core::conformation::Residue Class Reference

Instance Residue class, used for placed residues and rotamers. More...

#include <Residue.hh>

Inheritance diagram for core::conformation::Residue:

Public Types
typedef chemical::AtomType	AtomType
typedef chemical::ResidueType	ResidueType
typedef chemical::ResidueTypeCOP	ResidueTypeCOP
typedef chemical::AtomIndices	AtomIndices

Public Member Functions
	Residue (ResidueTypeCOP rsd_type_in, bool const dummy_arg)
	constructor with a ResidueTypeCOP. The dummy arg is there to prevent implicit casts from a ResidueTypeCOP to a Residue. More...
	Residue (ResidueType const &rsd_type_in, bool const dummy_arg)
	constructor with a ResidueType const &. The dummy arg is there to prevent implicit casts from a ResidueType to a Residue. More...
	Residue (ResidueType const &rsd_type_in, Residue const &current_rsd, Conformation const &conformation, bool preserve_c_beta=false, bool allow_alternate_backbone_matching=false)
	Rotamer-style constructor; orients ideal coords onto backbone of current_rsd. More...
	Residue (Residue const &src)
	Copy constructor. More...
	~Residue () override
	Destructor. More...
ResidueOP	clone () const
	Copy this residue( allocate actual memory for it ) More...
ResidueOP	clone_flipping_chirality (core::chemical::ResidueTypeSet const &residue_type_set) const
	Copy this residue( allocate actual memory for it ), keeping everything the same EXCEPT the type. More...
void	show (std::ostream &output=std::cout, bool output_atomic_details=false) const
	Generate string representation of Residue for debugging purposes. More...
ResidueCOP	get_self_ptr () const
	self pointers More...
ResidueOP	get_self_ptr ()
ResidueCAP	get_self_weak_ptr () const
ResidueAP	get_self_weak_ptr ()
AtomType const &	atom_type (Size const atomno) const
	Returns the AtomType of this residue's atom with index number <atomno> More...
chemical::AtomTypeSet const &	atom_type_set () const
	Returns the AtomTypeSet of this residue. More...
Size	atom_type_index (Size const atomno) const
	Returns the atom_type_index of this residue's atom with index number <atomno> atom_type_index is used to query this atom's AtomType from an AtomTypeSet, example: AtomTypeSet[atom_type_index] = AtomType. More...
Real	atomic_charge (Size const atomno) const
	Returns the atom charge of this residue's atom with index number <atomno> More...
bool	is_virtual (Size const atomno) const
	Check if atom is virtual. AMW TODO: somehow SWA spends literally 3.7% of its time calling this function. More...
bool	is_repulsive (Size const atomno) const
	Check if atom is repulsive. More...
bool	is_virtual_residue () const
	Check if residue is virtual. More...
Size	atom_index (std::string const &atm) const
	Returns the index number of the <atm> in this residue example: residue.atom_index("CA") returns 2 for a normal amino acid. More...
Size	natoms () const
	Returns the number of atoms in this residue. More...
Size	n_hbond_acceptors () const
	number of hbond_donors More...
Size	n_hbond_donors () const
	number of hbond_donors More...
Size	nheavyatoms () const
	Returns the number of heavyatoms in this residue. More...
AtomIndices const &	Hpos_polar () const
	Returns the AtomIndices of this residue's polar hydrogens. More...
AtomIndices const &	all_bb_atoms () const
	Returns the AtomIndices of this residue's backbone atoms. More...
AtomIndices const &	Haro_index () const
	Returns the AtomIndices of this residue's aromatic hydrogens. More...
AtomIndices const &	Hpol_index () const
	Returns the AtomIndices of this residue's polar hydrogens. More...
AtomIndices const &	Hpos_apolar () const
	Returns the AtomIndices of this residue's apolar hydrogens. More...
AtomIndices const &	Hpos_polar_sc () const
	Returns the AtomIndices of this residue's polar sidechain hydrogens. More...
AtomIndices const &	accpt_pos () const
	Returns the AtomIndices of this residue's h-bond acceptor atoms. More...
AtomIndices const &	accpt_pos_sc () const
	Returns the AtomIndices of this residue's sidechain h-bond acceptor atoms. More...
void	get_metal_binding_atoms (AtomIndices &metal_binding_indices) const
	Gets the AtomIndices of the atoms in this residue that can bind to metals. More...
core::Size	n_virtual_atoms () const
	Returns the number of virtual atoms in this residue. More...
bool	heavyatom_has_polar_hydrogens (Size ind) const
	Is a particular atom a heavy atom with chemically bound polar hydrogens? (i.e. a donor heavy atom) More...
bool	heavyatom_is_an_acceptor (Size ind) const
	Is a particular atom a heavy atom acceptor? More...
bool	atom_is_polar_hydrogen (Size ind) const
	Is a particular atom a polar hydrogen? More...
Atoms const &	atoms () const
	Returns this residue's Atoms (const), a vector1 of Atom objects. More...
Atoms &	atoms ()
	Returns this residue's Atoms (non-const), a vector1 of Atom objects. More...
Atoms::iterator	atom_begin ()
	begin interator, to iterate over atoms More...
Atoms::iterator	atom_end ()
	end interator, to iterate over atoms More...
Atoms::const_iterator	atom_begin () const
Atoms::const_iterator	atom_end () const
Atoms::const_iterator	sidechainAtoms_begin () const
	should be safe, given the atom ordering rules? More...
Atoms::const_iterator	heavyAtoms_end () const
Atom const &	atom (Size const atm_index) const
	Returns this residue's Atom with index number <atm_index> (const) More...
Atom &	atom (Size const atm_index)
	Returns this residue's Atom with index number <atm_index> (non-const) More...
Atom const &	atom (std::string const &atm_name) const
	Returns this residue's Atom with name <atm_name> (const) More...
Atom &	atom (std::string const &atm_name)
	Returns this residue's Atom with name <atm_name> (non-const) More...
Vector const &	xyz (Size const atm_index) const
	Returns the position of this residue's atom with index number <atm_index> More...
Vector const &	xyz (std::string const &atm_name) const
	Returns the position of this residue's atom with name <atm_name> More...
void	set_xyz (core::Size const atm_index, Vector const &xyz_in)
	Sets the position of this residue's atom with index number <atm_index> More...
void	set_xyz (std::string const &atm_name, Vector const &xyz_in)
	Sets the position of this residue's atom with name <atm_name> More...
Size	last_backbone_atom () const
	Returns the index number of the last backbone heavyatom. More...
Size	first_sidechain_atom () const
	Returns the index number of the first sidechain heavyatom. More...
Size	first_sidechain_hydrogen () const
	Returns the index number of the first sidechain hydrogen. More...
Size	attached_H_begin (Size const atom) const
	Returns the index number of the first hydrogen attached to the atom with index number <atom> More...
Size	attached_H_end (Size const atom) const
	Returns the index number of the last hydrogen attached to the atom with index number <atom> More...
AtomIndices const &	attached_H_begin () const
	Returns the AtomIndices of the first hydrogen attached to each heavyatom. More...
AtomIndices const &	attached_H_end () const
	Returns the AtomIndices of the last hydrogen attached to each heavyatom. More...
bool	has_lower_connect () const
	Returns true if residue has a valid lower connection. More...
Size	lower_connect_atom () const
	Returns the index number of this residue's atom which connects to the residue before it in sequence. More...
bool	has_upper_connect () const
	Returns true if residue has a valid upper connection. More...
Size	upper_connect_atom () const
	Returns the index number of this residue's atom which connects to the residue after it in sequence. More...
Size	connect_atom (Residue const &other) const
	Returns the index number of this residue's atom connected to the <other> Residue. More...
core::chemical::AtomIndices	get_adjacent_heavy_atoms (uint const atom_index) const
	Get a list of heavy atoms connected to a given atom. More...
uint	first_adjacent_heavy_atom (uint const atom_index) const
	Scan through the list of atoms connected to a given atom and return the 1st heavy atom found. More...
core::chemical::AtomIndices	get_atoms_exocyclic_to_ring_atom (uint const atom_index) const
	Get a list of exocyclic atoms connected to a given ring atom. More...
core::chemical::AtomIndices	get_substituents_to_ring_atom (uint const atom_index) const
	Get a list of substituent atoms connected to a given ring atom. More...
core::chemical::AtomIndices	get_hydrogens_bonded_to_ring_atom (uint const atom_index) const
	Get a list of hydrogen atoms connected to a given ring atom. More...
utility::vector1< int > const &	path_distance (Size atom) const
	Returns the shortest path distance from <atom> to any other atom in this residue. More...
utility::vector1 < utility::vector1< int > > const &	path_distances () const
	Returns the shortest path distance for any atom pair in this residue example: path_distances()[atom1][atom2]. More...
int	path_distance (Size at1, Size at2) const
	Returns the number of bonds separating atom <at1> from <at2> More...
bool	atom_is_backbone (Size const atomno) const
	Returns true if this residue's atom with index number <atomno> is a backbone atom. More...
bool	atom_is_hydrogen (Size const atomno) const
	Returns true if this residue's atom with index number <atomno> is a hydrogen. More...
Size	atom_base (Size const atomno) const
	Returns the atom index of the <atomno> atom's base atom. More...
Size	abase2 (Size const atomno) const
	Returns the atom index of the <atomno> atom's second base atom note: abase2 is this atom's first bonded neighbor other than this atom's base atom (unless it has only one neighbor) More...
AtomIndices const &	bonded_neighbor (Size const atm) const
	Returns the AtomIndices for all bonded neighbor atoms of <atm> More...
AtomIndices const &	mainchain_atoms () const
	Returns the AtomIndices of this residue's mainchain atoms. More...
Size	mainchain_atom (Size const i) const
	Returns the atom index of the residue's ith mainchain atom. More...
Size	n_mainchain_atoms () const
	Returns the number of the residue's mainchain atoms. More...
AtomIndices const &	actcoord_atoms () const
	Returns the AtomIndices of atoms that will be used to define this residue's actcoord. More...
Vector	build_atom_ideal (int const atomno, Conformation const &conformation) const
	Return coordinates for building an atom from ideal internal coordinates, used for building missing atoms. More...
Size	nbr_atom () const
	Returns the index number of this residue's atom used as a center for neighbor definition example: C-beta atom for some amino acids. More...
Real	nbr_radius () const
	Returns the distance cutoff value used as a radius for neighbor definition. More...
Vector const &	nbr_atom_xyz () const
AtomIndices const &	atoms_with_orb_index () const
Vector	build_orbital_xyz (Size const orbital_index) const
Vector const &	orbital_xyz (Size const orbital_index) const
void	set_orbital_xyz (core::Size const orbital_index, Vector const &xyz_in)
Size	n_orbitals () const
	Returns the number of orbitals in this residue. More...
utility::vector1< Size > const &	bonded_orbitals (Size const atm) const
std::string const &	orbital_name (Size const orbital_index) const
chemical::orbitals::OrbitalType const &	orbital_type (Size const orbital_index) const
Size	orbital_type_index (Size const orbital_index) const
void	update_orbital_coords ()
bool	misplaced () const
	Return whether or not the Residue was incorrectly oriented and placed within the polymer when created. More...
ResidueOP	create_rotamer () const
	Returns a ResidueOP for creating a rotamer of this residue Temporary hack until Residue hierarchy is worked out. More...
ResidueOP	create_residue () const
	Returns a ResidueOP for creating a copy of residue, same as clone() Temporary hack until Residue hierarchy is worked out. More...
ResidueType const &	type () const
	Returns this residue's ResidueType. More...
ResidueTypeCOP	type_ptr () const
	Returns this residue's ResidueType as a COP. More...
chemical::ResidueConnection const &	upper_connect () const
	Returns this residue's upper_connection a ResidueConnection has internal coords info on how to build the atom in the next residue which connects to this residue. More...
chemical::ResidueConnection const &	lower_connect () const
	Returns this residue's lower_connection a ResidueConnection has internal coords info on how to build the atom in the previous residue which connects to this residue. More...
bool	connections_match (Residue const &other) const
	Returns true if ??? More...
Size	n_possible_residue_connections () const
	Returns the number of ResidueConnections on this residue including polymeric residue connections. This is the total number of possible connections from the ResidueType. More...
Size	n_current_residue_connections () const
	Returns the number of ResidueConnections on this residue including polymeric residue connections. This is the total number of actual connections to other residues. The index here does not nessessarily match with the connection index as n_possible_residue_connections does!!!! More...
Size	n_polymeric_residue_connections () const
	Returns the number of polymeric ResidueConnections on this residue. More...
Size	n_non_polymeric_residue_connections () const
	Returns the number of non-polymeric ResidueConnections on this residue. More...
chemical::ResidueConnection const &	residue_connection (Size const resconn_index) const
	Returns this residue's ResidueConnection a ResidueConnection has internal coords info on how to build the atom in a different residue which connects to this residue. More...
Size	residue_connect_atom_index (Size const resconn_id) const
chemical::ResConnID	connect_map (Size resconn_index) const
void	mark_connect_incomplete (Size resconn_index)
core::Size	connect_map_size () const
	Returns the size (number of elements) in the connect_map_ object. More...
void	clear_residue_connections ()
void	update_connections_to_other_residue (Residue const &other_rsd)
	Search through the other residue for connections to this residue, and ensure that this residue's connect_map is up to date with that residue's connection indices (and residue number). More...
void	copy_residue_connections_from (Residue const &src)
bool	has_incomplete_connection () const
bool	has_incomplete_connection (core::Size const atomno) const
	Returns true is <atomno> has complete connectivity? More...
bool	connection_incomplete (Size resconnid) const
chemical::ResConnID	actual_residue_connection (Size resconnid) const
	Get the residue connection. How is this different than residue_connection? More...
id::AtomID	inter_residue_connection_partner (int connid, Conformation const &conformation) const
	This returns the AtomID of the atom in the other residue to which the "connection_index"-th connection of residue seqpos is connected to. More...
Size	connected_residue_at_resconn (Size const resconn_index) const
	Returns the residue number of a residue connected to this residue at this residue's connection resconn_index. More...
Size	connected_residue_at_upper () const
	Returns the residue number of a residue connected to this residue at this residue's upper_connect. More...
Size	connected_residue_at_lower () const
	Returns the residue number of a residue connected to this residue at this residue's lower_connect. More...
Size	residue_connection_partner (Size const resconn_index) const
	Returns the residue number of a residue connected to this residue at this residue's connection resconn_index. More...
void	copy_residue_connections (Residue const &src_rsd)
	attempt to take residue connection info from src_rsd More...
Size	residue_connection_conn_id (Size const resconn_index) const
	Returns the connection id on the OTHER residue connected to this residue at this residue's connection resconn_index. More...
void	residue_connection_partner (Size const resconn_index, Size const otherres, Size const other_connid)
	set a connection to this residue by adding its partner's residue number More...
Distance	connection_distance (conformation::Conformation const &conf, Size const resconn_index, Vector const &matchpoint) const
	Distance between a potential residue connection match and the position of the expected atom. More...
bool	is_bonded (Residue const &other) const
	Am I bonded to other? Meaningful for arbitrary topologies (e.g. circular peptides, disulfides) More...
bool	is_pseudo_bonded (Residue const &other) const
	Do I have any pseudobonds to other? More...
bool	is_bonded (Size const other_residue_index) const
	Am I bonded to other? Looks at all residue connections as opposed to doing arithmetic. More...
bool	is_pseudo_bonded (Size const other_index) const
	Do I have any pseudobonds to other? More...
bool	is_polymer_bonded (Residue const &other) const
	Am I polymer bonded to other? More...
bool	is_polymer_bonded (Size const other_index) const
	Am I polymer-bonded to other? checks lower and upper connections. More...
utility::vector1< Size > const &	connections_to_residue (Residue const &other) const
	Returns the vector1 of resconn ids that connect this residue to other. More...
utility::vector1< Size > const &	connections_to_residue (Size const other_resid) const
	Returns the vector1 of resconn ids that connect this residue to other. More...
PseudoBondCollectionCOP	get_pseudobonds_to_residue (Size resid) const
std::map< Size, PseudoBondCollectionCOP > const &	pseudobonds () const
void	set_pseudobonds_to_residue (Size resid, PseudoBondCollectionCOP pbs)
utility::vector1< std::pair < Real, Real > > const &	chi_rotamers (Size const chino) const
	Returns the chi rotamers available for this residue's chi angle <chino> More...
AtomIndices const &	cut_bond_neighbor (Size const atm) const
	atom indices for bonded neighbors to which atom-tree connections are disallowed. More...
core::Size	n_bonded_neighbor_all_res (core::Size const atomno, bool virt=false) const
	Returns the number of atoms bonded to <atomno> in all residues? More...
AtomIndices const &	nbrs (Size const atm) const
	Convenience synonym for bonded_neighbor. More...
utility::vector1< Real > const &	mainchain_torsions () const
	Returns the mainchain torsion angles of this residue (const) More...
utility::vector1< Real > &	mainchain_torsions ()
	Returns the mainchain torsion angles of this residue (non-const) More...
void	mainchain_torsions (utility::vector1< Real > const &torsions)
	Sets the mainchain torsion angles of this residue to <torsions> More...
Real	mainchain_torsion (Size const torsion) const
	Returns a specific mainchain torsion angle for this residue example: mainchain_torsion(2) will be the psi angle for an amino acid. More...
Size	nchi () const
	Returns the number of chi angles this residue has. More...
utility::vector1< Real > const &	chi () const
	Returns the chi torsion angles of this residue (const) More...
utility::vector1< Real > &	chi ()
	Returns the chi torsion angles of this residue (non-const) More...
void	chi (utility::vector1< Real > const &chis)
	Sets the chi torsion angles of this residue. More...
Real	chi (Size const chino) const
	get a specific chi torsion angle More...
utility::vector1< AtomIndices > const &	chi_atoms () const
	Returns the AtomIndices of each set of four atoms defining each chi angle. More...
AtomIndices const &	chi_atoms (Size const chino) const
	Returns the AtomIndices of the four atoms defining this residue's <chino> chi angle. More...
Size	n_nus () const
	Return the number of nu (internal ring) angles this residue has. More...
utility::vector1< core::Angle > const &	nus () const
	Return the nu (internal ring) torsion angles of this residue. More...
utility::vector1< core::Angle > &	nus ()
	Return the nu (internal ring) torsion angles of this residue. (non-const) More...
core::Angle	nu (core::uint const index) const
	Get a specific nu (internal ring) torsion angle by index. More...
utility::vector1< AtomIndices > const	nu_atoms () const
	Return the AtomIndices of each set of four atoms defining each nu angle. More...
AtomIndices const	nu_atoms (core::uint const index) const
	Return the AtomIndices of the four atoms defining the specified nu angle. More...
chemical::rings::RingConformer const &	ring_conformer (core::uint const ring_num, core::Real limit=90.0) const
	Return the current RingConformer of this residue's nth ring. More...
Size	seqpos () const
	Returns the sequence position of this residue. More...
void	seqpos (Size const setting)
	Sets this residue's sequence position to <setting> More...
Size	polymeric_sequence_distance (Residue const &other) const
	Returns the sequence separation distance between this residue and <other> More...
int	polymeric_oriented_sequence_distance (Residue const &other) const
	Returns the sequence separation distance between this residue and <other> positive if the other residue is downstream in sequence. More...
core::Size	chain () const
	Returns this residue's chain id. More...
void	chain (core::Size const setting)
	Sets this residue's chain id. More...
bool	requires_actcoord () const
	does this residue require an actcoord? More...
void	update_actcoord ()
	Updates actcoord for this residue. More...
Vector const &	actcoord () const
	Returns the coordinates used for pairE calculations (amino acids only) More...
Vector &	actcoord ()
	Returns the coordinates used for pairE calculations (amino acids only) More...
void	update_sequence_numbering (utility::vector1< Size > const &old2new)
	Updates the sequence numbers for this residue and the numbers stored about its non-polymer connections called by our owning conformation when the sequence numbers are remapped. More...
void	update_nus ()
	Calculate the set of nu dihedrals from the xyz coordinates and store them. More...
bool	is_polymer () const
	Returns true if this residue is a polymer. More...
bool	is_protein () const
	Returns true if this residue is an amino acid. More...
bool	is_peptoid () const
	Returns if this residue is a peptoid. More...
bool	is_aramid () const
	Returns if this residue is an aramid. More...
bool	is_ortho_aramid () const
	Returns if this residue is an ortho aramid. More...
bool	is_pre_methylene_ortho_aramid () const
	Returns if this residue is a pre methylene ortho aramid. More...
bool	is_post_methylene_ortho_aramid () const
	Returns if this residue is a post methylene ortho aramid. More...
bool	is_pre_methylene_post_methylene_ortho_aramid () const
	Returns if this residue is a post methylene ortho aramid. More...
bool	is_meta_aramid () const
	Returns if this residue is a meta aramid. More...
bool	is_pre_methylene_meta_aramid () const
	Returns if this residue is a pre methylene meta aramid. More...
bool	is_post_methylene_meta_aramid () const
	Returns if this residue is a post methylene meta aramid. More...
bool	is_pre_methylene_post_methylene_meta_aramid () const
	Returns if this residue is a post methylene meta aramid. More...
bool	is_para_aramid () const
	Returns if this residue is a para aramid. More...
bool	is_pre_methylene_para_aramid () const
	Returns if this residue is a pre methylene para aramid. More...
bool	is_post_methylene_para_aramid () const
	Returns if this residue is a post methylene para aramid. More...
bool	is_pre_methylene_post_methylene_para_aramid () const
	Returns if this residue is a post methylene para aramid. More...
bool	is_sri () const
	Is this one of SRI's special heteropolymer building blocks? More...
bool	is_triazolemer () const
	Returns true if and only if this residue is a triazolemer. More...
bool	is_DNA () const
	Returns true if this residue is a DNA residue. More...
bool	is_RNA () const
	Returns true if this residue is a RNA residue. More...
bool	is_TNA () const
	Returns true if this residue is a TNA residue. More...
bool	is_l_rna () const
	Returns true if this residue is a L-RNA residue. More...
bool	is_d_rna () const
	Returns true if this residue is a D-RNA residue. More...
bool	is_NA () const
	Returns true if this residue is a nucleic acid. More...
bool	is_purine () const
	Returns true if this residue is a purine. More...
bool	is_pyrimidine () const
	Returns true if this residue is a pyrimidine. More...
bool	is_carbohydrate () const
	Returns true if this residue is a carbohydrate. More...
bool	is_water () const
	Returns true if this residue is water. More...
bool	is_ligand () const
	Returns true if this residue is a ligand. More...
bool	is_metal () const
	Returns true if this residue is a metal ion, false otherwise. The METAL property is specified in the params file under PROPERTIES. More...
bool	is_metalbinding () const
	Returns true if this residue is a type capable of binding to a metal ion (e.g. His, Cys, etc.), false otherwise. The METALBINDING property is specified in the params file under PROPERTIES. More...
bool	is_surface () const
	Returns true if this residue is a surface residue. More...
bool	has_sc_orbitals () const
	Returns true if the residue has side chain orbitals. More...
bool	is_polar () const
	Returns true if the residue is polar. More...
bool	is_apolar () const
bool	is_charged () const
	Returns true if the residue is charged. More...
bool	is_aromatic () const
	Returns true if the residue is aromatic. More...
bool	is_coarse () const
	residue is coarse (used for RNA right now) More...
bool	is_terminus () const
	Returns true if the residue has a terminus property. More...
bool	is_upper_terminus () const
	Return true if the residue has an upper terminus property. More...
bool	is_lower_terminus () const
	Returns true if the residue has a lower terminus property. More...
bool	is_branch_point () const
	Return true if the residue is a branch point variant. More...
bool	is_similar_rotamer (Residue const &other) const
	Returns true if the chi angles of another residue all fall within 5 deg. More...
bool	is_similar_aa (Residue const &other) const
	Returns true if the aa residue types are the same. More...
bool	has_shadow_atoms () const
	Return true if and only if this residue's type has shadow atoms. More...
bool	has_property (std::string const &property) const
	Return true if the residue has <property>. More...
bool	has_variant_type (chemical::VariantType const variant_type) const
	Generic variant access. More...
std::string const &	atom_name (Size const atm) const
	Returns the name of this residue's atom with index number <atm> More...
std::string const &	mm_atom_name (Size const atom) const
	Returns the mm_atom_name of this residue's atom with index number <atom> More...
std::string const &	name () const
	Returns this residue's ResidueType name. More...
std::string const &	name3 () const
	Returns this residue's 3-letter representation. More...
char	name1 () const
	Returns this residue's 1-letter representation. More...
std::string	annotated_name (bool const show_all_variants=true) const
	Returns this residue's 1-letter representation, including details in square brackets. E.g., H[HIS_D]. More...
chemical::AA const &	aa () const
	Returns this residue's AA type, if any Used for knowledge-based scores, dunbrack, etc. could be "aa_unk" AA is enumeration. More...
chemical::AA const &	backbone_aa () const
	Returns this residue's backbone_aa type, if any. More...
chemical::AA const &	na_analogue () const
	Returns the nucleic acid type to be used for fragment sampling. More...
chemical::AtomICoor const &	icoor (Size const atm) const
	Returns the internal coordinates of this residue's atom with index number <atm> More...
bool	atom_depends_on_lower (core::Size const atom_index) const
	Does this atom depend on the LOWER_CONNECT? More...
bool	atom_depends_on_upper (core::Size const atom_index) const
	Does this atom depend on the UPPER_CONNECT? More...
void	set_d (int const chino, Real const setting)
	bondlength analog to set_chi like set_chi, assumes changes propagate to atomtree keyed off of chi#, so we only allow distances corresponding to chi angles to refine distance corresponds to the distance between atoms 3 and 4 defining the chi chino==0 ==> CA-CB distance, which allows us to refine ALA CB position for example More...
void	set_theta (int const chino, Real const setting)
	bondangle analog to set_chi same idea as set_d More...
void	set_tau (Size const nuno, Real const setting)
	set_theta for nus More...
void	set_all_nu (utility::vector1< Real > const &nus, utility::vector1< Real > const &taus)
void	set_all_ring_nu (Size start, Size end, utility::vector1< Real > const &nus, utility::vector1< Real > const &taus)
void	set_chi (int const chino, Real const setting)
	Sets this residue's chi angle <chino> to <setting> assuming that changes propagate according to the atom_base tree. More...
void	set_all_chi (utility::vector1< Real > const &chis)
	Sets all of this residue's chi angles using the set_chi function (wrapper function) More...
bool	has (std::string const &atm) const
	Returns true if this residue has an atom named <atm> More...
bool	fill_missing_atoms (utility::vector1< bool > &missing, Conformation const &conformation, bool fail=true)
	Builds coordinates for atoms missing from this residue assuming ideal internal coordinates. More...
void	select_orient_atoms (Size &center, Size &nbr1, Size &nbr2) const
	Selects three atoms for orienting this residue. More...
void	orient_onto_residue (Residue const &src)
	Orient our coords onto those of <src>, using the atoms from select_orient_atoms. More...
void	orient_onto_residue (Residue const &src, utility::vector1< std::pair< std::string, std::string > > const &atom_pairs)
	Orient our coords onto those of <src>, using the three atom pairs specified in the input. More...
void	orient_onto_residue_peptoid (Residue const &src, Conformation const &conformation)
	Orient our coords onto those of src, uses hard coded atom names (yuck) and will work for peptoid on to peptoid/peptide. More...
void	orient_onto_location (Size center, Size nbr1, Size nbr2, Vector center_locaton, Vector nbr1_locaton, Vector nbr2_locaton)
	Orients residue object onto atom locations. More...
void	orient_onto_location (Vector center_locaton, Vector nbr1_locaton, Vector nbr2_locaton)
	Orients residue object onto atom locations. More...
bool	place (Residue const &src, Conformation const &conformation, bool preserve_c_beta=false)
	Place this rotamer at the sequence position occupied by <src> by reorienting the ideal side chain coordinates to match. More...
void	apply_transform_Rx_plus_v (numeric::xyzMatrix< Real > R, Vector v)
	Applies a transform of the form Rx + v, where R is a rotation matrix, V is a vector, and x is the original position in xyz space. More...
core::chemical::rna::RNA_Info const &	RNA_info () const
	Return the RNA_residueType object. This is RNA specific. More...
core::chemical::carbohydrates::CarbohydrateInfoCOP	carbohydrate_info () const
	Return the CarbohydrateInfo object containing sugar-specific properties for this residue. More...
basic::datacache::BasicDataCacheCOP	data_ptr () const
	BasicDataCache indexed by enum in residue_datacache.hh. More...
basic::datacache::BasicDataCacheOP	nonconst_data_ptr ()
	BasicDataCache indexed by enum in residue_datacache.hh. More...
basic::datacache::BasicDataCache const &	data () const
	BasicDataCache indexed by enum in residue_datacache.hh. Beware, this will crash if a call to nonconst_data_ptr() or data_ptr() has not previously been made on this Residue – the datacache is created just-in-time. More...
basic::datacache::BasicDataCache &	nonconst_data ()
	BasicDataCache indexed by enum in residue_datacache.hh. Beware, this will crash if a call to nonconst_data_ptr() or data_ptr() has not previously been made on this Residue – the datacache is created just-in-time. More...
bool	mirrored_relative_to_type () const
	Is this residue mirrored relative to its coordinates in the ResidueType? More...
void	set_mirrored_relative_to_type (bool const setting)
	Set whether this residue is mirrored relative to its coordinates in the ResidueType. More...

Private Member Functions
	Residue (Residue const &src, core::chemical::ResidueTypeCOP new_restype, bool flip_chirality)
	Copy constructor that preserves everything EXCEPT the ResidueType This is deliberately private, as hot-swapping the ResidueType is not generally going to work. (In most instances, you should make a new Residue with the new ResidueType, and explicitly copy over the things you want to preserve. More...
void	init_residue_from_other (Residue const &src)
	Function called by both copy constructors, to avoid code duplication. More...
void	update_connections_to_residues ()
	Updates connections_to_residues_ using connect_map_. More...
void	apply_transform_downstream (core::Size const atomno, core::Size const upstream_atomno, numeric::xyzMatrix< Real > const &R, Vector const &v)
	apply transform of rotation R and translation V for all atoms downstream More...
void	determine_nonstandard_polymer_status ()
Residue const &	operator= (Residue const &rhs)
	Assignment operator does not work for class Residue. This function is intentionally unimplemented and private. More...
void	orient_onto_residue (Residue const &src, Size center, Size nbr1, Size nbr2, Size src_center, Size src_nbr1, Size src_nbr2)
	Orient coords onto those of <src>, using the specified atoms. More...
void	assign_orbitals ()
	Determine the set of orbitals that are needed and compute their coordinates; invoked from within the constructors. More...

Private Attributes
ResidueTypeCOP	rsd_type_ptr_
	Pointer to the ResidueType that this Residue derives its chemical identity from. The ResidueType is pointed to through both a pointer and a reference; the pointer for the sake of serialization, and the reference for access speed. More...
ResidueType const &	rsd_type_
	our Residue type More...
Atoms	atoms_
	our conformation atoms (not kinematic atom pointers) with xyz positions and atom type More...
utility::vector1 < orbitals::OrbitalXYZCoords >	orbitals_
Size	seqpos_
	the sequence position More...
bool	mirrored_relative_to_type_
	Is this residue mirrored relative to its coordinates in the ResidueType? More...
core::Size	chain_
	the chain id number, starting from 1 See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps. More...
utility::vector1< Real >	chi_
	our chi (side chain) torsion angles More...
utility::vector1< Angle >	nus_
	our nu (internal ring) torsion angles More...
utility::vector1< Real >	mainchain_torsions_
	our (possibly empty) backbone torsion angles More...
Vector	actcoord_
	the action coordinate, an interaction centroid for knowledge-based terms like fa-pair in fact, only for fa-pair More...
basic::datacache::BasicDataCacheOP	data_cache_
bool	misplaced_ = false
	Inter-residue connection data. More...
bool	nonstandard_polymer_
	true if is_polymer() and either upper_connect or lower_connect (if they exist) do not connect to seqpos()+1 or seqpos()-1 More...
utility::vector1 < chemical::ResConnID >	connect_map_
	map between connection ids on this residue and the connection points on other residues to which its bonded More...
std::map< Size, utility::vector1< Size > >	connections_to_residues_
	lists for each connected residue of the connection points on this residue that connect the pair. More...
std::map< Size, PseudoBondCollectionCOP >	pseudobonds_
	other residues within 4 bonds (connected through PseudoBonds) may include this residue (intra-residue pseudo-bonds) More...

Detailed Description

Instance Residue class, used for placed residues and rotamers.

This class is designed to be lightweight. It holds a const-reference ("rsd_type_") to a ResidueType object for access to information common to all instances of a single type, e.g., Alanine or Thymine. Residue stores any data unique to a placed residue or rotamer, currently:

• a vector1 of Atoms, which holds the positions (and also the atom-types for fast access during scoring);
• the sequence position and chain number, both integers (See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.)
• the backbone, side-chain, and internal ring (if applicable) torsion angles (of course backbone torsions are not unique to a rotamer, and the chi angles are derivable from the coordinates, but storing them in the residue is convenient for scoring purposes).
• the coordinates of an interaction center or centroid, used e.g., in the knowledge-based full-atom pair term ("actcoord_"). Maybe this will also hold the centroid position for centroid-mode scoring??

Member Typedef Documentation

typedef chemical::AtomIndices core::conformation::Residue::AtomIndices

typedef chemical::AtomType core::conformation::Residue::AtomType

typedef chemical::ResidueType core::conformation::Residue::ResidueType

typedef chemical::ResidueTypeCOP core::conformation::Residue::ResidueTypeCOP

Constructor & Destructor Documentation

core::conformation::Residue::Residue	(	ResidueTypeCOP	rsd_type_in,
		bool const	dummy_arg
	)

constructor with a ResidueTypeCOP. The dummy arg is there to prevent implicit casts from a ResidueTypeCOP to a Residue.

Constructor from ResidueTypeCOP; sets coords to ideal values create a residue of type residue_type_in.

Note

Dummmy arg to prevent secret type conversions from ResidueTypeCOP to Residue

References assign_orbitals(), core::chemical::ResidueType::atom_type_index(), atoms_, core::chemical::ResidueType::ideal_xyz(), core::chemical::ResidueType::mm_atom_type_index(), core::chemical::ResidueType::natoms(), rsd_type_, and update_nus().

Referenced by clone_flipping_chirality().

core::conformation::Residue::Residue	(	ResidueType const &	rsd_type_in,
		bool const	dummy_arg
	)

constructor with a ResidueType const &. The dummy arg is there to prevent implicit casts from a ResidueType to a Residue.

Constructor from residue type; sets coords to ideal values create a residue of type residue_type_in.

Note

Dummmy arg to prevent secret type conversions from ResidueType to Residue

References assign_orbitals(), core::chemical::ResidueType::atom_type_index(), atoms_, core::chemical::ResidueType::ideal_xyz(), core::chemical::ResidueType::mm_atom_type_index(), core::chemical::ResidueType::natoms(), rsd_type_, and update_nus().

core::conformation::Residue::Residue	(	ResidueType const &	rsd_type_in,
		Residue const &	current_rsd,
		Conformation const &	conformation,
		bool	preserve_c_beta = false,
		bool	allow_alternate_backbone_matching = false
	)

Rotamer-style constructor; orients ideal coords onto backbone of current_rsd.

Create a residue/rotamer of type rsd_type_in placed at the position occupied by current_rsd Used primarily in rotamer building. The newly created Residue has the same sequence position, chain id and mainchain torsion angles as current_rsd. It has a ResidueType as defined by rsd_type_in. Its side-chain chi angles are uninitialized as all 0.0 and sidechain atom coords are from ideal coords. Its backbone is aligned with that of current_rsd. Its residue connections and its pseudobonds must be initialized from the original residue.

Parameters

<allow_alternate_backbone_matching>

If true, the number of main-chain atoms in the input ResidueType need not match the number in the template Residue. A function will be called that will attempt to align the Residues' connections. If successful, the new Residue will be created; if unsuccessful, an empty Residue will be returned.

References assign_orbitals(), atom(), core::chemical::ResidueType::atom_type_index(), atoms_, chi_, core::chemical::ResidueType::chi_atoms(), chi_atoms(), copy_residue_connections(), core::chemical::ResidueType::ideal_xyz(), core::chemical::ResidueType::mainchain_atoms(), mainchain_torsions(), misplaced_, core::chemical::ResidueType::mm_atom_type_index(), core::chemical::ResidueType::n_nus(), n_nus(), core::chemical::ResidueType::n_possible_residue_connections(), core::chemical::ResidueType::natoms(), core::chemical::ResidueType::nchi(), nus_, place(), pseudobonds_, rsd_type_, core::conformation::TR(), type(), update_nus(), and xyz().

core::conformation::Residue::Residue

(

Residue const &

src

)

Copy constructor.

References init_residue_from_other().

core::conformation::Residue::~Residue ( )

overridedefault

Destructor.

core::conformation::Residue::Residue ( Residue const &  src, core::chemical::ResidueTypeCOP  new_restype, bool  flip_chirality  )

private

Copy constructor that preserves everything EXCEPT the ResidueType This is deliberately private, as hot-swapping the ResidueType is not generally going to work. (In most instances, you should make a new Residue with the new ResidueType, and explicitly copy over the things you want to preserve.

References atom(), chi_, core::chemical::ResidueType::chi_atoms(), chi_atoms(), init_residue_from_other(), mirrored_relative_to_type(), nchi(), rsd_type_, set_mirrored_relative_to_type(), type(), and xyz().

Member Function Documentation

chemical::AA const& core::conformation::Residue::aa ( ) const

inline

Returns this residue's AA type, if any Used for knowledge-based scores, dunbrack, etc. could be "aa_unk" AA is enumeration.

References core::chemical::ResidueTypeBase::aa(), and rsd_type_.

Referenced by protocols::protein_interface_design::movers::PlaceOnLoop::add_bb_csts_to_loop(), protocols::relax::add_coordinate_constraint_func_atoms(), protocols::protein_interface_design::movers::add_coordinate_constraints(), protocols::seeded_abinitio::add_coordinate_constraints(), protocols::relax::add_coordinate_constraints_to_pose(), protocols::loops::add_coordinate_constraints_to_pose(), protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_pose(), protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_wholepose(), protocols::hybridization::add_non_protein_cst(), protocols::denovo_design::components::advance_past_virtual_residues(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::append_metal_vsites(), protocols::simple_moves::VirtualRootMover::apply(), protocols::protein_interface_design::movers::RandomMutation::apply(), protocols::rbsegment_relax::IdealizeHelicesMover::apply(), protocols::protein_interface_design::filters::FilterScanFilter::apply(), protocols::constraint_generator::CoordinateConstraintGenerator::apply(), protocols::comparative_modeling::PartialThreadingMover::apply(), protocols::protein_interface_design::movers::PlacementAuctionMover::apply(), protocols::protein_interface_design::movers::DesignMinimizeHbonds::apply(), protocols::simple_moves::SetTorsion::apply(), protocols::membrane::AqueousPoreFinder::apply(), protocols::hybridization::CartesianHybridize::apply(), protocols::task_operations::ProteinInterfaceDesignOperation::apply(), protocols::fldsgn::filters::StrandCurvatureByLevels::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::protein_interface_design::Revert::apply(), protocols::enzdes::DetectProteinLigandInterface::apply(), protocols::symmetry::SetupNCSMover::apply(), protocols::idealize::IdealizeMover::apply(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::nmr::pre::PREMover::apply(), protocols::hybridization::CartesianSampler::apply_fragcsts(), protocols::seeded_abinitio::SegmentHybridizer::apply_frame(), protocols::hybridization::CartesianSampler::apply_frame(), protocols::stepwise::modeler::rna::apply_protonated_H1_adenosine_variant_type(), core::scoring::orbitals::OrbitalsScore::assign_orb_H_derivs(), core::scoring::methods::ProQ_Energy::atom13_0(), core::scoring::constraints::BackboneStubConstraint::BackboneStubConstraint(), core::scoring::constraints::BackboneStubLinearConstraint::BackboneStubLinearConstraint(), core::scoring::dna::DNA_BasePotential::base_string(), protocols::idealize::basic_idealize(), protocols::simple_moves::ExplicitWaterMover::build_backbone_rotamer_clouds(), protocols::LoopRebuild::build_loop_with_ccd_closure(), core::scoring::membrane::MPResidueLipophilicityEnergy::calc_energy(), protocols::protein_interface_design::ReportPSSMDifferences::calculate(), protocols::protein_interface_design::ReportSequenceDifferences::calculate(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::calculate_free_receptor_score(), core::scoring::FACTSPotential::calculate_GBpair_exact(), core::scoring::FACTSPotential::calculate_GBpair_fast(), core::scoring::methods::RG_Energy_Fast::calculate_rg_score(), core::scoring::dna::DNA_EnvPairPotential::centroid_xyz(), protocols::hybridization::HybridizeProtocol::check_and_create_fragments(), protocols::denovo_design::components::StructureData::check_pose(), protocols::denovo_design::DisulfidizeMover::check_residue_type(), core::scoring::rna::check_watson_crick_sequence(), protocols::loops::Loop::choose_cutpoint(), core::scoring::electron_density::ElectronDensity::clear_dCCdx_res_cache(), protocols::simple_filters::MembAccesResidueLipophilicityFilter::compute(), core::scoring::dssp::Dssp::compute(), protocols::flexpack::interaction_graph::OTFFlexbbEdge::compute_altbbconf_alternate_state_energy(), protocols::features::StructureScoresFeatures::compute_energies(), protocols::constraint_generator::compute_hnq_atoms(), protocols::calc_taskop_filters::RotamerBoltzmannWeight::compute_modified_ddG(), core::pack::interaction_graph::SurfacePotential::compute_pose_surface_energy(), protocols::relax::AtomCoordinateCstMover::compute_residue_subset(), core::pack::interaction_graph::SurfacePotential::compute_residue_surface_energy(), core::pack::interaction_graph::OnTheFlyNode::compute_rotamer_pair_energy(), core::pack::interaction_graph::SymmOnTheFlyNode::compute_rotamer_pair_energy(), protocols::flexpack::interaction_graph::OTFFlexbbEdge::compute_samebbconf_alternate_state_energy_first_node(), protocols::flexpack::interaction_graph::OTFFlexbbEdge::compute_samebbconf_alternate_state_energy_second_node(), core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric::compute_scores(), protocols::flexpack::rotamer_set::FlexbbRotamerSets::compute_sr_one_body_energies_for_flexsets(), protocols::abinitio::abscript::RigidChunkCM::configure(), protocols::stepwise::modeler::rna::create_alignment_id_map_legacy(), protocols::constraint_generator::CoordinateConstraintGenerator::create_residue_constraints(), protocols::cartesian::MolecularDynamics::createDihedralList(), protocols::vip::VIP_Mover::cull_mutatable_residues(), core::scoring::electron_density::ElectronDensity::dCCdB_fastRes(), core::scoring::electron_density::ElectronDensity::dCCdx_fastRes(), core::scoring::methods::ProClosureEnergy::defines_intrares_energy_for_residue(), core::scoring::electron_density::FastDensEnergy::defines_residue_pair_energy(), core::scoring::electron_density::ElecDensEnergy::defines_residue_pair_energy(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::defines_residue_pair_energy(), core::scoring::electron_density::ElecDensCenEnergy::defines_residue_pair_energy(), core::scoring::electron_density_atomwise::ElecDensAtomwiseEnergy::defines_residue_pair_energy(), core::scoring::methods::ProClosureEnergy::defines_score_for_residue_pair(), core::scoring::methods::PointWaterEnergy::defines_score_for_residue_pair(), core::scoring::methods::YHHPlanarityEnergy::defines_score_for_rsd(), protocols::cryst::MakeLatticeMover::detect_connecting_subunits(), protocols::antibody::design::AntibodySeqDesignTFCreator::disable_proline_design(), core::scoring::constraints::ResidueTypeLinkingConstraint::dist(), core::scoring::disulfides::CentroidDisulfidePotential::disulfide_params(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::disulfides_changed(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::do_checks_and_apply_protonated_H1_adenosine_variant(), core::scoring::electron_density::ElectronDensity::ElectronDensity(), core::scoring::saxs::FastSAXSEnergy::eval_atom_derivative(), core::scoring::fiber_diffraction::FiberDiffractionEnergy::eval_atom_derivative(), core::scoring::cryst::XtalMLEnergy::eval_atom_derivative(), core::scoring::methods::MembraneEnvSmoothEnergy::eval_atom_derivative(), core::scoring::methods::EnvSmoothEnergy::eval_atom_derivative(), core::scoring::membrane::FaMPEnvSmoothEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensCenEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensEnergy::eval_atom_derivative(), core::scoring::electron_density_atomwise::ElecDensAtomwiseEnergy::eval_atom_derivative(), core::scoring::dna::DNABFormPotential::eval_dna_bform_chi_torsion_score_residue(), core::scoring::methods::RamachandranEnergy::eval_dof_derivative(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd1(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd2(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd1(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd2(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_bond_energy(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_bond_length_derivs(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_improper_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_improper_energy(), core::scoring::methods::ProClosureEnergy::eval_intrares_derivatives(), core::scoring::elec::FA_ElecEnergy::eval_intrares_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_intrares_derivatives(), core::scoring::rna::RNA_TorsionPotential::eval_intrares_energy(), core::scoring::magnesium::MgEnergy::eval_intrares_energy(), core::scoring::methods::ProClosureEnergy::eval_intrares_energy(), core::scoring::elec::FA_ElecEnergy::eval_intrares_energy(), core::scoring::methods::CartesianBondedEnergy::eval_intrares_energy(), core::scoring::methods::CartesianBondedEnergy::eval_intraresidue_dof_derivative(), core::scoring::OmegaTether::eval_omega_score_residue(), core::scoring::Ramachandran2B::eval_rama_score_all(), core::scoring::Ramachandran::eval_rama_score_residue(), core::scoring::Ramachandran2B::eval_rama_score_residue(), core::scoring::Ramachandran::eval_rama_score_residue_nonstandard_connection(), core::scoring::methods::SmoothEnvEnergy::eval_residue_derivatives(), core::scoring::methods::CenRotEnvEnergy::eval_residue_derivatives(), core::pack::dunbrack::cenrot::CenRotDunEnergy::eval_residue_derivatives(), core::scoring::methods::RamachandranEnergy::eval_residue_dof_derivative(), core::scoring::methods::CenRotPairEnergy::eval_residue_pair_derivatives(), core::scoring::methods::SmoothCenPairEnergy::eval_residue_pair_derivatives(), core::scoring::methods::CenHBEnergy::eval_residue_pair_derivatives(), core::scoring::electron_density::FastDensEnergy::eval_residue_pair_derivatives(), core::scoring::methods::PointWaterEnergy::eval_residue_pair_derivatives(), core::scoring::methods::ProClosureEnergy::eval_residue_pair_derivatives(), core::scoring::methods::CenHBEnergy::eval_residue_pair_derivatives_soft(), core::scoring::methods::CartesianBondedEnergy::eval_residue_pair_derivatives_sorted(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_energy(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_improper_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_improper_energies(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_torsion_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_torsion_energies(), core::scoring::rna::data::RNA_DMS_LowResolutionPotential::evaluate(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_env_and_cbeta_deriv(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_env_and_cbeta_score(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_pair_deriv(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_pair_orientation_deriv(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_pair_orientation_score(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_pair_score(), core::scoring::MembranePotential::evaluate_env(), core::scoring::SmoothEnvPairPotential::evaluate_env_and_cbeta_deriv(), core::scoring::EnvPairPotential::evaluate_env_and_cbeta_scores(), core::scoring::SmoothEnvPairPotential::evaluate_env_and_cbeta_scores(), protocols::scoring::InterchainPotential::evaluate_env_score(), core::scoring::MembranePotential::evaluate_pair(), core::scoring::SmoothEnvPairPotential::evaluate_pair_and_cenpack_deriv(), core::scoring::SmoothEnvPairPotential::evaluate_pair_and_cenpack_score(), core::scoring::EnvPairPotential::evaluate_pair_and_cenpack_score(), protocols::scoring::InterchainPotential::evaluate_pair_and_vdw_score(), core::scoring::FACTSPotential::evaluate_polar_otf_energy(), core::scoring::rna::RNP_LowResPotential::evaluate_rnp_aa_rna_backbone_score(), core::scoring::rna::RNP_LowResPotential::evaluate_rnp_base_pair_score(), core::scoring::rna::RNP_LowResPotential::evaluate_rnp_pair_score(), core::scoring::rna::RNP_LowResStackData::evaluate_rnp_stack_xy_score(), core::scoring::constraints::BackboneStubLinearConstraint::fill_f1_f2(), core::scoring::constraints::BackboneStubConstraint::fill_f1_f2(), core::scoring::dssp::fill_hbond_bb_pair_score_dssp(), protocols::pmut_scan::PointMutScanDriver::fill_mutations_list(), core::io::silent::ProteinSilentStruct_Template< T >::fill_struct(), core::scoring::methods::MembraneLipo::finalize_total_energy(), protocols::simple_filters::TMsAACompFilter::find_aa_composition(), protocols::forge::remodel::RemodelDesignMover::find_disulfides_in_the_neighborhood(), protocols::constraint_movers::AddConstraintsToCurrentConformationMover::generate_atom_pair_constraints(), protocols::constraint_generator::AtomPairConstraintGenerator::generate_atom_pair_constraints(), protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMover::generate_csts(), protocols::constraint_generator::ResidueTypeConstraintGenerator::generate_residue_type_constraints(), protocols::ligand_docking::ga_ligand_dock::get_atomic_contacting_sidechains(), core::pose::motif::get_backbone_reference_frame_atomids(), core::scoring::hackaro::HackAroEnergy::get_base_coordinate_system(), core::scoring::dna::get_base_pair_y_axis_atom_xyz(), core::pack::interaction_graph::SimpleEdge::get_bb_index(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_calc_chem_shift_value_larmord(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_calc_chem_shift_value_nuchemics(), core::scoring::hackaro::HackAroEnergy::get_centroid(), core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::get_closest_rotamer(), protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::get_contacting_reslist(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_deriv_for_chemical_shift(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_deriv_for_chemical_shift_data_atom(), core::scoring::rna::data::RNA_DMS_Potential::get_features(), core::pose::motif::get_frame_ala(), core::pose::motif::get_frame_arg(), core::pose::motif::get_frame_asn(), core::pose::motif::get_frame_asp(), core::pose::motif::get_frame_cys(), core::pose::motif::get_frame_gln(), core::pose::motif::get_frame_glu(), core::pose::motif::get_frame_gly(), core::pose::motif::get_frame_his(), core::pose::motif::get_frame_ile(), core::pose::motif::get_frame_leu(), core::pose::motif::get_frame_lys(), core::pose::motif::get_frame_met(), core::pose::motif::get_frame_phe(), core::pose::motif::get_frame_pro(), core::pose::motif::get_frame_ser(), core::pose::motif::get_frame_thr(), core::pose::motif::get_frame_trp(), core::pose::motif::get_frame_tyr(), core::pose::motif::get_frame_val(), core::scoring::hbonds::get_hb_acc_chem_type(), core::scoring::hbonds::get_hb_don_chem_type(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_magnetic_anisotropy_deriv_for_src_atom(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_magnetic_anisotropy_deriv_for_src_base(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::get_matching_res_in_VDW_rep_screen_pose(), protocols::magnesium::get_mg_ligands(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::get_movable_scs(), core::scoring::rna::data::RNA_DMS_Potential::get_N1_lonepair_donor_angle(), protocols::optimize_weights::IterativeOptEDriver::get_nat_aa_opte_data(), protocols::optimize_weights::IterativeOptEDriver::get_nat_rot_opte_data(), protocols::cryst::get_nres_asu(), core::pose::motif::get_nterminal_peptide_bond_reference_frame(), core::pose::motif::get_nterminal_peptide_bond_reference_frame_atomids(), protocols::hybridization::get_num_residues_nonvirt(), core::scoring::P_AA::get_Paa_pp_deriv(), protocols::simple_filters::ResidueDepthCalculator::get_pose_crd_and_index(), protocols::simple_filters::ResidueDepthFilter::get_residue_similarity(), protocols::sic_dock::get_rg(), core::scoring::rna::chemical_shift::get_ring_current_deriv(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_ring_current_deriv_for_src_base(), core::chemical::rna::get_rna_base_coordinate_system(), core::scoring::rna::chemical_shift::get_rna_base_coordinate_system_from_CS_params(), core::scoring::rna::get_rna_motifs(), core::pose::motif::get_sidechain_reference_frame(), core::pose::motif::get_sidechain_reference_frame_atomids(), core::pose::motif::get_sidechain_reference_frame_atomids_with_downstream(), protocols::hybridization::CartesianSampler::get_transform(), core::scoring::dna::get_z_axis(), protocols::rbsegment_relax::guess_rbsegs_from_pose(), protocols::constel::has_aromatic(), protocols::seeded_abinitio::SegmentHybridizer::hybridize(), protocols::magnesium::MgHydrater::hydrate_magnesium_in_pose(), core::scoring::methods::CartesianBondedEnergy::idealize_proline_nvs(), protocols::hybridization::HybridizeProtocol::initialize_and_sample_loops(), protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::Initialize_base_stub_list(), protocols::match::upstream::OriginalBackboneBuildPoint::initialize_from_residue(), protocols::ligand_docking::ga_ligand_dock::GAOptimizer::initialize_rotamer_set_and_scores(), protocols::features::ResidueScoresFeatures::insert_residue_scores_rows(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::Is_magnetic_anisotropy_source_atom(), core::io::serialization::is_pseudoresidue(), is_similar_aa(), is_similar_rotamer(), protocols::stepwise::modeler::rna::is_virtual_base(), protocols::loops::loop_rmsd(), protocols::loops::loop_rmsd_with_superimpose_core(), core::scoring::rna::chemical_shift::magnetic_anisotropy_effect(), protocols::simple_filters::ResidueDepthFilter::make_context(), core::pack::make_symmetric_task(), core::scoring::methods::ProClosureEnergy::measure_chi4(), protocols::rotamer_recovery::RRComparerAutomorphicRMSD::measure_rotamer_recovery(), protocols::rotamer_recovery::RRComparerElecDensDiff::measure_rotamer_recovery(), protocols::rotamer_recovery::RRComparerRotBins::measure_rotamer_recovery(), protocols::rotamer_recovery::RRComparerChiDiff::measure_rotamer_recovery(), protocols::pose_metric_calculators::SequenceComparison::measure_sequence_recovery(), protocols::optimize_weights::IterativeOptEDriver::measure_sequence_recovery(), core::conformation::missing_stubs_build(), protocols::forge::build::SegmentRebuild::modify_impl(), protocols::motifs::mutate_loops_for_search(), protocols::motifs::mutate_position_vector_for_search(), protocols::ncbb::ncbb_design_main_loop(), protocols::protein_interface_design::movers::nearest_atom_for_constraint(), core::scoring::MembranePotential::non_helix_in_membrane_penalty(), core::conformation::WatsonCrickResidueMatcher::operator()(), protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo::output_silent_file(), core::scoring::P_AA::P_AA_energy(), core::scoring::P_AA::P_AA_pp_energy(), core::scoring::PairEPotential::pair_term_energy(), protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::partition(), protocols::match::NumNeighborsMPM::passes_com_vector_criterion(), protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturber::perturb_chain(), protocols::stepwise::modeler::rna::phosphate_base_phosphate_square_deviation(), protocols::stepwise::modeler::rna::phosphate_square_deviation(), protocols::hybridization::ChunkTrialMover::pick_random_chunk(), protocols::hotspot_hashing::HotspotStubSet::prepare_hashing_packer_task_(), core::scoring::Ramachandran2B::RamaE(), core::scoring::Ramachandran2B::RamaE_Lower(), core::scoring::Ramachandran2B::RamaE_Upper(), protocols::cryst::FitBfactorsMover::randomize_bs(), protocols::loop_grower::LoopGrower::refine_cycle(), protocols::protein_interface_design::movers::PlacementMinimizationMover::refresh_bbstub_constraints(), protocols::stepwise::modeler::rna::remove_all_variant_types(), protocols::features::ProteinResidueConformationFeatures::report_features(), protocols::features::ResidueConformationFeatures::report_features(), protocols::features::ProteinBackboneAtomAtomPairFeatures::report_features(), core::scoring::membrane::MPResidueLipophilicityEnergy::report_ressolv(), protocols::simple_moves::PeriodicBoxMover::report_thermodynamics(), core::scoring::methods::RamachandranEnergy::residue_energy(), core::scoring::nv::NVscore::residue_energy(), core::scoring::methods::EnvEnergy::residue_energy(), core::pack::dunbrack::cenrot::CenRotDunEnergy::residue_energy(), core::scoring::methods::SmoothEnvEnergy::residue_energy(), core::scoring::methods::CenRotEnvEnergy::residue_energy(), core::scoring::methods::MembraneCbetaEnergy::residue_energy(), core::scoring::membrane::MPCbetaEnergy::residue_energy(), core::scoring::methods::SequenceDependentRefEnergy::residue_energy(), core::scoring::methods::MembraneEnvEnergy::residue_energy(), core::scoring::methods::MembraneEnvSmoothEnergy::residue_energy(), core::scoring::methods::P_AA_ss_Energy::residue_energy(), core::scoring::membrane::MPTerminiPenalty::residue_energy(), core::scoring::membrane::MPNonHelixPenalty::residue_energy(), core::scoring::methods::EnvSmoothEnergy::residue_energy(), core::scoring::methods::ReferenceEnergy::residue_energy(), core::scoring::methods::NMerPSSMEnergy::residue_energy(), core::scoring::membrane::FaMPEnvSmoothEnergy::residue_energy(), core::scoring::membrane::MPEnvEnergy::residue_energy(), core::scoring::membrane::MPHelicalityEnergy::residue_energy(), protocols::fldsgn::potentials::AACompositionEnergy::residue_energy(), core::scoring::interface_::DDPscore::residue_pair_energy(), core::scoring::disulfides::CentroidDisulfideEnergy::residue_pair_energy(), core::scoring::methods::GaussianOverlapEnergy::residue_pair_energy(), core::scoring::methods::SmoothCenPairEnergy::residue_pair_energy(), core::scoring::methods::CenRotPairEnergy::residue_pair_energy(), core::scoring::methods::CenPairEnergy::residue_pair_energy(), core::scoring::membrane::MPPairEnergy::residue_pair_energy(), core::scoring::electron_density::FastDensEnergy::residue_pair_energy(), core::scoring::methods::CenHBEnergy::residue_pair_energy(), core::scoring::methods::ProClosureEnergy::residue_pair_energy(), core::scoring::methods::PointWaterEnergy::residue_pair_energy(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::residue_pair_energy(), core::scoring::electron_density::ElecDensCenEnergy::residue_pair_energy(), core::scoring::electron_density::ElecDensEnergy::residue_pair_energy(), core::scoring::electron_density_atomwise::ElecDensAtomwiseEnergy::residue_pair_energy(), core::scoring::methods::DNA_ReferenceEnergy::residue_pair_energy(), core::scoring::methods::CartesianBondedEnergy::residue_pair_energy_sorted(), core::scoring::electron_density_atomwise::ElectronDensityAtomwise::residue_score(), protocols::dna::PDBOutput::residues_are_different(), protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::restrict_sequence_profile(), core::scoring::rna::chemical_shift::ring_current_effect(), core::scoring::rna::chemical_shift::ring_current_effect_individual_ring(), core::scoring::rna::chemical_shift::ring_pos(), core::pack::dunbrack::rotamer_from_chi(), core::scoring::dna::DirectReadoutPotential::rsd_rsd_energy(), core::pack::annealer::FixbbPwatSimAnnealer::run(), core::scoring::constraints::BackboneStubLinearConstraint::score(), core::scoring::constraints::BackboneStubConstraint::score(), core::scoring::MembranePotential::score_normal_center(), protocols::relax::AtomCoordinateCstMover::set_constraints_on_func_groups(), protocols::hbnet::HBNet::setup(), protocols::simple_moves::ShakeStructureMover::setup_ca_constraints(), protocols::rna::denovo::movers::RNA_DeNovoMasterMover::setup_dock_into_density_mover(), core::scoring::saxs::FastSAXSEnergy::setup_for_derivatives(), core::scoring::methods::RG_LocalEnergy::setup_for_derivatives(), core::scoring::methods::RG_Energy_Fast::setup_for_derivatives(), core::scoring::hbonds::HBondEnergy::setup_for_packing(), core::scoring::lkball::LK_BallEnergy::setup_for_packing(), core::scoring::etable::BaseEtableEnergy< Derived >::setup_for_packing(), core::scoring::elec::FA_ElecEnergy::setup_for_packing(), core::scoring::hbonds::HBondSet::setup_for_residue_pair_energies(), core::scoring::methods::Abego::setup_for_scoring(), core::scoring::saxs::FastSAXSEnergy::setup_for_scoring(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::setup_for_scoring(), protocols::idealize::IdealizeMover::setup_idealize_constraints(), protocols::calc_taskop_movers::DesignRepackMover::setup_packer_and_movemap(), protocols::simple_moves::PeriodicBoxMover::setup_pose(), protocols::rbsegment_relax::setup_pose_from_rbsegs(), protocols::simple_filters::ShapeComplementarityFilter::setup_single_component_symm(), protocols::scoring::Interface::show(), protocols::hybridization::DDomainParse::split(), core::fragment::SingleResidueFragData::steal(), protocols::denovo_design::symmetric_fold_tree(), core::scoring::MembranePotential::termini_penalty(), core::pose::rna::update_edge_hbond_numbers(), core::pose::rna::update_edge_hbond_numbers_careful_hydrogen(), core::scoring::lkball::LK_BallEnergy::update_residue_for_packing(), core::pack::rotamers::SingleResidueRotamerLibrary::virtual_sidechain(), and protocols::simple_filters::ShapeComplementarityFilter::write_area().

Size core::conformation::Residue::abase2 ( Size const  atomno ) const

inline

Returns the atom index of the <atomno> atom's second base atom note: abase2 is this atom's first bonded neighbor other than this atom's base atom (unless it has only one neighbor)

References core::chemical::ResidueType::abase2(), and rsd_type_.

Referenced by core::scoring::hbonds::assign_abase_derivs(), core::pack::rotamer_set::build_acceptor_acceptor_waters(), protocols::simple_moves::ExplicitWaterMover::build_backbone_rotamer_clouds(), core::pack::rotamer_set::build_donor_acceptor_waters(), core::pack::rotamer_set::build_sew_waters_to_acceptor(), protocols::ligand_docking::ga_ligand_dock::GridScorer::calculate_grid(), core::scoring::hbonds::create_acc_orientation_vector(), core::scoring::hbonds::create_rotamer_descriptor(), protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), core::scoring::geometric_solvation::fill_atom_derivs_for_acceptor(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_1b_energy(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_2b_energy(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_acceptor_base_atm_xyz(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_acceptor(), core::scoring::magnesium::get_cos_theta(), protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::get_possible_hbond_acceptors(), core::scoring::WaterAdductHBondPotential::get_residue_residue_h2o_hbonds_1way(), core::scoring::WaterAdductHBondPotential::h2o_hbond_score_1way(), core::scoring::hbonds::hb_energy(), core::scoring::hbonds::HBondEnergy::hbond_derivs_1way(), core::scoring::hbonds::identify_hbonds_1way(), core::scoring::hbonds::identify_hbonds_1way_AHdist(), core::scoring::hbonds::identify_hbonds_1way_membrane(), core::scoring::hbonds::identify_intra_res_hbonds(), protocols::features::HBondFeatures::insert_hbond_geom_coords(), and protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::semiexpl_water_hbgeom_score().

AtomIndices const& core::conformation::Residue::accpt_pos ( ) const

inline

Returns the AtomIndices of this residue's h-bond acceptor atoms.

Note

: AtomIndices == vector1< Size >

example(s): residue.accpt_pos() See also: Residue Residue.accpt_pos_sc Residue.atoms Pose

References core::chemical::ResidueType::accpt_pos(), and rsd_type_.

Referenced by core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_intra(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_one_way(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_one_way_bb_bb(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_one_way_sc(), core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::atom_is_acceptor(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::atom_is_acceptor(), core::pose::rna::atom_is_acceptor(), core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::atom_is_valid_base(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::atom_is_valid_base(), core::scoring::carbon_hbonds::CarbonHBondEnergy::bb_bb_carbon_hbond_one_way(), core::scoring::carbon_hbonds::CarbonHBondEnergy::bb_sc_carbon_hbond_one_way(), protocols::simple_moves::ExplicitWaterMover::build_backbone_rotamer_clouds(), core::pack::rotamer_set::build_moving_O_bridge_waters(), protocols::ligand_docking::ga_ligand_dock::GridScorer::calculate_grid(), core::scoring::geometric_solvation::compute_exact_geosol(), core::pack::interaction_graph::create_hbonds_one_way(), protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), core::scoring::PointWaterPotential::eval_pointwater_derivs(), core::scoring::PointWaterPotential::eval_pointwater_score(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::eval_residue_pair_derivatives_one_way(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_1b_energy(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_2b_energy(), core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::get_atom_atom_occ_solvation(), core::scoring::WaterAdductHBondPotential::get_residue_residue_h2o_hbonds_1way(), core::scoring::WaterAdductHBondPotential::h2o_hbond_score_1way(), core::scoring::hbonds::HBondEnergy::hbond_derivs_1way(), core::scoring::hbonds::identify_hbonds_1way(), core::scoring::hbonds::identify_hbonds_1way_AHdist(), core::scoring::hbonds::identify_hbonds_1way_membrane(), core::scoring::hbonds::identify_intra_res_hbonds(), protocols::hbnet::HBNet::quick_and_dirty_heavy_atom_is_unsat(), protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::recompute(), core::scoring::carbon_hbonds::CarbonHBondEnergy::res_res_carbon_hbond_derivs_one_way(), core::scoring::carbon_hbonds::CarbonHBondEnergy::res_res_carbon_hbond_one_way(), core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::res_res_occ_sol_one_way(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::res_res_occ_sol_one_way(), core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::residue_energy(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::residue_energy(), protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::residue_partition(), core::scoring::carbon_hbonds::CarbonHBondEnergy::sc_bb_carbon_hbond_one_way(), and core::scoring::carbon_hbonds::CarbonHBondEnergy::sc_sc_carbon_hbond_one_way().

AtomIndices const& core::conformation::Residue::accpt_pos_sc ( ) const

inline

Returns the AtomIndices of this residue's sidechain h-bond acceptor atoms.

Note

: AtomIndices == vector1< Size >

example(s): residue.accpt_pos_sc() See also: Residue Residue.accpt_pos Residue.atoms Pose

References core::chemical::ResidueType::accpt_pos_sc(), and rsd_type_.

Referenced by protocols::hbnet::HBNet::quick_and_dirty_network_has_heavy_atom_unsat().

Vector const& core::conformation::Residue::actcoord ( ) const

inline

Returns the coordinates used for pairE calculations (amino acids only)

References actcoord_.

Referenced by core::scoring::rna::RNP_LowResPairDistPotential::calc_rnp_pair_dist_score(), core::scoring::methods::PairEnergy::eval_residue_pair_derivatives(), core::scoring::rna::RNA_VDW_Energy::evaluate_rnp_vdw_score(), core::pack::interaction_graph::SymmOnTheFlyNode::get_rotamer(), core::conformation::orient_residue_for_ideal_bond(), core::scoring::PairEPotential::pair_term_energy(), core::scoring::rna::RNP_LowResEnergy::residue_pair_energy(), protocols::features::OrbitalsFeatures::set_OrbH_features_data(), protocols::features::OrbitalsFeatures::set_OrbOrb_features_data(), core::scoring::rna::RNP_LowResEnergy::setup_for_scoring(), and update_actcoord().

Vector& core::conformation::Residue::actcoord ( )

inline

Returns the coordinates used for pairE calculations (amino acids only)

References actcoord_.

AtomIndices const& core::conformation::Residue::actcoord_atoms ( ) const

inline

Returns the AtomIndices of atoms that will be used to define this residue's actcoord.

References core::chemical::ResidueType::actcoord_atoms(), and rsd_type_.

Referenced by core::scoring::methods::PairEnergy::eval_residue_pair_derivatives().

chemical::ResConnID core::conformation::Residue::actual_residue_connection ( Size  resconnid ) const

inline

Get the residue connection. How is this different than residue_connection?

References connect_map_.

Referenced by core::conformation::Conformation::bonded_neighbor_all_res(), core::scoring::etable::count_pair::CountPairGeneric::CountPairGeneric(), and core::conformation::Conformation::detect_pseudobonds().

AtomIndices const& core::conformation::Residue::all_bb_atoms ( ) const

inline

Returns the AtomIndices of this residue's backbone atoms.

Note

: heavyatoms and hydrogens, AtomIndices == vector1< Size >

example(s): residue.all_bb_atoms() See also: Residue Residue.atoms Pose

References core::chemical::ResidueType::all_bb_atoms(), and rsd_type_.

Referenced by protocols::legacy_sewing::scoring::LegacyClashScorer::score().

std::string core::conformation::Residue::annotated_name

(

bool const

show_all_variants = true

)

const

Returns this residue's 1-letter representation, including details in square brackets. E.g., H[HIS_D].

References core::chemical::aa_from_oneletter_code(), core::pack::dunbrack::c, name(), name1(), core::chemical::name_from_aa(), and core::chemical::oneletter_code_specifies_aa().

Referenced by core::conformation::Conformation::annotated_sequence(), and core::scoring::rna::output_rna_motif().

void core::conformation::Residue::apply_transform_downstream ( core::Size const  atomno, core::Size const  upstream_atomno, numeric::xyzMatrix< Real > const &  R, Vector const &  v  )

private

apply transform of rotation R and translation V for all atoms downstream

Note

note this is not for general atom tree folding. only used in set_chi in which changes for a chi angle is fast propagated within one residue and not to invoke folding the whole atom tree.

xyz –> R * xyz + v
this uses information from atom_base array to transform all the downstream atoms along the side chain recursively. it assumes that the atom_base array will not get us into any infinite loops!

Note

this is not for general atom tree folding. only used in set_chi in which changes for a chi angle is fast propagated within one residue and not to invoke folding the whole atom tree.

References atom(), core::chemical::ResidueType::atom_base(), core::chemical::ResidueType::bonded_neighbor(), protocols::sic_dock::scores::nbr, nbrs(), core::chemical::ResidueType::root_atom(), rsd_type_, core::conformation::TR(), core::conformation::Atom::xyz(), and xyz().

Referenced by set_all_ring_nu(), set_chi(), set_d(), set_tau(), and set_theta().

void core::conformation::Residue::apply_transform_Rx_plus_v	(	numeric::xyzMatrix< Real >	R,
		Vector	v
	)

Applies a transform of the form Rx + v, where R is a rotation matrix, V is a vector, and x is the original position in xyz space.

References core::chemical::ResidueType::natoms(), set_xyz(), type(), and xyz().

void core::conformation::Residue::assign_orbitals ( )

private

Determine the set of orbitals that are needed and compute their coordinates; invoked from within the constructors.

References core::chemical::ResidueType::atoms_with_orb_index(), core::chemical::ResidueType::bonded_orbitals(), build_orbital_xyz(), core::chemical::ResidueTypeBase::orbital(), core::chemical::Orbital::orbital_type_index(), orbitals_, rsd_type_, and type().

Referenced by Residue().

Atom const& core::conformation::Residue::atom ( Size const  atm_index ) const

inline

Returns this residue's Atom with index number <atm_index> (const)

Note

: Atom object is xyz and atom_type

example(s): residue.atom(3) See also: Residue Residue.atoms Pose

References atoms_.

