A class for defining a type of residue. More...

#include <ResidueType.hh>

Inheritance diagram for core::chemical::ResidueType:

Public Member Functions
virtual	~ResidueType ()
	destructor More...

	ResidueType (AtomTypeSetCOP atom_types, ElementSetCOP element_types, MMAtomTypeSetCOP mm_atom_types, orbitals::OrbitalTypeSetCOP orbital_types)
	constructor More...

	ResidueType (ResidueType const &residue_type)

ResidueTypeOP	clone () const
	make a copy More...

ResidueTypeOP	placeholder_clone () const
	make a copy More...

ResidueType &	operator= (ResidueType const &src)
	Copies <src> into the ResidueType. More...

ResidueTypeCOP	get_self_ptr () const
	self pointers More...

ResidueTypeOP	get_self_ptr ()

ResidueTypeCAP	get_self_weak_ptr () const

ResidueTypeAP	get_self_weak_ptr ()

AtomTypeSet const &	atom_type_set () const
	access by reference the atomset for which this residue is constructed More...

ElementSet const &	element_set () const
	access by reference the element set for which this residue is constructed More...

ElementSetCOP	element_set_ptr () const
	access by const pointer the element set for which this residue is constructed More...

AtomTypeSetCOP	atom_type_set_ptr () const
	access by const pointer the atomset for which this residue is constructed More...

Atom &	atom (Size const atom_index)

Atom const &	atom (Size const atom_index) const

Atom &	atom (std::string const &atom_name)

Atom const &	atom (std::string const &atom_name) const

Atom &	atom (VD const atom_vd)

Atom const &	atom (VD const atom_vd) const

Orbital const &	orbital (Size const orbital_index) const

Orbital const &	orbital (std::string const &orbital_name) const

Bond &	bond (ED const ed)

Bond const &	bond (ED const ed) const

Bond &	bond (std::string const &atom1, std::string const &atom2)

Bond const &	bond (std::string const &atom1, std::string const &atom2) const

AtomType const &	atom_type (Size const atomno) const
	Get the chemical atom_type for this atom by it index number in this residue. More...

AtomType const &	atom_type (VD const vd) const
	Get the chemical atom_type for this atom by it index number in this residue. More...

Size	natoms () const
	number of atoms More...

Size	nheavyatoms () const
	number of heavy atoms More...

Size	n_hbond_acceptors () const
	number of hbond_acceptors More...

Size	n_hbond_donors () const
	number of hbond_donors More...

Size	nbonds () const
	number of bonds More...

Size	nbonds (Size atom) const
	number of bonds for given atom More...

Size	nbonds (VD atom) const
	number of bonds for given atom More...

int	path_distance (Size at1, Size at2) const
	path distance (number of bonds separated) between a pair of atoms More...

utility::vector1< int > const &	path_distance (Size atom) const
	shortest path distance for an atom to all other residue atoms More...

utility::vector1 < utility::vector1< int > > const &	path_distances () const
	accessor of path_distance_ data for this residue, which is a 2D array More...

Size	attached_H_begin (Size const atom) const
	index number of the first attached Hydrogen on an atom More...

Size	attached_H_end (Size const atom) const
	index number of the last attached Hydrogen on an atom More...

AtomIndices const &	attached_H_begin () const
	for all heavy atoms, index numbers of their first attached Hydrogen More...

AtomIndices const &	attached_H_end () const
	for all heavy atoms, index numbers of their last attached Hydrogen More...

Size	n_virtual_atoms () const
	Counts the number of virtual atoms and returns the count. More...

Size	number_bonded_hydrogens (Size const atomno) const
	indicates how many proton bonded neighbors an atom has More...

Size	number_bonded_heavyatoms (Size const atomno) const
	indicates how many heavyatom bonded neighbors an atom has More...

AtomIndices const &	bonded_neighbor (Size const atomno) const
	indices of the bonded neighbors for an atom More...

AdjacentIterPair	bonded_neighbor_iterators (VD const &atom) const

bool	atoms_are_bonded (core::Size const atomindex1, core::Size const atomindex2) const
	Indicates whether or not two atom indices have a chemical bond linking them. More...

utility::vector1< BondName > const &	bonded_neighbor_types (Size const atomno) const

AtomIndices const &	cut_bond_neighbor (Size const atomno) const
	indices of the bonded neighbors for an atom More...

AtomIndices const &	nbrs (Size const atomno) const
	indices of the bonded neighbors for an atom, shortcut for bonded_neighbor(atomno) More...

AtomIndices const &	chi_atoms (Size const chino) const
	indices of the atoms which are used to define a given chi angle (chino) More...

VDs const &	chi_atom_vds (Size const chino) const
	VDs of the atoms which are used to define a given chi angle (chino) More...

utility::vector1< AtomIndices > const &	chi_atoms () const
	indices of the atoms which are used to define all the chi angles More...

AtomIndices const &	nu_atoms (core::uint const nu_index) const
	Return indices of the atoms used to define a given nu (internal ring) angle. More...

utility::vector1< AtomIndices > const &	nu_atoms () const
	Return list of indices of the atoms used to define all the nu (internal ring) angles. More...

AtomIndices const &	ring_atoms (uint const ring_num) const
	Return list of indices of the atoms within this residue's nth cycle, not counting virtual atoms. More...

utility::vector1< AtomIndices > const &	ring_atoms () const
	Return list of indices of the atoms within this residue's cycles, not counting virtual atoms. More...

void	get_metal_binding_atoms (AtomIndices &metal_binding_indices) const
	Gets indices of all atoms that can form bonds to metals. More...

utility::vector1< std::string >	get_metal_binding_atoms () const

std::string	get_disulfide_atom_name () const
	Gets disulfide atom name. More...

void	set_disulfide_atom_name (std::string n)
	Sets disulfide atom name. More...

AtomIndices const &	all_bb_atoms () const
	Indices of all backbone atoms, hydrogens and heavyatoms. More...

AtomIndices const &	all_sc_atoms () const
	Indices of all sidechain atoms, hydrogens and heavyatoms. More...

AtomIndices const &	Haro_index () const
	return indices of aromatic Hydrogens More...

AtomIndices const &	Hpol_index () const
	return indices of polar Hydrogens More...

AtomIndices const &	Hpos_polar () const
	indices of polar hydrogens as Hbond donors More...

AtomIndices const &	Hpos_apolar () const
	indices of non-polar hydrogens as potential carbon Hbond donors More...

AtomIndices const &	Hpos_polar_sc () const

AtomIndices const &	accpt_pos () const
	indices of atoms as Hbond acceptors More...

AtomIndices const &	accpt_pos_sc () const
	indices of atoms as Hbond acceptors More...

bool	heavyatom_has_polar_hydrogens (Size atomno) const

bool	heavyatom_is_an_acceptor (Size atomno) const

bool	atom_is_polar_hydrogen (Size atomno) const

AtomIndices const &	mainchain_atoms () const
	indices of all mainchain atoms More...

Size	mainchain_atom (Size const atm) const
	index of mainchain atom More...

void	set_mainchain_atoms (AtomIndices const &mainchain)
	set indices of all mainchain atoms More...

bool	has (std::string const &atom_name) const
	is this atom present in this residue? More...

bool	has (VD const vd) const
	is this vertex descriptor present in this residue? More...

Size	atom_base (Size const atomno) const
	get index of an atom's base atom More...

VD	atom_base (VD const atomno) const
	get vd of an atom's base atom More...

Size	abase2 (Size const atomno) const
	get index of an atom's second base atom More...

std::string const &	atom_name (Size const index) const
	get atom name by index More...

std::string const &	atom_name (VD const vd) const
	get atom name by vertex descriptor More...

Size	atom_index (std::string const &name) const
	get atom index by name More...

Size	atom_index (VD const &vd) const
	get atom index by vertex descriptor More...

VD	atom_vertex (std::string const &name) const
	get the vertex descriptor from the name of the atom. More...

VD	atom_vertex (Size const &atomno) const
	Get the vertex descriptor from the atom index. More...

ResidueGraph const &	graph () const
	Constant access to the underlying graph. More...

void	dump_vd_info () const

void	show_all_atom_names (std::ostream &out) const

Size	last_backbone_atom () const
	index of the last backbone heavy atom More...

Size	first_sidechain_atom () const
	index of the first sidechain atom (heavy or hydrogen) More...

Size	first_sidechain_hydrogen () const
	index of the first sidehchain hydrogen More...

VIterPair	atom_iterators () const

EIterPair	bond_iterators () const

OutEdgeIterPair	bond_iterators (VD const &atom) const

bool	atom_is_backbone (Size const atomno) const
	is a backbone atom (heavy or hydrogen)? More...

bool	atom_is_hydrogen (Size const atomno) const
	quick lookup: is the atom with the given index a hydrogen or not? Atoms are sorted so that heavy atoms come first and hydrogen atoms come last. More...

utility::vector1< Size > const &	last_controlling_chi () const
	Read access to the last_controlling_chi_ array. More...

Size	last_controlling_chi (Size atomno) const
	The last_controlling_chi for an atom. 0 if an atom is controlled by no chi. More...

utility::vector1< AtomIndices > const &	atoms_last_controlled_by_chi () const
	Read access to the atoms_last_controlled_by_chi_ array. More...

AtomIndices const &	atoms_last_controlled_by_chi (Size chi) const
	Read access to the Atoms last controlled by a particular chi. More...

AtomIndices const &	actcoord_atoms () const
	get indices for atoms used to define actcoord More...

bool	is_virtual (Size const &atomno) const
	Check if atom is virtual. More...

bool	is_repulsive (Size const &atomno) const
	Check if atom is repulsive. More...

MMAtomType const &	mm_atom_type (Size const atomno) const
	Get the MM atom_type for this atom by its index number in this residue. More...

MMAtomTypeSetCOP	mm_atom_types_ptr () const
	Get the MM atom_type for this atom by its index number in this residue. More...

gasteiger::GasteigerAtomTypeDataCOP	gasteiger_atom_type (Size const atomno) const
	Get the MM atom_type index number for this atom by its index number in this residue. More...

gasteiger::GasteigerAtomTypeSetCOP	gasteiger_atom_typeset () const

chemical::orbitals::OrbitalType const &	orbital_type (int const orbital_index) const

Size	n_orbitals () const
	number of orbitals More...

utility::vector1< core::Size > const &	bonded_orbitals (Size const atomno) const
	indices of the orbitals bonded to an atom More...

bool	has_orbital (std::string const &orbital_name) const
	is this orbital present in this residue? More...

AtomIndices const &	atoms_with_orb_index () const

core::Size	orbital_index (std::string const &name) const
	get orbital index by name More...

orbitals::OrbitalTypeSetCOP	orbital_types_ptr () const
	Get the MM atom_type for this atom by its index number in this residue. More...

core::chemical::rings::RingConformerSetCOP	ring_conformer_set (core::uint ring_num) const
	Return a pointer to the object containing the set of ring conformers possible for this residue's nth cycle. More...

ResidueTypeSetCOP	residue_type_set () const
	Return an owning pointer to the ResidueTypeSet that this ResidueType belongs to; it will return a null pointer if this ResidueType does not belong to any ResidueTypeSet. More...

void	residue_type_set (ResidueTypeSetCAP set_in)
	set the residue type set of origin. More...

bool	in_residue_type_set () const

Size	nchi () const
	number of chi angles More...

Size	n_nus () const
	Return number of nu (internal ring) angles. More...

Size	n_rings () const
	Return the number of rings in this residue. More...

Size	n_proton_chi () const
	number of proton chis More...

bool	is_proton_chi (Size const chino) const
	number of proton chis More...

Size	proton_chi_2_chi (Size proton_chi_id) const
	translate proton_chi to global chi More...

Size	chi_2_proton_chi (Size chi_index) const

utility::vector1< Real > const &	proton_chi_samples (Size proton_chi) const

utility::vector1< Real > const &	proton_chi_extra_samples (Size proton_chi) const

utility::vector1< std::pair < Real, Real > > const &	chi_rotamers (Size const chino) const
	all rotamers bins (mean, std) for a given chi angle More...

ResidueConnection const &	lower_connect () const

Size	lower_connect_id () const

Size	lower_connect_atom () const
	index number of the atom which connects to the lower connection More...

void	set_lower_connect_atom (std::string const &atm_name)
	set the atom which connects to the lower connection More...

ResidueConnection const &	upper_connect () const

Size	upper_connect_id () const

Size	upper_connect_atom () const
	index number of the atom which connects to the upper connection More...

void	set_upper_connect_atom (std::string const &atm_name)
	set the atom which connects to the upper connection More...

utility::vector1< uint >	branch_connect_atoms () const
	Return a list of indices of atoms at non-polymer connections. More...

utility::vector1< std::string >	branch_connect_atom_names () const
	Return a list of names of atoms at non-polymer connections. More...

Size	n_possible_residue_connections () const
	number of ResidueConnections, counting polymeric residue connections More...

Size	n_polymeric_residue_connections () const

Size	n_non_polymeric_residue_connections () const

ResidueConnection const &	residue_connection (Size const i) const
	Get a ResidueConection. More...

ResidueConnection &	residue_connection (Size const i)
	Get a ResidueConection. More...

bool	atom_forms_residue_connection (Size const atomid)
	Does an atom form any inter-residue chemical bonds? More...

Size	n_residue_connections_for_atom (Size const atomid) const
	How many inter-residue chemical bonds does a particular atom form? More...

Size	residue_connection_id_for_atom (Size const atomid) const
	Convenience access function for the residue connection at a particular atom; requires that there is exactly one residue connection at this atom. More...

utility::vector1< Size > const &	residue_connections_for_atom (Size const atomid) const

bool	residue_connection_is_polymeric (Size const resconn_id) const

Size	residue_connect_atom_index (Size const resconn_id) const

bool	requires_actcoord () const
	require actcoord? More...

void	update_actcoord (conformation::Residue &rot) const
	update actcoord More...

VD	add_atom (std::string const &atom_name, std::string const &atom_type_name, std::string const &mm_atom_type_name, Real const charge)
	add an atom into this residue Will return the vertex descriptor of the added atom. More...

VD	add_atom (std::string const &atom_name="")
	add an atom into this residue, with just the name. Will return the vertex descriptor of the added atom. More...

VD	add_atom (Atom const &atom, AtomICoor const &icoor)

void	delete_atom (std::string const &name)
	flag an atom for deletion by adding its index to the delete_atom_ list More...

void	delete_atom (Size const index)
	flag an atom for deletion by adding its index to the delete_atom_ list More...

void	add_atom_alias (std::string const &rosetta_atom, std::string const &alias)
	Add an alias name for an atom. More...

void	delete_atom_alias (std::string const &alias)
	Remove a given alias name for an atom. More...

void	set_atom_type (std::string const &atom_name, std::string const &atom_type_name)
	set atom type More...

void	set_atom_type (VD atom, std::string const &atom_type_name)
	set atom type More...

void	set_mm_atom_type (std::string const &atom_name, std::string const &mm_atom_type_name)
	set mm atom type More...

void	set_gasteiger_typeset (gasteiger::GasteigerAtomTypeSetCOP gasteiger_atom_types)
	Manually set the gasteiger typeset - will use the default set otherwise. More...

void	set_gasteiger_atom_type (std::string const &atom_name, std::string const &gasteiger_atom_type_name)
	set gasteiger atom type More...

void	set_gasteiger_atom_type (VD atom, std::string const &gasteiger_atom_type_name)
	set gasteiger atom type More...

void	add_metalbinding_atom (std::string const atom_name)
	Add an atom to the list of atoms that can potentially form a bond to a metal ion. Note that the atom must exist in the residue type (the function checks for this at runtime). More...

void	delete_metalbinding_atom (std::string const &atom_name)
	Remove an atom from the list of atoms that can potentially form a bond to a metal ion (used in patching when it kills the valence that is thus used) More...

void	delete_act_coord_atom (std::string const &atom_name)
	Remove an atom from the list of act coord atoms (used in patching when it kills the valence that is thus used) More...

void	add_bond (std::string const &atom_name1, std::string const &atom_name2, BondName bondLabel=SingleBond)
	add a bond between atom1 and atom2, specifying a bond type (SingleBond, DoubleBond, TripleBond, AromaticBond) More...

void	add_bond (VD atom1, VD atom2, BondName bondLabel=SingleBond)
	add a bond between atom1 and atom2, specifying a bond type (SingleBond, DoubleBond, TripleBond, AromaticBond) More...

void	change_bond_type (std::string const &atom_name1, std::string const &atom_name2, BondName const old_bond_label, BondName const new_bond_label)
	Change the bond type of the given bond from one type to another. More...

void	add_cut_bond (std::string const &atom_name1, std::string const &atom_name2)
	add a bond between atom1 and atom2, if bond type is not specified, default to a SingleBond More...

VD	root_atom () const
	get root_atom used as the base of the icoor tree. More...

void	nbr_atom (std::string const &atom_name)
	set nbr_atom used to define residue-level neighbors More...

void	nbr_atom (VD vertex)
	set nbr_atom used to define residue-level neighbors More...

Size	nbr_atom () const
	get nbr_atom used to define residue-level neighbors More...

VD	nbr_vertex () const
	get VD used to define residue-level neighbors More...

void	nbr_radius (Real const radius)
	set nbr_radius_ used to define residue-level neighbors More...

Real	nbr_radius () const
	get nbr_radius_ used to define residue-level neighbors More...

core::Real const &	mass () const
	get the molecular weight of this residue More...

void	set_atom_base (std::string const &atom_name1, std::string const &atom_name2)
	sets atom_base[ atom1 ] = atom2 More...

void	set_atom_base (VD const &atom1, VD const &atom2)
	sets atom_base[ atom1 ] = atom2, vertex descriptor version More...

void	set_backbone_heavyatom (std::string const &name)
	set an atom as backbone heavy atom More...

void	debug_dump_icoor () const
	Dump out atomnames and icoor values. More...

AtomICoor const &	icoor (Size const atm) const
	AtomICoord of an atom. More...

AtomICoor const &	icoor (VD const atm) const
	AtomICoord of an atom. More...

void	set_icoor (std::string const &atm, Real const phi, Real const theta, Real const d, std::string const &stub_atom1, std::string const &stub_atom2, std::string const &stub_atom3, bool const update_xyz=false)
	set AtomICoor for an atom More...

void	set_icoor (VD const &atm, Real const phi, Real const theta, Real const d, VD const &stub_atom1, VD const &stub_atom2, VD const &stub_atom3, bool const update_xyz=false)
	set AtomICoor for an atom, vertex descriptor version More...

void	set_icoor (std::string const &atm, Real const phi, Real const theta, Real const d, ICoorAtomID const &stub_atom1, ICoorAtomID const &stub_atom2, ICoorAtomID const &stub_atom3, bool const update_xyz=false)
	set AtomICoor for an atom More...

void	reset_bond_distance_to_atom (std::string const &atm, core::Distance const d)
	Reset the bond distance to an atom whose internal coordinates have already been set. More...

void	assign_neighbor_atom ()

void	assign_internal_coordinates ()
	Assign internal coordinates from the set ideal xyz coordinates. Note that it currently does not obey mainchain designations or cut bonds. More...

void	assign_internal_coordinates (core::chemical::VD new_root)

void	set_ideal_xyz (std::string const &atm, Vector const &xyz_in)

void	set_ideal_xyz (Size index, Vector const &xyz_in)

void	set_ideal_xyz (VD atm, Vector const &xyz_in)

void	fill_ideal_xyz_from_icoor ()

void	set_shadowing_atom (std::string const &atom, std::string const &atom_being_shadowed)

void	clear_orbitals ()
	clear orbitals More...

void	add_orbital (std::string &orbital_name, std::string &orbital_type_name)
	add an orbital onto a residue based upon atom More...

void	add_orbital_bond (std::string const &atom_name1, std::string const &orbital_name)
	add an orbital bond between an atom and an orbital. More...

orbitals::ICoorOrbitalData const &	orbital_icoor_data (Size const orbital_index) const

orbitals::ICoorOrbitalData const &	new_orbital_icoor_data (Size const orbital_index) const

void	set_orbital_icoor_id (std::string const &orbital, Real const phi, Real const theta, Real const d, std::string const &stub_atom1, std::string const &stub_atom2, std::string const &stub_atom3)
	set OrbitalICoor for an orbital More...

const HeavyAtomGraph	heavy_atoms ()

const AcceptorAtomGraph	acceptor_atoms ()

const HeavyAtomWithPolarHydrogensGraph	heavy_atom_with_polar_hydrogens ()

const HeavyAtomWithHydrogensGraph	heavy_atom_with_hydrogens ()

const HydrogenAtomGraph	hydrogens ()

const PolarHydrogenGraph	polar_hydrogens ()

const APolarHydrogenGraph	apolar_hydrogens ()

const AromaticAtomGraph	aromatic_atoms ()

void	add_chi (Size const chino, VD atom1, VD atom2, VD atom3, VD atom4)
	Add a chi (side-chain) angle defined by four atoms. More...

void	add_chi (VD atom1, VD atom2, VD atom3, VD atom4)
	Add a chi (side-chain) angle defined by four atoms. More...

void	add_chi (Size const chino, std::string const &atom_name1, std::string const &atom_name2, std::string const &atom_name3, std::string const &atom_name4)
	Add a chi (side-chain) angle defined by four atoms. More...

void	add_chi (std::string const &atom_name1, std::string const &atom_name2, std::string const &atom_name3, std::string const &atom_name4)
	Add a chi (side-chain) angle defined by four atoms to the end of the list of chis. More...

void	add_nu (core::uint const nu_index, std::string const &atom_name1, std::string const &atom_name2, std::string const &atom_name3, std::string const &atom_name4)
	Add a nu (internal cyclic) angle defined by four atoms. More...

void	add_ring (core::uint const ring_num, utility::vector1< std::string > const &ring_atoms)
	Add a ring definition. More...

void	set_lowest_energy_ring_conformer (core::uint const ring_num, std::string const &conformer)
	Set this cyclic residue's lowest-energy ring conformer for the nth ring by IUPAC name. More...

void	set_low_energy_ring_conformers (core::uint const ring_num, utility::vector1< std::string > const &conformers)
	Set this cyclic residue's low-energy ring conformers for the nth ring by IUPAC name. More...

void	redefine_chi (Size const chino, std::string const &atom_name1, std::string const &atom_name2, std::string const &atom_name3, std::string const &atom_name4)
	redefine a chi angle based on four atoms More...

void	delete_terminal_chi ()
	delete terminal chi angle More...

void	set_proton_chi (Size chino, utility::vector1< Real > const &dihedral_samples, utility::vector1< Real > const &extra_samples)
	Annotate a given chi as a proton chi, and set the sampling behavior If the chi is already listed as a proton chi, change the sampling behavior. More...

void	add_chi_rotamer (Size const chino, Real const mean, Real const sdev)
	Add a rotamer bin for a given chi. More...

void	add_chi_rotamer_to_last_chi (core::Angle const mean, core::Angle const sdev)
	Adds a chi rotamer bin to the highest-indexed chi in the list of chis for this ResidueType. More...

void	clear_chi_rotamers (core::uint const chi_no)
	Delete all of the chi rotamer bins from the specified chi for this ResidueType. More...

void	autodetermine_chi_bonds (core::Size max_proton_chi_samples=500)
	Regenerate the rotatable chi bonds from the internal graph structure. If the number of proton chi samples would exceed max_proton_chi_samples, don't add extra sampling to proton chis. As a special case, if this is zero don't add any proton chi sampling at all. More...

void	finalize ()
	recalculate derived data, potentially reordering atom-indices More...

bool	finalized () const
	finalized? should always be true, except in very special case early in on-the-fly ResidueTypeSet. More...

void	require_final () const
	an assertion function to ensure an ResidueType has been finalized More...

Size	add_residue_connection (std::string const &atom_name)
	add a non-polymeric ResidueConnection More...

void	add_actcoord_atom (std::string const &atom)
	add an atom to the list for calculating actcoord center More...

ResidueProperties const &	properties () const
	Access the collection of properties for this ResidueType. More...

void	set_properties (ResiduePropertiesOP properties)
	Set the collection of properties for this ResidueType. More...

void	add_property (std::string const &property)
	Add a property to this ResidueType. More...

void	set_adduct_flag (bool adduct_in)

void	add_numeric_property (std::string const &tag, core::Real value)
	Add a numeric property. More...

void	add_string_property (std::string const &tag, std::string value)
	Add a string property. More...

void	delete_property (std::string const &property)
	Add a property of this ResidueType. More...

bool	is_base_type () const
	Is this ResidueType a base type? More...

ResidueTypeCOP	get_base_type_cop () const
	Get a pointer to this ResidueType's base ResidueType. More...

void	reset_base_type_cop ()
	Reset the base type COP to be null. This implies that this ResidueType is a base type. More...

void	set_base_type_cop (ResidueTypeCOP new_base_type)
	Set the base type COP. This implies that this ResidueType is NOT a base type. More...

bool	is_polymer () const
	is polymer? More...

bool	is_sidechain_thiol () const
	is thiol? More...

bool	is_disulfide_bonded () const
	is disulfide? More...

bool	is_sidechain_amine () const
	is sidechain amine? More...

bool	is_protein () const
	is protein? More...

bool	is_alpha_aa () const
	Is this an alpha-amino acid? More...

bool	is_beta_aa () const
	Is this a beta-amino acid? More...

bool	is_gamma_aa () const
	Is this a gamma-amino acid? More...

bool	is_sri () const
	Is this one of SRI's special heteropolymer building blocks? More...

bool	is_triazolemer () const
	Is this a triazolemer? More...

bool	is_d_aa () const
	is this a d-amino acid? More...

bool	is_l_aa () const
	is this an l-amino acid? More...

bool	is_achiral_backbone () const
	is this an achiral backbone? More...

bool	is_DNA () const
	is DNA? More...

bool	is_RNA () const
	is RNA? More...

bool	is_coarse () const
	is coarse? More...

bool	is_NA () const
	is Nucleic Acid? More...

bool	is_solvent () const
	Is this a solvent molecule (SOLVENT property)? More...

bool	is_canonical_nucleic () const
	Is this a canonical nucleic acid (CANONICAL_NUCLEIC property)? More...

bool	is_canonical_aa () const
	Is this a canonical amino acid (CANONICAL_AA property)? More...

bool	is_canonical () const
	Is this a canonical residue type (nucleic acid or amino acid)? More...

bool	is_peptoid () const
	is peptoid? More...

bool	is_carbohydrate () const
	is carbohydrate? More...

bool	is_ligand () const
	is ligand? More...

bool	is_lipid () const
	is lipid? More...

bool	is_metal () const
	Return true if this residue type is a metal ion, false otherwise. More...

bool	is_metalbinding () const
	Return true if this residue type is a type that can bind to a metal ion (e.g. His, Asp, Cys, etc.), false otherwise. More...

bool	is_membrane () const
	is membrane? More...

bool	is_surface () const
	is surface? (e.g. enamel) More...

bool	has_sc_orbitals () const
	does this residue have sidechain orbitals? More...

bool	is_polar () const
	is polar? More...

bool	is_charged () const
	is charged? More...

bool	is_aromatic () const
	is aromatic? More...

bool	is_cyclic () const
	is cyclic? More...

bool	is_terminus () const
	is terminus? More...

bool	is_lower_terminus () const
	is lower terminus? More...

bool	is_upper_terminus () const
	is upper terminus? More...

bool	is_branch_point () const
	is a branch-point residue? More...

bool	is_branch_lower_terminus () const
	is lower terminus of a branch? More...

bool	is_acetylated_nterminus () const
	is acetylated n terminus More...

bool	is_methylated_cterminus () const
	is methylated c terminus More...

bool	is_virtual_residue () const
	Check if residue is 'VIRTUAL_RESIDUE'. More...

bool	is_inverted_virtual_residue () const
	Check if atom is an inverted virtual. More...

bool	is_adduct () const
	is an adduct-modified residue? More...

bool	has_property (std::string const &property) const
	Generic property access. More...

bool	has_property (ResidueProperty const property) const
	Generic property access, by ResidueProperty. More...

core::Real	get_numeric_property (std::string const &tag) const
	Get a numeric property, if it exists. More...

std::string	get_string_property (std::string const &tag) const
	Get a string property, if it exists. More...

void	add_variant_type (VariantType const variant_type)
	Add a variant type to this ResidueType. More...

void	add_variant_type (std::string const &variant_type)
	Add a variant type to this ResidueType by string. More...

void	remove_variant_type (VariantType const variant_type)
	Remove a variant type to this ResidueType. More...

void	remove_variant_type (std::string const &variant_type)
	Remove a variant type to this ResidueType by string. More...

bool	has_variant_type (VariantType const variant_type) const
	Generic variant access. More...

bool	has_variant_type (std::string const &variant_type) const
	Generic variant access by string. More...

void	enable_custom_variant_types ()
	Turn on the ability to create VariantTypes "on-the-fly". More...

utility::vector1< std::string >	variant_types () const
	get all the variant types for this ResidueType More...

utility::vector1< VariantType >	variant_type_enums () const
	Get a vector of VariantType enums for this ResidueType. More...

utility::vector1< std::string > const &	custom_variant_types () const
	Get a list of custom VariantType strings for this ResidueType (by const reference). More...

void	aa (AA const &type)
	set our aa-type (could be "UNK") More...

void	aa (std::string const &type)
	set our aa-type (could be "UNK") More...

void	backbone_aa (std::string const &type)
	AA to use for backbone scoring. More...

void	rotamer_aa (std::string const &type)
	AA to use for rotamer scoring. More...

void	nondefault (bool const in)

std::string const &	base_name () const
	Get this ResidueType's base name (shared with other residue types with the same base type). More...

std::string const &	name () const
	get our (unique) residue name More...

void	base_name (std::string const &base_name_in)
	Set this ResidueType's base name (shared with other residue types with the same base type). More...

void	name (std::string const &name_in)
	set our (unique) residue name More...

std::string const &	name3 () const
	get our 3letter code. This is set in the ResidueType .params file through the IO_STRING tag along with the name1 string NOTE: The "name3" is not necessarily three characters long. e.g. Metal ions may be only two characters. More...

void	name3 (std::string const &name_in)
	set our 3letter code More...

char	name1 () const
	get our 1letter code. This is set in the ResidueType .params file through the IO_STRING tag along with the name3 string. More...

void	name1 (char const code)
	set our 1letter code More...

std::string	interchangeability_group () const
	get our interchangeability-group id. Used to determine if two residue types are equivalent, except for their variant status. E.g. ResidueTypes ALA and ALA_Nterm would be part of the same interchangeability group. This has a degree of subjectivity; are TYR and pTYR in the same interchangeability group? Probably not. This data can be specified in the ResidueTypes .params file with the INTERCHANGEABILITY_GROUP tag. More...

void	interchangeability_group (std::string setting)
	set our interchangeability-group id More...

void	remap_pdb_atom_names (bool rename)
	Turn on geometry-based atom renaming when loading this residue type from PDB files. More...

bool	remap_pdb_atom_names () const
	Are we using geometry-based atom renaming when loading this residue type from PDB. More...

AA const &	aa () const
	our traditional residue type, if any More...

AA const &	backbone_aa () const
	Returns the amino acid type to be used for backbone scoring (rama and p_aa_pp). More...

void	rotamer_library_specification (rotamers::RotamerLibrarySpecificationOP)

rotamers::RotamerLibrarySpecificationCOP	rotamer_library_specification () const

dihedral_atom_set const &	dihedral (Size const dihe) const
	dihedral methods More...

dihedral_atom_set const &	improper_dihedral (Size const dihe) const
	Return the indices for the set of atoms that define a particular intraresidue improper dihedral. More...

utility::vector1< Size > const &	dihedrals_for_atom (Size atomno) const
	Returns the list of all of the indices of all the intraresidue dihedrals a particular atom is involved in. Useful for calculating the derivatives for an atom. More...

utility::vector1< Size > const &	improper_dihedrals_for_atom (Size atomno) const
	Returns the list of all of the indices of all the intraresidue dihedrals a particular atom is involved in. Useful for calculating the derivatives for an atom. More...

Size	ndihe () const
	Return the number of intraresidue dihedrals. This covers all pairs of atoms that are separated by four bonds, and all pairs of intervening atoms. More...

void	print_dihedrals () const

bondangle_atom_set const &	bondangle (Size const bondang) const
	Return the indices for the set of atoms that define a particular intraresidue angle. More...

utility::vector1< Size > const &	bondangles_for_atom (Size atomno) const
	Returns the list of all of the indices of all the intraresidue bond angles a particular atom is involved in. Useful for calculating the derivatives for an atom. More...

Size	num_bondangles () const
	get number of intraresidue bond angles More...

bool	has_shadow_atoms () const
	Returns true if this residue has shadow atoms, false otherwise. More...

Size	atom_being_shadowed (Size atom_shadowing) const
	Return the index of the atom that the "atom_shadowing" atom is shadowing; returns zero if the "atom_shadowing" atom is not shadowing anyone. More...

void	print_bondangles () const
	print intraresidue bond angles to standard out More...

void	print_pretty_path_distances () const
	print chemical-bond path distances to standard out More...

utility::vector1< two_atom_set > const &	atoms_within_one_bond_of_a_residue_connection (Size resconn) const
	Returns a list of those atoms within one bond of a residue connection. For residue connection i, its position in this array is a list of pairs of atom-id's, the first of which is always the id for the atom forming residue connection i. More...

utility::vector1< std::pair < Size, Size > > const &	within1bonds_sets_for_atom (Size atomid) const
	Returns a list of pairs for atom# atomid where first == the residue_connection id that lists atomid as being within one bond of a residue connection, and second == the index of the entry containing this atom in the atoms_within_one_bond_of_a_residue_connection_[ first ] array. Useful for calculating the derivatives for an atom. More...

utility::vector1 < three_atom_set > const &	atoms_within_two_bonds_of_a_residue_connection (Size resconn) const
	Returns the list of those atoms within two bonds of residue connection # resconn. Each entry in this list is a triple of atom-id's, the first of which is always the id for the atom forming residue connection resconn. More...

utility::vector1< std::pair < Size, Size > >	within2bonds_sets_for_atom (Size atomid) const
	Returns a list of pairs for atom # atomid where first == the residue_connection id that lists this atom as being within two bonds of a residue connection, and second == the index of the entry containing this atom in the atoms_within_two_bonds_of_a_residue_connection_[ first ] array. Useful for calculating the derivatives for an atom. More...

core::chemical::rna::RNA_ResidueType const &	RNA_type () const

core::chemical::carbohydrates::CarbohydrateInfoCOP	carbohydrate_info () const
	Return the CarbohydrateInfo object containing sugar-specific properties for this residue. More...

void	force_nbr_atom_orient (bool force_orient)
	Set force_nbr_atom_orient_, used to control orient atoms selected by select_orient_atoms. More...

bool	force_nbr_atom_orient () const
	Return force_nbr_atom_orient_, used to control orient atoms selected by select_orient_atoms. More...

void	select_orient_atoms (Size &center, Size &nbr1, Size &nbr2) const
	Selects three atoms for orienting this residue type. More...

core::Size	smallest_ring_size (VD const &atom, core::Size const &max_size=999999) const
	A graph-based function to determine the size of the smallest ring that involves a given atom. More...

std::list< utility::vector1 < ED > > const &	rings ()

void	show (std::ostream &output=std::cout, bool output_atomic_details=false) const
	Generate string representation of ResidueType for debugging purposes. More...

utility::vector1< Adduct > const &	defined_adducts () const
	get the adducts defined for this residue More...

void	add_adduct (Adduct &adduct_in)

void	report_adducts ()

Static Public Attributes
static VD const	null_vertex = boost::graph_traits<ResidueGraph>::null_vertex()

Private Member Functions
void	setup_atom_ordering ()
	set up atom ordering map old2new, called by finalize() More...

void	order_atoms ()
	GRAPH FUNCTION to provide backward compatibility ////////. More...

void	generate_atom_indices ()
	reorder primary data in ResidueType given the old2new map, called by finalize() More...

void	update_derived_data ()
	update derived data in ResidueType, called by finalize() More...

void	perform_checks ()
	Final check of ResidueType data, called by finalize(). More...

void	update_residue_connection_mapping ()

void	update_last_controlling_chi ()
	compute the last controlling chi for an atom during the update_derived_data() stage. The last controlling chi is the furthest chi downstream of the mainchain which can change the location of an atom. More...

void	note_chi_controls_atom (Size chi, Size atomno)
	Recursive subroutine invoked by update_last_controlling_chi(). More...

void	set_icoor_private (std::string const &atm, ICoorAtomID const &id, AtomICoor const &ic, bool update_xyz)

Private Attributes
AtomTypeSetCOP	atom_types_
	The type set for Rosetta Atom types. – Primary used to define the set of allowed atomtypes for this residue and their properties Needs to be non-null by the time finalize() is called. More...

ElementSetCOP	elements_
	The set for element objects. – Primary, can be null. More...

MMAtomTypeSetCOP	mm_atom_types_
	The set for MMAtomTypes. – Primary, can be null. More...

gasteiger::GasteigerAtomTypeSetCOP	gasteiger_atom_types_
	The set for GasteigerAtomTypes. – Primary, can be null. More...

orbitals::OrbitalTypeSetCOP	orbital_types_
	The set for OrbitalTypes. – Primary, can be null. More...

utility::vector1 < rings::RingConformerSetOP >	conformer_sets_
	The sets of all possible ring conformers, one per ring – Derived, can be null. More...

ResidueTypeSetCAP	residue_type_set_
	The owning ResidueTypeSet, if any. – Primary, can be null. More...

ResidueGraph	graph_
	The Atoms and Bonds of the ResidueType, stored as Nodes and Edges. – Primary. More...

std::map< VD, Size >	vd_to_index_
	A map of graph VDs to vector indexes. – Derived, valid during Mutable. More...

std::map< VD, VD >	atom_base_
	The atom "one up" in the atom tree. – Derived, valid during Mutable. Updated in set_icoor. (also set_atom_base - TODO: Fix redundancy issue. More...

std::map< VD, VD >	abase2_
	The base of the atom base – Derived. More...

VDs	ordered_atoms_
	Vector of atoms for index->vd mapping. More...

utility::vector1< Orbital >	orbitals_
	The orbitals on the ResidueType, if any. – Primary. More...

Size	nheavyatoms_
	The number of heavy atoms – Derived. More...

Size	n_hbond_acceptors_
	The number of hbond_acceptors – Derived. More...

Size	n_hbond_donors_
	number of hbond_donors – Derived. More...

Size	n_backbone_heavyatoms_
	number of backbone heavy atoms – Derived. More...

Size	first_sidechain_hydrogen_
	the index of first sidechain hydrogen atom – Derived. More...

utility::vector1< AtomIndices >	bonded_neighbor_
	indices of the atoms psuedo bonded atoms. Used in orbital code – Derived More...

utility::vector1 < utility::vector1< BondName > >	bonded_neighbor_type_
	??? – Derived More...

std::map< VD, utility::vector1 < VD > >	cut_bond_neighbor_
	??? – Derived More...

utility::vector1< Size >	attached_H_begin_
	indices of each heavyatom's first attached hydrogen – Derived. More...

utility::vector1< Size >	attached_H_end_
	indices of each heavyatom's last attached hydrogen – Derived. More...

std::map< VD, AtomICoor >	icoor_
	Internal coordinates on how to build the given atom – Primary. More...

utility::vector1 < dihedral_atom_set >	dihedral_atom_sets_
	Data for the mm potentials. – Derived List all of the intra-residue dihedral angles and bond angles. vector of sets of atoms that make up dihedral angles in the residue Data for the mm potentials. More...

utility::vector1 < utility::vector1< Size > >	dihedrals_for_atom_
	all intra-residue dihedral angles that each atom "participates" in – Derived More...

utility::vector1 < dihedral_atom_set >	improper_dihedral_atom_sets_

utility::vector1 < utility::vector1< Size > >	improper_dihedrals_for_atom_

utility::vector1 < bondangle_atom_set >	bondangle_atom_sets_
	vector of sets of atoms that make up bond angles in the residue – Derived More...

utility::vector1 < utility::vector1< Size > >	bondangles_for_atom_
	??? – Derived More...

std::map< VD, VD >	atom_shadowed_
	Data to describe virtual atoms that should shadow other atoms for the sake of keeping intraresidue cycles closed when working with an atom tree, e.g. NV shadows N on proline. For each atom, the following vector lists the index of the atom it is shadowing. – Primary. More...

utility::vector1< Size >	last_controlling_chi_
	Data for controlling chi. – Derived. Computed in update_last_controlling_chi() for each atom 0 means an atom whose location is not determined by any chi. More...

utility::vector1< AtomIndices >	atoms_last_controlled_by_chi_
	for chi i, the list of atoms last controlled by i – Derived E.g. chi2 on LEU list cd1, 1hd1, 1hd2, 1hd3, cd2, 2hd1, 2hd2, 2hd3, and hg1 More...

AtomIndices	atoms_with_orb_index_
	indices of atoms with orbitals – Derived More...

AtomIndices	Haro_index_
	indices of haro hydrogens – Derived More...

AtomIndices	Hpol_index_
	indices of hpolar hydrogens – Derived More...

AtomIndices	accpt_pos_
	indices of Hbond acceptor positions – Derived More...

AtomIndices	Hpos_polar_
	indices of polar Hydrogens for Hbond donors – Derived More...

AtomIndices	Hpos_apolar_
	indices of apolar hydrogens – Derived More...

AtomIndices	accpt_pos_sc_
	indices of Hbond acceptor positions that are part of the sidechain – Derived must be a subset of the atoms listed in the accpt_pos_ array More...

AtomIndices	Hpos_polar_sc_
	indices of polar Hydrogens for Hbond donors that are part of the sidechain – Derived must be a subset of the atoms listed in the Hpos_polar_ array More...

AtomIndices	all_bb_atoms_
	Indices of all backbone atoms, hydrogens and heavyatoms – Derived. More...