Referenced by protocols::splice::Splice::add_coordinate_constraints(), protocols::splice::SpliceManager::add_coordinate_constraints(), protocols::splice::Splice::add_dihedral_constraints(), protocols::splice::SpliceManager::add_dihedral_constraints(), protocols::legacy_sewing::Assembly::add_loop_segment(), protocols::sewing::hashing::AlignmentFileGeneratorMover::add_pose_segments_to_segment_vector(), core::scoring::geometric_solvation::add_to_individual_sol_energies(), protocols::topology_broker::MembraneTopologyClaimer::addVirtualResAsRootMembrane(), protocols::loop_grower::SheetSampler::alignPerfectCA(), protocols::loop_grower::SheetSampler::alignStrand(), protocols::pockets::PocketGrid::alter_espGrid_with_bound_ligand(), core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr(), protocols::protein_interface_design::movers::SpinMover::apply(), protocols::rbsegment_relax::IdealizeHelicesMover::apply(), protocols::constraint_generator::MetalContactsConstraintGenerator::apply(), protocols::rigid::RollMover::apply(), protocols::task_operations::InteractingRotamerExplosion::apply(), protocols::simple_moves::chiral::ChiralMover::apply(), protocols::analysis::LoopAnalyzerMover::apply(), protocols::membrane::AqueousPoreFinder::apply(), protocols::simple_moves::Tumble::apply(), protocols::simple_filters::SheetFilter::apply(), protocols::hybridization::CartesianHybridize::apply(), protocols::rbsegment_relax::FragInsertAndAlignMover::apply(), protocols::loop_grower::FragmentExtension::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::docking::membrane::MPFindInterfaceMover::apply(), protocols::rbsegment_relax::SequenceShiftMover::apply(), protocols::hybridization::CartesianHybridize::apply_frag(), protocols::hybridization::CartesianSampler::apply_fragcsts(), protocols::seeded_abinitio::SegmentHybridizer::apply_frame(), protocols::hybridization::CartesianHybridize::apply_frame(), protocols::pockets::PlaidFingerprint::apply_rotation_offset_to_pose_(), apply_transform_downstream(), protocols::match::downstream::LigandConformerBuilder::assign_conformer_group_to_residue(), core::scoring::orbitals::OrbitalsScore::assign_haro_derivs_one_way(), core::scoring::orbitals::OrbitalsScore::assign_hpol_derivs_one_way(), protocols::qsar::scoring_grid::SolvationMetaGrid::atom_score(), core::conformation::membrane::MembraneInfo::atom_z_position(), core::scoring::atomic_depth::atomic_depth(), protocols::idealize::basic_idealize(), core::scoring::orbitals::OrbitalsStatistics::bb_stats(), protocols::sewing::hashing::LigandBindingResPlacer::best_rotamer_for_residue(), protocols::legacy_sewing::LegacyMonteCarloAssemblyMover::boltzman(), build_orbital_xyz(), protocols::peptide_deriver::PeptideDeriverFilter::build_receptor_peptide_pose(), core::conformation::build_residue_tree(), protocols::match::bump_grid_to_enclose_pose(), protocols::match::bump_grid_to_enclose_residue(), protocols::match::bump_grid_to_enclose_residue_backbone(), core::pack::dunbrack::cenrot::CentroidRotamerSampleData::cal_delta_internal_coordinates(), protocols::features::strand_assembly::cal_dis_angle_to_find_sheet(), core::pack::dunbrack::cenrot::CentroidRotamerSampleData::cal_distance_squared(), protocols::features::strand_assembly::cal_min_avg_dis_between_two_sheets_by_cen_res(), protocols::features::strand_assembly::cal_min_dis_between_two_sheets_by_all_res(), protocols::features::strand_assembly::cal_shortest_dis_between_facing_aro_in_sw(), core::scoring::sasa::LeGrandSasa::calc_atom_masks(), core::scoring::calc_atom_masks(), core::select::util::SelectResiduesByLayer::calc_sc_neighbors(), protocols::docking::EllipsoidalRandomizationMover::calculate_axes(), protocols::features::strand_assembly::calculate_dihedral_w_4_resnums(), protocols::ligand_docking::ga_ligand_dock::GridScorer::calculate_grid(), protocols::pockets::PlaidFingerprint::calculate_ligand_CoM(), core::scoring::lkball::LK_BallEnergy::calculate_lk_ball_atom_energies(), core::scoring::lkball::LK_BallEnergy::calculate_lk_ball_atom_energies_cp(), core::scoring::lkball::LK_BallEnergy::calculate_lk_desolvation_of_single_atom_by_residue(), core::scoring::lkball::LK_BallEnergy::calculate_lk_desolvation_of_single_atom_by_residue_no_count_pair(), protocols::docking::EllipsoidalRandomizationMover::calculate_plane_axes(), protocols::pockets::NonPlaidFingerprint::calculate_protein_CoM(), protocols::scoring::methods::pcsTs1::PCS_Energy_Ts1::calculate_scores_and_tensors_from_pose_and_PCS_data(), protocols::scoring::methods::pcsTs2::PCS_Energy_Ts2::calculate_scores_and_tensors_from_pose_and_PCS_data(), protocols::scoring::methods::pcsTs3::PCS_Energy_Ts3::calculate_scores_and_tensors_from_pose_and_PCS_data(), protocols::scoring::methods::pcsTs4::PCS_Energy_Ts4::calculate_scores_and_tensors_from_pose_and_PCS_data(), protocols::scoring::methods::pcs::PCS_Energy::calculate_scores_and_tensors_from_pose_and_PCS_data(), core::scoring::methods::ProQ_Energy::calculateZ(), core::select::util::cbeta_vector(), protocols::pose_length_moves::InsertResMover::center_of_mass(), protocols::simple_moves::Tumble::center_of_mass(), protocols::geometry::center_of_mass(), protocols::hybridization::FragmentBiasAssigner::chainbreak(), protocols::loop_grower::LoopGrower::check_coordinates(), protocols::features::strand_assembly::StrandBundleFeatures::check_strand_too_closeness(), protocols::features::strand_assembly::check_strand_too_closeness(), protocols::features::strand_assembly::check_whether_sheets_are_connected_with_near_bb_atoms(), protocols::features::strand_assembly::check_whether_sw_is_not_connected_with_continuous_atoms(), protocols::ligand_docking::ga_ligand_dock::GridScorer::clash_score(), protocols::simple_filters::AngleToVector::compute(), protocols::simple_filters::AtomicDistanceFilter::compute(), protocols::fldsgn::filters::HelixBendFilter::compute(), core::scoring::CenRotEnvPairPotential::compute_centroid_environment(), core::scoring::SmoothEnvPairPotential::compute_centroid_environment(), protocols::simple_filters::SymmetricMotifFilter::compute_d2(), core::scoring::CenRotEnvPairPotential::compute_dcentroid_environment(), core::scoring::SmoothEnvPairPotential::compute_dcentroid_environment(), core::scoring::MembranePotential::compute_membrane_embedding(), core::scoring::electron_density::ElectronDensity::compute_symm_rotations(), protocols::relax::RangeRelaxMover::constrain_to_reference(), core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms(), protocols::abinitio::copy_side_chains(), protocols::motif_grafting::movers::MotifGraftMover::count_clashes_between_two_poses(), core::scoring::hbonds::create_acc_orientation_vector(), core::scoring::hbonds::create_don_orientation_vector(), protocols::floppy_tail::create_extra_output(), protocols::legacy_sewing::create_model_from_pose(), core::scoring::hbonds::create_rotamer_descriptor(), core::scoring::elec::create_rotamer_descriptor(), core::scoring::lkball::create_rotamer_descriptor(), protocols::cryst::crystRMS(), protocols::cryst::crystRMSfast(), protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), core::conformation::Conformation::detect_bonds(), core::conformation::symmetry::SymmetricConformation::detect_disulfides(), core::conformation::Conformation::detect_disulfides(), protocols::features::strand_assembly::determine_core_heading_surface_heading_by_distance(), protocols::features::strand_assembly::determine_heading_direction_by_vector(), core::scoring::disulfides::DisulfideMatchingPotential::disulfide_RT(), core::scoring::methods::LinearChainbreakEnergy::do_score_dev(), core::scoring::methods::LinearChainbreakEnergy::do_score_ovp(), protocols::pockets::PlaidFingerprint::dump_oriented_pose_and_fp_to_pdb(), protocols::simple_ddg::ddG::duplicate_waters_across_jump(), protocols::metal_interface::MatchGrafter::ensure_proper_his_tautomers(), protocols::rigid::MovePoseToMembraneCenterMover::estimate_membrane_center(), core::scoring::methods::BranchEnergy::eval_atom_derivative(), core::scoring::methods::ChainbreakEnergy::eval_atom_derivative(), core::scoring::methods::MembraneEnvSmoothEnergy::eval_atom_derivative(), core::scoring::methods::EnvSmoothEnergy::eval_atom_derivative(), core::scoring::membrane::FaMPEnvSmoothEnergy::eval_atom_derivative(), core::scoring::rna::RNA_FullAtomVDW_BasePhosphate::eval_atom_derivative(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensCenEnergy::eval_atom_derivative(), core::scoring::hbonds::NPDHBondEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensEnergy::eval_atom_derivative(), core::scoring::etable::BaseEtableEnergy< Derived >::eval_atom_derivative(), core::scoring::lkball::LK_BallEnergy::eval_desolvation_derivs_no_count_pair(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd1(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd2(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_bond_energy(), core::scoring::methods::MMLJEnergyIntra::eval_intrares_derivatives(), core::scoring::etable::BaseEtableEnergy< Derived >::eval_intrares_derivatives(), core::scoring::methods::MMBondLengthEnergy::eval_intrares_energy(), core::scoring::methods::MMTorsionEnergy::eval_intrares_energy(), core::scoring::methods::MMBondAngleEnergy::eval_intrares_energy(), core::scoring::methods::MMLJEnergyIntra::eval_intrares_energy(), core::scoring::methods::MMLJEnergyIntra::eval_intrares_energy_ext(), core::scoring::etable::BaseEtableEnergy< Derived >::eval_intrares_energy_ext(), core::scoring::PointWaterPotential::eval_pointwater_derivs(), core::scoring::PointWaterPotential::eval_pointwater_score(), core::scoring::methods::SmoothEnvEnergy::eval_residue_derivatives(), core::scoring::methods::CenRotEnvEnergy::eval_residue_derivatives(), core::pack::dunbrack::cenrot::CenRotDunEnergy::eval_residue_derivatives(), core::scoring::methods::CenRotPairEnergy::eval_residue_pair_derivatives(), core::scoring::methods::SmoothCenPairEnergy::eval_residue_pair_derivatives(), core::scoring::methods::CenHBEnergy::eval_residue_pair_derivatives(), core::scoring::electron_density::FastDensEnergy::eval_residue_pair_derivatives(), core::scoring::methods::PointWaterEnergy::eval_residue_pair_derivatives(), core::scoring::methods::LK_PolarNonPolarEnergy::eval_residue_pair_derivatives(), core::scoring::etable::BaseEtableEnergy< Derived >::eval_residue_pair_derivatives(), core::scoring::methods::CenHBEnergy::eval_residue_pair_derivatives_soft(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_env_and_cbeta_deriv(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_pair_orientation_score(), core::scoring::SmoothEnvPairPotential::evaluate_env_and_cbeta_deriv(), core::scoring::lkball::evaluate_lk_ball_energy_for_atom_ranges(), protocols::scoring::InterchainPotential::evaluate_pair_and_vdw_score(), protocols::pockets::GenPharmacophore::extract_Hbond_atoms_from_protein_rna_complex(), protocols::pockets::GenPharmacophore::extract_rna_rings_from_protein_rna_complex(), protocols::pockets::DarcParticleSwarmMinimizer::fill_atom_arrays_for_electrostatics_(), protocols::match::fill_grid_with_backbone_heavyatom_spheres(), protocols::match::fill_grid_with_residue_heavyatom_spheres(), protocols::match::fill_grid_with_residue_spheres(), core::io::silent::BinarySilentStruct::fill_struct(), core::scoring::atomic_depth::AtomicDepth::fillvoxels(), core::scoring::methods::BranchEnergy::finalize_total_energy(), core::scoring::methods::LinearBranchEnergy::finalize_total_energy(), core::scoring::etable::BaseEtableEnergy< Derived >::finalize_total_energy(), protocols::features::strand_assembly::StrandBundleFeatures::find_antiparallel(), protocols::simple_moves::ExplicitWaterMover::find_closest(), protocols::simple_filters::HelixHelixAngleFilter::find_closest_res(), protocols::loophash::FastGapMover::find_next_gap(), protocols::features::strand_assembly::StrandBundleFeatures::find_parallel(), protocols::features::strand_assembly::find_sheet(), protocols::rigid::RigidBodyTiltMover::find_tilt_center(), protocols::metal_interface::ZincSiteFinder::find_zinc_site(), protocols::electron_density::findLoopFromDensity(), protocols::membrane::geometry::EmbeddingDef::from_span(), protocols::membrane::geometry::EmbeddingDef::from_span_positive_z(), protocols::loop_grower::LoopGrower::GDThatonative(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_1b_energy(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_2b_energy(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_acceptor_base_atm_xyz(), protocols::loops::loop_closure::ccd::CCDLoopClosureMover::get_anchors(), core::scoring::carbon_hbonds::CarbonHBondEnergy::get_atom_atom_carbon_hbond_energy(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_acceptor(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_donor(), core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::get_atom_atom_occ_solvation(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::get_atom_atom_occ_solvation(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::get_atom_lk_energy(), protocols::features::strand_assembly::StrandBundleFeatures::get_avg_dis_CA_CA(), protocols::features::strand_assembly::get_avg_dis_CA_CA(), protocols::features::strand_assembly::get_avg_dis_strands(), protocols::rna::denovo::movers::RNA_HelixMover::get_backbone_centroid(), protocols::features::strand_assembly::get_central_residues_in_each_of_two_edge_strands(), protocols::membrane::get_chain_and_z(), protocols::features::strand_assembly::get_closest_distance_between_strands(), core::scoring::magnesium::get_cos_theta(), core::scoring::disulfides::FullatomDisulfidePotential::get_disulfide_params(), core::scoring::orbitals::OrbitalsScore::get_E_haro_one_way(), core::scoring::orbitals::OrbitalsScore::get_E_hpol_one_way(), protocols::toolbox::match_enzdes_util::InvrotTreeNode::get_fixed_pt(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_grid_atomtypes(), protocols::pockets::GenPharmacophore::get_ideal_hydrogenBond_atoms(), protocols::features::strand_assembly::StrandBundleFeatures::get_nearest_res_from_strand(), core::scoring::methods::Fa_MbsolvEnergy::get_residue_pair_energy(), core::scoring::membrane::FaMPSolvEnergy::get_residue_pair_energy(), core::scoring::methods::LK_PolarNonPolarEnergy::get_residue_pair_energy_one_way(), protocols::hybridization::get_superposition_transformation(), protocols::hybridization::CartesianSampler::get_transform(), protocols::simple_moves::BBConRotMover::get_VdRdPhi(), protocols::simple_moves::BBGaussianMover::get_VdRdPhi(), protocols::cryst::getMW(), protocols::rbsegment_relax::guess_rbsegs_from_pose(), protocols::loops::has_severe_pep_bond_geom_issues(), core::scoring::hbonds::HBondEnergy::hbond_derivs_1way(), protocols::seeded_abinitio::SegmentHybridizer::hybridize(), core::scoring::hbonds::identify_hbonds_1way(), core::scoring::hbonds::identify_hbonds_1way_AHdist(), core::scoring::hbonds::identify_hbonds_1way_membrane(), core::scoring::hbonds::identify_intra_res_hbonds(), protocols::pockets::NonPlaidFingerprint::include_eggshell_points_based_on_known_ligand(), protocols::topology_broker::RigidChunkClaimer::initialize_dofs(), protocols::match::downstream::RigidLigandBuilder::initialize_from_residue(), protocols::match::downstream::LigandConformerBuilder::initialize_from_residue(), protocols::rbsegment_relax::FragInsertAndAlignMover::initialize_rb_fragments(), core::scoring::inline_intraresidue_atom_pair_energy(), core::scoring::inline_residue_atom_pair_energy(), protocols::features::HBondFeatures::insert_hbond_geom_coords(), protocols::features::HBondFeatures::insert_hbond_lennard_jones_row(), protocols::features::HBondFeatures::insert_site_atoms_row(), protocols::features::strand_assembly::is_this_strand_at_edge(), protocols::features::strand_assembly::StrandBundleFeatures::judge_facing(), protocols::features::strand_assembly::judge_facing(), protocols::loop_grower::LoopPartialSolution::LoopPartialSolution(), protocols::simple_moves::BBConRotMover::make_move(), core::scoring::electron_density::ElectronDensity::matchAtomFast(), core::scoring::electron_density::ElectronDensity::matchRes(), core::scoring::electron_density::ElectronDensity::matchResFast(), protocols::motifs::Motif::Motif(), core::scoring::nmr::NMRDummySpinlabelConformer::NMRDummySpinlabelConformer(), core::scoring::MembranePotential::non_helix_in_membrane_penalty(), orient_onto_location(), orient_onto_residue(), orient_onto_residue_peptoid(), protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::output_rep(), protocols::hybridization::MRMover::pack_missing_sidechains(), protocols::match::NumNeighborsMPM::passes_com_vector_criterion(), place(), protocols::motifs::Motif::place_atom_(), protocols::cryst::MakeLatticeMover::place_near_origin(), protocols::motifs::Motif::place_residue_helper(), core::scoring::PQR::PQR(), core::scoring::elec::FA_GrpElecEnergy::precalc_context(), protocols::viewer::print_node(), core::scoring::methods::PoissonBoltzmannEnergy::protein_position_equal_within(), core::conformation::symmetry::SymmetricConformation::recalculate_transforms(), protocols::pockets::PocketGrid::recenter(), protocols::qsar::scoring_grid::SolvationGrid::refresh(), protocols::toolbox::match_enzdes_util::InvrotTreeNode::remove_invrots_clashing_with_parent_res(), protocols::features::SmotifFeatures::report_features(), protocols::features::ModelFeatures::report_features(), protocols::features::OrbitalsFeatures::report_hpol_orbital_interactions(), protocols::features::ProteinBondGeometryFeatures::report_interres_angles(), protocols::features::ProteinBondGeometryFeatures::report_interres_lengths(), protocols::features::ProteinBondGeometryFeatures::report_intrares_angles(), protocols::features::ProteinBondGeometryFeatures::report_intrares_lengths(), protocols::features::ProteinBondGeometryFeatures::report_intrares_torsions(), Residue(), core::conformation::symmetry::residue_center_of_mass(), protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::residue_conformations_redundant(), core::scoring::methods::BurialEnergy::residue_energy(), core::scoring::methods::Fa_MbenvEnergy::residue_energy(), core::scoring::membrane::FaMPEnvEnergy::residue_energy(), core::scoring::methods::MembraneEnvSmoothEnergy::residue_energy(), core::scoring::rna::RNA_FullAtomVDW_BasePhosphate::residue_energy(), core::scoring::methods::EnvSmoothEnergy::residue_energy(), core::scoring::membrane::FaMPEnvSmoothEnergy::residue_energy(), core::scoring::rna::RNA_FullAtomVDW_BasePhosphate::residue_fast_pair_energy_attached_H(), core::scoring::residue_fast_pair_energy_attached_H(), core::scoring::methods::SmoothCenPairEnergy::residue_pair_energy(), core::scoring::methods::CenRotPairEnergy::residue_pair_energy(), core::scoring::methods::CenPairEnergy::residue_pair_energy(), core::scoring::methods::SuckerEnergy::residue_pair_energy(), core::scoring::methods::MembraneCenPairEnergy::residue_pair_energy(), core::scoring::membrane::MPPairEnergy::residue_pair_energy(), core::scoring::methods::CenHBEnergy::residue_pair_energy(), core::scoring::methods::MMBondLengthEnergy::residue_pair_energy(), core::scoring::methods::MMBondAngleEnergy::residue_pair_energy(), core::scoring::methods::PointWaterEnergy::residue_pair_energy(), core::scoring::rna::RNA_LJ_BaseEnergy::residue_pair_energy(), core::scoring::methods::LK_hack::residue_pair_energy(), core::scoring::methods::MMLJEnergyInter::residue_pair_energy(), core::scoring::methods::LK_PolarNonPolarEnergy::residue_pair_energy_ext(), core::scoring::etable::BaseEtableEnergy< Derived >::residue_pair_energy_ext(), core::conformation::membrane::MembraneInfo::residue_z_position(), core::conformation::symmetry::return_nearest_residue(), protocols::symmetry::SymmetrySlider::rg(), protocols::pockets::PlaidFingerprint::rmsd(), protocols::loop_grower::LoopGrower::RMStonative(), protocols::membrane::rsd_closest_to_chain_tm_com(), core::scoring::orbitals::OrbitalsStatistics::sc_H_orbital(), protocols::qsar::scoring_grid::SolvationMetaGrid::score(), core::scoring::MembranePotential::score_normal_center(), protocols::features::strand_assembly::see_whether_sheet_is_antiparallel(), core::select::util::select_coord_for_residue(), set_all_ring_nu(), set_chi(), protocols::hbnet::HBNet::set_constraints(), set_d(), protocols::features::OrbitalsFeatures::set_OrbH_features_data(), protocols::features::OrbitalsFeatures::set_OrbOrb_features_data(), set_tau(), set_theta(), protocols::scoring::methods::pcs2::GridSearchIteratorCA::set_vec(), set_xyz(), protocols::flexpep_docking::FlexPepDockingFlags::setDefaultAnchors(), core::scoring::saxs::FastSAXSEnergy::setup_for_derivatives(), core::scoring::saxs::FastSAXSEnergy::setup_for_scoring(), protocols::hybridization::setup_user_coordinate_constraints(), protocols::loop_grower::LoopPartialSolutionStore::skeleton_filter(), protocols::hybridization::DDomainParse::split(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::storeposedata(), core::scoring::lkball::LK_BallEnergy::sum_deriv_contributions_for_heavyatom_pair_one_way(), protocols::topology_broker::RigidChunkClaimer::switch_to_fullatom(), core::scoring::MembranePotential::termini_penalty(), protocols::loop_grower::transform_to_closest_symmunit(), protocols::hybridization::MRMover::trim_target_pose(), update_nus(), core::scoring::nmr::pcs::PCSSingleSet::update_spin_coordinates(), core::scoring::nmr::rdc::RDCMultiSet::update_spin_coordinates(), core::scoring::nmr::pre::PREMultiSet::update_spin_coordinates(), protocols::scoring::methods::pcs2::PcsDataCenter::update_X_Y_Z_all(), protocols::scoring::methods::pcsTs2::PCS_data_Ts2::update_X_Y_Z_all(), protocols::scoring::methods::pcsTs1::PCS_data_Ts1::update_X_Y_Z_all(), protocols::scoring::methods::pcsTs3::PCS_data_Ts3::update_X_Y_Z_all(), protocols::scoring::methods::pcs::PCS_data::update_X_Y_Z_all(), protocols::scoring::methods::pcsTs4::PCS_data_Ts4::update_X_Y_Z_all(), protocols::features::helixAssembly::HelixBundleFeatures::validate_bundle(), protocols::features::strand_assembly::write_number_of_electrostatic_interactions_of_residues_to_files(), protocols::features::strand_assembly::WriteToDB_ending_loop(), protocols::features::strand_assembly::WriteToDB_starting_loop(), core::chemical::ICoorAtomID::xyz(), and xyz().

Atom& core::conformation::Residue::atom ( Size const  atm_index )

inline

Returns this residue's Atom with index number <atm_index> (non-const)

Note

: Atom object is xyz and atom_type

example(s): residue.atom(3) See also: Residue Residue.atoms Pose

References atoms_.

Atom const& core::conformation::Residue::atom ( std::string const &  atm_name ) const

inline

Returns this residue's Atom with name <atm_name> (const)

Note

: Atom object is xyz and atom_type, slower but safer than hard-coding an integer index in code where you need a specific atom

example(s): residue.atom(3) See also: Residue Residue.atoms Pose

References atom_index(), and atoms_.

Atom& core::conformation::Residue::atom ( std::string const &  atm_name )

inline

Returns this residue's Atom with name <atm_name> (non-const)

Note

: Atom object is xyz and atom_type, slower but safer than hard-coding an integer index in code where you need a specific atom

example(s): residue.atom(3) See also: Residue Residue.atoms Pose

References atom_index(), and atoms_.

Size core::conformation::Residue::atom_base ( Size const  atomno ) const

inline

Returns the atom index of the <atomno> atom's base atom.

References core::chemical::ResidueType::atom_base(), and rsd_type_.

Referenced by core::scoring::geometric_solvation::add_to_individual_sol_energies(), protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::apply(), core::scoring::hbonds::assign_abase_derivs(), core::scoring::elec::assign_rna_atom_type(), core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::atom_is_valid_base(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::atom_is_valid_base(), core::pose::rna::bases_form_a_hydrogen_bond(), core::pack::rotamer_set::build_acceptor_acceptor_waters(), protocols::simple_moves::ExplicitWaterMover::build_backbone_rotamer_clouds(), core::pack::rotamer_set::build_donor_acceptor_waters(), core::pack::rotamer_set::build_donor_donor_waters(), core::pack::rotamer_set::build_sew_waters_to_acceptor(), core::pack::rotamer_set::build_sew_waters_to_donor(), protocols::ligand_docking::ga_ligand_dock::GridScorer::calculate_grid(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_donor_atom_energy(), core::scoring::geometric_solvation::compute_exact_geosol(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_polar_group_sol_energy(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_sho_donor_atom_energy(), core::scoring::hbonds::create_acc_orientation_vector(), core::scoring::hbonds::create_don_orientation_vector(), core::pack::interaction_graph::create_hbonds_one_way(), core::scoring::hbonds::create_rotamer_descriptor(), protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), core::pack::hbonds::determine_atom_level_edge_info(), core::scoring::hbonds::NPDHBondEnergy::eval_atom_derivative(), core::scoring::PointWaterPotential::eval_pointwater_derivs(), core::scoring::PointWaterPotential::eval_pointwater_score(), core::scoring::VdWTinkerPotential::eval_residue_pair_derivatives(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::eval_residue_pair_derivatives_one_way(), protocols::pockets::GenPharmacophore::extract_Hbond_atoms_from_protein_rna_complex(), core::scoring::geometric_solvation::fill_atom_derivs_for_donor(), protocols::generalized_kinematic_closure::GeneralizedKIC::generate_atomlist(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_1b_energy(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_2b_energy(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_acceptor_base_atm_xyz(), core::scoring::hbonds::HBond::get_AHDangle(), core::scoring::carbon_hbonds::CarbonHBondEnergy::get_atom_atom_carbon_hbond_energy(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_acceptor(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_donor(), core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::get_atom_atom_occ_solvation(), core::scoring::hbonds::HBond::get_BAHangle(), core::scoring::hbonds::HBond::get_BAtorsion(), core::scoring::magnesium::get_cos_theta(), protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::get_possible_hbond_acceptors(), core::scoring::VdWTinkerPotential::get_res_res_vdw(), core::scoring::WaterAdductHBondPotential::get_residue_residue_h2o_hbonds_1way(), core::scoring::WaterAdductHBondPotential::h2o_hbond_score_1way(), core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy::has_bb_hbond(), core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy::has_hbond(), core::scoring::hbonds::hb_energy(), core::scoring::hbonds::HBondEnergy::hbond_derivs_1way(), protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::hbond_energy(), protocols::protein_interface_design::hbonded_atom(), core::pose::rna::heavy_atom_is_polar(), core::scoring::hbonds::identify_hbonds_1way(), core::scoring::hbonds::identify_hbonds_1way_AHdist(), core::scoring::hbonds::identify_hbonds_1way_membrane(), core::scoring::hbonds::identify_intra_res_hbonds(), protocols::features::HBondFeatures::insert_hbond_geom_coords(), protocols::features::HBondFeatures::insert_hbond_lennard_jones_row(), protocols::features::HBondFeatures::insert_site_row(), core::scoring::elec::is_base_2(), core::scoring::elec::is_phosphate_2(), core::scoring::rna::StackElecEnergy::is_rna_base(), core::scoring::elec::is_sugar_2(), core::scoring::packing::PoseBalls::PoseBalls(), protocols::hbnet::HBNet::quick_and_dirty_heavy_atom_is_unsat(), protocols::hbnet::HBNet::quick_and_dirty_network_has_heavy_atom_unsat(), core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::res_res_occ_sol_one_way(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::res_res_occ_sol_one_way(), core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::residue_energy(), protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::semiexpl_water_hbgeom_score(), protocols::hbnet::HBNet::set_constraints(), protocols::features::OrbitalsFeatures::set_OrbH_features_data(), protocols::features::OrbitalsFeatures::set_OrbOrb_features_data(), core::scoring::hbonds::HBond::show(), and protocols::ligand_docking::ga_ligand_dock::LigandConformer::superimpose_to_alternative_frame().

Atoms::iterator core::conformation::Residue::atom_begin ( )

inline

begin interator, to iterate over atoms

References atoms_.

Referenced by core::select::util::any_atoms_within_cutoff(), protocols::dna::argrot_dna_dis2(), protocols::dna::close_to_dna(), protocols::environment::com_calc(), protocols::nmr::pcs::PCSLigandTransformMover::define_ligand_frame_origin(), protocols::hotspot_hashing::HotspotStubSet::find_neighboring_stubs(), and core::scoring::interface_::DDPscore::residue_pair_energy().

Atoms::const_iterator core::conformation::Residue::atom_begin ( ) const

inline

References atoms_.

bool core::conformation::Residue::atom_depends_on_lower

(

core::Size const

atom_index

)

const

Does this atom depend on the LOWER_CONNECT?

Now based on a simple lookup, based on data initialized during ResidueType::finalize().

Author

Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

References core::chemical::ResidueType::atom_depends_on_lower_polymeric_connection(), and rsd_type_.

Referenced by place(), and core::conformation::Conformation::rebuild_polymer_bond_dependent_atoms().

bool core::conformation::Residue::atom_depends_on_upper

(

core::Size const

atom_index

)

const

Does this atom depend on the UPPER_CONNECT?

Now based on a simple lookup, based on data initialized during ResidueType::finalize().

Author

Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

References core::chemical::ResidueType::atom_depends_on_upper_polymeric_connection(), and rsd_type_.

Referenced by place(), and core::conformation::Conformation::rebuild_polymer_bond_dependent_atoms().

Atoms::iterator core::conformation::Residue::atom_end ( )

inline

end interator, to iterate over atoms

References atoms_.

Referenced by protocols::nmr::pcs::PCSLigandTransformMover::define_ligand_frame_origin(), and protocols::hotspot_hashing::HotspotStubSet::find_neighboring_stubs().

Atoms::const_iterator core::conformation::Residue::atom_end ( ) const

inline

References atoms_.

Size core::conformation::Residue::atom_index ( std::string const &  atm ) const

inline

Returns the index number of the <atm> in this residue example: residue.atom_index("CA") returns 2 for a normal amino acid.

example(s): residue.atom_index("CA") See also: Residue AtomType Pose

References core::chemical::ResidueType::atom_index(), and rsd_type_.

Referenced by protocols::protein_interface_design::movers::PlaceOnLoop::add_bb_csts_to_loop(), protocols::jumping::JumpSample::add_chainbreaks_as_distance_constraint(), protocols::seeded_abinitio::add_coordinate_constraints(), protocols::splice::Splice::add_coordinate_constraints(), protocols::splice::SpliceManager::add_coordinate_constraints(), protocols::protein_interface_design::movers::add_coordinate_constraints(), core::util::add_covalent_linkage_helper(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::add_cyclic_constraints(), protocols::ncbb::SecStructMinimizeMover::add_dihedral_constraints_to_pose(), protocols::seeded_abinitio::add_dist_constraints(), core::scoring::dna::DNATorsionPotential::add_dna_base_distance_constraints(), protocols::antibody::constraints::add_harmonic_dihedral_cst_general(), protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_pose(), protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_wholepose(), protocols::motifs::add_motif_bb_constraints(), protocols::motifs::add_motif_sc_constraints(), core::import_pose::RNA_JumpMover::add_new_RNA_jump(), core::pose::ncbb::add_oop_constraint(), protocols::sewing::hashing::AlignmentFileGeneratorMover::add_pose_segments_to_segment_vector(), core::scoring::dna::DNATorsionPotential::add_sugar_ring_closure_constraints(), core::pose::ncbb::add_triazole_constraint(), protocols::loops::addScoresForLoopParts(), core::conformation::Conformation::align_virtual_atoms_in_carbohydrate_residue(), core::conformation::Conformation::append_residue(), core::pose::Pose::append_residue_by_atoms(), protocols::protein_interface_design::movers::TaskAwareCsts::apply(), protocols::simple_moves::oop::OopMover::apply(), protocols::simple_moves::triazolamer::TriazolamerMover::apply(), protocols::simple_moves::oop::OopRandomSmallMover::apply(), protocols::simple_moves::triazolamer::TriazolamerRandomSmallMover::apply(), protocols::constraint_generator::MetalContactsConstraintGenerator::apply(), protocols::protein_interface_design::movers::BestHotspotCstMover::apply(), protocols::protein_interface_design::movers::PlacementAuctionMover::apply(), protocols::helical_bundle::FitSimpleHelix::apply(), protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover::apply(), core::pack::task::operation::NoRepackDisulfides::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_Backrub::apply(), protocols::comparative_modeling::ExtraThreadingMover::apply(), protocols::splice::Splice::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::symmetry::SetupNCSMover::apply(), protocols::comparative_modeling::ThreadingMover::apply(), protocols::loop_grower::LoopGrower::apply(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_loop_bump_check(), protocols::constel::PresenceCommon::are_atoms_pres(), atom(), protocols::hydrate::atom_is_hydratable(), core::scoring::FACTSPotential::atompair_scale(), protocols::motifs::backbone_stub_match(), core::conformation::Conformation::backbone_torsion_angle_atoms(), protocols::simple_moves::ExplicitWaterMover::build_backbone_rotamer_clouds(), core::conformation::build_residue_tree(), core::select::util::SelectResiduesByLayer::calc_sc_neighbors(), core::scoring::methods::GoapEnergy::calculate_dipoles(), core::scoring::calpha_superimpose_pose(), core::sequence::calpha_superimpose_with_mapping(), protocols::sic_dock::cb_weight_map_from_pose(), protocols::antibody::cdr_backbone_rmsds(), core::scoring::rna::data::RNA_DMS_Potential::check_chbonded(), protocols::loop_grower::LoopGrower::check_coordinates(), core::import_pose::RNA_JumpMover::check_forward_backward(), protocols::simple_filters::AtomicDistanceFilter::compute(), protocols::simple_filters::SimpleHbondsToAtomFilter::compute(), protocols::enzdes::DiffAtomSasaFilter::compute(), protocols::constraint_generator::compute_ref_atom(), protocols::mpi_refinement::constrain_residue(), protocols::flxbb::constraints_sheet(), protocols::mpi_refinement::copy_pose_crd(), copy_residue_connections(), protocols::constraint_generator::CoordinateConstraintGenerator::create_ambiguous_constraint(), protocols::toolbox::DecoySetEvaluation::create_xyz_constraints_median(), protocols::cartesian::MolecularDynamics::createDihedral(), protocols::md::CartesianMD::cst_on_pose_simple(), protocols::relax::cyclize_pose(), core::conformation::Conformation::declare_chemical_bond(), core::scoring::disulfides::FullatomDisulfideEnergy::defines_score_for_residue_pair(), protocols::simple_moves::PeptideStapleMover::derive_staple_constraints_(), core::conformation::symmetry::SymmetricConformation::detect_disulfides(), core::conformation::Conformation::detect_disulfides(), protocols::helical_bundle::FitSimpleHelixMultiFunc::dfunc(), core::scoring::disulfides::DisulfideMatchingPotential::disulfide_RT(), core::scoring::disulfides::DisulfideAtomIndices::DisulfideAtomIndices(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::disulfides_changed(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::disulfides_changed(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::disulfides_changed(), core::scoring::methods::LinearChainbreakEnergy::do_score_ovp(), core::scoring::methods::BranchEnergy::eval_atom_derivative(), core::scoring::methods::MembraneEnvSmoothEnergy::eval_atom_derivative(), core::scoring::methods::EnvSmoothEnergy::eval_atom_derivative(), core::scoring::membrane::FaMPEnvSmoothEnergy::eval_atom_derivative(), core::scoring::methods::ProClosureEnergy::eval_intrares_derivatives(), core::scoring::elec::FA_ElecEnergy::eval_intrares_derivatives(), core::scoring::elec::FA_ElecEnergy::eval_intrares_energy(), core::scoring::PointWaterPotential::eval_pointwater_derivs(), core::scoring::PointWaterPotential::eval_pointwater_score(), core::scoring::HydroxylTorsionPotential::eval_residue_derivative(), core::pack::dunbrack::cenrot::CenRotDunEnergy::eval_residue_derivatives(), core::scoring::methods::CenRotEnvEnergy::eval_residue_derivatives(), core::scoring::methods::DNA_DihedralEnergy::eval_residue_derivatives(), core::scoring::methods::ArgCationPiEnergy::eval_residue_pair_derivatives(), core::scoring::methods::CenHBEnergy::eval_residue_pair_derivatives(), core::scoring::methods::ProClosureEnergy::eval_residue_pair_derivatives(), core::scoring::methods::CenHBEnergy::eval_residue_pair_derivatives_soft(), protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::figure_out_dof_ids_and_offsets(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_exact_cartmin(), protocols::abinitio::abscript::find_disulfide_partner(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::find_disulfides(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::find_disulfides(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::find_disulfides(), core::conformation::carbohydrates::find_seqpos_of_saccharides_child_residue_at(), protocols::metal_interface::ZincSiteFinder::find_zinc_site(), core::conformation::Conformation::fix_disulfides(), protocols::abinitio::abscript::fix_internal_coords_of_siblings(), protocols::topology_broker::fix_mainchain_connect(), protocols::abinitio::abscript::fix_mainchain_connect(), core::conformation::form_disulfide(), protocols::simple_moves::RepeatPropagationMover::generate_overlap(), protocols::pose_creation::MergePDBMover::generate_overlaps(), core::conformation::get_anchor_and_root_atoms(), core::conformation::get_anchor_atomno(), core::scoring::dna::DNATorsionPotential::get_atom_ids_by_torsion(), protocols::match::BfactorMPM::get_ca_bfactors(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_calc_chem_shift_value_nuchemics(), core::pose::get_constraints_from_link_records(), core::pose::motif::get_cterminal_peptide_bond_reference_frame_atomids(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_deriv_for_chemical_shift_data_atom(), protocols::cluster::GatherPosesMover::get_distance_measure(), core::conformation::get_disulf_partner(), core::scoring::disulfides::FullatomDisulfidePotential::get_disulfide_derivatives_old(), protocols::simple_moves::BBConRotMover::get_L_move(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_magnetic_anisotropy_deriv_for_src_atom(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_magnetic_anisotropy_deriv_for_src_base(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::get_matching_res_in_VDW_rep_screen_pose(), core::pose::motif::get_nterminal_peptide_bond_reference_frame_atomids(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_ring_current_deriv_for_src_base(), core::scoring::rna::chemical_shift::get_rna_base_coordinate_system_from_CS_params(), core::conformation::get_root_residue_root_atomno(), protocols::loophash::get_rt_over_leap_without_foldtree_bs(), protocols::toolbox::rigid_body::get_specific_atom_coordinate(), protocols::constel::has_aromatic(), protocols::protein_interface_design::hbonded_atom(), core::scoring::methods::CartesianBondedEnergy::idealize_proline_nvs(), protocols::relax::RelaxProtocolBase::initialize_movemap(), core::conformation::is_disulfide_bond(), core::scoring::is_protein_backbone(), core::scoring::is_protein_backbone_including_O(), core::scoring::is_protein_CA(), core::scoring::is_protein_CA_or_CB(), core::scoring::is_protein_CA_or_equiv(), protocols::loops::loop_rmsd_with_superimpose_core(), core::scoring::rna::chemical_shift::magnetic_anisotropy_effect(), core::pose::make_atom_map(), protocols::simple_moves::BBConRotMover::make_move(), protocols::pose_creation::MergePDBatOverlapMover::merge_poses(), protocols::peptide_deriver::PeptideDeriverFilter::minimize(), protocols::pose_creation::MergePDBatOverlapMover::minimize_overlap(), core::conformation::named_atom_id_to_atom_id(), protocols::fold_from_loops::movers::SplitAndMixPoseMover::NC_distance_filter(), orient_onto_residue(), orient_onto_residue_peptoid(), protocols::tcr::orient_tcr_chain(), protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo::output_silent_file(), protocols::constraint_generator::parse_custom_torsion(), protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::partition(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::perform_bump_check(), protocols::generalized_kinematic_closure::GeneralizedKIC::pick_pivots(), place(), protocols::viewer::print_node(), protocols::match::output::print_node(), core::conformation::print_node(), core::scoring::constraints::AngleConstraint::read_def(), protocols::loop_grower::LoopGrower::refine_cycle(), core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose(), protocols::protein_interface_design::movers::PlacementMinimizationMover::refresh_bbstub_constraints(), core::scoring::methods::MembraneEnvSmoothEnergy::residue_energy(), core::scoring::methods::EnvSmoothEnergy::residue_energy(), core::scoring::membrane::FaMPEnvSmoothEnergy::residue_energy(), core::scoring::methods::CenHBEnergy::residue_pair_energy(), protocols::ligand_docking::MinimizeBackbone::restrain_protein_Calpha(), core::scoring::rna::chemical_shift::ring_pos(), protocols::rbsegment_relax::set_constraints(), protocols::relax::AtomCoordinateCstMover::set_constraints_on_func_groups(), protocols::features::OrbitalsFeatures::set_OrbH_features_data(), protocols::rbsegment_relax::set_rb_constraints(), protocols::flexpep_docking::FlexPepDockingProtocol::set_receptor_constraints(), protocols::stepwise::modeler::rna::phosphate::PhosphateMover::setup_atom_and_neighbor_list(), protocols::simple_moves::ShakeStructureMover::setup_ca_constraints(), protocols::canonical_sampling::CanonicalSamplingMover::setup_constraints(), protocols::simple_moves::DisulfideInsertionMover::setup_constraints(), protocols::star::setup_constraints(), protocols::ddg::ddGMover::setup_constraints(), core::scoring::methods::MembraneEnvSmoothEnergy::setup_for_derivatives(), core::scoring::membrane::FaMPEnvSmoothEnergy::setup_for_derivatives(), core::conformation::setup_links(), core::scoring::setup_matching_atoms_with_given_names(), core::scoring::setup_matching_heavy_atoms(), protocols::stepwise::modeler::rna::setup_suite_atom_id_map(), protocols::loop_grower::LoopGrower::single_grow(), protocols::hotspot_hashing::stub_tgt_angle(), protocols::protein_interface_design::movers::PlaceStubMover::StubMinimize(), protocols::simple_moves::SuperimposeMover::superimpose(), protocols::grafting::superimpose_overhangs_heavy(), protocols::fibril::superimpose_pose_on_subset_bb(), protocols::toolbox::pose_manipulation::superimpose_pose_on_subset_CA(), protocols::mpi_refinement::WorkUnit_Sampler::superimpose_to_ref(), protocols::simple_moves::SuperimposeMover::superimposebb(), protocols::enzdes::ModifyStoredRBConfs::swap_coordinates_in_pose(), core::pose::swap_transform(), protocols::docking::ConformerSwitchMover::switch_conformer(), core::util::switch_to_centroid_rot_set(), core::import_pose::libraries::RNA_ChunkLibrary::update_atom_level_domain_map(), core::pose::rna::update_edge_hbond_numbers_careful_hydrogen(), protocols::simple_moves::oop::OopMover::update_hydrogens_(), protocols::simple_moves::triazolamer::TriazolamerMover::update_hydrogens_(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::use_in_rmsd(), and protocols::mpi_refinement::StructAvrgMover::weighted_average().

bool core::conformation::Residue::atom_is_backbone ( Size const  atomno ) const

inline

Returns true if this residue's atom with index number <atomno> is a backbone atom.

example(s): residue.atom_is_backbone(3) See also: Residue Residue.all_bb_atoms Residue.atom Residue.atoms Pose

References core::chemical::ResidueType::atom_is_backbone(), and rsd_type_.

Referenced by core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_one_way_bb_bb(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_one_way_sc(), core::scoring::hbonds::HBondSet::append_hbond(), protocols::comparative_modeling::PartialThreadingMover::apply(), protocols::hbnet::UnsatSelector::apply(), protocols::comparative_modeling::ThreadingMover::apply(), core::scoring::orbitals::OrbitalsScore::assign_haro_derivs_one_way(), core::scoring::orbitals::OrbitalsScore::assign_hpol_derivs_one_way(), core::scoring::orbitals::OrbitalsScore::assign_orb_H_derivs(), core::scoring::orbitals::OrbitalsScore::assign_orb_orb_derivs(), core::scoring::FACTSPotential::atompair_scale(), core::scoring::orbitals::OrbitalsStatistics::bb_stats(), core::pack::rotamer_set::build_moving_O_bridge_waters(), core::pack::rotamer_set::build_moving_O_water_rotamers_dependent(), core::scoring::lkball::build_optimal_water_Os_on_acceptor(), core::scoring::sasa::SasaCalc::calc_per_res_sasas(), protocols::simple_filters::HelixHelixAngleFilter::calc_shortest_dist_by_atoms(), core::scoring::FACTSPotential::calculate_GBpair_exact(), core::scoring::FACTSPotential::calculate_GBpair_fast(), protocols::simple_filters::BuriedUnsatHbondFilter::compute(), protocols::matdes::SymUnsatHbondFilter::compute(), protocols::simple_filters::HolesFilter::compute(), protocols::hbnet::UnsatSelector::compute(), core::scoring::hbonds::create_rotamer_descriptor(), core::scoring::elec::create_rotamer_descriptor(), protocols::vip::VIP_Mover::cull_mutatable_residues(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_one_way_bb_bb(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_one_way_sc(), core::scoring::PoissonBoltzmannPotential::eval_PB_energy_residue(), core::scoring::elec::FA_ElecEnergy::eval_residue_pair_derivatives(), core::scoring::FACTSPotential::evaluate_polar_otf_energy(), core::scoring::rna::RNA_VDW_Energy::evaluate_rnp_vdw_score(), core::scoring::elec::FA_ElecEnergy::finalize_total_energy(), core::util::find_metalbinding_atoms_helper(), protocols::hbnet::HBNet::find_unsats(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_acceptor(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_donor(), protocols::ligand_docking::ga_ligand_dock::get_atomic_contacting_sidechains(), core::scoring::dna::get_base_pair_stub_slow(), protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::get_contacting_reslist(), core::scoring::orbitals::OrbitalsScore::get_E_haro_one_way(), core::scoring::orbitals::OrbitalsScore::get_E_hpol_one_way(), core::scoring::hbonds::get_hb_acc_chem_type(), core::scoring::hbonds::get_hb_don_chem_type(), core::scoring::orbitals::OrbitalsScore::get_orb_orb_E(), core::scoring::hbonds::HBondEnergy::hbond_derivs_1way(), core::scoring::hbonds::identify_hbonds_1way(), core::scoring::hbonds::identify_hbonds_1way_membrane(), core::scoring::hbonds::identify_intra_res_hbonds(), protocols::relax::RelaxProtocolBase::initialize_movemap(), core::scoring::is_scatom(), protocols::pockets::PocketGrid::recenter(), protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::recompute(), protocols::features::OrbitalsFeatures::report_hpol_orbital_interactions(), core::scoring::carbon_hbonds::CarbonHBondEnergy::res_res_carbon_hbond_derivs_one_way(), core::scoring::carbon_hbonds::CarbonHBondEnergy::res_res_carbon_hbond_one_way(), protocols::rotamer_recovery::RRProtocolRelax::run(), core::scoring::orbitals::OrbitalsStatistics::sc_H_orbital(), core::scoring::elec::FA_ElecEnergy::score_atom_pair(), protocols::match::output::ResidueKinemageWriter::write_rsd_coords(), and core::conformation::ResidueKinWriter::write_rsd_coords().

bool core::conformation::Residue::atom_is_hydrogen ( Size const  atomno ) const

inline

Returns true if this residue's atom with index number <atomno> is a hydrogen.

example(s): residue.atom_is_backbone(3) See also: Residue Residue.all_bb_atoms Residue.atom Residue.atoms Pose

References core::chemical::ResidueType::atom_is_hydrogen(), and rsd_type_.

Referenced by protocols::splice::Splice::add_coordinate_constraints(), protocols::splice::SpliceManager::add_coordinate_constraints(), core::scoring::geometric_solvation::add_to_individual_sol_energies(), core::scoring::MultipoleElecPotential::align_residue_multipole_axes(), protocols::pockets::PocketGrid::alter_espGrid_with_bound_ligand(), core::scoring::elec::assign_rna_atom_type(), core::scoring::methods::LK_hack::calculate_orientation_vectors_and_pseudo_base_atoms(), core::scoring::hbonds::create_rotamer_descriptor(), protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), core::scoring::methods::LK_hack::distribute_pseudo_base_atom_derivatives(), core::scoring::lkball::LK_BallEnergy::eval_residue_pair_derivatives(), core::scoring::VdWTinkerPotential::eval_residue_pair_derivatives(), core::scoring::rna::RNA_VDW_Energy::evaluate_rnp_vdw_score(), protocols::contact_map::ContactMap::fill_contacts(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_2b_energy(), get_adjacent_heavy_atoms(), core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::get_atom_atom_occ_solvation(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::get_atom_atom_occ_solvation(), core::scoring::methods::LK_PolarNonPolarEnergy::get_base_vector(), get_hydrogens_bonded_to_ring_atom(), core::scoring::VdWTinkerPotential::get_res_res_vdw(), get_substituents_to_ring_atom(), core::scoring::ResidueNblistData::initialize(), core::scoring::ResiduePairNeighborList::initialize_from_residues(), core::scoring::elec::is_base_2(), core::scoring::is_heavyatom(), core::scoring::is_ligand_heavyatom(), core::scoring::is_ligand_heavyatom_residues(), core::scoring::is_non_peptide_heavy_atom(), core::scoring::elec::is_phosphate_2(), core::scoring::is_polymer_heavyatom(), core::scoring::rna::StackElecEnergy::is_rna_base(), core::scoring::elec::is_sugar_2(), protocols::comparative_modeling::randomize_selected_atoms(), protocols::pockets::PocketGrid::recenter(), protocols::toolbox::match_enzdes_util::replace_residue_keeping_all_atom_positions(), protocols::nmr::pcs::PCSLigandTransformMover::reset_grid_and_bounding_box(), core::scoring::methods::LK_hack::residue_pair_energy(), core::scoring::NeighborList::update_from_wide_nblist(), protocols::match::output::ResidueKinemageWriter::write_rsd_coords(), and core::conformation::ResidueKinWriter::write_rsd_coords().

bool core::conformation::Residue::atom_is_polar_hydrogen ( Size  ind ) const

inline

Is a particular atom a polar hydrogen?

References core::chemical::ResidueType::atom_is_polar_hydrogen(), and rsd_type_.

Referenced by protocols::hbnet::UnsatSelector::apply(), core::pack::rotamer_set::build_moving_O_water_rotamers_dependent(), protocols::simple_filters::BuriedUnsatHbondFilter::compute(), core::pack::interaction_graph::compute_alt_weights_for_npd_hbonds(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::eval_atom_energy(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::eval_intrares_derivatives(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::eval_residue_pair_derivatives(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_donor(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::residue_pair_energy_ext(), core::scoring::hbonds::weights_and_derivs_for_hbonds(), and core::scoring::hbonds::weights_for_hbonds().

std::string const& core::conformation::Residue::atom_name ( Size const  atm ) const

inline

Returns the name of this residue's atom with index number <atm>

References core::chemical::ResidueType::atom_name(), and rsd_type_.

Referenced by core::io::pose_to_sfr::PoseToStructFileRepConverter::add_atom_to_sfr(), core::util::add_constraints_to_metal(), protocols::splice::Splice::add_coordinate_constraints(), protocols::splice::SpliceManager::add_coordinate_constraints(), core::util::add_covalent_linkage(), core::util::add_covalent_linkage_helper(), protocols::forge::methods::add_cutpoint_variants(), protocols::denovo_design::add_cutpoints(), protocols::chemically_conjugated_docking::add_extra_bodies(), protocols::loops::add_single_cutpoint_variant(), core::scoring::sc::MolecularSurfaceCalculator::AddResidue(), protocols::topology_broker::MembraneTopologyClaimer::addVirtualResAsRootMembrane(), core::scoring::MultipoleElecPotential::align_residue_multipole_axes(), core::conformation::Conformation::align_virtual_atoms_in_carbohydrate_residue(), core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::append_metal_vsites(), core::conformation::Conformation::append_residue_by_bond(), protocols::pose_metric_calculators::append_rsd_by_jump_near_atom(), protocols::ligand_docking::AddHydrogen::apply(), protocols::comparative_modeling::PartialThreadingMover::apply(), protocols::minimization_packing::RotamerizeMover::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::comparative_modeling::ThreadingMover::apply(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_loop_bump_check(), core::scoring::VdWTinkerPotential::assign_residue_amoeba_type(), core::scoring::MultipoleElecPotential::assign_residue_amoeba_type(), core::scoring::methods::ProQ_Energy::atom13_0(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::atom_has_exp_chemical_shift_data(), core::pose::atom_id_to_named_atom_id(), core::conformation::atom_id_to_named_atom_id(), protocols::hydrate::atom_is_hydratable(), core::scoring::FACTSPotential::atompair_scale(), core::scoring::MultipoleElecPotential::build_frame_and_rotate(), protocols::LoopRebuild::build_loop_with_ccd_closure(), core::scoring::lkball::build_optimal_water_Os_on_acceptor(), core::pack::rotamer_set::RotamerSet_::build_optimize_H_rotamers(), protocols::rna::movers::bump_check(), core::scoring::sasa::LeGrandSasa::calc_atom_masks(), protocols::simple_filters::HelixHelixAngleFilter::calc_shortest_dist_by_atoms(), core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >::calculate_alt_state_hpatch_score(), protocols::hydrate::calculate_water_overcoordinated_hb_correction(), core::scoring::nmr::NMRDummySpinlabelEnsemble::clash_check(), protocols::enzdes::ModifyStoredRBConfs::closest_orient_atoms_msd(), core::scoring::constraints::combine_NMR_atom_string(), protocols::cryst::ReportGradientsMover::compute(), protocols::protein_interface_design::filters::AtomicContactCountFilter::compute(), protocols::simple_filters::BuriedUnsatHbondFilter::compute(), protocols::matdes::SymUnsatHbondFilter::compute(), protocols::matdes::ClashCheckFilter::compute(), protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::compute(), core::scoring::geometric_solvation::compute_exact_geosol(), protocols::simple_filters::InterfaceHbondsFilter::compute_hbonds(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_polar_group_sol_energy(), core::pack::interaction_graph::SurfacePotential::compute_pose_hpatch_score(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::copy_coords(), protocols::generalized_kinematic_closure::copy_loop_pose_to_original(), protocols::mpi_refinement::copy_pose_crd(), copy_residue_connections(), core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms(), protocols::constraint_generator::CoordinateConstraintGenerator::create_residue_constraints(), protocols::md::CartesianMD::cst_on_pose_dynamic(), core::pose::declare_cutpoint_chemical_bond(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::define_active_virtual_sites(), protocols::simple_moves::PeptideStapleMover::derive_staple_constraints_(), core::conformation::symmetry::SymmetricConformation::detect_disulfides(), core::scoring::methods::LinearChainbreakEnergy::do_score_ovp(), protocols::environment::dof_id_to_string(), core::scoring::methods::ChainbreakEnergy::eval_atom_derivative(), core::scoring::methods::BranchEnergy::eval_atom_derivative(), core::scoring::methods::DipolarCouplingEnergy::eval_atom_derivative(), core::scoring::methods::ChemicalShiftAnisotropyEnergy::eval_atom_derivative(), core::scoring::methods::ResidualDipolarCouplingEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensCenEnergy::eval_atom_derivative(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::eval_atom_derivative(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd1(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd2(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd1(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd2(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_bond_energy(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_bond_length_derivs(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_improper_energy(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_ring_energy(), core::scoring::methods::MMBondLengthEnergy::eval_intrares_energy(), core::scoring::methods::MMTorsionEnergy::eval_intrares_energy(), core::scoring::methods::MMBondAngleEnergy::eval_intrares_energy(), core::scoring::magnesium::MgEnergy::eval_mg_interaction(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_angle(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_bond(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_improper(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_torsion(), core::scoring::magnesium::MgEnergy::eval_residue_pair(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_angle(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_bond(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_improper(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_torsion(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_angle_energies(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_improper_energies(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_length_energies(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_ring_energies(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_torsion_energies(), core::scoring::rna::RNA_VDW_Energy::evaluate_rnp_vdw_score(), protocols::environment::EXCN_Env_Security_Exception::EXCN_Env_Security_Exception(), protocols::pockets::GenPharmacophore::extract_Hbond_atoms_from_protein_rna_complex(), protocols::pockets::GenPharmacophore::extract_rna_rings_from_protein_rna_complex(), core::pose::copydofs::CopyDofs::figure_out_dofs(), protocols::contact_map::ContactMap::fill_contacts(), core::conformation::Conformation::fill_missing_atoms(), fill_missing_atoms(), core::pack::rotamers::SingleBasicRotamerLibrary::fill_rotamer_vector(), protocols::metal_interface::find_closest_atom(), core::util::find_metalbinding_atoms_helper(), core::scoring::MultipoleElecPotential::find_params_and_neighbors(), protocols::hbnet::HBNet::find_unsats(), protocols::magnesium::MgWaterHydrogenPacker::find_water_neighbor_vecs(), protocols::toolbox::match_enzdes_util::EnzConstraintParameters::generate_active_pose_constraints(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_1b_energy(), core::scoring::carbon_hbonds::CarbonHBondEnergy::get_atom_atom_carbon_hbond_energy(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_acceptor(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_donor(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::get_atom_atom_occ_solvation(), core::scoring::rna::RNA_LowResolutionPotential::get_base_backbone(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_calc_chem_shift_value_larmord(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_deriv_for_chemical_shift_data_atom(), core::scoring::hbonds::get_hb_acc_chem_type(), core::scoring::hbonds::get_hb_don_chem_type(), core::conformation::carbohydrates::get_linkage_position_of_saccharide_residue(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_magnetic_anisotropy_deriv_for_src_atom(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_magnetic_anisotropy_deriv_for_src_base(), core::scoring::magnesium::MgKnowledgeBasedPotential::get_mg_potential_costheta_gaussian_parameter(), core::scoring::magnesium::MgKnowledgeBasedPotential::get_mg_potential_costheta_indirect_gaussian_parameter(), core::scoring::magnesium::MgKnowledgeBasedPotential::get_mg_potential_gaussian_parameter(), core::scoring::magnesium::MgKnowledgeBasedPotential::get_mg_potential_indirect_gaussian_parameter(), protocols::simple_filters::ResidueDepthCalculator::get_pose_crd_and_index(), core::select::get_pymol_selection_for_atoms(), core::scoring::methods::LK_PolarNonPolarEnergy::get_residue_pair_energy_one_way(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_ring_current_deriv_for_src_base(), core::conformation::idealize_hydrogens(), core::conformation::improper_build(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::init_from_ligand(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::init_from_ligand_pharmacophore(), core::scoring::MultipoleElecResidueInfo::initialize(), protocols::match::downstream::LigandConformerBuilder::initialize_conformers(), core::simple_metrics::per_residue_metrics::PerResidueClashMetric::is_clashing(), protocols::task_operations::CrystalContactsOperation::is_crystal_contact(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::Is_magnetic_anisotropy_source_atom(), protocols::ligand_docking::ga_ligand_dock::GridScorer::is_residue_in_grid(), protocols::toolbox::match_enzdes_util::EnzConstraintParameters::make_constraint_covalent(), protocols::toolbox::match_enzdes_util::EnzConstraintParameters::make_constraint_covalent_helper(), protocols::forge::methods::make_star_foldtree(), core::conformation::missing_stubs_build(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::model_loop(), protocols::loop_grower::LoopGrower::modifieddensity(), protocols::denovo_design::movers::new_jump_and_cutpoint(), core::scoring::nmr::NMRDummySpinlabelConformer::NMRDummySpinlabelConformer(), protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::output_rep(), core::chemical::sdf::MolWriter::output_residue(), protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo::output_silent_file(), place(), protocols::topology_broker::TMHTopologySamplerClaimer::pre_process(), core::conformation::print_atom(), protocols::stepwise::modeler::rna::print_heavy_atoms(), protocols::viewer::print_node(), protocols::analysis::InterfaceAnalyzerMover::print_pymol_selection_of_hbond_unsat(), core::conformation::Conformation::rebuild_polymer_bond_dependent_atoms(), protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::recompute(), core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose(), protocols::toolbox::match_enzdes_util::replace_residue_keeping_all_atom_positions(), protocols::features::ProteinBondGeometryFeatures::report_interres_angles(), protocols::features::ProteinBondGeometryFeatures::report_interres_lengths(), protocols::features::ProteinBondGeometryFeatures::report_intrares_angles(), protocols::features::ProteinBondGeometryFeatures::report_intrares_lengths(), protocols::features::ProteinBondGeometryFeatures::report_intrares_torsions(), protocols::nmr::pcs::PCSLigandTransformMover::reset_grid_and_bounding_box(), core::scoring::methods::MMBondLengthEnergy::residue_pair_energy(), core::scoring::methods::MMTorsionEnergy::residue_pair_energy(), core::scoring::methods::MMBondAngleEnergy::residue_pair_energy(), core::scoring::magnesium::RNA_MgPointEnergy::residue_pair_energy_one_way(), core::scoring::rms_at_all_corresponding_atoms(), core::scoring::rms_at_corresponding_atoms(), core::scoring::rna::RNA_LowResolutionPotential::rna_backbone_backbone_pair_energy_one_way(), core::scoring::rna::RNA_LowResolutionPotential::rna_repulsive_pair_energy_one_way(), core::scoring::SASAShouldItCount(), protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::semiexpl_water_hbgeom_score(), protocols::hbnet::HBNet::set_constraints(), core::conformation::symmetry::set_fold_tree_from_symm_data(), protocols::loops::set_loop_cutpoint_in_pose_fold_tree(), core::conformation::setup_corresponding_atoms(), core::scoring::electron_density::ElecDensCenEnergy::setup_for_scoring(), core::conformation::setup_links(), core::scoring::setup_matching_heavy_atoms(), core::scoring::ShouldItCount(), show(), core::scoring::hbonds::HBond::show(), protocols::nmr::pcs::PCSEnergy::show_additional_info(), protocols::nmr::pre::PREEnergy::show_additional_info(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::superimpose_to_alternative_frame(), protocols::enzdes::ModifyStoredRBConfs::swap_coordinates_in_pose(), core::import_pose::libraries::RNA_ChunkLibrary::update_atom_level_domain_map(), core::pose::rna::update_edge_hbond_numbers(), core::pose::rna::update_edge_hbond_numbers_careful_hydrogen(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::use_in_rmsd(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::use_in_rmsd_offset(), and core::scoring::VdWShouldItCount().

AtomType const& core::conformation::Residue::atom_type ( Size const  atomno ) const

inline

Returns the AtomType of this residue's atom with index number <atomno>

example(s): residue.atom_type(3) See also: Residue Residue.atom_index AtomType Pose

References core::chemical::ResidueType::atom_type(), and rsd_type_.

Referenced by core::io::pose_to_sfr::PoseToStructFileRepConverter::add_atom_to_sfr(), core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr(), protocols::hbnet::UnsatSelector::apply(), core::scoring::methods::ProQ_Energy::atom13_0(), core::scoring::elec::atom_is_aro(), core::scoring::elec::atom_is_aro2(), protocols::qsar::scoring_grid::HbaGrid::atom_score(), protocols::qsar::scoring_grid::HbdGrid::atom_score(), protocols::qsar::scoring_grid::VdwGrid::atom_score(), core::scoring::atomic_depth::AtomicDepth::boundbox(), core::scoring::atomic_depth::AtomicDepth::boundingatom(), core::pack::rotamer_set::build_acceptor_acceptor_waters(), protocols::simple_moves::ExplicitWaterMover::build_backbone_rotamer_clouds(), core::pack::rotamer_set::build_donor_acceptor_waters(), core::pack::rotamer_set::build_moving_O_bridge_waters(), core::pack::rotamer_set::build_sew_waters_to_acceptor(), core::pack::rotamer_set::build_single_edge_waters(), core::scoring::sasa::LeGrandSasa::calc_atom_masks(), core::scoring::calc_atom_masks(), core::scoring::calc_per_res_hydrophobic_sasa(), core::scoring::sasa::SasaCalc::calc_per_res_sasas(), core::simple_metrics::per_residue_metrics::PerResidueClashMetric::calculate(), core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >::calculate_alt_state_hpatch_score(), protocols::hydrate::calculate_water_overcoordinated_hb_correction(), protocols::simple_filters::AtomicDistanceFilter::compute(), protocols::protein_interface_design::filters::AtomicContactCountFilter::compute(), protocols::hbnet::UnsatSelector::compute(), protocols::simple_filters::BuriedSurfaceAreaFilter::compute(), protocols::scoring::methods::saxs::PDDFEnergy::compute_pddf(), protocols::scoring::methods::saxs::PDDFEnergy::compute_pddf_without_ff(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_polar_group_sol_energy(), core::scoring::power_diagram::PowerDiagram::construct_from_pose(), core::scoring::hbonds::create_acc_orientation_vector(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::define_active_virtual_sites(), core::import_pose::atom_tree_diffs::dump_atom_tree_diff(), protocols::hbnet::HBNet::estimate_saturation(), core::scoring::saxs::FastSAXSEnergy::eval_atom_derivative(), core::scoring::fiber_diffraction::FiberDiffractionEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensEnergy::eval_atom_derivative(), core::scoring::electron_density_atomwise::ElecDensAtomwiseEnergy::eval_atom_derivative(), core::scoring::magnesium::MgEnergy::eval_mg_interaction(), core::scoring::PointWaterPotential::eval_pointwater_derivs(), core::scoring::PointWaterPotential::eval_pointwater_score(), core::scoring::methods::LK_PolarNonPolarEnergy::eval_residue_pair_derivatives(), core::pose::xyzStripeHashPose::extract_pose_balls(), protocols::pose_metric_calculators::fast_clash_check(), protocols::forge::remodel::fast_clash_check(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::fast_full_atom_VDW_repulsion_screen(), core::conformation::Conformation::fill_missing_atoms(), core::scoring::atomic_depth::AtomicDepth::fillvoxels(), core::scoring::methods::D2H_SA_Energy::finalize_total_energy(), protocols::metal_interface::find_closest_atom(), core::util::find_metalbinding_atoms_for_complex(), core::util::find_metalbinding_atoms_helper(), protocols::hbnet::HBNet::find_unsats(), protocols::magnesium::MgWaterHydrogenPacker::find_water_neighbor_vecs(), protocols::ligand_docking::frac_atoms_within(), core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::get_atom_atom_occ_solvation(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::get_atom_atom_occ_solvation(), core::scoring::magnesium::get_cos_theta(), core::scoring::hbonds::get_hb_acc_chem_type(), core::conformation::carbohydrates::get_linkage_position_of_saccharide_residue(), protocols::membrane::scoring::FaWaterToBilayerEnergy::get_menv_params_for_residue(), core::scoring::magnesium::MgKnowledgeBasedPotential::get_mg_potential_costheta_gaussian_parameter(), core::scoring::magnesium::MgKnowledgeBasedPotential::get_mg_potential_costheta_indirect_gaussian_parameter(), core::scoring::magnesium::MgKnowledgeBasedPotential::get_mg_potential_gaussian_parameter(), core::scoring::magnesium::MgKnowledgeBasedPotential::get_mg_potential_indirect_gaussian_parameter(), core::select::get_pymol_selection_for_atoms(), core::scoring::methods::LK_PolarNonPolarEnergy::get_residue_pair_energy_one_way(), core::scoring::WaterAdductHBondPotential::get_residue_residue_h2o_hbonds_1way(), core::chemical::rna::get_rna_base_centroid(), core::scoring::MultipoleElecPotential::get_single_rotamer_effective_radii(), core::scoring::WaterAdductHBondPotential::h2o_hbond_score_1way(), core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy::has_bb_hbond(), core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy::has_hbond(), protocols::sic_dock::SICFast::init(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::init_from_ligand(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::init_from_ligand_pharmacophore(), core::scoring::GenBornResidueInfo::initialize(), protocols::toolbox::match_enzdes_util::LigandConformer::initialize_from_residue(), protocols::match::downstream::RigidLigandBuilder::initialize_from_residue(), protocols::match::downstream::LigandConformerBuilder::initialize_from_residue(), core::scoring::inline_intraresidue_atom_pair_energy(), core::scoring::inline_residue_atom_pair_energy(), protocols::features::HBondFeatures::insert_site_row(), core::simple_metrics::per_residue_metrics::PerResidueClashMetric::is_clashing(), protocols::task_operations::CrystalContactsOperation::is_crystal_contact(), core::pack::task::residue_selector::is_sc_bb_clash(), core::pack::task::residue_selector::is_sc_sc_clash(), protocols::stepwise::modeler::rna::is_virtual_base(), core::scoring::packstat::LeeRichards::LeeRichards(), protocols::protein_interface_design::make_hotspot_foldtree(), core::scoring::power_diagram::PowerDiagram::make_new_sphere(), protocols::motifs::Motif::Motif(), protocols::stepwise::modeler::rna::phosphate::PhosphateMover::pass_clash_check(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::perform_bump_check(), protocols::protein_interface_design::movers::PlaceStubMover::place_stub(), core::scoring::packing::PoseBalls::PoseBalls(), core::scoring::packing::PoseBallsLite::PoseBallsLite(), core::scoring::PQR::PQR(), protocols::stepwise::modeler::rna::print_atom_info(), protocols::stepwise::modeler::rna::print_individual_atom_info(), protocols::viewer::print_node(), protocols::simple_pose_metric_calculators::NumberHBondsCalculator::recompute(), protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::recompute(), protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::recompute(), protocols::qsar::scoring_grid::HbdGrid::refresh(), protocols::qsar::scoring_grid::HbaGrid::refresh(), protocols::qsar::scoring_grid::VdwGrid::refresh(), core::scoring::saxs::SAXSEnergy::rehash_form_factors(), protocols::simple_moves::PeriodicBoxMover::report_thermodynamics(), core::scoring::methods::WaterAdductIntraEnergy::residue_energy(), core::scoring::methods::GaussianOverlapEnergy::residue_pair_energy(), core::scoring::methods::LK_hack::residue_pair_energy(), core::scoring::methods::LK_PolarNonPolarEnergy::residue_pair_energy_ext(), core::scoring::magnesium::RNA_MgPointEnergy::residue_pair_energy_one_way(), core::scoring::rna::RNA_FullAtomStackingEnergy::residue_pair_energy_one_way(), core::scoring::residue_rmsd_nosuper(), core::scoring::residue_rmsd_super(), core::import_pose::atom_tree_diffs::rms_error_with_noise(), protocols::qsar::scoring_grid::HbaGrid::score(), protocols::qsar::scoring_grid::HbdGrid::score(), protocols::qsar::scoring_grid::VdwGrid::score(), protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::semiexpl_water_hbgeom_score(), protocols::features::OrbitalsFeatures::set_OrbH_features_data(), core::conformation::setup_links(), protocols::simple_moves::PeriodicBoxMover::setup_pose(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::update_VDW_screen_bin(), protocols::match::output::ResidueKinemageWriter::write_rsd_coords(), core::conformation::ResidueKinWriter::write_rsd_coords(), and core::pose::xyzStripeHashPose::xyzStripeHashPose().

Size core::conformation::Residue::atom_type_index ( Size const  atomno ) const

inline

Returns the atom_type_index of this residue's atom with index number <atomno> atom_type_index is used to query this atom's AtomType from an AtomTypeSet, example: AtomTypeSet[atom_type_index] = AtomType.

example(s): residue.atom_type_index(3) See also: Residue Residue.atom_index AtomType Pose

References atoms_.

Referenced by core::scoring::geometric_solvation::add_to_individual_sol_energies(), protocols::match::downstream::DownstreamAlgorithm::are_colliding(), core::scoring::orbitals::OrbitalsScore::assign_orb_orb_derivs(), core::scoring::atomic_depth::AtomicDepth::boundingatom(), core::scoring::geometric_solvation::compute_exact_geosol(), core::scoring::electron_density::ElectronDensity::dCCdB_fastRes(), core::scoring::electron_density::ElectronDensity::dCCdx_fastRes(), core::scoring::electron_density::ElectronDensity::ElectronDensity(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_angle(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_bond(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_improper(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_torsion(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_angle(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_bond(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_improper(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_torsion(), protocols::scoring::InterchainPotential::evaluate_pair_and_vdw_score(), core::scoring::carbon_hbonds::CarbonHBondEnergy::get_atom_atom_carbon_hbond_energy(), core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::get_atom_atom_occ_solvation(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::get_atom_atom_occ_solvation(), core::scoring::orbitals::OrbitalsScore::get_orb_orb_E(), core::chemical::rna::get_rna_base_centroid(), core::scoring::electron_density::ElectronDensity::matchAtomFast(), core::scoring::electron_density::ElectronDensity::matchRes(), core::scoring::electron_density::ElectronDensity::matchResFast(), core::conformation::orient_residue_for_ideal_bond(), protocols::match::output::UpstreamDownstreamCollisionFilter::passes_hardsphere_filter(), protocols::match::output::UpstreamCollisionFilter::passes_hardsphere_filter(), core::scoring::packing::PoseBalls::PoseBalls(), core::scoring::methods::HybridVDW_Energy::residue_pair_energy(), core::scoring::vdwaals::VDW_Energy::residue_pair_energy(), and protocols::simple_moves::PeriodicBoxMover::setup_LJcorrection().

chemical::AtomTypeSet const& core::conformation::Residue::atom_type_set ( ) const

inline

Returns the AtomTypeSet of this residue.

example(s): residue.atom_type_set() See also: Residue Residue.atom_type_index AtomType Pose

References core::chemical::ResidueTypeBase::atom_type_set(), and rsd_type_.

Referenced by core::scoring::calc_per_atom_sasa(), core::scoring::sasa::LeGrandSasa::calculate(), core::scoring::power_diagram::PowerDiagram::construct_from_pose(), core::scoring::hbonds::create_acc_orientation_vector(), core::scoring::hbonds::create_don_orientation_vector(), core::scoring::hbonds::create_rotamer_descriptor(), core::scoring::electron_density::ElectronDensity::dCCdB_fastRes(), core::scoring::electron_density::ElectronDensity::dCCdx_fastRes(), core::scoring::electron_density::ElectronDensity::ElectronDensity(), core::scoring::MultipoleElecPotential::get_effective_radii(), core::scoring::MultipoleElecPotential::get_single_rotamer_effective_radii(), core::scoring::GenBornResidueInfo::initialize(), core::scoring::power_diagram::PowerDiagram::make_new_sphere(), core::scoring::electron_density::ElectronDensity::matchAtomFast(), core::scoring::electron_density::ElectronDensity::matchRes(), core::scoring::electron_density::ElectronDensity::matchResFast(), and protocols::features::AtomTypesFeatures::report_features().

Real core::conformation::Residue::atomic_charge ( Size const  atomno ) const

inline

Returns the atom charge of this residue's atom with index number <atomno>

example(s): residue.atomic_charge(3) See also: Residue Residue.atom_index Pose

References core::chemical::ResidueType::atom_charge(), and rsd_type_.

Referenced by protocols::qsar::scoring_grid::ChargeGrid::atom_score(), core::scoring::elec::FA_ElecEnergy::backbone_backbone_energy(), core::scoring::elec::FA_ElecEnergy::backbone_sidechain_energy(), protocols::ligand_docking::ga_ligand_dock::GridScorer::calculate_grid(), core::scoring::elec::create_rotamer_descriptor(), protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), core::scoring::elec::FA_ElecEnergyAroAll::eval_atom_derivative_aro_aro(), core::scoring::elec::FA_ElecEnergyAroAro::eval_atom_derivative_aro_aro(), core::scoring::elec::RNA_FA_ElecEnergy::eval_atom_derivative_RNA(), core::scoring::elec::FA_ElecEnergy::eval_intrares_derivatives(), core::scoring::PoissonBoltzmannPotential::eval_PB_energy_residue(), core::scoring::rna::StackElecEnergy::eval_residue_pair_derivatives(), core::scoring::elec::RNA_FA_ElecEnergy::eval_residue_pair_derivatives(), core::scoring::elec::FA_ElecEnergy::eval_residue_pair_derivatives(), core::scoring::elec::GroupElec::eval_respair_group_coulomb(), core::scoring::elec::GroupElec::eval_respair_group_derivatives(), protocols::pockets::DarcParticleSwarmMinimizer::fill_atom_arrays_for_electrostatics_(), core::scoring::elec::RNA_FA_ElecEnergy::finalize_total_energy(), core::scoring::rna::StackElecEnergy::finalize_total_energy(), core::scoring::elec::FA_ElecEnergy::finalize_total_energy(), protocols::hbnet::HBNet::find_unsats(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_1b_energy(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_2b_energy(), core::scoring::GenBornPotential::get_res_res_elecE(), core::chemical::rna::get_rna_base_centroid(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::init_from_ligand_pharmacophore(), protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::recompute(), core::scoring::elec::FA_ElecEnergyAroAro::residue_pair_energy_aro_aro(), core::scoring::elec::FA_ElecEnergyAroAll::residue_pair_energy_aro_aro(), core::scoring::rna::StackElecEnergy::residue_pair_energy_ext(), core::scoring::rna::StackElecEnergy::residue_pair_energy_one_way(), core::scoring::elec::RNA_FA_ElecEnergy::rna_fa_elec_one_way(), protocols::qsar::scoring_grid::ChargeGrid::score(), core::scoring::elec::RNA_FA_ElecEnergy::score_atom_pair(), core::scoring::elec::FA_ElecEnergy::score_atom_pair(), protocols::qsar::scoring_grid::ChargeGrid::setup_charge_atoms(), and core::scoring::elec::FA_ElecEnergy::sidechain_sidechain_energy().

Atoms const& core::conformation::Residue::atoms ( ) const

inline

Returns this residue's Atoms (const), a vector1 of Atom objects.

example(s): residue.atoms() See also: Residue Pose

References atoms_.

Referenced by protocols::sewing::hashing::AlignmentFileGeneratorMover::add_pose_segments_to_segment_vector(), core::conformation::atom_id_to_named_atom_id(), core::pose::compare_atom_coordinates(), protocols::simple_moves::ConcatenatePosesMover::concatenate_poses(), core::conformation::Conformation::detect_bonds(), core::conformation::symmetry::SymmetricConformation::detect_disulfides(), core::conformation::Conformation::detect_disulfides(), protocols::contact_map::ContactMap::fill_contacts(), protocols::toolbox::match_enzdes_util::InvrotTreeNode::get_fixed_pt(), protocols::loops::loop_rmsd(), orient_onto_location(), orient_onto_residue_peptoid(), place(), core::conformation::setup_corresponding_atoms(), update_actcoord(), core::io::serialization::write_binary(), and protocols::environment::claims::XYZClaim::yield_elements().

Atoms& core::conformation::Residue::atoms ( )

inline

Returns this residue's Atoms (non-const), a vector1 of Atom objects.

example(s): residue.atoms() See also: Residue Pose

References atoms_.

AtomIndices const& core::conformation::Residue::atoms_with_orb_index ( ) const

inline

References core::chemical::ResidueType::atoms_with_orb_index(), and rsd_type_.

Referenced by core::scoring::orbitals::OrbitalsScore::assign_haro_derivs_one_way(), core::scoring::orbitals::OrbitalsScore::assign_hpol_derivs_one_way(), core::scoring::orbitals::OrbitalsScore::assign_orb_orb_derivs(), core::scoring::orbitals::OrbitalsStatistics::bb_stats(), core::scoring::orbitals::OrbitalsScore::get_E_haro_one_way(), core::scoring::orbitals::OrbitalsScore::get_E_hpol_one_way(), core::scoring::orbitals::OrbitalsScore::get_orb_orb_E(), protocols::features::OrbitalsFeatures::report_hpol_orbital_interactions(), core::scoring::orbitals::OrbitalsStatistics::sc_H_orbital(), core::conformation::Conformation::update_orbital_coords(), and update_orbital_coords().

Size core::conformation::Residue::attached_H_begin ( Size const  atom ) const

inline

Returns the index number of the first hydrogen attached to the atom with index number <atom>

example(s): residue.attached_H_begin() See also: Residue Residue.atom Residue.atoms Residue.attached_H_end Pose

References core::chemical::ResidueType::attached_H_begin(), and rsd_type_.

Referenced by core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_acceptor_atom_energy(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_donor_atom_energy(), core::scoring::hbonds::create_rotamer_descriptor(), core::scoring::elec::create_rotamer_descriptor(), core::scoring::trie::create_trie(), protocols::hbnet::HBNet::find_unsats(), core::scoring::cryst::fix_bfactorsH(), core::scoring::inline_intraresidue_atom_pair_energy(), core::scoring::inline_residue_atom_pair_energy(), protocols::comparative_modeling::randomize_selected_atoms(), protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::recompute(), core::pose::PDBInfo::replace_res_remap_bfactors(), core::scoring::rna::RNA_FullAtomVDW_BasePhosphate::residue_energy(), and core::scoring::elec::FA_ElecEnergy::residue_pair_energy().

AtomIndices const& core::conformation::Residue::attached_H_begin ( ) const

inline

Returns the AtomIndices of the first hydrogen attached to each heavyatom.

example(s): residue.attached_H_begin() See also: Residue Residue.atom Residue.atoms Residue.attached_H_end Residue.nheavyatoms Pose

References core::chemical::ResidueType::attached_H_begin(), and rsd_type_.

Size core::conformation::Residue::attached_H_end ( Size const  atom ) const

inline

Returns the index number of the last hydrogen attached to the atom with index number <atom>

example(s): residue.attached_H_end() See also: Residue Residue.atom Residue.atoms Residue.attached_H_begin Pose

References core::chemical::ResidueType::attached_H_end(), and rsd_type_.

Referenced by core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_acceptor_atom_energy(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_donor_atom_energy(), core::scoring::hbonds::create_rotamer_descriptor(), core::scoring::elec::create_rotamer_descriptor(), core::scoring::trie::create_trie(), protocols::hbnet::HBNet::find_unsats(), core::scoring::cryst::fix_bfactorsH(), core::scoring::inline_intraresidue_atom_pair_energy(), core::scoring::inline_residue_atom_pair_energy(), protocols::comparative_modeling::randomize_selected_atoms(), protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::recompute(), core::pose::PDBInfo::replace_res_remap_bfactors(), core::scoring::rna::RNA_FullAtomVDW_BasePhosphate::residue_energy(), and core::scoring::elec::FA_ElecEnergy::residue_pair_energy().

AtomIndices const& core::conformation::Residue::attached_H_end ( ) const

inline

Returns the AtomIndices of the last hydrogen attached to each heavyatom.

example(s): residue.attached_H_end() See also: Residue Residue.atom Residue.atoms Residue.attached_H_begin Residue.nheavyatoms Pose

References core::chemical::ResidueType::attached_H_end(), and rsd_type_.

chemical::AA const& core::conformation::Residue::backbone_aa ( ) const

inline

Returns this residue's backbone_aa type, if any.

This is used for noncanonical alpha-amino acids that are templated on canonicals. For example, 4,5-dihydroxyisoleucine uses the ramachandran and p_aa_pp scoring of isoleucine.

References core::chemical::ResidueTypeBase::backbone_aa(), and rsd_type_.

Referenced by protocols::loops::loop_closure::ccd::RamaCheck1B::compute_rama_score(), core::scoring::methods::RamachandranEnergy::eval_dof_derivative(), core::scoring::Ramachandran::eval_rama_score_residue(), core::scoring::Ramachandran::eval_rama_score_residue_nonstandard_connection(), core::scoring::methods::RamachandranEnergy::eval_residue_dof_derivative(), core::scoring::P_AA::get_Paa_pp_deriv(), core::scoring::P_AA::P_AA_energy(), core::scoring::P_AA::P_AA_pp_energy(), and core::scoring::methods::RamachandranEnergy::residue_energy().

AtomIndices const& core::conformation::Residue::bonded_neighbor ( Size const  atm ) const

inline

Returns the AtomIndices for all bonded neighbor atoms of <atm>

References core::chemical::ResidueType::bonded_neighbor(), and rsd_type_.

Referenced by core::scoring::MultipoleElecPotential::align_residue_multipole_axes(), protocols::constraint_generator::MetalContactsConstraintGenerator::apply(), core::scoring::orbitals::OrbitalsScore::assign_hpol_derivs_one_way(), core::scoring::orbitals::OrbitalsScore::assign_orb_H_derivs(), protocols::qsar::scoring_grid::HbaGrid::atom_score(), core::scoring::constraints::auto_detect_atoms(), core::scoring::orbitals::OrbitalsStatistics::bb_stats(), core::conformation::Conformation::bonded_neighbor_all_res(), core::scoring::methods::LK_hack::calculate_orientation_vectors_and_pseudo_base_atoms(), protocols::cartesian::MolecularDynamics::createBondList(), fill_missing_atoms(), get_adjacent_heavy_atoms(), get_atoms_exocyclic_to_ring_atom(), core::scoring::methods::LK_PolarNonPolarEnergy::get_base_vector(), core::scoring::orbitals::OrbitalsScore::get_E_haro_one_way(), core::scoring::orbitals::OrbitalsScore::get_E_hpol_one_way(), core::conformation::carbohydrates::get_linkage_position_of_saccharide_residue(), n_bonded_neighbor_all_res(), protocols::qsar::scoring_grid::HbdGrid::refresh(), protocols::features::OrbitalsFeatures::report_hpol_orbital_interactions(), core::scoring::methods::LK_hack::residue_pair_energy(), core::scoring::orbitals::OrbitalsStatistics::sc_H_orbital(), protocols::qsar::scoring_grid::HbaGrid::score(), and protocols::features::OrbitalsFeatures::set_OrbH_features_data().

utility::vector1< Size > const& core::conformation::Residue::bonded_orbitals ( Size const  atm ) const

inline

References core::chemical::ResidueType::bonded_orbitals(), and rsd_type_.

Referenced by core::scoring::orbitals::OrbitalsScore::assign_orb_H_derivs(), core::scoring::orbitals::OrbitalsScore::assign_orb_orb_derivs(), core::scoring::orbitals::OrbitalsStatistics::bb_stats(), core::scoring::orbitals::OrbitalsScore::get_orb_H_distance_and_energy(), core::scoring::orbitals::OrbitalsScore::get_orb_orb_E(), protocols::ligand_docking::rdf::RDFBinaryOrbitalFunction::operator()(), protocols::features::OrbitalsFeatures::report_hpol_orbital_interactions(), core::scoring::orbitals::OrbitalsStatistics::sc_H_orbital(), and core::conformation::Conformation::update_orbital_coords().

Vector core::conformation::Residue::build_atom_ideal ( int const  atomno, Conformation const &  conformation  ) const

inline

Return coordinates for building an atom from ideal internal coordinates, used for building missing atoms.

References core::chemical::AtomICoor::build(), and icoor().

Referenced by protocols::splice::Splice::apply(), and core::scoring::methods::CartesianBondedEnergy::idealize_proline_nvs().

Vector core::conformation::Residue::build_orbital_xyz ( Size const  orbital_index ) const

inline

References atom(), core::chemical::ResidueType::new_orbital_icoor_data(), rsd_type_, and xyz().

Referenced by assign_orbitals(), core::conformation::Conformation::update_orbital_coords(), and update_orbital_coords().

core::chemical::carbohydrates::CarbohydrateInfoCOP core::conformation::Residue::carbohydrate_info

(

)

const

Return the CarbohydrateInfo object containing sugar-specific properties for this residue.

References core::chemical::ResidueType::carbohydrate_info(), core::chemical::ResidueType::is_carbohydrate(), and rsd_type_.

Referenced by core::conformation::Conformation::align_virtual_atoms_in_carbohydrate_residue(), protocols::carbohydrates::IdealizeAnomericHydrogens::apply(), protocols::analysis::GlycanInfoMover::apply_const(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_ring_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_ring_energy(), core::scoring::methods::carbohydrates::SugarBackboneEnergy::eval_residue_dof_derivative(), core::conformation::carbohydrates::find_seqpos_of_saccharides_child_residue_at(), core::conformation::carbohydrates::find_seqpos_of_saccharides_mainchain_child(), core::conformation::carbohydrates::find_seqpos_of_saccharides_parent_residue(), protocols::analysis::GlycanInfoMover::get_attachment_point_string(), core::conformation::carbohydrates::get_linkage_position_of_saccharide_residue(), protocols::simple_moves::bb_sampler::SugarBBSampler::get_torsion(), core::conformation::carbohydrates::has_exocyclic_glycosidic_linkage(), core::pose::carbohydrates::idealize_last_n_glycans_in_pose(), core::conformation::carbohydrates::is_glycosidic_omega_torsion(), core::pose::carbohydrates::is_glycosidic_torsion(), core::scoring::methods::carbohydrates::SugarBackboneEnergy::residue_energy(), and core::scoring::constraints::SiteConstraint::setup_csts().

core::Size core::conformation::Residue::chain ( ) const

inline

Returns this residue's chain id.

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

References chain_.

Referenced by protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::add_rotamer_to_rotamer_set(), protocols::features::BetaTurnDetection::all_turn_residues_are_on_the_same_chain(), core::pack::rotamer_set::AddResiduesRotamerSetOperation::alter_rotamer_set(), protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::alter_rotamer_set_from_db(), protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::alter_rotamer_set_from_pdb(), core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr(), protocols::frag_picker::nonlocal::NonlocalFrags::apply(), protocols::task_operations::SelectResiduesWithinChainOperation::apply(), core::select::jump_selector::InterchainJumpSelector::apply(), protocols::protein_interface_design::movers::LoopFinder::apply(), protocols::simple_moves::CoupledMover::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::fold_from_loops::movers::NubInitioLoopClosureMover::apply_closure_trust(), core::pack::rotamer_set::RotamerSet_::build_dependent_rotamers_for_concrete(), core::pack::rotamer_set::RotamerSet_::build_filtered_tp3_water_rotamers(), core::pack::rotamer_set::RotamerSet_::build_optimize_H_rotamers(), core::pack::rotamer_set::RotamerSet_::build_rotamers_for_concrete(), core::pack::rotamer_set::RotamerSet_::build_tp3_water_rotamers(), core::pack::rotamer_set::RotamerSet_::build_virtualizable_rotatable_water_rotamers(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::calc_dist(), protocols::analysis::InterfaceAnalyzerMover::calc_per_residue_and_regional_data(), protocols::peptide_deriver::PeptideDeriverFilter::calculate_per_residue_interface_score(), core::pose::Pose::chain(), protocols::simple_filters::TerminusDistanceFilter::compute(), protocols::simple_filters::NetChargeFilter::compute(), protocols::protein_interface_design::filters::AtomicContactCountFilter::compute(), protocols::simple_filters::InterfaceHbondsFilter::compute_hbonds(), core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms(), protocols::matdes::dup_residue(), core::pack::rotamer_set::dup_residue(), core::pack::rotamers::dup_residue(), protocols::cutoutdomain::CutOutDomain::find_nearest_res(), protocols::rosetta_scripts::find_nearest_res(), core::io::pose_to_sfr::PoseToStructFileRepConverter::generate_secondary_structure_informations(), protocols::minimization_packing::ChainGroupDiscriminator::group_id(), protocols::antibody::AntibodyInfo::identify_antibody(), protocols::calc_taskop_filters::RotamerBoltzmannWeight::interface_interaction_energy(), protocols::loops::loopfinder(), protocols::ligand_docking::make_atr_rep_grid_without_ligands(), protocols::analysis::InterfaceAnalyzerMover::make_interface_set(), protocols::analysis::InterfaceAnalyzerMover::make_separated_pose(), protocols::forge::build::ConnectRight::modify_impl(), orient_onto_residue_peptoid(), core::pose::PDBInfo::PDBInfo(), polymeric_oriented_sequence_distance(), polymeric_sequence_distance(), core::scoring::PQR::PQR(), protocols::qsar::scoring_grid::VdwGrid::refresh(), protocols::antibody::AntibodyFeatures::report_features(), protocols::rotamer_recovery::RRReporterSQLite::report_rotamer_recovery_full(), core::scoring::rna::RNA_BulgeEnergy::residue_energy(), core::scoring::membrane::MPNonHelixPenalty::residue_energy(), core::scoring::methods::PoissonBoltzmannEnergy::residue_in_chains(), core::scoring::interface_::DDPscore::residue_pair_energy(), core::scoring::methods::RamachandranEnergy2B::residue_pair_energy(), core::scoring::methods::MotifDockEnergy::residue_pair_energy(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::RotamericSingleResidueDunbrackLibrary(), protocols::membrane::rsd_closest_to_chain_tm_com(), core::conformation::Conformation::sequence_matches(), protocols::qsar::scoring_grid::AtrGrid::set_ligand_rings(), protocols::docking::DockingHighResLegacy::setup_packing(), core::conformation::Conformation::update_polymeric_connection(), and core::io::serialization::write_binary().

void core::conformation::Residue::chain ( core::Size const  setting )

inline

Sets this residue's chain id.

Don't call directly – In almost all situations, this should be set by the owning Conformation

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

References chain_.

utility::vector1< Real > const& core::conformation::Residue::chi ( ) const

inline

Returns the chi torsion angles of this residue (const)

example(s): residue.chi() See also: Residue Residue.nchi Pose Pose.chi

References chi_.

Referenced by protocols::sewing::hashing::AlignmentFileGeneratorMover::add_pose_segments_to_segment_vector(), core::pack::dunbrack::RotamerConstraint::add_residue(), core::pose::add_variant_type_to_residue(), protocols::simple_moves::hbs::HbsPatcher::apply(), protocols::simple_moves::oop::OopPatcher::apply(), protocols::simple_moves::a3b_hbs::A3BHbsPatcher::apply(), protocols::simple_moves::sidechain_moves::SidechainMover::apply(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::bbdep_nrchi_score(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::best_rotamer_energy(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::best_rotamer_energy(), protocols::match::upstream::ProteinUpstreamBuilder::build(), core::pose::Pose::chi(), protocols::minimization_packing::MinimalRotamer::chi_matches_coords(), protocols::noesy_assign::FragsToAtomDist::compute_average_distances(), protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover::compute_proposal_density(), protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover::compute_proposal_density(), core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms(), protocols::legacy_sewing::create_model_from_pose(), protocols::stepwise::modeler::rna::create_rotamer_string(), core::conformation::Conformation::debug_residue_torsions(), core::io::raw_data::DecoyStruct::DecoyStruct(), protocols::ligand_docking::ResidueTorsionRestraints::disable(), protocols::dna::DNABase::DNABase(), protocols::metal_interface::dump_chis(), protocols::ligand_docking::ResidueTorsionRestraints::enable(), core::scoring::dna::DNABFormPotential::eval_dna_bform_chi_torsion_score_residue(), core::scoring::dna::DNA_DihedralPotential::eval_harmonic_sugar_pucker_dependent_chi_torsion_score_and_deriv(), core::scoring::rna::RNA_TorsionPotential::eval_intrares_energy(), core::scoring::methods::YHHPlanarityEnergy::eval_residue_dof_derivative(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::eval_rotameric_energy_deriv(), protocols::indexed_structure_store::extract_residue_entry(), core::pack::rotamers::SingleBasicRotamerLibrary::fill_rotamer_vector(), core::io::silent::RNA_SilentStruct::fill_struct(), core::io::silent::ProteinSilentStruct_Template< T >::fill_struct(), protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::get_chi_weight(), core::scoring::motif::MotifHash::get_matching_motifs(), protocols::optimize_weights::IterativeOptEDriver::get_nat_rot_opte_data(), core::chemical::rna::get_residue_base_state(), core::pack::get_residue_current_energy(), core::pack::interaction_graph::SymmOnTheFlyNode::get_rotamer(), core::pack::get_rotamer_angle_diffs(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::idealize_and_repack_pose(), protocols::features::RotamerInitializer< T, N >::initialize_rotamer(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::interpolate_rotamers(), is_similar_rotamer(), protocols::rotamer_recovery::RRComparerChiDiff::measure_rotamer_recovery(), protocols::make_rot_lib::MakeRotLibMover::minimize_rotamer(), protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::perturb(), protocols::stepwise::modeler::rna::print_torsion_info(), protocols::splice::printChi(), protocols::simple_moves::sidechain_moves::SidechainMover::proposal_density(), protocols::minimization_packing::MinimalRotamer::record_chi(), protocols::match::upstream::ProteinUpstreamBuilder::recover_hits(), core::pose::remove_variant_type_from_residue(), protocols::features::ResidueConformationFeatures::report_features(), protocols::features::ProteinResidueConformationFeatures::report_features(), core::scoring::methods::YHHPlanarityEnergy::residue_energy(), protocols::dna::PDBOutput::residues_are_different(), core::scoring::motif::ResPairMotif::ResPairMotif(), core::pack::dunbrack::rotamer_from_chi(), protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers::rotamer_set_contains_rotamer(), core::conformation::set_chi_according_to_coordinates(), core::pack::scmin::ResidueAtomTreeCollection::set_rescoords(), core::pack::rotamer_set::RotamerSubset::show(), core::pack::rotamer_set::RotamerSet_::show(), protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::update_chis(), protocols::legacy_sewing::Assembly::update_coords_from_pose(), protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::update_flexscs(), core::pack::scmin::ResidueAtomTreeCollection::update_residue(), and core::conformation::Conformation::update_residue_torsions().

utility::vector1< Real >& core::conformation::Residue::chi ( )

inline

Returns the chi torsion angles of this residue (non-const)

References chi_.

void core::conformation::Residue::chi ( utility::vector1< Real > const &  chis )

inline

Sets the chi torsion angles of this residue.

CAUTION: This function does not cause updating to any internal coordinate data. See Residue::set_chi() and Residue::set_all_chi() functions for versions which handle coordinate updates.

example(s):

See also: Residue Pose Pose.set_chi

References chi_.

Real core::conformation::Residue::chi ( Size const  chino ) const

inline

get a specific chi torsion angle

example(s): residue.chi(1) See also: Residue Pose Pose.chi

References chi_.

utility::vector1< AtomIndices > const& core::conformation::Residue::chi_atoms ( ) const

inline

Returns the AtomIndices of each set of four atoms defining each chi angle.

References core::chemical::ResidueType::chi_atoms(), and rsd_type_.

Referenced by protocols::splice::Splice::add_coordinate_constraints(), protocols::splice::SpliceManager::add_coordinate_constraints(), core::scoring::MultipoleElecPotential::align_residue_multipole_axes(), core::scoring::hackaro::chi2_torsion_atom_index(), protocols::simple_moves::PeptideStapleMover::derive_staple_constraints_(), core::scoring::dna::get_base_pair_stub_slow(), core::conformation::Conformation::get_torsion_angle_atom_ids(), core::conformation::carbohydrates::is_glycosidic_omega_torsion(), core::conformation::carbohydrates::is_glycosidic_psi_torsion(), core::pose::carbohydrates::is_glycosidic_torsion(), place(), Residue(), set_chi(), core::conformation::set_chi_according_to_coordinates(), set_d(), set_theta(), core::pack::scmin::AtomTreeSCMinMinimizerMap::setup(), core::conformation::setup_corresponding_atoms(), core::conformation::setup_links(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::superimpose_to_alternative_frame(), and core::pack::scmin::ResidueAtomTreeCollection::update_residue().

AtomIndices const& core::conformation::Residue::chi_atoms ( Size const  chino ) const

inline

Returns the AtomIndices of the four atoms defining this residue's <chino> chi angle.

References core::chemical::ResidueType::chi_atoms(), and rsd_type_.

utility::vector1< std::pair< Real, Real > > const& core::conformation::Residue::chi_rotamers ( Size const  chino ) const

inline

Returns the chi rotamers available for this residue's chi angle <chino>

References core::chemical::ResidueType::chi_rotamers(), and rsd_type_.

Referenced by core::pack::rotamer_set::build_rotamers_from_rotamer_bins().

void core::conformation::Residue::clear_residue_connections

(

)

References connect_map_, connections_to_residues_, nonstandard_polymer_, and pseudobonds_.

ResidueOP core::conformation::Residue::clone

(

)

const

Copy this residue( allocate actual memory for it )

make a copy of this residue( allocate actual memory for it )

Referenced by core::pack::rotamer_set::RotamerSubset::add_rotamer(), core::pack::rotamer_set::RotamerSet_::add_rotamer(), core::pack::rotamer_set::RotamerSubset::add_rotamer_into_existing_group(), core::pack::rotamer_set::RotamerSet_::add_rotamer_into_existing_group(), core::pose::add_variant_type_to_residue(), protocols::generalized_kinematic_closure::GeneralizedKIC::addloopgeometry(), protocols::generalized_kinematic_closure::GeneralizedKIC::addloweranchor(), protocols::generalized_kinematic_closure::GeneralizedKIC::addtailgeometry(), protocols::generalized_kinematic_closure::GeneralizedKIC::addupperanchor(), protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::alter_rotamer_set_from_pdb(), core::conformation::Conformation::append_polymer_residue_after_seqpos(), core::conformation::Conformation::append_residue_by_bond(), protocols::comparative_modeling::StealSideChainsMover::apply(), protocols::stepwise::modeler::packer::SideChainCopier::apply(), protocols::comparative_modeling::PartialThreadingMover::apply(), protocols::simple_moves::chiral::ChiralMover::apply(), protocols::comparative_modeling::ThreadingMover::apply(), protocols::enzdes::GenerateStoredRBConfs::apply(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::apply(), protocols::pockets::PocketGrid::autoexpanding_pocket_eval(), core::pack::rotamer_set::bb_independent_rotamers(), core::pack::rotamer_set::build_lib_dna_rotamers(), core::pack::rotamer_set::RotamerSet_::build_optimize_H_rotamers(), core::pack::rotamer_set::build_random_dna_rotamers(), protocols::motifs::MotifHit::build_rotamer(), core::pack::rotamer_set::RotamerSet_::build_rotamers_for_concrete(), protocols::seeded_abinitio::combine_two_poses(), core::pack::interaction_graph::SurfacePotential::compute_pose_hpatch_score(), create_residue(), create_rotamer(), protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::debug_note_considered_substitution(), core::io::pdb::dump_pdb_residue(), protocols::matdes::dup_residue(), core::pack::rotamer_set::dup_residue(), core::pack::rotamers::dup_residue(), core::pack::rotamers::SingleBasicRotamerLibrary::fill_rotamer_vector(), protocols::splice::RotLibOut::find_matching_res(), protocols::kinematic_closure::ClosureProblem::frame_lower_pivot(), protocols::kinematic_closure::ClosureProblem::frame_upper_pivot(), protocols::ligand_docking::get_ligand_torsion_constraints(), protocols::hbnet::HBNet::get_num_native_rot(), protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives::get_residue(), protocols::pockets::PocketGrid::getRelaxResidues(), protocols::magnesium::MgHydrater::hydrate_magnesium(), core::conformation::Conformation::insert_conformation_by_jump(), core::conformation::Conformation::insert_residue_by_bond(), protocols::motifs::BuildPosition::keep_rotamer(), protocols::stepwise::modeler::merge_two_poses(), protocols::hbnet::HBNet::minimize_network(), protocols::forge::build::SegmentInsert::modify_impl(), protocols::ligand_docking::LigandDockProtocol::optimize_orientation3(), core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::orient_rotamer_to_symmetric_partner(), core::pose::pdbslice(), protocols::cyclic_peptide::crosslinker::TMA_Helper::place_tma_asymmetric(), core::conformation::symmetry::SymmetricConformation::prepend_polymer_residue_before_seqpos(), core::conformation::Conformation::prepend_polymer_residue_before_seqpos(), protocols::hydrate::remove_high_energy_water_molecules(), protocols::hydrate::remove_non_buried_wat(), core::pose::remove_variant_type_from_residue(), protocols::simple_moves::RepeatPropagationMover::repeat_ligand(), core::conformation::symmetry::MirrorSymmetricConformation::replace_residue(), core::conformation::Conformation::residues_append(), core::conformation::Conformation::residues_insert(), core::conformation::Conformation::residues_replace(), protocols::denovo_design::components::Segment::set_template_pose(), core::pack::setup_bgres_cops(), protocols::relax::RepeatProteinRelax::setup_repeat_pose(), protocols::relax::RepeatProteinRelax::setup_repeat_pose_jumping(), protocols::stepwise::modeler::slice(), protocols::motifs::MotifHit::target_conformer(), protocols::legacy_sewing::Assembly::to_multichain_pose(), protocols::legacy_sewing::Assembly::to_pose(), protocols::sewing::data_storage::SmartAssembly::to_pose(), and protocols::vip::VIP_Mover::try_point_mutants().

ResidueOP core::conformation::Residue::clone_flipping_chirality

(

core::chemical::ResidueTypeSet const &

residue_type_set

)

const

Copy this residue( allocate actual memory for it ), keeping everything the same EXCEPT the type.

Switches the ResidueType to the mirror type (D->L or L->D). Preserves it for achiral residues. The passed ResidueTypeSet is the ResidueTypeSet you want the mirrored type to come from.

Note

This function is the best way to convert a D-residue to its L-counterpart, or an L-residue to its D-counterpart. It assumes that you've already mirrored all of the coordinates, and just allows you to generate a replacement residue of the mirror type that preserves all other Residue information (connections, seqpos, xyz coordinates of all atoms, variant types, etc.).

Author

Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References core::chemical::ResidueTypeSet::get_mirrored_type(), Residue(), and rsd_type_ptr_.

Referenced by core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::orient_rotamer_to_symmetric_partner().

Size core::conformation::Residue::connect_atom

(

Residue const &

other

)

const

Returns the index number of this residue's atom connected to the <other> Residue.

Returns the atom-index of my atom which is connected to the other residue.

example(s):

See also: Residue Residue.atom Residue.atoms Residue.lower_connect_atom Residue.upper_connect_atom Pose

so long as there is only a single connection to other... if there are multiple connections this will fail. If there are no connections this will fail. This is a convenience function that can fail; be careful! Fails if I'm not bonded to the other residue.

Note

not well defined if multiple connections to another residue – need more general function

References connections_to_residues_, is_lower_terminus(), is_polymer(), is_upper_terminus(), lower_connect_atom(), core::chemical::ResidueTypeBase::name(), nonstandard_polymer_, core::chemical::ResidueType::residue_connection(), rsd_type_, seqpos(), seqpos_, core::conformation::TR(), type(), and upper_connect_atom().

Referenced by core::conformation::Conformation::align_virtual_atoms_in_carbohydrate_residue(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_copy_backbone_dihedrals(), core::conformation::Conformation::branch_connection_torsion_angle_atoms(), protocols::cartesian::MolecularDynamics::createBondList(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_ring_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_ring_energy(), core::pose::symmetry::extract_asymmetric_unit(), core::conformation::form_disulfide(), core::io::pose_from_sfr::is_connected(), core::conformation::carbohydrates::is_glycosidic_omega_torsion(), core::conformation::carbohydrates::is_glycosidic_psi_torsion(), core::pose::carbohydrates::is_glycosidic_torsion(), core::scoring::carbon_hbonds::CarbonHBondEnergy::path_distance_OK(), and protocols::viewer::print_interres_bond().

chemical::ResConnID core::conformation::Residue::connect_map ( Size  resconn_index ) const

inline

References connect_map_.

Referenced by core::pose::add_custom_variant_type_to_pose_residue(), core::pose::add_variant_type_to_pose_residue(), protocols::cyclic_peptide::DeclareBond::apply(), protocols::cyclic_peptide::PeptideStubMover::apply(), core::chemical::ICoorAtomID::atom_id(), core::scoring::mm::connection_indices(), copy_residue_connections(), core::scoring::trie::create_cpdata_correspondence_for_rotamer(), core::scoring::disulfides::FullatomDisulfideEnergy::defines_score_for_residue_pair(), protocols::simple_moves::PeptideStapleMover::derive_staple_constraints_(), core::conformation::disulfide_bonds(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::disulfides_changed(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::disulfides_changed(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::disulfides_changed(), core::io::silent::BinarySilentStruct::fill_struct(), protocols::abinitio::abscript::find_disulfide_partner(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::find_disulfides(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::find_disulfides(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::find_disulfides(), core::conformation::form_disulfide(), core::scoring::methods::LK_PolarNonPolarEnergy::get_base_vector(), core::conformation::get_chemical_root_and_anchor_atomnos(), core::conformation::get_disulf_partner(), core::conformation::is_disulfide_bond(), core::pose::Pose::real_to_virtual(), protocols::cyclic_peptide::PeptideStubMover::rebuild_atoms(), core::pose::remove_variant_type_from_pose_residue(), core::scoring::methods::LK_hack::residue_pair_energy(), core::conformation::Conformation::show_residue_connections(), update_connections_to_other_residue(), core::conformation::carbohydrates::GlycanNode::update_connectivity_data(), and core::pose::Pose::virtual_to_real().

core::Size core::conformation::Residue::connect_map_size ( ) const

inline

Returns the size (number of elements) in the connect_map_ object.

References connect_map_.

Referenced by core::chemical::ICoorAtomID::atom_id(), core::scoring::Ramachandran::is_normally_connected(), and core::scoring::methods::lower_upper_connected_across_cutpoint().

Size core::conformation::Residue::connected_residue_at_lower

(

)

const

Returns the residue number of a residue connected to this residue at this residue's lower_connect.

This function returns 0 if this residue lacks a lower_connect or if it's not connected to anything at its lower_connect.

Author

Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References connected_residue_at_resconn(), has_lower_connect(), core::chemical::ResidueType::lower_connect_id(), and rsd_type_.

Referenced by protocols::cyclic_peptide::DeclareBond::apply(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::calc_dist(), protocols::simple_filters::LongestContinuousPolarSegmentFilter::compute(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_new_chainIDs(), core::pack::dunbrack::DunbrackEnergy::get_scratch_index(), core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy::has_bb_hbond_connection(), protocols::cyclic_peptide::RamaMutationSelector::is_terminus(), orient_onto_residue_peptoid(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::pose_from_posedata(), core::conformation::Conformation::rebuild_polymer_bond_dependent_atoms(), core::pose::set_reasonable_fold_tree(), and protocols::energy_based_clustering::EnergyBasedClusteringProtocol::storeposedata().

Size core::conformation::Residue::connected_residue_at_resconn ( Size const  resconn_index ) const

inline

Returns the residue number of a residue connected to this residue at this residue's connection resconn_index.

For example, in a normally-connected pose made of alpha-amino acids, calling residue_connection_partner(1) on residue 6 should return 5, since residue 6 is connected to residue 5 at the first connection of residue 6. Exactly the same as residue_connection_partner

References connect_map_.

Referenced by core::pose::add_custom_variant_type_to_pose_residue(), core::pose::add_variant_type_to_pose_residue(), protocols::cyclic_peptide::DeclareBond::apply(), protocols::cyclic_peptide::PeptideStubMover::apply(), protocols::farnesyl::SampleFarnesylMover::apply(), core::select::residue_selector::PhiSelector::apply(), core::select::residue_selector::BinSelector::apply(), protocols::cyclic_peptide::RamaMutationSelector::apply(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_copy_backbone_dihedrals(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_loop_bump_check(), connected_residue_at_lower(), connected_residue_at_upper(), core::scoring::trie::create_cpdata_correspondence_for_rotamer(), core::scoring::methods::CartesianBondedEnergy::eval_intraresidue_dof_derivative(), core::scoring::methods::CartesianBondedEnergy::eval_residue_pair_derivatives(), core::conformation::carbohydrates::fill_downstream_children_res_and_tips(), core::io::silent::BinarySilentStruct::fill_struct(), protocols::forge::methods::fold_tree_from_pose(), protocols::generalized_kinematic_closure::general_set_phi(), protocols::generalized_kinematic_closure::general_set_psi(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_connectivity_annotation_info(), core::conformation::carbohydrates::get_glycan_connecting_protein_branch_point(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_link_record(), core::conformation::carbohydrates::get_linkage_position_of_saccharide_residue(), protocols::cyclic_peptide::crosslinker::TMA_Helper::get_linker_index_asymmetric(), protocols::cyclic_peptide::crosslinker::TMA_Helper::get_linker_indices_symmetric(), core::conformation::get_second_atom_from_connection(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_ssbond_record(), protocols::denovo_design::components::StructureDataFactory::infer_from_pose(), core::scoring::PolymerBondedEnergyContainer::initialize_peptide_bonded_pair_indices(), core::scoring::PolymerBondedEnergyContainer::is_valid(), core::scoring::methods::lower_upper_connected_across_cutpoint(), n_current_residue_connections(), core::pose::Pose::real_to_virtual(), core::conformation::Conformation::rebuild_residue_connection_dependent_atoms(), core::pose::remove_variant_type_from_pose_residue(), core::scoring::GenericBondedPotential::residue_pair_derivatives(), core::scoring::GenericBondedPotential::residue_pair_energy(), core::scoring::methods::CartesianBondedEnergy::residue_pair_energy(), core::scoring::methods::CartesianBondedEnergy::residue_pair_energy_sorted(), update_connections_to_other_residue(), core::conformation::carbohydrates::GlycanNode::update_connectivity_data(), core::pose::Pose::virtual_to_real(), and core::conformation::ConformationKinWriter::write_coords().

Size core::conformation::Residue::connected_residue_at_upper

(

)

const

Returns the residue number of a residue connected to this residue at this residue's upper_connect.

This function returns 0 if this residue lacks an upper_connect or if it's not connected to anything at its upper_connect.

Author

Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References connected_residue_at_resconn(), has_upper_connect(), rsd_type_, and core::chemical::ResidueType::upper_connect_id().

Referenced by protocols::cyclic_peptide::DeclareBond::apply(), protocols::backbone_moves::RandomizeBBByRamaPrePro::apply(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::calc_dist(), protocols::simple_filters::LongestContinuousPolarSegmentFilter::compute(), core::scoring::methods::RamaPreProEnergy::eval_intraresidue_dof_derivative(), core::pose::symmetry::extract_asymmetric_unit(), core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy::has_bb_hbond_connection(), protocols::cyclic_peptide::RamaMutationSelector::is_terminus(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::pose_from_posedata(), protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::prepare_foldtree(), core::conformation::Conformation::rebuild_polymer_bond_dependent_atoms(), core::pose::carbohydrates::set_glycan_iupac_bb_torsions(), core::pose::set_reasonable_fold_tree(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::storeposedata(), and protocols::energy_based_clustering::EnergyBasedClusteringProtocol::use_this_atom().

Distance core::conformation::Residue::connection_distance	(	conformation::Conformation const &	conf,
		Size const	resconn_index,
		Vector const &	matchpoint
	)		const

Distance between a potential residue connection match and the position of the expected atom.

References core::chemical::AtomICoor::build(), core::chemical::ResidueConnection::icoor(), name(), core::chemical::ResidueType::residue_connection(), core::conformation::TR(), and type().

Referenced by core::conformation::Conformation::detect_bonds().

bool core::conformation::Residue::connection_incomplete

(

Size

resconnid

)

const

References connect_map_.

Referenced by core::conformation::Conformation::backbone_torsion_angle_atoms(), core::conformation::Conformation::bonded_neighbor_all_res(), core::scoring::trie::create_cpdata_correspondence_for_rotamer(), core::conformation::Conformation::detect_bonds(), protocols::generalized_kinematic_closure::general_set_phi(), protocols::generalized_kinematic_closure::general_set_psi(), has_incomplete_connection(), protocols::generalized_kinematic_closure::GeneralizedKIC::infer_anchor_connIDs(), core::scoring::Ramachandran::is_normally_connected(), protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::moves_for_pose(), n_bonded_neighbor_all_res(), core::scoring::polymeric_termini_incomplete(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::rama_energy(), and protocols::cyclic_peptide::PeptideStubMover::rebuild_atoms().

bool core::conformation::Residue::connections_match

(

Residue const &

other

)

const

Returns true if ???

References connect_map_, and pseudobonds_.

Referenced by core::conformation::Conformation::sequence_matches().

utility::vector1< Size > const& core::conformation::Residue::connections_to_residue ( Residue const &  other ) const

inline

Returns the vector1 of resconn ids that connect this residue to other.

References seqpos().

Referenced by core::scoring::etable::count_pair::CountPairGeneric::CountPairGeneric(), core::scoring::etable::count_pair::CountPairFactory::create_count_pair_function(), core::scoring::etable::count_pair::CountPairFactory::create_count_pair_function_and_invoke(), core::scoring::etable::count_pair::CountPairFactory::determine_residue_connection(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd1(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd2(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd1(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd2(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_bond_energy(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_bond_length_derivs(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_angle(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_bond(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_improper(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_torsion(), core::conformation::get_chemical_root_and_anchor_atomnos(), protocols::generalized_kinematic_closure::GeneralizedKIC::get_connection(), protocols::features::ProteinBondGeometryFeatures::report_interres_angles(), protocols::features::ProteinBondGeometryFeatures::report_interres_lengths(), core::scoring::methods::MMBondLengthEnergy::residue_pair_energy(), core::scoring::methods::MMTorsionEnergy::residue_pair_energy(), core::scoring::methods::MMBondAngleEnergy::residue_pair_energy(), and core::scoring::etable::etrie::TrieCountPairGeneric::TrieCountPairGeneric().

utility::vector1< Size > const& core::conformation::Residue::connections_to_residue ( Size const  other_resid ) const

inline

Returns the vector1 of resconn ids that connect this residue to other.

References connections_to_residues_.

void core::conformation::Residue::copy_residue_connections

(

Residue const &

src_rsd

)

attempt to take residue connection info from src_rsd

References atom_index(), atom_name(), core::chemical::ResidueConnection::atomno(), connect_map(), connect_map_, connections_to_residues_, core::chemical::ResConnID::connid(), has(), core::chemical::ResidueType::n_possible_residue_connections(), n_possible_residue_connections(), core::chemical::ResidueType::n_residue_connections_for_atom(), pseudobonds_, core::chemical::ResConnID::resid(), core::chemical::ResidueType::residue_connection(), core::chemical::ResidueType::residue_connection_id_for_atom(), residue_connection_partner(), core::chemical::ResidueType::residue_connections_for_atom(), seqpos(), core::conformation::TR(), and type().

Referenced by Residue().

void core::conformation::Residue::copy_residue_connections_from

(

Residue const &

src

)

References connect_map_, connections_to_residues_, nonstandard_polymer_, and pseudobonds_.

Referenced by protocols::toolbox::rotamer_set_operations::RigidBodyMoveBaseRSO::alter_rotamer_set(), and protocols::hbnet::hbnet_symm_one_body_energies().

ResidueOP core::conformation::Residue::create_residue ( ) const

inline

Returns a ResidueOP for creating a copy of residue, same as clone() Temporary hack until Residue hierarchy is worked out.

References clone().

ResidueOP core::conformation::Residue::create_rotamer ( ) const

inline

Returns a ResidueOP for creating a rotamer of this residue Temporary hack until Residue hierarchy is worked out.

References clone().

Referenced by core::pack::rotamer_set::RotamerSet_::build_dependent_rotamers(), core::pack::rotamer_set::RotamerSet_::build_filtered_tp3_water_rotamers(), core::pack::rotamer_set::RotamerSet_::build_rotamers(), core::pack::rotamer_set::RotamerSet_::build_rotamers_for_concrete(), core::pack::rotamer_set::build_rotamers_from_rotamer_bins(), core::pack::rotamer_set::RotamerSet_::build_tp3_water_rotamers(), core::pack::rotamer_set::RotamerSet_::build_virtualizable_rotatable_water_rotamers(), core::pack::rotamers::SingleResidueRotamerLibrary::current_rotamer(), and core::pack::hbonds::hbond_graph_from_partial_rotsets().

AtomIndices const& core::conformation::Residue::cut_bond_neighbor ( Size const  atm ) const

inline

atom indices for bonded neighbors to which atom-tree connections are disallowed.

References core::chemical::ResidueType::cut_bond_neighbor(), and rsd_type_.

Referenced by core::conformation::setup_links_simple().

basic::datacache::BasicDataCache const& core::conformation::Residue::data ( ) const

inline

BasicDataCache indexed by enum in residue_datacache.hh. Beware, this will crash if a call to nonconst_data_ptr() or data_ptr() has not previously been made on this Residue – the datacache is created just-in-time.

References data_cache_.

Referenced by core::conformation::annotated_atom_graph_from_conformation(), core::conformation::atom_graph_from_conformation(), core::scoring::lkball::LK_BallEnergy::backbone_backbone_energy(), core::scoring::lkball::LK_BallEnergy::backbone_sidechain_energy(), core::scoring::lkball::LK_BallEnergy::residue_pair_energy(), core::scoring::lkball::retrieve_lkb_resdata(), and core::scoring::lkball::LK_BallEnergy::sidechain_sidechain_energy().

basic::datacache::BasicDataCacheCOP core::conformation::Residue::data_ptr ( ) const

inline

BasicDataCache indexed by enum in residue_datacache.hh.

Return a COP to the data cache

Note

Might be a null pointer if the cache has not been initialized

References data_cache_.

Referenced by core::scoring::lkball::LK_BallEnergy::backbone_backbone_energy(), core::scoring::lkball::LK_BallEnergy::backbone_sidechain_energy(), protocols::ligand_docking::ga_ligand_dock::GridScorer::calculate_grid(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::define_active_virtual_sites(), core::conformation::Conformation::residue_data(), and core::scoring::lkball::LK_BallEnergy::sidechain_sidechain_energy().

void core::conformation::Residue::determine_nonstandard_polymer_status ( )

private

References connect_map_, is_lower_terminus(), is_polymer(), is_upper_terminus(), nonstandard_polymer_, seqpos(), and type().

Referenced by residue_connection_partner(), and update_sequence_numbering().

bool core::conformation::Residue::fill_missing_atoms	(	utility::vector1< bool > &	missing,
		Conformation const &	conformation,
		bool	fail = true
	)

Builds coordinates for atoms missing from this residue assuming ideal internal coordinates.

If fail is false, will return true if we can fill all the missing atoms, and false if we can't.

missing is passed by non-const ref: it will be updated for the atoms which are filled. (If fail is false, it will end up all false, or you'll get a utility_exit()

this uses ideal internal coords to build any missing atom from its three stub atoms. If any of the stub atoms are missing, build them first. Unable to build a missing atom whose stub atoms are from non-existing polymer connection and its input bogus value will not be changed.

References atom_name(), bonded_neighbor(), core::chemical::AtomICoor::build(), icoor(), core::conformation::improper_build(), core::chemical::INTERNAL, core::conformation::missing_stubs_build(), name(), natoms(), core::chemical::pretty_print_atomicoor(), seqpos(), seqpos_, set_xyz(), core::chemical::ResidueType::show_all_atom_names(), core::chemical::AtomICoor::stub_atom(), core::conformation::TR(), and type().

Referenced by core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms(), place(), and protocols::denovo_design::rebuild_missing_atoms().

uint core::conformation::Residue::first_adjacent_heavy_atom

(

uint const

atom_index

)

const

Scan through the list of atoms connected to a given atom and return the 1st heavy atom found.

Returns

The atom index of the 1st heavy atom next to the given atom (by index) or 0 if no heavy atom is found

This method does not count virtual atoms as heavy atoms.

Remarks

This method is crucial for determining atoms defining non-standard torsion angles, such as those found across branch connections or in glycosidic linkages.

Author

Labonte JWLab.nosp@m.onte.nosp@m.@jhu..nosp@m.edu

References get_adjacent_heavy_atoms(), and core::conformation::TR().

Referenced by core::conformation::Conformation::align_virtual_atoms_in_carbohydrate_residue(), and core::conformation::Conformation::branch_connection_torsion_angle_atoms().

Size core::conformation::Residue::first_sidechain_atom ( ) const

inline

Returns the index number of the first sidechain heavyatom.

example(s): residue.first_sidechain_atom() See also: Residue Residue.atom Residue.atoms Residue.last_backbone_atom Pose

References core::chemical::ResidueType::first_sidechain_atom(), and rsd_type_.

Referenced by core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_one_way_sc(), protocols::splice::Splice::add_coordinate_constraints(), protocols::splice::SpliceManager::add_coordinate_constraints(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::append_metal_vsites(), protocols::membrane::AqueousPoreFinder::apply(), protocols::match::downstream::DownstreamAlgorithm::are_colliding(), core::scoring::elec::assign_rna_atom_type(), protocols::stepwise::modeler::rna::base_atoms_square_deviation(), core::pose::rna::bases_form_a_hydrogen_bond(), protocols::recces::sampler::rna::calc_base_centroid_rmsd(), core::select::util::SelectResiduesByLayer::calc_sc_neighbors(), core::scoring::rna::RNA_FullAtomStackingEnergy::check_base_base_OK(), core::scoring::rna::RNA_LowResolutionPotential::check_for_base_neighbor(), protocols::protein_interface_design::filters::AtomicContactCountFilter::compute(), protocols::relax::derive_sc_sc_restraints(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_one_way_sc(), protocols::match::downstream::ActiveSiteGrid::enlargen_to_capture_volume_within_radius_of_backbone(), protocols::match::downstream::ActiveSiteGrid::enlargen_to_capture_volume_within_radius_of_sidechain(), protocols::hbnet::HBNet::estimate_saturation(), core::pose::rna::figure_out_number_base_contacts(), protocols::metal_interface::find_closest_atom(), protocols::enzdes::DetectProteinLigandInterface::find_design_interface(), protocols::enzdes::DetectProteinLigandInterface::find_design_interface_arg_sweep(), core::scoring::cryst::fix_bfactorsMissing(), core::scoring::dna::get_base_pair_stub_slow(), core::scoring::hackaro::HackAroEnergy::get_centroid(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::get_matching_res_in_VDW_rep_screen_pose(), protocols::simple_filters::ResidueDepthCalculator::get_pose_crd_and_index(), core::chemical::rna::get_rna_base_centroid(), core::chemical::rna::get_rna_base_coordinate_system(), protocols::motifs::LigandMotifSearch::get_sphere_aa(), protocols::stepwise::modeler::rna::get_surrounding_O2prime_hydrogen(), core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy::has_bb_hbond(), core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy::has_hbond(), protocols::simple_moves::ConstrainToIdealMover::i_want_this_atom_to_move(), core::scoring::inline_residue_atom_pair_energy_sidechain_backbone(), core::scoring::inline_residue_atom_pair_energy_sidechain_sidechain(), core::scoring::inline_residue_atom_pair_energy_sidechain_whole(), protocols::ligand_docking::ga_ligand_dock::GridScorer::is_residue_in_grid(), core::scoring::rna::StackElecEnergy::is_rna_base(), core::pack::task::residue_selector::is_sc_bb_clash(), core::pack::task::residue_selector::is_sc_sc_clash(), core::scoring::elec::is_sugar_2(), protocols::stepwise::modeler::rna::is_virtual_base(), protocols::ligand_docking::make_atr_rep_grid(), protocols::ligand_docking::make_atr_rep_grid_without_ligands(), protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::moving_res_contact_filter(), protocols::match::downstream::ActiveSiteGrid::or_within_radius_of_backbone(), protocols::match::downstream::ActiveSiteGrid::or_within_radius_of_sidechain(), protocols::hybridization::MRMover::pack_missing_sidechains(), protocols::match::output::UpstreamCollisionFilter::passes_hardsphere_filter(), protocols::stepwise::modeler::rna::phosphate_base_phosphate_square_deviation(), protocols::recces::print_base_centroid_atoms_for_rb_entropy(), core::pose::PDBInfo::replace_res_remap_bfactors(), core::scoring::rna::RNA_LJ_BaseEnergy::residue_pair_energy(), core::scoring::rna::RNA_FullAtomStackingEnergy::residue_pair_energy_one_way(), protocols::qsar::scoring_grid::AtrGrid::set_protein_rings(), core::pack::scmin::CartSCMinMinimizerMap::setup(), protocols::stepwise::modeler::rna::setup_suite_atom_id_map(), sidechainAtoms_begin(), protocols::hybridization::DDomainParse::split(), protocols::stepwise::modeler::rna::suite_square_deviation(), and protocols::dna::z_axis_dist().

Size core::conformation::Residue::first_sidechain_hydrogen ( ) const

inline

Returns the index number of the first sidechain hydrogen.

example(s): residue.first_sidechain_hydrogen() See also: Residue Residue.atom Residue.atoms Residue.first_sidechain_atom Pose

References core::chemical::ResidueType::first_sidechain_hydrogen(), and rsd_type_.

Referenced by core::scoring::carbon_hbonds::CarbonHBondEnergy::bb_bb_carbon_hbond_one_way(), core::scoring::carbon_hbonds::CarbonHBondEnergy::bb_sc_carbon_hbond_one_way(), protocols::ligand_docking::ga_ligand_dock::GridScorer::calculate_grid(), protocols::ligand_docking::ga_ligand_dock::GridScorer::debug_deriv(), protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_1b_energy(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_2b_energy(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_grid_atomtypes(), protocols::ligand_docking::ga_ligand_dock::GridScorer::is_residue_in_grid(), core::scoring::carbon_hbonds::CarbonHBondEnergy::sc_bb_carbon_hbond_one_way(), core::scoring::carbon_hbonds::CarbonHBondEnergy::sc_sc_carbon_hbond_one_way(), and core::pack::scmin::CartSCMinMinimizerMap::setup().

utility::vector1< uint > core::conformation::Residue::get_adjacent_heavy_atoms

(

uint const

atom_index

)

const

Get a list of heavy atoms connected to a given atom.

Returns

The atom indices of all heavy atoms bonded to the given atom (by index)

This method does not count virtual atoms as heavy atoms.

Author

Labonte JWLab.nosp@m.onte.nosp@m.@jhu..nosp@m.edu

References atom_is_hydrogen(), bonded_neighbor(), and is_virtual().

Referenced by first_adjacent_heavy_atom(), core::conformation::position_of_atom_on_ring(), and show().

core::chemical::AtomIndices core::conformation::Residue::get_atoms_exocyclic_to_ring_atom

(

uint const

atom_index

)

const

Get a list of exocyclic atoms connected to a given ring atom.

Returns

The atom indices of all atoms bonded to the given atom (by index) that are not a part of the ring.

This method does not count virtual atoms as atoms.

Author

Labonte JWLab.nosp@m.onte.nosp@m.@jhu..nosp@m.edu

References bonded_neighbor(), is_virtual(), and type().

Referenced by get_hydrogens_bonded_to_ring_atom(), and get_substituents_to_ring_atom().

core::chemical::AtomIndices core::conformation::Residue::get_hydrogens_bonded_to_ring_atom

(

uint const

atom_index

)

const

Get a list of hydrogen atoms connected to a given ring atom.

Returns

The atom indices of hydrogens bonded to the given ring atom (by index).

This method does not count virtual atoms as atoms.

Author

Labonte JWLab.nosp@m.onte.nosp@m.@jhu..nosp@m.edu

References atom_is_hydrogen(), and get_atoms_exocyclic_to_ring_atom().

void core::conformation::Residue::get_metal_binding_atoms ( AtomIndices &  metal_binding_indices ) const

inline

Gets the AtomIndices of the atoms in this residue that can bind to metals.

Note

: AtomIndices == vector1< Size >

Author

: Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References core::chemical::ResidueType::get_metal_binding_atoms(), and rsd_type_.

Referenced by protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::append_metal_vsites(), and core::util::find_metalbinding_atoms_helper().

PseudoBondCollectionCOP core::conformation::Residue::get_pseudobonds_to_residue

(

Size

resid

)

const

References pseudobonds_.

Referenced by core::scoring::etable::count_pair::CountPairGeneric::CountPairGeneric(), and core::scoring::etable::etrie::TrieCountPairGeneric::TrieCountPairGeneric().

ResidueCOP core::conformation::Residue::get_self_ptr ( ) const

inline

self pointers

Referenced by protocols::enzdes::SecondaryMatchProtocol::add_enz_cst_interaction_to_pose(), core::conformation::carbohydrates::align_virtual_atoms_in_carbohydrate_residue(), protocols::ligand_docking::WriteLigandMolFile::apply(), protocols::ligand_docking::AddHydrogens::apply(), protocols::ligand_docking::LigandDesign::apply(), protocols::ligand_docking::GrowLigand::apply(), protocols::ligand_docking::Transform::apply(), protocols::ligand_docking::TransformEnsemble::apply(), core::pack::rotamer_set::build_moving_O_water_rotamers_dependent(), protocols::toolbox::match_enzdes_util::constrain_pose_res_to_invrots(), core::scoring::disulfides::CentroidDisulfidePotential::disulfide_params(), protocols::hotspot_hashing::movers::PlaceProbeMover::execute_one_search(), protocols::hotspot_hashing::HotspotStubSet::fill(), core::scoring::aa_repeat_energy::AARepeatEnergy::finalize_total_energy(), core::scoring::aa_composition_energy::AACompositionEnergy::finalize_total_energy(), core::scoring::netcharge_energy::NetChargeEnergy::finalize_total_energy(), core::scoring::mhc_epitope_energy::MHCEpitopeEnergy::finalize_total_energy(), protocols::ligand_docking::LigandDesign::fragments_to_string(), protocols::cluster::GatherPosesMover::get_distance_measure(), core::conformation::carbohydrates::get_glycosidic_bond_residues(), protocols::ligand_docking::get_ligand_grid_scores(), core::pack::interaction_graph::ResidueArrayAnnealingEvaluator::initialize(), protocols::toolbox::match_enzdes_util::InvrotTreeNode::initialize_from_enzcst_io(), core::scoring::constraints::MembraneSpanConstraint::MembraneSpanConstraint(), core::scoring::constraints::MembraneSpanTermZConstraint::MembraneSpanTermZConstraint(), protocols::simple_moves::RepeatPropagationMover::repeat_ligand_constraints(), core::scoring::mhc_epitope_energy::MHCEpitopeEnergy::set_up_residuearrayannealableenergy_for_packing(), and protocols::ligand_docking::Transform::setup_conformers().

ResidueOP core::conformation::Residue::get_self_ptr ( )

inline

ResidueCAP core::conformation::Residue::get_self_weak_ptr ( ) const

inline

ResidueAP core::conformation::Residue::get_self_weak_ptr ( )

inline

core::chemical::AtomIndices core::conformation::Residue::get_substituents_to_ring_atom

(

uint const

atom_index

)

const

Get a list of substituent atoms connected to a given ring atom.

Returns

The atom indices of all heavy atoms bonded to the given atom (by index) that are not a part of the ring.

This method does not count virtual atoms as atoms.

Author

Labonte JWLab.nosp@m.onte.nosp@m.@jhu..nosp@m.edu

References atom_is_hydrogen(), and get_atoms_exocyclic_to_ring_atom().

AtomIndices const& core::conformation::Residue::Haro_index ( ) const

inline

Returns the AtomIndices of this residue's aromatic hydrogens.

Note

: AtomIndices == vector1< Size >

example(s): residue.Haro_index() See also: Residue Residue.atoms Residue.Hpol_index Pose

References core::chemical::ResidueType::Haro_index(), and rsd_type_.

Referenced by core::scoring::orbitals::OrbitalsScore::assign_haro_derivs_one_way(), core::scoring::orbitals::OrbitalsStatistics::bb_stats(), core::scoring::orbitals::OrbitalsScore::get_E_haro_one_way(), protocols::features::OrbitalsFeatures::report_hpol_orbital_interactions(), and core::scoring::orbitals::OrbitalsStatistics::sc_H_orbital().

bool core::conformation::Residue::has ( std::string const &  atm ) const

inline

Returns true if this residue has an atom named <atm>

References core::chemical::ResidueType::has(), and rsd_type_.

Referenced by core::pose::motif::a(), protocols::seeded_abinitio::add_coordinate_constraints(), core::util::add_covalent_linkage_helper(), protocols::mpi_refinement::StructAvrgMover::add_deviations(), core::pose::Pose::append_residue_by_atoms(), protocols::frag_picker::nonlocal::NonlocalFrags::apply(), protocols::constraint_generator::TerminiConstraintGenerator::apply(), protocols::comparative_modeling::ExtraThreadingMover::apply(), protocols::hybridization::FoldTreeHybridize::apply(), protocols::nmr::pre::PREMover::apply(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_atom_pair_distance(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_loop_bump_check(), protocols::constel::PresenceCommon::are_atoms_pres(), core::scoring::FACTSPotential::atompair_scale(), protocols::constraint_generator::AtomPairConstraintGenerator::atoms_to_constrain(), protocols::match::output::WriteUpstreamCoordinateKinemage::build(), protocols::simple_moves::ExplicitWaterMover::build_backbone_rotamer_clouds(), core::scoring::lkball::build_optimal_water_Os_on_acceptor(), protocols::mpi_refinement::CA_Sscore(), protocols::scoring::methods::pcsTs1::PCS_Energy_Ts1::calculate_scores_and_tensors_from_pose_and_PCS_data(), protocols::scoring::methods::pcsTs2::PCS_Energy_Ts2::calculate_scores_and_tensors_from_pose_and_PCS_data(), protocols::scoring::methods::pcsTs4::PCS_Energy_Ts4::calculate_scores_and_tensors_from_pose_and_PCS_data(), protocols::scoring::methods::pcsTs3::PCS_Energy_Ts3::calculate_scores_and_tensors_from_pose_and_PCS_data(), protocols::scoring::methods::pcs::PCS_Energy::calculate_scores_and_tensors_from_pose_and_PCS_data(), core::scoring::calpha_superimpose_pose(), core::sequence::calpha_superimpose_with_mapping(), protocols::sic_dock::cb_weight_map_from_pose(), protocols::sic_dock::cb_weights_from_pose(), core::select::util::cbeta_vector(), protocols::constraint_generator::HydrogenBondConstraintGenerator::choose_atoms(), protocols::enzdes::DiffAtomSasaFilter::compute(), protocols::constraint_generator::compute_ref_atom(), protocols::mpi_refinement::constrain_residue(), core::scoring::nmr::NMRDummySpinlabelEnsemble::coordinate_transform_from_target_site(), protocols::generalized_kinematic_closure::copy_loop_pose_to_original(), protocols::mpi_refinement::copy_pose_crd(), copy_residue_connections(), core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms(), protocols::sic_dock::count_CBs(), protocols::ligand_docking::ga_ligand_dock::count_neighbors(), protocols::ligand_docking::ga_ligand_dock::count_neighbors_on_coord(), protocols::cartesian::MolecularDynamics::createDihedralList(), protocols::md::CartesianMD::cst_on_pose_simple(), core::pose::declare_cutpoint_chemical_bond(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::do_initial_import_and_scoring(), core::scoring::methods::ProClosureEnergy::eval_intrares_derivatives(), core::scoring::elec::FA_ElecEnergy::eval_intrares_derivatives(), core::scoring::methods::ProClosureEnergy::eval_intrares_energy(), core::scoring::elec::FA_ElecEnergy::eval_intrares_energy(), core::scoring::PointWaterPotential::eval_pointwater_derivs(), core::scoring::PointWaterPotential::eval_pointwater_score(), core::scoring::HydroxylTorsionPotential::eval_residue_derivative(), core::scoring::HydroxylTorsionPotential::eval_residue_energy(), protocols::constraint_generator::existing_atoms(), protocols::nmr::filter_spinlabel_ensemble_by_packerenergy(), core::io::pose_from_sfr::PoseFromSFRBuilder::find_atom_tree_root_for_metal_ion(), protocols::ligand_docking::find_attach_pt(), protocols::enzdes::DetectProteinLigandInterface::find_design_interface(), protocols::enzdes::DetectProteinLigandInterface::find_design_interface_arg_sweep(), protocols::abinitio::abscript::find_disulfide_partner(), protocols::ligand_docking::LigandBaseProtocol::find_interface_backbone(), core::conformation::carbohydrates::find_seqpos_of_saccharides_child_residue_at(), protocols::helical_bundle::FitSimpleHelixMultiFunc::FitSimpleHelixMultiFunc(), protocols::topology_broker::fix_mainchain_connect(), protocols::abinitio::abscript::fix_mainchain_connect(), protocols::loops::loop_closure::ccd::CCDLoopClosureMover::get_anchors(), protocols::rna::denovo::movers::RNA_HelixMover::get_bb_pos(), protocols::sic_dock::get_CB_Vecs_from_pose(), protocols::cluster::GatherPosesMover::get_distance_measure(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::get_matching_res_in_VDW_rep_screen_pose(), core::scoring::rna::data::RNA_DMS_Potential::get_N1_lonepair_donor_angle(), protocols::stepwise::legacy::modeler::protein::get_pretend_phi_explicit(), core::scoring::rna::data::RNA_DMS_Potential::get_probe_xyz(), core::chemical::rna::get_rna_base_coordinate_system(), protocols::motifs::LigandMotifSearch::get_sphere_aa(), protocols::sic_dock::xyzStripeHashPoseWithMeta::init_with_pose(), protocols::match::upstream::OriginalBackboneBuildPoint::initialize_from_residue(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::is_beta_aminoacid(), core::scoring::is_protein_backbone(), core::scoring::is_protein_backbone_including_O(), core::scoring::is_protein_CA(), core::scoring::is_protein_CA_or_CB(), core::scoring::is_protein_CA_or_equiv(), protocols::sic_dock::scores::MotifHashRigidScore::MotifHashRigidScore(), protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo::output_silent_file(), protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::partition(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::perform_bump_check(), protocols::generalized_kinematic_closure::GeneralizedKIC::pick_pivots(), place(), protocols::rna::movers::ErraserMinimizerMover::process_entire_pose(), protocols::denovo_design::rebuild_missing_atoms(), protocols::qsar::scoring_grid::ClassicGrid::refresh(), protocols::qsar::scoring_grid::RepGrid::refresh(), protocols::ligand_docking::LigandBaseProtocol::reorder_foldtree_around_mobile_regions(), protocols::simple_moves::PeriodicBoxMover::report_thermodynamics(), core::scoring::methods::SymmetricLigandEnergy::residue_energy(), protocols::sic_dock::XfoxmScore::score(), core::select::util::select_coord_for_residue(), protocols::normalmode::NormalMode::set_harmonic_constant_map(), protocols::ligand_docking::set_repulsive_bb_cores(), core::conformation::setup_links(), core::scoring::setup_matching_heavy_atoms(), protocols::stepwise::modeler::rna::setup_suite_atom_id_map(), protocols::simple_moves::SuperimposeMover::superimpose(), protocols::mpi_refinement::WorkUnit_Sampler::superimpose_to_ref(), protocols::simple_moves::SuperimposeMover::superimposebb(), core::import_pose::libraries::RNA_ChunkLibrary::update_atom_level_domain_map(), core::pose::rna::update_edge_hbond_numbers_careful_hydrogen(), protocols::scoring::methods::pcs2::PcsDataCenter::update_X_Y_Z_all(), protocols::scoring::methods::pcsTs1::PCS_data_Ts1::update_X_Y_Z_all(), protocols::scoring::methods::pcsTs2::PCS_data_Ts2::update_X_Y_Z_all(), protocols::scoring::methods::pcsTs3::PCS_data_Ts3::update_X_Y_Z_all(), protocols::scoring::methods::pcs::PCS_data::update_X_Y_Z_all(), protocols::scoring::methods::pcsTs4::PCS_data_Ts4::update_X_Y_Z_all(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::use_in_rmsd(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::use_in_rmsd_offset(), and protocols::mpi_refinement::StructAvrgMover::weighted_average().

bool core::conformation::Residue::has_incomplete_connection

(

)

const

References connect_map_, and connection_incomplete().

Referenced by protocols::ligand_docking::CompleteConnectionsFilter::apply(), core::conformation::Conformation::detect_bonds(), protocols::ligand_docking::find_unconnected_residues(), protocols::ligand_docking::has_incomplete_connections(), and core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose().

bool core::conformation::Residue::has_incomplete_connection

(

core::Size const

atomno

)

const

Returns true is <atomno> has complete connectivity?

determine whether an atom is completely connected to all possible bonded partners

References connection_incomplete(), n_possible_residue_connections(), and residue_connect_atom_index().

bool core::conformation::Residue::has_lower_connect ( ) const

inline

Returns true if residue has a valid lower connection.

example(s): residue.has_lower_connect()

References core::chemical::ResidueTypeBase::is_polymer(), core::chemical::ResidueType::lower_connect_id(), and rsd_type_.

Referenced by core::conformation::Conformation::append_residue(), core::select::residue_selector::PhiSelector::apply(), core::select::residue_selector::BinSelector::apply(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_copy_backbone_dihedrals(), core::scoring::bin_transitions::BinTransitionCalculator::are_normally_bonded(), core::conformation::Conformation::backbone_torsion_angle_atoms(), connected_residue_at_lower(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::correct_termini_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd1(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd2(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_bond_length_derivs(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_improper_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_improper_energy(), core::scoring::methods::CartesianBondedEnergy::eval_intrares_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_intrares_energy(), core::scoring::methods::RamaPreProEnergy::eval_intraresidue_dof_derivative(), core::scoring::Ramachandran::eval_rama_score_residue(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_connectivity_annotation_info(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_phi_from_rsd(), core::chemical::rna::get_rna_base_centroid(), core::chemical::rna::get_rna_base_coordinate_system(), protocols::cyclic_peptide::crosslinker::TMA_Helper::get_sidechain_connect_index(), core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy::has_bb_hbond_connection(), protocols::cyclic_peptide::RamaMutationSelector::is_terminus(), core::scoring::methods::lower_upper_connected_across_cutpoint(), protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::moves_for_pose(), core::pose::set_reasonable_fold_tree(), and protocols::energy_based_clustering::EnergyBasedClusteringProtocol::storeposedata().

bool core::conformation::Residue::has_property ( std::string const &  property ) const

inline

Return true if the residue has <property>.

References core::chemical::ResidueTypeBase::has_property(), and rsd_type_.

Referenced by protocols::ligand_docking::MoveMapBuilder::build(), protocols::membrane::AddMembraneMover::check_pdb_for_mem(), core::scoring::P_AA::get_Paa_pp_deriv(), protocols::loops::loop_closure::kinematic_closure::TabooSamplingKinematicPerturber::get_random_phi_psi_for_residue(), protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturber::get_random_phi_psi_for_residue(), protocols::membrane::AddMembraneMover::initialize_membrane_residue(), protocols::ligand_docking::LigandBaseProtocol::make_movemap(), core::scoring::P_AA::P_AA_pp_energy(), protocols::hybridization::BackboneTorsionPerturbation::perturb(), protocols::hybridization::BackboneTorsionSampler::perturb(), protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturber::perturb_chain(), protocols::loops::loop_closure::kinematic_closure::NeighborDependentTorsionSamplingKinematicPerturber::perturb_chain(), protocols::loops::loop_closure::kinematic_closure::TorsionRestrictedKinematicPerturber::perturb_chain(), protocols::kinematic_closure::perturbers::RamaPerturber::perturb_subset(), and protocols::kinematic_closure::perturbers::Rama2bPerturber::perturb_subset().

bool core::conformation::Residue::has_sc_orbitals ( ) const

inline

Returns true if the residue has side chain orbitals.

References core::chemical::ResidueType::has_sc_orbitals(), and rsd_type_.

Referenced by core::scoring::orbitals::OrbitalsStatistics::sc_H_orbital().

bool core::conformation::Residue::has_shadow_atoms ( ) const

inline

Return true if and only if this residue's type has shadow atoms.

References core::chemical::ResidueType::has_shadow_atoms(), and rsd_type_.

Referenced by core::scoring::methods::RingClosureEnergy::eval_residue_derivatives(), and core::scoring::methods::RingClosureEnergy::residue_energy().

bool core::conformation::Residue::has_upper_connect ( ) const

inline

Returns true if residue has a valid upper connection.

example(s): residue.has_upper_connect()

References core::chemical::ResidueTypeBase::is_polymer(), rsd_type_, and core::chemical::ResidueType::upper_connect_id().

Referenced by core::select::residue_selector::PhiSelector::apply(), core::select::residue_selector::BinSelector::apply(), protocols::cyclic_peptide::RamaMutationSelector::apply(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_copy_backbone_dihedrals(), core::scoring::bin_transitions::BinTransitionCalculator::are_normally_bonded(), core::conformation::Conformation::backbone_torsion_angle_atoms(), connected_residue_at_upper(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::correct_termini_derivatives(), core::scoring::methods::ProClosureEnergy::defines_score_for_residue_pair(), core::scoring::methods::determine_lo_and_hi_residues(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd1(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd2(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_bond_length_derivs(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_improper_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_improper_energy(), core::scoring::methods::CartesianBondedEnergy::eval_intrares_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_intrares_energy(), core::scoring::methods::RamaPreProEnergy::eval_intraresidue_dof_derivative(), core::scoring::methods::CartesianBondedEnergy::eval_intraresidue_dof_derivative(), core::scoring::Ramachandran::eval_rama_score_residue(), core::scoring::methods::ProClosureEnergy::eval_residue_pair_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_residue_pair_derivatives(), core::scoring::MultipoleElecPotential::find_params_and_neighbors(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_connectivity_annotation_info(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_psi_from_rsd(), core::chemical::rna::get_rna_base_centroid(), core::chemical::rna::get_rna_base_coordinate_system(), protocols::cyclic_peptide::crosslinker::TMA_Helper::get_sidechain_connect_index(), core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy::has_bb_hbond_connection(), protocols::cyclic_peptide::RamaMutationSelector::is_terminus(), core::scoring::methods::lower_upper_connected_across_cutpoint(), core::scoring::methods::ProClosureEnergy::measure_chi4(), protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::moves_for_pose(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::rama_energy(), core::scoring::GenericBondedPotential::residue_pair_derivatives(), core::scoring::methods::ProClosureEnergy::residue_pair_energy(), core::scoring::GenericBondedPotential::residue_pair_energy(), core::scoring::methods::CartesianBondedEnergy::residue_pair_energy(), core::scoring::methods::CartesianBondedEnergy::residue_pair_energy_sorted(), core::pose::set_reasonable_fold_tree(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::storeposedata(), and protocols::energy_based_clustering::EnergyBasedClusteringProtocol::use_this_atom().

bool core::conformation::Residue::has_variant_type ( chemical::VariantType const  variant_type ) const

inline

Generic variant access.

References core::chemical::ResidueTypeBase::has_variant_type(), and rsd_type_.