AtomIndices	all_sc_atoms_
	Indices of all sidechain atoms, hydrogens and heavyatoms – Derived. More...

utility::vector1< std::string >	metal_binding_atoms_
	Names of all of the atoms that are able to make a bond to a metal, for metal-binding residue types. More...

std::string	disulfide_atom_name_
	Name of the disulfide-forming atom, if any. More...

utility::vector1< VD >	mainchain_atoms_
	Verticies of all mainchain atoms – Primary. More...

utility::vector1< VD >	actcoord_atoms_
	indices of action coordinate centers – Primary More...

utility::vector1 < utility::vector1< VD > >	chi_atoms_
	the four atoms to build each chi angle – Primary. More...

utility::vector1< bool >	is_proton_chi_
	Is the corresponding chi in chi_atoms_ a proton chi? – Primary. More...

utility::vector1< Size >	proton_chis_
	Indices of the chi_atoms_ vector for proton chis – Derived, valid during Mutable. More...

utility::vector1< Size >	chi_2_proton_chi_
	A "map" of chi indices to proteon_chi indices – Derived, valid during Mutable. More...

utility::vector1 < utility::vector1< Real > >	proton_chi_samples_
	For a proton chi, the primary samples to diversify the rotamer library with – Primary. More...

utility::vector1 < utility::vector1< Real > >	proton_chi_extra_samples_
	For a proton chi, how to handle extra ex_ levels – Primary. More...

utility::vector1 < utility::vector1< VD > >	nu_atoms_
	VDs of four atoms to build each nu angle – Primary. More...

utility::vector1 < utility::vector1< VD > >	ring_atoms_
	VDs of all ring atoms, not counting virtual atoms – Primary. More...

utility::vector1 < utility::vector1< int > >	path_distance_
	number of bonds separated between any pair of atoms in this residue – Derived. More...

std::map< std::string, VD >	atom_name_to_vd_
	atom index lookup by atom name string – Derived, valid during Mutable, with caveats More...

std::map< std::string, std::string >	atom_aliases_
	A mapping of alias atom names to canonical atom names – Primary Will be added to atom_name_to_vd_ during finalization. More...

std::map< std::string, int >	orbitals_index_
	index lookup for orbitals based on atom name – Derived, valid during Mutable Updated in add_orbital() More...

utility::vector1 < utility::vector1< std::pair < Real, Real > > >	chi_rotamers_
	Additional non-Dunbrack rotamer bins – Primary. More...

rotamers::RotamerLibrarySpecificationOP	rotamer_library_specification_
	How to construct a rotamer library for this ResidueType – Primary. More...

utility::vector1< Size >	ring_sizes_
	The size of each ring in this residue – Primary. More...

utility::vector1< std::string >	lowest_ring_conformer_
	Lowest-energy ring conformer for each ring – Primary. More...

utility::vector1 < utility::vector1 < std::string > >	low_ring_conformers_
	Low-energy ring conformers for each ring – Primary. More...

ResiduePropertiesOP	properties_
	Residue properties as defined in the residue topology (.params) files – Primary. More...

AA	aa_
	standard rosetta aa-type for knowledge-based potentials, may be aa_unk – Primary More...

AA	rotamer_aa_

AA	backbone_aa_

std::string	base_name_
	Residue id for the base type (i.e. sans variants). More...

ResidueTypeCOP	base_type_cop_
	Const-access owning pointer to the base residue type. More...

std::string	name_
	Residue id – Primary, should be unique. More...

std::string	name3_
	PDB-file id, need not be unique – Primary NOTE: The "name3" is not necessarily three characters long. e.g. Metal ions may be only two characters. More...

char	name1_
	one-letter code, also not necessarily unique – Primary More...

std::string	interchangeability_group_
	interchangeability group lets a ResidueType claim to be functionally interchangeable with any other ResidueType in the same group. This is used by the packer to decide which ResidueType from a desired group has the right set of variants to be placed at a particular position. E.g. if the interchangeability group is "ALA" and the packer is building rotamers for residue 1, (the N-terminal residue) then, the packer will select the "ALA:NTermProteinFull" ResidueType and build rotamers for it. Primary. More...

VD	root_atom_
	Atom at the nominal root of the ICOOR tree. More...

VD	nbr_atom_
	atom used for calculating residue-level neighbors – Primary More...

Real	nbr_radius_
	radius cutoff to define neighbors – Primary More...

bool	force_nbr_atom_orient_

bool	remap_pdb_atom_names_
	Should we attempt to rename atoms for this residue type when we read in PDB files? – Primary. More...

Real	mass_
	The isotopically averaged mass of the residue – Derived. More...

utility::vector1 < ResidueConnection >	residue_connections_
	Vector of inter-residue connections expected for this residuetype – Primary NOW includes the polymer connections, as well as disulf-type connections. More...

utility::vector1 < utility::vector1< Size > >	atom_2_residue_connection_map_
	Mapping of atom indicies to residue connections – Derived. More...

utility::vector1 < utility::vector1 < two_atom_set > >	atoms_within_one_bond_of_a_residue_connection_
	For calculating inter-residue bond angle and bond torsion energies, it is useful to have a list of those atoms within one bond of a residue connection atom. For residue connection i, its position in this array is a list of pairs of atom-id's, the first of which is always the id for the atom forming residue connection i. – Derived. More...

utility::vector1 < utility::vector1< std::pair < Size, Size > > >	within1bonds_sets_for_atom_
	For atom i, its position in this vector is a list of pairs where first == the residue_connection id that lists this atom as being within one bond of a residue connection, and second == the index of the entry containing this atom in the atoms_within_one_bond_of_a_residue_connection_[ first ] array. – Derived. More...

utility::vector1 < utility::vector1 < three_atom_set > >	atoms_within_two_bonds_of_a_residue_connection_
	For calculating inter-residue bond torsion energies, it is useful to have a list of those atoms within two bonds of a residue connection atom. For residue connection i, its position in this array is a list of triples of atom-id's, the first of which is always the id for the atom forming residue connection i. – Derived. More...

utility::vector1 < utility::vector1< std::pair < Size, Size > > >	within2bonds_sets_for_atom_
	For atom i, its position in this vector is a list of pairs where first == the residue_connection id that lists this atom as being within two bonds of a residue connection, and second == the index of the entry containing this atom in the atoms_within_two_bonds_of_a_residue_connection_[ first ] array. – Derived. More...

Size	lower_connect_id_
	Polymer lower connections – Derived, valid during Mutable Updated in set_lower_connect_atom() More...

Size	upper_connect_id_
	Polymer upper connections – Derived valid during Mutable Updated in set_upper_connect_atom() More...

Size	n_non_polymeric_residue_connections_
	Number of non-polymeric residue connections – Derived. More...

Size	n_polymeric_residue_connections_
	Number of polymeric residue connections – Derived. More...

utility::vector1< VD >	force_bb_
	atom indices forced to be considered backbone – Primary More...

core::chemical::rna::RNA_ResidueTypeOP	rna_residue_type_
	A container for properties unique to RNA. – Derived, can be null. More...

core::chemical::carbohydrates::CarbohydrateInfoOP	carbohydrate_info_
	A container for residue properties unique to carbohydrates. – Derived, can be null. More...

std::list< utility::vector1< ED > >	rings_and_their_edges_
	All the rings and the edges. Defaulted to null until defined – Derived. More...

utility::vector1< Size >	atom_base_indices_
	Index version of atom_base_ – Derived. More...

utility::vector1< Size >	abase2_indices_
	Index version of abase2_ – Derived. More...

utility::vector1< AtomIndices >	chi_atoms_indices_
	Index version of chi_atoms_ – Derived. More...

utility::vector1< AtomIndices >	nu_atoms_indices_
	Index version of nu_atoms_ – Derived. More...

utility::vector1< AtomIndices >	ring_atoms_indices_
	Index version of ring_atoms_ – Derived. More...

AtomIndices	mainchain_atoms_indices_
	Index version of mainchain_atoms_ – Derived. More...

Size	nbr_atom_indices_
	Index version of nbr_atom_ – Derived. More...

AtomIndices	actcoord_atoms_indices_
	Index version of actcoord_atoms_ – Derived. More...

utility::vector1< AtomIndices >	cut_bond_neighbor_indices_
	Index version of cut_bond_neighbor_ – Primary - will be converted to derived (from Bond.cut_bond()) More...

utility::vector1< Size >	atom_shadowed_indices_
	Index version of atom_shadowed_ – Derived. More...

bool	finalized_
	Is all the derived data appropriately updated? More...

utility::vector1< Adduct >	defined_adducts_
	Adducts defined for this residue – Primary. More...

bool	nondefault_

Detailed Description

A class for defining a type of residue.

This class contains the "chemical" information for residues as well as the ideal xyz and internal coordinates for a residue (generated xyz coordinates are found in core/conformation/Residue.hh). A ResidueType in Rosetta can be a ligand, DNA, amino acid, or basically anything. ResidueTypes are generated through .params files, which are read from the database chemical/residue_types. For ligands, a parameter has to be provided to rosetta through the -extra_res_fa flag. Primary data are set through the residue_io.cc class. The primary data that are set are: atoms, mmatoms, orbitals, and properties of the particular ResidueType. These properties can be modified through patches, which create new ResidueTypes, and are controlled through PatchOperations.cc.

The data structure of a ResidueType is based on a boost::graph implementation. Vertex descriptors (VD, yeah, I know, the name is kind of bad) are the atoms, while the edge descriptors (ED, yet another bad name) are the bonds. Initially, when a ResidueType is constructed, the following primary data are set:

atom_base_; chi_atoms_; nu_atoms_; ring_atoms_; mainchain_atoms_; nbr_atom_; actcoord_atoms_; cut_bond_neighbor_; atom_shadowed_;

When this data is set, it is set based on vertex descriptors. Because vertex descriptors never change, like atom indices, there is no need to reorder this primary data; however, because Rosetta relies heavily on atom indices to access data, atom indices for the above data have to be generated. To do this, when finalized is called, a function specifically designed to generate the atom indices for the primary data is called: generate_atom_indices. This function iterates over the vertex descriptors assigned in the primary data and creates private data based on atom indices. For example, atom_base_ has atom_base_indices_. When the function atom_base(atomno) is called, the private datum atom_base_indices_ is called. This allows for the external interface of ResidueType to be accessed by atom indices while the internal functions in ResidueType work off of vertex descriptors. This also removes the need to have the former old2new reordering scheme.

Atoms: Setting of atoms includes indexing the atoms into vectors, saving their names into vectors/maps, saving the associated mm_atom_type into a vector, saving bond connections into vectors, etc, etc. On any given residue, the heavy atoms are put into the vector first, (their indices are first,) and hydrogens are put in last.

Properties: Properties of a residue include things like DNA, PROTEIN, CHARGED, etc. These properties indicate the type of residue it is and what properties are associated with the residue. They are set when read in. To add new ResidueProperties, add them to core/chemical/residue_properties/general_properties.list.

Orbitals: Orbitals are indexed separately from atoms. They function much the same way as atoms, except for some key differences. To find atoms bonded to orbitals, you must provide the atom index, not the orbital index. (I haven't figured out how to get the reverse to work because of the separate indices.) Orbital xyz coordinates are not updated when atom coordinates are. This is to keep speed consistent with just having atoms. To output the orbitals, use the flag -output_orbitals.

Constructor & Destructor Documentation

core::chemical::ResidueType::~ResidueType ( )

virtual

destructor

References core::chemical::tr().

core::chemical::ResidueType::ResidueType	(	AtomTypeSetCOP	atom_types,
		ElementSetCOP	element_types,
		MMAtomTypeSetCOP	mm_atom_types,
		orbitals::OrbitalTypeSetCOP	orbital_types
	)

constructor

We use the AtomTypeSet object to assign atom_types to atoms inside add_atom, and to identify (polar) hydrogens, acceptors, etc.

Referenced by clone(), and placeholder_clone().

core::chemical::ResidueType::ResidueType ( ResidueType const & residue_type )

Member Function Documentation

void core::chemical::ResidueType::aa ( AA const & type )

inline

set our aa-type (could be "UNK")

References aa_.

void core::chemical::ResidueType::aa ( std::string const & type )

inline

set our aa-type (could be "UNK")

References aa_, and core::chemical::aa_from_name().

AA const& core::chemical::ResidueType::aa ( ) const

inline

our traditional residue type, if any

Used for knowledge-based scores, dunbrack, etc. could be "aa_unk".

AA is an enum. There are values for the 20 standard amino acids, the 19 canonical D-amino acids, common beta-amino acids and nucleic acids, and aa_unk as a general catch-all.

References aa_.

Referenced by placeholder_clone().

Size core::chemical::ResidueType::abase2 ( Size const atomno ) const

get index of an atom's second base atom

References abase2_indices_, and ordered_atoms_.

Referenced by core::conformation::Residue::abase2().

const AcceptorAtomGraph core::chemical::ResidueType::acceptor_atoms ( )

References atom_types_, graph(), and graph_.

AtomIndices const& core::chemical::ResidueType::accpt_pos ( ) const

inline

indices of atoms as Hbond acceptors

References accpt_pos_.

Referenced by core::conformation::Residue::accpt_pos().

AtomIndices const& core::chemical::ResidueType::accpt_pos_sc ( ) const

inline

indices of atoms as Hbond acceptors

References accpt_pos_sc_.

Referenced by core::conformation::Residue::accpt_pos_sc().

AtomIndices const& core::chemical::ResidueType::actcoord_atoms ( ) const

inline

get indices for atoms used to define actcoord

References actcoord_atoms_indices_.

Referenced by core::conformation::Residue::actcoord_atoms(), and core::chemical::write_topology_file().

void core::chemical::ResidueType::add_actcoord_atom ( std::string const & atom )

add an atom to the list for calculating actcoord center

References actcoord_atoms_, atom_index(), finalized_, is_protein(), name(), name_, ordered_atoms_, and core::chemical::tr().

void core::chemical::ResidueType::add_adduct ( Adduct & adduct_in )

inline

References defined_adducts_.

VD core::chemical::ResidueType::add_atom	(	std::string const &	atom_name,
		std::string const &	atom_type_name,
		std::string const &	mm_atom_type_name,
		Real const	charge
	)

add an atom into this residue Will return the vertex descriptor of the added atom.

Note: this does not set xyz coordinates for the added atom

References atom(), atom_2_residue_connection_map_, atom_base_, atom_name(), atom_name_to_vd_, bonded_neighbor_, bonded_neighbor_type_, finalized_, graph_, icoor_, mm_atom_types_, ordered_atoms_, set_atom_type(), core::chemical::strip_whitespace(), and vd_to_index_.

VD core::chemical::ResidueType::add_atom ( std::string const & atom_name = "" )

add an atom into this residue, with just the name. Will return the vertex descriptor of the added atom.

References atom_2_residue_connection_map_, atom_base_, atom_name(), atom_name_to_vd_, bonded_neighbor_, bonded_neighbor_type_, finalized_, graph_, icoor_, ordered_atoms_, core::chemical::strip_whitespace(), and vd_to_index_.

VD core::chemical::ResidueType::add_atom	(	Atom const &	atom,
		AtomICoor const &	icoor
	)

References atom_2_residue_connection_map_, atom_base_, atom_name(), atom_name_to_vd_, bonded_neighbor_, bonded_neighbor_type_, finalized_, graph_, icoor(), icoor_, core::chemical::Atom::name(), ordered_atoms_, core::chemical::strip_whitespace(), and vd_to_index_.

void core::chemical::ResidueType::add_atom_alias	(	std::string const &	rosetta_atom,
		std::string const &	alias
	)

Add an alias name for an atom.

References atom_aliases_, finalized_, has(), and core::chemical::strip_whitespace().

Referenced by core::chemical::AddAtomAlias::apply().

void core::chemical::ResidueType::add_bond	(	std::string const &	atom_name1,
		std::string const &	atom_name2,
		BondName	bondLabel = `SingleBond`
	)

add a bond between atom1 and atom2, specifying a bond type (SingleBond, DoubleBond, TripleBond, AromaticBond)

add a bond between atom1 and atom2 and add a BondType object referencing the bond using the specified bondName

References atom_index(), atom_name_to_vd_, bonded_neighbor_, bonded_neighbor_type_, finalized_, graph_, and has().

void core::chemical::ResidueType::add_bond	(	VD	atom1,
		VD	atom2,
		BondName	bondLabel = `SingleBond`
	)

add a bond between atom1 and atom2, specifying a bond type (SingleBond, DoubleBond, TripleBond, AromaticBond)

References atom_index(), bonded_neighbor_, bonded_neighbor_type_, finalized_, graph_, and has().

void core::chemical::ResidueType::add_chi	(	Size const	chino,
		VD	atom1,
		VD	atom2,
		VD	atom3,
		VD	atom4
	)

Add a chi (side-chain) angle defined by four atoms.

References chi_2_proton_chi_, chi_atoms_, chi_rotamers_, finalized_, has(), and is_proton_chi_.

Referenced by add_chi(), core::chemical::AddChi::apply(), core::chemical::ReplaceProtonWithMethoxy::apply(), core::chemical::ReplaceProtonWithEthyl::apply(), core::chemical::ReplaceProtonWithHydroxyl::apply(), autodetermine_chi_bonds(), and core::chemical::ResidueDatabaseIO::read_residue_type_chi().

void core::chemical::ResidueType::add_chi	(	VD	atom1,
		VD	atom2,
		VD	atom3,
		VD	atom4
	)

Add a chi (side-chain) angle defined by four atoms.

References add_chi(), and nchi().

void core::chemical::ResidueType::add_chi	(	Size const	chino,
		std::string const &	atom_name1,
		std::string const &	atom_name2,
		std::string const &	atom_name3,
		std::string const &	atom_name4
	)

Add a chi (side-chain) angle defined by four atoms.

References add_chi(), and atom_vertex().

void core::chemical::ResidueType::add_chi	(	std::string const &	atom_name1,
		std::string const &	atom_name2,
		std::string const &	atom_name3,
		std::string const &	atom_name4
	)

Add a chi (side-chain) angle defined by four atoms to the end of the list of chis.

This method is needed for combinatorial patching of ResidueTypes for which the number of chis is variable. Its primary purpose is to be used with add_chi_rotamer_to_last_chi() that adds rotamer bins to the last chi in the list. In this way, a new chi can be added by a patch file and its rotamer bins set without needing to designate a chi index.

Note: See also add_chi_rotamer_to_last_chi().

Author: Labonte

References add_chi(), and nchi().

void core::chemical::ResidueType::add_chi_rotamer	(	Size const	chino,
		Real const	mean,
		Real const	sdev
	)

Add a rotamer bin for a given chi.

A rotamer bin has the mean and standard deviation.

References chi_rotamers_.

Referenced by add_chi_rotamer_to_last_chi(), core::chemical::AddChiRotamer::apply(), core::chemical::ReplaceProtonWithMethoxy::apply(), core::chemical::ReplaceProtonWithEthyl::apply(), and core::chemical::ResidueDatabaseIO::read_residue_type_chi_rotamer().

void core::chemical::ResidueType::add_chi_rotamer_to_last_chi	(	core::Angle const	mean,
		core::Angle const	sdev
	)

Adds a chi rotamer bin to the highest-indexed chi in the list of chis for this ResidueType.

This method is needed for combinatorial patching of ResidueTypes for which the number of chis is variable. Its primary purpose is to be used with the overloaded version of add_chi() that adds a new chi to the end of the list. In this way, a new chi can be added by a patch file and its rotamer bins set without needing to designate a chi index.

Note: See also add_chi().

Author: Labonte

References add_chi_rotamer(), and nchi().

Referenced by core::chemical::AddChiRotamer::apply().

void core::chemical::ResidueType::add_cut_bond	(	std::string const &	atom_name1,
		std::string const &	atom_name2
	)

add a bond between atom1 and atom2, if bond type is not specified, default to a SingleBond

add a cut_bond between atom1 and atom2, which disallows an atom-tree connection, though the atoms are really bonded. update cut_bond_ and resize it as necessary

References atom_name_to_vd_, cut_bond_neighbor_, finalized_, graph_, has(), and core::chemical::tr().

Referenced by core::chemical::ResidueDatabaseIO::read_residue_type_cut_bond().

void core::chemical::ResidueType::add_metalbinding_atom ( std::string const atom_name )

Add an atom to the list of atoms that can potentially form a bond to a metal ion. Note that the atom must exist in the residue type (the function checks for this at runtime).

Add an atom to the list of atoms that can potentially form a bond to a metal ion.

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

References has(), metal_binding_atoms_, and name3().

void core::chemical::ResidueType::add_nu	(	core::uint const	nu_index,
		std::string const &	atom_name1,
		std::string const &	atom_name2,
		std::string const &	atom_name3,
		std::string const &	atom_name4
	)

Add a nu (internal cyclic) angle defined by four atoms.

References atom_index(), finalized_, has(), nu_atoms_, and ordered_atoms_.

void core::chemical::ResidueType::add_numeric_property	(	std::string const &	tag,
		core::Real	value
	)

Add a numeric property.

References properties_.

void core::chemical::ResidueType::add_orbital	(	std::string &	orbital_name,
		std::string &	orbital_type_name
	)

add an orbital onto a residue based upon atom

Note: this does not set xyz coordinates for the added orbital but sets the index of the orbital and maps it to the type of orbital.