Referenced by core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_intra(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_one_way(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_one_way_bb_bb(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_one_way_sc(), protocols::forge::methods::add_cutpoint_variants(), protocols::protein_interface_design::movers::SetAtomTree::add_cutpoint_variants(), core::pose::ncbb::add_oop_constraint(), core::pose::ncbb::add_triazole_constraint(), core::pose::add_variant_type_to_pose_residue(), core::pose::add_variant_type_to_residue(), protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::alter_rotamer_set_from_db(), protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::alter_rotamer_set_from_pdb(), protocols::cyclic_peptide::DeclareBond::apply(), protocols::simple_moves::hbs::HbsPatcher::apply(), protocols::simple_moves::oop::OopPatcher::apply(), protocols::simple_moves::oop::OopMover::apply(), protocols::simple_moves::triazolamer::TriazolamerMover::apply(), protocols::simple_moves::a3b_hbs::A3BHbsPatcher::apply(), protocols::simple_moves::oop::OopRandomPuckMover::apply(), protocols::simple_moves::oop::OopRandomSmallMover::apply(), protocols::simple_moves::triazolamer::TriazolamerRandomSmallMover::apply(), protocols::simple_moves::RepulsiveOnlyMover::apply(), protocols::fold_from_loops::movers::NubInitioLoopClosureMover::apply(), protocols::protein_interface_design::movers::DesignMinimizeHbonds::apply(), protocols::splice::SpliceIn::apply(), protocols::splice::SpliceInTail::apply(), protocols::splice::SpliceOut::apply(), protocols::farnesyl::SampleFarnesylMover::apply(), protocols::fold_from_loops::selectors::CutpointResidueSelector::apply(), core::pack::task::operation::NoRepackDisulfides::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::splice::Splice::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::ncbb::oop::OopCreatorMover::apply(), protocols::enzdes::DetectProteinLigandInterface::apply(), protocols::antibody_legacy::LoopRlxMover::apply(), protocols::fold_from_loops::movers::NubInitioLoopClosureMover::apply_closure_trust(), protocols::hybridization::CartesianSampler::apply_frame(), protocols::stepwise::modeler::rna::apply_protonated_H1_adenosine_variant_type(), core::pose::rna::apply_virtual_rna_residue_variant_type(), core::conformation::Conformation::backbone_torsion_angle_atoms(), core::pack::rotamer_set::RotamerSets::build_rotamers(), core::scoring::methods::RG_Energy_Fast::calculate_rg_score(), protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker::chain_break_screening_general(), protocols::topology_broker::TopologyBroker::check_chainbreak_variants(), core::scoring::loop_graph::LoopGraph::check_for_unexpected_cutpoints(), protocols::stepwise::screener::SugarInstantiator::check_moving_sugar(), core::scoring::rna::check_rna_loop(), protocols::antibody_legacy::CloseOneMover::close_one_loop_stem_helper(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_acceptor_atom_energy(), protocols::denovo_design::components::compute_cutpoints(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_donor_atom_energy(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_polar_group_sol_energy(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_sho_acceptor_atom_energy(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_sho_donor_atom_energy(), protocols::stepwise::modeler::rna::sugar::copy_bulge_res_and_sugar_torsion(), core::pack::rotamer_set::RotamerSets::copy_residue_conenctions_and_variants(), protocols::abinitio::copy_side_chains(), core::pose::correctly_add_2prime_connection_variants(), protocols::relax::cyclize_pose(), core::scoring::disulfides::FullatomDisulfideEnergy::defines_score_for_residue_pair(), core::scoring::rna::StackElecEnergy::defines_score_for_residue_pair(), core::conformation::symmetry::SymmetricConformation::detect_disulfides(), core::conformation::Conformation::detect_disulfides(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::disulfides_changed(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::disulfides_changed(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::disulfides_changed(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::do_checks_and_apply_protonated_H1_adenosine_variant(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_intra(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_one_way(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_one_way_bb_bb(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_one_way_sc(), protocols::anchored_design::dump_cutpoint_info(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::eval_atom_energy(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::eval_intrares_derivatives(), core::scoring::rna::RNA_TorsionPotential::eval_intrares_energy(), core::scoring::rna::RNA_TorsionEnergy::eval_intrares_energy(), core::scoring::magnesium::MgEnergy::eval_intrares_energy(), core::scoring::etable::TableLookupEtableEnergy::eval_intrares_energy(), core::scoring::etable::AnalyticEtableEnergy::eval_intrares_energy(), core::scoring::methods::SmoothEnvEnergy::eval_residue_derivatives(), core::scoring::methods::CenRotEnvEnergy::eval_residue_derivatives(), core::pack::dunbrack::cenrot::CenRotDunEnergy::eval_residue_derivatives(), core::scoring::methods::RamachandranEnergy::eval_residue_dof_derivative(), core::scoring::methods::YHHPlanarityEnergy::eval_residue_dof_derivative(), core::scoring::methods::OmegaTetherEnergy::eval_residue_dof_derivative(), core::scoring::methods::P_AA_pp_Energy::eval_residue_dof_derivative(), core::pack::dunbrack::DunbrackEnergy::eval_residue_dof_derivative(), core::scoring::methods::carbohydrates::SugarBackboneEnergy::eval_residue_dof_derivative(), core::pack::dunbrack::cenrot::CenRotDunEnergy::eval_residue_dof_derivative(), core::scoring::rna::RNA_SuiteEnergy::eval_residue_pair_derivatives(), core::scoring::rna::TNA_SuiteEnergy::eval_residue_pair_derivatives(), core::scoring::methods::CenRotPairEnergy::eval_residue_pair_derivatives(), core::scoring::methods::SmoothCenPairEnergy::eval_residue_pair_derivatives(), core::scoring::rna::StackElecEnergy::eval_residue_pair_derivatives(), core::scoring::disulfides::FullatomDisulfideEnergy::eval_residue_pair_derivatives(), core::scoring::methods::PairEnergy::eval_residue_pair_derivatives(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::eval_residue_pair_derivatives(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::eval_residue_pair_derivatives_one_way(), core::scoring::methods::CartesianBondedEnergy::eval_residue_pair_derivatives_sorted(), core::scoring::rna::TNA_SuitePotential::eval_score(), core::scoring::rna::data::RNA_DMS_LowResolutionPotential::evaluate(), core::scoring::rna::data::RNA_DMS_Potential::evaluate(), core::scoring::MembranePotential::evaluate_pair(), core::scoring::SmoothEnvPairPotential::evaluate_pair_and_cenpack_deriv(), core::scoring::EnvPairPotential::evaluate_pair_and_cenpack_score(), core::scoring::SmoothEnvPairPotential::evaluate_pair_and_cenpack_score(), core::scoring::rna::RNP_LowResPotential::evaluate_rnp_base_pair_score(), core::scoring::rna::RNP_LowResPairDistPotential::evaluate_rnp_pair_dist_score(), core::scoring::rna::RNP_LowResStackData::evaluate_rnp_stack_xy_score(), protocols::stepwise::modeler::working_parameters::figure_out_rebuild_bulge_mode(), protocols::stepwise::modeler::working_parameters::figure_out_sample_both_sugar_base_rotamer(), core::io::silent::BinarySilentStruct::fill_pose(), core::scoring::methods::LinearChainbreakEnergy::finalize_total_energy(), protocols::splice::RBOutMover::find_disulfide_postions(), protocols::splice::SpliceOutAntibody::find_disulfide_postions(), protocols::splice::RBInMover::find_disulfide_postions(), protocols::splice::SpliceInAntibody::find_disulfide_postions(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::find_disulfides(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::find_disulfides(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::find_disulfides(), protocols::forge::remodel::RemodelDesignMover::find_disulfides_in_the_neighborhood(), protocols::splice::find_disulfs_in_range(), protocols::rosetta_scripts::find_nearest_disulfide(), protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::find_uninstantiated_phosphates(), protocols::metal_interface::ZincSiteFinder::find_zinc_site(), protocols::splice::Splice::fold_tree(), core::conformation::form_disulfide(), protocols::stepwise::legacy::modeler::rna::full_length_rmsd_over_residue_list(), protocols::loops::loop_closure::ccd::CCDLoopClosureMover::get_anchors(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_acceptor(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_donor(), core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::get_atom_atom_occ_solvation(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::get_atom_atom_occ_solvation(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::get_atom_lk_energy(), core::scoring::rna::RNA_LowResolutionPotential::get_base_backbone(), core::scoring::hbonds::get_hb_acc_chem_type(), core::scoring::hbonds::get_hb_don_chem_type(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::get_main_chain_torsion_set_list(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::get_previously_closed_cutpoint_from_imported_silent_file(), protocols::recces::sampler::get_recces_turner_sampler_from_secstruct(), protocols::stepwise::modeler::rna::sugar::get_reference_res_for_each_virtual_sugar_based_on_fold_tree(), protocols::stepwise::modeler::rna::sugar::get_reference_res_for_each_virtual_sugar_without_fold_tree(), core::pose::rna::get_stub_stub(), core::scoring::SecondaryStructurePotential::identify_ss(), core::pose::ncbb::initialize_hbs(), protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::Initialize_is_virtual_base(), core::pose::ncbb::initialize_ncbbs(), core::pose::ncbb::initialize_oops(), protocols::recces::sampler::initialize_thermal_sampler(), protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::instantiate_sugars_at_cutpoint_closed(), protocols::fold_from_loops::movers::NubInitioLoopClosureMover::is_cutpoint_close(), core::scoring::methods::is_lower_cutpoint(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::is_old_individual_suite_cluster(), core::scoring::rna::RNA_BulgeEnergy::is_RNA_bulge(), protocols::stepwise::modeler::rna::sugar::is_sugar_virtual(), core::scoring::methods::is_upper_cutpoint(), protocols::stepwise::modeler::rna::is_virtual_base(), protocols::stepwise::modeler::rna::sugar::look_for_non_jump_reference_to_next(), protocols::stepwise::modeler::rna::sugar::look_for_non_jump_reference_to_previous(), protocols::antibody_legacy::CDRH3Modeler::loop_centroid_relax(), protocols::antibody_legacy::CDRH3Modeler::loop_fa_relax(), protocols::fold_from_loops::movers::NubInitioLoopClosureMover::make_cutpoints_coherent_to_foldtree(), protocols::enzdes::EnzdesFlexBBProtocol::modified_task(), protocols::stepwise::modeler::StepWiseMinimizer::move_side_chain(), protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::moves_for_pose(), orient_onto_residue_peptoid(), protocols::enzymatic_movers::NTerminalAcetyltransferaseMover::perform_reaction(), protocols::fold_from_loops::NubInitioMover::post_process(), protocols::peptide_deriver::PeptideDeriverFilter::prepare_pose(), core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose(), core::pose::carbohydrates::remove_carbohydrate_branch_point_variants(), protocols::forge::methods::remove_cutpoint_variants(), protocols::loops::remove_cutpoint_variants(), protocols::denovo_design::movers::SealFoldTreeMover::remove_cutpoints(), protocols::stepwise::modeler::rna::phosphate::remove_terminal_phosphates(), core::pose::remove_variant_type_from_pose_residue(), core::pose::remove_variant_type_from_residue(), core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::res_res_occ_sol_one_way(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::res_res_occ_sol_one_way(), protocols::hybridization::HybridizeFoldtreeDynamic::reset(), core::scoring::methods::RamachandranEnergy::residue_energy(), core::scoring::methods::OmegaTetherEnergy::residue_energy(), core::scoring::methods::YHHPlanarityEnergy::residue_energy(), protocols::scoring::methods::SpecialRotamerEnergy::residue_energy(), core::scoring::methods::P_AA_pp_Energy::residue_energy(), core::scoring::methods::EnvEnergy::residue_energy(), core::pack::dunbrack::cenrot::CenRotDunEnergy::residue_energy(), core::scoring::methods::SmoothEnvEnergy::residue_energy(), core::pack::dunbrack::DunbrackEnergy::residue_energy(), core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::residue_energy(), core::scoring::methods::CenRotEnvEnergy::residue_energy(), core::scoring::methods::ReferenceEnergyNoncanonical::residue_energy(), core::scoring::methods::FreeDOF_Energy::residue_energy(), core::scoring::methods::carbohydrates::SugarBackboneEnergy::residue_energy(), core::scoring::methods::EnvSmoothEnergy::residue_energy(), core::scoring::methods::ReferenceEnergy::residue_energy(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::residue_energy(), core::scoring::GenericBondedPotential::residue_pair_derivatives(), core::scoring::rna::TNA_SuiteEnergy::residue_pair_energy(), core::scoring::rna::RNA_SuiteEnergy::residue_pair_energy(), core::scoring::disulfides::DisulfideMatchingEnergy::residue_pair_energy(), core::scoring::disulfides::CentroidDisulfideEnergy::residue_pair_energy(), core::scoring::methods::GaussianOverlapEnergy::residue_pair_energy(), core::scoring::methods::CenPairEnergy::residue_pair_energy(), core::scoring::methods::CenRotPairEnergy::residue_pair_energy(), core::scoring::methods::SmoothCenPairEnergy::residue_pair_energy(), core::scoring::rna::RNA_JR_SuiteEnergy::residue_pair_energy(), core::scoring::rna::RNA_TorsionPotential::residue_pair_energy(), core::scoring::membrane::MPPairEnergy::residue_pair_energy(), core::scoring::rna::RNA_TorsionEnergy::residue_pair_energy(), core::scoring::rna::RNA_PairwiseLowResolutionEnergy::residue_pair_energy(), core::scoring::rna::StackElecEnergy::residue_pair_energy(), core::scoring::rna::data::RNA_DataBackboneEnergy::residue_pair_energy(), core::scoring::rna::RNP_LowResEnergy::residue_pair_energy(), core::scoring::rna::RNP_LowResPairDistEnergy::residue_pair_energy(), core::scoring::rna::RNP_LowResStackEnergy::residue_pair_energy(), core::scoring::rna::RNA_FullAtomStackingEnergy::residue_pair_energy(), core::scoring::rna::RNA_LJ_BaseEnergy::residue_pair_energy(), core::scoring::methods::PairEnergy::residue_pair_energy(), core::scoring::disulfides::FullatomDisulfideEnergy::residue_pair_energy(), core::scoring::GenericBondedPotential::residue_pair_energy(), core::scoring::disulfides::FullatomDisulfideEnergy::residue_pair_energy_ext(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::residue_pair_energy_ext(), core::scoring::rna::StackElecEnergy::residue_pair_energy_ext(), core::scoring::rna::RNA_FullAtomStackingEnergy::residue_pair_energy_one_way(), core::scoring::rna::StackElecEnergy::residue_pair_energy_one_way(), core::scoring::methods::CartesianBondedEnergy::residue_pair_energy_sorted(), protocols::stepwise::modeler::rna::rmsd_over_residue_list(), core::scoring::rna::RNA_LowResolutionPotential::rna_backbone_backbone_pair_energy_one_way(), core::scoring::rna::RNA_PairwiseLowResolutionEnergy::rna_base_axis_pairwise_pair_energy(), core::scoring::rna::RNA_PairwiseLowResolutionEnergy::rna_base_pair_pairwise_pair_energy(), core::scoring::rna::RNA_PairwiseLowResolutionEnergy::rna_base_stack_axis_pairwise_pair_energy(), core::scoring::rna::RNA_PairwiseLowResolutionEnergy::rna_base_stack_pairwise_pair_energy(), core::scoring::rna::RNA_PairwiseLowResolutionEnergy::rna_base_stagger_pairwise_pair_energy(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::RotamericSingleResidueDunbrackLibrary(), protocols::relax::RepeatProteinRelax::seal_jumps(), protocols::protein_interface_design::movers::SetAtomTree::set_ab_fold_tree(), protocols::splice::Splice::set_fold_tree(), protocols::rbsegment_relax::setup_disconnected(), core::scoring::methods::RG_LocalEnergy::setup_for_derivatives(), core::scoring::methods::RG_Energy_Fast::setup_for_derivatives(), core::scoring::disulfides::FullatomDisulfideEnergy::setup_for_minimizing_for_residue_pair(), core::conformation::setup_links(), protocols::rna::denovo::movers::RNA_Minimizer::setup_movemap(), core::pose::toolbox::AtomLevelDomainMap::setup_movemap(), protocols::rbsegment_relax::setup_pose_rbsegs_keep_loops(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList::setup_sugar_modeling_list(), protocols::stepwise::modeler::rna::phosphate::PhosphateMover::setup_variants_and_free_pose_for_five_prime_phosphate(), protocols::splice::Splice::superimpose_source_on_pose(), protocols::topology_broker::RigidChunkClaimer::switch_to_fullatom(), protocols::splice::Splice::tail_fold_tree(), core::conformation::Conformation::update_polymeric_connection(), core::conformation::Conformation::update_residue_torsions(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::virtualize_distal_partition(), and core::pose::rna::virtualize_free_rna_moieties().

bool core::conformation::Residue::heavyatom_has_polar_hydrogens ( Size  ind ) const

inline

Is a particular atom a heavy atom with chemically bound polar hydrogens? (i.e. a donor heavy atom)

References core::chemical::ResidueType::heavyatom_has_polar_hydrogens(), and rsd_type_.

Referenced by core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_acceptor_atom_energy(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_acceptor(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::get_atom_atom_occ_solvation(), protocols::magnesium::get_closest_non_hoh_contact(), core::scoring::methods::LK_PolarNonPolarEnergy::get_residue_pair_energy_one_way(), and protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::init_from_ligand_pharmacophore().

bool core::conformation::Residue::heavyatom_is_an_acceptor ( Size  ind ) const

inline

Is a particular atom a heavy atom acceptor?

References core::chemical::ResidueType::heavyatom_is_an_acceptor(), and rsd_type_.

Referenced by core::pack::rotamer_set::build_moving_O_water_rotamers_dependent(), core::pack::interaction_graph::compute_alt_weights_for_npd_hbonds(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_donor_atom_energy(), protocols::hbnet::HBNet::estimate_saturation(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::eval_atom_energy(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::eval_intrares_derivatives(), core::scoring::magnesium::MgEnergy::eval_mg_interaction(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::eval_residue_pair_derivatives(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_acceptor(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_donor(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::get_atom_atom_occ_solvation(), protocols::magnesium::get_closest_non_hoh_contact(), core::scoring::magnesium::get_cos_theta(), protocols::magnesium::SampleGrid::get_mg_positions(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::residue_pair_energy_ext(), and core::scoring::magnesium::RNA_MgPointEnergy::residue_pair_energy_one_way().

Atoms::const_iterator core::conformation::Residue::heavyAtoms_end ( ) const

inline

References atoms_, and nheavyatoms().

Referenced by core::select::util::any_atoms_within_cutoff(), protocols::dna::argrot_dna_dis2(), protocols::dna::close_to_dna(), protocols::environment::com_calc(), and core::scoring::interface_::DDPscore::residue_pair_energy().

AtomIndices const& core::conformation::Residue::Hpol_index ( ) const

inline

Returns the AtomIndices of this residue's polar hydrogens.

Note

: AtomIndices == vector1< Size >

example(s): residue.Hpol_index() See also: Residue Residue.atoms Residue.Hpol_index Residue.Hpos_apolar Residue.Hpos_polar Pose

References core::chemical::ResidueType::Hpol_index(), and rsd_type_.

Referenced by core::scoring::orbitals::OrbitalsScore::assign_hpol_derivs_one_way(), core::scoring::orbitals::OrbitalsStatistics::bb_stats(), protocols::hbnet::HBNet::estimate_saturation(), core::scoring::orbitals::OrbitalsScore::get_E_hpol_one_way(), protocols::features::OrbitalsFeatures::report_hpol_orbital_interactions(), and core::scoring::orbitals::OrbitalsStatistics::sc_H_orbital().

AtomIndices const& core::conformation::Residue::Hpos_apolar ( ) const

inline

Returns the AtomIndices of this residue's apolar hydrogens.

Note

: AtomIndices == vector1< Size >

example(s): residue.Hpos_apolar() See also: Residue Residue.atoms Residue.Hpol_index() Residue.Hpos_polar Pose

References core::chemical::ResidueType::Hpos_apolar(), and rsd_type_.

Referenced by core::scoring::carbon_hbonds::CarbonHBondEnergy::bb_bb_carbon_hbond_one_way(), core::scoring::carbon_hbonds::CarbonHBondEnergy::bb_sc_carbon_hbond_one_way(), core::scoring::rna::data::RNA_DMS_Potential::check_chbonded(), core::scoring::carbon_hbonds::CarbonHBondEnergy::res_res_carbon_hbond_derivs_one_way(), core::scoring::carbon_hbonds::CarbonHBondEnergy::res_res_carbon_hbond_one_way(), core::scoring::carbon_hbonds::CarbonHBondEnergy::sc_bb_carbon_hbond_one_way(), and core::scoring::carbon_hbonds::CarbonHBondEnergy::sc_sc_carbon_hbond_one_way().

AtomIndices const& core::conformation::Residue::Hpos_polar ( ) const

inline

Returns the AtomIndices of this residue's polar hydrogens.

Note

: AtomIndices == vector1< Size >

example(s): residue.Hpos_polar() See also: Residue Residue.atoms Residue.Hpol_index Residue.Hpos_apolar Pose

References core::chemical::ResidueType::Hpos_polar(), and rsd_type_.

Referenced by core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::atom_is_donor_h(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::atom_is_donor_h(), core::pose::rna::atom_is_polar(), core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::atom_is_valid_base(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::atom_is_valid_base(), protocols::simple_moves::ExplicitWaterMover::build_backbone_rotamer_clouds(), core::pack::rotamer_set::build_moving_O_bridge_waters(), protocols::ligand_docking::ga_ligand_dock::GridScorer::calculate_grid(), core::scoring::geometric_solvation::compute_exact_geosol(), core::pack::interaction_graph::create_hbonds_one_way(), protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_intra(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_one_way(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_one_way_bb_bb(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_one_way_sc(), core::scoring::PointWaterPotential::eval_pointwater_derivs(), core::scoring::PointWaterPotential::eval_pointwater_score(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::eval_residue_pair_derivatives_one_way(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_1b_energy(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_2b_energy(), core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::get_atom_atom_occ_solvation(), core::scoring::WaterAdductHBondPotential::get_residue_residue_h2o_hbonds_1way(), core::scoring::WaterAdductHBondPotential::h2o_hbond_score_1way(), core::scoring::hbonds::HBondEnergy::hbond_derivs_1way(), core::pose::rna::heavy_atom_is_polar(), protocols::simple_moves::ConstrainToIdealMover::i_want_this_atom_to_move(), core::scoring::hbonds::identify_hbonds_1way(), core::scoring::hbonds::identify_hbonds_1way_AHdist(), core::scoring::hbonds::identify_hbonds_1way_membrane(), core::scoring::hbonds::identify_intra_res_hbonds(), protocols::stepwise::modeler::StepWiseMinimizer::move_side_chain(), protocols::hbnet::HBNet::quick_and_dirty_heavy_atom_is_unsat(), protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::recompute(), core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::res_res_occ_sol_one_way(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::res_res_occ_sol_one_way(), core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::residue_energy(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::residue_energy(), and protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::residue_partition().

AtomIndices const& core::conformation::Residue::Hpos_polar_sc ( ) const

inline

Returns the AtomIndices of this residue's polar sidechain hydrogens.

Note

: AtomIndices == vector1< Size >

example(s): residue.Hpos_polar_sc() See also: Residue Residue.atoms Residue.Hpol_index Residue.Hpos_polar Pose

References core::chemical::ResidueType::Hpos_polar_sc(), and rsd_type_.

Referenced by protocols::hbnet::HBNet::quick_and_dirty_network_has_heavy_atom_unsat().

chemical::AtomICoor const& core::conformation::Residue::icoor ( Size const  atm ) const

inline

Returns the internal coordinates of this residue's atom with index number <atm>

References core::chemical::ResidueType::icoor(), and rsd_type_.

Referenced by core::conformation::Conformation::backbone_torsion_angle_atoms(), build_atom_ideal(), core::select::util::SelectResiduesByLayer::calc_sc_neighbors(), core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::detect_intra_residue_hydrogen_bonds(), core::conformation::Conformation::fill_missing_atoms(), fill_missing_atoms(), core::conformation::idealize_hydrogens(), core::conformation::missing_stubs_build(), orient_onto_residue_peptoid(), protocols::cyclic_peptide::PeptideStubMover::rebuild_atoms(), core::conformation::Conformation::rebuild_polymer_bond_dependent_atoms(), core::conformation::Conformation::rebuild_residue_connection_dependent_atoms(), and core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose().

void core::conformation::Residue::init_residue_from_other ( Residue const &  src )

private

Function called by both copy constructors, to avoid code duplication.

As private member variables are added, add them to this to copy them.

Author

Vikram K. Mulligan.

References actcoord_, atoms_, chain_, chi_, connect_map_, connections_to_residues_, data_cache_, mainchain_torsions_, mirrored_relative_to_type_, misplaced_, nonstandard_polymer_, nus_, orbitals_, pseudobonds_, and seqpos_.

Referenced by Residue().

id::AtomID core::conformation::Residue::inter_residue_connection_partner	(	int	connid,
		Conformation const &	conformation
	)		const

This returns the AtomID of the atom in the other residue to which the "connection_index"-th connection of residue seqpos is connected to.

References core::id::GLOBAL_BOGUS_ATOM_ID, name(), core::chemical::ResidueType::residue_connect_atom_index(), residue_connection_conn_id(), residue_connection_partner(), core::conformation::Conformation::residue_type(), seqpos(), core::conformation::Conformation::size(), and core::conformation::TR().

Referenced by core::chemical::ICoorAtomID::atom_id().

bool core::conformation::Residue::is_apolar ( ) const

inline

true if the residue is apolar

Note

: apolar is classified as NOT polar, aromatic, or charged

References core::chemical::ResidueType::is_aromatic(), core::chemical::ResidueType::is_charged(), core::chemical::ResidueType::is_polar(), and rsd_type_.

bool core::conformation::Residue::is_aramid ( ) const

inline

Returns if this residue is an aramid.

References core::chemical::ResidueType::is_aramid(), and rsd_type_.

Referenced by core::scoring::methods::AromaticBackboneRestraintEnergy::eval_residue_derivatives(), and core::scoring::methods::AromaticBackboneRestraintEnergy::residue_energy().

bool core::conformation::Residue::is_aromatic ( ) const

inline

Returns true if the residue is aromatic.

References core::chemical::ResidueType::is_aromatic(), and rsd_type_.

Referenced by protocols::analysis::InterfaceAnalyzerMover::calc_per_residue_and_regional_data(), core::scoring::methods::PairEnergy::defines_score_for_residue_pair(), core::scoring::hackaro::HackAroEnergy::eval_atom_derivative_aro_aro(), core::scoring::methods::PairEnergy::eval_residue_pair_derivatives(), core::scoring::elec::FA_ElecEnergyAroAll::evaluate_rotamer_background_energies(), core::scoring::elec::FA_ElecEnergyAroAro::evaluate_rotamer_background_energies(), core::scoring::methods::PairEnergy::evaluate_rotamer_background_energies(), core::scoring::methods::PairEnergy::evaluate_rotamer_background_energy_maps(), protocols::constel::has_aromatic(), core::scoring::PairEPotential::pair_term_energy(), core::scoring::PairEPotential::pair_term_energy_exists(), core::scoring::hackaro::HackAroEnergy::residue_pair_energy(), core::scoring::methods::PairEnergy::residue_pair_energy(), core::scoring::elec::FA_ElecEnergyAroAro::residue_pair_energy(), core::scoring::elec::FA_ElecEnergyAroAll::residue_pair_energy(), core::scoring::hackaro::HackAroEnergy::residue_pair_energy_aro_aro(), and core::scoring::elec::FA_ElecEnergyAroAro::residue_pair_energy_aro_aro().

bool core::conformation::Residue::is_bonded ( Residue const &  other ) const

inline

Am I bonded to other? Meaningful for arbitrary topologies (e.g. circular peptides, disulfides)

See Also: For atom-atom bonding, see conformation.is_bonded(AtomID, AtomID)

first check if it is polymer upper or lower connected to the other residue. then check if it is boned to the other residue through non-polymer connection.

References connections_to_residues_, and seqpos().

Referenced by protocols::generalized_kinematic_closure::GeneralizedKIC::addtailgeometry(), protocols::simple_filters::AveragePathLengthFilter::apply(), protocols::simple_filters::DisulfideEntropyFilter::apply(), core::scoring::elec::FA_ElecEnergy::backbone_backbone_energy(), core::scoring::elec::FA_ElecEnergy::backbone_sidechain_energy(), core::scoring::FACTSPotential::calculate_GBpair_exact(), core::scoring::FACTSPotential::calculate_GBpair_fast(), core::scoring::FACTSPotential::calculate_GBpair_v1trunk(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::check_path_distance(), protocols::simple_filters::DisulfideEntropyFilter::compute(), protocols::simple_filters::DisulfideEntropyFilter::compute_residual(), core::scoring::etable::count_pair::CountPairGeneric::CountPairGeneric(), core::scoring::methods::ProClosureEnergy::defines_score_for_residue_pair(), core::scoring::methods::GenericBondedEnergy::defines_score_for_residue_pair(), core::scoring::etable::count_pair::CountPairFactory::determine_residue_connection(), protocols::viewer::dump_residue_kinemage(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_ring_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_ring_energy(), core::scoring::methods::ProClosureEnergy::eval_residue_pair_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_residue_pair_derivatives_sorted(), core::scoring::elec::GroupElec::eval_respair_group_coulomb(), core::scoring::elec::GroupElec::eval_respair_group_derivatives(), core::scoring::MembranePotential::evaluate_pair(), core::scoring::SmoothEnvPairPotential::evaluate_pair_and_cenpack_deriv(), core::scoring::SmoothEnvPairPotential::evaluate_pair_and_cenpack_score(), core::scoring::EnvPairPotential::evaluate_pair_and_cenpack_score(), core::scoring::FACTSPotential::evaluate_polar_otf_energy(), protocols::denovo_design::DisulfidizeMover::find_current_disulfides(), protocols::forge::remodel::RemodelDesignMover::find_disulfides_in_the_neighborhood(), protocols::toolbox::CovalentResidueNetwork::generate_edges(), core::conformation::get_chemical_root_and_anchor_atomnos(), core::scoring::methods::LK_PolarNonPolarEnergy::get_count_pair_function(), core::scoring::rna::StackElecEnergy::get_count_pair_function(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_count_pair_function(), core::scoring::elec::FA_GrpElecEnergy::get_count_pair_function(), core::scoring::elec::FA_ElecEnergy::get_count_pair_function(), core::scoring::GenBornPotential::get_res_res_elecE(), protocols::generalized_kinematic_closure::GeneralizedKIC::has_geometric_connection(), core::scoring::trie::initialize_cpdata_for_atom(), core::scoring::methods::ProClosureEnergy::measure_chi4(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::model_loop(), core::scoring::carbon_hbonds::CarbonHBondEnergy::path_distance_OK(), protocols::features::ProteinBondGeometryFeatures::report_interres_angles(), protocols::features::ProteinBondGeometryFeatures::report_interres_lengths(), core::scoring::methods::GaussianOverlapEnergy::residue_pair_energy(), core::scoring::membrane::MPPairEnergy::residue_pair_energy(), core::scoring::methods::HybridVDW_Energy::residue_pair_energy(), core::scoring::methods::PeptideBondEnergy::residue_pair_energy(), core::scoring::methods::ProClosureEnergy::residue_pair_energy(), core::scoring::methods::MMBondLengthEnergy::residue_pair_energy(), core::scoring::methods::MMTorsionEnergy::residue_pair_energy(), core::scoring::methods::RamaPreProEnergy::residue_pair_energy(), core::scoring::methods::MMBondAngleEnergy::residue_pair_energy(), core::scoring::vdwaals::VDW_Energy::residue_pair_energy(), core::scoring::elec::FA_ElecEnergy::residue_pair_energy(), core::scoring::methods::CartesianBondedEnergy::residue_pair_energy_sorted(), core::pose::set_reasonable_fold_tree(), protocols::hbnet::HBNetStapleInterface::setup_packer_task_and_starting_residues(), core::scoring::elec::FA_ElecEnergy::sidechain_sidechain_energy(), and core::scoring::etable::etrie::TrieCountPairGeneric::TrieCountPairGeneric().

bool core::conformation::Residue::is_bonded ( Size const  other_residue_index ) const

inline

Am I bonded to other? Looks at all residue connections as opposed to doing arithmetic.

See Also: For atom-atom bonding, see conformation.is_bonded(AtomID, AtomID)

References connections_to_residues_.

bool core::conformation::Residue::is_branch_point ( ) const

inline

Return true if the residue is a branch point variant.

References core::chemical::ResidueType::is_branch_point(), and rsd_type_.

Referenced by protocols::analysis::GlycanInfoMover::apply_const(), core::conformation::Conformation::branch_connection_torsion_angle_atoms(), core::pose::carbohydrates::delete_carbohydrate_branch(), core::conformation::carbohydrates::get_carbohydrate_residues_and_tips_of_branch(), core::conformation::carbohydrates::get_glycan_connecting_protein_branch_point(), and core::pose::carbohydrates::remove_carbohydrate_branch_point_variants().

bool core::conformation::Residue::is_carbohydrate ( ) const

inline

Returns true if this residue is a carbohydrate.

References core::chemical::ResidueType::is_carbohydrate(), and rsd_type_.

Referenced by protocols::loops::add_single_cutpoint_variant(), core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr(), core::select::residue_selector::RandomGlycanFoliageSelector::apply(), core::select::residue_selector::GlycanResidueSelector::apply(), protocols::carbohydrates::GlycanTreeModeler::apply(), protocols::analysis::GlycanInfoMover::apply_const(), core::conformation::Conformation::backbone_torsion_angle_atoms(), core::scoring::electron_density::calculate_rama(), core::pose::carbohydrates::create_glycan_movemap_from_residue_selector(), core::pose::carbohydrates::delete_carbohydrate_branch(), core::scoring::methods::LinearChainbreakEnergy::do_score_dev(), core::scoring::methods::LinearChainbreakEnergy::do_score_ovp(), core::io::carbohydrates::dump_gws(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_ring_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_ring_energy(), core::scoring::methods::carbohydrates::SugarBackboneEnergy::eval_residue_dof_derivative(), core::conformation::carbohydrates::fill_downstream_children_res_and_tips(), core::scoring::methods::LinearBranchEnergy::finalize_total_energy(), core::scoring::methods::LinearChainbreakEnergy::finalize_total_energy(), core::conformation::carbohydrates::find_seqpos_of_saccharides_child_residue_at(), core::conformation::carbohydrates::find_seqpos_of_saccharides_parent_residue(), protocols::loops::fold_tree_from_loops(), core::pose::get_bb_torsion(), core::conformation::carbohydrates::get_carbohydrate_residues_and_tips_of_branch(), core::conformation::carbohydrates::get_distance_to_start(), core::conformation::carbohydrates::get_glycan_connecting_protein_branch_point(), core::conformation::carbohydrates::get_glycan_start_points(), core::conformation::carbohydrates::get_glycosidic_TorsionIDs(), core::conformation::carbohydrates::get_linkage_position_of_saccharide_residue(), core::pose::carbohydrates::get_resnums_in_leaf(), core::pose::carbohydrates::get_resnums_in_leaf_on_the_fly(), core::chemical::rna::get_rna_base_coordinate_system(), protocols::simple_moves::bb_sampler::SugarBBSampler::get_torsion(), core::conformation::carbohydrates::has_exocyclic_glycosidic_linkage(), protocols::carbohydrates::GlycanSampler::init_objects(), core::conformation::carbohydrates::is_glycosidic_omega_torsion(), core::conformation::carbohydrates::is_glycosidic_phi_torsion(), core::conformation::carbohydrates::is_glycosidic_psi_torsion(), core::pose::carbohydrates::is_glycosidic_torsion(), core::scoring::is_protein_CA_or_equiv(), core::conformation::carbohydrates::GlycanTreeSet::on_length_change(), core::pose::carbohydrates::remove_carbohydrate_branch_point_variants(), core::scoring::methods::carbohydrates::SugarBackboneEnergy::residue_energy(), protocols::denovo_design::components::residue_is_compatible(), core::pose::set_bb_torsion(), core::pose::carbohydrates::set_glycan_iupac_bb_torsions(), core::scoring::constraints::SiteConstraint::setup_csts(), protocols::carbohydrates::GlycanSampler::setup_movers(), and core::conformation::carbohydrates::GlycanNode::update_connectivity_data().

bool core::conformation::Residue::is_charged ( ) const

inline

Returns true if the residue is charged.

References core::chemical::ResidueType::is_charged(), and rsd_type_.

bool core::conformation::Residue::is_coarse ( ) const

inline

residue is coarse (used for RNA right now)

References core::chemical::ResidueType::is_coarse(), and rsd_type_.

Referenced by core::import_pose::RNA_JumpMover::check_forward_backward(), core::conformation::Conformation::detect_pseudobonds(), core::scoring::rna::data::RNA_DataBackboneEnergy::get_sugar_env_score(), core::scoring::rna::RNA_LowResolutionPotential::rna_backbone_backbone_pair_energy_one_way(), core::scoring::rna::RNA_LowResolutionPotential::rna_base_backbone_pair_energy_one_way(), core::scoring::rna::RNA_LowResolutionPotential::rna_repulsive_pair_energy_one_way(), core::pose::toolbox::AtomLevelDomainMap::set_phosphate_domain(), and core::pose::toolbox::AtomLevelDomainMap::set_sugar_domain().

bool core::conformation::Residue::is_d_rna ( ) const

inline

Returns true if this residue is a D-RNA residue.

References core::chemical::ResidueTypeBase::is_d_rna(), and rsd_type_.

Referenced by core::scoring::rna::RNA_TorsionPotential::eval_intrares_energy(), and core::scoring::rna::RNA_TorsionPotential::residue_pair_energy().

bool core::conformation::Residue::is_DNA ( ) const

inline

Returns true if this residue is a DNA residue.

References core::chemical::ResidueTypeBase::is_DNA(), and rsd_type_.

Referenced by core::scoring::dna::DNATorsionPotential::add_sugar_ring_closure_constraints(), core::scoring::hbonds::HBondSet::append_hbond(), protocols::motifs::Motif::apply_check(), core::scoring::hbonds::HBondEnergy::backbone_backbone_energy(), core::scoring::hbonds::HBondEnergy::backbone_sidechain_energy(), core::scoring::lkball::build_optimal_water_Os_on_acceptor(), protocols::dna::DNAParameters::calculate(), core::scoring::etable::BaseEtableEnergy< TableLookupEtableEnergy >::calculate_interres(), core::scoring::hbonds::calculate_intra_res_hbonds(), core::scoring::etable::BaseEtableEnergy< TableLookupEtableEnergy >::calculate_intra_xover4(), core::scoring::etable::BaseEtableEnergy< TableLookupEtableEnergy >::calculate_intrares(), core::scoring::dna::DNA_EnvPairPotential::centroid_xyz(), core::scoring::hbonds::create_rotamer_descriptor(), core::scoring::methods::DNA_DihedralEnergy::defines_score_for_residue(), core::scoring::elec::FA_GrpElecEnergy::defines_score_for_residue_pair(), core::scoring::elec::FA_ElecEnergy::defines_score_for_residue_pair(), protocols::forge::remodel::RemodelMover::design_refine(), protocols::dna::DNABase::DNABase(), protocols::dna::DNABasepair::DNABasepair(), protocols::dna::DNABasestep::DNABasestep(), core::scoring::dna::DNABFormPotential::eval_dna_bform_bb_torsion_score_residue(), core::scoring::dna::DNABFormPotential::eval_dna_bform_chi_torsion_score_residue(), core::scoring::dna::DNAChiEnergy::eval_dof_derivative(), core::scoring::methods::FACTSEnergy::eval_intrares_energy(), core::scoring::methods::GenBornEnergy::eval_intrares_energy(), core::scoring::methods::VdWTinkerEnergy::eval_intrares_energy(), core::scoring::methods::MultipoleElecEnergy::eval_intrares_energy(), core::scoring::methods::VdWTinkerEnergy::eval_intrares_energy_ext(), core::scoring::methods::MultipoleElecEnergy::eval_intrares_energy_ext(), core::scoring::methods::SASAEnergy::eval_intrares_energy_ext(), core::scoring::methods::FACTSEnergy::evaluate_rotamer_background_energies(), core::scoring::methods::GenBornEnergy::evaluate_rotamer_background_energies(), core::scoring::methods::VdWTinkerEnergy::evaluate_rotamer_background_energies(), core::scoring::methods::MultipoleElecEnergy::evaluate_rotamer_background_energies(), core::scoring::elec::FA_GrpElecEnergy::evaluate_rotamer_background_energies(), core::scoring::hbonds::HBondEnergy::evaluate_rotamer_background_energies(), core::scoring::methods::FACTSEnergy::evaluate_rotamer_background_energy_maps(), core::scoring::methods::GenBornEnergy::evaluate_rotamer_background_energy_maps(), core::scoring::methods::VdWTinkerEnergy::evaluate_rotamer_background_energy_maps(), core::scoring::methods::MultipoleElecEnergy::evaluate_rotamer_background_energy_maps(), core::scoring::hbonds::get_hb_acc_chem_type(), core::scoring::dna::get_z_axis(), protocols::dna::make_base_pair_aware_fold_tree(), protocols::relax::make_dna_rigid(), protocols::motifs::Motif::Motif(), core::scoring::methods::DirectReadoutEnergy::my_residue_pair_energy(), protocols::fold_from_loops::NubInitioMover::post_process(), core::scoring::dna::DNAChiEnergy::residue_energy(), core::scoring::methods::DNA_DihedralEnergy::residue_energy(), core::scoring::methods::DNA_BaseEnergy::residue_pair_energy(), core::scoring::methods::FACTSEnergy::residue_pair_energy(), core::scoring::methods::DNA_ReferenceEnergy::residue_pair_energy(), core::scoring::hbonds::HBondEnergy::residue_pair_energy(), core::scoring::methods::GenBornEnergy::residue_pair_energy(), core::scoring::methods::SASAEnergy::residue_pair_energy(), core::scoring::methods::VdWTinkerEnergy::residue_pair_energy(), core::scoring::methods::MultipoleElecEnergy::residue_pair_energy(), core::scoring::methods::SASAEnergy::residue_pair_energy_ext(), core::scoring::methods::MultipoleElecEnergy::residue_pair_energy_ext(), core::scoring::methods::VdWTinkerEnergy::residue_pair_energy_ext(), core::scoring::dna::DirectReadoutPotential::rsd_rsd_energy(), core::conformation::setup_corresponding_atoms(), and core::scoring::dna::DNA_DihedralPotential::skip_torsion().

bool core::conformation::Residue::is_l_rna ( ) const

inline

Returns true if this residue is a L-RNA residue.

References core::chemical::ResidueTypeBase::is_l_rna(), and rsd_type_.

Referenced by core::scoring::rna::RNA_TorsionPotential::residue_pair_energy().

bool core::conformation::Residue::is_ligand ( ) const

inline

Returns true if this residue is a ligand.

References core::chemical::ResidueType::is_ligand(), and rsd_type_.

Referenced by core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr(), core::conformation::Conformation::append_residue(), protocols::enzdes::EnzdesFlexBBProtocol::apply(), protocols::rbsegment_relax::RBSegmentRelax::apply(), protocols::enzdes::DetectProteinLigandInterface::apply(), protocols::simple_moves::ExplicitWaterMover::build_backbone_rotamer_clouds(), protocols::scoring::Interface::calculate(), protocols::enzdes::PackRotamersMoverPartGreedy::choose_n_best(), protocols::enzdes::EnzdesBaseProtocol::create_enzdes_movemap(), core::scoring::methods::GenericBondedEnergy::defines_score_for_residue_pair(), protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), core::scoring::etable::BaseEtableEnergy< Derived >::determine_crossover_behavior(), protocols::metal_interface::MatchGrafter::ensure_proper_his_tautomers(), core::scoring::methods::GenericBondedEnergy::eval_intrares_derivatives(), core::scoring::elec::FA_ElecEnergy::eval_intrares_derivatives(), core::scoring::methods::GenericBondedEnergy::eval_intrares_energy(), core::scoring::elec::FA_ElecEnergy::eval_intrares_energy(), protocols::cutoutdomain::CutOutDomain::find_nearest_res(), protocols::rosetta_scripts::find_nearest_res(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_1b_energy(), protocols::toolbox::IGLigandDesignEdgeUpweighter::get_edge_reweight(), core::scoring::elec::FA_ElecEnergy::get_intrares_countpair(), protocols::hbnet::HBNet::get_native_networks(), core::chemical::rna::get_rna_base_coordinate_system(), protocols::sic_dock::make_Cx(), protocols::ligand_docking::ProtLigEnsemble::make_packer_task(), protocols::ligand_docking::HighResDocker::make_packer_task_from_vector(), protocols::motifs::Motif::Motif(), protocols::hbnet::HBNetStapleInterface::network_meets_final_criteria(), protocols::hbnet::HBNet::rec_trav_native(), protocols::simple_moves::RepeatPropagationMover::repeat_ligand_constraints(), protocols::features::ResidueConformationFeatures::report_features(), protocols::denovo_design::components::residue_is_compatible(), core::scoring::elec::FA_ElecEnergy::residue_pair_energy(), protocols::ligand_docking::restrict_to_protein_residues(), core::pose::symmetry::sealed_symmetric_fold_tree(), protocols::denovo_design::components::SegmentCounts::SegmentCounts(), protocols::scoring::Interface::set_pack(), protocols::hbnet::HBNet::traverse_native(), and protocols::toolbox::match_enzdes_util::EnzConstraintParameters::update_pdb_remarks().

bool core::conformation::Residue::is_lower_terminus ( ) const

inline

Returns true if the residue has a lower terminus property.

References core::chemical::ResidueType::is_lower_terminus(), and rsd_type_.

Referenced by protocols::cryst::MakeLatticeMover::add_monomers_to_lattice(), protocols::cryst::MakeLayerMover::add_monomers_to_layer(), protocols::loops::add_single_cutpoint_variant(), protocols::denovo_design::components::add_to_pose(), protocols::frags::add_vall_cheating_fragments(), core::conformation::Conformation::align_virtual_atoms_in_carbohydrate_residue(), core::conformation::Conformation::append_polymer_residue_after_seqpos(), core::conformation::Conformation::append_residue(), core::pose::append_subpose_to_pose(), protocols::protein_interface_design::movers::AddChainBreak::apply(), protocols::fldsgn::filters::HelixKinkFilter::apply(), protocols::task_operations::DsspDesignOperation::apply(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::apply(), protocols::fldsgn::CircularPermutation::apply(), protocols::flxbb::LayerDesignOperation::apply(), core::chemical::ICoorAtomID::atom_id(), protocols::idealize::basic_idealize(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::calc_dist(), core::scoring::membrane::MPResidueLipophilicityEnergy::calc_energy(), core::scoring::geometric_solvation::compute_exact_geosol(), core::scoring::packing::compute_holes_deriv_res(), core::scoring::packing::compute_holes_score_res(), connect_atom(), protocols::topology_broker::copy_internal_coords(), protocols::denovo_design::movers::AlignResiduesMover::copy_residue(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::correct_termini_derivatives(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::count_bb_atoms(), protocols::forge::methods::count_cutpoints(), protocols::relax::cyclize_pose(), determine_nonstandard_polymer_status(), core::scoring::dna::DNA_DihedralPotential::eval_harmonic_backbone_torsion_score_and_deriv(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd1(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd2(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_bond_length_derivs(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_improper_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_improper_energy(), core::scoring::elec::FA_ElecEnergy::eval_intrares_derivatives(), core::scoring::elec::FA_ElecEnergy::eval_intrares_energy(), protocols::forge::methods::find_cutpoint(), protocols::ligand_docking::LigandBaseProtocol::find_interface_backbone(), core::conformation::carbohydrates::find_seqpos_of_saccharides_parent_residue(), protocols::generalized_kinematic_closure::general_set_phi(), protocols::generalized_kinematic_closure::general_set_psi(), core::conformation::get_anchor_atomno(), core::scoring::dna::get_DNA_backbone_bin(), core::scoring::hbonds::get_hb_don_chem_type(), core::pose::motif::get_nterminal_peptide_bond_reference_frame(), core::pose::motif::get_nterminal_peptide_bond_reference_frame_atomids(), core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::get_phi_from_rsd(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_phi_from_rsd(), core::conformation::get_root_atomno(), protocols::sic_dock::get_termini_from_pose(), protocols::forge::methods::grow_left_r(), protocols::rbsegment_relax::guess_rbsegs_from_pose(), protocols::forge::build::SegmentSwap::init(), protocols::forge::build::SegmentInsert::init(), protocols::abinitio::abscript::RigidChunkCM::initialize(), protocols::match::upstream::OriginalBackboneBuildPoint::initialize_from_residue(), core::conformation::Conformation::insert_polymer_residue(), protocols::frags::insert_random_fragments_in_flexible_protein_regions(), core::pose::is_lower_terminus(), core::scoring::Ramachandran::is_normally_connected(), protocols::loops::Loop::is_terminal(), protocols::denovo_design::loop_stop_without_overlap(), protocols::sic_dock::make_Cx(), protocols::forge::build::Bridge::modify_impl(), protocols::forge::build::SegmentRebuild::modify_impl(), protocols::forge::build::ConnectRight::modify_impl(), protocols::forge::build::SegmentInsert::modify_impl(), protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturber::perturb_chain(), protocols::denovo_design::components::pose_matches_description(), protocols::denovo_design::components::prepend_new_residues(), core::conformation::symmetry::SymmetricConformation::prepend_polymer_residue_before_seqpos(), core::conformation::Conformation::prepend_polymer_residue_before_seqpos(), core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose(), core::scoring::methods::DNA_DihedralEnergy::residue_energy(), core::scoring::methods::carbohydrates::SugarBackboneEnergy::residue_energy(), core::scoring::membrane::MPHelicalityEnergy::residue_energy(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::RotamericSingleResidueDunbrackLibrary(), protocols::loops::loop_closure::kinematic_closure::KinematicPerturber::set_pose_after_closure(), protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturber::set_pose_after_closure(), protocols::denovo_design::components::Segment::set_template_pose(), protocols::rbsegment_relax::setup_disconnected(), protocols::rbsegment_relax::setup_pose_rbsegs_keep_loops(), core::scoring::dna::DNA_DihedralPotential::skip_torsion(), protocols::fldsgn::CircularPermutation::split_chains(), and core::conformation::Conformation::update_polymeric_connection().

bool core::conformation::Residue::is_meta_aramid ( ) const

inline

Returns if this residue is a meta aramid.

References core::chemical::ResidueType::is_meta_aramid(), and rsd_type_.

Referenced by core::scoring::methods::AromaticBackboneRestraintEnergy::eval_residue_derivatives(), and core::scoring::methods::AromaticBackboneRestraintEnergy::residue_energy().

bool core::conformation::Residue::is_metal ( ) const

inline

Returns true if this residue is a metal ion, false otherwise. The METAL property is specified in the params file under PROPERTIES.

Author

Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References core::chemical::ResidueType::is_metal(), and rsd_type_.

Referenced by core::util::add_covalent_linkages_to_metal(), core::util::auto_setup_all_metal_bonds(), core::util::auto_setup_all_metal_constraints(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::define_active_virtual_sites(), protocols::simple_moves::SetupMetalsMover::find_metal_resnums(), core::util::find_metalbinding_atoms(), core::scoring::GenericBondedPotential::residue_derivatives(), core::scoring::GenericBondedPotential::residue_energy(), and core::scoring::GenericBondedPotential::setup_for_scoring().

bool core::conformation::Residue::is_metalbinding ( ) const

inline

Returns true if this residue is a type capable of binding to a metal ion (e.g. His, Cys, etc.), false otherwise. The METALBINDING property is specified in the params file under PROPERTIES.

Author

Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References core::chemical::ResidueType::is_metalbinding(), and rsd_type_.

Referenced by core::io::pose_from_sfr::PoseFromSFRBuilder::find_atom_tree_root_for_metal_ion(), and core::util::find_metalbinding_atoms_helper().

bool core::conformation::Residue::is_NA ( ) const

inline

Returns true if this residue is a nucleic acid.

References core::chemical::ResidueType::is_NA(), and rsd_type_.

Referenced by core::io::pose_to_sfr::PoseToStructFileRepConverter::append_residue_info_to_sfr(), protocols::simple_moves::ExplicitWaterMover::build_backbone_rotamer_clouds(), core::pack::rotamer_set::build_lib_dna_rotamers(), protocols::scoring::Interface::calculate(), core::scoring::loop_graph::get_6D_trans_rot_potential_evaluator(), core::chemical::rna::get_rna_base_centroid(), core::chemical::rna::get_rna_base_coordinate_system(), protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::Initialize_base_stub_list(), and protocols::stepwise::modeler::rna::is_virtual_base().

bool core::conformation::Residue::is_ortho_aramid ( ) const

inline

Returns if this residue is an ortho aramid.

References core::chemical::ResidueType::is_ortho_aramid(), and rsd_type_.

Referenced by core::scoring::methods::AromaticBackboneRestraintEnergy::eval_residue_derivatives(), and core::scoring::methods::AromaticBackboneRestraintEnergy::residue_energy().

bool core::conformation::Residue::is_para_aramid ( ) const

inline

Returns if this residue is a para aramid.

References core::chemical::ResidueType::is_para_aramid(), and rsd_type_.

Referenced by core::scoring::methods::AromaticBackboneRestraintEnergy::eval_residue_derivatives(), and core::scoring::methods::AromaticBackboneRestraintEnergy::residue_energy().

bool core::conformation::Residue::is_peptoid ( ) const

inline

Returns if this residue is a peptoid.

References core::chemical::ResidueTypeBase::is_peptoid(), and rsd_type_.

Referenced by core::scoring::hbonds::calculate_intra_res_hbonds(), core::scoring::etable::BaseEtableEnergy< TableLookupEtableEnergy >::calculate_intra_xover4(), core::scoring::etable::BaseEtableEnergy< Derived >::determine_crossover_behavior(), core::scoring::etable::BaseEtableEnergy< Derived >::eval_atom_derivative(), core::scoring::etable::BaseEtableEnergy< Derived >::eval_intrares_derivatives(), core::scoring::etable::TableLookupEtableEnergy::eval_intrares_energy(), core::scoring::etable::AnalyticEtableEnergy::eval_intrares_energy(), core::scoring::etable::BaseEtableEnergy< Derived >::eval_intrares_energy_ext(), core::scoring::OmegaTether::eval_omega_score_residue(), core::scoring::methods::OmegaTetherEnergy::eval_residue_dof_derivative(), core::scoring::etable::BaseEtableEnergy< Derived >::finalize_total_energy(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_phi_from_rsd(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_psi_from_rsd(), core::pack::dunbrack::DunbrackEnergy::get_scratch_index(), core::pose::is_lower_terminus(), core::pose::is_upper_terminus(), place(), and core::scoring::methods::OmegaTetherEnergy::residue_energy().

bool core::conformation::Residue::is_polar ( ) const

inline

Returns true if the residue is polar.

References core::chemical::ResidueType::is_polar(), and rsd_type_.

Referenced by protocols::vip::VIP_Mover::cull_mutatable_residues(), core::scoring::methods::PairEnergy::defines_score_for_residue_pair(), core::scoring::methods::PairEnergy::eval_residue_pair_derivatives(), core::scoring::methods::PairEnergy::evaluate_rotamer_background_energies(), core::scoring::methods::PairEnergy::evaluate_rotamer_background_energy_maps(), protocols::task_operations::CrystalContactsOperation::is_crystal_contact(), core::scoring::PairEPotential::pair_term_energy(), core::scoring::PairEPotential::pair_term_energy_exists(), and core::scoring::methods::PairEnergy::residue_pair_energy().

bool core::conformation::Residue::is_polymer ( ) const

inline

Returns true if this residue is a polymer.

References core::chemical::ResidueTypeBase::is_polymer(), and rsd_type_.

Referenced by protocols::jumping::JumpSample::add_chainbreaks(), protocols::cryst::MakeLatticeMover::add_monomers_to_lattice(), core::pose::addVirtualResAsRoot(), core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr(), protocols::ligand_docking::LigandDockProtocol::append_ligand_docking_scores(), core::conformation::Conformation::append_residue_by_bond(), protocols::hybridization::MRMover::apply(), protocols::cyclic_peptide::RamaMutationSelector::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), core::scoring::elec::FA_ElecEnergy::backbone_backbone_energy(), core::scoring::elec::FA_ElecEnergy::backbone_sidechain_energy(), protocols::idealize::basic_idealize(), core::select::util::SelectResiduesByLayer::calc_sc_neighbors(), connect_atom(), protocols::enzdes::EnzdesBaseProtocol::create_enzdes_movemap(), core::scoring::methods::GenericBondedEnergy::defines_score_for_residue_pair(), core::scoring::etable::BaseEtableEnergy< Derived >::determine_crossover_behavior(), protocols::enzdes::EnzdesFlexBBProtocol::determine_flexible_regions(), determine_nonstandard_polymer_status(), protocols::rna::movers::determine_residues_to_rebuild(), protocols::ligand_docking::InterfaceBuilder::enforce_minimum_length(), core::scoring::methods::GenericBondedEnergy::eval_intrares_derivatives(), core::scoring::elec::FA_ElecEnergy::eval_intrares_derivatives(), core::scoring::methods::GenericBondedEnergy::eval_intrares_energy(), core::scoring::elec::FA_ElecEnergy::eval_intrares_energy(), protocols::loophash::FastGapMover::find_next_gap(), protocols::electron_density::findLoopFromDensity(), protocols::forge::methods::fold_tree_from_pose(), core::conformation::get_anchor_atomno(), core::scoring::elec::FA_ElecEnergy::get_intrares_countpair(), protocols::ligand_docking::LigandBaseProtocol::get_ligand_id(), core::chemical::rna::get_rna_base_centroid(), core::chemical::rna::get_rna_base_coordinate_system(), core::conformation::get_root_atomno(), protocols::denovo_design::components::StructureDataFactory::infer_from_pose(), core::pose::toolbox::AtomID_Mapper::initialize(), core::scoring::is_ligand_heavyatom(), core::scoring::is_ligand_heavyatom_residues(), core::pose::is_lower_terminus(), core::scoring::is_polymer_heavyatom(), core::pose::is_upper_terminus(), protocols::ligand_docking::LigandBaseProtocol::make_movemap(), protocols::ligand_docking::LigandBaseProtocol::make_packer_task_ligand_only(), protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::moves_for_pose(), polymeric_oriented_sequence_distance(), polymeric_sequence_distance(), protocols::ligand_docking::LigandDockProtocol::random_conformer(), protocols::ligand_docking::LigandBaseProtocol::reorder_foldtree_around_mobile_regions(), protocols::ligand_docking::reorder_with_first_non_mobile_as_root(), core::scoring::elec::FA_ElecEnergy::residue_pair_energy(), protocols::ligand_docking::LigandDockProtocol::restrain_ligand_chis(), core::pose::set_reasonable_fold_tree(), core::scoring::elec::FA_ElecEnergy::sidechain_sidechain_energy(), protocols::protein_interface_design::star_fold_tree(), protocols::hybridization::MRMover::trim_target_pose(), and core::conformation::Conformation::update_polymeric_connection().

bool core::conformation::Residue::is_polymer_bonded ( Residue const &  other ) const

inline

Am I polymer bonded to other?

References seqpos().

Referenced by protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_perturb_backbone_by_bins(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_randomize_backbone_by_bins(), core::scoring::lkball::LK_BallEnergy::backbone_backbone_energy(), core::scoring::lkball::LK_BallEnergy::backbone_sidechain_energy(), core::scoring::lkball::LK_BallEnergy::calculate_lk_ball_atom_energies(), core::scoring::lkball::LK_BallEnergy::calculate_lk_desolvation_of_single_atom_by_residue(), core::scoring::etable::BaseEtableEnergy< Derived >::determine_crossover_behavior(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_improper_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_improper_energy(), core::scoring::lkball::LK_BallEnergy::get_count_pair_function_trie(), protocols::forge::build::ConnectRight::modify_impl(), core::scoring::lkball::LK_BallEnergy::residue_pair_energy(), core::scoring::lkball::LK_BallEnergy::setup_for_minimizing_for_residue_pair(), and core::scoring::lkball::LK_BallEnergy::sidechain_sidechain_energy().

bool core::conformation::Residue::is_polymer_bonded ( Size const  other_index ) const

inline

Am I polymer-bonded to other? checks lower and upper connections.

References core::chemical::ResidueTypeBase::is_polymer(), core::chemical::ResidueType::lower_connect_id(), residue_connection_partner(), rsd_type_, and core::chemical::ResidueType::upper_connect_id().

bool core::conformation::Residue::is_post_methylene_meta_aramid ( ) const

inline

Returns if this residue is a post methylene meta aramid.

References core::chemical::ResidueType::is_post_methylene_meta_aramid(), and rsd_type_.

Referenced by core::scoring::methods::AromaticBackboneRestraintEnergy::eval_residue_derivatives(), and core::scoring::methods::AromaticBackboneRestraintEnergy::residue_energy().

bool core::conformation::Residue::is_post_methylene_ortho_aramid ( ) const

inline

Returns if this residue is a post methylene ortho aramid.

References core::chemical::ResidueType::is_post_methylene_ortho_aramid(), and rsd_type_.

Referenced by core::scoring::methods::AromaticBackboneRestraintEnergy::eval_residue_derivatives(), and core::scoring::methods::AromaticBackboneRestraintEnergy::residue_energy().

bool core::conformation::Residue::is_post_methylene_para_aramid ( ) const

inline

Returns if this residue is a post methylene para aramid.

References core::chemical::ResidueType::is_post_methylene_para_aramid(), and rsd_type_.

Referenced by core::scoring::methods::AromaticBackboneRestraintEnergy::eval_residue_derivatives(), and core::scoring::methods::AromaticBackboneRestraintEnergy::residue_energy().

bool core::conformation::Residue::is_pre_methylene_meta_aramid ( ) const

inline

Returns if this residue is a pre methylene meta aramid.

References core::chemical::ResidueType::is_pre_methylene_meta_aramid(), and rsd_type_.

Referenced by core::scoring::methods::AromaticBackboneRestraintEnergy::eval_residue_derivatives(), and core::scoring::methods::AromaticBackboneRestraintEnergy::residue_energy().

bool core::conformation::Residue::is_pre_methylene_ortho_aramid ( ) const

inline

Returns if this residue is a pre methylene ortho aramid.

References core::chemical::ResidueType::is_pre_methylene_ortho_aramid(), and rsd_type_.

Referenced by core::scoring::methods::AromaticBackboneRestraintEnergy::eval_residue_derivatives(), and core::scoring::methods::AromaticBackboneRestraintEnergy::residue_energy().

bool core::conformation::Residue::is_pre_methylene_para_aramid ( ) const

inline

Returns if this residue is a pre methylene para aramid.

References core::chemical::ResidueType::is_pre_methylene_para_aramid(), and rsd_type_.

Referenced by core::scoring::methods::AromaticBackboneRestraintEnergy::eval_residue_derivatives(), and core::scoring::methods::AromaticBackboneRestraintEnergy::residue_energy().

bool core::conformation::Residue::is_pre_methylene_post_methylene_meta_aramid ( ) const

inline

Returns if this residue is a post methylene meta aramid.

References core::chemical::ResidueType::is_pre_methylene_post_methylene_meta_aramid(), and rsd_type_.

Referenced by core::scoring::methods::AromaticBackboneRestraintEnergy::eval_residue_derivatives(), and core::scoring::methods::AromaticBackboneRestraintEnergy::residue_energy().

bool core::conformation::Residue::is_pre_methylene_post_methylene_ortho_aramid ( ) const

inline

Returns if this residue is a post methylene ortho aramid.

References core::chemical::ResidueType::is_pre_methylene_post_methylene_ortho_aramid(), and rsd_type_.

Referenced by core::scoring::methods::AromaticBackboneRestraintEnergy::eval_residue_derivatives(), and core::scoring::methods::AromaticBackboneRestraintEnergy::residue_energy().

bool core::conformation::Residue::is_pre_methylene_post_methylene_para_aramid ( ) const

inline

Returns if this residue is a post methylene para aramid.

References core::chemical::ResidueType::is_pre_methylene_post_methylene_para_aramid(), and rsd_type_.

Referenced by core::scoring::methods::AromaticBackboneRestraintEnergy::eval_residue_derivatives(), and core::scoring::methods::AromaticBackboneRestraintEnergy::residue_energy().

bool core::conformation::Residue::is_protein ( ) const

inline

Returns true if this residue is an amino acid.

References core::chemical::ResidueTypeBase::is_protein(), and rsd_type_.

Referenced by protocols::loops::loop_closure::ccd::RamaCheckBase::accept_new_conformation(), protocols::simple_filters::SpanTopologyMatchPoseFilter::actual_topology(), protocols::hybridization::HybridizeProtocol::add_fragment_csts(), protocols::loop_grower::LoopGrower::add_fragment_csts(), protocols::hybridization::add_non_protein_cst(), protocols::sewing::hashing::AlignmentFileGeneratorMover::add_pose_segments_to_segment_vector(), protocols::mpi_refinement::add_poseinfo_to_ss(), protocols::loops::add_single_cutpoint_variant(), core::pose::ncbb::add_triazole_constraint(), protocols::frags::add_vall_cheating_fragments(), protocols::frags::add_vall_fragments(), protocols::loops::addScoresForLoopParts(), protocols::forge::remodel::RemodelGlobalFrame::align_segment(), protocols::hybridization::TMalign::alignment2AtomMap(), protocols::pockets::PocketGrid::alter_espGrid_with_bound_ligand(), core::scoring::hbonds::HBondSet::append_hbond(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::append_metal_vsites(), core::io::pose_to_sfr::PoseToStructFileRepConverter::append_residue_info_to_sfr(), core::pose::append_subpose_to_pose(), protocols::RBSegmentRelaxImpl::apply(), protocols::simple_filters::EnergyPerResidueFilter::apply(), protocols::protein_interface_design::movers::RandomMutation::apply(), protocols::simple_moves::WriteSSEMover::apply(), protocols::matdes::SchemePlaceMotifsMover::apply(), protocols::protein_interface_design::movers::PrepackMover::apply(), protocols::simple_filters::SSMotifFinder::apply(), protocols::frag_picker::nonlocal::NonlocalFrags::apply(), protocols::task_operations::SelectBySASAOperation::apply(), protocols::abinitio::DomainAssembly::apply(), protocols::enzdes::BackboneSampler::apply(), protocols::protein_interface_design::filters::FilterScanFilter::apply(), protocols::hbnet::ConstrainHBondNetwork::apply(), protocols::protein_interface_design::movers::BackrubDDMover::apply(), protocols::rna::denovo::movers::RNA_Minimizer::apply(), protocols::protein_interface_design::movers::DesignMinimizeHbonds::apply(), protocols::task_operations::CrystalContactsOperation::apply(), protocols::evolution::NucleotideMutation::apply(), protocols::fold_from_loops::selectors::ProteinResidueSelector::apply(), core::select::residue_selector::ResidueInMembraneSelector::apply(), protocols::hybridization::CartesianSampler::apply(), protocols::pose_creation::MakePolyXMover::apply(), protocols::hybridization::CartesianHybridize::apply(), protocols::fldsgn::SheetConstraintGenerator::apply(), protocols::minimization_packing::BoltzmannRotamerMover::apply(), protocols::simple_moves::CoupledMover::apply(), protocols::denovo_design::movers::FastDesign::apply(), protocols::task_operations::DsspDesignOperation::apply(), protocols::fldsgn::CircularPermutation::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::hybridization::FoldTreeHybridize::apply(), protocols::enzdes::ProteinLigandInterfaceUpweighter::apply(), protocols::enzdes::RepackLigandSiteWithoutLigandMover::apply(), protocols::flxbb::LayerDesignOperation::apply(), protocols::rbsegment_relax::SequenceShiftMover::apply(), protocols::hybridization::TMalign::apply(), protocols::frags::TorsionFragmentMover::apply(), protocols::minimization_packing::MinMover::apply_dof_tasks_to_movemap(), protocols::hybridization::CartesianHybridize::apply_frame(), protocols::loops::apply_sequence_mapping(), core::scoring::atomic_depth::AtomicDepth::AtomicDepth(), protocols::pockets::PocketGrid::autoexpanding_pocket_eval(), core::scoring::hbonds::HBondEnergy::backbone_sidechain_energy(), core::scoring::constraints::BackboneStubConstraint::BackboneStubConstraint(), core::scoring::constraints::BackboneStubLinearConstraint::BackboneStubLinearConstraint(), protocols::idealize::basic_idealize(), protocols::simple_moves::ExplicitWaterMover::build_backbone_rotamer_clouds(), protocols::simple_moves::StructProfileMover::calc_cenlist(), protocols::analysis::InterfaceAnalyzerMover::calc_per_residue_and_regional_data(), protocols::protein_interface_design::ReportPSSMDifferences::calculate(), protocols::protein_interface_design::ReportSequenceDifferences::calculate(), protocols::simple_ddg::DdGScan::calculate(), protocols::docking::EllipsoidalRandomizationMover::calculate_axes(), core::scoring::electron_density::calculate_density_nbr(), core::scoring::hbonds::calculate_intra_res_hbonds(), core::scoring::etable::BaseEtableEnergy< TableLookupEtableEnergy >::calculate_intra_xover4(), core::scoring::etable::BaseEtableEnergy< TableLookupEtableEnergy >::calculate_intrares(), protocols::docking::EllipsoidalRandomizationMover::calculate_plane_axes(), protocols::pockets::NonPlaidFingerprint::calculate_protein_CoM(), core::scoring::electron_density::calculate_rama(), protocols::geometry::center_of_mass(), protocols::fldsgn::BluePrintBDR::centroid_build(), protocols::forge::components::BDR::centroid_build(), protocols::hybridization::HybridizeProtocol::check_and_create_fragments(), core::scoring::rna::RNA_FullAtomStackingEnergy::check_base_base_OK(), protocols::denovo_design::DisulfidizeMover::check_residue_type(), protocols::simple_filters::TMsSpanMembraneFilter::compute(), protocols::simple_filters::MembAccesResidueLipophilicityFilter::compute(), protocols::denovo_design::filters::SSPredictionFilter::compute(), protocols::denovo_design::filters::ExposedHydrophobicsFilter::compute(), core::scoring::dssp::Dssp::compute(), protocols::fldsgn::filters::SecondaryStructureHasResidueFilter::compute(), protocols::fldsgn::filters::SecondaryStructureFilter::compute(), protocols::enzdes::RepackWithoutLigandFilter::compute(), protocols::enzdes::PackRotamersMoverPartGreedy::compute_designable_neighbors(), protocols::pockets::PlaidFingerprint::compute_ligand_resnum(), core::pack::interaction_graph::SurfacePotential::compute_pose_hpatch_score(), protocols::simple_filters::ResidueIEFilter::compute_resnums(), protocols::optimize_weights::IterativeOptEDriver::compute_rotamers_around_ligands(), protocols::denovo_design::construct_poly_ala_pose(), protocols::abinitio::AbrelaxApplication::copy_structure(), protocols::stepwise::modeler::align::create_alignment_id_map_legacy(), protocols::hybridization::create_fragment_set(), protocols::hybridization::create_fragment_set_no_ssbias(), core::scoring::hbonds::create_rotamer_descriptor(), core::scoring::membrane::MPSpanInsertionEnergy::create_updated_span(), protocols::cryst::crystRMS(), protocols::cryst::crystRMSfast(), protocols::simple_ddg::AlaScan::ddG_for_single_residue(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::define_active_virtual_sites(), core::scoring::methods::PointWaterEnergy::defines_score_for_residue_pair(), core::scoring::methods::PairEnergy::defines_score_for_residue_pair(), core::scoring::elec::FA_GrpElecEnergy::defines_score_for_residue_pair(), core::scoring::elec::FA_ElecEnergy::defines_score_for_residue_pair(), protocols::rna::denovo::delete_non_protein_from_pose(), protocols::cryst::MakeLatticeMover::detect_connecting_subunits(), core::scoring::etable::BaseEtableEnergy< Derived >::determine_crossover_behavior(), protocols::pockets::EggshellGrid::EggshellGrid(), protocols::metal_interface::MatchGrafter::ensure_proper_his_tautomers(), protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::EntropyEstimator(), core::scoring::membrane::MPSpanInsertionEnergy::eval_atom_derivative(), core::scoring::methods::MembraneEnvSmoothEnergy::eval_atom_derivative(), core::scoring::membrane::MPSpanAngleEnergy::eval_atom_derivative(), core::scoring::methods::EnvSmoothEnergy::eval_atom_derivative(), core::scoring::membrane::FaMPEnvSmoothEnergy::eval_atom_derivative(), core::scoring::membrane::MPHelicalityEnergy::eval_atom_derivative(), core::scoring::membrane::MPResidueLipophilicityEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensCenEnergy::eval_atom_derivative(), core::scoring::etable::BaseEtableEnergy< Derived >::eval_atom_derivative(), core::scoring::methods::RamachandranEnergy2B::eval_dof_derivative(), core::scoring::methods::RamachandranEnergy::eval_dof_derivative(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_improper_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_improper_energy(), core::scoring::etable::BaseEtableEnergy< Derived >::eval_intrares_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_intrares_derivatives(), core::scoring::methods::RamachandranEnergy2B::eval_intrares_energy(), core::scoring::methods::CartesianBondedEnergy::eval_intrares_energy(), core::scoring::etable::TableLookupEtableEnergy::eval_intrares_energy(), core::scoring::etable::AnalyticEtableEnergy::eval_intrares_energy(), core::scoring::etable::BaseEtableEnergy< Derived >::eval_intrares_energy_ext(), core::scoring::methods::CartesianBondedEnergy::eval_intraresidue_dof_derivative(), core::scoring::OmegaTether::eval_omega_score_residue(), core::scoring::PointWaterPotential::eval_pointwater_derivs(), core::scoring::PointWaterPotential::eval_pointwater_score(), core::scoring::Ramachandran::eval_rama_score_all(), core::scoring::Ramachandran2B::eval_rama_score_all(), core::scoring::Ramachandran::eval_rama_score_residue(), core::scoring::Ramachandran2B::eval_rama_score_residue(), core::scoring::methods::RamachandranEnergy::eval_residue_dof_derivative(), core::scoring::methods::OmegaTetherEnergy::eval_residue_dof_derivative(), core::pack::dunbrack::cenrot::CenRotDunEnergy::eval_residue_dof_derivative(), core::scoring::methods::PointWaterEnergy::eval_residue_pair_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_residue_pair_derivatives_sorted(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_torsion(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_angle_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_angle_energies(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_ring_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_ring_energies(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_torsion_derivatives(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_env_and_cbeta_deriv(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_env_and_cbeta_score(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_pair_orientation_deriv(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_pair_orientation_score(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_pair_score(), core::scoring::MembranePotential::evaluate_env(), core::scoring::SmoothEnvPairPotential::evaluate_env_and_cbeta_deriv(), core::scoring::EnvPairPotential::evaluate_env_and_cbeta_scores(), core::scoring::SmoothEnvPairPotential::evaluate_env_and_cbeta_scores(), protocols::scoring::InterchainPotential::evaluate_env_score(), core::scoring::MembranePotential::evaluate_pair(), core::scoring::SmoothEnvPairPotential::evaluate_pair_and_cenpack_deriv(), core::scoring::EnvPairPotential::evaluate_pair_and_cenpack_score(), core::scoring::SmoothEnvPairPotential::evaluate_pair_and_cenpack_score(), protocols::scoring::InterchainPotential::evaluate_pair_and_vdw_score(), core::scoring::rna::RNP_LowResPotential::evaluate_rnp_base_pair_score(), core::scoring::rna::RNP_LowResPairDistPotential::evaluate_rnp_pair_dist_score(), core::scoring::rna::RNP_LowResPotential::evaluate_rnp_pair_score(), core::scoring::rna::RNP_LowResStackData::evaluate_rnp_stack_xy_score(), core::scoring::methods::PairEnergy::evaluate_rotamer_background_energies(), core::scoring::methods::PairEnergy::evaluate_rotamer_background_energy_maps(), protocols::indexed_structure_store::extract_residue_entries(), 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protocols::optimize_weights::IterativeOptEDriver::get_nat_aa_opte_data(), protocols::md::CartesianMD::get_native_info(), core::scoring::motif::get_nbrs(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_new_chainIDs(), protocols::cryst::get_nres_asu(), core::pose::motif::get_nterminal_peptide_bond_reference_frame(), core::pose::motif::get_nterminal_peptide_bond_reference_frame_atomids(), protocols::hybridization::get_num_residues_prot(), core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::get_phi_from_rsd(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_phi_from_rsd(), protocols::simple_filters::AbinitioBaseFilter::get_protein_sstype(), core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::get_psi_from_rsd(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_psi_from_rsd(), protocols::rna::denovo::get_residues_within_dist_of_RNA(), protocols::rna::denovo::get_rnp_docking_fold_tree(), protocols::loophash::get_rt_over_leap_without_foldtree_bs(), protocols::motifs::LigandMotifSearch::get_sphere_aa(), protocols::sic_dock::get_termini_from_pose(), protocols::loops::has_severe_pep_bond_geom_issues(), protocols::pockets::NonPlaidFingerprint::include_eggshell_points_based_on_known_ligand(), protocols::hybridization::FragmentBiasAssigner::init(), protocols::simple_moves::RepeatPropagationMover::initial_constrained_residues(), protocols::hybridization::HybridizeFoldtreeDynamic::initialize(), core::pose::toolbox::AtomID_Mapper::initialize(), protocols::fldsgn::topology::SS_Info2::initialize(), protocols::match::upstream::OriginalBackboneBuildPoint::initialize_from_residue(), protocols::topology_broker::TopologyBroker::initialize_sequence(), protocols::loops::loop_closure::ccd::RamaCheckBase::initialize_starting_rama_scores(), protocols::features::HBondFeatures::insert_hbond_dehydron_row(), protocols::frags::insert_random_fragments_in_flexible_protein_regions(), core::conformation::is_disulfide_bond(), core::pose::is_lower_terminus(), core::scoring::is_non_peptide_heavy_atom(), core::scoring::is_protein_backbone(), core::scoring::is_protein_backbone_including_O(), core::scoring::is_protein_CA(), core::scoring::is_protein_CA_or_CB(), core::scoring::is_protein_CA_or_equiv(), protocols::loops::Loop::is_terminal(), core::pose::is_upper_terminus(), protocols::constel::NeighTeller::isneigh(), protocols::constraint_generator::last_protein_residue(), core::pack::dunbrack::load_unboundrot(), protocols::denovo_design::loop_start_without_overlap(), protocols::denovo_design::loop_stop_without_overlap(), protocols::ligand_docking::make_atr_rep_grid(), protocols::ligand_docking::make_atr_rep_grid_without_ligands(), protocols::dna::make_base_pair_aware_fold_tree(), protocols::struct_fragment::StructFragmentMover::make_fragment_picker(), protocols::optimize_weights::IterativeOptEDriver::measure_rotamer_recovery(), protocols::pose_metric_calculators::SequenceComparison::measure_sequence_recovery(), protocols::optimize_weights::IterativeOptEDriver::measure_sequence_recovery(), protocols::peptide_deriver::PeptideDeriverFilter::minimize(), protocols::protein_interface_design::MinimizeInterface(), protocols::motifs::Motif::Motif(), protocols::stepwise::modeler::StepWiseMinimizer::move_side_chain(), core::scoring::methods::DirectReadoutEnergy::my_residue_pair_energy(), protocols::hbnet::HBNetStapleInterface::network_meets_final_criteria(), protocols::hybridization::AllResiduesChanged::operator()(), protocols::abinitio::AllResiduesChanged::operator()(), protocols::rna::denovo::movers::RNA_Minimizer::packing_trials(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::pair_sets_with_positions(), core::scoring::PairEPotential::pair_term_energy_exists(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::parse_my_tag(), protocols::protein_interface_design::movers::PlaceStubMover::parse_my_tag(), protocols::protein_interface_design::movers::parse_stub_sets(), protocols::hybridization::partial_align(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::perform_bump_check(), core::scoring::UnfoldedStatePotential::pose_raw_unfolded_state_energymap(), protocols::fold_from_loops::NubInitioMover::post_process(), core::scoring::methods::PoissonBoltzmannEnergy::protein_position_equal_within(), protocols::rna::denovo::movers::RNP_HighResMover::protein_sidechain_packing(), protocols::toolbox::DecoySetEvaluation::push_back_CA_xyz_from_silent_file(), core::scoring::Ramachandran2B::RamaE(), core::scoring::Ramachandran2B::RamaE_Lower(), core::scoring::Ramachandran2B::RamaE_Upper(), protocols::rna::denovo::movers::RNA_DeNovoMasterMover::randomize_rnp_rigid_body_orientations(), core::pose::read_psipred_ss2_file(), protocols::hbnet::HBNet::rec_trav_native(), core::conformation::symmetry::SymmetricConformation::recalculate_transforms(), protocols::pockets::PocketGrid::recenter(), protocols::qsar::scoring_grid::ClassicGrid::refresh(), protocols::qsar::scoring_grid::AtrGrid::refresh(), protocols::qsar::scoring_grid::HbaGrid::refresh(), protocols::qsar::scoring_grid::RepGrid::refresh(), protocols::qsar::scoring_grid::HbdGrid::refresh(), protocols::simple_moves::RepeatPropagationMover::repeat_ligand(), protocols::simple_moves::RepeatPropagationMover::repeat_ligand_constraints(), core::pose::PDBInfo::replace_res_remap_bfactors(), protocols::simple_filters::EnergyPerResidueFilter::report(), protocols::simple_ddg::AlaScan::report(), protocols::features::ResidueSecondaryStructureFeatures::report_features(), protocols::features::ProteinBackboneAtomAtomPairFeatures::report_features(), protocols::features::ProteinBackboneTorsionAngleFeatures::report_features(), protocols::features::HelixCapFeatures::report_features(), protocols::features::HBondFeatures::report_features(), protocols::features::ProteinBondGeometryFeatures::report_interres_angles(), protocols::features::ProteinBondGeometryFeatures::report_interres_lengths(), protocols::features::ProteinBondGeometryFeatures::report_intrares_angles(), protocols::features::ProteinBondGeometryFeatures::report_intrares_lengths(), protocols::features::ProteinBondGeometryFeatures::report_intrares_torsions(), core::scoring::membrane::MPResidueLipophilicityEnergy::report_ressolv(), protocols::simple_filters::EnergyPerResidueFilter::report_sm(), protocols::fldsgn::filters::SecondaryStructureFilter::report_sm(), protocols::simple_ddg::AlaScan::report_symmetry(), core::conformation::symmetry::residue_center_of_mass(), core::scoring::methods::RamachandranEnergy::residue_energy(), core::scoring::methods::OmegaTetherEnergy::residue_energy(), protocols::membrane::scoring::FaWaterToBilayerEnergy::residue_energy(), core::scoring::methods::MembraneEnvSmoothEnergy::residue_energy(), core::scoring::methods::EnvSmoothEnergy::residue_energy(), core::scoring::membrane::MPEnvEnergy::residue_energy(), core::scoring::membrane::FaMPEnvSmoothEnergy::residue_energy(), core::scoring::membrane::MPHelicalityEnergy::residue_energy(), core::scoring::membrane::MPResidueLipophilicityEnergy::residue_energy(), core::scoring::methods::RamachandranEnergy2B::residue_pair_energy(), core::scoring::membrane::MPPairEnergy::residue_pair_energy(), core::scoring::rna::RNA_VDW_Energy::residue_pair_energy(), core::scoring::methods::HybridVDW_Energy::residue_pair_energy(), core::scoring::rna::RNP_LowResEnergy::residue_pair_energy(), core::scoring::rna::RNP_LowResPairDistEnergy::residue_pair_energy(), core::scoring::rna::RNP_LowResStackEnergy::residue_pair_energy(), core::scoring::rna::RNA_FullAtomStackingEnergy::residue_pair_energy(), core::scoring::methods::PairEnergy::residue_pair_energy(), core::scoring::hbonds::HBondEnergy::residue_pair_energy(), core::scoring::rna::RNA_FullAtomStackingEnergy::residue_pair_energy_one_way(), core::scoring::methods::CartesianBondedEnergy::residue_pair_energy_sorted(), protocols::features::BetaTurnDetection::residue_range_is_protein(), protocols::ligand_docking::MinimizeBackbone::restrain_protein_Calpha(), protocols::ligand_docking::LigandBaseProtocol::restrain_protein_Calphas(), core::conformation::symmetry::return_nearest_residue(), core::pose::return_nearest_residue(), protocols::symmetry::SymmetrySlider::rg(), protocols::membrane::rsd_closest_to_chain_tm_com(), core::scoring::dna::DirectReadoutPotential::rsd_rsd_energy(), protocols::motifs::LigandMotifSearch::run(), protocols::denovo_design::same_pose(), protocols::environment::ClientMover::sandboxed_copy(), protocols::sic_dock::XfoxmScore::score(), core::scoring::constraints::BackboneStubLinearConstraint::score(), core::scoring::constraints::BackboneStubConstraint::score(), protocols::rna::denovo::movers::RNA_DeNovoMasterMover::search_rigid_body_orientation(), protocols::simple_filters::SaveResfileToDiskFilter::select_residues(), protocols::ligand_docking::MoveMapBuilder::set_all_bb(), core::conformation::set_chi_according_to_coordinates(), protocols::rbsegment_relax::set_constraints(), protocols::vip::VIP_Mover::set_excluded_positions(), protocols::normalmode::NormalMode::set_harmonic_constant_map(), protocols::hybridization::AllResiduesChanged::set_initial_pose(), protocols::abinitio::AllResiduesChanged::set_initial_pose(), protocols::rbsegment_relax::set_rb_constraints(), protocols::ligand_docking::set_repulsive_bb_cores(), protocols::denovo_design::components::Segment::set_template_pose(), protocols::hbnet::HBNet::setup(), protocols::enzdes::EnzdesBaseProtocol::setup_bbmin_ft_and_csts(), protocols::simple_moves::ShakeStructureMover::setup_ca_constraints(), protocols::forge::remodel::RemodelGlobalFrame::setup_CM_helical_constraint(), protocols::ddg::ddGMover::setup_constraints(), core::scoring::constraints::SiteConstraint::setup_csts(), core::scoring::hbonds::HBondEnergy::setup_for_minimizing_for_residue(), core::scoring::rna::RNP_LowResEnergy::setup_for_scoring(), core::scoring::electron_density::ElecDensCenEnergy::setup_for_scoring(), protocols::forge::remodel::RemodelGlobalFrame::setup_helical_constraint(), protocols::simple_moves::BBGaussianMover::setup_list(), protocols::rna::denovo::movers::RNA_Minimizer::setup_movemap(), protocols::stepwise::modeler::packer::StepWisePacker::setup_pack_task(), protocols::calc_taskop_movers::DesignRepackMover::setup_packer_and_movemap(), protocols::hbnet::HBNetStapleInterface::setup_packer_task_and_starting_residues(), protocols::hbnet::HBNet::setup_packer_task_and_starting_residues(), protocols::rbsegment_relax::setup_pose_from_rbsegs(), protocols::rna::denovo::movers::RNA_DeNovoMasterMover::setup_rna_protein_docking_mover(), protocols::denovo_design::filters::SSShapeComplementarityFilter::setup_sc(), protocols::enzdes::EnzdesBaseProtocol::setup_sequence_recovery_cache(), protocols::hybridization::AllResiduesChanged::show_unmoved(), protocols::abinitio::AllResiduesChanged::show_unmoved(), protocols::simple_filters::SpanTopologyMatchPoseFilter::span_file_topology(), protocols::hybridization::DDomainParse::split(), protocols::loops::split_by_ca_ca_dist(), protocols::loops::split_by_resSeq(), protocols::fldsgn::CircularPermutation::split_chains(), core::util::switch_to_residue_type_set(), protocols::protein_interface_design::SymMinimizeInterface(), and protocols::hbnet::HBNet::traverse_native().

bool core::conformation::Residue::is_pseudo_bonded ( Residue const &  other ) const

inline

Do I have any pseudobonds to other?

References seqpos().

Referenced by core::scoring::elec::FA_ElecEnergy::backbone_backbone_energy(), core::scoring::elec::FA_ElecEnergy::backbone_sidechain_energy(), core::scoring::FACTSPotential::calculate_GBpair_exact(), core::scoring::FACTSPotential::calculate_GBpair_fast(), core::scoring::FACTSPotential::calculate_GBpair_v1trunk(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::check_path_distance(), core::scoring::etable::count_pair::CountPairGeneric::CountPairGeneric(), core::scoring::etable::count_pair::CountPairFactory::determine_residue_connection(), core::scoring::elec::GroupElec::eval_respair_group_coulomb(), core::scoring::elec::GroupElec::eval_respair_group_derivatives(), core::scoring::FACTSPotential::evaluate_polar_otf_energy(), core::scoring::methods::LK_PolarNonPolarEnergy::get_count_pair_function(), core::scoring::rna::StackElecEnergy::get_count_pair_function(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_count_pair_function(), core::scoring::elec::FA_GrpElecEnergy::get_count_pair_function(), core::scoring::elec::FA_ElecEnergy::get_count_pair_function(), core::scoring::GenBornPotential::get_res_res_elecE(), core::scoring::vdwaals::VDW_Energy::residue_pair_energy(), core::scoring::elec::FA_ElecEnergy::residue_pair_energy(), core::scoring::elec::FA_ElecEnergy::sidechain_sidechain_energy(), and core::scoring::etable::etrie::TrieCountPairGeneric::TrieCountPairGeneric().

bool core::conformation::Residue::is_pseudo_bonded ( Size const  other_index ) const

inline

Do I have any pseudobonds to other?

References pseudobonds_.

bool core::conformation::Residue::is_purine ( ) const

inline

Returns true if this residue is a purine.

References core::chemical::ResidueType::is_purine(), and rsd_type_.

Referenced by protocols::pockets::GenPharmacophore::extract_rna_rings_from_protein_rna_complex(), and protocols::rna::denovo::movers::RNA_HelixMover::get_bb_pos().

bool core::conformation::Residue::is_pyrimidine ( ) const

inline

Returns true if this residue is a pyrimidine.

References core::chemical::ResidueType::is_pyrimidine(), and rsd_type_.

Referenced by protocols::rna::denovo::movers::RNA_HelixMover::get_bb_pos().

bool core::conformation::Residue::is_repulsive ( Size const  atomno ) const

inline

Check if atom is repulsive.

Note

A misnomer; this should really be called "is_repulsive_atom()". ~Labonte

References core::chemical::ResidueType::atom_type(), core::chemical::AtomType::is_repulsive(), and rsd_type_.

Referenced by core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_intra(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_one_way(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_one_way_bb_bb(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_one_way_sc(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::atom_is_heavy(), protocols::recces::sampler::rna::calc_base_centroid_rmsd(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_acceptor_atom_energy(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_donor_atom_energy(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_polar_group_sol_energy(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_sho_acceptor_atom_energy(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_sho_donor_atom_energy(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_intra(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_one_way(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_one_way_bb_bb(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_one_way_sc(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::eval_atom_energy(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::eval_intrares_derivatives(), core::scoring::rna::StackElecEnergy::eval_residue_pair_derivatives(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::eval_residue_pair_derivatives(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::eval_residue_pair_derivatives_one_way(), core::scoring::rna::StackElecEnergy::finalize_total_energy(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_acceptor(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_donor(), core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::get_atom_atom_occ_solvation(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::get_atom_atom_occ_solvation(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::get_atom_lk_energy(), core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::res_res_occ_sol_one_way(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::res_res_occ_sol_one_way(), core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::residue_energy(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::residue_energy(), core::scoring::rna::RNA_LJ_BaseEnergy::residue_pair_energy(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::residue_pair_energy_ext(), core::scoring::rna::StackElecEnergy::residue_pair_energy_ext(), core::scoring::rna::RNA_FullAtomStackingEnergy::residue_pair_energy_one_way(), and core::scoring::rna::StackElecEnergy::residue_pair_energy_one_way().

bool core::conformation::Residue::is_RNA ( ) const

inline

Returns true if this residue is a RNA residue.

References core::chemical::ResidueTypeBase::is_RNA(), and rsd_type_.

Referenced by core::scoring::methods::FreeDOF_Energy::accumulate_stack_energy(), core::import_pose::RNA_JumpMover::add_new_RNA_jump(), core::scoring::rna::RNA_SugarCloseEnergy::add_sugar_ring_closure_constraints(), protocols::rna::denovo::movers::RNA_Minimizer::apply(), core::pose::rna::RNA_SuiteName::assign(), core::conformation::Conformation::backbone_torsion_angle_atoms(), core::scoring::hbonds::calculate_intra_res_hbonds(), core::scoring::rna::RNA_FullAtomStackingEnergy::check_base_base_OK(), protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker::check_chain_closable_geometry(), protocols::stepwise::modeler::rna::check_for_messed_up_structure(), core::import_pose::RNA_JumpMover::check_forward_backward(), protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::check_moved(), core::scoring::rna::check_rna_loop(), protocols::stepwise::screener::TagDefinition::check_screen(), protocols::stepwise::modeler::rna::copy_all_o2prime_torsions(), core::pose::correctly_add_cutpoint_variants(), protocols::stepwise::modeler::rna::create_standard_o2prime_pack_task(), core::scoring::elec::FA_GrpElecEnergy::defines_score_for_residue_pair(), core::scoring::elec::FA_ElecEnergy::defines_score_for_residue_pair(), core::scoring::etable::BaseEtableEnergy< Derived >::determine_crossover_behavior(), protocols::rna::denovo::movers::RNA_DeNovoMasterMover::do_random_moves(), core::scoring::rna::RNA_TorsionPotential::eval_atom_derivative(), core::scoring::rna::RNA_FullAtomVDW_BasePhosphate::eval_atom_derivative(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::eval_intrares_derivatives(), core::scoring::rna::RNA_TorsionPotential::eval_intrares_energy(), core::scoring::methods::LK_PolarNonPolarEnergy::eval_intrares_energy(), core::scoring::rna::StackElecEnergy::eval_residue_pair_derivatives(), core::scoring::rna::RNA_LowResolutionPotential::eval_rna_base_pair_energy_one_way(), core::scoring::rna::RNP_LowResPotential::evaluate_rnp_base_pair_score(), core::scoring::rna::RNP_LowResPairDistPotential::evaluate_rnp_pair_dist_score(), core::scoring::rna::RNP_LowResStackData::evaluate_rnp_stack_xy_score(), core::scoring::elec::RNA_FA_ElecEnergy::evaluate_rotamer_background_energies(), protocols::pockets::GenPharmacophore::extract_Hbond_atoms_from_protein_rna_complex(), protocols::pockets::GenPharmacophore::extract_rna_rings_from_protein_rna_complex(), core::io::rna::RDAT::fill_header_information(), core::scoring::methods::FreeDOF_Energy::finalize_total_energy(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::finalize_total_energy(), core::scoring::dna::get_base_pair_stub_slow(), core::scoring::rna::RNA_FullAtomStackingEnergy::get_count_pair_function(), protocols::cluster::GatherPosesMover::get_distance_measure(), core::scoring::hbonds::get_hb_acc_chem_type(), core::scoring::hbonds::get_hb_don_chem_type(), core::scoring::magnesium::MgKnowledgeBasedPotential::get_mg_potential_gaussian_parameter(), core::scoring::magnesium::MgKnowledgeBasedPotential::get_mg_potential_indirect_gaussian_parameter(), protocols::rna::denovo::get_residues_within_dist_of_RNA(), core::chemical::rna::get_rna_base_centroid(), core::scoring::rna::chemical_shift::get_rna_base_coordinate_system_from_CS_params(), core::scoring::rna::RNA_LowResolutionPotential::get_rna_basepair_xy(), protocols::pockets::GenPharmacophore::get_RNAring_sasa(), protocols::rna::denovo::get_rnp_docking_fold_tree(), core::scoring::dna::get_z_axis(), protocols::simple_moves::ConstrainToIdealMover::i_want_this_atom_to_move(), protocols::stepwise::modeler::rna::o2prime::O2PrimePacker::initialize_o2prime_green_packer(), protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::initialize_phosphate_move_list(), protocols::toolbox::rigid_body::initialize_stub(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::insert_base_pair_jumps(), core::chemical::rna::is_base_phosphate_atom_pair(), core::scoring::is_protein_CA_or_equiv(), core::scoring::rna::RNA_BulgeEnergy::is_RNA_bulge(), core::pose::rna::make_phosphate_nomenclature_matches_mini(), protocols::stepwise::modeler::StepWiseMinimizer::move_side_chain(), protocols::rna::denovo::movers::RNA_Minimizer::packing_trials(), place(), core::scoring::UnfoldedStatePotential::pose_raw_unfolded_state_energymap(), protocols::fold_from_loops::NubInitioMover::post_process(), protocols::rna::denovo::movers::RNP_HighResMover::protein_sidechain_packing(), protocols::rna::denovo::movers::RNA_DeNovoMasterMover::randomize_rnp_rigid_body_orientations(), core::conformation::Conformation::rebuild_polymer_bond_dependent_atoms(), protocols::stepwise::modeler::rna::remove_virtual_O2Prime_hydrogen(), core::scoring::rna::RNA_FullAtomVDW_BasePhosphate::residue_energy(), core::scoring::methods::ReferenceEnergy::residue_energy(), core::scoring::rna::RNA_TorsionPotential::residue_pair_energy(), core::scoring::rna::RNA_VDW_Energy::residue_pair_energy(), core::scoring::magnesium::RNA_MgPointEnergy::residue_pair_energy(), core::scoring::rna::data::RNA_DataBackboneEnergy::residue_pair_energy(), core::scoring::rna::RNP_LowResPairDistEnergy::residue_pair_energy(), core::scoring::rna::RNP_LowResEnergy::residue_pair_energy(), core::scoring::rna::RNP_LowResStackEnergy::residue_pair_energy(), core::scoring::rna::RNA_FullAtomStackingEnergy::residue_pair_energy(), core::scoring::rna::RNA_LJ_BaseEnergy::residue_pair_energy(), core::scoring::elec::RNA_FA_ElecEnergy::residue_pair_energy(), core::scoring::elec::RNA_FA_ElecEnergy::residue_pair_energy_ext(), core::scoring::rna::StackElecEnergy::residue_pair_energy_ext(), core::scoring::magnesium::RNA_MgPointEnergy::residue_pair_energy_one_way(), core::scoring::rna::RNA_FullAtomStackingEnergy::residue_pair_energy_one_way(), core::scoring::rna::StackElecEnergy::residue_pair_energy_one_way(), core::pack::task::ResidueLevelTask_::ResidueLevelTask_(), core::scoring::rna::RNA_LowResolutionPotential::rna_backbone_backbone_pair_energy_one_way(), core::scoring::rna::RNA_LowResolutionPotential::rna_base_backbone_pair_energy_one_way(), core::scoring::rna::RNA_LowResolutionPotential::rna_repulsive_pair_energy_one_way(), protocols::rna::denovo::movers::RNA_DeNovoMasterMover::search_rigid_body_orientation(), core::conformation::setup_corresponding_atoms(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_fold_tree_legacy(), core::scoring::rna::RNP_LowResEnergy::setup_for_scoring(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_jumps(), protocols::stepwise::modeler::packer::StepWisePacker::setup_pack_task(), protocols::rna::denovo::movers::RNA_DeNovoMasterMover::setup_rna_protein_docking_mover(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_virtual_phosphate_variants(), core::import_pose::libraries::RNA_ChunkLibrary::update_atom_level_domain_map(), protocols::rna::denovo::movers::RNA_Minimizer::update_atom_level_domain_map_with_extra_minimize_res(), and core::scoring::carbon_hbonds::CarbonHBondEnergy::use_orientation_dep_rna_ch_o_bonds().

bool core::conformation::Residue::is_similar_aa ( Residue const &  other ) const

inline

Returns true if the aa residue types are the same.

References core::chemical::ResidueTypeBase::aa(), aa(), and rsd_type_.

bool core::conformation::Residue::is_similar_rotamer

(

Residue const &

other

)

const

Returns true if the chi angles of another residue all fall within 5 deg.

References core::chemical::ResidueTypeBase::aa(), aa(), chi(), chi_, core::chemical::ResidueTypeBase::name3(), name3(), and rsd_type_.

bool core::conformation::Residue::is_sri ( ) const

inline

Is this one of SRI's special heteropolymer building blocks?

References core::chemical::ResidueType::is_sri(), and rsd_type_.

bool core::conformation::Residue::is_surface ( ) const

inline

Returns true if this residue is a surface residue.

References core::chemical::ResidueType::is_surface(), and rsd_type_.

Referenced by protocols::vip::VIP_Mover::cull_mutatable_residues().

bool core::conformation::Residue::is_terminus ( ) const

inline

Returns true if the residue has a terminus property.

References core::chemical::ResidueType::is_terminus(), and rsd_type_.

Referenced by protocols::ligand_docking::MinimizeBackbone::add_cut_points(), protocols::simple_moves::PeptideStapleMover::apply(), protocols::anchored_design::AnchoredPerturbMover::apply(), protocols::anchored_design::AnchoredRefineMover::apply(), protocols::pockets::PocketGrid::autoexpanding_pocket_eval(), protocols::denovo_design::components::StructureData::check_improper_termini(), core::scoring::methods::RamachandranEnergy2B::eval_dof_derivative(), core::scoring::methods::RamachandranEnergy2B::eval_intrares_energy(), core::scoring::methods::RamaPreProEnergy::eval_intraresidue_dof_derivative(), core::scoring::Ramachandran::eval_rama_score_all(), core::scoring::Ramachandran2B::eval_rama_score_all(), core::scoring::Ramachandran::eval_rama_score_residue(), core::scoring::Ramachandran2B::eval_rama_score_residue(), core::scoring::Ramachandran::eval_rama_score_residue_nonstandard_connection(), protocols::analysis::LoopAnalyzerMover::find_positions(), core::scoring::P_AA::get_Paa_pp_deriv(), protocols::floppy_tail::FloppyTailMover::init_on_new_input(), protocols::cyclic_peptide::RamaMutationSelector::is_terminus(), core::scoring::P_AA::P_AA_pp_energy(), protocols::denovo_design::components::pose_matches_description(), core::scoring::Ramachandran2B::RamaE(), core::scoring::Ramachandran2B::RamaE_Lower(), core::scoring::Ramachandran2B::RamaE_Upper(), protocols::ligand_docking::LigandBaseProtocol::reorder_foldtree_around_mobile_regions(), protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue(), core::scoring::membrane::MPTerminiPenalty::residue_energy(), core::pose::symmetry::sealed_symmetric_fold_tree(), and core::scoring::MembranePotential::termini_penalty().

bool core::conformation::Residue::is_TNA ( ) const

inline

Returns true if this residue is a TNA residue.

References core::chemical::ResidueType::is_TNA(), and rsd_type_.

Referenced by core::scoring::rna::RNA_SugarCloseEnergy::add_sugar_ring_closure_constraints(), core::scoring::rna::RNA_FullAtomStackingEnergy::check_base_base_OK(), protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker::check_chain_closable_geometry(), protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker::check_chain_closable_geometry_strict(), core::scoring::rna::TNA_SuitePotential::eval_score(), protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker::get_C4_C3_distance_range(), core::scoring::rna::RNA_FullAtomStackingEnergy::get_count_pair_function(), and core::scoring::rna::RNA_FullAtomStackingEnergy::residue_pair_energy_one_way().

bool core::conformation::Residue::is_triazolemer ( ) const

inline

Returns true if and only if this residue is a triazolemer.

References core::chemical::ResidueType::is_triazolemer(), and rsd_type_.

bool core::conformation::Residue::is_upper_terminus ( ) const

inline

Return true if the residue has an upper terminus property.

References core::chemical::ResidueType::is_upper_terminus(), and rsd_type_.

Referenced by protocols::loops::add_single_cutpoint_variant(), protocols::frags::add_vall_cheating_fragments(), core::conformation::Conformation::align_virtual_atoms_in_carbohydrate_residue(), protocols::denovo_design::components::append_new_residues(), core::conformation::Conformation::append_polymer_residue_after_seqpos(), protocols::denovo_design::components::append_residues_from_template_segment(), protocols::protein_interface_design::movers::AddChainBreak::apply(), protocols::hybridization::MRMover::apply(), protocols::task_operations::DsspDesignOperation::apply(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::apply(), protocols::fldsgn::CircularPermutation::apply(), protocols::antibody_legacy::LoopRlxMover::apply(), protocols::flxbb::LayerDesignOperation::apply(), core::chemical::ICoorAtomID::atom_id(), protocols::idealize::basic_idealize(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::calc_dist(), core::scoring::membrane::MPResidueLipophilicityEnergy::calc_energy(), protocols::dna::DNAParameters::calculate(), protocols::antibody_legacy::CloseOneMover::close_one_loop_stem_helper(), core::scoring::packing::compute_holes_deriv_res(), core::scoring::packing::compute_holes_score_res(), connect_atom(), protocols::topology_broker::copy_internal_coords(), protocols::denovo_design::movers::AlignResiduesMover::copy_residue(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::correct_termini_derivatives(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::count_bb_atoms(), protocols::forge::methods::count_cutpoints(), protocols::relax::cyclize_pose(), determine_nonstandard_polymer_status(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd1(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd2(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd1(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd2(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_bond_energy(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_bond_length_derivs(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_improper_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_improper_energy(), core::scoring::OmegaTether::eval_omega_score_residue(), protocols::anchored_design::AnchoredDesignMover::filter(), protocols::forge::methods::find_cutpoint(), protocols::ligand_docking::LigandBaseProtocol::find_interface_backbone(), core::conformation::carbohydrates::find_seqpos_of_saccharides_child_residue_at(), protocols::generalized_kinematic_closure::general_set_psi(), core::conformation::get_anchor_atomno(), core::pose::motif::get_cterminal_peptide_bond_reference_frame(), core::pose::motif::get_cterminal_peptide_bond_reference_frame_atomids(), core::scoring::dna::get_DNA_backbone_bin(), core::scoring::hbonds::get_hb_acc_chem_type(), core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::get_psi_from_rsd(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_psi_from_rsd(), core::conformation::get_root_atomno(), protocols::sic_dock::get_termini_from_pose(), protocols::forge::methods::grow_right_r(), protocols::rbsegment_relax::guess_rbsegs_from_pose(), protocols::abinitio::abscript::RigidChunkCM::initialize(), protocols::match::upstream::OriginalBackboneBuildPoint::initialize_from_residue(), core::conformation::Conformation::insert_polymer_residue(), protocols::frags::insert_random_fragments_in_flexible_protein_regions(), core::conformation::carbohydrates::is_glycosidic_omega_torsion(), core::conformation::carbohydrates::is_glycosidic_phi_torsion(), core::conformation::carbohydrates::is_glycosidic_psi_torsion(), core::pose::carbohydrates::is_glycosidic_torsion(), core::scoring::Ramachandran::is_normally_connected(), protocols::loops::Loop::is_terminal(), core::pose::is_upper_terminus(), protocols::antibody_legacy::CDRH3Modeler::loop_centroid_relax(), protocols::antibody_legacy::CDRH3Modeler::loop_fa_relax(), protocols::denovo_design::loop_start_without_overlap(), protocols::forge::build::Bridge::modify_impl(), protocols::forge::build::SegmentRebuild::modify_impl(), protocols::forge::build::ConnectRight::modify_impl(), protocols::forge::build::SegmentInsert::modify_impl(), protocols::cryst::MakeLayerMover::place_near_origin(), protocols::cryst::MakeLatticeMover::place_near_origin(), protocols::denovo_design::components::pose_matches_description(), core::conformation::Conformation::prepend_polymer_residue_before_seqpos(), core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose(), core::scoring::methods::DNA_DihedralEnergy::residue_energy(), core::scoring::membrane::MPHelicalityEnergy::residue_energy(), core::scoring::methods::DNA_ReferenceEnergy::residue_pair_energy(), core::io::carbohydrates::residue_range_gws_string(), core::scoring::elec::FA_GrpElecEnergy::set_nres_mono(), core::scoring::elec::FA_ElecEnergy::set_nres_mono(), protocols::denovo_design::components::Segment::set_template_pose(), protocols::rbsegment_relax::setup_disconnected(), protocols::rbsegment_relax::setup_pose_rbsegs_keep_loops(), core::scoring::dna::DNA_DihedralPotential::skip_torsion(), and protocols::fldsgn::CircularPermutation::split_chains().

bool core::conformation::Residue::is_virtual ( Size const  atomno ) const

inline

Check if atom is virtual. AMW TODO: somehow SWA spends literally 3.7% of its time calling this function.

Note

A misnomer; this should really be called "is_virtual_atom()". ~Labonte

References core::chemical::ResidueType::atom_type(), core::chemical::AtomType::is_virtual(), and rsd_type_.

Referenced by core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_intra(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_one_way(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_one_way_bb_bb(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_one_way_sc(), core::import_pose::RNA_JumpMover::add_new_RNA_jump(), core::scoring::sc::ElectrostaticComplementarityCalculator::AddResidue(), core::scoring::sc::MolecularSurfaceCalculator::AddResidue(), core::scoring::MultipoleElecPotential::align_residue_multipole_axes(), core::scoring::electron_density_atomwise::ElectronDensityAtomwise::atom_gradient(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::atom_is_heavy(), protocols::stepwise::modeler::rna::base_atoms_square_deviation(), core::conformation::Conformation::bonded_neighbor_all_res(), protocols::recces::sampler::rna::calc_base_centroid_rmsd(), core::scoring::MultipoleElecPotential::calculate_res_res_fixed_fields_for_polarization(), core::scoring::MultipoleElecPotential::calculate_res_res_induced_fields_for_polarization(), protocols::stepwise::modeler::packer::check_o2prime_contact(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_acceptor_atom_energy(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_donor_atom_energy(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_polar_group_sol_energy(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_sho_acceptor_atom_energy(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_sho_donor_atom_energy(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_intra(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_one_way(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_one_way_bb_bb(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_one_way_sc(), core::scoring::saxs::FastSAXSEnergy::eval_atom_derivative(), core::scoring::rna::RNA_FullAtomVDW_BasePhosphate::eval_atom_derivative(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::eval_atom_energy(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::eval_intrares_derivatives(), core::scoring::magnesium::MgEnergy::eval_mg_interaction(), core::scoring::rna::StackElecEnergy::eval_residue_pair_derivatives(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::eval_residue_pair_derivatives(), core::scoring::SASAPotential::eval_residue_pair_derivatives(), core::scoring::VdWTinkerPotential::eval_residue_pair_derivatives(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::eval_residue_pair_derivatives_one_way(), protocols::scoring::InterchainPotential::evaluate_pair_and_vdw_score(), core::scoring::rna::RNA_VDW_Energy::evaluate_rnp_vdw_score(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::fast_full_atom_VDW_repulsion_screen(), core::conformation::Conformation::fill_missing_atoms(), protocols::scoring::VDW_GridEnergy::finalize_total_energy(), core::scoring::rna::StackElecEnergy::finalize_total_energy(), protocols::metal_interface::find_closest_atom(), protocols::magnesium::MgWaterHydrogenPacker::find_water_neighbor_vecs(), get_adjacent_heavy_atoms(), core::scoring::carbon_hbonds::CarbonHBondEnergy::get_atom_atom_carbon_hbond_energy(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_acceptor(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_donor(), core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::get_atom_atom_occ_solvation(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::get_atom_atom_occ_solvation(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::get_atom_lk_energy(), get_atoms_exocyclic_to_ring_atom(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::get_matching_res_in_VDW_rep_screen_pose(), protocols::magnesium::get_mg_ligands(), protocols::magnesium::SampleGrid::get_mg_positions(), core::scoring::rna::data::RNA_DMS_Potential::get_occupancy_densities(), core::scoring::MultipoleElecPotential::get_res_res_elecE(), core::scoring::SASAPotential::get_res_res_sasa(), core::scoring::VdWTinkerPotential::get_res_res_vdw(), core::scoring::MultipoleElecPotential::get_single_rotamer_effective_radii(), protocols::stepwise::modeler::rna::get_surrounding_O2prime_hydrogen(), protocols::simple_moves::ConstrainToIdealMover::i_want_this_atom_to_move(), core::scoring::rna::StackElecEnergy::is_rna_base(), protocols::stepwise::modeler::rna::is_virtual_base(), n_bonded_neighbor_all_res(), protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo::output_silent_file(), protocols::stepwise::modeler::rna::phosphate::PhosphateMover::pass_clash_check(), core::scoring::per_res_rms_at_corresponding_atoms_no_super(), protocols::stepwise::modeler::rna::phosphate_base_phosphate_square_deviation(), protocols::stepwise::modeler::rna::phosphate_square_deviation(), core::scoring::packing::PoseBalls::PoseBalls(), core::scoring::packing::PoseBallsLite::PoseBallsLite(), protocols::recces::print_base_centroid_atoms_for_rb_entropy(), protocols::toolbox::match_enzdes_util::replace_residue_keeping_all_atom_positions(), core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::res_res_occ_sol_one_way(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::res_res_occ_sol_one_way(), core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::residue_energy(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::residue_energy(), core::scoring::rna::RNA_VDW_Energy::residue_pair_energy(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::residue_pair_energy_ext(), core::scoring::rna::StackElecEnergy::residue_pair_energy_ext(), core::scoring::magnesium::RNA_MgPointEnergy::residue_pair_energy_one_way(), core::scoring::rna::RNA_FullAtomStackingEnergy::residue_pair_energy_one_way(), core::scoring::rna::StackElecEnergy::residue_pair_energy_one_way(), core::scoring::electron_density_atomwise::ElectronDensityAtomwise::residue_score(), core::scoring::methods::PoissonBoltzmannEnergy::revamp_weight_by_burial(), protocols::rotamer_recovery::RRProtocolRelax::run(), core::import_pose::libraries::ChunkSet::setup_atom_id_mask(), core::scoring::saxs::FastSAXSEnergy::setup_for_derivatives(), core::scoring::saxs::FastSAXSEnergy::setup_for_scoring(), core::scoring::setup_matching_atoms_with_given_names(), core::scoring::setup_matching_heavy_atoms(), protocols::stepwise::modeler::rna::setup_suite_atom_id_map(), show(), protocols::stepwise::modeler::rna::suite_square_deviation(), core::import_pose::libraries::RNA_ChunkLibrary::update_atom_level_domain_map(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::update_VDW_screen_bin(), and protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::VDW_rep_screen().

bool core::conformation::Residue::is_virtual_residue ( ) const

inline

Check if residue is virtual.

References core::chemical::ResidueType::is_virtual_residue(), and rsd_type_.

Referenced by protocols::mpi_refinement::add_init_dev_penalty(), core::io::pose_to_sfr::PoseToStructFileRepConverter::append_residue_info_to_sfr(), protocols::antibody::snugdock::SnugDockProtocol::apply(), protocols::scoring::Interface::calculate(), protocols::pose_creation::MergePDBMover::check_duplicate(), core::scoring::nmr::NMRDummySpinlabelEnsemble::clash_check(), protocols::simple_ddg::ddG::clean_pose(), protocols::simple_filters::TMsSpanMembraneFilter::compute(), protocols::ligand_docking::ga_ligand_dock::count_neighbors(), protocols::ligand_docking::ga_ligand_dock::count_neighbors_on_coord(), core::pose::rna::detect_sugar_contacts(), core::scoring::methods::MMTorsionEnergy::eval_intrares_derivatives(), core::scoring::methods::ProClosureEnergy::eval_intrares_derivatives(), core::scoring::methods::ProClosureEnergy::eval_intrares_energy(), core::scoring::OmegaTether::eval_omega_score_residue(), core::scoring::Ramachandran::eval_rama_score_all(), core::scoring::Ramachandran::eval_rama_score_residue(), core::scoring::methods::RingClosureEnergy::eval_residue_derivatives(), core::scoring::methods::AromaticBackboneRestraintEnergy::eval_residue_derivatives(), core::scoring::methods::carbohydrates::SugarBackboneEnergy::eval_residue_dof_derivative(), core::pack::dunbrack::cenrot::CenRotDunEnergy::eval_residue_dof_derivative(), core::scoring::rna::data::RNA_DMS_LowResolutionPotential::evaluate(), protocols::magnesium::SampleGrid::figure_out_box_bounds(), core::scoring::fill_rmsd_coordinates(), protocols::topology_broker::MembraneTopologyClaimer::generate_claims(), core::pose::full_model_info::get_move_elements_from_full_model_info_const(), protocols::simple_filters::ResidueDepthFilter::get_n8(), core::scoring::P_AA::get_Paa_pp_deriv(), protocols::simple_filters::ResidueDepthCalculator::get_pose_crd_and_index(), protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::get_possible_hbond_acceptors(), protocols::electron_density::DockIntoDensityMover::get_spectrum(), protocols::loops::has_severe_pep_bond_geom_issues(), protocols::simple_filters::ResidueDepthFilter::make_context(), protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::moves_for_pose(), core::scoring::P_AA::P_AA_pp_energy(), core::scoring::per_res_rms_at_corresponding_atoms_no_super(), protocols::stepwise::modeler::rna::phosphate_base_phosphate_square_deviation(), protocols::nmr::pcs::PCSLigandTransformMover::reset_grid_and_bounding_box(), core::scoring::methods::RingClosureEnergy::residue_energy(), core::scoring::methods::AromaticBackboneRestraintEnergy::residue_energy(), core::pack::dunbrack::DunbrackEnergy::residue_energy(), core::scoring::methods::carbohydrates::SugarBackboneEnergy::residue_energy(), core::scoring::rna::data::RNA_DataBackboneEnergy::residue_pair_energy(), core::scoring::methods::ProClosureEnergy::residue_pair_energy(), core::scoring::methods::PoissonBoltzmannEnergy::revamp_weight_by_burial(), protocols::topology_broker::TMHTopologySamplerClaimer::set_pose_torsions(), protocols::carbohydrates::GlycanSampler::setup_default_task_factory(), and core::pose::rna::virtualize_free_rna_moieties().

bool core::conformation::Residue::is_water ( ) const

inline

Returns true if this residue is water.

References core::chemical::ResidueType::is_water(), and rsd_type_.

Referenced by protocols::task_operations::RestrictToInterfaceVectorOperation::apply(), protocols::simple_task_operations::RestrictToInterface::apply(), protocols::simple_ddg::ddG::clean_pose(), protocols::simple_ddg::ddG::do_minimize(), protocols::simple_ddg::ddG::duplicate_waters_across_jump(), protocols::simple_moves::ExplicitWaterMover::find_closest(), protocols::scoring::Interface::protein_calculate(), core::scoring::GenericBondedPotential::residue_derivatives(), core::scoring::GenericBondedPotential::residue_energy(), core::scoring::GenericBondedPotential::setup_for_scoring(), and protocols::simple_ddg::ddG::setup_solvated_task().

Size core::conformation::Residue::last_backbone_atom ( ) const

inline

Returns the index number of the last backbone heavyatom.

Note

The heavyatoms come first in atom ordering, first backbone then sidechain, hydrogens follow the order of their attached heavyatom.

example(s): residue.last_backbone_atom() See also: Residue Residue.atom Residue.atoms Residue.first_sidechain_atom Pose

References core::chemical::ResidueType::last_backbone_atom(), and rsd_type_.

Referenced by core::scoring::constraints::add_coordinate_constraints(), core::scoring::carbon_hbonds::CarbonHBondEnergy::bb_bb_carbon_hbond_one_way(), core::scoring::carbon_hbonds::CarbonHBondEnergy::bb_sc_carbon_hbond_one_way(), protocols::match::bump_grid_to_enclose_residue_backbone(), protocols::ligand_docking::ga_ligand_dock::GridScorer::calculate_grid(), protocols::constraint_generator::CoordinateConstraintGenerator::create_residue_constraints(), protocols::ligand_docking::ga_ligand_dock::GridScorer::debug_deriv(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::define_active_virtual_sites(), protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), core::import_pose::atom_tree_diffs::dump_atom_tree_diff(), core::scoring::saxs::FastSAXSEnergy::eval_atom_derivative(), core::scoring::electron_density::FastDensEnergy::eval_residue_pair_derivatives(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_torsion(), protocols::match::fill_grid_with_backbone_heavyatom_spheres(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_1b_energy(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_2b_energy(), protocols::rna::denovo::movers::RNA_HelixMover::get_backbone_centroid(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_grid_atomtypes(), protocols::simple_filters::ResidueDepthCalculator::get_pose_crd_and_index(), core::scoring::inline_residue_atom_pair_energy_backbone_backbone(), core::scoring::inline_residue_atom_pair_energy_sidechain_backbone(), core::pack::task::residue_selector::is_sc_bb_clash(), core::scoring::electron_density::ElectronDensity::matchRes(), core::scoring::electron_density::ElectronDensity::matchResFast(), core::pose::PDBInfo::replace_res_remap_bfactors(), core::scoring::methods::PoissonBoltzmannEnergy::revamp_weight_by_burial(), core::import_pose::atom_tree_diffs::rms_error_with_noise(), core::scoring::carbon_hbonds::CarbonHBondEnergy::sc_bb_carbon_hbond_one_way(), core::scoring::carbon_hbonds::CarbonHBondEnergy::sc_sc_carbon_hbond_one_way(), protocols::qsar::scoring_grid::AtrGrid::set_protein_rings(), core::scoring::saxs::FastSAXSEnergy::setup_for_derivatives(), and core::scoring::saxs::FastSAXSEnergy::setup_for_scoring().

chemical::ResidueConnection const& core::conformation::Residue::lower_connect ( ) const

inline

Returns this residue's lower_connection a ResidueConnection has internal coords info on how to build the atom in the previous residue which connects to this residue.

References core::chemical::ResidueType::lower_connect(), and rsd_type_.

Referenced by core::conformation::Conformation::append_polymer_residue_after_seqpos(), core::conformation::Conformation::append_residue_by_bond(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd1(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd2(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_bond_length_derivs(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_improper_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_improper_energy(), core::scoring::methods::CartesianBondedEnergy::eval_intrares_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_intrares_energy(), protocols::loops::loop_closure::ccd::get_deviation(), protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger::KIC_loop_close(), core::conformation::symmetry::SymmetricConformation::prepend_polymer_residue_before_seqpos(), and core::conformation::Conformation::prepend_polymer_residue_before_seqpos().

Size core::conformation::Residue::lower_connect_atom ( ) const

inline

Returns the index number of this residue's atom which connects to the residue before it in sequence.

Note

: polymers only, example: for an amino acid, residue.lower_connect_atom() = atom_index("N")

example(s): residue.lower_connect_atom() See also: Residue Residue.atom Residue.atoms Residue.upper_connect_atom Pose

References core::chemical::ResidueType::lower_connect_atom(), and rsd_type_.

Referenced by protocols::forge::methods::add_cutpoint_variants(), protocols::denovo_design::add_cutpoints(), protocols::loops::add_single_cutpoint_variant(), core::conformation::Conformation::append_residue(), core::conformation::Conformation::append_residue_by_bond(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::idealize::basic_idealize(), protocols::LoopRebuild::build_loop_with_ccd_closure(), connect_atom(), core::pose::declare_cutpoint_chemical_bond(), protocols::loophash::FastGapMover::find_next_gap(), core::conformation::get_anchor_atomno(), core::conformation::get_root_atomno(), core::scoring::methods::lower_upper_connected_across_cutpoint(), protocols::forge::methods::make_star_foldtree(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::model_loop(), protocols::denovo_design::movers::new_jump_and_cutpoint(), and protocols::loops::set_loop_cutpoint_in_pose_fold_tree().

Size core::conformation::Residue::mainchain_atom ( Size const  i ) const

inline

Returns the atom index of the residue's ith mainchain atom.

References core::chemical::ResidueType::mainchain_atom(), and rsd_type_.

Referenced by core::scoring::MultipoleElecPotential::align_residue_multipole_axes(), core::conformation::Conformation::backbone_torsion_angle_atoms(), core::conformation::get_anchor_atomno(), protocols::loops::loop_closure::ccd::CCDLoopClosureMover::get_anchors(), core::conformation::get_root_atomno(), core::conformation::Conformation::set_torsion(), protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::store_target_icoors(), and core::kinematics::jacobian::ModuleType1::update_screw_vectors().

AtomIndices const& core::conformation::Residue::mainchain_atoms ( ) const

inline

Returns the AtomIndices of this residue's mainchain atoms.

References core::chemical::ResidueType::mainchain_atoms(), and rsd_type_.

Referenced by core::scoring::MultipoleElecPotential::align_residue_multipole_axes(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_loop_bump_check(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_perturb_backbone_by_bins(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_randomize_backbone_by_bins(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_set_backbone_bin(), core::conformation::Conformation::backbone_torsion_angle_atoms(), protocols::loops::loop_closure::ccd::CCDLoopClosureMover::compute_closure_metrics(), core::conformation::Conformation::debug_residue_torsions(), core::scoring::methods::LinearChainbreakEnergy::do_score_dev(), core::scoring::methods::LinearChainbreakEnergy::do_score_ovp(), core::scoring::methods::ChainbreakEnergy::eval_atom_derivative(), core::scoring::methods::AromaticBackboneRestraintEnergy::eval_residue_derivatives(), core::scoring::methods::LinearChainbreakEnergy::finalize_total_energy(), core::conformation::get_anchor_atomno(), protocols::loops::loop_closure::ccd::CCDLoopClosureMover::get_anchors(), protocols::loops::loop_closure::ccd::get_deviation(), core::conformation::get_root_atomno(), core::pose::rna::get_stub_stub(), protocols::loops::loop_closure::ccd::CCDLoopClosureMover::get_torsion_axis(), protocols::relax::RelaxProtocolBase::initialize_movemap(), core::pose::rna::RNA_IdealCoord::is_torsion_exists(), core::conformation::Conformation::set_torsion(), core::conformation::setup_corresponding_atoms(), and core::conformation::setup_links().

Real core::conformation::Residue::mainchain_torsion ( Size const  torsion ) const

inline

Returns a specific mainchain torsion angle for this residue example: mainchain_torsion(2) will be the psi angle for an amino acid.

example(s): residue.mainchain_torsion(2) See also: Residue Pose Pose.omega Pose.phi Pose.psi

References mainchain_torsions_.

Referenced by core::scoring::rna::RNA_SugarCloseEnergy::add_sugar_ring_closure_constraints(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_backbone_bin(), protocols::simple_moves::apply_ideal_coordinates_for_alternative_pucker(), core::pose::rna::RNA_SuiteName::assign(), protocols::pose_metric_calculators::RotamerRecovery::bb_bins_from_pose(), core::pack::rotamer_set::ContinuousRotamerSet::build_rotamers(), core::pose::rna::RNA_SuiteName::closest_by_dist4(), core::pose::rna::RNA_SuiteName::closest_suite(), protocols::stepwise::modeler::rna::create_rotamer_string(), core::conformation::Conformation::debug_residue_torsions(), core::io::raw_data::DecoyStruct::DecoyStruct(), protocols::dna::DNABase::DNABase(), core::scoring::rna::RNA_TorsionPotential::eval_atom_derivative(), core::scoring::dna::DNABFormPotential::eval_dna_bform_bb_torsion_score_residue(), core::scoring::dna::DNA_DihedralPotential::eval_harmonic_backbone_torsion_score_and_deriv(), core::scoring::methods::CartesianBondedEnergy::eval_intrares_derivatives(), core::scoring::rna::RNA_TorsionPotential::eval_intrares_energy(), core::scoring::methods::CartesianBondedEnergy::eval_intrares_energy(), core::scoring::methods::RamaPreProEnergy::eval_intraresidue_dof_derivative(), core::scoring::methods::CartesianBondedEnergy::eval_intraresidue_dof_derivative(), core::scoring::OmegaTether::eval_omega_score_residue(), core::scoring::Ramachandran::eval_rama_score_residue(), core::scoring::Ramachandran2B::eval_rama_score_residue(), core::scoring::methods::OmegaTetherEnergy::eval_residue_dof_derivative(), core::scoring::methods::CartesianBondedEnergy::eval_residue_pair_derivatives_sorted(), protocols::indexed_structure_store::extract_residue_entry(), core::io::silent::ProteinSilentStruct_Template< T >::fill_struct(), protocols::topology_broker::fix_mainchain_connect(), protocols::abinitio::abscript::fix_mainchain_connect(), core::scoring::dna::get_DNA_backbone_bin(), core::scoring::P_AA::get_Paa_pp_deriv(), core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::get_phi_from_rsd(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_phi_from_rsd(), core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::get_psi_from_rsd(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_psi_from_rsd(), core::chemical::rna::get_residue_pucker_state(), core::scoring::dna::get_sugar_torsions(), protocols::match::upstream::OriginalBackboneBuildPoint::initialize_from_residue(), protocols::ligand_docking::ga_ligand_dock::GAOptimizer::initialize_rotamer_set_and_scores(), core::pose::Pose::mu(), core::pose::Pose::omega(), core::scoring::P_AA::P_AA_pp_energy(), core::pose::Pose::phi(), protocols::stepwise::legacy::modeler::rna::print_backbone_torsions(), protocols::stepwise::modeler::rna::print_torsion_info(), core::pose::Pose::psi(), core::scoring::Ramachandran2B::RamaE(), core::scoring::Ramachandran2B::RamaE_Lower(), core::scoring::Ramachandran2B::RamaE_Upper(), protocols::features::ProteinResidueConformationFeatures::report_features(), protocols::features::ResidueConformationFeatures::report_features(), protocols::features::ProteinBackboneTorsionAngleFeatures::report_features(), core::scoring::methods::OmegaTetherEnergy::residue_energy(), core::scoring::methods::DNA_DihedralEnergy::residue_energy(), core::scoring::rna::RNA_TorsionPotential::residue_pair_energy(), core::scoring::methods::CartesianBondedEnergy::residue_pair_energy_sorted(), protocols::stepwise::sampler::screener::RNA_TorsionScreener::screen(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::storeposedata(), and core::pose::Pose::theta().

utility::vector1< Real > const& core::conformation::Residue::mainchain_torsions ( ) const

inline

Returns the mainchain torsion angles of this residue (const)

example(s): residue.mainchain_torsions() See also: Residue Pose Pose.omega Pose.phi Pose.psi

References mainchain_torsions_.

Referenced by protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_pose(), protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_wholepose(), protocols::ncbb::SecStructMinimizeMover::apply(), protocols::cyclic_peptide::RamaMutationSelector::apply(), protocols::simple_moves::bin_transitions::InitializeByBins::apply(), protocols::simple_moves::bin_transitions::PerturbByBins::apply(), protocols::symmetry::SetupNCSMover::apply(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_backbone_bin(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_copy_backbone_dihedrals(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_rama_prepro_check(), core::conformation::Conformation::backbone_torsion_angle_atoms(), protocols::match::upstream::ProteinUpstreamBuilder::build(), core::pack::rotamer_set::RotamerSet_::build_optimize_H_rotamers(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::calc_dist(), protocols::minimization_packing::GreenPacker::compare_input_pose_geometry_to_reference(), protocols::helical_bundle::copy_helix_dihedrals(), protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::figure_out_movemap(), core::io::silent::RNA_SilentStruct::fill_struct(), core::scoring::bin_transitions::BinTransitionCalculator::find_data_and_bin(), core::pack::interaction_graph::SymmOnTheFlyNode::get_rotamer(), core::pack::dunbrack::DunbrackEnergy::get_scratch_index(), protocols::helical_bundle_predict::HBPHelix::get_torsions_for_helix(), core::scoring::bin_transitions::BinTransitionData::in_bin_i(), core::scoring::bin_transitions::BinTransitionData::in_bin_iplus1(), protocols::cyclic_peptide::CycpepSymmetryFilter::mainchain_torsions_differ(), protocols::make_rot_lib::MakeRotLibMover::minimize_rotamer(), core::scoring::bin_transitions::BinTransitionCalculator::p_i_given_iplus1(), core::scoring::bin_transitions::BinTransitionCalculator::p_iplus1_given_i(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::pose_from_posedata(), core::scoring::bin_transitions::BinTransitionCalculator::random_mainchain_torsions_from_bin(), core::scoring::bin_transitions::BinTransitionCalculator::random_mainchain_torsions_from_bins(), Residue(), core::scoring::methods::AromaticBackboneRestraintEnergy::residue_energy(), protocols::dna::PDBOutput::residues_are_different(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::RotamericSingleResidueDunbrackLibrary(), core::conformation::Conformation::set_torsion(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_chainbreak_variants(), core::pose::toolbox::AtomLevelDomainMap::setup_movemap(), core::pack::rotamer_set::RotamerSubset::show(), core::pack::rotamer_set::RotamerSet_::show(), protocols::minimization_packing::GreenPacker::store_reference_pose_geometry(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::storeposedata(), core::conformation::Conformation::update_residue_torsions(), protocols::comparative_modeling::features::TorsionFeature::values_from_pose(), and protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::which_torsions().

utility::vector1< Real >& core::conformation::Residue::mainchain_torsions ( )

inline

Returns the mainchain torsion angles of this residue (non-const)

References mainchain_torsions_.

void core::conformation::Residue::mainchain_torsions ( utility::vector1< Real > const &  torsions )

inline

Sets the mainchain torsion angles of this residue to <torsions>

example(s): residue.mainchain_torsions() See also: Residue Pose Pose.set_omega Pose.set_phi Pose.set_psi

References mainchain_torsions_.

void core::conformation::Residue::mark_connect_incomplete

(

Size

resconn_index

)

References connect_map_, and connections_to_residues_.

Referenced by core::conformation::Conformation::sever_chemical_bond().

bool core::conformation::Residue::mirrored_relative_to_type ( ) const

inline

Is this residue mirrored relative to its coordinates in the ResidueType?

Only used for achiral residues like glycine in the context of mirror symmetry and other mirror-image structures.

References mirrored_relative_to_type_.

Referenced by Residue(), core::scoring::methods::RamachandranEnergy::residue_energy(), and show().

bool core::conformation::Residue::misplaced ( ) const

inline

Return whether or not the Residue was incorrectly oriented and placed within the polymer when created.

References misplaced_.

std::string const& core::conformation::Residue::mm_atom_name ( Size const  atom ) const

inline

Returns the mm_atom_name of this residue's atom with index number <atom>

References core::chemical::ResidueType::mm_name(), and rsd_type_.

Size core::conformation::Residue::n_bonded_neighbor_all_res	(	core::Size const	atomno,
		bool	virt = false
	)		const

Returns the number of atoms bonded to <atomno> in all residues?

determine how many atoms n the residue and adjacent residues are bonded to the given atom (by default, intraresidue virtual atoms are excluded)

References bonded_neighbor(), connection_incomplete(), is_virtual(), n_possible_residue_connections(), and residue_connect_atom_index().

Referenced by protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::recompute(), and protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::recompute().

core::Size core::conformation::Residue::n_current_residue_connections

(

)

const

Returns the number of ResidueConnections on this residue including polymeric residue connections. This is the total number of actual connections to other residues. The index here does not nessessarily match with the connection index as n_possible_residue_connections does!!!!

References connected_residue_at_resconn(), and n_possible_residue_connections().

Referenced by core::conformation::carbohydrates::fill_downstream_children_res_and_tips(), core::pose::carbohydrates::get_resnums_in_leaf(), and core::pose::carbohydrates::get_resnums_in_leaf_on_the_fly().

Size core::conformation::Residue::n_hbond_acceptors ( ) const

inline

number of hbond_donors

References core::chemical::ResidueType::n_hbond_acceptors(), and rsd_type_.

Referenced by core::pose::num_hbond_acceptors().

Size core::conformation::Residue::n_hbond_donors ( ) const

inline

number of hbond_donors

References core::chemical::ResidueType::n_hbond_donors(), and rsd_type_.

Referenced by core::pose::num_hbond_donors().

Size core::conformation::Residue::n_mainchain_atoms ( ) const

inline

Returns the number of the residue's mainchain atoms.

References core::chemical::ResidueType::mainchain_atoms(), and rsd_type_.

Referenced by protocols::helical_bundle::align_mainchain_atoms_of_residue_range(), protocols::helical_bundle::FitSimpleHelix::apply(), protocols::helical_bundle::copy_helix_bondangles(), protocols::helical_bundle::copy_helix_bondlengths(), core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms(), protocols::helical_bundle::generate_atom_positions(), core::conformation::get_anchor_atomno(), core::conformation::carbohydrates::get_downstream_residue_that_this_torsion_moves(), core::conformation::get_root_atomno(), protocols::mpi_refinement::get_touched_res(), core::conformation::carbohydrates::is_glycosidic_omega_torsion(), core::conformation::carbohydrates::is_glycosidic_phi_torsion(), core::conformation::carbohydrates::is_glycosidic_psi_torsion(), and core::pose::carbohydrates::is_glycosidic_torsion().

Size core::conformation::Residue::n_non_polymeric_residue_connections ( ) const

inline

Returns the number of non-polymeric ResidueConnections on this residue.

References core::chemical::ResidueType::n_non_polymeric_residue_connections(), and rsd_type_.

Referenced by core::conformation::Conformation::branch_connection_torsion_angle_atoms(), core::conformation::carbohydrates::get_downstream_residue_that_this_torsion_moves(), protocols::denovo_design::components::StructureDataFactory::infer_from_pose(), core::conformation::carbohydrates::is_glycosidic_omega_torsion(), core::conformation::carbohydrates::is_glycosidic_phi_torsion(), core::conformation::carbohydrates::is_glycosidic_psi_torsion(), core::pose::carbohydrates::is_glycosidic_torsion(), core::conformation::Conformation::show_residue_connections(), and core::pack::rotamers::SingleResidueRotamerLibrary::virtual_sidechain().

Size core::conformation::Residue::n_nus ( ) const

inline

Return the number of nu (internal ring) angles this residue has.

Example: residue.n_nus()
See also:
Residue
Residue.nu
Residue.nus
Pose.set_ring_conformation
Pose
Pose.nu

References core::chemical::ResidueType::n_nus(), and rsd_type_.

Referenced by Residue(), ring_conformer(), update_nus(), and core::conformation::Conformation::update_residue_torsions().

Size core::conformation::Residue::n_orbitals ( ) const

inline

Returns the number of orbitals in this residue.

References core::chemical::ResidueTypeBase::n_orbitals(), and rsd_type_.

Size core::conformation::Residue::n_polymeric_residue_connections ( ) const

inline

Returns the number of polymeric ResidueConnections on this residue.

References core::chemical::ResidueType::n_polymeric_residue_connections(), and rsd_type_.

Referenced by core::conformation::Conformation::branch_connection_torsion_angle_atoms(), core::conformation::carbohydrates::get_downstream_residue_that_this_torsion_moves(), core::conformation::carbohydrates::is_glycosidic_omega_torsion(), core::conformation::carbohydrates::is_glycosidic_phi_torsion(), core::conformation::carbohydrates::is_glycosidic_psi_torsion(), core::pose::carbohydrates::is_glycosidic_torsion(), core::scoring::polymeric_termini_incomplete(), core::pose::carbohydrates::set_glycan_iupac_bb_torsions(), and core::conformation::Conformation::show_residue_connections().

Size core::conformation::Residue::n_possible_residue_connections ( ) const

inline

Returns the number of ResidueConnections on this residue including polymeric residue connections. This is the total number of possible connections from the ResidueType.

References core::chemical::ResidueType::n_possible_residue_connections(), and rsd_type_.

Referenced by protocols::generalized_kinematic_closure::GeneralizedKIC::addloopgeometry(), protocols::generalized_kinematic_closure::GeneralizedKIC::addtailgeometry(), protocols::generalized_kinematic_closure::GeneralizedKIC::addupperanchor(), core::pose::Pose::append_residue_by_atoms(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_loop_bump_check(), core::conformation::Conformation::bonded_neighbor_all_res(), core::scoring::mm::connection_indices(), copy_residue_connections(), protocols::generalized_kinematic_closure::correct_polymer_dependent_atoms_in_pose_segment(), core::scoring::trie::create_cpdata_correspondence_for_rotamer(), core::conformation::Conformation::declare_chemical_bond(), core::pose::symmetry::extract_asymmetric_unit(), core::conformation::carbohydrates::fill_downstream_children_res_and_tips(), protocols::ligand_docking::LigandDesign::fragments_to_string(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_connectivity_annotation_info(), core::conformation::carbohydrates::get_glycan_connecting_protein_branch_point(), core::conformation::carbohydrates::get_linkage_position_of_saccharide_residue(), protocols::cyclic_peptide::crosslinker::TBMB_Helper::get_linker_index_asymmetric(), protocols::cyclic_peptide::crosslinker::TBMB_Helper::get_linker_indices_symmetric(), protocols::cyclic_peptide::crosslinker::TMA_Helper::get_sidechain_connect_index(), has_incomplete_connection(), protocols::generalized_kinematic_closure::GeneralizedKIC::infer_anchor_connIDs(), protocols::denovo_design::components::StructureDataFactory::infer_from_pose(), core::scoring::PolymerBondedEnergyContainer::initialize_peptide_bonded_pair_indices(), core::scoring::PolymerBondedEnergyContainer::is_valid(), n_bonded_neighbor_all_res(), n_current_residue_connections(), protocols::cyclic_peptide::PeptideStubMover::rebuild_atoms(), core::pose::carbohydrates::set_glycan_iupac_bb_torsions(), core::conformation::setup_corresponding_atoms(), core::conformation::Conformation::show_residue_connections(), update_connections_to_residues(), and core::conformation::carbohydrates::GlycanNode::update_connectivity_data().

core::Size core::conformation::Residue::n_virtual_atoms ( ) const

inline

Returns the number of virtual atoms in this residue.

This calls the function with the same name in ResidueType, which counts virts on the fly (memory-efficient, performance-poor). This being the case, don't call this function repeatedly! Call it once, and store the return value!

Author

Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References core::chemical::ResidueType::n_virtual_atoms(), and rsd_type_.

chemical::AA const& core::conformation::Residue::na_analogue ( ) const

inline

Returns the nucleic acid type to be used for fragment sampling.

References core::chemical::ResidueTypeBase::na_analogue(), and rsd_type_.

Referenced by core::scoring::rna::check_watson_crick_sequence(), and core::scoring::rna::get_rna_motifs().

std::string const& core::conformation::Residue::name ( ) const

inline

Returns this residue's ResidueType name.

Note

: for proteins, this will be the amino acid type and variant type

References core::chemical::ResidueTypeBase::name(), and rsd_type_.

Referenced by core::pose::motif::a(), protocols::relax::add_coordinate_constraint_func_atoms(), protocols::protein_interface_design::movers::add_coordinate_constraints(), protocols::seeded_abinitio::add_coordinate_constraints(), core::pose::ncbb::add_oop_constraint(), core::pose::ncbb::add_triazole_constraint(), protocols::topology_broker::MembraneTopologyClaimer::addVirtualResAsRootMembrane(), core::scoring::MultipoleElecPotential::align_residue_multipole_axes(), protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::analyze_trajectory(), annotated_name(), core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::append_metal_vsites(), core::conformation::Conformation::append_residue(), protocols::simple_moves::hbs::HbsPatcher::apply(), protocols::simple_moves::a3b_hbs::A3BHbsPatcher::apply(), protocols::simple_filters::ResidueCountFilter::apply(), protocols::ligand_docking::CompleteConnectionsFilter::apply(), core::select::residue_selector::ResidueNameSelector::apply(), protocols::cyclic_peptide::RamaMutationSelector::apply(), protocols::denovo_design::residue_selectors::NamedSegmentSelector::apply(), protocols::enzdes::GenerateStoredRBConfs::apply(), protocols::simple_filters::ResidueDepthFilter::apply(), protocols::vip::are_seqs_different(), core::scoring::VdWTinkerPotential::assign_residue_amoeba_type(), core::scoring::MultipoleElecPotential::assign_residue_amoeba_type(), core::chemical::ICoorAtomID::atom_id(), core::scoring::dna::DNA_BasePotential::base_string(), protocols::match::downstream::ClassicMatchAlgorithm::build(), core::pack::rotamer_set::RotamerSet_::build_dependent_rotamers(), core::pack::rotamer_set::RotamerSet_::build_filtered_tp3_water_rotamers(), core::pack::rotamer_set::build_moving_O_bridge_waters(), core::pack::rotamer_set::build_moving_O_water_rotamers_dependent(), core::pack::rotamer_set::build_moving_O_water_rotamers_independent(), core::scoring::lkball::build_optimal_water_Os_on_acceptor(), core::pack::rotamer_set::RotamerSet_::build_optimize_H_rotamers(), core::pack::rotamer_set::RotamerSet_::build_rotamers(), core::pack::rotamer_set::RotamerSet_::build_rotamers_for_concrete(), core::pack::rotamer_set::build_single_edge_waters(), core::pack::rotamer_set::RotamerSet_::build_tp3_water_rotamers(), core::pack::rotamer_set::RotamerSet_::build_virtualizable_rotatable_water_rotamers(), core::simple_metrics::per_residue_metrics::WaterMediatedHbondMetric::calculate(), protocols::denovo_design::DisulfidizeMover::check_residue_type(), protocols::constraint_generator::HydrogenBondConstraintGenerator::choose_atoms(), protocols::simple_filters::ResidueCountFilter::compute(), protocols::denovo_design::filters::SSShapeComplementarityFilter::compute_from_selector(), protocols::vip::VIP_Mover::compute_number_cavities(), core::pack::rotamer_set::RotamerSet_::compute_one_body_energies(), protocols::constraint_generator::compute_ref_atom(), protocols::denovo_design::filters::PreProlineFilter::compute_simple(), connection_distance(), core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms(), core::scoring::hbonds::HBondEnergy::create_rotamer_trie(), core::scoring::trie::create_trie(), protocols::md::CartesianMD::cst_on_pose_dynamic(), protocols::md::CartesianMD::cst_on_pose_simple(), core::pack::rotamers::SingleResidueRotamerLibrary::current_rotamer(), core::conformation::Conformation::declare_chemical_bond(), protocols::simple_moves::ExplicitWaterMover::delete_waters(), protocols::simple_moves::PeptideStapleMover::derive_staple_constraints_(), core::conformation::Conformation::detect_bonds(), protocols::jobdist::PlainPdbJobDistributor::dump_scores(), protocols::hydrate::enforce_all_waters(), core::scoring::methods::SuckerEnergy::eval_atom_derivative(), core::scoring::methods::Fa_MbsolvEnergy::eval_intrares_energy(), core::scoring::methods::GenericBondedEnergy::eval_intrares_energy(), core::scoring::methods::PointWaterEnergy::eval_intrares_energy(), core::scoring::Ramachandran2B::eval_rama_score_all(), core::scoring::methods::AromaticBackboneRestraintEnergy::eval_residue_derivatives(), core::scoring::methods::PointWaterEnergy::eval_residue_pair_derivatives(), core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::eval_rotameric_energy_deriv(), core::scoring::FACTSPotential::evaluate_nonpolar_energy(), core::scoring::FACTSPotential::evaluate_polar_energy(), core::pose::copydofs::CopyDofs::figure_out_dofs(), core::conformation::Conformation::fill_missing_atoms(), fill_missing_atoms(), core::io::silent::BinarySilentStruct::fill_pose(), core::scoring::MultipoleElecPotential::find_params_and_neighbors(), protocols::ligand_docking::LigandDesign::fragments_to_string(), core::scoring::loop_graph::get_6D_trans_rot_potential_evaluator(), core::scoring::rna::get_bin(), protocols::vip::VIP_Mover::get_cavity_positions(), protocols::vip::VIP_Report::get_GOE_packstat_report(), protocols::vip::VIP_Report::get_GOE_relaxed_report(), protocols::vip::VIP_Report::get_GOE_repack_report(), core::scoring::hbonds::get_hb_acc_chem_type(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_link_record(), protocols::hydrate::get_ready_for_sew_packing(), protocols::stepwise::sampler::copy_dofs::ResidueAlternativeStepWiseSampler::get_residue_at_origin_with_matching_type(), core::chemical::rna::get_rna_base_centroid(), protocols::simple_moves::ExplicitWaterMover::get_water_recovery(), core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_pose_energies_table(), protocols::ligand_docking::has_incomplete_connections(), protocols::hydrate::hydrate_cavities(), core::scoring::hbonds::identify_hbonds_1way(), core::scoring::hbonds::identify_hbonds_1way_membrane(), core::scoring::MultipoleElecResidueInfo::initialize(), protocols::flexpack::interaction_graph::FlexbbInteractionGraph::initialize(), protocols::match::downstream::LigandConformerBuilder::initialize_conformers(), protocols::topology_broker::TopologyBroker::initialize_cuts(), protocols::match::downstream::LigandConformerBuilder::initialize_from_residue(), protocols::stepwise::sampler::copy_dofs::ResidueAlternativeStepWiseSampler::initialize_residues_for_type(), core::scoring::inline_residue_atom_pair_energy(), protocols::features::ResidueFeatures::insert_residue_rows(), inter_residue_connection_partner(), protocols::toolbox::match_enzdes_util::EnzConstraintParameters::make_constraint_covalent(), protocols::rotamer_recovery::RRComparerAutomorphicRMSD::measure_rotamer_recovery(), protocols::rotamer_recovery::RRComparerElecDensDiff::measure_rotamer_recovery(), protocols::rotamer_recovery::RRComparerRotBins::measure_rotamer_recovery(), protocols::rotamer_recovery::RRComparerChiDiff::measure_rotamer_recovery(), protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::moves_for_pose(), protocols::denovo_design::movers::new_jump_and_cutpoint(), orient_onto_residue(), protocols::hydrate::place_de_novo_wat_at_anchor(), protocols::simple_moves::CopyDofMover::pose_string(), core::conformation::print_atom(), protocols::hydrate::print_residues_near_water(), protocols::forge::remodel::RemodelDesignMover::reduce_task(), protocols::hydrate::remove_all_anchors_and_ENF(), protocols::denovo_design::movers::SealFoldTreeMover::remove_cutpoints(), protocols::hydrate::remove_high_energy_water_molecules(), protocols::hydrate::remove_non_buried_wat(), protocols::calc_taskop_filters::RotamerBoltzmannWeight2::report(), core::scoring::methods::Fa_MbenvEnergy::residue_energy(), core::scoring::methods::WaterSpecificEnergy::residue_energy(), core::scoring::methods::AromaticBackboneRestraintEnergy::residue_energy(), core::scoring::methods::ReferenceEnergy::residue_energy(), core::scoring::GenericBondedPotential::residue_energy(), core::scoring::hbonds::residue_near_water(), protocols::hydrate::residue_near_water(), core::scoring::sym_e::symEnergy::residue_pair_energy(), core::scoring::methods::SuckerEnergy::residue_pair_energy(), core::scoring::methods::PointWaterEnergy::residue_pair_energy(), core::scoring::methods::Fa_MbsolvEnergy::residue_pair_energy(), core::scoring::GenericBondedPotential::residue_pair_energy(), core::conformation::Conformation::residues_insert(), core::scoring::rms_at_all_corresponding_atoms(), core::scoring::rms_at_corresponding_atoms(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::rotamer_energy_deriv(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::rotamer_energy_deriv_bbdep(), core::pose::symmetry::rotate_anchor_to_x_axis(), protocols::denovo_design::same_pose(), protocols::hydrate::set_dew_waters_not_to_be_included(), protocols::match::set_ligpose_rotamer(), protocols::hydrate::set_task_and_movemap(), protocols::hydrate::set_task_with_de_novo_water_using_resfile(), protocols::hydrate::set_water_info_and_add_de_novo_water(), core::pack::rotamer_set::RotamerSubset::show(), core::pack::rotamer_set::RotamerSet_::show(), core::conformation::Conformation::show_residue_connections(), protocols::vip::VIP_Mover::sort_fill_energies(), core::import_pose::libraries::RNA_ChunkLibrary::update_atom_level_domain_map(), update_connections_to_other_residue(), core::pose::rna::update_map(), protocols::simple_moves::ExplicitWaterMover::update_packer_task(), protocols::environment::CoMTrackerCM::update_tracking_residue(), protocols::match::output::ResidueKinemageWriter::write_rsd_coords(), and core::conformation::ResidueKinWriter::write_rsd_coords().

char core::conformation::Residue::name1 ( ) const

inline

Returns this residue's 1-letter representation.

Note

: for proteins, this will be the 1-letter amino acid code

References core::chemical::ResidueTypeBase::name1(), and rsd_type_.

Referenced by core::pack::task::residue_selector::add_clashes_to_shell(), protocols::splice::Splice::add_coordinate_constraints(), protocols::splice::SpliceManager::add_coordinate_constraints(), protocols::loop_grower::LoopGrower::add_fragment_csts(), annotated_name(), protocols::simple_moves::PSSM2BfactorMover::apply(), protocols::cutoutdomain::CutOutDomain::apply(), protocols::symmetry::DetectSymmetry::apply(), protocols::protein_interface_design::filters::Torsion::apply(), protocols::protein_interface_design::filters::FilterScanFilter::apply(), protocols::task_operations::RestrictIdentitiesAtAlignedPositionsOperation::apply(), protocols::hbnet::ConstrainHBondNetwork::apply(), protocols::simple_moves::ShortBackrubMover::apply(), protocols::design_opt::GreedyOptMutationMover::apply(), protocols::matdes::MatDesGreedyOptMutationMover::apply(), protocols::simple_moves::sidechain_moves::SidechainMCMover::apply(), protocols::splice::Splice::apply(), protocols::comparative_modeling::ThreadingMover::apply(), protocols::indexed_structure_store::apply_residue_entries_to_pose(), protocols::loops::apply_sequence_mapping(), protocols::hbnet::HBNet::atom_hbonds_to_bridging_water(), protocols::fold_from_loops::utils::attach_unfolded_pose_to_pose_c_term(), protocols::fold_from_loops::utils::attach_unfolded_pose_to_pose_n_term(), protocols::idealize::basic_idealize(), core::scoring::rna::RNP_LowResPairDistPotential::calc_rnp_pair_dist_score(), protocols::analysis::simple_metrics::SequenceRecoveryMetric::calculate(), protocols::forge::components::VarLengthBuild::centroid_build(), core::import_pose::libraries::RNA_ChunkLibrary::check_res_map(), protocols::splice::SpliceManager::check_sequence_profile(), protocols::denovo_design::filters::SSPredictionFilter::compute(), protocols::simple_filters::MotifScoreFilter::compute(), protocols::denovo_design::filters::ExposedHydrophobicsFilter::compute(), protocols::pose_metric_calculators::RotamerBoltzCalculator::compute_boltz_weight_packrotamers(), protocols::denovo_design::filters::PreProlineFilter::compute_spline(), protocols::antibody::AntibodyInfo::detect_and_set_regular_CDR_H3_stem_type(), protocols::antibody::AntibodyInfo::detect_and_set_regular_CDR_H3_stem_type_new_rule(), protocols::antibody_legacy::Antibody::detect_regular_CDR_H3_stem_type(), core::scoring::dna::DNA_DihedralPotential::eval_harmonic_sugar_pucker_dependent_chi_torsion_score_and_deriv(), core::scoring::dna::DNA_DihedralPotential::eval_sugar_torsion_score_and_deriv(), core::scoring::rna::RNP_LowResPotential::evaluate_rnp_base_pair_score(), core::scoring::rna::RNP_LowResPotential::evaluate_rnp_pair_score(), core::scoring::rna::RNP_LowResStackData::evaluate_rnp_stack_xy_score(), protocols::indexed_structure_store::extract_residue_entry(), core::pose::copydofs::CopyDofs::figure_out_dofs(), core::io::rna::RDAT::fill_header_information(), protocols::pmut_scan::PointMutScanDriver::fill_mutations_list(), core::scoring::methods::CenPairMotifDegreeEnergy::finalize_total_energy(), core::scoring::methods::CenPairMotifEnergy::finalize_total_energy(), protocols::splice::RotLibOut::find_matching_res(), protocols::cutoutdomain::CutOutDomain::find_nearest_res(), protocols::splice::SpliceOut::find_non_active_site_cut_site(), protocols::splice::Splice::find_non_active_site_cut_site(), protocols::hbnet::HBNet::find_unsats(), core::scoring::gdtha(), core::scoring::gdtsc(), protocols::splice::Splice::generate_sequence_profile(), core::scoring::carbon_hbonds::CarbonHBondEnergy::get_atom_atom_carbon_hbond_energy(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_acceptor(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_donor(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::get_atom_atom_occ_solvation(), core::scoring::rna::get_bin(), protocols::recon_design::get_designable_sequence(), core::scoring::hbonds::get_hb_don_chem_type(), core::scoring::motif::MotifHash::get_matching_motifs(), core::scoring::dna::DNA_DihedralPotential::get_mean_sugar_pucker_dependent_chi(), protocols::hbnet::HBNet::get_num_native_rot(), protocols::hbnet::HBNet::get_num_native_seq(), core::scoring::rna::data::RNA_DMS_Potential::get_probe_xyz(), core::scoring::methods::NMerRefEnergy::get_residue_energy_by_table(), core::scoring::methods::LK_PolarNonPolarEnergy::get_residue_pair_energy_one_way(), core::scoring::methods::SSElementMotifContactEnergy::get_SSelements_in_contact(), protocols::simple_filters::SSElementMotifContactFilter::get_SSelements_in_contact(), core::scoring::dna::DNA_DihedralPotential::get_sugar_torsion_mean_and_sdev(), protocols::hbnet::HBNetStapleInterface::has_pH_His(), protocols::hbnet::his_tyr_connectivity(), protocols::antibody::AntibodyInfo::identify_antibody(), protocols::abinitio::abscript::RigidChunkCM::initialize(), protocols::antibody::AntibodyInfo::kink_anion_atoms(), protocols::antibody::AntibodyInfo::kink_cation_atoms(), protocols::antibody::kink_dihedral(), protocols::tcr::match_template_and_target_sequence(), protocols::hbnet::HBNetStapleInterface::network_meets_final_criteria(), protocols::hbnet::HBNetStapleInterface::num_intermolecular_hbonds(), protocols::protein_interface_design::movers::MapHotspot::output_pose(), core::pack::pack_rotamers_loop(), protocols::splice::SpliceOut::place_cut_site_in_segment(), protocols::read_in_mutations(), protocols::pmut_scan::PointMutScanDriver::read_mutants_list_file(), protocols::hbnet::HBNet::rec_trav_native(), protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::recompute(), core::scoring::sasa::rel_per_res_sc_sasa(), protocols::rotamer_recovery::RRReporterSQLite::report_rotamer_recovery_full(), core::scoring::methods::ProQ_Energy::res6(), core::scoring::methods::MotifDockEnergy::residue_pair_energy(), core::scoring::rna::RNP_LowResEnergy::residue_pair_energy(), core::scoring::motif::ResPairMotif::ResPairMotif(), core::scoring::rna::RNA_LowResolutionPotential::rna_backbone_backbone_pair_energy_one_way(), protocols::simple_moves::StructProfileMover::save_MSAcst_file(), protocols::hbnet::HBNet::select_best_networks(), protocols::toolbox::match_enzdes_util::EnzdesSeqRecoveryCache::sequence_recovery(), core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >::set_rotamer_dots_for_node_state(), protocols::toolbox::match_enzdes_util::EnzdesSeqRecoveryCache::set_sequence(), core::conformation::setup_corresponding_atoms(), protocols::simple_moves::BBGaussianMover::setup_list(), protocols::stepwise::modeler::rna::setup_suite_atom_id_map(), core::scoring::dna::show_base_pair_params(), core::scoring::dna::show_base_pair_params_with_z_scores(), core::scoring::dna::show_new_base_step_params(), core::scoring::motif::MotifHits::stat_motifs(), protocols::simple_moves::sidechain_moves::SidechainMoverBase::suggest_residue_number(), protocols::calc_taskop_filters::RelativePoseFilter::thread_seq(), protocols::hbnet::HBNet::traverse_native(), core::pose::rna::update_edge_hbond_numbers(), protocols::antibody_legacy::Antibody::update_sequence(), and protocols::simple_filters::SaveResfileToDiskFilter::write_resfile().

std::string const& core::conformation::Residue::name3 ( ) const

inline

Returns this residue's 3-letter representation.

Note

: for proteins, this will be the 3-letter amino acid code

References core::chemical::ResidueTypeBase::name3(), and rsd_type_.