References finalized_, orbital_types_, orbitals_, orbitals_index_, and core::chemical::strip_whitespace().

void core::chemical::ResidueType::add_orbital_bond	(	std::string const &	atom_name1,
		std::string const &	orbital_name
	)

add an orbital bond between an atom and an orbital.

Note: NOTE!!!!! This is indexed based upon atoms, not orbitals. That means that in your params file you must have the atom as the first and orbital as the second.

References atom_index(), atom_name_to_vd_, finalized_, graph_, has(), has_orbital(), orbitals_index_, and ordered_atoms_.

void core::chemical::ResidueType::add_property ( std::string const & property )

Add a property to this ResidueType.

References core::chemical::ACHIRAL_BACKBONE, finalized_, core::chemical::LOWER_TERMINUS, core::chemical::PHOSPHONATE, core::chemical::POLYMER, properties_, core::chemical::PROTEIN, and core::chemical::UPPER_TERMINUS.

Referenced by core::chemical::AddProperty::apply(), core::chemical::ChiralFlipAtoms::apply(), core::chemical::ResidueDatabaseIO::read_residue_type_properties(), core::chemical::sdf::MolFileIOMolecule::set_from_extra_data(), and core::chemical::setup_patch_atomic_charge_reassignments_from_commandline().

Size core::chemical::ResidueType::add_residue_connection ( std::string const & atom_name )

add a non-polymeric ResidueConnection

For polymeric connections, see set_lower_connect() and set_upper_connect() Doesn't set the ideal geometry – maybe it should?

References atom_index(), finalized_, n_non_polymeric_residue_connections_, ordered_atoms_, residue_connections_, and update_residue_connection_mapping().

Referenced by core::chemical::AddConnect::apply(), core::chemical::AddConnectAndTrackingVirt::apply(), and core::chemical::AddConnectDeleteChildProton::apply().

void core::chemical::ResidueType::add_ring	(	core::uint const	ring_num,
		utility::vector1< std::string > const &	ring_atoms
	)

Add a ring definition.

References atom_index(), finalized_, has(), low_ring_conformers_, lowest_ring_conformer_, ordered_atoms_, and ring_atoms_.

void core::chemical::ResidueType::add_string_property	(	std::string const &	tag,
		std::string	value
	)

Add a string property.

References properties_.

Referenced by core::chemical::sdf::MolFileIOMolecule::set_from_extra_data().

void core::chemical::ResidueType::add_variant_type ( VariantType const variant_type )

Add a variant type to this ResidueType.

References finalized_, and properties_.

Referenced by core::chemical::AddConnectAndTrackingVirt::apply(), core::chemical::AddConnectDeleteChildProton::apply(), and core::chemical::ResidueDatabaseIO::read_residue_type_variant().

void core::chemical::ResidueType::add_variant_type ( std::string const & variant_type )

Add a variant type to this ResidueType by string.

References finalized_, and properties_.

AtomIndices const& core::chemical::ResidueType::all_bb_atoms ( ) const

inline

Indices of all backbone atoms, hydrogens and heavyatoms.

References all_bb_atoms_.

Referenced by core::conformation::Residue::all_bb_atoms(), core::scoring::elec::FA_ElecEnergy::backbone_backbone_energy(), core::scoring::elec::FA_ElecEnergy::backbone_sidechain_energy(), core::scoring::sasa::get_sc_bb_sasa(), and core::scoring::sasa::get_sc_bb_sasa_per_res().

AtomIndices const& core::chemical::ResidueType::all_sc_atoms ( ) const

inline

Indices of all sidechain atoms, hydrogens and heavyatoms.

References all_sc_atoms_.

Referenced by protocols::simple_moves::chiral::ChiralMover::apply(), core::scoring::elec::FA_ElecEnergy::backbone_sidechain_energy(), core::scoring::sasa::get_sc_bb_sasa(), core::scoring::sasa::get_sc_bb_sasa_per_res(), and core::scoring::elec::FA_ElecEnergy::sidechain_sidechain_energy().

const APolarHydrogenGraph core::chemical::ResidueType::apolar_hydrogens ( )

References atom_types_, and graph_.

const AromaticAtomGraph core::chemical::ResidueType::aromatic_atoms ( )

References atom_types_, and graph_.

void core::chemical::ResidueType::assign_internal_coordinates ( )

Assign internal coordinates from the set ideal xyz coordinates. Note that it currently does not obey mainchain designations or cut bonds.

References nbr_atom_, null_vertex, ordered_atoms_, and root_atom_.

void core::chemical::ResidueType::assign_internal_coordinates ( core::chemical::VD new_root )

@ recursive function to assign internal coordinates Note that it currently does not work well with polymers.

References graph_, n_possible_residue_connections(), name(), null_vertex, core::chemical::reroot_restype(), root_atom_, and core::chemical::tr().

void core::chemical::ResidueType::assign_neighbor_atom ( )

References atom_is_hydrogen(), core::conformation::membrane::center, core::kinematics::distance(), graph_, protocols::ddg::min_index(), name(), nbr_atom(), ordered_atoms_, and protocols::analysis::total.

Atom & core::chemical::ResidueType::atom ( Size const atom_index )

References atom_index(), graph_, and ordered_atoms_.

Atom const & core::chemical::ResidueType::atom ( Size const atom_index ) const

References atom_index(), graph_, and ordered_atoms_.

Atom & core::chemical::ResidueType::atom ( std::string const & atom_name )

References atom_name(), atom_name_to_vd_, and graph_.

Atom const & core::chemical::ResidueType::atom ( std::string const & atom_name ) const

References atom_name_to_vd_, and graph_.

Atom & core::chemical::ResidueType::atom ( VD const atom_vd )

References graph_, and has().

Atom const & core::chemical::ResidueType::atom ( VD const atom_vd ) const

References graph_, and has().

Size core::chemical::ResidueType::atom_base ( Size const atomno ) const

get index of an atom's base atom

References atom_base_indices_, and ordered_atoms_.

Referenced by core::chemical::ConnectSulfurAndMakeVirtualProton::apply(), core::conformation::Residue::apply_transform_downstream(), core::conformation::Residue::atom_base(), core::util::auto_setup_all_metal_constraints(), core::scoring::hbonds::create_rotamer_descriptor(), core::scoring::disulfides::DisulfideAtomIndices::DisulfideAtomIndices(), core::chemical::find_chi_bonds(), protocols::generalized_kinematic_closure::GeneralizedKIC::get_path(), protocols::stepwise::modeler::rna::phosphate::get_phosphate_atom_and_neighbor_list(), note_chi_controls_atom(), core::scoring::lkball::LKB_ResidueInfo::remove_irrelevant_waters(), select_orient_atoms(), core::conformation::Residue::set_chi(), core::conformation::Residue::set_d(), core::conformation::Residue::set_theta(), update_derived_data(), update_last_controlling_chi(), and core::chemical::ResidueTypeKinWriter::write_restype().

VD core::chemical::ResidueType::atom_base ( VD const atomno ) const

get vd of an atom's base atom

References atom_base_, and has().

Size core::chemical::ResidueType::atom_being_shadowed ( Size atom_shadowing ) const

inline

Return the index of the atom that the "atom_shadowing" atom is shadowing; returns zero if the "atom_shadowing" atom is not shadowing anyone.

References atom_shadowed_indices_.

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

bool core::chemical::ResidueType::atom_forms_residue_connection ( Size const atomid )

inline

Does an atom form any inter-residue chemical bonds?

References atom_2_residue_connection_map_.

Size core::chemical::ResidueType::atom_index ( std::string const & name ) const

get atom index by name

References atom_name_to_vd_, graph_, is_membrane(), is_protein(), name(), name3(), ordered_atoms_, show_all_atom_names(), and core::chemical::tr().

Size core::chemical::ResidueType::atom_index ( VD const & vd ) const

get atom index by vertex descriptor

References vd_to_index_.

bool core::chemical::ResidueType::atom_is_backbone ( Size const atomno ) const

inline

is a backbone atom (heavy or hydrogen)?

References finalized_, first_sidechain_hydrogen_, n_backbone_heavyatoms_, natoms(), and nheavyatoms_.

Referenced by core::conformation::Residue::atom_is_backbone(), core::scoring::hbonds::create_rotamer_descriptor(), core::pose::motif::get_backbone_reference_frame_atomids_with_downstream(), core::scoring::orbitals::OrbitalsScore::get_orb_orb_E(), core::scoring::FACTSRsdTypeInfo::initialize_intrascale(), core::conformation::Residue::place(), core::chemical::ResidueDatabaseIO::report_residue_type_atom(), core::scoring::constraints::requires_CB_mapping(), select_orient_atoms(), core::scoring::lkball::LKB_ResidueInfo::setup_atom_weights(), core::scoring::lkball::setup_water_builders_for_residue_type(), and core::scoring::orbitals::surrogate_atom_for_orbital().

bool core::chemical::ResidueType::atom_is_hydrogen ( Size const atomno ) const

inline

quick lookup: is the atom with the given index a hydrogen or not? Atoms are sorted so that heavy atoms come first and hydrogen atoms come last.

References finalized_, natoms(), and nheavyatoms_.

Referenced by core::chemical::SetAllAtomsRepulsive::apply(), assign_neighbor_atom(), core::conformation::Residue::atom_is_hydrogen(), core::scoring::methods::YHHPlanarityEnergy::defines_score_for_rsd(), core::pose::motif::get_backbone_reference_frame_atomids_with_downstream(), core::scoring::is_protein_sidechain_heavyatom(), core::conformation::Residue::place(), and core::scoring::lkball::LKB_ResidueInfo::remove_irrelevant_waters().

bool core::chemical::ResidueType::atom_is_polar_hydrogen ( Size atomno ) const

inline

References finalized_, graph_, and ordered_atoms_.

Referenced by core::conformation::Residue::atom_is_polar_hydrogen(), core::scoring::elec::GroupElec::build_groupinfo(), core::pose::motif::get_backbone_reference_frame_atomids_with_downstream(), and core::scoring::lkball::setup_water_builders_for_residue_type().

VIterPair core::chemical::ResidueType::atom_iterators ( ) const

inline

References graph_.

Referenced by core::chemical::gasteiger::assign_gasteiger_atom_types(), and core::chemical::calculate_rigid_matrix().

std::string const & core::chemical::ResidueType::atom_name ( Size const index ) const

get atom name by index

Get the atom name by index.

References graph_, and ordered_atoms_.

std::string const & core::chemical::ResidueType::atom_name ( VD const vd ) const

get atom name by vertex descriptor

Get atom name by vertex descriptor.

References graph_, and has().

AtomType const& core::chemical::ResidueType::atom_type ( Size const atomno ) const

inline

Get the chemical atom_type for this atom by it index number in this residue.

If we want the atom_type index (integer), we get this from the conformation::Atom itself, as seen in the code below

References atom_types_, graph_, and ordered_atoms_.

Referenced by protocols::simple_moves::chiral::ChiralMover::apply(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_loop_bump_check(), core::conformation::Residue::atom_type(), core::scoring::elec::GroupElec::build_groupinfo(), core::scoring::SplitUnfoldedTwoBodyPotential::calculate_residue_emap(), core::chemical::sdf::MolWriter::compose_typeinfo(), core::pack::interaction_graph::SurfacePotential::compute_pose_hpatch_score(), protocols::motif_grafting::movers::MotifGraftMover::count_clashes_between_two_poses(), core::scoring::methods::MMBondLengthEnergy::eval_atom_derivative(), core::scoring::methods::MMBondAngleEnergy::eval_atom_derivative(), core::scoring::methods::MMBondLengthEnergy::eval_intrares_energy(), core::scoring::methods::MMBondAngleEnergy::eval_intrares_energy(), 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(), core::scoring::FACTSRsdTypeInfo::initialize_intrascale(), core::scoring::FACTSRsdTypeInfo::initialize_parameters(), core::conformation::Residue::is_repulsive(), is_repulsive(), core::conformation::Residue::is_virtual(), is_virtual(), protocols::ligand_docking::rdf::RDFBinaryOrbitalFunction::operator()(), print_bondangles(), print_dihedrals(), protocols::match::output::print_node(), core::conformation::print_node(), protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::recompute(), protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::recompute(), core::chemical::ResidueDatabaseIO::report_residue_type_atom(), core::scoring::methods::MMBondLengthEnergy::residue_pair_energy(), core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::set_rotamer(), core::pack::interaction_graph::HPatchNode< V, E, G >::set_rotamers(), core::scoring::lkball::LKB_ResidueInfo::setup_atom_weights(), core::scoring::lkball::setup_water_builders_for_residue_type(), core::chemical::ResidueTypeKinWriter::write_restype(), and core::chemical::write_topology_file().

AtomType const & core::chemical::ResidueType::atom_type ( VD const vd ) const

Get the chemical atom_type for this atom by it index number in this residue.

References atom_types_, graph_, and ordered_atoms_.

AtomTypeSet const& core::chemical::ResidueType::atom_type_set ( ) const

inline

access by reference the atomset for which this residue is constructed

References atom_types_.

Referenced by core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr(), core::conformation::Residue::atom_type_set(), core::scoring::FACTSRsdTypeInfo::initialize_parameters(), protocols::features::AtomAtomPairFeatures::report_atom_pairs(), core::chemical::rosetta_recharge_fullatom(), core::chemical::rosetta_retype_fullatom(), core::chemical::sdf::MolFileIOMolecule::set_from_extra_data(), and core::scoring::lkball::LKB_ResidueInfo::setup_atom_weights().

AtomTypeSetCOP core::chemical::ResidueType::atom_type_set_ptr ( ) const

inline

access by const pointer the atomset for which this residue is constructed

References atom_types_.

Referenced by core::scoring::etable::TableLookupEtableEnergy::setup_for_scoring_(), and core::scoring::etable::AnalyticEtableEnergy::setup_for_scoring_().

VD core::chemical::ResidueType::atom_vertex ( std::string const & name ) const

get the vertex descriptor from the name of the atom.

References atom_name_to_vd_, name3(), show_all_atom_names(), and core::chemical::tr().

Referenced by add_chi(), core::chemical::AtomICoor::AtomICoor(), bond(), debug_dump_icoor(), core::chemical::find_nbr_dist(), and core::chemical::ICoorAtomID::ICoorAtomID().

VD core::chemical::ResidueType::atom_vertex ( Size const & atomno ) const

Get the vertex descriptor from the atom index.

References ordered_atoms_.

bool core::chemical::ResidueType::atoms_are_bonded	(	core::Size const	atom_index1,
		core::Size const	atom_index2
	)		const

Indicates whether or not two atom indices have a chemical bond linking them.

Note that this assumes that the Rosetta machinery is set up so that if atom 1 is bonded to atom 2, atom 2 is bonded to atom 1. This function breaks if that assumption breaks.

Author: Vikram K. Mulligan

References nbrs().

utility::vector1< AtomIndices > const& core::chemical::ResidueType::atoms_last_controlled_by_chi ( ) const

inline

Read access to the atoms_last_controlled_by_chi_ array.

References atoms_last_controlled_by_chi_.

Referenced by protocols::match::upstream::UpstreamResTypeGeometry::initialize_from_residue_type().

AtomIndices const& core::chemical::ResidueType::atoms_last_controlled_by_chi ( Size chi ) const

inline

Read access to the Atoms last controlled by a particular chi.

References atoms_last_controlled_by_chi_.

AtomIndices const& core::chemical::ResidueType::atoms_with_orb_index ( ) const

inline

References atoms_with_orb_index_.

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

utility::vector1< two_atom_set > const& core::chemical::ResidueType::atoms_within_one_bond_of_a_residue_connection ( Size resconn ) const

inline

Returns a list of those atoms within one bond of a residue connection. For residue connection i, its position in this array is a list of pairs of atom-id's, the first of which is always the id for the atom forming residue connection i.

References atoms_within_one_bond_of_a_residue_connection_.

Referenced by core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), 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(), protocols::features::ProteinBondGeometryFeatures::report_interres_angles(), core::scoring::methods::MMTorsionEnergy::residue_pair_energy(), and core::scoring::methods::MMBondAngleEnergy::residue_pair_energy().

utility::vector1< three_atom_set > const& core::chemical::ResidueType::atoms_within_two_bonds_of_a_residue_connection ( Size resconn ) const

inline

Returns the list of those atoms within two bonds of residue connection # resconn. Each entry in this list is a triple of atom-id's, the first of which is always the id for the atom forming residue connection resconn.

References atoms_within_two_bonds_of_a_residue_connection_.

Referenced by core::scoring::methods::MMTorsionEnergy::residue_pair_energy().

Size core::chemical::ResidueType::attached_H_begin ( Size const atom ) const

inline

index number of the first attached Hydrogen on an atom

References atom(), and attached_H_begin_.

AtomIndices const& core::chemical::ResidueType::attached_H_begin ( ) const

inline

for all heavy atoms, index numbers of their first attached Hydrogen

References attached_H_begin_.

Size core::chemical::ResidueType::attached_H_end ( Size const atom ) const

inline

index number of the last attached Hydrogen on an atom

References atom(), and attached_H_end_.

Referenced by core::conformation::Residue::attached_H_end(), protocols::simple_moves::MinimalRotamer::has_ideal_geometry(), protocols::toolbox::pose_metric_calculators::NumberHBondsCalculator::recompute(), protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::recompute(), protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::recompute(), and protocols::simple_moves::MinimalRotamer::record_internal_geometry().

AtomIndices const& core::chemical::ResidueType::attached_H_end ( ) const

inline

for all heavy atoms, index numbers of their last attached Hydrogen

References attached_H_end_.

void core::chemical::ResidueType::autodetermine_chi_bonds ( core::Size max_proton_chi_samples = 500 )

Regenerate the rotatable chi bonds from the internal graph structure. If the number of proton chi samples would exceed max_proton_chi_samples, don't add extra sampling to proton chis. As a special case, if this is zero don't add any proton chi sampling at all.

Requires that Icoor and atom base records are up-to-date, and that ring bonds have been annotated.

References add_chi(), atom(), chi_2_proton_chi_, chi_atoms_, chi_rotamers_, finalized_, core::chemical::find_chi_bonds(), core::chemical::element::H, is_proton_chi_, core::chemical::is_sp2_proton_chi(), name(), nchi(), proton_chi_extra_samples_, proton_chi_samples_, proton_chis_, set_proton_chi(), and core::chemical::tr().

void core::chemical::ResidueType::backbone_aa ( std::string const & type )

inline

AA to use for backbone scoring.

References core::chemical::aa_from_name(), and backbone_aa_.

Referenced by core::conformation::Residue::backbone_aa(), core::scoring::methods::RamaPreProEnergy::eval_intraresidue_dof_derivative(), and core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::eval_rotameric_energy_deriv().

AA const& core::chemical::ResidueType::backbone_aa ( ) const

inline

Returns the amino acid type to be used for backbone scoring (rama and p_aa_pp).

References aa_, core::chemical::aa_unk, and backbone_aa_.

std::string const& core::chemical::ResidueType::base_name ( ) const

inline

Get this ResidueType's base name (shared with other residue types with the same base type).

References base_name_.

Referenced by core::io::pose_to_sfr::PoseToStructFileRepConverter::append_residue_info_to_sfr().

void core::chemical::ResidueType::base_name ( std::string const & base_name_in )

inline

Set this ResidueType's base name (shared with other residue types with the same base type).

References base_name_.

Bond & core::chemical::ResidueType::bond ( ED const ed )

References graph_.

Referenced by core::chemical::complex_ring_detection(), core::chemical::RigidDistanceVisitor::examine_edge(), core::chemical::find_bonds_in_rings(), core::chemical::find_chi_bonds(), generate_atom_indices(), core::chemical::is_sp2_proton_chi(), and core::chemical::quick_ring_detection().

Bond const & core::chemical::ResidueType::bond ( ED const ed ) const

References graph_.

Bond & core::chemical::ResidueType::bond	(	std::string const &	atom1,
		std::string const &	atom2
	)

References atom_vertex(), graph_, and name().

Bond const & core::chemical::ResidueType::bond	(	std::string const &	atom1,
		std::string const &	atom2
	)		const

References atom_vertex(), graph_, and name().

EIterPair core::chemical::ResidueType::bond_iterators ( ) const

inline

References graph_.

Referenced by core::chemical::find_chi_bonds(), core::chemical::is_sp2_proton_chi(), and core::io::pose_from_sfr::score_mapping().

OutEdgeIterPair core::chemical::ResidueType::bond_iterators ( VD const & atom ) const

inline

References graph_.

bondangle_atom_set const& core::chemical::ResidueType::bondangle ( Size const bondang ) const

inline

Return the indices for the set of atoms that define a particular intraresidue angle.

References bondangle_atom_sets_.

Referenced by core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), core::scoring::methods::MMBondAngleEnergy::eval_atom_derivative(), core::scoring::methods::MMBondAngleEnergy::eval_intrares_energy(), core::scoring::mm::MMBondAngleResidueTypeParam::init(), and protocols::features::ProteinBondGeometryFeatures::report_intrares_angles().

utility::vector1< Size > const& core::chemical::ResidueType::bondangles_for_atom ( Size atomno ) const

inline

Returns the list of all of the indices of all the intraresidue bond angles a particular atom is involved in. Useful for calculating the derivatives for an atom.