Referenced by protocols::splice::Splice::add_coordinate_constraints(), protocols::splice::SpliceManager::add_coordinate_constraints(), protocols::environment::add_variant(), core::scoring::sc::MolecularSurfaceCalculator::AddResidue(), protocols::toolbox::rotamer_set_operations::RigidBodyMoveBaseRSO::alter_rotamer_set(), core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr(), core::io::pose_to_sfr::PoseToStructFileRepConverter::append_residue_info_to_sfr(), protocols::simple_filters::ResidueBurialFilter::apply(), protocols::protein_interface_design::movers::ShoveResidueMover::apply(), protocols::simple_filters::EnergyPerResidueFilter::apply(), protocols::protein_interface_design::movers::RandomMutation::apply(), protocols::protein_interface_design::movers::SetAtomTree::apply(), protocols::protein_interface_design::filters::Torsion::apply(), protocols::simple_filters::NeighborTypeFilter::apply(), protocols::task_operations::SelectBySASAOperation::apply(), protocols::matdes::ExtractSubposeMover::apply(), protocols::simple_filters::ResidueCountFilter::apply(), protocols::task_operations::SelectByDeltaScoreOperation::apply(), protocols::protein_interface_design::filters::FilterScanFilter::apply(), protocols::splice::FindEndpointsOperation::apply(), protocols::magnesium::MgHydrater::apply(), protocols::dna::RestrictDesignToProteinDNAInterface::apply(), core::select::residue_selector::ScoreTermValueBasedSelector::apply(), protocols::simple_filters::LongestContinuousPolarSegmentFilter::apply(), protocols::hbnet::ConstrainHBondNetwork::apply(), protocols::matdes::BuildingBlockInterfaceOperation::apply(), protocols::evolution::NucleotideMutation::apply(), protocols::task_operations::RestrictIdentitiesOperation::apply(), protocols::motifs::MotifDnaPacker::apply(), protocols::protein_interface_design::movers::SaveAndRetrieveSidechains::apply(), protocols::task_operations::RestrictNativeResiduesOperation::apply(), core::select::residue_selector::ResidueNameSelector::apply(), protocols::pose_creation::MakePolyXMover::apply(), protocols::abinitio::abscript::AbscriptLoopCloserCM::apply(), protocols::splice::Splice::apply(), protocols::protein_interface_design::Revert::apply(), protocols::protein_interface_design::movers::PlaceStubMover::apply(), protocols::loop_grower::SheetSampler::apply(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_alpha_aa_rama_check(), protocols::motifs::Motif::apply_check(), protocols::analysis::GlycanInfoMover::apply_const(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_rama_prepro_check(), core::scoring::methods::ProQ_Energy::atom13_0(), protocols::fold_from_loops::utils::attach_unfolded_pose_to_pose_c_term(), protocols::fold_from_loops::utils::attach_unfolded_pose_to_pose_n_term(), protocols::motifs::Motif::backward_check(), protocols::LoopRebuild::barcode_extend_stems(), core::scoring::orbitals::OrbitalsStatistics::bb_stats(), protocols::seeded_abinitio::SeedFoldTree::best_by_ala_scan(), core::conformation::break_disulfide(), core::scoring::MultipoleElecPotential::build_frame_and_rotate(), protocols::motifs::MotifSearch::BuildPosition_from_Size(), core::scoring::sasa::LeGrandSasa::calc_atom_masks(), core::scoring::calc_per_res_hydrophobic_sasa(), core::select::util::SelectResiduesByLayer::calc_sc_neighbors(), protocols::protein_interface_design::ReportSequenceDifferences::calculate(), protocols::simple_ddg::DdGScan::calculate(), protocols::antibody::CDR_H3_cter_filter(), protocols::antibody_legacy::CDRH3Modeler::CDR_H3_filter(), protocols::antibody::CDR_H3_filter_legacy_code_with_old_rule(), protocols::membrane::AddMembraneMover::check_pdb_for_mem(), protocols::constraint_generator::HydrogenBondConstraintGenerator::choose_atoms(), core::scoring::nmr::NMRDummySpinlabelEnsemble::clash_check(), protocols::enzdes::ModifyStoredRBConfs::closest_orient_atoms_msd(), protocols::simple_filters::TotalSasaFilter::compute(), protocols::cryst::ReportGradientsMover::compute(), protocols::simple_filters::MutationsFilter::compute(), protocols::protein_interface_design::filters::DesignableResiduesFilter::compute(), protocols::calc_taskop_filters::RotamerBoltzmannWeight::compute(), protocols::simple_filters::TaskAwareScoreTypeFilter::compute(), protocols::frag_picker::FragmentScoreFilter::compute(), protocols::simple_filters::BuriedUnsatHbondFilter::compute(), protocols::denovo_design::filters::ExposedHydrophobicsFilter::compute(), protocols::simple_filters::ResidueCountFilter::compute(), protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter::compute(), protocols::matdes::SymUnsatHbondFilter::compute(), protocols::matdes::ClashCheckFilter::compute(), protocols::simple_filters::TaskAwareSASAFilter::compute(), protocols::calc_taskop_filters::RotamerBoltzmannWeight::compute_modified_ddG(), protocols::calc_taskop_filters::RotamerBoltzmannWeight2::compute_modified_ddg(), core::membrane::concave_shell(), protocols::abinitio::abscript::RigidChunkCM::configure(), protocols::loop_grower::LoopGrower::coordinate_filter(), protocols::protein_interface_design::movers::SetAtomTree::create_atom_tree(), protocols::toolbox::ResidueNetwork::create_from_pose(), protocols::enzdes::enzutil::create_remark_headers_from_cstcache(), core::scoring::bin_transitions::BinTransitionData::criteria_match_i(), core::scoring::bin_transitions::BinTransitionData::criteria_match_iplus1(), protocols::simple_ddg::DdGScan::ddG_for_single_residue(), protocols::toolbox::rotamer_set_operations::RigidBodyMoveBaseRSO::determine_largest_nbr_atom_distance(), protocols::antibody::GraftCDRLoopsProtocol::display_constraint_residues(), protocols::antibody::AntibodyModelerProtocol::display_constraint_residues(), protocols::antibody_legacy::AntibodyModeler::display_constraint_residues(), protocols::magnesium::MgScanner::distance_to_closest_magnesium(), protocols::environment::dof_id_to_string(), protocols::ligand_docking::HighResDocker::enable_ligand_rotamer_packing(), protocols::ligand_docking::ProtLigEnsemble::enable_ligand_rotamer_packing(), protocols::simple_moves::DumpSingleResidueRotamers::enumerate_aa_rotamer(), core::scoring::magnesium::MgEnergy::eval_intrares_energy(), core::scoring::methods::GenericBondedEnergy::eval_intrares_energy(), core::scoring::magnesium::MgEnergy::eval_mg_interaction(), core::scoring::rna::RNA_LowResolutionPotential::eval_rna_base_pair_energy_one_way(), core::scoring::rna::RNA_VDW_Energy::evaluate_rnp_vdw_score(), protocols::enzdes::EnzdesBaseProtocol::exchange_ligands_in_pose(), protocols::magnesium::SampleGrid::figure_out_box_bounds(), protocols::frag_picker::scores::FragmentDME::fill_CA_coords(), protocols::frag_picker::scores::FragmentCrmsd::fill_CA_coords(), protocols::frag_picker::scores::FragmentCrmsdResDepth::fill_CA_coords(), protocols::contact_map::ContactMap::fill_contacts(), protocols::frag_picker::scores::FragmentAllAtomCrmsd::fill_coords(), protocols::membrane::MPLipidAccessibility::fill_up_slices(), protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::find_in_pose_if_missing_from_header(), protocols::flxbb::find_ligands(), protocols::splice::SpliceOut::find_non_active_site_cut_site(), protocols::splice::Splice::find_non_active_site_cut_site(), protocols::metal_interface::ZincSiteFinder::find_zinc_site(), protocols::calc_taskop_filters::RotamerBoltzmannWeight::first_pass_ala_scan(), protocols::splice::Splice::fold_tree(), core::conformation::form_disulfide(), protocols::motifs::Motif::forward_check(), protocols::docking::membrane::MPFindInterfaceMover::fractions_small_residues(), protocols::kinematic_closure::ClosureProblem::frame(), protocols::loop_grower::LoopGrower::GDThatonative(), protocols::topology_broker::MembraneTopologyClaimer::generate_claims(), protocols::enzdes::EnzdesBaseProtocol::generate_explicit_ligand_rotamer_poses(), protocols::helical_bundle::BundleReporterFilter::generate_full_tracer_report(), core::scoring::rna::RNA_LowResolutionPotential::get_base_backbone(), core::scoring::rna::data::RNA_DMS_Potential::get_binding_energy(), protocols::magnesium::get_closest_non_hoh_contact(), protocols::enzdes::ResidueConformerFilter::get_current_conformer(), core::pose::symmetry::get_full_intracomponent_and_neighbor_subs(), protocols::magnesium::get_hoh_xyz(), core::pose::symmetry::get_intracomponent_and_neighbor_subs(), protocols::cyclic_peptide::crosslinker::TBMB_Helper::get_linker_index_asymmetric(), protocols::cyclic_peptide::crosslinker::TBMB_Helper::get_linker_indices_symmetric(), protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::get_pose_data(), protocols::magnesium::get_res_with_name(), protocols::rna::denovo::get_residues_within_dist_of_RNA(), core::chemical::rna::get_rna_base_coordinate_system(), core::pack::get_rotamer_angle_diffs(), protocols::magnesium::MgScanner::get_score(), protocols::magnesium::MgScanner::get_unique_mg_res(), core::pose::carbohydrates::glycosylate_pose(), core::pose::carbohydrates::glycosylate_pose_by_file(), protocols::motifs::MotifSearch::identify_motif_BuildPositions(), protocols::motifs::MotifSearch::incorporate_motifs(), protocols::motifs::LigandMotifSearch::incorporate_motifs(), protocols::sic_dock::SICFast::init(), protocols::abinitio::abscript::RigidChunkCM::initialize(), protocols::motifs::MotifSearch::initialize(), protocols::topology_broker::TopologyBroker::initialize_cuts(), core::pack::palette::PackerPalette::initialize_residue_level_task(), protocols::features::ResidueFeatures::insert_residue_rows(), core::pose::symmetry::intracomponent_contact(), protocols::pockets::GenPharmacophore::is_buried_ring(), protocols::task_operations::CrystalContactsOperation::is_crystal_contact(), is_similar_rotamer(), protocols::antibody::kink_bb_Hbond(), protocols::antibody::kink_Trp_Hbond(), protocols::loop_grower::LoopPartialSolution::LoopPartialSolution(), protocols::motifs::make_dna_mutations(), protocols::protein_interface_design::make_hotspot_foldtree(), protocols::simple_moves::MutateResidue::make_mutation(), protocols::rotamer_recovery::RRComparerElecDensDiff::measure_rotamer_recovery(), protocols::enzdes::EnzdesFlexBBProtocol::modified_task(), protocols::loop_grower::LoopGrower::modifieddensity(), protocols::motifs::Motif::Motif(), protocols::kinematic_closure::ClosureProblem::mutate_residues(), core::conformation::ExactResidueMatcher::operator()(), core::io::sequence_comparation::DesignContrast::output_sqc_file(), protocols::antibody::paratope_charge(), core::pose::parse_selection_block(), protocols::enzymatic_movers::DNAMethyltransferaseMover::perform_reaction(), protocols::motifs::Motif::place_atoms(), protocols::motifs::Motif::place_residue(), protocols::antibody::pose_charge(), core::scoring::UnfoldedStatePotential::pose_raw_unfolded_state_energymap(), core::scoring::packing::PoseBalls::PoseBalls(), protocols::splice::printChi(), protocols::toolbox::match_enzdes_util::EnzConstraintIO::process_pdb_header(), protocols::membrane::MPLipidAccessibility::protein_in_membrane(), core::scoring::bin_transitions::BinTransitionCalculator::random_bin(), core::scoring::bin_transitions::BinTransitionCalculator::random_bin_based_on_previous(), protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::recompute(), protocols::magnesium::remove_mg_bound_waters(), protocols::magnesium::remove_waters_except_mg_bound(), protocols::simple_moves::RepeatPropagationMover::repeat_ligand(), protocols::simple_moves::RepeatPropagationMover::repeat_ligand_constraints(), protocols::toolbox::match_enzdes_util::replace_residue_keeping_all_atom_positions(), protocols::simple_filters::ResidueBurialFilter::report(), protocols::simple_filters::TotalSasaFilter::report(), protocols::simple_filters::NeighborTypeFilter::report(), protocols::calc_taskop_filters::RotamerBoltzmannWeight::report(), protocols::simple_filters::EnergyPerResidueFilter::report(), protocols::simple_ddg::AlaScan::report(), protocols::simple_filters::LongestContinuousPolarSegmentFilter::report(), protocols::features::OrbitalsFeatures::report_hpol_orbital_interactions(), protocols::rotamer_recovery::RRReporterSQLite::report_rotamer_recovery_full(), protocols::simple_ddg::AlaScan::report_symmetry(), protocols::membrane::scoring::FaWaterToBilayerEnergy::residue_energy(), core::scoring::methods::SymmetricLigandEnergy::residue_energy(), core::scoring::methods::ReferenceEnergyNoncanonical::residue_energy(), core::scoring::magnesium::MgEnergy::residue_pair_energy(), core::scoring::methods::GoapEnergy::residue_pair_energy(), protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::restrict_sequence_profile(), protocols::multistate_design::restrict_to_canonical_aas(), protocols::environment::rm_variant(), protocols::loop_grower::LoopGrower::RMStonative(), core::scoring::rna::RNA_LowResolutionPotential::rna_repulsive_pair_energy_one_way(), protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers::rotamer_set_contains_rotamer(), core::pack::annealer::SequenceSymmetricAnnealer::run(), core::scoring::orbitals::OrbitalsStatistics::sc_H_orbital(), protocols::magnesium::MgScanner::scan_magnesiums(), protocols::relax::AtomCoordinateCstMover::set_constraints_on_func_groups(), protocols::features::OrbitalsFeatures::set_OrbH_features_data(), protocols::features::OrbitalsFeatures::set_OrbOrb_features_data(), protocols::enzymatic_movers::EnzymaticMover::set_pose_reactive_sites(), protocols::topology_broker::TMHTopologySamplerClaimer::set_pose_torsions(), protocols::magnesium::set_water_numbers_to_zero(), core::import_pose::libraries::ChunkSet::setup_atom_id_mask(), core::scoring::constraints::FabConstraint::setup_csts(), core::scoring::packstat::MultiProbePoseAccumulator::show(), protocols::protein_interface_design::filters::FilterScanFilter::single_substitution(), protocols::magnesium::strip_out_magnesiums(), protocols::magnesium::MgHydrater::update_full_model_info_with_new_waters(), protocols::toolbox::match_enzdes_util::EnzConstraintParameters::update_pdb_remarks(), protocols::splice::SpliceOutTail::write_database_to_file(), protocols::splice::SpliceOut::write_database_to_file(), and protocols::simple_ddg::DdGScan::write_to_pdb().

Size core::conformation::Residue::natoms ( ) const

inline

Returns the number of atoms in this residue.

example(s): residue.natoms() See also: Residue Pose

References core::chemical::ResidueType::natoms(), and rsd_type_.

Referenced by protocols::splice::Splice::add_coordinate_constraints(), protocols::splice::SpliceManager::add_coordinate_constraints(), protocols::sewing::hashing::AlignmentFileGeneratorMover::add_pose_segments_to_segment_vector(), core::scoring::geometric_solvation::add_to_individual_sol_energies(), core::scoring::sc::ElectrostaticComplementarityCalculator::AddResidue(), protocols::topology_broker::MembraneTopologyClaimer::addVirtualResAsRootMembrane(), core::scoring::MultipoleElecPotential::align_residue_multipole_axes(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::align_to_current_phore_match(), protocols::loop_grower::SheetSampler::alignPerfectCA(), protocols::loop_grower::SheetSampler::alignStrand(), core::conformation::all_atom_center(), protocols::pockets::PocketGrid::alter_espGrid_with_bound_ligand(), core::scoring::APBSConfig::APBSConfig(), core::conformation::symmetry::SymmetricConformation::append_polymer_residue_after_seqpos(), core::conformation::Conformation::append_polymer_residue_after_seqpos(), core::conformation::symmetry::SymmetricConformation::append_residue_by_jump(), protocols::simple_moves::PSSM2BfactorMover::apply(), protocols::protein_interface_design::movers::SetTemperatureFactor::apply(), protocols::simple_moves::CombinePoseMover::apply(), protocols::cyclic_peptide::FlipChiralityMover::apply(), core::select::residue_selector::BondedResidueSelector::apply(), protocols::comparative_modeling::PartialThreadingMover::apply(), protocols::helical_bundle::FitSimpleHelix::apply(), protocols::membrane::MPLipidAccessibility::apply(), protocols::hbnet::UnsatSelector::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::comparative_modeling::MultiThreadingMover::apply(), protocols::comparative_modeling::ThreadingMover::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::rbsegment_relax::SequenceShiftMover::apply(), protocols::cryst::MakeLatticeMover::apply(), protocols::minimization_packing::MinMover::apply_dof_tasks_to_movemap(), protocols::hybridization::CartesianHybridize::apply_frag(), protocols::hybridization::CartesianSampler::apply_frame(), protocols::indexed_structure_store::apply_residue_entries_to_pose(), core::conformation::Conformation::apply_transform_Rx_plus_v(), protocols::rbsegment_relax::RBSegmentMover::applyTransformation(), protocols::rbsegment_relax::RBSegmentMover::applyTranslation(), core::scoring::VdWTinkerPotential::assign_residue_amoeba_type(), core::scoring::MultipoleElecPotential::assign_residue_amoeba_type(), protocols::hybridization::atom_map_valid_size(), protocols::rna::movers::atoms_have_bond_to_bonded_atoms(), protocols::rna::movers::atoms_have_mutual_bond_to_atom(), protocols::sewing::hashing::LigandBindingResPlacer::best_rotamer_for_residue(), core::scoring::biggest_residue_deviation_no_super(), core::scoring::biggest_residue_deviation_no_super_subset(), protocols::nmr::pcs::PCSLigandTransformMover::build_ligand_atom_xyz_table(), core::pack::rotamer_set::build_moving_O_water_rotamers_dependent(), core::conformation::build_residue_tree(), core::pack::rotamer_set::ContinuousRotamerSet::build_rotamers(), core::chemical::ICoorAtomID::buildable(), protocols::rna::movers::bump_check(), protocols::match::bump_grid_to_enclose_pose(), protocols::match::bump_grid_to_enclose_residue(), protocols::match::bump_grid_to_enclose_residue_backbone(), core::scoring::sasa::LeGrandSasa::calc_atom_masks(), core::scoring::calc_atom_masks(), protocols::flexpep_docking::FlexPepDockingPoseMetrics::calc_frac_atoms_kA_to_native(), core::scoring::calc_per_res_hydrophobic_sasa(), core::scoring::sasa::SasaCalc::calc_per_res_sasas(), core::simple_metrics::per_residue_metrics::PerResidueClashMetric::calculate(), core::scoring::MultipoleElecPotential::calculate_and_store_all_derivs(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::calculate_free_ligand_score(), core::scoring::FACTSPotential::calculate_GBpair_exact(), core::scoring::FACTSPotential::calculate_GBpair_fast(), core::scoring::FACTSPotential::calculate_GBpair_v1trunk(), protocols::ligand_docking::ga_ligand_dock::GridScorer::calculate_grid(), core::scoring::MultipoleElecPotential::calculate_res_res_fixed_fields_for_polarization(), core::scoring::MultipoleElecPotential::calculate_res_res_induced_fields_for_polarization(), protocols::antibody::AntibodyFeatures::calculate_residue_atomic_contacts(), protocols::hydrate::calculate_water_overcoordinated_hb_correction(), protocols::sic_dock::cb_weights_from_map(), core::pose::Pose::center(), core::scoring::membrane::MPHelicalityEnergy::centroid_neighbors(), core::scoring::membrane::MPResidueLipophilicityEnergy::centroid_neighbors(), protocols::geometry::centroids_by_jump(), protocols::geometry::centroids_by_jump_int(), protocols::ligand_docking::ga_ligand_dock::GridScorer::clash_score(), protocols::environment::collect_dofs(), core::pack::compare_simple_inteaction_graph_alt_state_and_energy_graph(), protocols::simple_filters::AtomicDistanceFilter::compute(), protocols::cryst::ReportGradientsMover::compute(), protocols::hbnet::UnsatSelector::compute(), protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::compute(), core::pack::interaction_graph::compute_alt_weights_for_npd_hbonds(), protocols::pockets::PlaidFingerprint::compute_ligand_natoms(), protocols::pockets::PlaidFingerprint::compute_ligand_natoms_with_hydrogens(), protocols::scoring::methods::saxs::PDDFEnergy::compute_pddf(), protocols::scoring::methods::saxs::PDDFEnergy::compute_pddf_without_ff(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_sho_acceptor_atom_energy(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_sho_donor_atom_energy(), core::scoring::power_diagram::PowerDiagram::construct_from_pose(), core::pack::scmin::ResidueAtomTreeCollectionMomento::copy_coords(), protocols::generalized_kinematic_closure::copy_loop_pose_to_original(), protocols::mpi_refinement::copy_pose_crd(), core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms(), protocols::abinitio::copy_side_chains(), protocols::pockets::counting_atoms_in_residue(), core::scoring::hbonds::create_rotamer_descriptor(), core::scoring::elec::create_rotamer_descriptor(), core::pack::create_scmin_minimizer_map(), core::scoring::trie::create_trie(), protocols::ligand_docking::ga_ligand_dock::GridScorer::debug_deriv(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::define_active_virtual_sites(), protocols::nmr::pcs::PCSLigandTransformMover::define_ligand_frame_origin(), protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), protocols::relax::derive_sc_sc_restraints(), core::scoring::constraints::AtomPairConstraint::dist(), protocols::match::downstream::RigidLigandBuilder::downstream_pose_from_hit(), protocols::match::downstream::LigandConformerBuilder::downstream_pose_from_hit(), core::import_pose::atom_tree_diffs::dump_atom_tree_diff(), protocols::pockets::PlaidFingerprint::dump_oriented_pose_and_fp_to_pdb(), protocols::viewer::dump_residue_kinemage(), core::scoring::rna::RNA_FullAtomVDW_BasePhosphate::eval_atom_derivative(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::eval_atom_derivative(), core::scoring::elec::FA_ElecEnergyAroAll::eval_atom_derivative_aro_aro(), core::scoring::elec::FA_ElecEnergyAroAro::eval_atom_derivative_aro_aro(), core::scoring::methods::dfire::DFIRE_Potential::eval_dfire_pair_energy(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::eval_intrares_derivatives(), core::scoring::elec::FA_ElecEnergy::eval_intrares_derivatives(), core::scoring::constraints::ConstraintsEnergy::eval_intrares_derivatives(), core::scoring::elec::FA_ElecEnergy::eval_intrares_energy(), core::scoring::PoissonBoltzmannPotential::eval_PB_energy_residue(), core::scoring::methods::RingClosureEnergy::eval_residue_derivatives(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_bond(), core::scoring::rna::StackElecEnergy::eval_residue_pair_derivatives(), core::scoring::lkball::LK_BallEnergy::eval_residue_pair_derivatives(), core::scoring::SASAPotential::eval_residue_pair_derivatives(), core::scoring::constraints::ConstraintsEnergy::eval_residue_pair_derivatives(), core::scoring::etable::BaseEtableEnergy< Derived >::eval_residue_pair_derivatives(), core::scoring::VdWTinkerPotential::eval_residue_pair_derivatives(), core::scoring::MultipoleElecPotential::eval_residue_pair_derivatives(), core::scoring::elec::GroupElec::eval_respair_group_derivatives(), core::scoring::FACTSPotential::evaluate_nonpolar_energy(), protocols::scoring::InterchainPotential::evaluate_pair_and_vdw_score(), core::scoring::FACTSPotential::evaluate_polar_otf_energy(), core::scoring::rna::RNA_VDW_Energy::evaluate_rnp_vdw_score(), protocols::environment::EXCN_Env_Security_Exception::EXCN_Env_Security_Exception(), protocols::pose_metric_calculators::fast_clash_check(), protocols::forge::remodel::fast_clash_check(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::fast_full_atom_VDW_repulsion_screen(), protocols::magnesium::SampleGrid::figure_out_box_bounds(), protocols::match::fill_grid_with_residue_spheres(), core::conformation::Conformation::fill_missing_atoms(), fill_missing_atoms(), core::io::silent::BinarySilentStruct::fill_pose(), core::scoring::fill_rmsd_coordinates(), core::io::silent::BinarySilentStruct::fill_struct(), protocols::scoring::VDW_GridEnergy::finalize_total_energy(), core::scoring::elec::RNA_FA_ElecEnergy::finalize_total_energy(), core::scoring::rna::StackElecEnergy::finalize_total_energy(), core::scoring::elec::FA_ElecEnergy::finalize_total_energy(), core::scoring::etable::BaseEtableEnergy< Derived >::finalize_total_energy(), protocols::nmr::pcs::PCSLigandTransformMover::find_best_ligand_pose_with_grid_search(), core::util::find_metalbinding_atoms_for_complex(), core::scoring::MultipoleElecPotential::find_params_and_neighbors(), protocols::enzdes::PredesignPerturbMover::find_rotation_center(), protocols::magnesium::MgWaterHydrogenPacker::find_water_neighbor_vecs(), protocols::electron_density::findLoopFromDensity(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_1b_energy(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_2b_energy(), protocols::toolbox::rigid_body::get_atom_coordinates(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_calc_chem_shift_value_larmord(), protocols::sic_dock::get_CB_Vecs_from_map(), protocols::simple_moves::AddCavitiesMover::get_closest_heavy_atom(), core::scoring::magnesium::get_closest_orbital_axis(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_deriv_for_chemical_shift(), protocols::pockets::NonPlaidFingerprint::get_electrostatics_energy(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_grid_atomtypes(), core::pose::get_hash_excluding_chain(), core::pose::get_hash_from_chain(), protocols::pockets::GenPharmacophore::get_ideal_hydrogenBond_atoms(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::get_matching_res_in_VDW_rep_screen_pose(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::get_movable_scs(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::get_nearest_dist_to_O2prime(), core::pack::interaction_graph::NPDHBSimpleNode::get_npdhb_deltaE_for_substitution(), core::scoring::rna::data::RNA_DMS_Potential::get_occupancy_densities(), protocols::generalized_kinematic_closure::GeneralizedKIC::get_path(), protocols::stepwise::monte_carlo::rna::RNA_O2PrimeMover::get_random_o2prime_residue_near_moving_residue(), core::scoring::GenBornPotential::get_res_res_elecE(), core::scoring::MultipoleElecPotential::get_res_res_elecE(), core::scoring::SASAPotential::get_res_res_sasa(), core::scoring::VdWTinkerPotential::get_res_res_vdw(), core::pack::get_residue_current_energy(), core::scoring::WaterAdductHBondPotential::get_residue_residue_h2o_hbonds_1way(), core::pack::interaction_graph::SymmOnTheFlyNode::get_rotamer(), core::conformation::get_second_atom_from_connection(), core::pose::get_sha1_hash_excluding_chains(), core::pose::get_sha1_hash_from_chains(), core::scoring::FACTSPotential::get_single_rotamer_born_radii(), core::scoring::GenBornPotential::get_single_rotamer_born_radii(), core::scoring::MultipoleElecPotential::get_single_rotamer_effective_radii(), protocols::hybridization::get_superposition_transformation(), protocols::stepwise::modeler::rna::get_surrounding_O2prime_hydrogen(), protocols::cryst::getMW(), core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_conect_records_for_atom(), core::scoring::WaterAdductHBondPotential::h2o_hbond_score_1way(), core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy::has_bb_hbond(), core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy::has_hbond(), protocols::magnesium::MgHydrater::hydrate_magnesium(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::idealize_and_repack_pose(), core::conformation::idealize_hydrogens(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::init_from_ligand(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::init_from_ligand_pharmacophore(), protocols::abinitio::abscript::RigidChunkCM::initialize(), core::scoring::VdWTinkerResidueInfo::initialize(), core::scoring::GenBornResidueInfo::initialize(), core::scoring::FACTSResidueInfo::initialize(), core::scoring::ResidueNblistData::initialize(), core::scoring::MultipoleElecResidueInfo::initialize(), protocols::flexpack::interaction_graph::FlexbbInteractionGraph::initialize(), core::pose::initialize_dof_id_map(), protocols::toolbox::match_enzdes_util::LigandConformer::initialize_from_residue(), protocols::match::downstream::RigidLigandBuilder::initialize_from_residue(), protocols::match::downstream::LigandConformerBuilder::initialize_from_residue(), core::scoring::ResiduePairNeighborList::initialize_from_residues(), protocols::relax::RelaxProtocolBase::initialize_movemap(), core::scoring::FACTSPoseInfo::is_changed(), protocols::task_operations::CrystalContactsOperation::is_crystal_contact(), protocols::qsar::scoring_grid::SingleGrid::is_in_grid(), protocols::ligand_docking::ga_ligand_dock::GridScorer::is_residue_in_grid(), protocols::ligand_docking::ComputeLigandRDF::ligand_protein_rdf(), core::pose::symmetry::make_symmetric_movemap(), core::pose::MiniPose::MiniPose(), core::conformation::missing_stubs_build(), protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::moving_res_contact_filter(), protocols::hybridization::natom_aligned(), core::scoring::membrane::MPHelicalityEnergy::neighboring_atoms(), core::scoring::membrane::MPResidueLipophilicityEnergy::neighboring_atoms(), core::scoring::nmr::NMRDummySpinlabelConformer::NMRDummySpinlabelConformer(), core::pose::num_atoms(), core::pose::PDBInfo::on_identity_change(), core::pose::PDBInfo::on_length_change(), protocols::qsar::scoring_grid::AllAtomNormalization::operator()(), core::scoring::func::ResidueXYZ::operator()(), core::scoring::func::ResiduePairXYZ::operator()(), core::conformation::orient_residue_for_ideal_bond(), protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::output_rep(), core::chemical::sdf::MolWriter::output_residue(), protocols::hybridization::MRMover::pack_missing_sidechains(), protocols::stepwise::modeler::rna::phosphate::PhosphateMover::pass_clash_check(), core::scoring::per_res_rms_at_corresponding_atoms_no_super(), protocols::simple_moves::PeriodicBoxMover::perturb_molecule_move(), place(), protocols::motifs::Motif::place_residue_(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::pose_from_posedata(), core::scoring::packing::PoseBalls::PoseBalls(), core::scoring::packing::PoseBallsLite::PoseBallsLite(), core::scoring::PQR::PQR(), protocols::topology_broker::TMHTopologySamplerClaimer::pre_process(), core::pack::interaction_graph::NPDHBSimpleNode::prepare_for_neighbors_substitution(), core::scoring::NeighborList::prepare_for_scoring(), protocols::ligand_docking::ga_ligand_dock::GridScorer::prepare_grid(), core::conformation::Conformation::prepend_polymer_residue_before_seqpos(), protocols::stepwise::modeler::rna::print_atom_info(), protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::print_sho_energies(), core::scoring::methods::PoissonBoltzmannEnergy::protein_position_equal_within(), protocols::ligand_docking::ComputeLigandRDF::protein_protein_rdf(), protocols::cryst::FitBfactorsMover::randomize_bs(), protocols::cyclic_peptide::PeptideStubMover::rebuild_atoms(), core::conformation::Conformation::rebuild_polymer_bond_dependent_atoms(), core::conformation::Conformation::rebuild_residue_connection_dependent_atoms(), protocols::simple_moves::PeriodicBoxMover::recenter_pose(), protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::recompute(), protocols::vardist_solaccess::VarSolDistSasaCalculator::recompute(), protocols::minimization_packing::MinimalRotamer::record_internal_geometry(), core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose(), protocols::qsar::scoring_grid::HbaGrid::refresh(), protocols::qsar::scoring_grid::HbdGrid::refresh(), protocols::qsar::scoring_grid::VdwGrid::refresh(), protocols::qsar::scoring_grid::SolvationGrid::refresh(), core::scoring::saxs::SAXSEnergy::rehash_form_factors(), core::pose::PDBInfo::replace_res_remap_bfactors(), core::conformation::symmetry::SymmetricConformation::replace_residue(), protocols::toolbox::match_enzdes_util::replace_residue_keeping_all_atom_positions(), protocols::features::ResidueConformationFeatures::report_features(), protocols::features::ProteinResidueConformationFeatures::report_features(), protocols::simple_moves::PeriodicBoxMover::report_thermodynamics(), core::scoring::FACTSPotential::res_res_burial(), core::scoring::GenBornPotential::res_res_burial(), core::scoring::FACTSPotential::res_res_burial_for_scoring(), core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::res_res_occ_sol_one_way(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::res_res_occ_sol_one_way(), core::optimization::CartesianMinimizerMap::reset(), core::optimization::MinimizerMap::reset(), protocols::nmr::pcs::PCSLigandTransformMover::reset_grid_and_bounding_box(), core::pack::interaction_graph::NPDHBSimpleNode::reset_hbs(), core::scoring::methods::WaterAdductIntraEnergy::residue_energy(), core::scoring::methods::RingClosureEnergy::residue_energy(), core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::residue_energy(), core::scoring::methods::HybridVDW_Energy::residue_pair_energy(), core::scoring::vdwaals::VDW_Energy::residue_pair_energy(), core::scoring::methods::GoapEnergy::residue_pair_energy(), core::scoring::elec::FA_ElecEnergyAroAll::residue_pair_energy_aro_aro(), core::scoring::elec::FA_ElecEnergyAroAro::residue_pair_energy_aro_aro(), core::scoring::magnesium::MgEnergy::residue_pair_energy_one_way(), core::scoring::rna::StackElecEnergy::residue_pair_energy_one_way(), core::conformation::Conformation::residues_append(), core::conformation::Conformation::residues_insert(), core::conformation::Conformation::residues_replace(), core::pose::PDBInfo::resize_atom_records(), protocols::toolbox::pose_manipulation::rigid_body_move(), core::import_pose::atom_tree_diffs::rms_error_with_noise(), core::scoring::rmsd_no_super(), core::scoring::rmsd_with_super(), core::scoring::elec::RNA_FA_ElecEnergy::rna_fa_elec_one_way(), protocols::toolbox::sample_around::rotate_into_nucleobase_frame(), protocols::rotamer_recovery::RRProtocolRelax::run(), protocols::qsar::scoring_grid::HbaGrid::score(), protocols::qsar::scoring_grid::HbdGrid::score(), protocols::qsar::scoring_grid::VdwGrid::score(), protocols::qsar::scoring_grid::SolvationMetaGrid::score(), protocols::qsar::scoring_grid::ShapeGrid::score(), protocols::qsar::scoring_grid::ChargeGrid::score(), protocols::qsar::scoring_grid::SingleGrid::score(), protocols::qsar::scoring_grid::PCSSingleGrid::score(), protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::semiexpl_water_hbgeom_score(), protocols::features::serialize_residue_xyz_coords(), core::pose::set_bfactors_from_atom_id_map(), protocols::match::output::UpstreamDownstreamCollisionFilter::set_downstream_pose(), core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::set_pose(), core::pack::scmin::ResidueAtomTreeCollection::set_rescoords(), core::pack::interaction_graph::SymmOnTheFlyNode::set_rotamers(), core::pack::scmin::CartSCMinMinimizerMap::setup(), core::pack::scmin::AtomTreeSCMinMinimizerMap::setup(), core::scoring::NeighborList::setup(), core::import_pose::libraries::ChunkSet::setup_atom_id_mask(), protocols::qsar::scoring_grid::ChargeGrid::setup_charge_atoms(), protocols::forge::remodel::RemodelGlobalFrame::setup_CM_helical_constraint(), core::conformation::setup_corresponding_atoms(), protocols::rbsegment_relax::setup_disconnected(), core::scoring::hbonds::HBondEnergy::setup_for_minimizing_for_residue(), core::scoring::electron_density::FastDensEnergy::setup_for_scoring(), core::scoring::methods::GoapEnergy::setup_for_scoring(), core::conformation::setup_links(), core::conformation::setup_links_simple(), protocols::simple_moves::PeriodicBoxMover::setup_LJcorrection(), protocols::simple_moves::PeriodicBoxMover::setup_pose(), protocols::rbsegment_relax::setup_pose_rbsegs_keep_loops(), protocols::features::strand_assembly::StrandBundleFeatures::shortest_dis_sidechain(), show(), core::scoring::FACTSResidueInfo::store_xyz(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::storeposedata(), core::scoring::superimpose_pose(), protocols::enzdes::ModifyStoredRBConfs::swap_coordinates_in_pose(), core::pose::swap_transform(), protocols::topology_broker::RigidChunkClaimer::switch_to_fullatom(), core::scoring::sym_rmsd_with_super_subset(), protocols::electron_density::symmetrizeBfactors(), core::optimization::symmetry::SymMinimizerMap::SymMinimizerMap(), protocols::protein_interface_design::PatchdockReader::transform_pose(), core::import_pose::libraries::RNA_ChunkLibrary::update_atom_level_domain_map(), protocols::rna::denovo::movers::RNA_Minimizer::update_atom_level_domain_map_with_extra_minimize_res(), protocols::hybridization::update_atom_map(), core::pack::scmin::ResidueAtomTreeCollection::update_atom_tree(), protocols::environment::update_pdb_info(), core::pack::scmin::ResidueAtomTreeCollection::update_residue(), core::conformation::Conformation::update_residue_coordinates(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::update_VDW_screen_bin(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::VDW_rep_screen(), protocols::mpi_refinement::StructAvrgMover::weighted_average(), core::scoring::PoissonBoltzmannPotential::write_config(), protocols::match::output::ResidueKinemageWriter::write_rsd_coords(), core::conformation::ResidueKinWriter::write_rsd_coords(), and protocols::kinmatch::xform_rsd_gl2().

Size core::conformation::Residue::nbr_atom ( ) const

inline

Returns the index number of this residue's atom used as a center for neighbor definition example: C-beta atom for some amino acids.

References core::chemical::ResidueType::nbr_atom(), and rsd_type_.

Referenced by protocols::task_operations::InteractingRotamerExplosion::apply(), protocols::task_operations::DesignAroundOperation::apply(), protocols::task_operations::RestrictToMoveMapChiOperation::apply(), protocols::simple_task_operations::RestrictToInterface::apply(), protocols::simple_filters::EnergyPerResidueFilter::apply_helper(), protocols::constraint_generator::AtomPairConstraintGenerator::atoms_to_constrain(), core::scoring::sasa::LeGrandSasa::calc_atom_masks(), core::scoring::calc_atom_masks(), core::select::util::SelectResiduesByLayer::calc_sc_neighbors(), core::scoring::membrane::MPHelicalityEnergy::centroid_neighbors(), core::scoring::membrane::MPResidueLipophilicityEnergy::centroid_neighbors(), protocols::ligand_docking::ligand_options::check_neighbor_ligand_atom(), core::scoring::nmr::NMRDummySpinlabelEnsemble::clash_check(), core::pack::interaction_graph::SurfacePotential::compute_pose_surface_energy(), core::pack::interaction_graph::SurfacePotential::compute_residue_surface_energy(), protocols::optimize_weights::IterativeOptEDriver::compute_rotamers_around_ligands(), protocols::constraint_generator::DistanceConstraintGenerator::create_constraint(), protocols::flexpack::interaction_graph::OTFFlexbbNode::declare_all_rotamers_initialized(), core::conformation::Conformation::detect_bonds(), core::conformation::symmetry::SymmetricConformation::detect_disulfides(), core::conformation::Conformation::detect_disulfides(), core::pack::interaction_graph::SurfaceNode< V, E, G >::detect_neighborship_with_node(), protocols::toolbox::rotamer_set_operations::RigidBodyMoveBaseRSO::determine_largest_nbr_atom_distance(), protocols::flexpack::rotamer_set::FlexbbRotamerSets::determine_res_cb_deviation(), protocols::simple_ddg::ddG::duplicate_waters_across_jump(), core::scoring::methods::RG_LocalEnergy::eval_atom_derivative(), core::scoring::methods::RG_Energy_Fast::eval_atom_derivative(), core::scoring::elec::FA_GrpElecEnergy::eval_context_derivatives(), core::scoring::methods::SmoothEnvEnergy::eval_residue_derivatives(), core::scoring::methods::CenRotEnvEnergy::eval_residue_derivatives(), core::scoring::methods::CenRotPairEnergy::eval_residue_pair_derivatives(), core::scoring::methods::SmoothCenPairEnergy::eval_residue_pair_derivatives(), core::scoring::hbonds::HBondEnergy::eval_residue_pair_derivatives(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_env_and_cbeta_deriv(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_pair_orientation_score(), core::scoring::SmoothEnvPairPotential::evaluate_env_and_cbeta_deriv(), protocols::scoring::InterchainPotential::evaluate_pair_and_vdw_score(), core::select::filter_neighbors_by_distance(), core::scoring::methods::D2H_SA_Energy::finalize_total_energy(), protocols::simple_moves::ExplicitWaterMover::find_closest(), protocols::simple_filters::HelixHelixAngleFilter::find_closest_res(), protocols::ligand_docking::LigandBaseProtocol::find_interface_rsds(), protocols::ddg::ddGMover::find_nbrs(), protocols::protein_interface_design::find_nearest_residue(), protocols::protein_interface_design::movers::find_nearest_residue_to_coord(), protocols::simple_filters::ResidueDepthCalculator::get_pose_crd_and_index(), protocols::neighbor::in_ngbat_sphere(), protocols::sic_dock::xyzStripeHashPoseWithMeta::init_with_pose(), protocols::ligand_docking::InterfaceBuilder::is_interface_residue(), core::scoring::is_nbr_atom(), protocols::ligand_docking::ga_ligand_dock::GridScorer::is_residue_in_grid(), protocols::scoring::Interface::ligand_calculate(), protocols::protein_interface_design::make_hotspot_foldtree(), protocols::ddg::ddGMover::neighborhood_of_mutations(), core::scoring::membrane::MPHelicalityEnergy::neighboring_atoms(), core::scoring::membrane::MPResidueLipophilicityEnergy::neighboring_atoms(), protocols::match::output::UpstreamDownstreamCollisionFilter::passes_hardsphere_filter(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::perform_bump_check(), protocols::cryst::MakeLatticeMover::place_near_origin(), protocols::protein_interface_design::movers::PlaceStubMover::place_stub(), protocols::flexpack::interaction_graph::OTFFlexbbEdge::prepare_for_simulated_annealing(), core::scoring::methods::BurialEnergy::residue_energy(), protocols::simple_filters::NonSequentialNeighborsFilter::residue_neighbors(), core::scoring::methods::CenPairEnergy::residue_pair_energy(), core::scoring::methods::CenRotPairEnergy::residue_pair_energy(), core::scoring::methods::SmoothCenPairEnergy::residue_pair_energy(), core::scoring::methods::MembraneCenPairEnergy::residue_pair_energy(), core::scoring::membrane::MPPairEnergy::residue_pair_energy(), core::scoring::methods::PairEnergy::residue_pair_energy(), core::scoring::hbonds::HBondEnergy::residue_pair_energy_ext(), core::conformation::residue_point_graph_from_conformation(), core::scoring::methods::residues_interact(), core::select::util::select_coord_for_residue(), core::pack::interaction_graph::SymmOnTheFlyEdge::set_residues_adjacent_for_subunit_pair(), core::scoring::constraints::SiteConstraint::setup_csts(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::superimpose_to_alternative_frame(), core::util::switch_to_centroid_rot_set(), core::pack::interaction_graph::SurfaceNode< V, E, G >::verify_patch_areas_correct(), and core::conformation::ResidueKinWriter::write_kin_header().

Vector const& core::conformation::Residue::nbr_atom_xyz ( ) const

inline

References atoms_, core::chemical::ResidueType::nbr_atom(), and rsd_type_.

Referenced by protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::append_metal_vsites(), protocols::hbnet::HBNet::atom_hbonds_to_bridging_water(), core::scoring::orbitals::OrbitalsStatistics::bb_stats(), core::pack::rotamer_set::build_anchorless_water_rotamers(), core::pack::rotamer_set::RotamerSet_::build_rotamers_for_concrete(), protocols::docking::EllipsoidalRandomizationMover::calculate_axes(), core::scoring::methods::ContactOrderEnergy::calculate_contact_order(), protocols::docking::EllipsoidalRandomizationMover::calculate_plane_axes(), core::scoring::methods::RG_Energy_Fast::calculate_rg_score(), protocols::scoring::Interface::center(), protocols::geometry::center_of_mass(), core::scoring::dna::DNA_EnvPairPotential::centroid_xyz(), protocols::denovo_design::DisulfidizeMover::check_disulfide_cb_distance(), core::scoring::nmr::NMRDummySpinlabelEnsemble::clash_check(), protocols::dna::close_to_dna(), protocols::fold_from_loops::utils::Nub::closest_binder(), protocols::scoring::Interface::closest_interface_residue(), protocols::ligand_docking::ga_ligand_dock::count_neighbors(), protocols::ligand_docking::ga_ligand_dock::count_neighbors_on_coord(), core::scoring::membrane::MPSpanInsertionEnergy::create_updated_span(), core::pose::rna::detect_base_contacts(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::eval_residue_pair_derivatives_one_way(), core::scoring::methods::FACTSEnergy::evaluate_rotamer_background_energies(), core::scoring::methods::GenBornEnergy::evaluate_rotamer_background_energies(), core::scoring::methods::MultipoleElecEnergy::evaluate_rotamer_background_energies(), core::scoring::methods::VdWTinkerEnergy::evaluate_rotamer_background_energies(), core::scoring::elec::FA_GrpElecEnergy::evaluate_rotamer_background_energies(), core::scoring::methods::FACTSEnergy::evaluate_rotamer_background_energy_maps(), core::scoring::methods::GenBornEnergy::evaluate_rotamer_background_energy_maps(), core::scoring::methods::MultipoleElecEnergy::evaluate_rotamer_background_energy_maps(), core::scoring::methods::VdWTinkerEnergy::evaluate_rotamer_background_energy_maps(), protocols::magnesium::SampleGrid::figure_out_scan_res(), core::scoring::methods::D2H_SA_Energy::finalize_total_energy(), protocols::ligand_docking::find_attach_pt(), protocols::ligand_docking::ga_ligand_dock::get_atomic_contacting_sidechains(), protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::get_contacting_reslist(), protocols::matdes::get_intra_contacts(), core::pose::rna::get_phosphate_atom_and_neighbor_list(), protocols::sic_dock::get_rg(), protocols::mpi_refinement::get_touched_res(), protocols::hbnet::HBNetStapleInterface::interhelical_contact(), protocols::match::NumNeighborsMPM::modified_match_positions(), protocols::ligand_docking::LigandDockProtocol::optimize_orientation3(), protocols::magnesium::pdbslice(), protocols::simple_moves::point_graph_dme(), protocols::hbnet::HBNet::quick_and_dirty_heavy_atom_is_unsat(), protocols::ligand_docking::LigandBaseProtocol::reorder_foldtree_around_mobile_regions(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::res_res_occ_sol_one_way(), core::conformation::symmetry::residue_center_of_mass(), core::scoring::nv::NVscore::residue_energy(), core::conformation::symmetry::return_nearest_residue(), core::scoring::orbitals::OrbitalsStatistics::sc_H_orbital(), core::scoring::methods::RG_LocalEnergy::setup_for_derivatives(), core::scoring::methods::RG_Energy_Fast::setup_for_derivatives(), protocols::sic_dock::scores::TrisBpyScore::TrisBpyScore(), core::scoring::methods::Burial_v2Energy::using_atom_distance(), protocols::hbnet::HBNet::water_clashes(), and protocols::dna::z_axis_dist().

Real core::conformation::Residue::nbr_radius ( ) const

inline

Returns the distance cutoff value used as a radius for neighbor definition.

References core::chemical::ResidueType::nbr_radius(), and rsd_type_.

Referenced by core::select::residue_selector::CloseContactResidueSelector::apply(), core::scoring::sasa::LeGrandSasa::calc_atom_masks(), core::scoring::calc_atom_masks(), core::scoring::nmr::NMRDummySpinlabelEnsemble::clash_check(), protocols::optimize_weights::IterativeOptEDriver::compute_rotamers_around_ligands(), core::conformation::Conformation::detect_bonds(), core::conformation::symmetry::SymmetricConformation::detect_disulfides(), core::conformation::Conformation::detect_disulfides(), core::scoring::hbonds::HBondEnergy::eval_residue_pair_derivatives(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::eval_residue_pair_derivatives_one_way(), core::scoring::methods::FACTSEnergy::evaluate_rotamer_background_energies(), core::scoring::methods::GenBornEnergy::evaluate_rotamer_background_energies(), core::scoring::methods::VdWTinkerEnergy::evaluate_rotamer_background_energies(), core::scoring::methods::MultipoleElecEnergy::evaluate_rotamer_background_energies(), core::scoring::elec::FA_GrpElecEnergy::evaluate_rotamer_background_energies(), core::scoring::methods::FACTSEnergy::evaluate_rotamer_background_energy_maps(), core::scoring::methods::GenBornEnergy::evaluate_rotamer_background_energy_maps(), core::scoring::methods::VdWTinkerEnergy::evaluate_rotamer_background_energy_maps(), core::scoring::methods::MultipoleElecEnergy::evaluate_rotamer_background_energy_maps(), protocols::ligand_docking::LigandBaseProtocol::find_interface_rsds(), core::pack::find_residue_max_radii(), protocols::task_operations::CrystalContactsOperation::is_crystal_contact(), protocols::ligand_docking::InterfaceBuilder::is_interface_residue(), protocols::ligand_docking::ga_ligand_dock::GridScorer::is_residue_in_grid(), protocols::scoring::Interface::ligand_calculate(), protocols::match::output::UpstreamDownstreamCollisionFilter::passes_hardsphere_filter(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::perform_bump_check(), core::pose::pose_max_nbr_radius(), core::pack::rotamer_set::RotamerSets::prepare_otf_graph(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::res_res_occ_sol_one_way(), core::scoring::methods::PairEnergy::residue_pair_energy(), core::scoring::hbonds::HBondEnergy::residue_pair_energy_ext(), core::scoring::methods::residues_interact(), core::pack::interaction_graph::SymmOnTheFlyEdge::set_residues_adjacent_for_subunit_pair(), and core::scoring::NeighborList::setup().

AtomIndices const& core::conformation::Residue::nbrs ( Size const  atm ) const

inline

Convenience synonym for bonded_neighbor.

References core::chemical::ResidueType::bonded_neighbor(), and rsd_type_.

Referenced by apply_transform_downstream(), core::scoring::hbonds::HBondEnergy::backbone_backbone_energy(), core::scoring::hbonds::HBondEnergy::backbone_sidechain_energy(), protocols::hbnet::UnsatSelector::compute(), protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::compute(), protocols::viewer::dump_residue_kinemage(), core::scoring::MultipoleElecPotential::find_params_and_neighbors(), core::scoring::hbonds::HBondEnergy::residue_pair_energy(), core::conformation::setup_links_simple(), protocols::match::output::ResidueKinemageWriter::write_rsd_coords(), and core::conformation::ResidueKinWriter::write_rsd_coords().

Size core::conformation::Residue::nchi ( ) const

inline

Returns the number of chi angles this residue has.

example(s): residue.nchi() See also: Residue Pose Pose.chi Pose.set_chi

References core::chemical::ResidueType::nchi(), and rsd_type_.

Referenced by protocols::splice::Splice::add_coordinate_constraints(), protocols::splice::SpliceManager::add_coordinate_constraints(), core::pose::add_variant_type_to_residue(), core::scoring::MultipoleElecPotential::align_residue_multipole_axes(), protocols::ligand_docking::LigandDockProtocol::append_ligand_docking_scores(), protocols::simple_moves::sidechain_moves::SetChiMover::apply(), protocols::pose_creation::MakePolyXMover::apply(), protocols::symmetry::SetupNCSMover::apply(), protocols::indexed_structure_store::apply_residue_entries_to_pose(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::assign_chi_for_interpolated_rotamer(), core::pack::rotamer_set::bb_independent_rotamers(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::best_rotamer_energy(), protocols::pose_metric_calculators::RotamerRecovery::chis_from_pose(), core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms(), core::conformation::Conformation::debug_residue_torsions(), protocols::metal_interface::dump_chis(), protocols::indexed_structure_store::extract_residue_entry(), core::io::raw_data::DecoyStruct::fill_pose(), core::scoring::motif::ResPairMotif::fill_pose_with_motif(), core::pack::rotamers::SingleBasicRotamerLibrary::fill_rotamer_vector(), core::io::silent::ProteinSilentStruct_Template< T >::fill_struct(), protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::get_chi_weight(), protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::get_contacting_reslist(), core::scoring::motif::MotifHash::get_matching_motifs(), protocols::ligand_docking::ga_ligand_dock::GAOptimizer::initialize_rotamer_set_and_scores(), protocols::optimize_weights::IterativeOptEDriver::measure_rotamer_recovery(), protocols::rotamer_recovery::RRComparerChiDiff::measure_rotamer_recovery(), core::pose::num_chi_angles(), protocols::qsar::scoring_grid::ChiAngleNormalization::operator()(), protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::perturb(), protocols::cryst::DockLatticeMover::perturb_chis(), protocols::simple_moves::PeriodicBoxMover::perturb_molecule_move(), core::scoring::motif::Xfres::place_sidechain_in_pose(), protocols::simple_moves::sidechain_moves::SidechainMover::proposal_density(), protocols::cryst::DockLatticeMover::randomize_chis(), core::pose::remove_variant_type_from_residue(), protocols::features::ProteinResidueConformationFeatures::report_features(), protocols::features::ResidueConformationFeatures::report_features(), Residue(), core::scoring::methods::FreeDOF_Energy::residue_energy(), core::scoring::motif::ResPairMotif::ResPairMotif(), protocols::loop_grower::ResTorsions::ResTorsions(), protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers::rotamer_set_contains_rotamer(), protocols::environment::ClientMover::sandboxed_copy(), set_all_chi(), core::conformation::set_chi_according_to_coordinates(), core::pack::scmin::ResidueAtomTreeCollection::set_rescoords(), core::pack::scmin::AtomTreeSCMinMinimizerMap::setup(), protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::setup_trj(), core::pack::scmin::ResidueAtomTreeCollection::update_residue(), core::conformation::Conformation::update_residue_torsions(), and core::pack::rotamers::SingleResidueRotamerLibrary::virtual_sidechain().

Size core::conformation::Residue::nheavyatoms ( ) const

inline

Returns the number of heavyatoms in this residue.

example(s): residue.nheavyatoms() See also: Residue Pose

References core::chemical::ResidueType::nheavyatoms(), and rsd_type_.

Referenced by core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_intra(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_one_way(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_one_way_bb_bb(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_one_way_sc(), protocols::hybridization::add_non_protein_cst(), core::scoring::sc::MolecularSurfaceCalculator::AddResidue(), core::scoring::methods::LK_hack::allocate_appropriate_memory(), core::scoring::Membrane_FAEmbed::allocate_appropriate_memory(), protocols::ligand_docking::LigandDockProtocol::append_ligand_docking_scores(), protocols::electron_density::ScaleMapIntensities::apply(), protocols::electron_density::ReportFSC::apply(), protocols::task_operations::SelectBySASAOperation::apply(), protocols::matdes::BuildingBlockInterfaceOperation::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::match::downstream::DownstreamAlgorithm::are_colliding(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::atom_is_heavy(), protocols::hydrate::atom_is_hydratable(), core::scoring::automorphic_rmsd(), protocols::electron_density::BfactorMultifunc::BfactorMultifunc(), core::scoring::atomic_depth::AtomicDepth::boundbox(), core::scoring::atomic_depth::AtomicDepth::boundingatom(), core::pack::rotamer_set::RotamerSet_::build_optimize_H_rotamers(), core::scoring::lkball::LKB_ResidueInfo::build_waters(), protocols::recces::sampler::rna::calc_base_centroid_rmsd(), core::scoring::calc_per_res_hydrophobic_sasa(), protocols::simple_filters::HelixHelixAngleFilter::calc_shortest_dist_by_atoms(), protocols::ligand_docking::ga_ligand_dock::GridScorer::calculate_grid(), core::scoring::lkball::LK_BallEnergy::calculate_lk_desolvation_of_single_atom_by_residue(), core::scoring::lkball::LK_BallEnergy::calculate_lk_desolvation_of_single_atom_by_residue_no_count_pair(), core::scoring::methods::LK_hack::calculate_orientation_vectors_and_pseudo_base_atoms(), protocols::pockets::NonPlaidFingerprint::calculate_protein_CoM(), core::scoring::fiber_diffraction::FiberDiffractionEnergyDens::calculate_rho_fast2(), core::scoring::packstat::cavity_distance_constraint(), protocols::ligand_docking::ligand_options::check_all_ligand_atoms(), core::scoring::rna::RNA_FullAtomStackingEnergy::check_base_base_OK(), core::scoring::rna::RNA_LowResolutionPotential::check_for_base_neighbor(), protocols::stepwise::modeler::packer::check_o2prime_contact(), protocols::scoring::ImplicitFastClashCheck::clash_check_trimer(), core::scoring::electron_density::ElectronDensity::clear_dCCdx_res_cache(), protocols::matdes::InterfacePackingFilter::compute(), protocols::protein_interface_design::filters::AtomicContactCountFilter::compute(), protocols::simple_filters::BuriedUnsatHbondFilter::compute(), protocols::matdes::SymUnsatHbondFilter::compute(), protocols::simple_filters::TaskAwareSASAFilter::compute(), core::scoring::packstat::compute_atom_packing_scores(), protocols::pockets::PlaidFingerprint::compute_ligand_natoms(), core::scoring::electron_density_atomwise::ElectronDensityAtomwise::compute_normalization(), core::pack::interaction_graph::SurfacePotential::compute_pose_hpatch_score(), protocols::optimize_weights::IterativeOptEDriver::compute_rotamers_around_ligands(), protocols::flexpack::rotamer_set::FlexbbRotamerSets::compute_sr_one_body_energies_for_flexsets(), protocols::pockets::counting_atoms_in_residue(), protocols::constraint_generator::CoordinateConstraintGenerator::create_residue_constraints(), core::scoring::hbonds::create_rotamer_descriptor(), core::scoring::elec::create_rotamer_descriptor(), core::scoring::lkball::create_rotamer_descriptor(), core::scoring::trie::create_trie(), protocols::cryst::crystRMS(), core::scoring::electron_density::ElectronDensity::dCCdBs(), protocols::ligand_docking::ga_ligand_dock::GridScorer::debug_deriv(), protocols::flexpack::interaction_graph::OTFFlexbbNode::declare_all_rotamers_initialized(), protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), protocols::cryst::MakeLatticeMover::detect_connecting_subunits(), core::pose::rna::detect_sugar_contacts(), protocols::electron_density::BfactorMultifunc::dfunc(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_intra(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_one_way(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_one_way_bb_bb(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_one_way_sc(), protocols::pockets::EggshellGrid::EggshellGrid(), core::scoring::electron_density::ElectronDensity::ElectronDensity(), protocols::match::downstream::ActiveSiteGrid::enlargen_to_capture_volume_within_radius_of_backbone(), protocols::match::downstream::ActiveSiteGrid::enlargen_to_capture_volume_within_radius_of_residue(), protocols::match::downstream::ActiveSiteGrid::enlargen_to_capture_volume_within_radius_of_sidechain(), protocols::hbnet::HBNet::estimate_saturation(), core::scoring::saxs::FastSAXSEnergy::eval_atom_derivative(), core::scoring::methods::SuckerEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensEnergy::eval_atom_derivative(), core::scoring::magnesium::MgEnergy::eval_mg_interaction(), core::scoring::magnesium::MgEnergy::eval_residue_pair(), core::scoring::electron_density::FastDensEnergy::eval_residue_pair_derivatives(), core::scoring::methods::LK_PolarNonPolarEnergy::eval_residue_pair_derivatives(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::eval_residue_pair_derivatives_one_way(), protocols::pockets::GenPharmacophore::extract_rna_rings_from_protein_rna_complex(), core::scoring::Membrane_FAPotential::fa_projection(), core::pose::rna::figure_out_number_base_contacts(), protocols::match::fill_grid_with_residue_heavyatom_spheres(), core::io::silent::BinarySilentStruct::fill_pose(), core::scoring::atomic_depth::AtomicDepth::fillvoxels(), protocols::metal_interface::find_closest_atom(), protocols::enzdes::DetectProteinLigandInterface::find_design_interface(), protocols::enzdes::DetectProteinLigandInterface::find_design_interface_arg_sweep(), protocols::ligand_docking::LigandBaseProtocol::find_interface_backbone(), protocols::ligand_docking::LigandBaseProtocol::find_interface_rsds(), core::scoring::fiber_diffraction::find_max_r(), core::scoring::fiber_diffraction::find_min_xyz(), core::scoring::fiber_diffraction::find_num_scattering_atoms(), protocols::hbnet::HBNet::find_unsats(), core::scoring::cryst::fix_bfactorsH(), core::scoring::cryst::fix_bfactorsMissing(), protocols::ligand_docking::frac_atoms_within(), protocols::constraint_movers::AddConstraintsToCurrentConformationMover::generate_coordinate_constraints(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_1b_energy(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_2b_energy(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::get_atom_lk_energy(), protocols::ligand_docking::ga_ligand_dock::get_atomic_contacting_sidechains(), core::scoring::dna::get_base_pair_stub_slow(), protocols::vip::VIP_Mover::get_cav_approx(), core::scoring::hackaro::HackAroEnergy::get_centroid(), protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::get_chi_weight(), protocols::magnesium::get_closest_non_hoh_contact(), protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::get_contacting_reslist(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_grid_atomtypes(), core::scoring::motif::MotifHash::get_matching_motifs(), protocols::magnesium::get_mg_ligands(), protocols::vip::VIP_Mover::get_neighbors(), protocols::simple_filters::ResidueDepthCalculator::get_pose_crd_and_index(), protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::get_possible_hbond_acceptors(), core::scoring::methods::Fa_MbsolvEnergy::get_residue_pair_energy(), core::scoring::membrane::FaMPSolvEnergy::get_residue_pair_energy(), core::scoring::methods::LK_PolarNonPolarEnergy::get_residue_pair_energy_one_way(), core::chemical::rna::get_rna_base_centroid(), protocols::pockets::GenPharmacophore::get_RNAring_sasa(), protocols::motifs::LigandMotifSearch::get_sphere_aa(), core::scoring::rna::data::RNA_DataBackboneEnergy::get_sugar_env_score(), protocols::ligand_docking::grid_rotamer_trials_atr_rep(), protocols::ligand_docking::grid_score(), protocols::ligand_docking::grid_score_atr_rep(), heavyAtoms_end(), protocols::magnesium::MgHydrater::hydrate_magnesium_in_pose(), core::conformation::idealize_hydrogens(), protocols::pockets::NonPlaidFingerprint::include_eggshell_points_based_on_known_ligand(), core::scoring::membrane::FaMPEnvEnergy::init(), core::scoring::membrane::FaMPSolvEnergy::init(), core::scoring::sasa::SasaCalc::init(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::init_from_ligand(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::init_from_ligand_pharmacophore(), protocols::match::downstream::LigandConformerBuilder::initialize_conformers(), protocols::toolbox::match_enzdes_util::LigandConformer::initialize_from_residue(), core::scoring::inline_intraresidue_atom_pair_energy(), core::scoring::inline_residue_atom_pair_energy(), core::scoring::inline_residue_atom_pair_energy_sidechain_backbone(), core::scoring::inline_residue_atom_pair_energy_sidechain_sidechain(), core::scoring::inline_residue_atom_pair_energy_sidechain_whole(), protocols::hydrate::is_inside(), protocols::ligand_docking::ga_ligand_dock::GridScorer::is_residue_in_grid(), core::scoring::rna::StackElecEnergy::is_rna_base(), core::pack::task::residue_selector::is_sc_bb_clash(), core::pack::task::residue_selector::is_sc_sc_clash(), protocols::stepwise::modeler::rna::is_virtual_base(), protocols::flexpep_docking::FlexPepDockingPoseMetrics::isInContact(), core::scoring::packstat::LeeRichards::LeeRichards(), protocols::scoring::Interface::ligand_calculate(), protocols::ligand_docking::make_atr_rep_grid(), protocols::ligand_docking::make_atr_rep_grid_without_ligands(), core::scoring::electron_density::ElectronDensity::matchPose(), core::scoring::electron_density::ElectronDensity::matchRes(), core::scoring::electron_density::ElectronDensity::matchResFast(), protocols::rotamer_recovery::RRComparerElecDensDiff::measure_rotamer_recovery(), protocols::rotamer_recovery::RRComparerAutomorphicRMSD::measure_rotamer_recovery(), protocols::loop_grower::LoopGrower::modifieddensity(), protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::moving_res_contact_filter(), core::pose::num_heavy_atoms(), protocols::electron_density::BfactorMultifunc::operator()(), protocols::qsar::scoring_grid::HeavyAtomNormalization::operator()(), protocols::ligand_docking::LigandDockProtocol::optimize_orientation3(), protocols::match::downstream::ActiveSiteGrid::or_within_radius_of_residue(), protocols::match::downstream::ActiveSiteGrid::or_within_radius_of_sidechain(), protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo::output_silent_file(), protocols::match::output::UpstreamDownstreamCollisionFilter::passes_hardsphere_filter(), protocols::match::output::UpstreamCollisionFilter::passes_hardsphere_filter(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::perform_bump_check(), protocols::kinmatch::BruteFunGroupTK::place_c(), protocols::kinmatch::BruteFunGroupTK::place_d(), protocols::recces::print_base_centroid_atoms_for_rb_entropy(), protocols::stepwise::modeler::rna::print_heavy_atoms(), protocols::pockets::PocketGrid::recenter(), protocols::simple_pose_metric_calculators::NumberHBondsCalculator::recompute(), protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::recompute(), protocols::toolbox::match_enzdes_util::InvrotTreeNode::remove_invrots_clashing_with_parent_res(), core::pose::PDBInfo::replace_res_remap_bfactors(), core::scoring::electron_density::ElectronDensity::rescale_fastscoring_temp_bins(), core::scoring::methods::Fa_MbenvEnergy::residue_energy(), protocols::membrane::scoring::FaWaterToBilayerEnergy::residue_energy(), core::scoring::membrane::FaMPEnvEnergy::residue_energy(), core::scoring::rna::RNA_FullAtomVDW_BasePhosphate::residue_energy(), core::pose::rna::residue_is_bulge(), protocols::sic_dock::residue_is_floppy(), core::scoring::hbonds::residue_near_water(), protocols::hydrate::residue_near_water(), core::scoring::methods::GaussianOverlapEnergy::residue_pair_energy(), core::scoring::methods::SuckerEnergy::residue_pair_energy(), core::scoring::rna::RNA_LJ_BaseEnergy::residue_pair_energy(), core::scoring::methods::LK_hack::residue_pair_energy(), core::scoring::elec::FA_ElecEnergy::residue_pair_energy(), core::scoring::methods::LK_PolarNonPolarEnergy::residue_pair_energy_ext(), core::scoring::rna::RNA_FullAtomStackingEnergy::residue_pair_energy_one_way(), core::scoring::electron_density_atomwise::ElectronDensityAtomwise::residue_score(), protocols::dna::PDBOutput::residues_are_different(), core::scoring::methods::PoissonBoltzmannEnergy::revamp_weight_by_burial(), protocols::pockets::PlaidFingerprint::rmsd(), protocols::qsar::scoring_grid::AtrGrid::set_ligand_rings(), protocols::qsar::scoring_grid::AtrGrid::set_protein_rings(), core::pack::scmin::CartSCMinMinimizerMap::setup(), core::scoring::saxs::FastSAXSEnergy::setup_for_derivatives(), core::scoring::membrane::FaMPEnvEnergy::setup_for_fullatom(), core::scoring::membrane::FaMPSolvEnergy::setup_for_fullatom(), core::scoring::saxs::FastSAXSEnergy::setup_for_scoring(), core::import_pose::setup_jumps(), core::scoring::setup_matching_heavy_atoms(), protocols::stepwise::modeler::rna::setup_suite_atom_id_map(), core::scoring::packstat::MultiProbePoseAccumulator::show(), protocols::hybridization::DDomainParse::split(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::superimpose_to_alternative_frame(), and protocols::electron_density::VoxelSpacingMultifunc::VoxelSpacingMultifunc().

basic::datacache::BasicDataCache& core::conformation::Residue::nonconst_data ( )

inline

BasicDataCache indexed by enum in residue_datacache.hh. Beware, this will crash if a call to nonconst_data_ptr() or data_ptr() has not previously been made on this Residue – the datacache is created just-in-time.

References data_cache_.

basic::datacache::BasicDataCacheOP core::conformation::Residue::nonconst_data_ptr ( )

inline

BasicDataCache indexed by enum in residue_datacache.hh.

Return an OP to the datacache

Note

Will create new one if not already initialized

References data_cache_, and core::conformation::residue_datacache::n_cacheable_types.

Referenced by core::pack::interaction_graph::SymmOnTheFlyNode::get_rotamer(), and core::conformation::Conformation::residue_data().

core::Angle core::conformation::Residue::nu ( core::uint const  index ) const

inline

Get a specific nu (internal ring) torsion angle by index.

Example: residue.nu(1)
See also:
Residue
Residue.nus
Residue.n_nus
Pose.set_ring_conformation
Pose
Pose.nu

Note

It is intentional that there is no set_nu() function; nu angles should only be modified together. Use Pose.set_ring_conformation() instead.

References nus_.

utility::vector1<AtomIndices> const core::conformation::Residue::nu_atoms ( ) const

inline

Return the AtomIndices of each set of four atoms defining each nu angle.

References core::chemical::ResidueType::nu_atoms(), and rsd_type_.

Referenced by core::conformation::Conformation::get_torsion_angle_atom_ids(), set_all_ring_nu(), set_tau(), and update_nus().

AtomIndices const core::conformation::Residue::nu_atoms ( core::uint const  index ) const

inline

Return the AtomIndices of the four atoms defining the specified nu angle.

References core::chemical::ResidueType::nu_atoms(), and rsd_type_.

utility::vector1<core::Angle> const& core::conformation::Residue::nus ( ) const

inline

Return the nu (internal ring) torsion angles of this residue.

Example: residue.nus()
See also:
Residue
Residue.nu
Residue.n_nus
Pose.set_ring_conformation
Pose
Pose.nu

References nus_.

Referenced by ring_conformer(), set_all_nu(), core::pack::rotamer_set::RotamerSubset::show(), core::pack::rotamer_set::RotamerSet_::show(), and core::conformation::Conformation::update_residue_torsions().

utility::vector1<core::Angle>& core::conformation::Residue::nus ( )

inline

Return the nu (internal ring) torsion angles of this residue. (non-const)

References nus_.

Residue const& core::conformation::Residue::operator= ( Residue const &  rhs )

private

Assignment operator does not work for class Residue. This function is intentionally unimplemented and private.

std::string const& core::conformation::Residue::orbital_name ( Size const  orbital_index ) const

inline

References core::chemical::Orbital::name(), core::chemical::ResidueTypeBase::orbital(), and rsd_type_.

chemical::orbitals::OrbitalType const& core::conformation::Residue::orbital_type ( Size const  orbital_index ) const

inline

References core::chemical::ResidueTypeBase::orbital_type(), and rsd_type_.

Referenced by core::scoring::orbitals::OrbitalsStatistics::bb_stats(), protocols::ligand_docking::rdf::RDFBinaryOrbitalFunction::operator()(), core::scoring::orbitals::OrbitalsStatistics::sc_H_orbital(), protocols::features::OrbitalsFeatures::set_OrbH_features_data(), and protocols::features::OrbitalsFeatures::set_OrbOrb_features_data().

Size core::conformation::Residue::orbital_type_index ( Size const  orbital_index ) const

inline

References orbitals_.

Referenced by core::scoring::orbitals::OrbitalsScore::assign_orb_H_derivs(), core::scoring::orbitals::OrbitalsScore::assign_orb_orb_derivs(), core::scoring::orbitals::OrbitalsScore::compute_orb_orb_E(), and core::scoring::orbitals::OrbitalsScore::get_orb_H_distance_and_energy().

Vector const& core::conformation::Residue::orbital_xyz ( Size const  orbital_index ) const

inline

References orbitals_.

Referenced by core::scoring::orbitals::OrbitalsScore::assign_orb_H_derivs(), core::scoring::orbitals::OrbitalsScore::assign_orb_orb_derivs(), core::scoring::orbitals::OrbitalsStatistics::bb_stats(), core::scoring::orbitals::OrbitalsScore::compute_orb_orb_E(), core::scoring::orbitals::OrbitalsScore::get_orb_H_distance_and_energy(), protocols::features::OrbitalsFeatures::report_hpol_orbital_interactions(), and core::scoring::orbitals::OrbitalsStatistics::sc_H_orbital().

void core::conformation::Residue::orient_onto_location	(	Size	center,
		Size	nbr1,
		Size	nbr2,
		Vector	center_locaton,
		Vector	nbr1_locaton,
		Vector	nbr2_locaton
	)

Orients residue object onto atom locations.

Note

Orients onto the atom numbers center, nbr1, nbr2.

References atom(), atoms(), core::chemical::ResidueType::natoms(), rsd_type_, and xyz().

Referenced by protocols::indexed_structure_store::apply_residue_entries_to_pose(), orient_onto_location(), and orient_onto_residue().

void core::conformation::Residue::orient_onto_location	(	Vector	center_locaton,
		Vector	nbr1_locaton,
		Vector	nbr2_locaton
	)

Orients residue object onto atom locations.

Note

Orients using default orient atoms taken from select_orient_atoms

References core::conformation::membrane::center, protocols::sic_dock::scores::nbr1(), protocols::sic_dock::scores::nbr2(), orient_onto_location(), and select_orient_atoms().

void core::conformation::Residue::orient_onto_residue

(

Residue const &

src

)

Orient our coords onto those of <src>, using the atoms from select_orient_atoms.

Helper function: selects atoms to orient on and transforms all of my atoms to orient onto another residue. Used by place(). Need to think a bit more about the restrictions on src...

References atom_index(), core::chemical::ResidueType::atom_index(), core::chemical::ResidueType::atom_name(), core::conformation::membrane::center, core::chemical::ResidueType::has(), core::chemical::ResidueTypeBase::name(), name(), protocols::sic_dock::scores::nbr1(), protocols::sic_dock::scores::nbr2(), rsd_type_, select_orient_atoms(), core::conformation::TR(), and type().

Referenced by protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_pose(), protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_wholepose(), protocols::simple_moves::chiral::ChiralMover::apply(), protocols::hbnet::hbnet_symm_one_body_energies(), orient_onto_residue(), place(), and core::conformation::Conformation::replace_residue().

void core::conformation::Residue::orient_onto_residue	(	Residue const &	src,
		utility::vector1< std::pair< std::string, std::string > > const &	atom_pairs
	)

Orient our coords onto those of <src>, using the three atom pairs specified in the input.

Parameters

atom_pairs

References atom_index(), and orient_onto_residue().

void core::conformation::Residue::orient_onto_residue ( Residue const &  src, Size  center, Size  nbr1, Size  nbr2, Size  src_center, Size  src_nbr1, Size  src_nbr2  )

private

Orient coords onto those of <src>, using the specified atoms.

References atom(), orient_onto_location(), and core::conformation::Atom::xyz().

void core::conformation::Residue::orient_onto_residue_peptoid	(	Residue const &	src,
		Conformation const &	conformation
	)

Orient our coords onto those of src, uses hard coded atom names (yuck) and will work for peptoid on to peptoid/peptide.

oritent onto residue for peptoids Not too proud of this as I think there is probably a more general way but at the moment it is alluding me To align a peptoid the N is the center and the nbrs are the lower connect and the CA. The lower connect is not stored in the atom index so we need to get the xyz coord a different way.

References core::chemical::ACETYLATED_NTERMINUS_VARIANT, atom(), atom_index(), atoms(), chain(), core::conformation::Conformation::chain_end(), connected_residue_at_lower(), core::chemical::AtomICoor::d(), has_variant_type(), icoor(), core::chemical::ResidueType::is_lower_terminus(), core::chemical::ResidueTypeBase::is_peptoid(), core::chemical::ResidueType::natoms(), core::conformation::Conformation::num_chains(), core::chemical::AtomICoor::phi(), core::conformation::Conformation::residue(), rsd_type_, core::conformation::Conformation::size(), core::chemical::AtomICoor::theta(), type(), core::conformation::Atom::xyz(), and xyz().

Referenced by place().

utility::vector1< int > const& core::conformation::Residue::path_distance ( Size  atom ) const

inline

Returns the shortest path distance from <atom> to any other atom in this residue.

example(s):

See also: Residue Residue.atom Residue.atoms Pose

References core::chemical::ResidueType::path_distance(), and rsd_type_.

Referenced by core::scoring::FACTSPotential::calculate_GBpair_v1trunk(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::check_path_distance(), core::scoring::etable::count_pair::CountPairGeneric::CountPairGeneric(), core::conformation::Conformation::detect_pseudobonds(), core::scoring::rna::RNA_FullAtomVDW_BasePhosphate::eval_atom_derivative(), core::scoring::MultipoleElecPotential::find_params_and_neighbors(), core::scoring::hbonds::identify_intra_res_hbonds(), core::scoring::trie::initialize_cpdata_for_atom(), core::chemical::rna::is_base_phosphate_atom_pair(), and core::scoring::carbon_hbonds::CarbonHBondEnergy::path_distance_OK().

int core::conformation::Residue::path_distance ( Size  at1, Size  at2  ) const

inline

Returns the number of bonds separating atom <at1> from <at2>

example(s):

See also: Residue Residue.atom Residue.atoms Residue.path_distance Pose

References core::chemical::ResidueType::path_distance(), and rsd_type_.

utility::vector1< utility::vector1< int > > const& core::conformation::Residue::path_distances ( ) const

inline

Returns the shortest path distance for any atom pair in this residue example: path_distances()[atom1][atom2].

example(s):

See also: Residue Residue.atom Residue.atoms Residue.path_distance Pose

References core::chemical::ResidueType::path_distances(), and rsd_type_.

bool core::conformation::Residue::place	(	Residue const &	src,
		Conformation const &	conformation,
		bool	preserve_c_beta = false
	)

Place this rotamer at the sequence position occupied by <src> by reorienting the ideal side chain coordinates to match.

Place/orient "this" Residue onto "src" Residue by backbone superimposition. This function is mainly used to place a rotamer onto the backbone of "src" residue. Meanwhile, it can also be used to add sidechains to one pose/conformation from another pose/conformation.
Current logic:

• Find backbone atom with bonded neighbors in sidechain, and which is the base_atom of those neighbors.
• Take that backbone atom and find two neighboring backbone heavyatoms.
• The three atoms to be superimposed with are
  • the center/base atom,
  • the backbone neighbor 1,
  • and the mid-point of backbone neighbor 1 and 2. This way, we can avoid large perturbation on backbone neighbor 2 after superimpostion if the two sets of backbone atoms are not perfectly superimposable, (e.g., with slightly different backbone geometry).
• After all atoms in "this" Residue are oriented, copy any corresponding backbone atom coords from "src", and if there are any backbone atoms missing from "src", (for example, src is a proline with HN missing), build them using ideal internal coords. (That is why "conformation" is needed as an input argument).
• For residues without any backbone atoms, (e.g., some ligands,) center on nbr_atom instead and two of its bonded neighbors, (preferring heavy atoms to hydrogens if possible.)

  Returns

  true on success; false on failure

References atom(), atom_depends_on_lower(), atom_depends_on_upper(), atom_index(), core::chemical::ResidueType::atom_is_backbone(), core::chemical::ResidueType::atom_is_hydrogen(), core::chemical::ResidueType::atom_name(), atom_name(), core::chemical::ICoorAtomID::atomno(), atoms(), chi_atoms(), core::chemical::AtomICoor::depends_on_polymer_lower(), core::chemical::AtomICoor::depends_on_polymer_upper(), fill_missing_atoms(), core::chemical::ResidueType::first_sidechain_atom(), core::chemical::ResidueType::has(), has(), core::chemical::ResidueType::icoor(), core::chemical::ResidueType::is_lower_terminus(), core::chemical::ResidueType::is_NA(), core::chemical::ResidueTypeBase::is_peptoid(), is_peptoid(), core::chemical::ResidueTypeBase::is_polymer(), is_RNA(), core::chemical::ResidueType::natoms(), natoms(), core::chemical::ResidueType::nheavyatoms(), orient_onto_residue(), orient_onto_residue_peptoid(), rsd_type_, core::chemical::AtomICoor::stub_atom1(), type(), core::conformation::Atom::xyz(), and xyz().

Referenced by protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::add_rotamer_to_rotamer_set(), core::pack::rotamer_set::AddResiduesRotamerSetOperation::alter_rotamer_set(), and Residue().

int core::conformation::Residue::polymeric_oriented_sequence_distance ( Residue const &  other ) const

inline

Returns the sequence separation distance between this residue and <other> positive if the other residue is downstream in sequence.

References chain(), chain_, is_polymer(), protocols::mean_field::max(), and seqpos_.

Referenced by core::scoring::hbonds::HBEvalTuple::HBEvalTuple(), and core::scoring::hbonds::hbond_evaluation_type().

Size core::conformation::Residue::polymeric_sequence_distance ( Residue const &  other ) const

inline

Returns the sequence separation distance between this residue and <other>

Note

: magnitude of distance only

References chain(), chain_, is_polymer(), and seqpos_.

Referenced by protocols::stepwise::screener::PartitionContactScreener::check_screen(), core::scoring::etable::count_pair::CountPairFactory::create_count_pair_function(), core::scoring::etable::count_pair::CountPairFactory::create_count_pair_function_and_invoke(), core::scoring::methods::CenHBEnergy::eval_residue_pair_derivatives(), core::scoring::methods::CenHBEnergy::eval_residue_pair_derivatives_soft(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_pair_deriv(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_pair_orientation_deriv(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_pair_orientation_score(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_pair_score(), core::scoring::MembranePotential::evaluate_pair(), core::scoring::SmoothEnvPairPotential::evaluate_pair_and_cenpack_deriv(), core::scoring::EnvPairPotential::evaluate_pair_and_cenpack_score(), core::scoring::SmoothEnvPairPotential::evaluate_pair_and_cenpack_score(), core::scoring::PairEPotential::pair_term_energy(), core::scoring::methods::GaussianOverlapEnergy::residue_pair_energy(), core::scoring::membrane::MPPairEnergy::residue_pair_energy(), and core::scoring::methods::CenHBEnergy::residue_pair_energy().

std::map< Size, PseudoBondCollectionCOP > const& core::conformation::Residue::pseudobonds ( ) const

inline

References pseudobonds_.

Referenced by core::scoring::trie::create_cpdata_correspondence_for_rotamer().

bool core::conformation::Residue::requires_actcoord ( ) const

inline

does this residue require an actcoord?

References core::chemical::ResidueType::requires_actcoord(), and rsd_type_.

Size core::conformation::Residue::residue_connect_atom_index ( Size const  resconn_id ) const

inline

References core::chemical::ResidueType::residue_connect_atom_index(), and rsd_type_.

Referenced by core::pose::Pose::append_residue_by_atoms(), protocols::ligand_docking::AddHydrogen::apply(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_perturb_backbone_by_bins(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_randomize_backbone_by_bins(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_set_backbone_bin(), core::conformation::Conformation::bonded_neighbor_all_res(), core::scoring::Ramachandran::eval_rama_score_residue_nonstandard_connection(), core::pose::symmetry::extract_asymmetric_unit(), protocols::generalized_kinematic_closure::general_set_phi(), protocols::generalized_kinematic_closure::general_set_psi(), protocols::generalized_kinematic_closure::GeneralizedKIC::generate_atomlist(), core::conformation::carbohydrates::get_linkage_position_of_saccharide_residue(), core::conformation::get_second_atom_from_connection(), has_incomplete_connection(), protocols::denovo_design::components::StructureDataFactory::infer_from_pose(), core::scoring::trie::initialize_cpdata_for_atom(), core::scoring::methods::lower_upper_connected_across_cutpoint(), n_bonded_neighbor_all_res(), protocols::cyclic_peptide::PeptideStubMover::rebuild_atoms(), core::conformation::Conformation::show_residue_connections(), and core::conformation::ConformationKinWriter::write_coords().

chemical::ResidueConnection const& core::conformation::Residue::residue_connection ( Size const  resconn_index ) const

inline

Returns this residue's ResidueConnection a ResidueConnection has internal coords info on how to build the atom in a different residue which connects to this residue.

References core::chemical::ResidueType::residue_connection(), and rsd_type_.

Referenced by core::util::add_constraints_to_metal(), core::conformation::Conformation::append_residue_by_bond(), protocols::ligand_docking::AddHydrogen::apply(), core::scoring::mm::connection_indices(), core::scoring::etable::count_pair::CountPairGeneric::CountPairGeneric(), core::scoring::etable::count_pair::CountPairFactory::create_count_pair_function(), core::scoring::etable::count_pair::CountPairFactory::create_count_pair_function_and_invoke(), core::conformation::Conformation::declare_chemical_bond(), core::conformation::Conformation::detect_bonds(), core::conformation::Conformation::detect_pseudobonds(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd1(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd2(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd1(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd2(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_bond_energy(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_bond_length_derivs(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_angle(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_bond(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_improper(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_torsion(), core::io::silent::BinarySilentStruct::fill_struct(), core::conformation::get_chemical_root_and_anchor_atomnos(), core::conformation::Conformation::insert_residue_by_bond(), protocols::features::ProteinBondGeometryFeatures::report_interres_angles(), protocols::features::ProteinBondGeometryFeatures::report_interres_lengths(), core::scoring::methods::MMBondLengthEnergy::residue_pair_energy(), core::scoring::methods::MMTorsionEnergy::residue_pair_energy(), and core::scoring::methods::MMBondAngleEnergy::residue_pair_energy().

Size core::conformation::Residue::residue_connection_conn_id ( Size const  resconn_index ) const

inline

Returns the connection id on the OTHER residue connected to this residue at this residue's connection resconn_index.

For example, if this were a normally-connected alpha amino acid, residue_connection_conn_id(1) would return 2, since the first connection in this residue is attached to the second connection in the previous residue.

References connect_map_.

Referenced by core::conformation::Conformation::backbone_torsion_angle_atoms(), core::conformation::Conformation::backbone_torsion_angle_atoms_meta_aramid(), core::conformation::Conformation::backbone_torsion_angle_atoms_oligourea(), core::conformation::Conformation::backbone_torsion_angle_atoms_ortho_aramid(), core::conformation::Conformation::backbone_torsion_angle_atoms_para_aramid(), core::pose::correctly_add_2prime_connection_variants(), core::pose::declare_cutpoint_chemical_bond(), core::conformation::Conformation::detect_pseudobonds(), core::scoring::methods::MMBondLengthEnergy::eval_atom_derivative(), core::scoring::methods::MMTorsionEnergy::eval_atom_derivative(), core::scoring::methods::MMBondAngleEnergy::eval_atom_derivative(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd1(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd2(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd1(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd2(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_bond_energy(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_bond_length_derivs(), core::scoring::methods::MMTorsionEnergy::eval_intrares_derivatives(), core::scoring::Ramachandran::eval_rama_score_residue_nonstandard_connection(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_angle(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_bond(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_improper(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_torsion(), core::scoring::methods::find_relevant_connections(), core::scoring::methods::find_relevant_connections_onersd(), protocols::generalized_kinematic_closure::general_set_phi(), protocols::generalized_kinematic_closure::general_set_psi(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_connectivity_annotation_info(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_link_record(), core::conformation::carbohydrates::get_linkage_position_of_saccharide_residue(), core::conformation::get_second_atom_from_connection(), inter_residue_connection_partner(), core::scoring::methods::lower_upper_connected_across_cutpoint(), protocols::features::ProteinBondGeometryFeatures::report_interres_angles(), protocols::features::ProteinBondGeometryFeatures::report_interres_lengths(), core::scoring::methods::MMBondLengthEnergy::residue_pair_energy(), core::scoring::methods::MMTorsionEnergy::residue_pair_energy(), core::scoring::methods::MMBondAngleEnergy::residue_pair_energy(), protocols::cyclic_peptide::crosslinker::TMA_Helper::update_tma_amide_bond_dependent_atoms_asymmetric(), and protocols::cyclic_peptide::crosslinker::TMA_Helper::update_tma_amide_bond_dependent_atoms_symmetric().

Size core::conformation::Residue::residue_connection_partner ( Size const  resconn_index ) const

inline

Returns the residue number of a residue connected to this residue at this residue's connection resconn_index.

For example, in a normally-connected pose made of alpha-amino acids, calling residue_connection_partner(1) on residue 6 should return 5, since residue 6 is connected to residue 5 at the first connection of residue 6.

References connect_map_.

Referenced by protocols::generalized_kinematic_closure::GeneralizedKIC::addloopgeometry(), protocols::generalized_kinematic_closure::GeneralizedKIC::addloweranchor(), protocols::generalized_kinematic_closure::GeneralizedKIC::addtailgeometry(), protocols::generalized_kinematic_closure::GeneralizedKIC::addupperanchor(), core::conformation::Conformation::align_virtual_atoms_in_carbohydrate_residue(), protocols::simple_moves::hbs::HbsPatcher::apply(), protocols::simple_moves::a3b_hbs::A3BHbsPatcher::apply(), core::pack::task::operation::NoRepackDisulfides::apply(), core::scoring::bin_transitions::BinTransitionCalculator::are_normally_bonded(), core::chemical::ICoorAtomID::atom_id(), core::conformation::Conformation::backbone_torsion_angle_atoms(), core::conformation::Conformation::branch_connection_torsion_angle_atoms(), copy_residue_connections(), core::conformation::Conformation::declare_chemical_bond(), core::scoring::methods::ProClosureEnergy::defines_score_for_residue_pair(), core::conformation::Conformation::detect_pseudobonds(), core::scoring::methods::determine_lo_and_hi_residues(), protocols::viewer::dump_residue_kinemage(), core::scoring::methods::MMBondLengthEnergy::eval_atom_derivative(), core::scoring::methods::MMTorsionEnergy::eval_atom_derivative(), core::scoring::methods::MMBondAngleEnergy::eval_atom_derivative(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd1(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd2(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd1(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd2(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_bond_energy(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_bond_length_derivs(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_improper_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_improper_energy(), core::scoring::methods::MMTorsionEnergy::eval_intrares_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_intrares_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_intrares_energy(), core::scoring::Ramachandran::eval_rama_score_residue(), core::scoring::Ramachandran::eval_rama_score_residue_nonstandard_connection(), core::scoring::methods::ProClosureEnergy::eval_residue_pair_derivatives(), core::conformation::carbohydrates::find_seqpos_of_saccharides_child_residue_at(), core::conformation::carbohydrates::find_seqpos_of_saccharides_parent_residue(), core::conformation::carbohydrates::get_downstream_residue_that_this_torsion_moves(), protocols::cyclic_peptide::crosslinker::TBMB_Helper::get_linker_index_asymmetric(), protocols::cyclic_peptide::crosslinker::TBMB_Helper::get_linker_indices_symmetric(), protocols::generalized_kinematic_closure::GeneralizedKIC::infer_anchor_connIDs(), core::scoring::PolymerBondedEnergyContainer::initialize_peptide_bonded_pair_indices(), inter_residue_connection_partner(), core::conformation::carbohydrates::is_glycosidic_omega_torsion(), core::conformation::carbohydrates::is_glycosidic_phi_torsion(), core::conformation::carbohydrates::is_glycosidic_psi_torsion(), core::pose::carbohydrates::is_glycosidic_torsion(), core::scoring::Ramachandran::is_normally_connected(), is_polymer_bonded(), core::scoring::PolymerBondedEnergyContainer::is_valid(), core::scoring::methods::ProClosureEnergy::measure_chi4(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::rama_energy(), core::scoring::methods::ProClosureEnergy::residue_pair_energy(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::RotamericSingleResidueDunbrackLibrary(), core::pose::carbohydrates::set_glycan_iupac_bb_torsions(), and update_connections_to_other_residue().

void core::conformation::Residue::residue_connection_partner	(	Size const	resconn_index,
		Size const	otherres,
		Size const	other_connid
	)

set a connection to this residue by adding its partner's residue number

set a connection to this residue by adding its partner's residue number

References connect_map_, determine_nonstandard_polymer_status(), and update_connections_to_residues().

chemical::rings::RingConformer const & core::conformation::Residue::ring_conformer	(	core::uint const	ring_num,
		core::Real	limit = 90.0
	)		const

Return the current RingConformer of this residue's nth ring.

References core::chemical::rings::AROMATIC, core::chemical::ResidueType::is_cyclic(), n_nus(), core::chemical::ResidueType::n_rings(), nus(), nus_, core::chemical::ResidueType::ring_atoms(), core::chemical::ResidueType::ring_conformer_set(), core::chemical::ResidueType::ring_saturation_type(), and rsd_type_.

Referenced by core::scoring::methods::CartesianBondedEnergy::eval_singleres_ring_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_ring_energies(), and show().

core::chemical::rna::RNA_Info const& core::conformation::Residue::RNA_info ( ) const

inline

Return the RNA_residueType object. This is RNA specific.

References core::chemical::ResidueType::RNA_info(), and rsd_type_.

Referenced by core::scoring::rna::RNA_SugarCloseEnergy::add_sugar_ring_closure_constraints(), protocols::pockets::GenPharmacophore::extract_rna_rings_from_protein_rna_complex(), core::chemical::rna::get_rna_base_centroid(), protocols::pockets::GenPharmacophore::get_RNAring_sasa(), and core::chemical::rna::is_base_phosphate_atom_pair().

void core::conformation::Residue::select_orient_atoms	(	Size &	center,
		Size &	nbr1,
		Size &	nbr2
	)		const

Selects three atoms for orienting this residue.

References rsd_type_, and core::chemical::ResidueType::select_orient_atoms().

Referenced by core::conformation::get_stub_from_residue(), orient_onto_location(), and orient_onto_residue().

Size core::conformation::Residue::seqpos ( ) const

inline

Returns the sequence position of this residue.

References seqpos_.

Referenced by protocols::simple_filters::SpanTopologyMatchPoseFilter::actual_topology(), core::io::pose_to_sfr::PoseToStructFileRepConverter::add_atom_to_sfr(), core::pack::task::residue_selector::add_clashes_to_shell(), core::scoring::dna::DNATorsionPotential::add_sugar_ring_closure_constraints(), core::scoring::rna::RNA_SugarCloseEnergy::add_sugar_ring_closure_constraints(), protocols::environment::add_variant(), core::scoring::sc::MolecularSurfaceCalculator::AddResidue(), core::scoring::MultipoleElecPotential::align_residue_multipole_axes(), protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers::alter_rotamer_set(), core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr(), core::scoring::hbonds::HBondSet::append_hbond(), core::select::residue_selector::ResidueInMembraneSelector::apply(), protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::apply(), core::scoring::bin_transitions::BinTransitionCalculator::are_normally_bonded(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::atom_has_exp_chemical_shift_data(), core::chemical::ICoorAtomID::atom_id(), protocols::qsar::scoring_grid::PCSSingleGrid::atom_score(), core::scoring::methods::atoms_interact(), core::scoring::automorphic_rmsd(), core::scoring::hbonds::HBondEnergy::backbone_backbone_energy(), core::scoring::hbonds::HBondEnergy::backbone_sidechain_energy(), core::scoring::dna::DNA_BasePotential::base_step_score(), core::scoring::orbitals::OrbitalsStatistics::bb_stats(), core::conformation::Conformation::branch_connection_torsion_angle_atoms(), protocols::match::downstream::SecondaryMatcherToDownstreamResidue::build(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::build_bbdep_rotamers(), core::scoring::MultipoleElecPotential::build_frame_and_rotate(), core::pack::rotamer_set::build_moving_O_bridge_waters(), core::pack::rotamer_set::RotamerSet_::build_optimize_H_rotamers(), core::conformation::build_residue_tree(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::build_rotamers(), core::pack::rotamer_set::RotamerSet_::build_rotamers_for_concrete(), core::scoring::sasa::LeGrandSasa::calc_atom_masks(), core::scoring::calc_atom_masks(), core::scoring::methods::MembraneEnvSmoothEnergy::calc_energy(), core::scoring::membrane::FaMPEnvSmoothEnergy::calc_energy(), core::scoring::membrane::MPHelicalityEnergy::calc_energy(), core::scoring::membrane::MPResidueLipophilicityEnergy::calc_energy(), core::scoring::methods::GoapEnergy::calculate_dipoles(), core::scoring::FACTSPotential::calculate_GBpair_exact(), core::scoring::FACTSPotential::calculate_GBpair_fast(), core::scoring::FACTSPotential::calculate_GBpair_v1trunk(), core::scoring::lkball::LK_BallEnergy::calculate_lk_ball_atom_energies_cp(), core::scoring::MultipoleElecPotential::calculate_res_res_fixed_fields_for_polarization(), core::scoring::MultipoleElecPotential::calculate_res_res_induced_fields_for_polarization(), core::scoring::membrane::MPHelicalityEnergy::centroid_neighbors(), core::scoring::membrane::MPResidueLipophilicityEnergy::centroid_neighbors(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::check_path_distance(), protocols::constraint_generator::HydrogenBondConstraintGenerator::choose_atoms(), protocols::simple_filters::TMsSpanMembraneFilter::compute(), protocols::simple_filters::InterfaceHbondsFilter::compute_hbonds(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_polar_group_sol_energy(), core::pack::interaction_graph::SurfacePotential::compute_pose_hpatch_score(), protocols::constraint_generator::compute_ref_atom(), core::pack::interaction_graph::SymmOnTheFlyNode::compute_rotamer_pair_energy(), connect_atom(), core::scoring::mm::connection_indices(), connections_to_residue(), core::pack::interaction_graph::NPDHBondEdge< V, E, G >::consider_alternate_state_step1(), copy_residue_connections(), core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms(), core::scoring::etable::count_pair::CountPairGeneric::CountPairGeneric(), protocols::constraint_generator::CoordinateConstraintGenerator::create_ambiguous_constraint(), core::scoring::etable::count_pair::CountPairFactory::create_count_pair_function(), core::scoring::etable::count_pair::CountPairFactory::create_count_pair_function_and_invoke(), core::scoring::trie::create_cpdata_correspondence_for_rotamer(), core::pack::interaction_graph::create_hbonds_one_way(), protocols::constraint_generator::HydrogenBondConstraintGenerator::create_residue_constraint(), protocols::constraint_generator::CoordinateConstraintGenerator::create_residue_constraints(), core::scoring::hbonds::create_rotamer_descriptor(), core::scoring::hbonds::HBondEnergy::create_rotamer_trie(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::create_rotamers_from_chisets(), protocols::cartesian::MolecularDynamics::createDihedral(), core::pack::rotamers::SingleResidueRotamerLibrary::current_rotamer(), core::scoring::electron_density::ElectronDensity::dCCdB_fastRes(), core::scoring::electron_density::ElectronDensity::dCCdx_fastRes(), protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::debug_note_considered_substitution(), core::pack::palette::PackerPalette::decide_what_to_do_with_base_type(), core::pack::palette::PackerPalette::decide_what_to_do_with_existing_type(), core::scoring::methods::ProClosureEnergy::defines_score_for_residue_pair(), core::scoring::disulfides::FullatomDisulfideEnergy::defines_score_for_residue_pair(), core::scoring::methods::LK_PolarNonPolarEnergy::defines_score_for_residue_pair(), core::scoring::rna::StackElecEnergy::defines_score_for_residue_pair(), core::scoring::elec::FA_GrpElecEnergy::defines_score_for_residue_pair(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::defines_score_for_residue_pair(), core::scoring::elec::FA_ElecEnergy::defines_score_for_residue_pair(), core::pack::hbonds::determine_atom_level_edge_info(), core::scoring::etable::BaseEtableEnergy< Derived >::determine_crossover_behavior(), determine_nonstandard_polymer_status(), core::scoring::etable::count_pair::CountPairFactory::determine_residue_connection(), protocols::viewer::dump_residue_kinemage(), protocols::matdes::dup_residue(), core::pack::rotamer_set::dup_residue(), core::pack::rotamers::dup_residue(), core::scoring::methods::MembraneEnvSmoothEnergy::eval_atom_derivative(), core::scoring::methods::EnvSmoothEnergy::eval_atom_derivative(), core::scoring::membrane::FaMPEnvSmoothEnergy::eval_atom_derivative(), core::scoring::dna::DNA_BasePotential::eval_base_pair_derivative(), core::scoring::dna::DNA_BasePotential::eval_base_step_derivative(), core::scoring::dna::DNA_BasePotential::eval_base_step_Z_scores(), protocols::match::downstream::ScoringSecMatchRPE::eval_cd_2b_residues(), core::scoring::elec::FA_GrpElecEnergy::eval_context_derivatives(), core::scoring::methods::dfire::DFIRE_Potential::eval_dfire_pair_energy(), core::scoring::methods::RamachandranEnergy2B::eval_dof_derivative(), core::scoring::dna::DNA_DihedralPotential::eval_harmonic_backbone_torsion_score_and_deriv(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd1(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd2(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd1(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd2(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_bond_energy(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_bond_length_derivs(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_improper_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_improper_energy(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_ring_energy(), core::scoring::hbonds::HBondEnergy::eval_intrares_derivatives(), core::scoring::elec::FA_GrpElecEnergy::eval_intrares_derivatives(), core::scoring::constraints::ConstraintsEnergy::eval_intrares_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_intrares_derivatives(), core::scoring::rna::RNA_TorsionPotential::eval_intrares_energy(), core::scoring::dna::DNATorsionEnergy::eval_intrares_energy(), core::scoring::methods::MMBondLengthEnergy::eval_intrares_energy(), core::scoring::methods::MMTorsionEnergy::eval_intrares_energy(), core::scoring::methods::MMBondAngleEnergy::eval_intrares_energy(), core::scoring::methods::Fa_MbsolvEnergy::eval_intrares_energy(), core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty::eval_intrares_energy(), core::scoring::methods::FACTSEnergy::eval_intrares_energy(), core::scoring::methods::GenBornEnergy::eval_intrares_energy(), core::scoring::elec::FA_GrpElecEnergy::eval_intrares_energy(), core::scoring::methods::MultipoleElecEnergy::eval_intrares_energy(), core::scoring::methods::VdWTinkerEnergy::eval_intrares_energy(), core::scoring::constraints::ConstraintSet::eval_intrares_energy(), core::scoring::hbonds::HBondEnergy::eval_intrares_energy(), core::scoring::methods::CartesianBondedEnergy::eval_intrares_energy(), core::scoring::methods::RamaPreProEnergy::eval_intraresidue_dof_derivative(), core::scoring::methods::CartesianBondedEnergy::eval_intraresidue_dof_derivative(), core::scoring::methods::DNA_DihedralEnergy::eval_residue_derivatives(), core::pack::dunbrack::cenrot::CenRotDunEnergy::eval_residue_dof_derivative(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_angle(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_bond(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_improper(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_torsion(), core::scoring::rna::StackElecEnergy::eval_residue_pair_derivatives(), core::scoring::methods::ProClosureEnergy::eval_residue_pair_derivatives(), core::scoring::rna::RNA_SuiteEnergy::eval_residue_pair_derivatives(), core::scoring::rna::TNA_SuiteEnergy::eval_residue_pair_derivatives(), core::scoring::methods::PairEnergy::eval_residue_pair_derivatives(), core::scoring::elec::FA_GrpElecEnergy::eval_residue_pair_derivatives(), core::scoring::SASAPotential::eval_residue_pair_derivatives(), core::scoring::constraints::ConstraintsEnergy::eval_residue_pair_derivatives(), core::scoring::elec::RNA_FA_ElecEnergy::eval_residue_pair_derivatives(), core::scoring::hbonds::HBondEnergy::eval_residue_pair_derivatives(), core::scoring::elec::FA_ElecEnergy::eval_residue_pair_derivatives(), core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy::eval_residue_pair_derivatives(), core::scoring::VdWTinkerPotential::eval_residue_pair_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_residue_pair_derivatives(), core::scoring::MultipoleElecPotential::eval_residue_pair_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_residue_pair_derivatives_sorted(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_angle(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_bond(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_improper(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_torsion(), core::scoring::elec::GroupElec::eval_respair_group_coulomb(), core::scoring::elec::GroupElec::eval_respair_group_derivatives(), core::scoring::rna::RNA_LowResolutionPotential::eval_rna_base_pair_energy_one_way(), core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::eval_rotameric_energy_deriv(), core::scoring::rna::TNA_SuitePotential::eval_score(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_angle_energies(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_improper_energies(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_length_energies(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_ring_energies(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_torsion_energies(), core::scoring::MembranePotential::evaluate_cbeta(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_env_and_cbeta_deriv(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_env_and_cbeta_score(), core::scoring::MembranePotential::evaluate_env(), core::scoring::SmoothEnvPairPotential::evaluate_env_and_cbeta_deriv(), core::scoring::EnvPairPotential::evaluate_env_and_cbeta_scores(), core::scoring::SmoothEnvPairPotential::evaluate_env_and_cbeta_scores(), protocols::scoring::InterchainPotential::evaluate_env_score(), core::scoring::FACTSPotential::evaluate_nonpolar_energy(), core::scoring::MembranePotential::evaluate_pair(), core::scoring::FACTSPotential::evaluate_polar_energy(), core::scoring::FACTSPotential::evaluate_polar_otf_energy(), core::scoring::rna::RNA_VDW_Energy::evaluate_rnp_vdw_score(), core::scoring::methods::MMLJEnergyInter::evaluate_rotamer_background_energies(), core::scoring::methods::FACTSEnergy::evaluate_rotamer_background_energies(), core::scoring::methods::GenBornEnergy::evaluate_rotamer_background_energies(), core::scoring::methods::MultipoleElecEnergy::evaluate_rotamer_background_energies(), core::scoring::methods::VdWTinkerEnergy::evaluate_rotamer_background_energies(), core::scoring::elec::FA_GrpElecEnergy::evaluate_rotamer_background_energies(), core::scoring::hbonds::HBondEnergy::evaluate_rotamer_background_energies(), core::scoring::elec::FA_ElecEnergy::evaluate_rotamer_background_energies(), core::scoring::etable::BaseEtableEnergy< Derived >::evaluate_rotamer_background_energies(), core::scoring::lkball::LK_BallEnergy::evaluate_rotamer_background_energies(), core::scoring::methods::FACTSEnergy::evaluate_rotamer_background_energy_maps(), core::scoring::methods::GenBornEnergy::evaluate_rotamer_background_energy_maps(), core::scoring::methods::MultipoleElecEnergy::evaluate_rotamer_background_energy_maps(), core::scoring::methods::VdWTinkerEnergy::evaluate_rotamer_background_energy_maps(), core::scoring::elec::FA_GrpElecEnergy::evaluate_rotamer_pair_energies(), protocols::pockets::GenPharmacophore::extract_Hbond_atoms_from_protein_rna_complex(), protocols::pockets::GenPharmacophore::extract_rna_rings_from_protein_rna_complex(), core::conformation::Conformation::fill_missing_atoms(), fill_missing_atoms(), core::pack::rotamers::SingleBasicRotamerLibrary::fill_rotamer_vector(), core::pack::rotamers::SingleLigandRotamerLibrary::fill_rotamer_vector(), core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::fill_rotamer_vector(), core::scoring::methods::MembraneLipo::finalize_total_energy(), core::pack::hbonds::find_hbonds_in_residue_pair(), core::scoring::MultipoleElecPotential::find_params_and_neighbors(), core::conformation::carbohydrates::find_seqpos_of_saccharides_child_residue_at(), core::scoring::loop_graph::get_6D_trans_rot_potential_evaluator(), core::conformation::get_anchor_and_root_atoms(), core::conformation::get_anchor_atomno(), core::scoring::carbon_hbonds::CarbonHBondEnergy::get_atom_atom_carbon_hbond_energy(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_acceptor(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_donor(), core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::get_atom_atom_occ_solvation(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::get_atom_atom_occ_solvation(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::get_atom_lk_energy(), core::scoring::rna::RNA_LowResolutionPotential::get_base_backbone(), core::scoring::dna::get_base_step_params(), core::scoring::rna::RNA_PairwiseLowResolutionEnergy::get_centroid_information(), core::scoring::rna::RNA_FullAtomStackingEnergy::get_count_pair_function(), core::scoring::vdwaals::VDW_Energy::get_count_pair_function_trie(), core::scoring::methods::MMLJEnergyInter::get_count_pair_function_trie(), core::scoring::elec::FA_ElecEnergy::get_count_pair_function_trie(), core::scoring::lkball::LK_BallEnergy::get_count_pair_function_trie(), core::scoring::etable::BaseEtableEnergy< Derived >::get_count_pair_function_trie(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_deriv_for_chemical_shift_data_atom(), core::scoring::disulfides::FullatomDisulfidePotential::get_disulfide_derivatives_old(), core::scoring::hbonds::get_hb_acc_chem_type(), core::scoring::hbonds::get_hb_don_chem_type(), core::conformation::carbohydrates::get_linkage_position_of_saccharide_residue(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_magnetic_anisotropy_deriv_for_src_atom(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_magnetic_anisotropy_deriv_for_src_base(), protocols::membrane::scoring::FaWaterToBilayerEnergy::get_menv_params_for_residue(), core::scoring::GenBornPotential::get_res_res_elecE(), core::scoring::MultipoleElecPotential::get_res_res_elecE(), core::scoring::SASAPotential::get_res_res_sasa(), core::scoring::VdWTinkerPotential::get_res_res_vdw(), core::conformation::get_residue_connections(), core::scoring::methods::Fa_MbsolvEnergy::get_residue_pair_energy(), core::scoring::membrane::FaMPSolvEnergy::get_residue_pair_energy(), core::scoring::methods::LK_PolarNonPolarEnergy::get_residue_pair_energy_one_way(), core::scoring::WaterAdductHBondPotential::get_residue_residue_h2o_hbonds_1way(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_ring_current_deriv_for_src_base(), core::conformation::get_root_residue_root_atomno(), core::pack::dunbrack::DunbrackEnergy::get_scratch_index(), core::conformation::get_second_atom_from_connection(), core::scoring::MultipoleElecPotential::get_single_rotamer_effective_radii(), core::scoring::hbonds::get_ssdep_weight(), core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy::has_bb_hbond_connection(), core::scoring::hbonds::hb_energy(), core::scoring::hbonds::HBondEnergy::hbond_derivs_1way(), protocols::simple_moves::ConstrainToIdealMover::i_want_this_atom_to_move(), core::scoring::hbonds::identify_hbonds_1way(), core::scoring::hbonds::identify_hbonds_1way_membrane(), protocols::neighbor::in_nrg_graph(), core::scoring::MultipoleElecResidueInfo::initialize(), protocols::match::upstream::ProteinUpstreamBuilder::initialize_rescoords(), core::pack::palette::PackerPalette::initialize_residue_level_task(), core::scoring::inline_intraresidue_atom_pair_energy(), core::scoring::inline_residue_atom_pair_energy(), core::conformation::Conformation::insert_residue_by_bond(), core::conformation::Conformation::insert_residue_by_jump(), core::conformation::insert_residue_into_atom_tree(), inter_residue_connection_partner(), core::chemical::rna::is_base_phosphate_atom_pair(), is_bonded(), protocols::task_operations::CrystalContactsOperation::is_crystal_contact(), protocols::scoring::Interface::is_interface(), core::scoring::Ramachandran::is_normally_connected(), protocols::scoring::Interface::is_pair(), is_polymer_bonded(), is_pseudo_bonded(), protocols::ligand_docking::ga_ligand_dock::GridScorer::is_residue_in_grid(), protocols::stepwise::modeler::rna::is_virtual_base(), core::scoring::methods::lower_upper_connected_across_cutpoint(), core::scoring::electron_density::ElectronDensity::matchAtomFast(), core::scoring::electron_density::ElectronDensity::matchResFast(), core::scoring::methods::ProClosureEnergy::measure_chi4(), protocols::rotamer_recovery::RRComparerElecDensDiff::measure_rotamer_recovery(), protocols::rotamer_recovery::RRComparerAutomorphicRMSD::measure_rotamer_recovery(), protocols::topology_broker::TMHTopologySamplerClaimer::move_spans(), core::scoring::membrane::MPHelicalityEnergy::neighboring_atoms(), core::scoring::membrane::MPResidueLipophilicityEnergy::neighboring_atoms(), core::scoring::MembranePotential::non_helix_in_membrane_penalty(), core::conformation::carbohydrates::GlycanTreeSet::on_length_change(), core::scoring::func::ResidueXYZ::operator()(), core::scoring::func::ResiduePairXYZ::operator()(), core::scoring::bin_transitions::BinTransitionCalculator::p_i_given_iplus1(), core::scoring::bin_transitions::BinTransitionCalculator::p_iplus1_given_i(), core::scoring::PairEPotential::pair_term_energy(), core::scoring::carbon_hbonds::CarbonHBondEnergy::path_distance_OK(), protocols::kinmatch::BruteFunGroupTK::place_c(), protocols::kinmatch::KinFunGroupTK::place_c(), protocols::kinmatch::BruteFunGroupTK::place_d(), protocols::kinmatch::KinFunGroupTK::place_h(), core::conformation::print_atom(), protocols::viewer::print_interres_bond(), protocols::viewer::print_node(), core::pack::reinitialize_mingraph_neighborhood_for_residue(), core::scoring::ScoreFunction::reinitialize_minnode_for_residue(), core::conformation::replace_residue_in_atom_tree(), protocols::features::ProteinBondGeometryFeatures::report_interres_angles(), protocols::features::ProteinBondGeometryFeatures::report_interres_lengths(), protocols::rotamer_recovery::RRReporterSQLite::report_predicted_features(), core::scoring::membrane::MPResidueLipophilicityEnergy::report_ressolv(), protocols::rotamer_recovery::PerNativeRRReporterHuman::report_rotamer_recovery(), protocols::rotamer_recovery::RRReporterSQLite::report_rotamer_recovery_features(), protocols::rotamer_recovery::RRReporterSQLite::report_rotamer_recovery_full(), core::scoring::FACTSPotential::res_res_burial(), core::scoring::GenBornPotential::res_res_burial(), core::scoring::FACTSPotential::res_res_burial_for_scoring(), core::scoring::func::ResidueXYZ::residue(), core::scoring::func::ResiduePairXYZ::residue(), core::scoring::methods::HRF_MSLabelingEnergy::residue_energy(), core::scoring::methods::BurialEnergy::residue_energy(), core::scoring::methods::CovalentLabelingFAEnergy::residue_energy(), core::scoring::methods::CovalentLabelingEnergy::residue_energy(), core::scoring::methods::Fa_MbenvEnergy::residue_energy(), core::scoring::rna::RNA_BulgeEnergy::residue_energy(), core::scoring::nv::NVscore::residue_energy(), core::scoring::methods::EnvEnergy::residue_energy(), core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::residue_energy(), core::scoring::methods::MembraneCbetaEnergy::residue_energy(), core::scoring::methods::SequenceDependentRefEnergy::residue_energy(), core::scoring::membrane::FaMPEnvEnergy::residue_energy(), core::scoring::membrane::MPCbetaEnergy::residue_energy(), core::scoring::methods::FreeDOF_Energy::residue_energy(), core::scoring::methods::MembraneEnvEnergy::residue_energy(), core::scoring::methods::MembraneEnvSmoothEnergy::residue_energy(), core::scoring::methods::P_AA_ss_Energy::residue_energy(), core::scoring::membrane::MPTerminiPenalty::residue_energy(), core::scoring::membrane::MPNonHelixPenalty::residue_energy(), core::scoring::methods::carbohydrates::SugarBackboneEnergy::residue_energy(), core::scoring::methods::EnvSmoothEnergy::residue_energy(), core::scoring::methods::NMerPSSMEnergy::residue_energy(), core::scoring::membrane::FaMPEnvSmoothEnergy::residue_energy(), core::scoring::membrane::MPEnvEnergy::residue_energy(), core::scoring::methods::NMerRefEnergy::residue_energy(), core::scoring::membrane::MPHelicalityEnergy::residue_energy(), protocols::fldsgn::potentials::AACompositionEnergy::residue_energy(), core::scoring::methods::NMerSVMEnergy::residue_energy(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::residue_energy(), core::scoring::GenericBondedPotential::residue_energy(), core::scoring::GenericBondedPotential::residue_pair_derivatives(), core::scoring::interface_::DDPscore::residue_pair_energy(), core::scoring::methods::RamachandranEnergy2B::residue_pair_energy(), core::scoring::sym_e::symEnergy::residue_pair_energy(), core::scoring::disulfides::DisulfideMatchingEnergy::residue_pair_energy(), core::scoring::disulfides::CentroidDisulfideEnergy::residue_pair_energy(), core::scoring::rna::RNA_StubCoordinateEnergy::residue_pair_energy(), core::scoring::methods::GaussianOverlapEnergy::residue_pair_energy(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::residue_pair_energy(), core::scoring::methods::CenPairEnergy::residue_pair_energy(), core::scoring::methods::MotifDockEnergy::residue_pair_energy(), core::scoring::methods::SuckerEnergy::residue_pair_energy(), core::scoring::methods::MembraneCenPairEnergy::residue_pair_energy(), core::scoring::rna::RNA_JR_SuiteEnergy::residue_pair_energy(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::residue_pair_energy(), core::scoring::rna::RNA_TorsionPotential::residue_pair_energy(), core::scoring::membrane::MPPairEnergy::residue_pair_energy(), core::scoring::rna::RNA_VDW_Energy::residue_pair_energy(), core::scoring::magnesium::RNA_MgPointEnergy::residue_pair_energy(), core::scoring::electron_density::FastDensEnergy::residue_pair_energy(), core::scoring::methods::PeptideBondEnergy::residue_pair_energy(), core::scoring::methods::DNA_BaseEnergy::residue_pair_energy(), core::scoring::rna::data::RNA_DataBackboneEnergy::residue_pair_energy(), core::scoring::methods::ProClosureEnergy::residue_pair_energy(), core::scoring::methods::MMBondLengthEnergy::residue_pair_energy(), core::scoring::methods::MMTorsionEnergy::residue_pair_energy(), core::scoring::methods::RamaPreProEnergy::residue_pair_energy(), core::scoring::methods::MMBondAngleEnergy::residue_pair_energy(), core::scoring::rna::RNA_FullAtomStackingEnergy::residue_pair_energy(), protocols::comparative_modeling::IgnoreSubsetConstraintSet::residue_pair_energy(), core::scoring::methods::Fa_MbsolvEnergy::residue_pair_energy(), core::scoring::methods::CustomAtomPairEnergy::residue_pair_energy(), core::scoring::electron_density::ElecDensEnergy::residue_pair_energy(), core::scoring::methods::PairEnergy::residue_pair_energy(), core::scoring::methods::AspartimidePenaltyEnergy::residue_pair_energy(), core::scoring::methods::FACTSEnergy::residue_pair_energy(), core::scoring::methods::DNA_ReferenceEnergy::residue_pair_energy(), core::scoring::hbonds::HBondEnergy::residue_pair_energy(), protocols::constraints_additional::MaxSeqSepConstraintSet::residue_pair_energy(), core::scoring::methods::GenBornEnergy::residue_pair_energy(), core::scoring::methods::PoissonBoltzmannEnergy::residue_pair_energy(), core::scoring::methods::GoapEnergy::residue_pair_energy(), core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty::residue_pair_energy(), core::scoring::elec::FA_GrpElecEnergy::residue_pair_energy(), core::scoring::disulfides::FullatomDisulfideEnergy::residue_pair_energy(), core::scoring::etable::BaseEtableEnergy< Derived >::residue_pair_energy(), core::scoring::methods::MultipoleElecEnergy::residue_pair_energy(), core::scoring::methods::VdWTinkerEnergy::residue_pair_energy(), core::scoring::GenericBondedPotential::residue_pair_energy(), core::scoring::constraints::ConstraintSet::residue_pair_energy(), core::scoring::methods::CartesianBondedEnergy::residue_pair_energy(), core::scoring::disulfides::FullatomDisulfideEnergy::residue_pair_energy_ext(), core::scoring::elec::RNA_FA_ElecEnergy::residue_pair_energy_ext(), core::scoring::methods::MultipoleElecEnergy::residue_pair_energy_ext(), core::scoring::methods::VdWTinkerEnergy::residue_pair_energy_ext(), core::scoring::hbonds::HBondEnergy::residue_pair_energy_ext(), core::scoring::rna::StackElecEnergy::residue_pair_energy_ext(), core::scoring::elec::FA_GrpElecEnergy::residue_pair_energy_ext(), core::scoring::elec::FA_ElecEnergy::residue_pair_energy_ext(), core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy::residue_pair_energy_ext(), core::scoring::magnesium::RNA_MgPointEnergy::residue_pair_energy_one_way(), core::scoring::rna::RNA_FullAtomStackingEnergy::residue_pair_energy_one_way(), core::scoring::rna::StackElecEnergy::residue_pair_energy_one_way(), core::scoring::methods::CartesianBondedEnergy::residue_pair_energy_sorted(), core::scoring::electron_density_atomwise::ElectronDensityAtomwise::residue_score(), core::pack::scmin::ResidueAtomTreeCollection::ResidueAtomTreeCollection(), protocols::environment::rm_variant(), core::scoring::rna::RNA_LowResolutionPotential::rna_backbone_backbone_pair_energy_one_way(), core::scoring::rna::RNA_PairwiseLowResolutionEnergy::rna_base_axis_pairwise_pair_energy(), core::scoring::rna::RNA_LowResolutionPotential::rna_base_backbone_pair_energy_one_way(), core::scoring::rna::RNA_PairwiseLowResolutionEnergy::rna_base_pair_pairwise_pair_energy(), core::scoring::rna::RNA_PairwiseLowResolutionEnergy::rna_base_stack_axis_pairwise_pair_energy(), core::scoring::rna::RNA_PairwiseLowResolutionEnergy::rna_base_stack_pairwise_pair_energy(), core::scoring::rna::RNA_PairwiseLowResolutionEnergy::rna_base_stagger_pairwise_pair_energy(), core::scoring::rna::RNA_LowResolutionPotential::rna_repulsive_pair_energy_one_way(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::rotamer_energy_deriv(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::rotamer_energy_deriv_bbdep(), core::scoring::same_polarization_group(), core::scoring::SASAShouldItCount(), core::scoring::orbitals::OrbitalsStatistics::sc_H_orbital(), protocols::qsar::scoring_grid::PCSSingleGrid::score(), core::scoring::MembranePotential::score_normal_center(), protocols::features::OrbitalsFeatures::set_OrbH_features_data(), protocols::features::OrbitalsFeatures::set_OrbOrb_features_data(), core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >::set_rotamer_dots_for_node_state(), core::conformation::setup_corresponding_atoms(), core::scoring::ScoreFunction::setup_for_lr2benmeth_minimization_for_respair(), core::scoring::ScoreFunction::setup_for_minimizing_for_node(), protocols::comparative_modeling::IgnoreSubsetConstraintSet::setup_for_minimizing_for_residue(), core::scoring::methods::MultipoleElecEnergy::setup_for_minimizing_for_residue(), core::scoring::methods::VdWTinkerEnergy::setup_for_minimizing_for_residue(), core::scoring::hbonds::HBondEnergy::setup_for_minimizing_for_residue(), core::scoring::constraints::ConstraintSet::setup_for_minimizing_for_residue(), core::scoring::disulfides::FullatomDisulfideEnergy::setup_for_minimizing_for_residue_pair(), protocols::comparative_modeling::IgnoreSubsetConstraintSet::setup_for_minimizing_for_residue_pair(), core::scoring::elec::RNA_FA_ElecEnergy::setup_for_minimizing_for_residue_pair(), protocols::constraints_additional::MaxSeqSepConstraintSet::setup_for_minimizing_for_residue_pair(), core::scoring::elec::FA_GrpElecEnergy::setup_for_minimizing_for_residue_pair(), core::scoring::elec::FA_ElecEnergy::setup_for_minimizing_for_residue_pair(), core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy::setup_for_minimizing_for_residue_pair(), core::scoring::constraints::ConstraintSet::setup_for_minimizing_for_residue_pair(), core::scoring::methods::GoapEnergy::setup_for_scoring(), protocols::stepwise::modeler::rna::setup_suite_atom_id_map(), core::scoring::ShouldItCount(), protocols::scoring::Interface::show(), core::scoring::dna::show_base_pair_params(), core::scoring::dna::show_base_pair_params_with_z_scores(), core::scoring::dna::show_new_base_step_params(), core::scoring::hbonds::HBondEnergy::sidechain_sidechain_energy(), protocols::enzdes::ModifyStoredRBConfs::swap_coordinates_in_pose(), core::scoring::MembranePotential::termini_penalty(), core::scoring::etable::etrie::TrieCountPairGeneric::TrieCountPairGeneric(), update_connections_to_other_residue(), core::conformation::carbohydrates::GlycanTree::update_on_length_change(), core::scoring::VdWShouldItCount(), protocols::symmetry::SymmetrySlider::very_far_away(), protocols::match::output::ResidueKinemageWriter::write_rsd_coords(), and core::conformation::ResidueKinWriter::write_rsd_coords().

void core::conformation::Residue::seqpos ( Size const  setting )

inline

Sets this residue's sequence position to <setting>

References seqpos_.

void core::conformation::Residue::set_all_chi

(

utility::vector1< Real > const &

chis

)

Sets all of this residue's chi angles using the set_chi function (wrapper function)

References nchi(), and set_chi().

Referenced by protocols::simple_moves::hbs::HbsPatcher::apply(), protocols::simple_moves::oop::OopPatcher::apply(), protocols::simple_moves::a3b_hbs::A3BHbsPatcher::apply(), and protocols::simple_moves::sidechain_moves::SidechainMover::dunbrack_accept().

void core::conformation::Residue::set_all_nu	(	utility::vector1< Real > const &	nus,
		utility::vector1< Real > const &	taus
	)

References nus(), nus_, and set_all_ring_nu().

void core::conformation::Residue::set_all_ring_nu	(	Size	start,
		Size	end,
		utility::vector1< Real > const &	nus,
		utility::vector1< Real > const &	taus
	)

References apply_transform_downstream(), atom(), core::chemical::ResidueType::nu_atoms(), nu_atoms(), nus_, rsd_type_, set_tau(), update_actcoord(), and xyz().

Referenced by set_all_nu().

void core::conformation::Residue::set_chi	(	int const	chino,
		Real const	setting
	)

Sets this residue's chi angle <chino> to <setting> assuming that changes propagate according to the atom_base tree.

this assumes that change propagates according to the information from atom_base array, not from atom tree. So be sure not to get into an endless loop.

References apply_transform_downstream(), atom(), core::chemical::ResidueType::atom_base(), chi_, core::chemical::ResidueType::chi_atoms(), chi_atoms(), rsd_type_, update_actcoord(), and xyz().

Referenced by protocols::protein_interface_design::movers::DisulfideMover::apply(), core::scoring::atomic_depth::AtomicDepth::AtomicDepth(), protocols::forge::remodel::build_and_score_disulfide(), core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms(), protocols::ligand_docking::ga_ligand_dock::GAOptimizer::initialize_rotamer_set_and_scores(), protocols::rotamer_recovery::RRProtocolRelax::run(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::run_docking(), and set_all_chi().

void core::conformation::Residue::set_d	(	int const	chino,
		Real const	setting
	)

bondlength analog to set_chi like set_chi, assumes changes propagate to atomtree keyed off of chi#, so we only allow distances corresponding to chi angles to refine distance corresponds to the distance between atoms 3 and 4 defining the chi chino==0 ==> CA-CB distance, which allows us to refine ALA CB position for example

Author

fpd

References apply_transform_downstream(), atom(), core::chemical::ResidueType::atom_base(), core::chemical::ResidueType::chi_atoms(), chi_atoms(), rsd_type_, update_actcoord(), and xyz().

void core::conformation::Residue::set_mirrored_relative_to_type ( bool const  setting )

inline

Set whether this residue is mirrored relative to its coordinates in the ResidueType.

Only used for achiral residues like glycine in the context of mirror symmetry and other mirror-image structures.

References mirrored_relative_to_type_.

Referenced by Residue().

void core::conformation::Residue::set_orbital_xyz ( core::Size const  orbital_index, Vector const &  xyz_in  )

inline

References core::chemical::ResidueTypeBase::orbital(), core::chemical::Orbital::orbital_type_index(), orbitals_, and rsd_type_.

Referenced by core::conformation::Conformation::update_orbital_coords(), and update_orbital_coords().

void core::conformation::Residue::set_pseudobonds_to_residue	(	Size	resid,
		PseudoBondCollectionCOP	pbs
	)

References pseudobonds_.

void core::conformation::Residue::set_tau	(	Size const	nuno,
		Real const	setting
	)

set_theta for nus

References apply_transform_downstream(), atom(), core::chemical::ResidueType::nu_atoms(), nu_atoms(), nus_, rsd_type_, update_actcoord(), and xyz().

Referenced by set_all_ring_nu().

void core::conformation::Residue::set_theta	(	int const	chino,
		Real const	setting
	)

bondangle analog to set_chi same idea as set_d

Author

fpd

References apply_transform_downstream(), atom(), core::chemical::ResidueType::atom_base(), core::chemical::ResidueType::chi_atoms(), chi_atoms(), rsd_type_, update_actcoord(), and xyz().

void core::conformation::Residue::set_xyz	(	core::Size const	atm_index,
		Vector const &	xyz_in
	)

Sets the position of this residue's atom with index number <atm_index>

example(s):

See also: Residue Residue.atom Residue.atoms Residue.xyz Pose

References atoms_.

Referenced by core::conformation::symmetry::SymmetricConformation::append_polymer_residue_after_seqpos(), core::conformation::symmetry::SymmetricConformation::append_residue_by_jump(), protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::apply(), protocols::splice::Splice::apply(), apply_transform_Rx_plus_v(), protocols::match::downstream::SecondaryMatcherToDownstreamResidue::build(), protocols::match::upstream::ProteinUpstreamBuilder::build(), protocols::enzdes::DiversifyStoredRBConfs::diversify_all_confs(), protocols::match::downstream::RigidLigandBuilder::downstream_pose_from_hit(), protocols::match::downstream::LigandConformerBuilder::downstream_pose_from_hit(), fill_missing_atoms(), protocols::splice::fix_chain_break_residue(), core::pack::interaction_graph::SymmOnTheFlyNode::get_rotamer(), core::conformation::idealize_hydrogens(), protocols::match::upstream::ProteinUpstreamBuilder::initialize_rescoords(), core::conformation::orient_residue_for_ideal_bond(), protocols::motifs::Motif::place_atoms_(), protocols::motifs::Motif::place_residue_(), protocols::match::downstream::SecondaryMatcherToDownstreamResidue::prepare_for_hit_generation_at_target_build_point(), protocols::enzdes::MinimizeStoredRBConfs::rb_minimize_all_confs(), protocols::match::upstream::ProteinUpstreamBuilder::recover_hits(), core::conformation::symmetry::SymmetricConformation::replace_residue(), protocols::simple_moves::PeriodicBoxMover::setup_pose(), protocols::enzdes::ModifyStoredRBConfs::swap_coordinates_in_pose(), core::pack::scmin::ResidueAtomTreeCollection::update_residue(), core::conformation::Conformation::update_residue_coordinates(), and protocols::kinmatch::xform_rsd_gl2().

void core::conformation::Residue::set_xyz	(	std::string const &	atm_name,
		Vector const &	xyz_in
	)

Sets the position of this residue's atom with name <atm_name>

example(s):

See also: Residue Residue.atom Residue.atoms Residue.xyz Pose

References atom(), and core::conformation::Atom::xyz().

void core::conformation::Residue::show	(	std::ostream &	output = std::cout,
		bool	output_atomic_details = false
	)		const

Generate string representation of Residue for debugging purposes.

Author

Labonte JWLab.nosp@m.onte.nosp@m.@jhu..nosp@m.edu

References atom_name(), atoms_, core::chemical::rings::AXIAL, core::chemical::rings::EQUATORIAL, get_adjacent_heavy_atoms(), core::conformation::is_atom_axial_or_equatorial_to_ring(), core::chemical::ResidueType::is_cyclic(), is_virtual(), mirrored_relative_to_type(), core::chemical::ResidueType::n_rings(), natoms(), core::chemical::rings::NEITHER, core::chemical::ResidueType::ring_atoms(), ring_conformer(), rsd_type_, seqpos_, core::conformation::Atom::show(), and core::chemical::ResidueType::show().

Referenced by core::conformation::operator<<().

Atoms::const_iterator core::conformation::Residue::sidechainAtoms_begin ( ) const

inline

should be safe, given the atom ordering rules?

References atoms_, and first_sidechain_atom().

Referenced by core::select::util::any_atoms_within_cutoff(), protocols::dna::argrot_dna_dis2(), protocols::dna::close_to_dna(), and protocols::simple_filters::AtomicContactFilter::compute().

ResidueType const& core::conformation::Residue::type ( ) const

inline

Returns this residue's ResidueType.

example(s): residue.type() See also: Residue Residue.type_ptr Residue.atom_type

References rsd_type_.

Referenced by core::util::add_constraints_to_metal(), protocols::relax::add_coordinate_constraint_func_atoms(), protocols::protein_interface_design::movers::add_coordinate_constraints(), protocols::ncbb::SecStructMinimizeMover::add_dihedral_constraints_to_pose(), protocols::legacy_sewing::Assembly::add_loop_segment(), protocols::motifs::add_motif_bb_constraints(), protocols::sewing::hashing::AlignmentFileGeneratorMover::add_pose_segments_to_segment_vector(), core::pack::dunbrack::RotamerConstraint::add_residue(), core::pack::rotamer_set::RotamerSubset::add_rotamer(), core::pack::rotamer_set::RotamerSet_::add_rotamer(), core::scoring::rna::RNA_SugarCloseEnergy::add_sugar_ring_closure_constraints(), core::pose::add_variant_type_to_residue(), core::scoring::sc::MolecularSurfaceCalculator::AddResidue(), core::scoring::MultipoleElecPotential::align_residue_multipole_axes(), protocols::denovo_design::movers::AlignResiduesMover::align_residues(), core::conformation::Conformation::align_virtual_atoms_in_carbohydrate_residue(), protocols::task_operations::PruneBuriedUnsats_RotamerSetsOperation::alter_rotamer_sets(), protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::analyze_trajectory(), core::select::util::any_atoms_within_cutoff(), core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr(), core::conformation::Conformation::append_residue(), core::conformation::Conformation::append_residue_by_bond(), core::io::pose_to_sfr::PoseToStructFileRepConverter::append_residue_info_to_sfr(), protocols::simple_moves::hbs::HbsPatcher::apply(), protocols::simple_moves::oop::OopPatcher::apply(), protocols::protein_interface_design::movers::PrepackMover::apply(), protocols::simple_moves::a3b_hbs::A3BHbsPatcher::apply(), protocols::ligand_docking::AddHydrogen::apply(), protocols::abinitio::DomainAssembly::apply(), protocols::cyclic_peptide::FlipChiralityMover::apply(), protocols::denovo_design::movers::DeclareStructureDataCovalentBondMover::apply(), protocols::simple_moves::SetTorsion::apply(), core::select::residue_selector::PhiSelector::apply(), protocols::cyclic_peptide::TryDisulfPermutations::apply(), protocols::ncbb::SecStructFinder::apply(), protocols::simple_moves::DumpSingleResidueRotamers::apply(), protocols::simple_moves::ReturnSidechainMover::apply(), core::pack::task::operation::NoRepackDisulfides::apply(), protocols::simple_moves::sidechain_moves::SidechainMover::apply(), protocols::denovo_design::movers::FastDesign::apply(), protocols::dna_dock::PropagateClashCheckFilter::apply(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::nmr::pre::PREMover::apply(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_alpha_aa_rama_check(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_loop_bump_check(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_perturb_dihedral_bbg(), protocols::loops::apply_sequence_mapping(), apply_transform_Rx_plus_v(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::apply_virtual_phosphate_variants(), core::scoring::bin_transitions::BinTransitionCalculator::are_normally_bonded(), assign_orbitals(), core::chemical::ICoorAtomID::atom_id(), protocols::minimization_packing::MinimalRotamer::atom_is_ideal(), core::scoring::atomic_depth::atomic_depth(), protocols::constraint_generator::AtomPairConstraintGenerator::atoms_to_constrain(), core::scoring::automorphic_rmsd(), core::scoring::elec::FA_ElecEnergy::backbone_backbone_energy(), core::scoring::elec::FA_ElecEnergy::backbone_sidechain_energy(), protocols::motifs::backbone_stub_match(), core::conformation::Conformation::backbone_torsion_angle_atoms(), protocols::stepwise::modeler::rna::base_atoms_square_deviation(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::bbdep_nrchi_score(), core::pack::dunbrack::RotamerLibrary::best_rotamer_energy(), protocols::sewing::hashing::LigandBindingResPlacer::best_rotamer_for_residue(), core::conformation::Conformation::bonded_neighbor_all_res(), core::scoring::atomic_depth::AtomicDepth::boundingatom(), core::conformation::break_disulfide(), protocols::match::downstream::RigidLigandBuilder::build(), protocols::match::downstream::ClassicMatchAlgorithm::build(), protocols::match::upstream::ProteinUpstreamBuilder::build(), protocols::simple_moves::ExplicitWaterMover::build_backbone_rotamer_clouds(), protocols::match::downstream::LigandConformerBuilder::build_conformer_group(), core::pack::rotamer_set::build_moving_O_bridge_waters(), core::pack::rotamer_set::build_moving_O_water_rotamers_dependent(), core::io::pose_from_sfr::PoseFromSFRBuilder::build_pdb_info_2_temps(), protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover::build_rotamer_list(), core::pack::rotamer_set::ContinuousRotamerSet::build_rotamers(), core::pack::rotamer_set::RotamerSet_::build_rotamers_for_concrete(), core::pack::rotamer_set::build_rotamers_from_rotamer_bins(), core::pack::rotamer_set::build_single_edge_waters(), core::scoring::lkball::LKB_ResidueInfo::build_waters(), core::scoring::sc::ElectrostaticComplementarityCalculator::Calc(), core::scoring::sc::MolecularSurfaceCalculator::Calc(), core::scoring::sasa::SasaCalc::calc_per_res_sasas(), core::scoring::rna::RNP_LowResPairDistPotential::calc_rnp_pair_dist_score(), protocols::antibody::AntibodyFeatures::calculate_cdr_aromatic_nres(), protocols::fldsgn::BluePrintBDR::centroid_build(), protocols::forge::components::BDR::centroid_build(), core::io::carbohydrates::chain_gws_string(), core::conformation::check_good_cutpoint_neighbour(), protocols::minimization_packing::MinimalRotamer::chi_matches_coords(), protocols::simple_filters::AtomicDistanceFilter::compute(), protocols::simple_filters::ResidueChiralityFilter::compute(), core::scoring::compute_bb_centroid(), core::scoring::compute_bb_radius(), core::scoring::compute_sc_centroid(), core::scoring::compute_sc_radius(), protocols::constraint_generator::HydrogenBondConstraintGenerator::compute_valid_atoms(), connect_atom(), connection_distance(), protocols::denovo_design::construct_poly_ala_pose(), protocols::toolbox::pose_manipulation::construct_poly_uniq_restype_pose(), copy_residue_connections(), core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::correct_termini_derivatives(), protocols::match::downstream::SecondaryMatcherToUpstreamResidue::count_rotamer(), protocols::constraint_generator::DistanceConstraintGenerator::create_constraint(), core::scoring::etable::count_pair::CountPairFactory::create_count_pair_function_and_invoke(), protocols::legacy_sewing::create_model_from_pose(), protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::create_random_fragments(), protocols::constraint_generator::HydrogenBondConstraintGenerator::create_residue_constraint(), protocols::rna::denovo::create_rna_vall_torsions(), core::scoring::hbonds::create_rotamer_descriptor(), core::scoring::elec::create_rotamer_descriptor(), core::pack::palette::PackerPalette::decide_what_to_do_with_base_type(), core::pack::palette::PackerPalette::decide_what_to_do_with_existing_type(), core::scoring::methods::ArgCationPiEnergy::defines_score_for_residue_pair(), core::scoring::disulfides::FullatomDisulfideEnergy::defines_score_for_residue_pair(), core::scoring::methods::GenericBondedEnergy::defines_score_for_residue_pair(), core::scoring::methods::YHHPlanarityEnergy::defines_score_for_rsd(), protocols::simple_moves::PeptideStapleMover::derive_staple_constraints_(), core::conformation::Conformation::detect_bonds(), core::conformation::symmetry::SymmetricConformation::detect_disulfides(), core::conformation::Conformation::detect_disulfides(), core::conformation::Conformation::detect_pseudobonds(), core::scoring::etable::BaseEtableEnergy< Derived >::determine_crossover_behavior(), core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup::determine_max_accepted_hbond_count(), determine_nonstandard_polymer_status(), core::scoring::constraints::NonResidueTypeConstraint::dist(), core::scoring::constraints::ResidueTypeConstraint::dist(), core::scoring::constraints::SequenceProfileConstraint::dist(), core::conformation::disulfide_bonds(), core::scoring::disulfides::DisulfideAtomIndices::DisulfideAtomIndices(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::disulfides_changed(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::disulfides_changed(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::disulfides_changed(), core::scoring::methods::LinearChainbreakEnergy::do_score_ovp(), core::io::carbohydrates::dump_gws(), protocols::viewer::dump_residue_kinemage(), protocols::ligand_docking::HighResDocker::enable_ligand_rotamer_packing(), protocols::ligand_docking::ProtLigEnsemble::enable_ligand_rotamer_packing(), protocols::simple_moves::DumpSingleResidueRotamers::enumerate_aa_rotamer(), core::scoring::rna::RNA_TorsionPotential::eval_atom_derivative(), core::scoring::methods::MembraneEnvSmoothEnergy::eval_atom_derivative(), core::scoring::methods::EnvSmoothEnergy::eval_atom_derivative(), core::scoring::membrane::FaMPEnvSmoothEnergy::eval_atom_derivative(), core::scoring::methods::dfire::DFIRE_Potential::eval_dfire_pair_energy(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd1(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd2(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd1(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd2(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_bond_energy(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_bond_length_derivs(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_improper_energy(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_ring_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_ring_energy(), core::scoring::methods::GenericBondedEnergy::eval_intrares_derivatives(), core::scoring::methods::MMTorsionEnergy::eval_intrares_derivatives(), core::scoring::elec::FA_ElecEnergy::eval_intrares_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_intrares_derivatives(), core::scoring::rna::RNA_TorsionPotential::eval_intrares_energy(), core::scoring::methods::MMBondLengthEnergy::eval_intrares_energy(), core::scoring::methods::MMTorsionEnergy::eval_intrares_energy(), core::scoring::methods::MMBondAngleEnergy::eval_intrares_energy(), core::scoring::methods::GenericBondedEnergy::eval_intrares_energy(), core::scoring::methods::MMLJEnergyIntra::eval_intrares_energy(), core::scoring::elec::FA_ElecEnergy::eval_intrares_energy(), core::scoring::methods::CartesianBondedEnergy::eval_intrares_energy(), core::scoring::methods::RamaPreProEnergy::eval_intraresidue_dof_derivative(), core::scoring::methods::CartesianBondedEnergy::eval_intraresidue_dof_derivative(), core::scoring::OmegaTether::eval_omega_score_residue(), core::scoring::Ramachandran2B::eval_rama_score_residue(), core::scoring::Ramachandran::eval_rama_score_residue(), core::scoring::Ramachandran::eval_rama_score_residue_nonstandard_connection(), core::scoring::HydroxylTorsionPotential::eval_residue_derivative(), core::pack::dunbrack::cenrot::CenRotDunEnergy::eval_residue_derivatives(), core::scoring::methods::RingClosureEnergy::eval_residue_derivatives(), core::scoring::methods::OmegaTetherEnergy::eval_residue_dof_derivative(), core::pack::dunbrack::DunbrackEnergy::eval_residue_dof_derivative(), core::pack::dunbrack::cenrot::CenRotDunEnergy::eval_residue_dof_derivative(), core::scoring::HydroxylTorsionPotential::eval_residue_energy(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_angle(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_bond(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_improper(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_torsion(), core::scoring::methods::ArgCationPiEnergy::eval_residue_pair_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_residue_pair_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_residue_pair_derivatives_sorted(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_angle(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_improper(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_torsion(), core::scoring::elec::GroupElec::eval_respair_group_coulomb(), core::scoring::elec::GroupElec::eval_respair_group_derivatives(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::eval_rotameric_energy_deriv(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_angle_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_angle_energies(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_improper_energies(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_length_energies(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_ring_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_ring_energies(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_torsion_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_torsion_energies(), core::scoring::EnvPairPotential::evaluate_pair_and_cenpack_score(), core::scoring::rna::RNA_VDW_Energy::evaluate_rnp_vdw_score(), protocols::constraint_generator::existing_atoms(), protocols::frag_picker::scores::FragmentCrmsd::fill_CA_coords(), core::conformation::Conformation::fill_missing_atoms(), fill_missing_atoms(), core::pack::rotamers::SingleBasicRotamerLibrary::fill_rotamer_vector(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::fill_rotamer_vector(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::fill_rotamer_vector_bbdep(), protocols::nmr::pcs::PCSLigandTransformMover::find_best_ligand_pose_with_grid_search(), protocols::denovo_design::DisulfidizeMover::find_current_disulfides(), protocols::abinitio::abscript::find_disulfide_partner(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::find_disulfides(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::find_disulfides(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::find_disulfides(), protocols::denovo_design::DisulfidizeMover::find_possible_disulfides(), core::conformation::carbohydrates::find_seqpos_of_saccharides_child_residue_at(), core::conformation::carbohydrates::find_seqpos_of_saccharides_parent_residue(), core::conformation::Conformation::fix_disulfides(), core::conformation::form_disulfide(), core::conformation::form_disulfide_helper(), protocols::ligand_docking::frac_atoms_within(), protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::fragment_check(), protocols::generalized_kinematic_closure::general_set_phi(), protocols::generalized_kinematic_closure::general_set_psi(), core::conformation::get_anchor_and_root_atoms(), core::scoring::custom_pair_distance::PairFuncMap::get_atom_pair_func_list(), get_atoms_exocyclic_to_ring_atom(), core::scoring::dna::get_base_stub(), core::scoring::methods::LK_PolarNonPolarEnergy::get_base_vector(), core::scoring::rna::get_bin(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_connectivity_annotation_info(), core::pose::get_constraints_from_link_records(), protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::get_contacting_reslist(), core::conformation::get_disulf_partner(), core::scoring::disulfides::FullatomDisulfidePotential::get_disulfide_derivatives(), core::scoring::orbitals::OrbitalsScore::get_E_haro_one_way(), core::scoring::orbitals::OrbitalsScore::get_E_hpol_one_way(), core::scoring::hbonds::get_hb_acc_chem_type(), core::scoring::hbonds::get_hb_don_chem_type(), protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::get_ideal_hxyz_positions(), core::scoring::elec::FA_ElecEnergy::get_intrares_countpair(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::get_matching_res_in_VDW_rep_screen_pose(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::get_movable_scs(), core::scoring::orbitals::OrbitalsScore::get_orb_orb_E(), core::scoring::P_AA::get_Paa_pp_deriv(), protocols::generalized_kinematic_closure::GeneralizedKIC::get_path(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_phi_from_rsd(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_psi_from_rsd(), protocols::enzdes::ModifyStoredRBConfs::get_rigid_body_confs(), core::scoring::methods::ArgCationPiEnergy::get_ring(), core::scoring::methods::ArgCationPiEnergy::get_ring_params(), core::chemical::rna::get_rna_base_centroid(), core::chemical::rna::get_rna_base_coordinate_system(), core::conformation::get_root_atomno(), core::conformation::get_root_residue_root_atomno(), core::pack::interaction_graph::SymmOnTheFlyNode::get_rotamer(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_rotamer_from_chi_static_voronoi(), protocols::loophash::get_rt_over_leap_without_foldtree_bs(), core::pack::dunbrack::DunbrackEnergy::get_scratch_index(), core::conformation::get_second_atom_from_connection(), core::pose::rna::get_sugar_centroid(), protocols::enzdes::EnzdesFlexBBProtocol::get_tenA_neighbor_residues(), core::pack::palette::PackerPalette::get_types_on_residue(), core::scoring::lkball::LKB_ResidueInfo::get_water_builder(), core::scoring::dna::get_y_axis(), protocols::cryst::getMW(), protocols::minimization_packing::MinimalRotamer::has_ideal_geometry(), core::scoring::bin_transitions::BinTransitionData::has_property(), protocols::simple_moves::ConstrainToIdealMover::i_want_this_atom_to_move(), core::conformation::idealize_position(), core::conformation::improper_build(), protocols::motifs::LigandMotifSearch::incorporate_motifs(), protocols::denovo_design::components::StructureDataFactory::infer_from_pose(), protocols::abinitio::abscript::RigidChunkCM::initialize(), core::scoring::FACTSPoseInfo::initialize(), protocols::match::downstream::LigandConformerBuilder::initialize_conformers(), protocols::topology_broker::TopologyBroker::initialize_cuts(), protocols::relax::RelaxProtocolBase::initialize_movemap(), protocols::stepwise::sampler::copy_dofs::ResidueAlternativeStepWiseSampler::initialize_residues_for_type(), protocols::features::RotamerInitializer< T, N >::initialize_rotamer(), protocols::ligand_docking::ga_ligand_dock::GAOptimizer::initialize_rotamer_set_and_scores(), protocols::toolbox::rigid_body::initialize_stub(), core::conformation::insert_ideal_bonds_at_polymer_junction(), core::conformation::insert_ideal_mainchain_bonds(), core::conformation::Conformation::insert_polymer_residue(), core::conformation::Conformation::insert_residue_by_bond(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::interpolate_rotamers(), core::conformation::is_atom_axial_or_equatorial(), core::conformation::is_disulfide_bond(), core::conformation::is_ideal_position(), core::scoring::sasa::SasaMethod::is_polar_atom(), core::scoring::rna::StackElecEnergy::is_rna_base(), core::pose::rna::is_rna_chainbreak(), core::pose::rna::is_tna_chainbreak(), core::scoring::lkball::LKB_ResidueInfo::LKB_ResidueInfo(), core::pack::dunbrack::load_unboundrot(), core::scoring::methods::IdealParametersDatabase::lookup_angle_legacy(), core::scoring::methods::IdealParametersDatabase::lookup_length_legacy(), core::pose::mass(), protocols::environment::ProtectedConformation::match_variants(), protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::max_allowed_hbonds(), core::scoring::methods::ProClosureEnergy::measure_chi4(), protocols::rotamer_recovery::RRComparerAutomorphicRMSD::measure_rotamer_recovery(), protocols::rotamer_recovery::RRComparerElecDensDiff::measure_rotamer_recovery(), protocols::rotamer_recovery::RRComparerRotBins::measure_rotamer_recovery(), protocols::rotamer_recovery::RRComparerChiDiff::measure_rotamer_recovery(), core::conformation::missing_stubs_build(), protocols::denovo_design::DisulfidizeMover::mixed_disulfide(), protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::moves_for_pose(), protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::moving_res_contact_filter(), protocols::denovo_design::DisulfidizeMover::mutate_disulfides_to_ala(), protocols::legacy_sewing::Assembly::native_positions(), core::scoring::OmegaTether::omega_index(), protocols::qsar::scoring_grid::MolecularWeightNormalization::operator()(), protocols::ligand_docking::rdf::RDFBinaryOrbitalFunction::operator()(), orient_onto_residue(), orient_onto_residue_peptoid(), core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::orient_rotamer_to_symmetric_partner(), core::chemical::sdf::MolWriter::output_residue(), core::scoring::OmegaTether::phi_index(), protocols::stepwise::modeler::rna::phosphate_base_phosphate_square_deviation(), place(), protocols::stepwise::modeler::rna::print_atom_info(), protocols::stepwise::modeler::rna::print_individual_atom_info(), protocols::match::output::print_node(), core::conformation::print_node(), protocols::simple_moves::sidechain_moves::SidechainMover::proposal_density(), core::scoring::OmegaTether::psi_index(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::rama_energy(), core::scoring::Ramachandran2B::RamaE(), core::scoring::Ramachandran2B::RamaE_Lower(), core::scoring::Ramachandran2B::RamaE_Upper(), protocols::denovo_design::rebuild_missing_atoms(), core::conformation::Conformation::rebuild_residue_connection_dependent_atoms(), protocols::simple_pose_metric_calculators::NumberHBondsCalculator::recompute(), protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::recompute(), protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::recompute(), protocols::minimization_packing::MinimalRotamer::record_chi(), protocols::minimization_packing::MinimalRotamer::record_internal_geometry(), protocols::loop_grower::LoopGrower::refine_cycle(), core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose(), protocols::stepwise::modeler::rna::remove_all_variant_types(), protocols::toolbox::match_enzdes_util::InvrotTreeNode::remove_invrots_clashing_with_parent_res(), core::pose::remove_variant_type_from_residue(), protocols::environment::ProtectedConformation::replace_residue_sandbox(), protocols::features::AtomAtomPairFeatures::report_atom_pairs(), protocols::features::ProteinBondGeometryFeatures::report_interres_angles(), protocols::features::ProteinBondGeometryFeatures::report_intrares_angles(), protocols::features::ProteinBondGeometryFeatures::report_intrares_lengths(), protocols::features::ProteinBondGeometryFeatures::report_intrares_torsions(), protocols::rotamer_recovery::RRReporterSQLite::report_rotamer_recovery_full(), protocols::nmr::pcs::PCSLigandTransformMover::reset_grid_and_bounding_box(), Residue(), protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::residue_conformations_redundant(), core::scoring::GenericBondedPotential::residue_derivatives(), core::scoring::methods::CovalentLabelingFAEnergy::residue_energy(), core::scoring::methods::UnfoldedStateEnergy::residue_energy(), core::scoring::methods::SplitUnfoldedTwoBodyEnergy::residue_energy(), core::scoring::methods::RamachandranEnergy::residue_energy(), core::scoring::methods::OmegaTetherEnergy::residue_energy(), core::scoring::methods::pHEnergy::residue_energy(), core::scoring::methods::RingClosureEnergy::residue_energy(), core::pack::dunbrack::cenrot::CenRotDunEnergy::residue_energy(), core::pack::dunbrack::DunbrackEnergy::residue_energy(), core::scoring::methods::ReferenceEnergyNoncanonical::residue_energy(), core::scoring::methods::ReferenceEnergy::residue_energy(), core::scoring::GenericBondedPotential::residue_energy(), core::scoring::GenericBondedPotential::residue_pair_derivatives(), core::scoring::methods::ArgCationPiEnergy::residue_pair_energy(), core::scoring::disulfides::DisulfideMatchingEnergy::residue_pair_energy(), core::scoring::disulfides::CentroidDisulfideEnergy::residue_pair_energy(), core::scoring::rna::RNA_VDW_Energy::residue_pair_energy(), core::scoring::methods::PeptideBondEnergy::residue_pair_energy(), core::scoring::methods::HybridVDW_Energy::residue_pair_energy(), core::scoring::methods::MMBondLengthEnergy::residue_pair_energy(), core::scoring::methods::MMTorsionEnergy::residue_pair_energy(), core::scoring::rna::RNP_LowResEnergy::residue_pair_energy(), core::scoring::rna::RNP_LowResPairDistEnergy::residue_pair_energy(), core::scoring::methods::RamaPreProEnergy::residue_pair_energy(), core::scoring::methods::MMBondAngleEnergy::residue_pair_energy(), core::scoring::methods::LK_hack::residue_pair_energy(), core::scoring::methods::CustomAtomPairEnergy::residue_pair_energy(), core::scoring::methods::MMLJEnergyInter::residue_pair_energy(), core::scoring::disulfides::FullatomDisulfideEnergy::residue_pair_energy(), core::scoring::elec::FA_ElecEnergy::residue_pair_energy(), core::scoring::GenericBondedPotential::residue_pair_energy(), core::scoring::methods::CartesianBondedEnergy::residue_pair_energy(), core::scoring::methods::CartesianBondedEnergy::residue_pair_energy_sorted(), core::scoring::residue_rmsd_nosuper(), core::scoring::residue_rmsd_super(), core::pack::dunbrack::RotamerLibrary::rotamer_energy(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::rotamer_energy_deriv(), core::pack::dunbrack::RotamerLibrary::rotamer_energy_deriv(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::rotamer_energy_deriv_bbdep(), core::pack::dunbrack::rotamer_from_chi(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::RotamericSingleResidueDunbrackLibrary(), core::scoring::ResidueExclParams::same_rsdpairs(), protocols::qsar::scoring_grid::LigandPropertyScore::score(), core::scoring::ProQPotential::score(), protocols::constraints_additional::SequenceCoupling1BDConstraint::score(), protocols::constraints_additional::SequenceCouplingConstraint::score(), core::scoring::constraints::SequenceProfileConstraint::score(), core::scoring::disulfides::FullatomDisulfidePotential::score_this_disulfide(), core::select::util::select_coord_for_residue(), protocols::loops::select_loop_residues(), core::conformation::Conformation::sequence_matches(), core::pack::scmin::ResidueAtomTreeCollection::set_rescoords(), core::pose::Pose::set_ring_conformation(), protocols::simple_moves::CyclizationMover::setup_connections(), protocols::simple_moves::CyclizationMover::setup_constraints(), core::conformation::setup_corresponding_atoms(), core::scoring::elec::FA_ElecEnergy::setup_for_minimizing_for_residue_pair(), core::scoring::elec::FA_ElecEnergy::setup_for_packing(), protocols::constraints_additional::BindingSiteConstraint::setup_for_scoring(), protocols::constraints_additional::COMCoordinateConstraint::setup_for_scoring(), core::scoring::methods::GoapEnergy::setup_for_scoring(), core::scoring::GenericBondedPotential::setup_for_scoring(), core::scoring::etable::TableLookupEtableEnergy::setup_for_scoring_(), core::scoring::etable::AnalyticEtableEnergy::setup_for_scoring_(), protocols::rna::denovo::movers::RNA_Minimizer::setup_movemap(), protocols::calc_taskop_movers::DesignRepackMover::setup_packer_and_movemap(), protocols::stepwise::modeler::rna::setup_suite_atom_id_map(), protocols::simple_moves::RandomOmegaFlipMover::setup_torsion_list(), protocols::simple_moves::RandomTorsionMover::setup_torsion_list(), core::scoring::hbonds::HBond::show(), core::scoring::elec::FA_ElecEnergy::sidechain_sidechain_energy(), protocols::match::downstream::SecondaryMatcherToUpstreamResidue::store_rotamer_coords(), core::scoring::orbitals::surrogate_atom_for_orbital(), protocols::enzdes::ModifyStoredRBConfs::swap_coordinates_in_pose(), protocols::denovo_design::movers::RotateSegmentMover::target_atoms(), core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::three_body_approximate_buried_unsat_calculation(), protocols::legacy_sewing::Assembly::to_multichain_pose(), protocols::legacy_sewing::Assembly::to_pose(), protocols::sewing::data_storage::SmartAssembly::to_pose(), update_connections_to_other_residue(), core::pose::rna::update_edge_hbond_numbers(), core::pose::rna::update_edge_hbond_numbers_careful_hydrogen(), core::pose::rna::update_map(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::update_VDW_screen_bin(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::use_this_atom(), protocols::mpi_refinement::StructAvrgMover::weighted_average(), core::io::serialization::write_binary(), and core::chemical::ICoorAtomID::xyz().