References bondangles_for_atom_.

Referenced by core::scoring::methods::MMBondAngleEnergy::eval_atom_derivative().

AtomIndices const & core::chemical::ResidueType::bonded_neighbor ( Size const atomno ) const

indices of the bonded neighbors for an atom

References bonded_neighbor_.

AdjacentIterPair core::chemical::ResidueType::bonded_neighbor_iterators ( VD const & atom ) const

References graph_.

Referenced by core::chemical::find_nbr_dist(), and core::chemical::RigidDistanceVisitor::is_nub().

utility::vector1< BondName > const & core::chemical::ResidueType::bonded_neighbor_types ( Size const atomno ) const

References bonded_neighbor_type_.

Referenced by core::chemical::sdf::MolWriter::compose_bonds(), and core::chemical::ResidueDatabaseIO::report_residue_type_bond().

utility::vector1<core::Size> const& core::chemical::ResidueType::bonded_orbitals ( Size const atomno ) const

inline

indices of the orbitals bonded to an atom

References graph_, and ordered_atoms_.

Referenced by core::conformation::Residue::assign_orbitals(), core::conformation::Residue::bonded_orbitals(), generate_atom_indices(), operator=(), and core::conformation::Residue::update_orbital_coords().

utility::vector1< std::string > core::chemical::ResidueType::branch_connect_atom_names ( ) const

Return a list of names of atoms at non-polymer connections.

References atom_name(), and branch_connect_atoms().

Referenced by core::pose::append_pose_with_glycan_residues(), and show().

utility::vector1< uint > core::chemical::ResidueType::branch_connect_atoms ( ) const

Return a list of indices of atoms at non-polymer connections.

References is_branch_lower_terminus(), lower_connect_id_, n_non_polymeric_residue_connections_, n_possible_residue_connections(), residue_connect_atom_index(), and upper_connect_id_.

Referenced by branch_connect_atom_names().

core::chemical::carbohydrates::CarbohydrateInfoCOP core::chemical::ResidueType::carbohydrate_info ( ) const

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

References carbohydrate_info_.

Referenced by core::conformation::Residue::carbohydrate_info(), and core::chemical::Selector_UPPER_POSITION::operator[]().

void core::chemical::ResidueType::change_bond_type	(	std::string const &	atom_name1,
		std::string const &	atom_name2,
		BondName const	old_bond_label,
		BondName const	new_bond_label
	)

Change the bond type of the given bond from one type to another.

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

References atom_index(), atom_name_to_vd_, bonded_neighbor_type_, core::sequence::end, finalized_, graph_, and has().

Referenced by core::chemical::ChangeBondType::apply().

Size core::chemical::ResidueType::chi_2_proton_chi ( Size chi_index ) const

inline

References chi_2_proton_chi_.

Referenced by core::pack::rotamers::RotamericSingleResiduePeptoidLibrary< T, N >::chisamples_for_rotamer_and_chi(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::chisamples_for_rotamer_and_chi(), protocols::match::upstream::FullChiSampleSet::expand_non_dunbrack_chi(), and protocols::rotamer_recovery::RRComparerChiDiff::measure_rotamer_recovery().

VDs const& core::chemical::ResidueType::chi_atom_vds ( Size const chino ) const

inline

VDs of the atoms which are used to define a given chi angle (chino)

References chi_atoms_.

Referenced by core::chemical::is_sp2_proton_chi().

AtomIndices const& core::chemical::ResidueType::chi_atoms ( Size const chino ) const

inline

indices of the atoms which are used to define a given chi angle (chino)

References chi_atoms_indices_.

Referenced by protocols::simple_moves::MinimalRotamer::atom_is_ideal(), protocols::stepwise::modeler::polar_hydrogens::check_if_proton_chi_atom(), protocols::simple_moves::check_if_proton_chi_atom(), core::conformation::Residue::chi_atoms(), protocols::simple_moves::MinimalRotamer::chi_matches_coords(), core::pack::rotamers::RotamericSingleResiduePeptoidLibrary< T, N >::chisamples_for_rotamer_and_chi(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::chisamples_for_rotamer_and_chi(), core::scoring::methods::YHHPlanarityEnergy::defines_score_for_rsd(), core::pack::rotamers::SingleBasicRotamerLibrary::fill_rotamer_vector(), protocols::match::upstream::FullChiSampleSet::FullChiSampleSet(), protocols::match::upstream::UpstreamResTypeGeometry::initialize_from_residue_type(), core::chemical::print_chis(), core::chemical::ResidueDatabaseIO::report_residue_type_chi(), core::conformation::Residue::Residue(), core::conformation::Residue::set_chi(), core::conformation::Residue::set_d(), core::conformation::Residue::set_theta(), protocols::ligand_docking::torsion_constraints_from_mean_sd(), core::chemical::ResidueTypeKinWriter::write_restype(), and core::chemical::write_topology_file().

utility::vector1< AtomIndices > const& core::chemical::ResidueType::chi_atoms ( ) const

inline

indices of the atoms which are used to define all the chi angles

References chi_atoms_indices_.

Referenced by generate_atom_indices(), and update_last_controlling_chi().

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

inline

all rotamers bins (mean, std) for a given chi angle

References chi_rotamers_.

Referenced by core::conformation::Residue::chi_rotamers(), core::pack::rotamers::RotamericSingleResiduePeptoidLibrary< T, N >::chisamples_for_rotamer_and_chi(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::chisamples_for_rotamer_and_chi(), core::chemical::ResidueDatabaseIO::report_residue_type_chi_rotamer(), and protocols::ligand_docking::torsion_constraints_from_chi_rotamers().

void core::chemical::ResidueType::clear_chi_rotamers ( core::uint const chi_no )

Delete all of the chi rotamer bins from the specified chi for this ResidueType.

This method is useful if one has redefined a chi within a patch file such that the old rotamer bins need to be regenerated.

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

References chi_rotamers_.

Referenced by core::chemical::ClearChiRotamers::apply().

void core::chemical::ResidueType::clear_orbitals ( )

clear orbitals

References graph_, natoms(), orbitals_, orbitals_index_, and ordered_atoms_.

ResidueTypeOP core::chemical::ResidueType::clone ( ) const

make a copy

References ResidueType().

Referenced by protocols::ligand_docking::AddHydrogen::apply(), core::chemical::PatchCase::apply(), and core::scoring::FACTSRsdTypeInfo::initialize_parameters().

utility::vector1< std::string > const & core::chemical::ResidueType::custom_variant_types ( ) const

Get a list of custom VariantType strings for this ResidueType (by const reference).

This ONLY includes custom, on-the-fly variants, not standard variants.

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

References properties_.

AtomIndices const& core::chemical::ResidueType::cut_bond_neighbor ( Size const atomno ) const

inline

indices of the bonded neighbors for an atom

References cut_bond_neighbor_indices_.

Referenced by core::conformation::Residue::cut_bond_neighbor(), and core::chemical::ResidueDatabaseIO::report_residue_type_cut_bond().

void core::chemical::ResidueType::debug_dump_icoor ( ) const

Dump out atomnames and icoor values.

References atom(), atom_name(), atom_vertex(), core::chemical::Atom::ideal_xyz(), name3(), natoms(), core::chemical::pretty_print_atomicoor(), and core::chemical::tr().

utility::vector1< Adduct > const& core::chemical::ResidueType::defined_adducts ( ) const

inline

get the adducts defined for this residue

References defined_adducts_.

Referenced by core::chemical::apply_adducts_to_residue(), core::chemical::create_adduct_combinations(), core::chemical::error_check_requested_adducts(), and core::chemical::place_adducts().

void core::chemical::ResidueType::delete_act_coord_atom ( std::string const & atom_name )

Remove an atom from the list of act coord atoms (used in patching when it kills the valence that is thus used)

Author: Andrew Watkins (amw57.nosp@m.9@ny.nosp@m.u.edu)

References actcoord_atoms_, actcoord_atoms_indices_, atom_index(), atom_name(), atom_name_to_vd_, has(), and name3().

Referenced by core::chemical::DeleteActCoordAtom::apply().

void core::chemical::ResidueType::delete_atom ( std::string const & name )

flag an atom for deletion by adding its index to the delete_atom_ list

References atom_index(), and has().

void core::chemical::ResidueType::delete_atom ( Size const index )

flag an atom for deletion by adding its index to the delete_atom_ list

References finalized_, graph_, and ordered_atoms_.

void core::chemical::ResidueType::delete_atom_alias ( std::string const & alias )

Remove a given alias name for an atom.

References atom_aliases_, finalized_, and core::chemical::strip_whitespace().

void core::chemical::ResidueType::delete_metalbinding_atom ( std::string const & atom_name )

Remove an atom from the list of atoms that can potentially form a bond to a metal ion (used in patching when it kills the valence that is thus used)

Author: Andrew Watkins (amw57.nosp@m.9@ny.nosp@m.u.edu)

References atom_name(), has(), metal_binding_atoms_, and name3().

Referenced by core::chemical::DeleteMetalbindingAtom::apply().

void core::chemical::ResidueType::delete_property ( std::string const & property )

Add a property of this ResidueType.

This is needed for deleting properties, which occurs in certain PTMs.

References finalized_, and properties_.

Referenced by core::chemical::DeleteProperty::apply(), and core::chemical::ChiralFlipAtoms::apply().

void core::chemical::ResidueType::delete_terminal_chi ( )

delete terminal chi angle

Author: Andrew M. Watkins (April 2015)

References chi_2_proton_chi_, chi_atoms_, chi_rotamers_, finalized_, is_proton_chi_, and proton_chis_.

Referenced by core::chemical::DeleteTerminalChi::apply().

dihedral_atom_set const& core::chemical::ResidueType::dihedral ( Size const dihe ) const

inline

dihedral methods

Return the indices for the set of atoms that define a particular intraresidue dihedral

References dihedral_atom_sets_.

Referenced by core::scoring::methods::MMTorsionEnergy::eval_atom_derivative(), core::scoring::methods::MMTorsionEnergy::eval_intrares_energy(), and protocols::features::ProteinBondGeometryFeatures::report_intrares_torsions().

utility::vector1< Size > const& core::chemical::ResidueType::dihedrals_for_atom ( Size atomno ) const

inline

Returns the list of all of the indices of all the intraresidue dihedrals a particular atom is involved in. Useful for calculating the derivatives for an atom.

References dihedrals_for_atom_.

Referenced by core::scoring::methods::MMTorsionEnergy::eval_atom_derivative().

void core::chemical::ResidueType::dump_vd_info ( ) const

References atom_name(), graph_, has(), name(), ordered_atoms_, and core::chemical::tr().

ElementSet const& core::chemical::ResidueType::element_set ( ) const

inline

access by reference the element set for which this residue is constructed

References elements_.

ElementSetCOP core::chemical::ResidueType::element_set_ptr ( ) const

inline

access by const pointer the element set for which this residue is constructed

References elements_.

void core::chemical::ResidueType::enable_custom_variant_types ( )

Turn on the ability to create VariantTypes "on-the-fly".

"Custom" VariantTypes as strings are permitted for the enzdes and metalloproteins cases. Do not enable unless you have a good reason to, as string look-ups are less efficient and more error-prone.

References properties_.

Referenced by core::chemical::AddConnectAndTrackingVirt::apply(), and core::chemical::AddConnectDeleteChildProton::apply().

void core::chemical::ResidueType::fill_ideal_xyz_from_icoor ( )

References core::chemical::fill_ideal_xyz_from_icoor(), graph_, icoor_, and natoms().

Referenced by core::chemical::ChiralFlipAtoms::apply().

void core::chemical::ResidueType::finalize ( )

recalculate derived data, potentially reordering atom-indices

recalculate derived data, potentially reordering atom-indices This routine updates all the derived data.
Atom order will probably change after this call, so if you add a new property that depends on atom-indices that will have to be updated below.

References finalized_, generate_atom_indices(), perform_checks(), setup_atom_ordering(), and update_derived_data().

bool core::chemical::ResidueType::finalized ( ) const

inline

finalized? should always be true, except in very special case early in on-the-fly ResidueTypeSet.

References finalized_.

Referenced by core::chemical::ResidueTypeSet::apply_patches(), core::chemical::ResidueTypeSet::generate_residue_type(), and core::chemical::place_adducts().

Size core::chemical::ResidueType::first_sidechain_atom ( ) const

inline

index of the first sidechain atom (heavy or hydrogen)

References n_backbone_heavyatoms_, natoms(), and nheavyatoms_.

Referenced by protocols::simple_moves::chiral::ChiralMover::apply(), core::scoring::compute_bb_centroid(), core::scoring::compute_bb_radius(), core::scoring::compute_sc_centroid(), core::scoring::compute_sc_radius(), protocols::stepwise::modeler::rna::bulge::detect_base_contacts(), protocols::stepwise::modeler::align::StepWisePoseAligner::do_checks(), core::conformation::Residue::first_sidechain_atom(), protocols::simple_moves::MinimalRotamer::has_ideal_geometry(), core::scoring::is_protein_sidechain_heavyatom(), core::conformation::Residue::place(), protocols::simple_moves::MinimalRotamer::record_internal_geometry(), select_orient_atoms(), and protocols::mpi_refinement::StructAvrgMover::weighted_average().

Size core::chemical::ResidueType::first_sidechain_hydrogen ( ) const

inline

index of the first sidehchain hydrogen

References finalized_, and first_sidechain_hydrogen_.

Referenced by protocols::stepwise::modeler::align::StepWisePoseAligner::do_checks(), and core::conformation::Residue::first_sidechain_hydrogen().

void core::chemical::ResidueType::force_nbr_atom_orient ( bool force_orient )

inline

Set force_nbr_atom_orient_, used to control orient atoms selected by select_orient_atoms.

References force_nbr_atom_orient_.

Referenced by core::chemical::SetOrientAtom::apply(), and core::chemical::write_topology_file().

bool core::chemical::ResidueType::force_nbr_atom_orient ( ) const

inline

Return force_nbr_atom_orient_, used to control orient atoms selected by select_orient_atoms.

References force_nbr_atom_orient_.

Referenced by select_orient_atoms().

gasteiger::GasteigerAtomTypeDataCOP core::chemical::ResidueType::gasteiger_atom_type ( Size const atomno ) const

Get the MM atom_type index number for this atom by its index number in this residue.

Get the Gasteiger atom_type for this atom by its index number in this residue.

Get the MM atom_type for this atom by its index number in this residue

References graph_, and ordered_atoms_.

gasteiger::GasteigerAtomTypeSetCOP core::chemical::ResidueType::gasteiger_atom_typeset ( ) const

References gasteiger_atom_types_.

Referenced by core::chemical::gasteiger::assign_gasteiger_atom_types().

void core::chemical::ResidueType::generate_atom_indices ( )

private

reorder primary data in ResidueType given the old2new map, called by finalize()

The private data for ResidueType is based on vertex descriptors (VD). Rosetta relies on atom indices to access the private data. In order to keep this interface, the VDs must be converted into atom indices. These are called *_indices, where the primary data is a VD but the indices_data is the atom indices. Because the atom indices change during the setup atom ordering, we must regenerate the cached data. This would not have to occur if Rosetta relied on VDs instead of atom indices.

First, the private data that relies on atom ordering, atom_name_to_vd_ and vd_to_index_ is created by iterating over the total number of atoms in the graph.

Second, the bonded neighbors are generated based on the graph structure.

Finally, all the cached data is generated by iterating over the VDs.

– Assumes that ordered_atoms_ is updated appropriately. Derived data set in this method: atom_name_to_vd_ vd_to_index_ atom_base_indices_ chi_atoms_indices_ nu_atoms_indices_ ring_atoms_indices_ mainchain_atoms_indices_ nbr_atom_indices_ actcoord_atoms_indices_ cut_bond_neighbor_indices_ atom_shadowed_indices_ bonded_neighbor_ bonded_neighbor_type_ atom_2_residue_connection_map_

References actcoord_atoms_, actcoord_atoms_indices_, atom_2_residue_connection_map_, atom_aliases_, atom_base_, atom_base_indices_, atom_index(), atom_name_to_vd_, atom_shadowed_, atom_shadowed_indices_, core::chemical::ICoorAtomID::atomno(), bond(), bonded_neighbor_, bonded_neighbor_type_, bonded_orbitals(), chi_atoms(), chi_atoms_, chi_atoms_indices_, cut_bond_neighbor_, cut_bond_neighbor_indices_, graph_, icoor_, core::chemical::ICoorAtomID::INTERNAL, mainchain_atoms_, mainchain_atoms_indices_, name(), natoms(), nbr_atom_, nbr_atom_indices_, nu_atoms_, nu_atoms_indices_, orbitals_, ordered_atoms_, core::chemical::pretty_print_atomicoor(), residue_connections_, ring_atoms_, ring_atoms_indices_, core::chemical::strip_whitespace(), core::chemical::AtomICoor::stub_atom(), core::chemical::tr(), core::chemical::ICoorAtomID::type(), update_residue_connection_mapping(), vd_to_index_, and core::chemical::ICoorAtomID::vertex().

Referenced by finalize().

ResidueTypeCOP core::chemical::ResidueType::get_base_type_cop ( ) const

Get a pointer to this ResidueType's base ResidueType.

Returns the base_type_cop_ pointer if not null, self pointer if null.

References base_type_cop_, and get_self_ptr().

Referenced by core::chemical::ResidueTypeSet::generate_residue_type().

std::string core::chemical::ResidueType::get_disulfide_atom_name ( ) const

inline

Gets disulfide atom name.

Author: Andrew M. Watkins (amw57.nosp@m.9@ny.nosp@m.u.edu).

References disulfide_atom_name_.

Referenced by protocols::cyclic_peptide::TryDisulfPermutations::apply(), core::pack::task::operation::NoRepackDisulfides::apply(), core::chemical::ConnectSulfurAndMakeVirtualProton::apply(), core::scoring::disulfides::FullatomDisulfideEnergy::defines_score_for_residue_pair(), core::conformation::symmetry::SymmetricConformation::detect_disulfides(), core::conformation::Conformation::detect_disulfides(), core::scoring::disulfides::DisulfideAtomIndices::DisulfideAtomIndices(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::find_disulfides(), core::conformation::Conformation::fix_disulfides(), core::conformation::form_disulfide(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_connectivity_annotation_info(), core::conformation::get_disulf_partner(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_ssbond_record(), core::conformation::is_disulfide_bond(), and protocols::toolbox::match_enzdes_util::EnzConstraintParameters::make_constraint_covalent_helper().

void core::chemical::ResidueType::get_metal_binding_atoms ( AtomIndices & metal_binding_indices ) const

inline

Gets indices of all atoms that can form bonds to metals.

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

References atom_index(), has(), and metal_binding_atoms_.

Referenced by core::conformation::Residue::get_metal_binding_atoms().

utility::vector1< std::string > core::chemical::ResidueType::get_metal_binding_atoms ( ) const

inline

References metal_binding_atoms_.

core::Real core::chemical::ResidueType::get_numeric_property ( std::string const & tag ) const

Get a numeric property, if it exists.

References name3_, and properties_.

Referenced by protocols::qsar::scoring_grid::LigandPropertyScore::score().

ResidueTypeCOP core::chemical::ResidueType::get_self_ptr ( ) const

inline

self pointers

Referenced by protocols::toolbox::rotamer_set_operations::RigidBodyMoveBaseRSO::alter_rotamer_set(), protocols::ligand_docking::RandomConformerMover::apply(), protocols::simple_moves::ModifyVariantTypeMover::apply(), core::scoring::BB_Pos::bbindices_up_to_date(), protocols::match::downstream::SecondaryMatcherToUpstreamResidue::build(), protocols::toolbox::pose_manipulation::construct_poly_uniq_restype_pose(), protocols::match::downstream::SecondaryMatcherToUpstreamResidue::count_rotamer(), protocols::match::Matcher::create_ds_builder(), protocols::dna::DnaInterfacePacker::current_working_sequence(), protocols::dna::design_residues_list(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::find_disulfides(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::find_disulfides(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::find_disulfides(), core::chemical::ResidueTypeSet::generate_residue_type(), get_base_type_cop(), protocols::ligand_docking::LigandBaseProtocol::get_non_bb_clashing_rotamers(), protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::get_pose_data(), protocols::dna::DnaInterfacePacker::get_targeted_sequence(), protocols::dna::DnaInterfacePacker::init_standard(), core::scoring::lkball::LKB_ResidueInfo::initialize(), protocols::toolbox::match_enzdes_util::LigandConformer::initialize_from_residue(), protocols::match::downstream::RigidLigandBuilder::initialize_from_residue(), protocols::match::downstream::LigandConformerBuilder::initialize_from_residue(), protocols::dna::DnaInterfacePacker::measure_specificities(), protocols::dna::DnaInterfacePacker::protein_scan(), core::scoring::methods::GoapEnergy::read_angle_definitions(), protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::residue_conformations_redundant(), core::pose::residue_types_from_saccharide_sequence(), core::pose::residue_types_from_sequence(), core::pack::task::ResidueLevelTask_::ResidueLevelTask_(), protocols::dna::DnaInterfacePacker::reversion_scan(), protocols::ligand_docking::rotamers_for_trials(), protocols::match::downstream::SecondaryMatcherToUpstreamResidue::store_rotamer_coords(), protocols::simple_moves::RotamerizeMover::task_is_valid(), protocols::simple_moves::MinPackMover::task_is_valid(), protocols::simple_moves::PackRotamersMover::task_is_valid(), and protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::template_atom_inds().

ResidueTypeOP core::chemical::ResidueType::get_self_ptr ( )

inline

ResidueTypeCAP core::chemical::ResidueType::get_self_weak_ptr ( ) const

inline

Referenced by update_derived_data().

ResidueTypeAP core::chemical::ResidueType::get_self_weak_ptr ( )

inline

std::string core::chemical::ResidueType::get_string_property ( std::string const & tag ) const

Get a string property, if it exists.

References name3_, and properties_.

ResidueGraph const& core::chemical::ResidueType::graph ( ) const

inline

Constant access to the underlying graph.

References graph_.

AtomIndices const& core::chemical::ResidueType::Haro_index ( ) const

inline

return indices of aromatic Hydrogens

References Haro_index_.

Referenced by core::conformation::Residue::Haro_index().

bool core::chemical::ResidueType::has ( std::string const & atom_name ) const

inline

is this atom present in this residue?

References atom_name_to_vd_.

bool core::chemical::ResidueType::has ( VD const vd ) const

inline

is this vertex descriptor present in this residue?

References graph_, and core::chemical::has().

bool core::chemical::ResidueType::has_orbital ( std::string const & orbital_name ) const

inline

is this orbital present in this residue?

References orbitals_index_.

Referenced by add_orbital_bond().

bool core::chemical::ResidueType::has_property ( std::string const & property ) const

Generic property access.

References properties_.

Referenced by core::io::pose_to_sfr::PoseToStructFileRepConverter::get_connectivity_annotation_info(), core::conformation::Residue::has_property(), core::pack::task::operation::ResidueHasProperty::operator()(), core::chemical::Selector_PROPERTY::operator[](), and core::scoring::aa_composition_energy::AACompositionPropertiesSet::properties_match_this().

bool core::chemical::ResidueType::has_property ( ResidueProperty const property ) const

Generic property access, by ResidueProperty.

References properties_.

bool core::chemical::ResidueType::has_sc_orbitals ( ) const

does this residue have sidechain orbitals?

References properties_, and core::chemical::SC_ORBITALS.

Referenced by core::conformation::Residue::has_sc_orbitals().

bool core::chemical::ResidueType::has_shadow_atoms ( ) const

inline

Returns true if this residue has shadow atoms, false otherwise.

References atom_shadowed_.

Referenced by core::conformation::Residue::has_shadow_atoms().

bool core::chemical::ResidueType::has_variant_type ( VariantType const variant_type ) const

Generic variant access.

References properties_.

bool core::chemical::ResidueType::has_variant_type ( std::string const & variant_type ) const

Generic variant access by string.

References properties_.

const HeavyAtomWithHydrogensGraph core::chemical::ResidueType::heavy_atom_with_hydrogens ( )

References atom_types_, graph(), and graph_.

const HeavyAtomWithPolarHydrogensGraph core::chemical::ResidueType::heavy_atom_with_polar_hydrogens ( )

References atom_types_, graph(), and graph_.

const HeavyAtomGraph core::chemical::ResidueType::heavy_atoms ( )

References atom_types_, and graph_.

bool core::chemical::ResidueType::heavyatom_has_polar_hydrogens ( Size atomno ) const

inline

References finalized_, graph_, and ordered_atoms_.

Referenced by protocols::stepwise::modeler::rna::sugar::detect_sugar_contacts(), core::conformation::Residue::heavyatom_has_polar_hydrogens(), and core::scoring::lkball::setup_water_builders_for_residue_type().

bool core::chemical::ResidueType::heavyatom_is_an_acceptor ( Size atomno ) const

inline

References finalized_, graph_, and ordered_atoms_.

Referenced by core::scoring::elec::GroupElec::build_groupinfo(), protocols::stepwise::modeler::rna::sugar::detect_sugar_contacts(), protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::get_possible_hbond_acceptors(), and core::conformation::Residue::heavyatom_is_an_acceptor().

AtomIndices const& core::chemical::ResidueType::Hpol_index ( ) const

inline

return indices of polar Hydrogens

References Hpol_index_.

Referenced by core::conformation::Residue::Hpol_index(), and perform_checks().

AtomIndices const& core::chemical::ResidueType::Hpos_apolar ( ) const

inline

indices of non-polar hydrogens as potential carbon Hbond donors

References Hpos_apolar_.

Referenced by core::conformation::Residue::Hpos_apolar().

AtomIndices const& core::chemical::ResidueType::Hpos_polar ( ) const

inline

indices of polar hydrogens as Hbond donors

References Hpos_polar_.

Referenced by protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::check_other_partition_for_contact(), protocols::stepwise::modeler::rna::phosphate::get_phosphate_atom_and_neighbor_list(), and core::conformation::Residue::Hpos_polar().

AtomIndices const& core::chemical::ResidueType::Hpos_polar_sc ( ) const

inline

References Hpos_polar_sc_.

Referenced by core::conformation::Residue::Hpos_polar_sc().

const HydrogenAtomGraph core::chemical::ResidueType::hydrogens ( )

References atom_types_, and graph_.

Referenced by setup_atom_ordering().

AtomICoor const & core::chemical::ResidueType::icoor ( Size const atm ) const

AtomICoord of an atom.

References icoor_, and ordered_atoms_.

AtomICoor const & core::chemical::ResidueType::icoor ( VD const atm ) const

AtomICoord of an atom.

References has(), and icoor_.

dihedral_atom_set const& core::chemical::ResidueType::improper_dihedral ( Size const dihe ) const

inline

Return the indices for the set of atoms that define a particular intraresidue improper dihedral.

References improper_dihedral_atom_sets_.

utility::vector1< Size > const& core::chemical::ResidueType::improper_dihedrals_for_atom ( Size atomno ) const

inline

Returns the list of all of the indices of all the intraresidue dihedrals a particular atom is involved in. Useful for calculating the derivatives for an atom.

References improper_dihedrals_for_atom_.

bool core::chemical::ResidueType::in_residue_type_set ( ) const

References residue_type_set_.

std::string core::chemical::ResidueType::interchangeability_group ( ) const

inline

get our interchangeability-group id. Used to determine if two residue types are equivalent, except for their variant status. E.g. ResidueTypes ALA and ALA_Nterm would be part of the same interchangeability group. This has a degree of subjectivity; are TYR and pTYR in the same interchangeability group? Probably not. This data can be specified in the ResidueTypes .params file with the INTERCHANGEABILITY_GROUP tag.

References interchangeability_group_.

Referenced by core::chemical::SetInterchangeabilityGroup_String::apply(), core::chemical::ChiralFlipNaming::apply(), placeholder_clone(), and core::chemical::sdf::MolFileIOMolecule::set_from_extra_data().

void core::chemical::ResidueType::interchangeability_group ( std::string setting )

inline

set our interchangeability-group id

References interchangeability_group_.

bool core::chemical::ResidueType::is_acetylated_nterminus ( ) const

is acetylated n terminus

References core::chemical::ACETYLATED_NTERMINUS, and properties_.

bool core::chemical::ResidueType::is_achiral_backbone ( ) const

is this an achiral backbone?

References core::chemical::ACHIRAL_BACKBONE, and properties_.

bool core::chemical::ResidueType::is_adduct ( ) const

is an adduct-modified residue?

References core::chemical::ADDUCT, and properties_.

bool core::chemical::ResidueType::is_alpha_aa ( ) const

Is this an alpha-amino acid?

References core::chemical::ALPHA_AA, and properties_.

Referenced by protocols::ncbb::SecStructMinimizeMover::add_dihedral_constraints_to_pose(), protocols::cyclic_peptide::DeclareBond::apply(), protocols::simple_moves::SetTorsion::apply(), protocols::ncbb::SecStructMinimizeMover::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::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_randomize_alpha_backbone_by_rama(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_sample_cis_peptide_bond(), core::scoring::methods::RamaPreProEnergy::eval_intraresidue_dof_derivative(), core::conformation::form_disulfide_helper(), protocols::generalized_kinematic_closure::general_set_phi(), protocols::generalized_kinematic_closure::general_set_psi(), core::scoring::P_AA::get_Paa_pp_deriv(), core::scoring::bin_transitions::BinTransitionData::has_property(), core::scoring::methods::RamaPreProEnergy::residue_pair_energy(), and protocols::helical_bundle::MakeBundleHelix::set_tail_dihedrals().

bool core::chemical::ResidueType::is_aromatic ( ) const

is aromatic?

References core::chemical::AROMATIC, and properties_.

Referenced by protocols::antibody::AntibodyFeatures::calculate_cdr_aromatic_nres(), core::pack::task::ResidueLevelTask_::extrachi_sample_level(), core::scoring::bin_transitions::BinTransitionData::has_property(), core::conformation::Residue::is_apolar(), and core::conformation::Residue::is_aromatic().

bool core::chemical::ResidueType::is_base_type ( ) const

Is this ResidueType a base type?

Checks the base_type_cop_ pointer. If it's null, this is assumed to be a base type.

References base_type_cop_.

bool core::chemical::ResidueType::is_beta_aa ( ) const

Is this a beta-amino acid?

References core::chemical::BETA_AA, and properties_.

Referenced by protocols::ncbb::SecStructMinimizeMover::add_dihedral_constraints_to_pose(), protocols::cyclic_peptide::DeclareBond::apply(), protocols::simple_moves::SetTorsion::apply(), protocols::ncbb::SecStructFinder::apply(), protocols::ncbb::SecStructMinimizeMover::apply(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_loop_bump_check(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_sample_cis_peptide_bond(), core::pack::rotamer_set::ContinuousRotamerSet::build_rotamers(), core::scoring::bin_transitions::BinTransitionData::has_property(), core::scoring::OmegaTether::omega_index(), core::scoring::OmegaTether::phi_index(), core::scoring::OmegaTether::psi_index(), and protocols::helical_bundle::MakeBundleHelix::set_tail_dihedrals().

bool core::chemical::ResidueType::is_branch_lower_terminus ( ) const

is lower terminus of a branch?

References core::chemical::BRANCH_LOWER_TERMINUS, and properties_.

Referenced by branch_connect_atoms(), core::conformation::Residue::is_branch_lower_terminus(), and core::pose::set_reasonable_fold_tree().

bool core::chemical::ResidueType::is_branch_point ( ) const

is a branch-point residue?

References core::chemical::BRANCH_POINT, and properties_.

Referenced by core::conformation::Residue::is_branch_point(), and show().

bool core::chemical::ResidueType::is_canonical ( ) const

Is this a canonical residue type (nucleic acid or amino acid)?

Calls is_canonical_aa() and is_canonical_nucleic().

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

References is_canonical_aa(), and is_canonical_nucleic().

Referenced by core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_conect_records_for_atom().

bool core::chemical::ResidueType::is_canonical_aa ( ) const

Is this a canonical amino acid (CANONICAL_AA property)?

Only the standard amino acid types (ACDEFGHIKLMNPQRSTVWY) are canonical.

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

References core::chemical::CANONICAL_AA, and properties_.

Referenced by is_canonical().

bool core::chemical::ResidueType::is_canonical_nucleic ( ) const

Is this a canonical nucleic acid (CANONICAL_NUCLEIC property)?

Only the standard nucliec acid types (dA, dC, dG, dT, A, C, G, U) are canonical.

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

References core::chemical::CANONICAL_NUCLEIC, and properties_.

Referenced by is_canonical().

bool core::chemical::ResidueType::is_carbohydrate ( ) const

is carbohydrate?

References core::chemical::CARBOHYDRATE, and properties_.

Referenced by core::conformation::Residue::carbohydrate_info(), core::conformation::Residue::is_carbohydrate(), and core::chemical::Selector_UPPER_POSITION::operator[]().

bool core::chemical::ResidueType::is_charged ( ) const

is charged?

References core::chemical::CHARGED, and properties_.

Referenced by core::scoring::bin_transitions::BinTransitionData::has_property(), core::conformation::Residue::is_apolar(), and core::conformation::Residue::is_charged().

bool core::chemical::ResidueType::is_coarse ( ) const

is coarse?

References core::chemical::COARSE, and properties_.

Referenced by core::conformation::Residue::is_coarse(), and protocols::toolbox::AtomID_Mapper::renumber_after_variant_changes().

bool core::chemical::ResidueType::is_cyclic ( ) const

is cyclic?

References core::chemical::CYCLIC, and properties_.

Referenced by core::scoring::bin_transitions::BinTransitionData::has_property(), core::conformation::Residue::ring_conformer(), core::pose::Pose::set_ring_conformation(), core::conformation::Residue::show(), and show().

bool core::chemical::ResidueType::is_d_aa ( ) const

is this a d-amino acid?

References core::chemical::D_AA, and properties_.

Referenced by protocols::simple_moves::oop::OopRandomPuckMover::apply(), protocols::ncbb::oop::OopCreatorMover::apply(), protocols::denovo_design::construct_poly_ala_pose(), core::scoring::OmegaTether::eval_omega_score_residue(), core::conformation::form_disulfide_helper(), protocols::simple_moves::chiral::get_chiral_residue_type(), core::scoring::disulfides::FullatomDisulfidePotential::get_disulfide_derivatives(), core::scoring::bin_transitions::BinTransitionData::has_property(), protocols::denovo_design::DisulfidizeMover::mixed_disulfide(), protocols::denovo_design::DisulfidizeMover::mutate_disulfides_to_ala(), and core::scoring::disulfides::FullatomDisulfidePotential::score_this_disulfide().

bool core::chemical::ResidueType::is_disulfide_bonded ( ) const

is disulfide?

References core::chemical::DISULFIDE_BONDED, and properties_.

Referenced by protocols::protein_interface_design::movers::PrepackMover::apply(), protocols::abinitio::DomainAssembly::apply(), protocols::cyclic_peptide::TryDisulfPermutations::apply(), protocols::hybridization::HybridizeProtocol::apply(), core::conformation::break_disulfide(), protocols::denovo_design::construct_poly_ala_pose(), core::conformation::symmetry::SymmetricConformation::detect_disulfides(), core::conformation::Conformation::detect_disulfides(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::disulfides_changed(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::disulfides_changed(), core::scoring::EnvPairPotential::evaluate_pair_and_cenpack_score(), protocols::denovo_design::DisulfidizeMover::find_current_disulfides(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::find_disulfides(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::find_disulfides(), protocols::denovo_design::DisulfidizeMover::find_possible_disulfides(), core::conformation::get_disulf_partner(), protocols::enzdes::EnzdesFlexBBProtocol::get_tenA_neighbor_residues(), protocols::loops::get_tenA_neighbor_residues(), core::scoring::bin_transitions::BinTransitionData::has_property(), core::conformation::is_disulfide_bond(), protocols::toolbox::match_enzdes_util::EnzConstraintParameters::make_constraint_covalent_helper(), core::scoring::disulfides::DisulfideMatchingEnergy::residue_pair_energy(), core::scoring::disulfides::FullatomDisulfideEnergy::residue_pair_energy(), protocols::loops::select_loop_residues(), protocols::simple_moves::DesignRepackMover::setup_packer_and_movemap(), and core::pose::full_model_info::update_disulfides_from_full_model_info().

bool core::chemical::ResidueType::is_DNA ( ) const

is DNA?

References core::chemical::DNA, and properties_.

Referenced by protocols::dna::RestrictDesignToProteinDNAInterface::apply(), protocols::motifs::MotifDnaPacker::apply(), protocols::dna::design_residues_list(), protocols::dna::DnaInterfaceFinder::determine_dna_interface(), protocols::dna::DnaInterfaceFinder::determine_interface(), protocols::dna::DnaInterfaceFinder::determine_protein_interface(), core::pack::task::ResidueLevelTask_::extrachi_sample_level(), protocols::simple_moves::AddConstraintsToCurrentConformationMover::generate_coordinate_constraints(), core::conformation::Residue::is_DNA(), is_NA(), protocols::motifs::MotifSearch::position_vector_setup(), protocols::motifs::LigandMotifSearch::position_vector_setup(), protocols::dna::DnaInterfacePacker::protein_scan(), and core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose().

bool core::chemical::ResidueType::is_gamma_aa ( ) const

Is this a gamma-amino acid?

References core::chemical::GAMMA_AA, and properties_.

bool core::chemical::ResidueType::is_inverted_virtual_residue ( ) const

Check if atom is an inverted virtual.

Check if residue is 'INVERTING_VIRTUAL_RESIDUE'.

Used by the symmetry machinery for mirror symmetry operations.

References core::chemical::INVERTED_VIRTUAL_RESIDUE, and properties_.

Referenced by core::conformation::symmetry::calculate_inverting_virtuals(), and core::pose::symmetry::make_symmetric_pose().

bool core::chemical::ResidueType::is_l_aa ( ) const

is this an l-amino acid?

References core::chemical::L_AA, and properties_.

Referenced by protocols::ncbb::oop::OopCreatorMover::apply(), protocols::denovo_design::construct_poly_ala_pose(), protocols::simple_moves::chiral::get_chiral_residue_type(), and core::scoring::bin_transitions::BinTransitionData::has_property().

bool core::chemical::ResidueType::is_ligand ( ) const

is ligand?

References core::chemical::LIGAND, and properties_.

bool core::chemical::ResidueType::is_lipid ( ) const

is lipid?

References core::chemical::LIPID, and properties_.

Referenced by core::io::carbohydrates::chain_gws_string(), and core::io::carbohydrates::dump_gws().

bool core::chemical::ResidueType::is_lower_terminus ( ) const

is lower terminus?

References core::chemical::LOWER_TERMINUS, and properties_.

Referenced by 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::simple_moves::a3b_hbs::A3BHbsRandomSmallMover::apply(), protocols::simple_moves::MissingDensityToJumpMover::apply(), protocols::simple_moves::chiral::ChiralMover::apply(), protocols::flexpep_docking::FlexPepDockingPoseMetrics::calc_phipsi_RMSD(), core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), core::scoring::dna::DNATorsionPotential::get_atom_ids_by_torsion(), protocols::rbsegment_relax::guess_rbsegs_from_pose(), core::scoring::FACTSRsdTypeInfo::initialize_parameters(), core::conformation::Residue::is_lower_terminus(), is_terminus(), core::pose::make_pose_from_sequence(), core::conformation::Residue::orient_onto_residue_peptoid(), core::conformation::Residue::place(), core::pose::remove_ligand_canonical_residues(), core::chemical::ResidueDatabaseIO::report_residue_type(), protocols::dna::set_base_segment_chainbreak_constraints(), core::scoring::lkball::LKB_ResidueInfo::setup_atom_weights(), protocols::sewing::Assembly::to_pose(), and core::chemical::write_topology_file().

bool core::chemical::ResidueType::is_membrane ( ) const

is membrane?

References core::chemical::MEMBRANE, and properties_.

Referenced by atom_index().

bool core::chemical::ResidueType::is_metal ( ) const

Return true if this residue type 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::METAL, and properties_.

Referenced by core::scoring::sc::MolecularSurfaceCalculator::AddResidue(), core::scoring::sc::MolecularSurfaceCalculator::Calc(), core::conformation::Residue::is_metal(), and perform_checks().

bool core::chemical::ResidueType::is_metalbinding ( ) const

Return true if this residue type is a type that can bind to a metal ion (e.g. His, Asp, 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::METALBINDING, and properties_.

Referenced by core::scoring::bin_transitions::BinTransitionData::has_property(), core::conformation::Residue::is_metalbinding(), and perform_checks().

bool core::chemical::ResidueType::is_methylated_cterminus ( ) const

is methylated c terminus

References core::chemical::METHYLATED_CTERMINUS, and properties_.

bool core::chemical::ResidueType::is_NA ( ) const

is Nucleic Acid?

References is_DNA(), and is_RNA().

Referenced by protocols::simple_moves::RotamerizeMover::apply(), core::pose::correctly_add_cutpoint_variants(), protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::fragment_check(), core::scoring::methods::get_restag(), core::pose::rna::get_suite_torsion_info(), and core::conformation::Residue::is_NA().

bool core::chemical::ResidueType::is_peptoid ( ) const

is peptoid?

References core::chemical::PEPTOID, and properties_.

Referenced by protocols::simple_moves::SetTorsion::apply(), protocols::ncbb::SecStructMinimizeMover::apply(), core::pose::get_constraints_from_link_records(), core::conformation::Residue::is_peptoid(), core::conformation::Residue::orient_onto_residue_peptoid(), protocols::simple_moves::CyclizationMover::setup_connections(), protocols::simple_moves::RandomOmegaFlipMover::setup_torsion_list(), and protocols::simple_moves::RandomTorsionMover::setup_torsion_list().

bool core::chemical::ResidueType::is_polar ( ) const

is polar?