ResidueTypeCOP core::conformation::Residue::type_ptr ( ) const

inline

Returns this residue's ResidueType as a COP.

example(s): residue.typei_ptr() See also: Residue Residue.type Residue.atom_type

References rsd_type_ptr_.

Referenced by protocols::match::downstream::SecondaryMatcherToUpstreamResidue::build(), protocols::toolbox::pose_manipulation::construct_poly_uniq_restype_pose(), protocols::match::downstream::SecondaryMatcherToUpstreamResidue::count_rotamer(), core::scoring::trie::create_trie(), core::pack::palette::PackerPalette::decide_what_to_do_with_base_type(), core::pack::palette::PackerPalette::decide_what_to_do_with_existing_type(), core::scoring::methods::RamaPreProEnergy::eval_intraresidue_dof_derivative(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_chem_comp_type(), protocols::toolbox::match_enzdes_util::LigandConformer::initialize_from_residue(), protocols::match::downstream::RigidLigandBuilder::initialize_from_residue(), protocols::match::downstream::LigandConformerBuilder::initialize_from_residue(), protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::residue_conformations_redundant(), core::scoring::GenericBondedPotential::residue_derivatives(), core::scoring::GenericBondedPotential::residue_energy(), core::scoring::GenericBondedPotential::residue_pair_derivatives(), core::scoring::GenericBondedPotential::residue_pair_energy(), and protocols::match::downstream::SecondaryMatcherToUpstreamResidue::store_rotamer_coords().

void core::conformation::Residue::update_actcoord

(

)

Updates actcoord for this residue.

loop over all actcoord atoms for this ResidueType, average their actual positions in this residue.

References actcoord(), core::chemical::ResidueType::actcoord_atoms(), atoms(), and rsd_type_.

Referenced by set_all_ring_nu(), set_chi(), set_d(), protocols::features::OrbitalsFeatures::set_OrbH_features_data(), protocols::features::OrbitalsFeatures::set_OrbOrb_features_data(), set_tau(), set_theta(), and core::conformation::Conformation::update_residue_coordinates().

void core::conformation::Residue::update_connections_to_other_residue

(

Residue const &

other_rsd

)

Search through the other residue for connections to this residue, and ensure that this residue's connect_map is up to date with that residue's connection indices (and residue number).

Author

Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

Throws an error if this residue doesn't have a connection id indicated by the other residue. Overwrites connection ids otherwise, with no consideration of whether the original connection was to other_rsd.

Author

Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References connect_map(), connect_map_, connected_residue_at_resconn(), core::chemical::ResConnID::connid(), core::chemical::ResidueType::n_possible_residue_connections(), name(), residue_connection_partner(), seqpos(), core::conformation::TR(), and type().

void core::conformation::Residue::update_connections_to_residues ( )

private

Updates connections_to_residues_ using connect_map_.

Private function to keep the connections_to_residues_ array up to date

Note

This could be made faster – connections_to_residues_ is a std::map< > so operator[] calls are slow

References connect_map_, connections_to_residues_, and n_possible_residue_connections().

Referenced by residue_connection_partner(), and update_sequence_numbering().

void core::conformation::Residue::update_nus

(

)

Calculate the set of nu dihedrals from the xyz coordinates and store them.

References atom(), core::chemical::ResidueType::n_nus(), n_nus(), core::chemical::ResidueType::nu_atoms(), nu_atoms(), nus_, rsd_type_, and xyz().

Referenced by Residue().

void core::conformation::Residue::update_orbital_coords ( )

inline

References core::chemical::ResidueType::atoms_with_orb_index(), atoms_with_orb_index(), core::chemical::ResidueType::bonded_orbitals(), build_orbital_xyz(), rsd_type_, and set_orbital_xyz().

Referenced by core::scoring::orbitals::OrbitalsScore::setup_for_minimizing_for_residue_pair().

void core::conformation::Residue::update_sequence_numbering

(

utility::vector1< Size > const &

old2new

)

Updates the sequence numbers for this residue and the numbers stored about its non-polymer connections called by our owning conformation when the sequence numbers are remapped.

update sequence numbers for this residue and the numbers stored about its connections. called by our owning conformation when the sequence numbers are remapped

References connect_map_, determine_nonstandard_polymer_status(), pseudobonds_, seqpos_, and update_connections_to_residues().

chemical::ResidueConnection const& core::conformation::Residue::upper_connect ( ) const

inline

Returns this residue's upper_connection a ResidueConnection has internal coords info on how to build the atom in the next residue which connects to this residue.

References rsd_type_, and core::chemical::ResidueType::upper_connect().

Referenced by core::conformation::Conformation::append_polymer_residue_after_seqpos(), core::conformation::Conformation::append_residue_by_bond(), core::scoring::methods::ProClosureEnergy::defines_score_for_residue_pair(), core::scoring::methods::determine_lo_and_hi_residues(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd1(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd2(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd1(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd2(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_bond_energy(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_bond_length_derivs(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_improper_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_improper_energy(), core::scoring::methods::CartesianBondedEnergy::eval_intrares_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_intrares_energy(), core::scoring::methods::ProClosureEnergy::eval_residue_pair_derivatives(), protocols::loops::loop_closure::ccd::get_deviation(), protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger::KIC_loop_close(), core::scoring::methods::ProClosureEnergy::measure_chi4(), core::conformation::Conformation::prepend_polymer_residue_before_seqpos(), and core::scoring::methods::ProClosureEnergy::residue_pair_energy().

Size core::conformation::Residue::upper_connect_atom ( ) const

inline

Returns the index number of this residue's atom which connects to the residue after it in sequence.

Note

: polymers only, example: for an amino acid, residue.upper_connect_atom() = atom_index("C")

example(s): residue.upper_connect_atom() See also: Residue Residue.atom Residue.atoms Residue.lower_connect_atom Pose

References rsd_type_, and core::chemical::ResidueType::upper_connect_atom().

Referenced by protocols::forge::methods::add_cutpoint_variants(), protocols::denovo_design::add_cutpoints(), protocols::loops::add_single_cutpoint_variant(), core::conformation::Conformation::append_residue_by_bond(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::idealize::basic_idealize(), protocols::LoopRebuild::build_loop_with_ccd_closure(), connect_atom(), core::pose::declare_cutpoint_chemical_bond(), protocols::loophash::FastGapMover::find_next_gap(), core::scoring::MultipoleElecPotential::find_params_and_neighbors(), core::conformation::get_anchor_atomno(), core::conformation::get_root_atomno(), core::scoring::methods::lower_upper_connected_across_cutpoint(), protocols::forge::methods::make_star_foldtree(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::model_loop(), protocols::denovo_design::movers::new_jump_and_cutpoint(), and protocols::loops::set_loop_cutpoint_in_pose_fold_tree().

Vector const& core::conformation::Residue::xyz ( Size const  atm_index ) const

inline

Returns the position of this residue's atom with index number <atm_index>

Note

: position is a Vector

example(s): residue.xyz(3) See also: Residue Residue.atom Residue.atoms Residue.set_xyz Pose

References atoms_.

Referenced by core::pose::motif::a(), protocols::LoopRebuild::acceptable_rmsd_change(), protocols::rna::movers::RNAThreadAndMinimizeMover::accomodate_length_change(), protocols::hybridization::add_constraints(), protocols::constraint_generator::AtomPairConstraintGenerator::add_constraints(), core::util::add_constraints_to_metal(), protocols::relax::add_coordinate_constraint_func_atoms(), protocols::protein_interface_design::movers::add_coordinate_constraints(), protocols::seeded_abinitio::add_coordinate_constraints(), protocols::splice::Splice::add_coordinate_constraints(), protocols::splice::SpliceManager::add_coordinate_constraints(), core::util::add_covalent_linkage(), protocols::mpi_refinement::StructAvrgMover::add_deviations(), protocols::seeded_abinitio::add_dist_constraints(), protocols::mpi_refinement::add_init_dev_penalty(), protocols::motifs::add_motif_bb_constraints(), protocols::motifs::add_motif_sc_constraints(), protocols::hybridization::add_non_protein_cst(), protocols::hybridization::add_strand_pairs_cst(), core::scoring::sc::MolecularSurfaceCalculator::AddResidue(), protocols::hybridization::HybridizeProtocol::align_by_domain(), core::scoring::MultipoleElecPotential::align_residue_multipole_axes(), protocols::forge::remodel::RemodelGlobalFrame::align_segment(), protocols::cyclic_peptide::SymmetricCycpepAlign::align_to_origin(), protocols::cyclic_peptide::SymmetricCycpepAlign::align_to_zaxis(), core::conformation::all_atom_center(), protocols::matdes::MotifHitsRotamersOperation::alter_rotamer_set(), core::scoring::APBSConfig::APBSConfig(), protocols::ligand_docking::LigandDockProtocol::append_ligand_docking_scores(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::append_metal_vsites(), core::conformation::symmetry::SymmetricConformation::append_polymer_residue_after_seqpos(), core::conformation::symmetry::SymmetricConformation::append_residue_by_jump(), protocols::simple_moves::ReportXYZ::apply(), protocols::protein_interface_design::movers::AddChainBreak::apply(), protocols::magnesium::MgMinimizer::apply(), protocols::symmetry::DetectSymmetry::apply(), protocols::antibody::CloseOneCDRLoop::apply(), protocols::ligand_docking::RigidSearchMover::apply(), protocols::simple_moves::CombinePoseMover::apply(), protocols::frag_picker::nonlocal::NonlocalFrags::apply(), protocols::domain_assembly::PostDockAssemblyScorer::apply(), protocols::matdes::ExtractSubposeMover::apply(), protocols::stepwise::modeler::packer::SideChainCopier::apply(), protocols::splice::FindEndpointsOperation::apply(), protocols::topology_broker::RigidBodyRandomTMHMover::apply(), protocols::comparative_modeling::PartialThreadingMover::apply(), protocols::protein_interface_design::movers::PlacementAuctionMover::apply(), protocols::fold_from_loops::constraint_generator::AutomaticSheetConstraintGenerator::apply(), protocols::matdes::BuildingBlockInterfaceOperation::apply(), protocols::constraint_generator::DihedralConstraintGenerator::apply(), protocols::task_operations::DesignAroundOperation::apply(), protocols::protein_interface_design::movers::LoopFinder::apply(), protocols::simple_moves::ShortBackrubMover::apply(), protocols::flexpep_docking::FlexPepDockingProtocol::apply(), protocols::simple_filters::SheetFilter::apply(), protocols::fldsgn::filters::StrandCurvatureByLevels::apply(), protocols::membrane_benchmark::MembraneEnergyLandscapeSampler::apply(), protocols::minimization_packing::RotamerizeMover::apply(), core::select::residue_selector::CloseContactResidueSelector::apply(), protocols::ligand_docking::TransformEnsemble::apply(), protocols::task_operations::RestrictToMoveMapChiOperation::apply(), protocols::splice::Splice::apply(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::simple_task_operations::RestrictToInterface::apply(), protocols::antibody_legacy::CloseOneMover::apply(), protocols::cryst::MakeLatticeMover::apply(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_atom_pair_distance(), protocols::hybridization::CartesianHybridize::apply_frag(), protocols::hybridization::CartesianSampler::apply_frame(), protocols::simple_filters::EnergyPerResidueFilter::apply_helper(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_loop_bump_check(), apply_transform_downstream(), apply_transform_Rx_plus_v(), protocols::match::downstream::DownstreamAlgorithm::are_colliding(), core::scoring::methods::ResidualDipolarCouplingEnergy_Rohl::assemble_datamatrix(), core::scoring::orbitals::OrbitalsScore::assign_orb_H_derivs(), core::scoring::orbitals::OrbitalsScore::assign_orb_orb_derivs(), core::scoring::MultipoleElecPotential::assign_residue_amoeba_type(), protocols::match::upstream::ProteinUpstreamBuilder::atom_coordinate_unacceptable(), protocols::splice::atom_dist_with_zero(), protocols::simple_filters::atom_distance(), protocols::protein_interface_design::filters::atom_distance(), core::scoring::electron_density_atomwise::ElectronDensityAtomwise::atom_gradient(), protocols::hbnet::HBNet::atom_hbonds_to_bridging_water(), protocols::hydrate::atom_is_hydratable(), protocols::minimization_packing::MinimalRotamer::atom_is_ideal(), protocols::qsar::scoring_grid::HbaGrid::atom_score(), protocols::qsar::scoring_grid::HbdGrid::atom_score(), protocols::qsar::scoring_grid::VdwGrid::atom_score(), protocols::qsar::scoring_grid::ShapeGrid::atom_score(), protocols::qsar::scoring_grid::ChargeGrid::atom_score(), protocols::qsar::scoring_grid::SingleGrid::atom_score(), protocols::qsar::scoring_grid::PCSSingleGrid::atom_score(), protocols::motifs::atom_specific_rms(), protocols::stepwise::modeler::rna::atom_square_deviation(), core::scoring::methods::atoms_interact(), core::scoring::elec::FA_ElecEnergy::backbone_backbone_energy(), core::scoring::elec::FA_ElecEnergy::backbone_sidechain_energy(), protocols::motifs::backbone_stub_match(), core::scoring::constraints::BackboneStubConstraint::BackboneStubConstraint(), core::scoring::constraints::BackboneStubLinearConstraint::BackboneStubLinearConstraint(), core::scoring::carbon_hbonds::CarbonHBondEnergy::bb_bb_carbon_hbond_one_way(), core::scoring::carbon_hbonds::CarbonHBondEnergy::bb_sc_carbon_hbond_one_way(), protocols::features::BetaTurnDetection::beta_turn_present(), core::scoring::biggest_residue_deviation_no_super(), core::scoring::biggest_residue_deviation_no_super_subset(), core::scoring::atomic_depth::AtomicDepth::boundbox(), protocols::match::downstream::RigidLigandBuilder::build(), core::scoring::lkball::WaterBuilder::build(), protocols::match::output::WriteUpstreamCoordinateKinemage::build(), core::pack::rotamer_set::build_acceptor_acceptor_waters(), protocols::simple_moves::ExplicitWaterMover::build_backbone_rotamer_clouds(), protocols::match::downstream::LigandConformerBuilder::build_conformer_group(), core::pack::rotamer_set::build_donor_acceptor_waters(), core::pack::rotamer_set::build_donor_donor_waters(), core::scoring::MultipoleElecPotential::build_frame_and_rotate(), protocols::match::downstream::ClassicMatchAlgorithm::build_from_three_coords(), protocols::cryst::MakeLatticeMover::build_lattice_of_virtuals(), protocols::cryst::MakeLayerMover::build_layer_of_virtuals(), core::pack::rotamer_set::build_lib_dna_rotamers(), protocols::nmr::pcs::PCSLigandTransformMover::build_ligand_atom_xyz_table(), core::pack::rotamer_set::build_moving_O_bridge_waters(), core::scoring::lkball::build_optimal_water_Os_on_acceptor(), core::pack::rotamer_set::RotamerSet_::build_optimize_H_rotamers(), build_orbital_xyz(), core::pack::rotamer_set::build_random_dna_rotamers(), core::pack::rotamer_set::ContinuousRotamerSet::build_rotamers(), core::pack::rotamer_set::build_rotated_water_rotamers(), core::pack::rotamer_set::build_sew_waters_to_acceptor(), core::pack::rotamer_set::build_sew_waters_to_donor(), protocols::rna::movers::bump_check(), protocols::match::bump_grid_to_enclose_pose(), protocols::match::bump_grid_to_enclose_residue(), protocols::match::bump_grid_to_enclose_residue_backbone(), protocols::simple_moves::Ca_coord(), protocols::fold_from_loops::movers::Ca_coord(), protocols::simple_moves::Ca_coords(), protocols::splice::Ca_coords(), protocols::protein_interface_design::filters::Ca_coords(), protocols::mpi_refinement::CA_Sscore(), protocols::features::strand_assembly::cal_dis_angle_to_find_sheet(), protocols::recces::sampler::rna::calc_base_centroid_rmsd(), protocols::flexpep_docking::FlexPepDockingPoseMetrics::calc_frac_atoms_kA_to_native(), protocols::membrane::calc_helix_axis(), core::scoring::rna::RNP_LowResPairDistPotential::calc_rnp_pair_dist_score(), protocols::simple_filters::HelixHelixAngleFilter::calc_shortest_dist_by_atoms(), protocols::fldsgn::topology::calc_strand_helix_angle(), protocols::features::strand_assembly::calculate_dihedral_w_4_resnums(), core::scoring::methods::GoapEnergy::calculate_dipoles(), core::scoring::FACTSPotential::calculate_GBpair_exact(), core::scoring::FACTSPotential::calculate_GBpair_fast(), core::scoring::FACTSPotential::calculate_GBpair_v1trunk(), protocols::ligand_docking::ga_ligand_dock::GridScorer::calculate_grid(), protocols::simple_filters::RepeatParameterFilter::calculate_helical_parameters_helper(), core::scoring::lkball::LK_BallEnergy::calculate_lk_ball_atom_energies(), core::scoring::lkball::LK_BallEnergy::calculate_lk_ball_atom_energies_cp(), core::scoring::lkball::LK_BallEnergy::calculate_lk_desolvation_of_single_atom_by_residue(), core::scoring::lkball::LK_BallEnergy::calculate_lk_desolvation_of_single_atom_by_residue_no_count_pair(), core::scoring::methods::LK_hack::calculate_orientation_vectors_and_pseudo_base_atoms(), core::scoring::MultipoleElecPotential::calculate_res_res_fixed_fields_for_polarization(), core::scoring::MultipoleElecPotential::calculate_res_res_induced_fields_for_polarization(), protocols::antibody::AntibodyFeatures::calculate_residue_atomic_contacts(), protocols::splice::calculate_rmsd(), core::scoring::methods::ProQ_Energy::calculateZ(), core::scoring::packstat::cavity_distance_constraint(), protocols::antibody::cdr_CN_anchor_distance(), protocols::antibody::CDR_H3_cter_filter(), protocols::antibody::CDR_H3_filter_legacy_code_with_old_rule(), protocols::ub_e2c::ubi_e2c_modeler::centroid_mode_perturbation(), core::scoring::membrane::MPHelicalityEnergy::centroid_neighbors(), core::scoring::membrane::MPResidueLipophilicityEnergy::centroid_neighbors(), core::scoring::dna::DNA_EnvPairPotential::centroid_xyz(), protocols::geometry::centroids_by_jump(), protocols::geometry::centroids_by_jump_int(), protocols::simple_moves::CutChainMover::chain_cut(), protocols::splice::SpliceManager::chainbreak_check(), protocols::splice::Splice::chainbreak_check(), protocols::ligand_docking::ligand_options::check_all_ligand_atoms(), protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker::check_chain_closable_geometry(), protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker::check_chain_closable_geometry_strict(), core::scoring::rna::data::RNA_DMS_Potential::check_chbonded(), protocols::pose_creation::MergePDBMover::check_duplicate(), core::scoring::rna::RNA_LowResolutionPotential::check_for_base_neighbor(), protocols::ligand_docking::ligand_options::check_neighbor_ligand_atom(), protocols::stepwise::modeler::packer::check_o2prime_contact(), protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::check_other_partition_for_contact(), protocols::hybridization::InsertChunkMover::check_overlap(), protocols::kinematic_closure::ClosureSolution::check_overlap(), protocols::stepwise::modeler::rna::phosphate::PhosphateMover::check_phosphate_contacts_donor(), core::pose::rna::check_phosphate_contacts_donor(), core::scoring::MembranePotential::check_spanning(), protocols::features::strand_assembly::check_whether_sheets_are_connected_with_near_bb_atoms(), protocols::minimization_packing::MinimalRotamer::chi_matches_coords(), protocols::ligand_docking::ga_ligand_dock::GridScorer::clash_score(), protocols::pose_creation::MergePDBatOverlapMover::closest_non_overlap_residue(), protocols::pose_creation::MergePDBMover::closest_non_overlap_residue(), protocols::enzdes::ModifyStoredRBConfs::closest_orient_atoms_msd(), protocols::constel::cnl_com(), protocols::rna::movers::com_of_true_residues(), core::pack::compare_simple_inteaction_graph_alt_state_and_energy_graph(), protocols::simple_filters::ChainBreak::compute(), protocols::matdes::InterfacePackingFilter::compute(), protocols::simple_filters::MotifScoreFilter::compute(), protocols::protein_interface_design::filters::AtomicContactCountFilter::compute(), protocols::fldsgn::filters::HelixBendFilter::compute(), core::scoring::compute_bb_centroid(), core::scoring::compute_bb_radius(), core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid::compute_bounding_box(), protocols::forge::remodel::compute_center_of_mass(), core::scoring::saxs::SAXSEnergy::compute_distance_histogram(), core::scoring::orbitals::OrbitalsScore::compute_orb_orb_E(), protocols::scoring::methods::saxs::PDDFEnergy::compute_pddf(), protocols::scoring::methods::saxs::PDDFEnergy::compute_pddf_without_ff(), core::pack::interaction_graph::SurfacePotential::compute_pose_surface_energy(), core::pack::interaction_graph::SurfacePotential::compute_residue_surface_energy(), protocols::optimize_weights::IterativeOptEDriver::compute_rotamers_around_ligands(), protocols::flexpack::interaction_graph::OTFFlexbbEdge::compute_samebbconf_alternate_state_energy_first_node(), protocols::flexpack::interaction_graph::OTFFlexbbEdge::compute_samebbconf_alternate_state_energy_second_node(), core::scoring::compute_sc_centroid(), core::scoring::compute_sc_radius(), protocols::flexpack::rotamer_set::FlexbbRotamerSets::compute_sr_one_body_energies_for_flexsets(), protocols::features::LoopAnchorFeatures::compute_transform_and_write_to_db(), protocols::forge::remodel::RemodelMover::confirm_sequence(), core::scoring::power_diagram::PowerDiagram::construct_from_pose(), core::scoring::nmr::NMRDummySpinlabelEnsemble::coordinate_transform_from_target_site(), protocols::simple_filters::coords(), protocols::splice::coords(), core::pack::scmin::ResidueAtomTreeCollectionMomento::copy_coords(), protocols::generalized_kinematic_closure::copy_loop_pose_to_original(), protocols::mpi_refinement::copy_pose_crd(), protocols::ligand_docking::ga_ligand_dock::count_neighbors(), protocols::ligand_docking::ga_ligand_dock::count_neighbors_on_coord(), protocols::constraint_generator::CoordinateConstraintGenerator::create_coordinate_constraint(), core::pack::interaction_graph::create_hbonds_one_way(), core::pack::rotamer_set::create_oriented_water_rotamer(), protocols::rna::denovo::create_rna_vall_torsions(), core::scoring::hbonds::create_rotamer_descriptor(), protocols::cryst::crystRMSfast(), protocols::antibody_legacy::CDRH3Modeler::cutpoint_separation(), protocols::antibody::cutpoint_separation(), core::scoring::electron_density::ElectronDensity::dCCdB_fastRes(), protocols::flexpack::interaction_graph::OTFFlexbbNode::declare_all_rotamers_initialized(), core::io::raw_data::DecoyStruct::DecoyStruct(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::define_active_virtual_sites(), core::scoring::lkball::WaterBuilder::derivatives(), protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), protocols::relax::derive_sc_sc_restraints(), core::pose::rna::detect_base_contacts(), core::conformation::Conformation::detect_bonds(), protocols::cryst::MakeLayerMover::detect_connecting_subunits(), protocols::cryst::MakeLatticeMover::detect_connecting_subunits(), core::pack::interaction_graph::SurfaceNode< V, E, G >::detect_neighborship_with_node(), core::pose::rna::detect_sugar_contacts(), protocols::toolbox::rotamer_set_operations::RigidBodyMoveBaseRSO::determine_largest_nbr_atom_distance(), protocols::flexpack::rotamer_set::FlexbbRotamerSets::determine_res_cb_deviation(), protocols::helical_bundle::FitSimpleHelixMultiFunc::dfunc(), protocols::hybridization::discontinued_lower(), protocols::hybridization::discontinued_upper(), protocols::protein_interface_design::filters::RmsdSimpleFilter::dist_bb(), protocols::magnesium::MgScanner::distance_to_closest_magnesium(), protocols::simple_ddg::ddG::duplicate_waters_across_jump(), core::scoring::electron_density::ElectronDensity::ElectronDensity(), protocols::match::downstream::ActiveSiteGrid::enlargen_to_capture_volume_within_radius_of_backbone(), protocols::match::downstream::ActiveSiteGrid::enlargen_to_capture_volume_within_radius_of_residue(), protocols::match::downstream::ActiveSiteGrid::enlargen_to_capture_volume_within_radius_of_sidechain(), protocols::rna::denovo::ensure_phosphate_nomenclature_matches_mini(), protocols::rigid::MovePoseToMembraneCenterMover::estimate_membrane_center(), core::scoring::methods::eval(), core::scoring::methods::MMBondLengthEnergy::eval_atom_derivative(), core::scoring::methods::MMTorsionEnergy::eval_atom_derivative(), core::scoring::methods::MMBondAngleEnergy::eval_atom_derivative(), core::scoring::elec::FA_ElecEnergyAroAll::eval_atom_derivative_aro_aro(), core::scoring::elec::FA_ElecEnergyAroAro::eval_atom_derivative_aro_aro(), core::scoring::elec::RNA_FA_ElecEnergy::eval_atom_derivative_RNA(), core::scoring::FACTSPotential::eval_atom_nonpolar_derivative(), core::scoring::FACTSPotential::eval_atom_polar_derivative(), core::scoring::elec::FA_GrpElecEnergy::eval_context_derivatives(), core::scoring::methods::dfire::DFIRE_Potential::eval_dfire_pair_energy(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd1(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd2(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd1(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd2(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_bond_energy(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_bond_length_derivs(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_improper_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_improper_energy(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_ring_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_ring_energy(), core::scoring::methods::MMTorsionEnergy::eval_intrares_derivatives(), core::scoring::methods::ProClosureEnergy::eval_intrares_derivatives(), core::scoring::elec::FA_ElecEnergy::eval_intrares_derivatives(), core::scoring::methods::ProClosureEnergy::eval_intrares_energy(), core::scoring::methods::CartesianBondedEnergy::eval_intraresidue_dof_derivative(), core::scoring::magnesium::MgEnergy::eval_mg_interaction(), core::scoring::PoissonBoltzmannPotential::eval_PB_energy_residue(), core::scoring::Ramachandran::eval_rama_score_residue_nonstandard_connection(), core::scoring::HydroxylTorsionPotential::eval_residue_derivative(), core::scoring::methods::RingClosureEnergy::eval_residue_derivatives(), core::scoring::HydroxylTorsionPotential::eval_residue_energy(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_angle(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_bond(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_improper(), core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_torsion(), core::scoring::methods::ArgCationPiEnergy::eval_residue_pair_derivatives(), core::scoring::rna::StackElecEnergy::eval_residue_pair_derivatives(), core::scoring::methods::ProClosureEnergy::eval_residue_pair_derivatives(), core::scoring::methods::LK_PolarNonPolarEnergy::eval_residue_pair_derivatives(), core::scoring::lkball::LK_BallEnergy::eval_residue_pair_derivatives(), core::scoring::elec::RNA_FA_ElecEnergy::eval_residue_pair_derivatives(), core::scoring::hbonds::HBondEnergy::eval_residue_pair_derivatives(), core::scoring::elec::FA_ElecEnergy::eval_residue_pair_derivatives(), core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy::eval_residue_pair_derivatives(), core::scoring::VdWTinkerPotential::eval_residue_pair_derivatives(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::eval_residue_pair_derivatives_one_way(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_angle(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_bond(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_improper(), core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_torsion(), core::scoring::elec::GroupElec::eval_respair_group_coulomb(), core::scoring::elec::GroupElec::eval_respair_group_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_angle_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_angle_energies(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_improper_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_improper_energies(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_length_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_length_energies(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_ring_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_ring_energies(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_torsion_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_torsion_energies(), core::scoring::MembranePotential::evaluate_env(), core::scoring::lkball::evaluate_lk_ball_energy_for_atom_ranges(), protocols::scoring::InterchainPotential::evaluate_pair_and_vdw_score(), core::scoring::FACTSPotential::evaluate_polar_otf_energy(), protocols::match::downstream::AtomDistanceSecMatchRPE::evaluate_residues(), protocols::match::downstream::AtomAngleSecMatchRPE::evaluate_residues(), protocols::match::downstream::AtomDihedralSecMatchRPE::evaluate_residues(), core::scoring::rna::RNA_VDW_Energy::evaluate_rnp_vdw_score(), protocols::kinematic_closure::ClosureProblem::extract_cartesian_coordinates(), protocols::indexed_structure_store::extract_residue_entry(), protocols::normalmode::NormalModeRelaxMover::extrapolate_mode_on_crd(), core::scoring::Membrane_FAPotential::fa_projection(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::fast_full_atom_VDW_repulsion_screen(), protocols::magnesium::SampleGrid::figure_out_box_bounds(), core::pose::rna::figure_out_number_base_contacts(), protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger::fill_chainTORS_info(), core::scoring::constraints::BackboneStubLinearConstraint::fill_f1_f2(), core::scoring::constraints::BackboneStubConstraint::fill_f1_f2(), protocols::match::fill_grid_with_backbone_heavyatom_spheres(), protocols::match::fill_grid_with_residue_heavyatom_spheres(), protocols::match::fill_grid_with_residue_spheres(), core::conformation::Conformation::fill_missing_atoms(), core::io::silent::RNA_SilentStruct::fill_pose(), core::scoring::fill_rmsd_coordinates(), core::io::silent::RNA_SilentStruct::fill_struct(), core::io::silent::ProteinSilentStruct_Template< T >::fill_struct(), protocols::membrane::MPLipidAccessibility::fill_up_slices(), protocols::cyclic_peptide::crosslinker::TBMB_Helper::filter_by_sidechain_distance_asymmetric(), protocols::cyclic_peptide::crosslinker::TMA_Helper::filter_by_sidechain_distance_asymmetric(), protocols::cyclic_peptide::crosslinker::Metal_HelperBase::filter_by_sidechain_distance_asymmetric(), protocols::cyclic_peptide::crosslinker::TBMB_Helper::filter_by_sidechain_distance_symmetric(), protocols::cyclic_peptide::crosslinker::TMA_Helper::filter_by_sidechain_distance_symmetric(), protocols::cyclic_peptide::crosslinker::Metal_HelperBase::filter_by_sidechain_distance_symmetric(), protocols::stepwise::monte_carlo::mover::filter_for_proximity(), core::select::filter_neighbors_by_distance(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_exact_cartmin(), core::scoring::methods::CenPairMotifDegreeEnergy::finalize_total_energy(), core::scoring::methods::CenPairMotifEnergy::finalize_total_energy(), protocols::scoring::VDW_GridEnergy::finalize_total_energy(), core::scoring::elec::RNA_FA_ElecEnergy::finalize_total_energy(), core::scoring::rna::StackElecEnergy::finalize_total_energy(), core::scoring::elec::FA_ElecEnergy::finalize_total_energy(), core::io::pose_from_sfr::PoseFromSFRBuilder::find_atom_tree_root_for_metal_ion(), protocols::ligand_docking::find_attach_pt(), protocols::constraint_movers::AddConstraintsToCurrentConformationMover::find_best_anchor(), protocols::nmr::pcs::PCSLigandTransformMover::find_best_ligand_pose_with_grid_search(), protocols::magnesium::find_bound_waters_that_are_daughters_in_fold_tree(), protocols::metal_interface::find_closest_atom(), protocols::enzdes::DetectProteinLigandInterface::find_design_interface(), protocols::enzdes::DetectProteinLigandInterface::find_design_interface_arg_sweep(), protocols::forge::remodel::RemodelDesignMover::find_disulfides_in_the_neighborhood(), protocols::splice::find_disulfs_in_range(), protocols::environment::find_implied_cut(), protocols::ligand_docking::LigandBaseProtocol::find_interface_backbone(), protocols::ligand_docking::LigandBaseProtocol::find_interface_rsds(), protocols::recces::scratch::find_likely_first_chain_ending(), core::util::find_metalbinding_atoms_helper(), protocols::ddg::ddGMover::find_nbrs(), protocols::rna::movers::find_nearby_res(), protocols::cutoutdomain::CutOutDomain::find_nearest_res(), protocols::rosetta_scripts::find_nearest_res(), protocols::protein_interface_design::find_nearest_residue(), protocols::protein_interface_design::movers::find_nearest_residue_to_coord(), core::pose::carbohydrates::find_neighbor(), protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockMoveRbJumpMover::find_new_jump_residue(), core::pose::symmetry::find_new_symmetric_jump_residues(), protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::find_phosphate_contacts_other_partition(), protocols::enzdes::PredesignPerturbMover::find_rotation_center(), protocols::magnesium::MgWaterHydrogenPacker::find_water_neighbor_vecs(), protocols::splice::fix_chain_break_residue(), protocols::flexpep_docking::FlexPepDockingProtocol::flip_in_pcs(), protocols::ligand_docking::frac_atoms_within(), protocols::motif_grafting::movers::MotifGraftMover::fragments_permutation_test_by_CA_distances(), protocols::features::LoopAnchorFeatures::frame_for_residue(), protocols::ub_e2c::ubi_e2c_modeler::fullatom_mode_perturbation(), protocols::comparative_modeling::gather_coords(), protocols::normalmode::NormalModeRelaxMover::gen_coord_constraint(), protocols::constraint_movers::AddConstraintsToCurrentConformationMover::generate_atom_pair_constraints(), protocols::generalized_kinematic_closure::GeneralizedKIC::generate_atomlist(), protocols::constraint_movers::AddConstraintsToCurrentConformationMover::generate_coordinate_constraints(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_1b_energy(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_2b_energy(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_acceptor_base_atm_xyz(), core::scoring::hbonds::HBond::get_AHDangle(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_acceptor(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::get_atom_lk_energy(), protocols::ligand_docking::ga_ligand_dock::get_atomic_contacting_sidechains(), core::scoring::sc::ElectrostaticComplementarityCalculator::get_atoms_within_radius(), core::scoring::hbonds::HBond::get_BAHangle(), core::scoring::rna::RNA_LowResolutionPotential::get_base_backbone(), core::scoring::hackaro::HackAroEnergy::get_base_coordinate_system(), core::scoring::dna::get_base_pair_stub_slow(), core::scoring::dna::get_base_pair_y_axis_atom_xyz(), core::scoring::dna::get_base_pucker(), core::scoring::dna::get_base_stub(), core::scoring::methods::LK_PolarNonPolarEnergy::get_base_vector(), core::scoring::hbonds::HBond::get_BAtorsion(), protocols::motif_grafting::movers::MotifGraftMover::get_bb_alignment_and_transformation(), protocols::motif_grafting::movers::MotifGraftMover::get_bb_alignment_and_transformation_wTipsExtraInfo(), protocols::motif_grafting::movers::MotifGraftMover::get_bb_distance(), protocols::rna::denovo::movers::RNA_HelixMover::get_bb_pos(), protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::get_best_hxyz(), protocols::stepwise::modeler::rna::get_binary_rna_silent_struct_safe(), core::scoring::rna::data::RNA_DMS_Potential::get_binding_energy(), protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker::get_C4_C3_distance_range(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_calc_chem_shift_value_larmord(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_calc_chem_shift_value_nuchemics(), protocols::vip::VIP_Mover::get_cav_approx(), protocols::sic_dock::get_CB_Vecs_from_map(), protocols::sic_dock::get_CB_Vecs_from_pose(), core::scoring::hackaro::HackAroEnergy::get_centroid(), protocols::rna::movers::RNA_LoopCloser::get_chainbreak_xyz(), protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::get_chi_weight(), protocols::magnesium::get_closest_non_hoh_contact(), core::scoring::magnesium::get_closest_orbital_axis(), protocols::simple_filters::get_contact_features(), protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::get_contacting_reslist(), protocols::cryst::get_corresponding_CAs(), core::scoring::magnesium::get_cos_theta(), core::io::silent::BinarySilentStruct::get_debug_rmsd(), core::io::silent::RNA_SilentStruct::get_debug_rmsd(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_deriv_for_chemical_shift(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_deriv_for_chemical_shift_data_atom(), protocols::splice::RBOutMover::get_disulf_jump(), core::scoring::disulfides::FullatomDisulfidePotential::get_disulfide_derivatives(), core::scoring::orbitals::OrbitalsScore::get_E_haro_one_way(), core::scoring::orbitals::OrbitalsScore::get_E_hpol_one_way(), protocols::motif_grafting::movers::MotifGraftMover::get_fragments_by_CA_distances_and_NCpoints_restrains(), core::pose::symmetry::get_full_intracomponent_and_neighbor_subs(), protocols::rna::movers::RNA_LoopCloser::get_gap_distance(), core::scoring::elec::GroupElec::get_grpdis2(), core::scoring::hbonds::HBond::get_HAdist(), protocols::forge::remodel::RemodelGlobalFrame::get_helical_params(), protocols::indexed_structure_store::SSHashedFragmentStore::get_hits_below_rms(), protocols::magnesium::get_hoh_xyz(), protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::get_ideal_hxyz_positions(), core::pose::symmetry::get_intracomponent_and_neighbor_subs(), protocols::sic_dock::get_leap_lower_stub(), protocols::sic_dock::get_leap_upper_stub(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_link_record(), protocols::pose_length_moves::AnalyzeLoopModeling::get_loop_rmsd(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_magnetic_anisotropy_deriv_for_src_atom(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_magnetic_anisotropy_deriv_for_src_base(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::get_matching_res_in_VDW_rep_screen_pose(), protocols::membrane::scoring::FaWaterToBilayerEnergy::get_menv_params_for_residue(), protocols::magnesium::get_mg_ligands(), protocols::magnesium::SampleGrid::get_mg_positions(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::get_movable_scs(), core::scoring::rna::data::RNA_DMS_Potential::get_N1_lonepair_donor_angle(), core::scoring::motif::get_nbrs(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::get_nearest_dist_to_O2prime(), protocols::hotspot_hashing::HotspotStub::get_nearest_residue(), protocols::vip::VIP_Mover::get_neighbors(), core::scoring::rna::data::RNA_DMS_Potential::get_occupancy_densities(), core::pose::rna::get_phosphate_atom_and_neighbor_list(), protocols::simple_filters::ResidueDepthCalculator::get_pose_crd_and_index(), protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::get_possible_hbond_acceptors(), core::scoring::rna::data::RNA_DMS_Potential::get_probe_xyz(), protocols::stepwise::monte_carlo::rna::RNA_O2PrimeMover::get_random_o2prime_residue_near_moving_residue(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::get_reference_xyz(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::get_reference_xyz_average(), protocols::membrane::MPMutateRelaxMover::get_repack_residues(), core::scoring::GenBornPotential::get_res_res_elecE(), core::scoring::MultipoleElecPotential::get_res_res_elecE(), core::scoring::VdWTinkerPotential::get_res_res_vdw(), core::pack::get_residue_current_energy(), core::scoring::methods::Fa_MbsolvEnergy::get_residue_pair_energy(), core::scoring::membrane::FaMPSolvEnergy::get_residue_pair_energy(), core::scoring::methods::LK_PolarNonPolarEnergy::get_residue_pair_energy_one_way(), core::scoring::WaterAdductHBondPotential::get_residue_residue_h2o_hbonds_1way(), protocols::rna::denovo::get_residues_within_dist_of_RNA(), core::scoring::methods::ArgCationPiEnergy::get_ring(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_ring_current_deriv_for_src_base(), core::scoring::methods::ArgCationPiEnergy::get_ring_params(), protocols::normalmode::NormalModeRelaxMover::get_RMSD(), core::chemical::rna::get_rna_base_centroid(), core::chemical::rna::get_rna_base_coordinate_system(), core::scoring::rna::chemical_shift::get_rna_base_coordinate_system_from_CS_params(), core::scoring::rna::get_rna_motifs(), core::pack::interaction_graph::SymmOnTheFlyNode::get_rotamer(), protocols::magnesium::MgScanner::get_score(), protocols::simple_filters::ResidueDepthFilter::get_SDE_score(), core::scoring::MultipoleElecPotential::get_single_rotamer_effective_radii(), protocols::toolbox::rigid_body::get_specific_atom_coordinate(), protocols::motifs::LigandMotifSearch::get_sphere_aa(), protocols::relax::RangeRelaxMover::get_spherical_repack_residues(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_ssbond_record(), core::scoring::methods::SSElementMotifContactEnergy::get_SSelements_in_contact(), protocols::simple_filters::SSElementMotifContactFilter::get_SSelements_in_contact(), core::conformation::get_stub_from_residue(), core::pose::rna::get_stub_stub(), core::pose::rna::get_sugar_centroid(), core::scoring::rna::data::RNA_DataBackboneEnergy::get_sugar_env_score(), core::scoring::dna::get_sugar_pucker(), core::scoring::dna::get_sugar_torsions(), protocols::stepwise::modeler::rna::get_surrounding_O2prime_hydrogen(), core::pose::symmetry::get_symm_axis(), protocols::loops::loop_closure::ccd::CCDLoopClosureMover::get_torsion_axis(), protocols::mpi_refinement::get_touched_res(), protocols::simple_moves::ExplicitWaterMover::get_water_recovery(), core::scoring::rna::data::RNA_DMS_LowResolutionPotential::get_wc_near_o2prime(), protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives::get_xyz(), core::scoring::dna::get_y_axis(), core::scoring::dna::get_z_axis(), protocols::rbsegment_relax::RBSegmentMover::getCoM(), protocols::rbsegment_relax::HelicalGaussianMover::getCoordinateTransformation(), protocols::rbsegment_relax::StrandTwistingMover::getCoordinateTransformation(), protocols::sic_dock::getxform(), protocols::ligand_docking::grid_score(), protocols::ligand_docking::grid_score_atr_rep(), core::scoring::WaterAdductHBondPotential::h2o_hbond_score_1way(), core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy::has_bb_hbond(), core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy::has_hbond(), protocols::constel::has_prox_termini(), core::scoring::hbonds::hb_energy(), core::scoring::hbonds::HBondEnergy::hbond_derivs_1way(), protocols::magnesium::MgHydrater::hydrate_magnesium_in_pose(), protocols::magnesium::MgHydrater::hydrate_magnesium_with_orbital_frame(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::idealize_and_repack_pose(), core::scoring::hbonds::identify_hbonds_1way(), core::scoring::hbonds::identify_hbonds_1way_AHdist(), core::scoring::hbonds::identify_hbonds_1way_membrane(), core::scoring::hbonds::identify_intra_res_hbonds(), protocols::neighbor::in_ngbat_sphere(), protocols::motifs::MotifSearch::incorporate_motifs(), protocols::motifs::LigandMotifSearch::incorporate_motifs(), core::scoring::membrane::FaMPEnvEnergy::init(), core::scoring::membrane::FaMPSolvEnergy::init(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::init_from_ligand(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::init_from_ligand_pharmacophore(), core::scoring::MembranePotential::init_membrane_center_normal(), protocols::ub_e2c::ubi_e2c_modeler::initial_perturbation(), core::scoring::ResidueNblistData::initialize(), core::scoring::MultipoleElecResidueInfo::initialize(), protocols::flexpack::interaction_graph::FlexbbInteractionGraph::initialize(), protocols::match::downstream::LigandConformerBuilder::initialize_conformers(), protocols::toolbox::match_enzdes_util::LigandConformer::initialize_from_residue(), protocols::match::upstream::OriginalBackboneBuildPoint::initialize_from_residue(), core::scoring::ResiduePairNeighborList::initialize_from_residues(), core::conformation::symmetry::MirrorSymmetricConformation::insert_conformation_by_jump(), core::conformation::symmetry::SymmetricConformation::insert_conformation_by_jump(), core::fragment::rna::FullAtomRNA_Fragments::insert_fragment(), protocols::features::HBondFeatures::insert_hbond_dehydron_row(), protocols::magnesium::instantiate_water_at_octahedral_vertex(), core::pose::symmetry::intracomponent_contact(), protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::inverse_rotamers_against_residue(), core::conformation::is_atom_axial_or_equatorial_to_ring(), core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::is_buried(), core::scoring::FACTSPoseInfo::is_changed(), core::simple_metrics::per_residue_metrics::PerResidueClashMetric::is_clashing(), protocols::task_operations::CrystalContactsOperation::is_crystal_contact(), protocols::fold_from_loops::movers::NubInitioLoopClosureMover::is_cutpoint_close(), protocols::qsar::scoring_grid::SingleGrid::is_in_grid(), protocols::hydrate::is_inside(), protocols::ligand_docking::InterfaceBuilder::is_interface_residue(), protocols::ligand_docking::ga_ligand_dock::GridScorer::is_residue_in_grid(), protocols::constel::FilterByIndoleCOO::is_satisfied(), protocols::constel::FilterByTryptamine::is_satisfied(), protocols::constel::FilterByAmphetamine::is_satisfied(), protocols::constel::FilterByProxTerm::is_satisfied(), protocols::constel::FilterByHistamine::is_satisfied(), core::pack::task::residue_selector::is_sc_bb_clash(), core::pack::task::residue_selector::is_sc_sc_clash(), protocols::flexpep_docking::FlexPepDockingPoseMetrics::isInContact(), protocols::features::strand_assembly::StrandBundleFeatures::judge_facing(), protocols::features::strand_assembly::judge_facing(), protocols::antibody::AntibodyInfo::kink_anion_atoms(), protocols::antibody::kink_bb_Hbond(), protocols::antibody::AntibodyInfo::kink_cation_atoms(), protocols::antibody::kink_dihedral(), protocols::antibody::kink_Trp_Hbond(), protocols::scoring::Interface::ligand_calculate(), protocols::ligand_docking::ComputeLigandRDF::ligand_protein_rdf(), protocols::indexed_structure_store::FragmentLookup::lookup_closest_pose_fragments(), protocols::indexed_structure_store::FragmentLookup::lookup_pose_fragments(), protocols::loops::loop_local_rmsd(), protocols::loops::loop_rmsd(), core::scoring::rna::chemical_shift::magnetic_anisotropy_effect(), protocols::ligand_docking::make_atr_rep_grid(), protocols::ligand_docking::make_atr_rep_grid_without_ligands(), protocols::dna::make_base_pair_aware_fold_tree(), protocols::simple_filters::ResidueDepthFilter::make_context(), protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover::make_disjointed_foldtree(), core::scoring::power_diagram::PowerDiagram::make_new_sphere(), core::fragment::make_pose_from_frags(), core::scoring::methods::ProClosureEnergy::measure_chi4(), core::conformation::membrane::MembraneInfo::membrane_center(), core::conformation::membrane::MembraneInfo::membrane_normal(), core::pack::min_pack_optimize(), protocols::pose_creation::MergePDBatOverlapMover::minimize_overlap(), protocols::protein_interface_design::MinimizeInterface(), core::pose::MiniPose::MiniPose(), protocols::sic_dock::scores::MotifHashRigidScore::MotifHashRigidScore(), protocols::topology_broker::TMHTopologySamplerClaimer::move_spans(), protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer::moving_res_contact_filter(), protocols::fold_from_loops::movers::SplitAndMixPoseMover::NC_distance_filter(), protocols::ddg::ddGMover::neighborhood_of_mutations(), core::scoring::membrane::MPHelicalityEnergy::neighboring_atoms(), core::scoring::membrane::MPResidueLipophilicityEnergy::neighboring_atoms(), protocols::splice::neighbors_in_vector(), protocols::frag_picker::FragmentPicker::nonlocal_pairs(), protocols::helical_bundle::FitSimpleHelixMultiFunc::operator()(), core::scoring::func::ResidueXYZ::operator()(), core::scoring::func::ResiduePairXYZ::operator()(), protocols::ub_e2c::ubi_e2c_modeler::optimize_cov_bond(), protocols::match::downstream::ActiveSiteGrid::or_within_radius_of_backbone(), protocols::match::downstream::ActiveSiteGrid::or_within_radius_of_residue(), protocols::match::downstream::ActiveSiteGrid::or_within_radius_of_sidechain(), orient_onto_location(), orient_onto_residue_peptoid(), core::conformation::orient_residue_for_ideal_bond(), core::chemical::sdf::MolWriter::output_residue(), protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo::output_silent_file(), protocols::magnesium::MgWaterHydrogenPacker::pack_mg_water_hydrogens_in_pose(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::pair_sets_with_positions(), protocols::stepwise::modeler::rna::phosphate::PhosphateMover::pass_clash_check(), protocols::match::output::UpstreamCollisionFilter::passes_hardsphere_filter(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::perform_bump_check(), protocols::simple_moves::PeriodicBoxMover::perturb_molecule_move(), protocols::comparative_modeling::pick_loops_chainbreak(), place(), protocols::motifs::Motif::place_atom_(), protocols::motifs::Motif::place_atoms_(), protocols::kinmatch::BruteFunGroupTK::place_c(), protocols::kinmatch::BruteFunGroupTK::place_d(), protocols::hydrate::place_de_novo_wat_at_anchor(), protocols::cryst::MakeLayerMover::place_near_origin(), protocols::flexpep_docking::FlexPepDockingProtocol::place_peptide_on_binding_site(), protocols::motifs::Motif::place_residue_(), protocols::cyclic_peptide::crosslinker::TMA_Helper::place_tma_asymmetric(), protocols::antibody::snugdock::SnugDockProtocol::place_VRT_at_residue_COM(), protocols::hotspot_hashing::StubGenerator::placeResidueAtTransform(), protocols::magnesium::MgOrbitalFrameFinder::point_orbitals_to_closest_ligands(), protocols::stepwise::modeler::rna::phosphate::position_five_prime_phosphate(), core::scoring::NeighborList::prepare_for_scoring(), protocols::flexpack::interaction_graph::OTFFlexbbEdge::prepare_for_simulated_annealing(), protocols::ligand_docking::ga_ligand_dock::GridScorer::prepare_grid(), core::pose::rna::prepare_scratch_residue(), core::conformation::symmetry::SymmetricConformation::prepend_polymer_residue_before_seqpos(), protocols::recces::print_base_centroid_atoms_for_rb_entropy(), protocols::match::output::print_node(), core::conformation::print_node(), protocols::membrane::MPLipidAccessibility::protein_in_membrane(), protocols::hbnet::HBNet::quick_and_dirty_heavy_atom_is_unsat(), protocols::hybridization::TMalign::read_pose(), core::conformation::symmetry::SymmetricConformation::recalculate_transforms(), protocols::pockets::PocketGrid::recenter(), protocols::simple_moves::PeriodicBoxMover::recenter_pose(), protocols::minimization_packing::MinimalRotamer::record_internal_geometry(), protocols::qsar::scoring_grid::ClassicGrid::refresh(), protocols::qsar::scoring_grid::RepGrid::refresh(), protocols::hydrate::remove_non_buried_wat(), protocols::ligand_docking::LigandBaseProtocol::reorder_foldtree_around_mobile_regions(), protocols::relax::RangeRelaxMover::repack_spherical_range(), protocols::simple_moves::RepeatPropagationMover::repeat_ligand(), core::conformation::symmetry::MirrorSymmetricConformation::replace_residue(), core::conformation::symmetry::SymmetricConformation::replace_residue(), protocols::toolbox::match_enzdes_util::replace_residue_keeping_all_atom_positions(), protocols::features::ProteinResidueConformationFeatures::report_features(), protocols::features::ResidueConformationFeatures::report_features(), protocols::features::ProteinBackboneAtomAtomPairFeatures::report_features(), protocols::simple_moves::PeriodicBoxMover::report_thermodynamics(), core::scoring::FACTSPotential::res_res_burial(), core::scoring::GenBornPotential::res_res_burial(), core::scoring::FACTSPotential::res_res_burial_for_scoring(), core::scoring::carbon_hbonds::CarbonHBondEnergy::res_res_carbon_hbond_derivs_one_way(), core::scoring::carbon_hbonds::CarbonHBondEnergy::res_res_carbon_hbond_one_way(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::res_res_occ_sol_one_way(), protocols::nmr::pcs::PCSLigandTransformMover::reset_grid_and_bounding_box(), Residue(), core::scoring::methods::HRF_MSLabelingEnergy::residue_energy(), core::scoring::methods::CovalentLabelingEnergy::residue_energy(), core::scoring::methods::CovalentLabelingFAEnergy::residue_energy(), core::scoring::methods::WaterSpecificEnergy::residue_energy(), core::scoring::methods::RingClosureEnergy::residue_energy(), core::scoring::methods::SymmetricLigandEnergy::residue_energy(), core::pose::rna::residue_is_bulge(), protocols::sic_dock::residue_is_floppy(), core::scoring::hbonds::residue_near_water(), protocols::hydrate::residue_near_water(), protocols::simple_filters::NonSequentialNeighborsFilter::residue_neighbors(), core::scoring::methods::GaussianOverlapEnergy::residue_pair_energy(), core::scoring::methods::SuckerEnergy::residue_pair_energy(), core::scoring::rna::RNA_VDW_Energy::residue_pair_energy(), core::scoring::methods::HybridVDW_Energy::residue_pair_energy(), core::scoring::methods::PeptideBondEnergy::residue_pair_energy(), core::scoring::rna::RNP_LowResEnergy::residue_pair_energy(), core::scoring::methods::MMTorsionEnergy::residue_pair_energy(), core::scoring::rna::RNP_LowResStackEnergy::residue_pair_energy(), core::scoring::rna::RNA_LJ_BaseEnergy::residue_pair_energy(), core::scoring::methods::LK_hack::residue_pair_energy(), core::scoring::vdwaals::VDW_Energy::residue_pair_energy(), core::scoring::methods::CustomAtomPairEnergy::residue_pair_energy(), core::scoring::methods::PairEnergy::residue_pair_energy(), core::scoring::methods::GoapEnergy::residue_pair_energy(), core::scoring::elec::FA_ElecEnergy::residue_pair_energy(), core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy::residue_pair_energy(), core::scoring::elec::FA_ElecEnergyAroAll::residue_pair_energy_aro_aro(), core::scoring::elec::FA_ElecEnergyAroAro::residue_pair_energy_aro_aro(), core::scoring::methods::LK_PolarNonPolarEnergy::residue_pair_energy_ext(), core::scoring::hbonds::HBondEnergy::residue_pair_energy_ext(), core::scoring::rna::StackElecEnergy::residue_pair_energy_ext(), core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy::residue_pair_energy_ext(), core::scoring::magnesium::RNA_MgPointEnergy::residue_pair_energy_one_way(), core::scoring::rna::RNA_FullAtomStackingEnergy::residue_pair_energy_one_way(), core::scoring::rna::StackElecEnergy::residue_pair_energy_one_way(), core::conformation::residue_point_graph_from_conformation(), core::scoring::residue_rmsd_nosuper(), core::scoring::residue_rmsd_super(), core::scoring::electron_density_atomwise::ElectronDensityAtomwise::residue_score(), core::scoring::methods::residues_interact(), protocols::ligand_docking::MinimizeBackbone::restrain_protein_Calpha(), protocols::ligand_docking::LigandBaseProtocol::restrain_protein_Calphas(), protocols::enzdes::SecondaryMatchProtocol::restype_possible_at_position(), core::scoring::methods::PoissonBoltzmannEnergy::revamp_weight_by_burial(), core::scoring::rna::chemical_shift::ring_pos(), protocols::protein_interface_design::filters::RmsdSimpleFilter::rmsd_bb(), core::scoring::rmsd_no_super(), core::scoring::rmsd_with_super(), core::scoring::rna::RNA_LowResolutionPotential::rna_backbone_backbone_pair_energy_one_way(), core::scoring::elec::RNA_FA_ElecEnergy::rna_fa_elec_one_way(), core::scoring::rna::RNA_LowResolutionPotential::rna_repulsive_pair_energy_one_way(), core::pose::symmetry::rotate_anchor_to_x_axis(), protocols::toolbox::sample_around::rotate_into_nucleobase_frame(), protocols::toolbox::sample_around::rotate_into_phosphate_frame(), core::scoring::dna::DirectReadoutPotential::rsd_rsd_energy(), core::pack::RTMin::rtmin(), core::scoring::carbon_hbonds::CarbonHBondEnergy::sc_bb_carbon_hbond_one_way(), core::scoring::carbon_hbonds::CarbonHBondEnergy::sc_sc_carbon_hbond_one_way(), protocols::qsar::scoring_grid::HbaGrid::score(), protocols::qsar::scoring_grid::HbdGrid::score(), protocols::qsar::scoring_grid::VdwGrid::score(), protocols::qsar::scoring_grid::ShapeGrid::score(), protocols::sic_dock::XfoxmScore::score(), protocols::qsar::scoring_grid::ChargeGrid::score(), core::scoring::constraints::BackboneStubLinearConstraint::score(), protocols::qsar::scoring_grid::SingleGrid::score(), core::scoring::constraints::BackboneStubConstraint::score(), protocols::qsar::scoring_grid::PCSSingleGrid::score(), core::scoring::elec::RNA_FA_ElecEnergy::score_atom_pair(), core::scoring::elec::FA_ElecEnergy::score_atom_pair(), core::select::util::select_coord_for_residue(), protocols::features::serialize_residue_xyz_coords(), set_all_ring_nu(), set_chi(), core::conformation::set_chi_according_to_coordinates(), protocols::rbsegment_relax::set_constraints(), protocols::match::downstream::TargetRotamerCoords::set_coordinates_for_rotamer(), set_d(), protocols::normalmode::NormalMode::set_harmonic_constant_map(), protocols::qsar::scoring_grid::AtrGrid::set_ligand_rings(), protocols::cyclic_peptide::crosslinker::Metal_HelperBase::set_metal_bond_length(), protocols::features::OrbitalsFeatures::set_OrbH_features_data(), protocols::features::OrbitalsFeatures::set_OrbOrb_features_data(), protocols::qsar::scoring_grid::AtrGrid::set_protein_rings(), protocols::rbsegment_relax::set_rb_constraints(), protocols::ligand_docking::set_repulsive_bb_cores(), core::pack::scmin::ResidueAtomTreeCollection::set_rescoords(), core::pack::interaction_graph::SymmOnTheFlyEdge::set_residues_adjacent_for_subunit_pair(), protocols::hydrate::set_task_and_movemap(), set_tau(), protocols::denovo_design::components::Segment::set_template_pose(), set_theta(), core::scoring::NeighborList::setup(), protocols::simple_moves::ShakeStructureMover::setup_ca_constraints(), protocols::canonical_sampling::CanonicalSamplingMover::setup_constraints(), protocols::ddg::ddGMover::setup_constraints(), core::scoring::constraints::FabConstraint::setup_csts(), core::scoring::FACTSPotential::setup_for_derivatives(), core::scoring::rna::RNP_LowResEnergy::setup_for_scoring(), core::import_pose::setup_jumps(), protocols::simple_moves::PeriodicBoxMover::setup_pose(), protocols::relax::RepeatProteinRelax::setup_repeat_pose_jumping(), core::pose::rna::setup_three_prime_phosphate_based_on_next_residue(), protocols::features::strand_assembly::StrandBundleFeatures::sheet_dis_by_terminals(), protocols::features::strand_assembly::StrandBundleFeatures::sheet_torsion(), protocols::features::strand_assembly::StrandBundleFeatures::shortest_dis_sidechain(), core::scoring::elec::FA_ElecEnergy::sidechain_sidechain_energy(), protocols::loops::split_by_ca_ca_dist(), core::pack::scmin::CartSCMinMinimizerMap::starting_dofs(), protocols::minimization_packing::GreenPacker::store_reference_pose_geometry(), core::scoring::FACTSResidueInfo::store_xyz(), core::scoring::dna::strand_orientation_vector(), protocols::hotspot_hashing::stub_tgt_angle(), protocols::protein_interface_design::movers::PlaceStubMover::StubMinimize(), core::scoring::lkball::LK_BallEnergy::sum_deriv_contributions_for_heavyatom_pair_one_way(), core::scoring::superimpose_pose(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::superimpose_to_alternative_frame(), protocols::enzdes::ModifyStoredRBConfs::swap_coordinates_in_pose(), core::scoring::sym_rmsd_with_super_subset(), protocols::protein_interface_design::movers::test_res_res_aln(), core::scoring::MembranePotential::tm_projection_penalty(), protocols::sic_dock::scores::TrisBpyScore::TrisBpyScore(), protocols::rna::denovo::coarse::MultipleDomainMover::try_to_slide_into_contact(), core::pack::scmin::ResidueAtomTreeCollection::update_atom_tree(), protocols::legacy_sewing::Assembly::update_coords_from_pose(), core::pose::rna::update_edge_hbond_numbers_careful_hydrogen(), protocols::simple_moves::oop::OopMover::update_hydrogens_(), protocols::simple_moves::triazolamer::TriazolamerMover::update_hydrogens_(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::update_ligand_coord(), update_nus(), protocols::environment::CoMTrackerCM::update_tracking_residue(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::update_VDW_screen_bin(), core::scoring::methods::Burial_v2Energy::using_atom_distance(), protocols::features::helixAssembly::HelixBundleFeatures::validate_bundle(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::VDW_rep_screen(), core::pack::interaction_graph::SurfaceNode< V, E, G >::verify_patch_areas_correct(), protocols::antibody::vl_vh_orientation_coords(), protocols::mpi_refinement::StructAvrgMover::weighted_average(), core::scoring::PoissonBoltzmannPotential::write_config(), core::conformation::ResidueKinWriter::write_kin_header(), protocols::kinmatch::xform_rsd_gl2(), and protocols::dna::z_axis_dist().

Vector const& core::conformation::Residue::xyz ( std::string const &  atm_name ) const

inline

Returns the position of this residue's atom with name <atm_name>

Note

: position is a Vector

example(s): residue.xyz("CA") See also: Residue Residue.atom Residue.atoms Residue.set_xyz Pose

References atom(), and core::conformation::Atom::xyz().

Member Data Documentation

Vector core::conformation::Residue::actcoord_

private

the action coordinate, an interaction centroid for knowledge-based terms like fa-pair in fact, only for fa-pair

Referenced by actcoord(), and init_residue_from_other().

Atoms core::conformation::Residue::atoms_

private

our conformation atoms (not kinematic atom pointers) with xyz positions and atom type

Referenced by atom(), atom_begin(), atom_end(), atom_type_index(), atoms(), heavyAtoms_end(), init_residue_from_other(), nbr_atom_xyz(), Residue(), set_xyz(), show(), sidechainAtoms_begin(), and xyz().

core::Size core::conformation::Residue::chain_

private

the chain id number, starting from 1 See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

Referenced by chain(), init_residue_from_other(), polymeric_oriented_sequence_distance(), and polymeric_sequence_distance().

utility::vector1< Real > core::conformation::Residue::chi_

private

our chi (side chain) torsion angles

Referenced by chi(), init_residue_from_other(), is_similar_rotamer(), Residue(), and set_chi().

utility::vector1< chemical::ResConnID > core::conformation::Residue::connect_map_

private

map between connection ids on this residue and the connection points on other residues to which its bonded

Referenced by actual_residue_connection(), clear_residue_connections(), connect_map(), connect_map_size(), connected_residue_at_resconn(), connection_incomplete(), connections_match(), copy_residue_connections(), copy_residue_connections_from(), determine_nonstandard_polymer_status(), has_incomplete_connection(), init_residue_from_other(), mark_connect_incomplete(), residue_connection_conn_id(), residue_connection_partner(), update_connections_to_other_residue(), update_connections_to_residues(), and update_sequence_numbering().

std::map< Size, utility::vector1< Size > > core::conformation::Residue::connections_to_residues_

private

lists for each connected residue of the connection points on this residue that connect the pair.

Referenced by clear_residue_connections(), connect_atom(), connections_to_residue(), copy_residue_connections(), copy_residue_connections_from(), init_residue_from_other(), is_bonded(), mark_connect_incomplete(), and update_connections_to_residues().

basic::datacache::BasicDataCacheOP core::conformation::Residue::data_cache_

private

Referenced by data(), data_ptr(), init_residue_from_other(), nonconst_data(), and nonconst_data_ptr().

utility::vector1< Real > core::conformation::Residue::mainchain_torsions_

private

our (possibly empty) backbone torsion angles

Referenced by init_residue_from_other(), mainchain_torsion(), and mainchain_torsions().

bool core::conformation::Residue::mirrored_relative_to_type_

private

Is this residue mirrored relative to its coordinates in the ResidueType?

Only used for achiral residues like glycine in the context of mirror symmetry and other mirror-image structures. False by default.

Referenced by init_residue_from_other(), mirrored_relative_to_type(), and set_mirrored_relative_to_type().

bool core::conformation::Residue::misplaced_ = false

private

Inter-residue connection data.

Was the Residue incorrectly oriented and placed within the polymer when created?

Referenced by init_residue_from_other(), misplaced(), and Residue().

bool core::conformation::Residue::nonstandard_polymer_

private

true if is_polymer() and either upper_connect or lower_connect (if they exist) do not connect to seqpos()+1 or seqpos()-1

Referenced by clear_residue_connections(), connect_atom(), copy_residue_connections_from(), determine_nonstandard_polymer_status(), and init_residue_from_other().

utility::vector1<Angle> core::conformation::Residue::nus_

private

our nu (internal ring) torsion angles

Referenced by init_residue_from_other(), nu(), nus(), Residue(), ring_conformer(), set_all_nu(), set_all_ring_nu(), set_tau(), and update_nus().

utility::vector1< orbitals::OrbitalXYZCoords > core::conformation::Residue::orbitals_

private

Referenced by assign_orbitals(), init_residue_from_other(), orbital_type_index(), orbital_xyz(), and set_orbital_xyz().

std::map< Size, PseudoBondCollectionCOP > core::conformation::Residue::pseudobonds_

private

other residues within 4 bonds (connected through PseudoBonds) may include this residue (intra-residue pseudo-bonds)

Referenced by clear_residue_connections(), connections_match(), copy_residue_connections(), copy_residue_connections_from(), get_pseudobonds_to_residue(), init_residue_from_other(), is_pseudo_bonded(), pseudobonds(), Residue(), set_pseudobonds_to_residue(), and update_sequence_numbering().

ResidueType const& core::conformation::Residue::rsd_type_

private

our Residue type

Referenced by aa(), abase2(), accpt_pos(), accpt_pos_sc(), actcoord_atoms(), all_bb_atoms(), apply_transform_downstream(), assign_orbitals(), atom_base(), atom_depends_on_lower(), atom_depends_on_upper(), atom_index(), atom_is_backbone(), atom_is_hydrogen(), atom_is_polar_hydrogen(), atom_name(), atom_type(), atom_type_set(), atomic_charge(), atoms_with_orb_index(), attached_H_begin(), attached_H_end(), backbone_aa(), bonded_neighbor(), bonded_orbitals(), build_orbital_xyz(), carbohydrate_info(), chi_atoms(), chi_rotamers(), connect_atom(), connected_residue_at_lower(), connected_residue_at_upper(), cut_bond_neighbor(), first_sidechain_atom(), first_sidechain_hydrogen(), get_metal_binding_atoms(), Haro_index(), has(), has_lower_connect(), has_property(), has_sc_orbitals(), has_shadow_atoms(), has_upper_connect(), has_variant_type(), heavyatom_has_polar_hydrogens(), heavyatom_is_an_acceptor(), Hpol_index(), Hpos_apolar(), Hpos_polar(), Hpos_polar_sc(), icoor(), is_apolar(), is_aramid(), is_aromatic(), is_branch_point(), is_carbohydrate(), is_charged(), is_coarse(), is_d_rna(), is_DNA(), is_l_rna(), is_ligand(), is_lower_terminus(), is_meta_aramid(), is_metal(), is_metalbinding(), is_NA(), is_ortho_aramid(), is_para_aramid(), is_peptoid(), is_polar(), is_polymer(), is_polymer_bonded(), is_post_methylene_meta_aramid(), is_post_methylene_ortho_aramid(), is_post_methylene_para_aramid(), is_pre_methylene_meta_aramid(), is_pre_methylene_ortho_aramid(), is_pre_methylene_para_aramid(), is_pre_methylene_post_methylene_meta_aramid(), is_pre_methylene_post_methylene_ortho_aramid(), is_pre_methylene_post_methylene_para_aramid(), is_protein(), is_purine(), is_pyrimidine(), is_repulsive(), is_RNA(), is_similar_aa(), is_similar_rotamer(), is_sri(), is_surface(), is_terminus(), is_TNA(), is_triazolemer(), is_upper_terminus(), is_virtual(), is_virtual_residue(), is_water(), last_backbone_atom(), lower_connect(), lower_connect_atom(), mainchain_atom(), mainchain_atoms(), mm_atom_name(), n_hbond_acceptors(), n_hbond_donors(), n_mainchain_atoms(), n_non_polymeric_residue_connections(), n_nus(), n_orbitals(), n_polymeric_residue_connections(), n_possible_residue_connections(), n_virtual_atoms(), na_analogue(), name(), name1(), name3(), natoms(), nbr_atom(), nbr_atom_xyz(), nbr_radius(), nbrs(), nchi(), nheavyatoms(), nu_atoms(), orbital_name(), orbital_type(), orient_onto_location(), orient_onto_residue(), orient_onto_residue_peptoid(), path_distance(), path_distances(), place(), requires_actcoord(), Residue(), residue_connect_atom_index(), residue_connection(), ring_conformer(), RNA_info(), select_orient_atoms(), set_all_ring_nu(), set_chi(), set_d(), set_orbital_xyz(), set_tau(), set_theta(), show(), type(), update_actcoord(), update_nus(), update_orbital_coords(), upper_connect(), and upper_connect_atom().

ResidueTypeCOP core::conformation::Residue::rsd_type_ptr_

private

Pointer to the ResidueType that this Residue derives its chemical identity from. The ResidueType is pointed to through both a pointer and a reference; the pointer for the sake of serialization, and the reference for access speed.

Referenced by clone_flipping_chirality(), and type_ptr().

Size core::conformation::Residue::seqpos_

private

the sequence position

Referenced by connect_atom(), fill_missing_atoms(), init_residue_from_other(), polymeric_oriented_sequence_distance(), polymeric_sequence_distance(), seqpos(), show(), and update_sequence_numbering().

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The documentation for this class was generated from the following files:

• src/core/conformation/Residue.hh
• src/core/conformation/Residue.cc