References core::chemical::POLAR, and properties_.

Referenced by core::scoring::bin_transitions::BinTransitionData::has_property(), core::conformation::Residue::is_apolar(), and core::conformation::Residue::is_polar().

bool core::chemical::ResidueType::is_polymer ( ) const

is polymer?

References core::chemical::POLYMER, and properties_.

Referenced by protocols::simple_moves::MissingDensityToJumpMover::apply(), protocols::loophash::BackboneSegment::apply_to_pose(), core::chemical::gasteiger::assign_gasteiger_atom_types(), core::io::pose_from_sfr::PoseFromSFRBuilder::build_initial_pose(), protocols::ligand_docking::constrain_ligand_torsions(), core::scoring::etable::BaseEtableEnergy< Derived >::determine_crossover_behavior(), core::scoring::lkball::determine_crossover_behavior(), protocols::hybridization::discontinued_lower(), protocols::hybridization::discontinued_upper(), protocols::ligand_docking::LigandBaseProtocol::find_interface_backbone(), protocols::loops::find_non_protein_chunks(), protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::fragment_check(), core::pose::full_model_info::FullModelParameters::get_cutpoint_open_from_pdb_info(), protocols::loophash::get_rt_over_leap_fast(), core::conformation::Residue::has_lower_connect(), core::conformation::Residue::has_upper_connect(), core::conformation::Residue::is_polymer(), core::conformation::Residue::is_polymer_bonded(), core::pose::make_pose_from_sequence(), core::scoring::PolymerBondedEnergyContainer::other_res_index(), core::io::pose_from_sfr::PoseFromSFRBuilder::pass_3_verify_sufficient_backbone_atoms(), core::conformation::Residue::place(), core::io::serialization::read_binary(), core::chemical::ResidueDatabaseIO::report_residue_type(), and core::chemical::write_topology_file().

bool core::chemical::ResidueType::is_protein ( ) const

is protein?

References properties_, and core::chemical::PROTEIN.

bool core::chemical::ResidueType::is_proton_chi ( Size const chino ) const

inline

number of proton chis

References proton_chis_.

Referenced by core::pack::rotamers::RotamericSingleResiduePeptoidLibrary< T, N >::chisamples_for_rotamer_and_chi(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::chisamples_for_rotamer_and_chi(), protocols::match::upstream::FullChiSampleSet::expand_non_dunbrack_chi(), core::scoring::methods::IdealParametersDatabase::lookup_torsion_legacy(), core::chemical::print_chis(), and core::chemical::write_topology_file().

bool core::chemical::ResidueType::is_repulsive ( Size const & atomno ) const

Check if atom is repulsive.

References atom_type().

bool core::chemical::ResidueType::is_RNA ( ) const

is RNA?

References properties_, and core::chemical::RNA.

bool core::chemical::ResidueType::is_sidechain_amine ( ) const

is sidechain amine?

References properties_, and core::chemical::SIDECHAIN_AMINE.

bool core::chemical::ResidueType::is_sidechain_thiol ( ) const

is thiol?

References properties_, and core::chemical::SIDECHAIN_THIOL.

Referenced by core::pack::task::operation::OptCysHG::apply(), core::conformation::symmetry::SymmetricConformation::detect_disulfides(), core::conformation::Conformation::detect_disulfides(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::disulfides_changed(), core::scoring::bin_transitions::BinTransitionData::has_property(), core::conformation::is_disulfide_bond(), core::scoring::disulfides::DisulfideMatchingEnergy::residue_pair_energy(), core::scoring::disulfides::FullatomDisulfideEnergy::residue_pair_energy(), and core::pose::full_model_info::update_disulfides_from_full_model_info().

bool core::chemical::ResidueType::is_solvent ( ) const

Is this a solvent molecule (SOLVENT property)?

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

References properties_, and core::chemical::SOLVENT.

Referenced by core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_conect_records_for_atom().

bool core::chemical::ResidueType::is_sri ( ) const

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

References properties_, and core::chemical::SRI.

Referenced by core::conformation::Residue::is_sri().

bool core::chemical::ResidueType::is_surface ( ) const

is surface? (e.g. enamel)

References properties_, and core::chemical::SURFACE.

Referenced by core::conformation::Residue::is_surface(), and core::chemical::write_topology_file().

bool core::chemical::ResidueType::is_terminus ( ) const

is terminus?

References is_lower_terminus(), and is_upper_terminus().

Referenced by protocols::fldsgn::potentials::sspot::get_foldtree_seqsep(), core::scoring::SecondaryStructurePotential::get_foldtree_seqsep(), core::conformation::Residue::is_terminus(), and core::scoring::methods::GoapEnergy::setup_for_scoring().

bool core::chemical::ResidueType::is_triazolemer ( ) const

Is this a triazolemer?

References properties_, and core::chemical::TRIAZOLE_LINKER.

Referenced by core::conformation::Residue::is_triazolemer().

bool core::chemical::ResidueType::is_upper_terminus ( ) const

is upper terminus?

References properties_, and core::chemical::UPPER_TERMINUS.

Referenced by protocols::simple_moves::chiral::ChiralMover::apply(), protocols::flexpep_docking::FlexPepDockingPoseMetrics::calc_phipsi_RMSD(), core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), protocols::loops::find_non_protein_chunks(), core::scoring::dna::DNATorsionPotential::get_atom_ids_by_torsion(), protocols::rbsegment_relax::guess_rbsegs_from_pose(), core::scoring::FACTSRsdTypeInfo::initialize_parameters(), is_terminus(), core::conformation::Residue::is_upper_terminus(), core::pose::make_pose_from_sequence(), core::pose::remove_ligand_canonical_residues(), core::chemical::ResidueDatabaseIO::report_residue_type(), protocols::fldsgn::potentials::sspot::HSPairPotential::score(), protocols::fldsgn::potentials::sspot::SSPairPotential::score(), protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential::score(), protocols::dna::set_base_segment_chainbreak_constraints(), core::scoring::lkball::LKB_ResidueInfo::setup_atom_weights(), protocols::sewing::Assembly::to_pose(), and core::chemical::write_topology_file().

bool core::chemical::ResidueType::is_virtual ( Size const & atomno ) const

Check if atom is virtual.

References atom_type().

Referenced by protocols::stepwise::modeler::rna::bulge::detect_base_contacts(), protocols::stepwise::modeler::rna::sugar::detect_sugar_contacts(), protocols::stepwise::modeler::align::StepWisePoseAligner::do_checks(), core::scoring::elec::GroupElec::get_group(), protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::get_possible_hbond_acceptors(), n_virtual_atoms(), perform_checks(), and protocols::toolbox::match_enzdes_util::InvrotTreeNode::remove_invrots_clashing_with_parent_res().

bool core::chemical::ResidueType::is_virtual_residue ( ) const

Check if residue is 'VIRTUAL_RESIDUE'.

References properties_, and core::chemical::VIRTUAL_RESIDUE.

Referenced by core::conformation::Residue::is_virtual_residue().

Size core::chemical::ResidueType::last_backbone_atom ( ) const

inline

index of the last backbone heavy atom

References n_backbone_heavyatoms_.

Referenced by protocols::hybridization::FragmentBiasAssigner::bfactors(), protocols::simple_moves::AddConstraintsToCurrentConformationMover::generate_coordinate_constraints(), core::conformation::Residue::last_backbone_atom(), and protocols::hybridization::InsertChunkMover::set_bb_xyz_aligned().

utility::vector1< Size > const& core::chemical::ResidueType::last_controlling_chi ( ) const

inline

Read access to the last_controlling_chi_ array.

References last_controlling_chi_.

Referenced by protocols::match::upstream::UpstreamResTypeGeometry::initialize_from_residue_type().

Size core::chemical::ResidueType::last_controlling_chi ( Size atomno ) const

inline

The last_controlling_chi for an atom. 0 if an atom is controlled by no chi.

References last_controlling_chi_.

ResidueConnection const & core::chemical::ResidueType::lower_connect ( ) const

References lower_connect_id_, core::chemical::POLYMER, properties_, and residue_connections_.

Referenced by core::chemical::gasteiger::assign_gasteiger_atom_types(), core::scoring::methods::CartesianBondedEnergy::eval_intraresidue_dof_derivative(), core::chemical::has_assigned_coords(), core::conformation::Conformation::insert_ideal_geometry_at_polymer_bond(), core::conformation::Residue::lower_connect(), core::chemical::write_topology_file(), and core::chemical::ICoorAtomID::xyz().

Size core::chemical::ResidueType::lower_connect_atom ( ) const

index number of the atom which connects to the lower connection

References lower_connect_id_, core::chemical::POLYMER, properties_, residue_connections_, and vd_to_index_.

Referenced by protocols::denovo_design::components::StructureData::are_connectable(), core::chemical::ICoorAtomID::atom_id(), core::conformation::Residue::lower_connect_atom(), and core::chemical::ResidueDatabaseIO::report_residue_type().

Size core::chemical::ResidueType::lower_connect_id ( ) const

inline

References lower_connect_id_.

Referenced by core::conformation::Conformation::append_residue_by_bond(), protocols::cyclic_peptide::DeclareBond::apply(), protocols::cyclic_peptide::PeptideStubMover::apply(), core::scoring::bin_transitions::BinTransitionCalculator::are_normally_bonded(), core::chemical::gasteiger::assign_gasteiger_atom_types(), core::conformation::Conformation::backbone_torsion_angle_atoms(), core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), core::io::silent::BinarySilentStruct::fill_struct(), core::conformation::Residue::has_lower_connect(), core::conformation::Residue::is_polymer_bonded(), and core::chemical::ICoorAtomID::xyz().

Size core::chemical::ResidueType::mainchain_atom ( Size const atm ) const

inline

index of mainchain atom

References mainchain_atoms_indices_.

Referenced by core::conformation::Conformation::insert_ideal_geometry_at_polymer_bond(), and core::conformation::Residue::mainchain_atom().

AtomIndices const& core::chemical::ResidueType::mainchain_atoms ( ) const

inline

indices of all mainchain atoms

References mainchain_atoms_indices_.

Referenced by core::scoring::MultipoleElecPotential::align_residue_multipole_axes(), core::chemical::PrependMainchainAtom::apply(), core::chemical::AppendMainchainAtom::apply(), core::chemical::ReplaceMainchainAtom::apply(), core::chemical::rotamers::NCAARotamerLibrarySpecification::cache_tag(), core::pack::rotamers::SingleNCAARotamerLibraryCreator::create(), core::conformation::Conformation::insert_ideal_geometry_at_polymer_bond(), core::conformation::Residue::mainchain_atoms(), core::conformation::Residue::n_mainchain_atoms(), core::io::pose_from_sfr::PoseFromSFRBuilder::pass_3_verify_sufficient_backbone_atoms(), core::conformation::Residue::Residue(), and core::chemical::ResidueTypeKinWriter::write_restype().

core::Real const& core::chemical::ResidueType::mass ( ) const

inline

get the molecular weight of this residue

References mass_.

Referenced by core::pose::mass(), and protocols::qsar::scoring_grid::MolecularWeightNormalization::operator()().

MMAtomType const & core::chemical::ResidueType::mm_atom_type ( Size const atomno ) const

Get the MM atom_type for this atom by its index number in this residue.

References graph_, mm_atom_types_, and ordered_atoms_.

Referenced by core::scoring::mm::MMBondAngleResidueTypeParam::init(), print_bondangles(), print_dihedrals(), core::chemical::ResidueTypeKinWriter::write_restype(), and core::chemical::write_topology_file().

MMAtomTypeSetCOP core::chemical::ResidueType::mm_atom_types_ptr ( ) const

inline

Get the MM atom_type for this atom by its index number in this residue.

References mm_atom_types_.

Size core::chemical::ResidueType::n_hbond_acceptors ( ) const

inline

number of hbond_acceptors

References n_hbond_acceptors_.

Referenced by core::conformation::Residue::n_hbond_acceptors().

Size core::chemical::ResidueType::n_hbond_donors ( ) const

inline

number of hbond_donors

References n_hbond_donors_.

Referenced by core::conformation::Residue::n_hbond_donors().

Size core::chemical::ResidueType::n_non_polymeric_residue_connections ( ) const

inline

References n_non_polymeric_residue_connections_.

Referenced by core::conformation::Residue::n_non_polymeric_residue_connections().

Size core::chemical::ResidueType::n_nus ( ) const

inline

Return number of nu (internal ring) angles.

References nu_atoms_.

Referenced by core::conformation::Residue::assign_nus(), core::conformation::Residue::n_nus(), and core::chemical::write_topology_file().

Size core::chemical::ResidueType::n_orbitals ( ) const

number of orbitals

References orbitals_.

Referenced by core::conformation::Residue::n_orbitals().

Size core::chemical::ResidueType::n_polymeric_residue_connections ( ) const

inline

References n_polymeric_residue_connections_.

Referenced by core::chemical::AddConnectAndTrackingVirt::apply(), and core::conformation::Residue::n_polymeric_residue_connections().

Size core::chemical::ResidueType::n_possible_residue_connections ( ) const

number of ResidueConnections, counting polymeric residue connections

References residue_connections_.

Size core::chemical::ResidueType::n_proton_chi ( ) const

inline

number of proton chis

References proton_chis_.

Referenced by protocols::stepwise::modeler::polar_hydrogens::check_if_proton_chi_atom(), protocols::simple_moves::check_if_proton_chi_atom(), core::pack::rotamers::SingleResidueRotamerLibrary::compute_proton_chi_samplings(), core::pack::rotamers::SingleResiduePeptoidLibraryCreator::create(), core::pack::rotamers::SingleNCAARotamerLibraryCreator::create(), core::pack::rotamers::SingleResidueRotamerLibrary::expand_proton_chis(), and core::chemical::ResidueDatabaseIO::report_residue_type_proton_chi().

Size core::chemical::ResidueType::n_residue_connections_for_atom ( Size const atomid ) const

inline

How many inter-residue chemical bonds does a particular atom form?

References atom_2_residue_connection_map_.

Referenced by core::chemical::gasteiger::assign_gasteiger_atom_types(), core::conformation::Residue::copy_residue_connections(), core::conformation::Conformation::detect_bonds(), core::scoring::methods::LK_PolarNonPolarEnergy::get_base_vector(), and core::scoring::methods::LK_hack::residue_pair_energy().

Size core::chemical::ResidueType::n_rings ( ) const

inline

Return the number of rings in this residue.

References ring_atoms_.

Referenced by core::conformation::Residue::ring_conformer(), core::pose::Pose::set_ring_conformation(), core::conformation::Residue::show(), show(), and update_derived_data().

Size core::chemical::ResidueType::n_virtual_atoms ( ) const

Counts the number of virtual atoms and returns the count.

The virtual count is not stored in the resiude type. This count is performed on the fly, and can hurt performance if reapeatedly carried out. Not intended for use in large loops – instead, call once and store the value.

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

The virtual count is not stored in the residue type. This count is performed on the fly, and can hurt performance if repeatedly carried out. Not intended for use in large loops – instead, call once and store the value.

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

References is_virtual(), and natoms().

Referenced by core::chemical::AddConnectAndTrackingVirt::apply(), and core::conformation::Residue::n_virtual_atoms().

std::string const& core::chemical::ResidueType::name ( ) const

inline

get our (unique) residue name

References name_.

void core::chemical::ResidueType::name ( std::string const & name_in )

inline

set our (unique) residue name

References name_.

char core::chemical::ResidueType::name1 ( ) const

inline

get our 1letter code. This is set in the ResidueType .params file through the IO_STRING tag along with the name3 string.

References name1_.

Referenced by core::chemical::SetIO_String::apply(), core::pose::full_model_info::check_full_model_info_OK(), protocols::membrane::MPMutateRelaxMover::check_mutant_file(), protocols::stepwise::modeler::rna::bulge::detect_base_contacts(), protocols::contact_map::ContactMap::fill_contacts(), protocols::loophash::get_rt_over_leap_without_foldtree_bs(), core::conformation::Residue::name1(), core::chemical::Selector_NAME1::operator[](), protocols::simple_filters::ScoreCutoffFilter::output_residue_pair_energies(), placeholder_clone(), protocols::hybridization::TMalign::read_pose(), core::chemical::ResidueDatabaseIO::read_residue_type(), core::chemical::ResidueDatabaseIO::report_residue_type(), core::chemical::sdf::MolFileIOMolecule::set_from_extra_data(), core::scoring::lkball::LKB_ResidueInfo::setup_atom_weights(), core::chemical::setup_patch_atomic_charge_reassignments_from_commandline(), core::chemical::ResidueTypeKinWriter::write_kin_header(), and core::chemical::write_topology_file().

void core::chemical::ResidueType::name1 ( char const code )

inline

set our 1letter code

References name1_.

std::string const& core::chemical::ResidueType::name3 ( ) const

inline

get our 3letter code. This is set in the ResidueType .params file through the IO_STRING tag along with the name1 string NOTE: The "name3" is not necessarily three characters long. e.g. Metal ions may be only two characters.

If you need three characters, the PDB convention is to right pad.

References name3_.

void core::chemical::ResidueType::name3 ( std::string const & name_in )

inline

set our 3letter code

References name3_.

Size core::chemical::ResidueType::natoms ( ) const

inline

number of atoms

References graph_.

Size core::chemical::ResidueType::nbonds ( ) const

inline

number of bonds

References graph_.

Referenced by core::chemical::sdf::MolWriter::compose_ctab(), and core::chemical::sdf::MolWriter::compose_metadata().

Size core::chemical::ResidueType::nbonds ( Size atom ) const

inline

number of bonds for given atom

References graph_, and ordered_atoms_.

Size core::chemical::ResidueType::nbonds ( VD atom ) const

inline

number of bonds for given atom

References graph_.

void core::chemical::ResidueType::nbr_atom ( std::string const & atom_name )

inline

set nbr_atom used to define residue-level neighbors

References atom_index(), nbr_atom_, nbr_atom_indices_, and ordered_atoms_.

Referenced by core::chemical::SetNbrAtom::apply(), protocols::denovo_design::constraints::CoordinateConstraintGenerator::create_coordinate_cst(), protocols::denovo_design::connection::BridgeChains::create_coordinate_cst(), core::scoring::methods::MembraneEnvSmoothEnergy::eval_atom_derivative(), core::scoring::methods::EnvSmoothEnergy::eval_atom_derivative(), core::scoring::membrane::FaMPEnvSmoothEnergy::eval_atom_derivative(), protocols::simple_moves::AddConstraintsToCurrentConformationMover::generate_atom_pair_constraints(), core::conformation::Residue::nbr_atom(), core::conformation::Residue::nbr_atom_xyz(), core::chemical::ResidueDatabaseIO::read_residue_type(), core::chemical::ResidueDatabaseIO::report_residue_type(), core::chemical::sdf::MolFileIOMolecule::set_from_extra_data(), core::chemical::ResidueTypeKinWriter::write_restype(), and core::chemical::write_topology_file().

void core::chemical::ResidueType::nbr_atom ( VD vertex )

inline

set nbr_atom used to define residue-level neighbors

References atom_index(), nbr_atom_, and nbr_atom_indices_.

Size core::chemical::ResidueType::nbr_atom ( ) const

inline

get nbr_atom used to define residue-level neighbors

References nbr_atom_indices_.

Referenced by assign_neighbor_atom(), and select_orient_atoms().

void core::chemical::ResidueType::nbr_radius ( Real const radius )

inline

set nbr_radius_ used to define residue-level neighbors

References nbr_radius_.

Referenced by core::chemical::SetNbrRadius::apply(), core::pack::rotamer_set::RotamerSubset::different_resgroup(), core::pack::rotamer_set::RotamerSet_::different_resgroup(), core::conformation::Residue::nbr_radius(), core::pose::pose_max_nbr_radius(), core::chemical::ResidueDatabaseIO::read_residue_type(), core::chemical::ResidueDatabaseIO::report_residue_type(), core::scoring::Energies::require_context_graph_(), core::chemical::sdf::MolFileIOMolecule::set_from_extra_data(), core::scoring::symmetry::SymmetricEnergies::update_neighbor_links(), core::scoring::Energies::update_neighbor_links(), core::chemical::ResidueTypeKinWriter::write_restype(), and core::chemical::write_topology_file().

Real core::chemical::ResidueType::nbr_radius ( ) const

inline

get nbr_radius_ used to define residue-level neighbors

References nbr_radius_.

VD core::chemical::ResidueType::nbr_vertex ( ) const

inline

get VD used to define residue-level neighbors

References nbr_atom_.

AtomIndices const& core::chemical::ResidueType::nbrs ( Size const atomno ) const

inline

indices of the bonded neighbors for an atom, shortcut for bonded_neighbor(atomno)

References bonded_neighbor().

Referenced by atoms_are_bonded(), core::chemical::AutomorphismIterator::can_pair(), core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), core::chemical::AutomorphismIterator::edges_match(), core::scoring::methods::MMBondLengthEnergy::eval_atom_derivative(), core::scoring::methods::MMBondLengthEnergy::eval_intrares_energy(), core::chemical::get_residue_path_distances(), note_chi_controls_atom(), protocols::features::ProteinBondGeometryFeatures::report_intrares_lengths(), select_orient_atoms(), core::scoring::lkball::setup_water_builders_for_residue_type(), core::scoring::orbitals::surrogate_atom_for_orbital(), and core::chemical::write_topology_file().

Size core::chemical::ResidueType::nchi ( ) const

inline

number of chi angles

References chi_atoms_.

Size core::chemical::ResidueType::ndihe ( ) const

inline

Return the number of intraresidue dihedrals. This covers all pairs of atoms that are separated by four bonds, and all pairs of intervening atoms.

References dihedral_atom_sets_.

Referenced by core::scoring::methods::MMTorsionEnergy::eval_intrares_energy(), print_dihedrals(), and protocols::features::ProteinBondGeometryFeatures::report_intrares_torsions().

orbitals::ICoorOrbitalData const & core::chemical::ResidueType::new_orbital_icoor_data ( Size const orbital_index ) const

References orbital_index(), and orbitals_.

Referenced by core::conformation::Residue::build_orbital_xyz().

Size core::chemical::ResidueType::nheavyatoms ( ) const

inline

number of heavy atoms

References nheavyatoms_.

Referenced by core::chemical::AutomorphismIterator::AutomorphismIterator(), core::scoring::elec::GroupElec::build_groupinfo(), protocols::analysis::InterfaceAnalyzerMover::calc_hbond_sasaE(), core::scoring::calc_per_res_hydrophobic_sasa(), protocols::pose_length_moves::InsertResMover::center_of_mass(), protocols::simple_moves::Tumble::center_of_mass(), core::chemical::sdf::MolWriter::compose_atoms(), core::pack::interaction_graph::SurfacePotential::compute_pose_hpatch_score(), core::scoring::compute_sc_centroid(), core::scoring::compute_sc_radius(), protocols::stepwise::modeler::align::StepWisePoseAligner::create_coordinate_constraints(), protocols::stepwise::modeler::rna::bulge::detect_base_contacts(), protocols::stepwise::modeler::align::StepWisePoseAligner::do_checks(), protocols::stepwise::modeler::align::StepWisePoseAligner::get_calc_rms_atom_id_map(), protocols::simple_moves::MinimalRotamer::has_ideal_geometry(), core::chemical::heavy_atom_names_match(), core::scoring::lkball::LKB_ResidueInfo::initialize(), core::pose::initialize_atomid_map_heavy_only(), core::conformation::Residue::nheavyatoms(), protocols::ligand_docking::LigandDockProtocol::optimize_orientation3(), protocols::enzdes::ResidueConformerFilter::parse_my_tag(), core::conformation::Residue::place(), protocols::simple_moves::MinimalRotamer::record_internal_geometry(), select_orient_atoms(), core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::set_rotamer(), core::pack::interaction_graph::HPatchNode< V, E, G >::set_rotamers(), core::scoring::lkball::LKB_ResidueInfo::setup_atom_weights(), core::scoring::lkball::setup_water_builders_for_residue_type(), and protocols::stepwise::modeler::align::StepWisePoseAligner::update_superimpose_atom_id_map().

void core::chemical::ResidueType::nondefault ( bool const in )

inline

References nondefault_.

void core::chemical::ResidueType::note_chi_controls_atom	(	Size	chi,
		Size	atomno
	)

private

Recursive subroutine invoked by update_last_controlling_chi().

O(N) recursive algorithm for determining the last chi for each atom. Each atom is visited at most twice.

References atom_base(), bonded_neighbor(), last_controlling_chi_, and nbrs().

Referenced by update_last_controlling_chi().

AtomIndices const& core::chemical::ResidueType::nu_atoms ( core::uint const nu_index ) const

inline

Return indices of the atoms used to define a given nu (internal ring) angle.

References nu_atoms_indices_.

Referenced by core::conformation::Residue::assign_nus(), core::conformation::Residue::nu_atoms(), core::conformation::Residue::set_all_ring_nu(), core::pose::Pose::set_ring_conformation(), core::conformation::Residue::set_tau(), and core::chemical::write_topology_file().

utility::vector1< AtomIndices > const& core::chemical::ResidueType::nu_atoms ( ) const

inline

Return list of indices of the atoms used to define all the nu (internal ring) angles.

References nu_atoms_indices_.

Size core::chemical::ResidueType::num_bondangles ( ) const

inline

get number of intraresidue bond angles

References bondangle_atom_sets_.

Referenced by core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), core::scoring::methods::MMBondAngleEnergy::eval_intrares_energy(), core::scoring::mm::MMBondAngleResidueTypeParam::init(), and protocols::features::ProteinBondGeometryFeatures::report_intrares_angles().

Size core::chemical::ResidueType::number_bonded_heavyatoms ( Size const atomno ) const

indicates how many heavyatom bonded neighbors an atom has

References bonded_neighbor(), and number_bonded_hydrogens().

Referenced by core::chemical::sdf::MolWriter::compose_atoms(), and core::scoring::orbitals::surrogate_atom_for_orbital().

Size core::chemical::ResidueType::number_bonded_hydrogens ( Size const atomno ) const

inline

indicates how many proton bonded neighbors an atom has

References attached_H_begin_, and attached_H_end_.

ResidueType & core::chemical::ResidueType::operator= ( ResidueType const & src )

Copies <src> into the ResidueType.

References core::pose::motif::a(), aa_, abase2_, abase2_indices_, accpt_pos_, accpt_pos_sc_, actcoord_atoms_, actcoord_atoms_indices_, all_bb_atoms_, all_sc_atoms_, atom_2_residue_connection_map_, atom_aliases_, atom_base_, atom_base_indices_, atom_name_to_vd_, atom_shadowed_, atom_shadowed_indices_, atom_types_, core::chemical::ICoorAtomID::atomno(), atoms_last_controlled_by_chi_, atoms_with_orb_index_, atoms_within_one_bond_of_a_residue_connection_, atoms_within_two_bonds_of_a_residue_connection_, attached_H_begin_, attached_H_end_, backbone_aa_, base_name_, base_type_cop_, bondangle_atom_sets_, bondangles_for_atom_, bonded_neighbor_, bonded_neighbor_type_, bonded_orbitals(), core::chemical::AtomICoor::built_atom_vertex(), carbohydrate_info_, chi_2_proton_chi_, chi_atoms_, chi_atoms_indices_, chi_rotamers_, conformer_sets_, cut_bond_neighbor_, cut_bond_neighbor_indices_, defined_adducts_, dihedral_atom_sets_, dihedrals_for_atom_, disulfide_atom_name_, elements_, core::sequence::end, finalized_, first_sidechain_hydrogen_, force_bb_, force_nbr_atom_orient_, gasteiger_atom_types_, graph_, Haro_index_, Hpol_index_, Hpos_apolar_, Hpos_polar_, Hpos_polar_sc_, icoor_, improper_dihedral_atom_sets_, improper_dihedrals_for_atom_, interchangeability_group_, core::chemical::ICoorAtomID::INTERNAL, is_proton_chi_, last_controlling_chi_, low_ring_conformers_, lower_connect_id_, lowest_ring_conformer_, mainchain_atoms_, mainchain_atoms_indices_, mass_, metal_binding_atoms_, mm_atom_types_, n_backbone_heavyatoms_, n_hbond_acceptors_, n_hbond_donors_, n_non_polymeric_residue_connections_, n_polymeric_residue_connections_, core::chemical::Atom::name(), name1_, name3_, name_, natoms(), nbr_atom_, nbr_atom_indices_, nbr_radius_, nheavyatoms_, nondefault_, nu_atoms_, nu_atoms_indices_, null_vertex, orbital_types_, orbitals_, orbitals_index_, ordered_atoms_, path_distance_, properties_, proton_chi_extra_samples_, proton_chi_samples_, proton_chis_, remap_pdb_atom_names_, residue_connections_, residue_type_set_, ring_atoms_, ring_atoms_indices_, rings_and_their_edges_, rna_residue_type_, root_atom_, rotamer_aa_, rotamer_library_specification_, core::chemical::strip_whitespace(), core::chemical::AtomICoor::stub_atom(), upper_connect_id_, vd_to_index_, core::chemical::ICoorAtomID::vertex(), within1bonds_sets_for_atom_, and within2bonds_sets_for_atom_.

Orbital const & core::chemical::ResidueType::orbital ( Size const orbital_index ) const

References orbital_index(), and orbitals_.

Referenced by core::conformation::Residue::assign_orbitals(), core::conformation::Residue::orbital_name(), and core::conformation::Residue::set_orbital_xyz().

Orbital const & core::chemical::ResidueType::orbital ( std::string const & orbital_name ) const

References orbital_index(), and orbitals_.

orbitals::ICoorOrbitalData const & core::chemical::ResidueType::orbital_icoor_data ( Size const orbital_index ) const

References orbital_index(), and orbitals_.

core::Size core::chemical::ResidueType::orbital_index ( std::string const & name ) const

get orbital index by name

References name3(), and orbitals_index_.

Referenced by new_orbital_icoor_data(), orbital(), orbital_icoor_data(), orbital_type(), and set_orbital_icoor_id().

orbitals::OrbitalType const & core::chemical::ResidueType::orbital_type ( int const orbital_index ) const

References orbital_index(), orbital_types_, and orbitals_.

Referenced by core::conformation::Residue::orbital_type().

orbitals::OrbitalTypeSetCOP core::chemical::ResidueType::orbital_types_ptr ( ) const

inline

Get the MM atom_type for this atom by its index number in this residue.

References orbital_types_.

void core::chemical::ResidueType::order_atoms ( )

private

GRAPH FUNCTION to provide backward compatibility ////////.

int core::chemical::ResidueType::path_distance	(	Size	at1,
		Size	at2
	)		const

inline

path distance (number of bonds separated) between a pair of atoms

References path_distance_.

Referenced by core::chemical::AutomorphismIterator::bonded(), core::chemical::AutomorphismIterator::bonded2(), core::scoring::etable::count_pair::CountPairGeneric::CountPairGeneric(), core::scoring::FACTSRsdTypeInfo::initialize_intrascale(), and core::conformation::Residue::path_distance().

utility::vector1< int > const& core::chemical::ResidueType::path_distance ( Size atom ) const

inline

shortest path distance for an atom to all other residue atoms

References atom(), and path_distance_.

utility::vector1< utility::vector1< int > > const& core::chemical::ResidueType::path_distances ( ) const

inline

accessor of path_distance_ data for this residue, which is a 2D array

References path_distance_.

Referenced by core::conformation::Residue::path_distances(), and update_derived_data().

void core::chemical::ResidueType::perform_checks ( )

private

Final check of ResidueType data, called by finalize().

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

These checks are meant to be quick and low-expense, and are only called on finalize(), so they shouldn't generally add much to Rosetta processing time.

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

References core::chemical::aa_unk, core::chemical::ALPHA_AA, atom_name(), backbone_aa_, core::chemical::BETA_AA, core::chemical::D_AA, Hpol_index(), Hpol_index_, Hpos_polar_, is_metal(), is_metalbinding(), is_virtual(), core::chemical::L_AA, metal_binding_atoms_, name(), nheavyatoms_, and properties_.

Referenced by finalize().

ResidueTypeOP core::chemical::ResidueType::placeholder_clone ( ) const

make a copy

make a copy, but only with all the stuff needed by patch selectors needs to be filled.

References aa(), interchangeability_group(), name(), name1(), name3(), properties(), properties_, and ResidueType().

Referenced by core::chemical::PatchCase::apply().

const PolarHydrogenGraph core::chemical::ResidueType::polar_hydrogens ( )

References atom_types_, and graph_.

void core::chemical::ResidueType::print_bondangles ( ) const

print intraresidue bond angles to standard out

References atom_type(), bondangle_atom_sets_, graph_, mm_atom_type(), core::chemical::MMAtomType::name(), core::chemical::AtomType::name(), ordered_atoms_, and core::chemical::tr().

void core::chemical::ResidueType::print_dihedrals ( ) const

References atom_type(), dihedral_atom_sets_, graph_, mm_atom_type(), core::chemical::MMAtomType::name(), core::chemical::AtomType::name(), ndihe(), ordered_atoms_, and core::chemical::tr().

void core::chemical::ResidueType::print_pretty_path_distances ( ) const

print chemical-bond path distances to standard out

References graph_, natoms(), ordered_atoms_, path_distance_, and core::chemical::tr().

ResidueProperties const & core::chemical::ResidueType::properties ( ) const

Access the collection of properties for this ResidueType.

References properties_.

Referenced by protocols::enzdes::SecondaryMatchProtocol::add_enz_cst_interaction_to_pose(), protocols::simple_moves::a3b_hbs::A3BHbsPatcher::apply(), protocols::simple_moves::hbs::HbsPatcher::apply(), protocols::protein_interface_design::movers::SaveAndRetrieveSidechains::apply(), protocols::toolbox::pose_manipulation::construct_poly_uniq_restype_pose(), protocols::toolbox::pose_manipulation::construct_poly_XXX_pose(), protocols::enzdes::EnzdesBaseProtocol::cst_minimize(), core::conformation::form_disulfide_helper(), protocols::simple_moves::chiral::get_chiral_residue_type(), core::chemical::ResidueTypeSet::get_residue_type_with_variant_added(), core::chemical::ResidueTypeSet::get_residue_type_with_variant_removed(), protocols::abinitio::abscript::RigidChunkCM::initialize(), protocols::environment::ProtectedConformation::match_variants(), core::chemical::ResidueTypeSelector::match_variants(), core::pose::MiniPose::MiniPose(), core::chemical::Selector_MATCH_VARIANTS::operator[](), core::chemical::Selector_NO_VARIANTS::operator[](), placeholder_clone(), protocols::stepwise::modeler::rna::remove_all_variant_types(), protocols::toolbox::match_enzdes_util::CovalentConnectionReplaceInfo::remove_covalent_connection_from_pose(), core::chemical::ResidueDatabaseIO::report_residue_type_properties(), core::chemical::ResidueDatabaseIO::report_residue_type_variant(), set_properties(), core::chemical::variants_match_with_exceptions(), and core::chemical::write_topology_file().

Size core::chemical::ResidueType::proton_chi_2_chi ( Size proton_chi_id ) const

inline

translate proton_chi to global chi

References proton_chis_.

Referenced by protocols::stepwise::modeler::polar_hydrogens::check_if_proton_chi_atom(), protocols::simple_moves::check_if_proton_chi_atom(), core::pack::rotamers::SingleResidueRotamerLibrary::compute_proton_chi_samplings(), core::pack::rotamers::SingleResidueRotamerLibrary::expand_proton_chis(), and core::chemical::ResidueDatabaseIO::report_residue_type_proton_chi().

utility::vector1< Real > const& core::chemical::ResidueType::proton_chi_extra_samples ( Size proton_chi ) const

inline

References proton_chi_extra_samples_.

Referenced by core::pack::rotamers::RotamericSingleResiduePeptoidLibrary< T, N >::chisamples_for_rotamer_and_chi(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::chisamples_for_rotamer_and_chi(), core::pack::rotamers::SingleResidueRotamerLibrary::compute_proton_chi_samplings(), protocols::match::upstream::FullChiSampleSet::expand_non_dunbrack_chi(), core::chemical::ResidueDatabaseIO::report_residue_type_proton_chi(), and core::chemical::write_topology_file().

utility::vector1< Real > const& core::chemical::ResidueType::proton_chi_samples ( Size proton_chi ) const

inline

References proton_chi_samples_.

Referenced by core::pack::rotamers::RotamericSingleResiduePeptoidLibrary< T, N >::chisamples_for_rotamer_and_chi(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::chisamples_for_rotamer_and_chi(), core::pack::rotamers::SingleResidueRotamerLibrary::compute_proton_chi_samplings(), protocols::match::upstream::FullChiSampleSet::expand_non_dunbrack_chi(), core::scoring::methods::IdealParametersDatabase::lookup_torsion_legacy(), core::chemical::ResidueDatabaseIO::report_residue_type_proton_chi(), and core::chemical::write_topology_file().

void core::chemical::ResidueType::redefine_chi	(	Size const	chino,
		std::string const &	atom_name1,
		std::string const &	atom_name2,
		std::string const &	atom_name3,
		std::string const &	atom_name4
	)

redefine a chi angle based on four atoms

This function is almost an exact copy of the add_chi function except that vector resizing does NOT occur. It is needed for certain PTMs that affect proton chis (e.g., phosphorylation and sulfation).

Author: Andy M. Chen (June 2009)

References atom_index(), chi_2_proton_chi_, chi_atoms_, finalized_, has(), is_proton_chi_, and ordered_atoms_.

Referenced by core::chemical::RedefineChi::apply().

void core::chemical::ResidueType::remap_pdb_atom_names ( bool rename )

inline

Turn on geometry-based atom renaming when loading this residue type from PDB files.

References remap_pdb_atom_names_.

Referenced by core::io::pose_from_sfr::PoseFromSFRBuilder::fill_name_map(), and core::chemical::rename_atoms().

bool core::chemical::ResidueType::remap_pdb_atom_names ( ) const

inline

Are we using geometry-based atom renaming when loading this residue type from PDB.

References remap_pdb_atom_names_.

void core::chemical::ResidueType::remove_variant_type ( VariantType const variant_type )

Remove a variant type to this ResidueType.

References finalized_, and properties_.

Referenced by core::chemical::DeleteVariantType::apply().

void core::chemical::ResidueType::remove_variant_type ( std::string const & variant_type )

Remove a variant type to this ResidueType by string.

References finalized_, and properties_.

void core::chemical::ResidueType::report_adducts ( )

References core::chemical::Adduct::adduct_name(), core::chemical::Adduct::atom_name(), defined_adducts_, name3(), and core::chemical::tr().

void core::chemical::ResidueType::require_final ( ) const

inline

an assertion function to ensure an ResidueType has been finalized

References finalized_.

bool core::chemical::ResidueType::requires_actcoord ( ) const

require actcoord?

References actcoord_atoms_, core::chemical::AROMATIC, core::chemical::POLAR, properties_, and core::chemical::PROTEIN.

Referenced by core::conformation::Residue::requires_actcoord().

void core::chemical::ResidueType::reset_base_type_cop ( )

Reset the base type COP to be null. This implies that this ResidueType is a base type.

References base_type_cop_.

void core::chemical::ResidueType::reset_bond_distance_to_atom	(	std::string const &	atm,
		core::Distance const	d
	)

Reset the bond distance to an atom whose internal coordinates have already been set.

Looks up the internal coordinates to build the given atom and then resets the bond distance, updating the xyz coordinates afterward.
One cannot currently reset the bond distance of residue connections using this method.

Parameters

<atm>	the string name of the atom
<d>	the new bond distance in angstroms

Note: This method is primarily useful for patch operations, which may need to change the hybridization of an atom and thus the bond length from the atom to which it is attached.

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

References atom_index(), core::chemical::AtomICoor::built_atom_vertex(), icoor(), core::chemical::AtomICoor::is_internal(), core::chemical::AtomICoor::phi(), set_icoor(), core::chemical::AtomICoor::stub_atom1(), core::chemical::AtomICoor::stub_atom2(), core::chemical::AtomICoor::stub_atom3(), core::chemical::AtomICoor::theta(), and core::chemical::ICoorAtomID::vertex().

Referenced by core::chemical::ResetBondLength::apply().

Size core::chemical::ResidueType::residue_connect_atom_index ( Size const resconn_id ) const

References residue_connections_, and vd_to_index_.

Referenced by branch_connect_atoms(), core::conformation::Residue::residue_connect_atom_index(), and core::chemical::ICoorAtomID::xyz().

ResidueConnection const & core::chemical::ResidueType::residue_connection ( Size const i ) const

Get a ResidueConection.

References residue_connections_.

Referenced by protocols::cyclic_peptide::PeptideStubMover::apply(), core::conformation::Residue::connect_atom(), core::conformation::Residue::connection_distance(), core::conformation::Residue::copy_residue_connections(), protocols::simple_moves::PeptideStapleMover::derive_staple_constraints_(), core::conformation::Conformation::detect_bonds(), core::conformation::Conformation::detect_pseudobonds(), core::conformation::disulfide_bonds(), core::scoring::methods::MMBondLengthEnergy::eval_atom_derivative(), core::scoring::methods::MMBondAngleEnergy::eval_atom_derivative(), core::scoring::methods::MMTorsionEnergy::eval_atom_derivative(), core::scoring::methods::MMTorsionEnergy::eval_intrares_derivatives(), 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::conformation::get_disulf_partner(), core::chemical::has_assigned_coords(), core::scoring::mm::MMBondAngleResidueTypeParam::init(), core::conformation::is_disulfide_bond(), core::conformation::Residue::residue_connection(), core::conformation::setup_corresponding_atoms(), and core::chemical::ICoorAtomID::xyz().

ResidueConnection & core::chemical::ResidueType::residue_connection ( Size const i )

Get a ResidueConection.

References residue_connections_.

Size core::chemical::ResidueType::residue_connection_id_for_atom ( Size const atomid ) const

inline

Convenience access function for the residue connection at a particular atom; requires that there is exactly one residue connection at this atom.

References atom_2_residue_connection_map_.

Referenced by protocols::cyclic_peptide::PeptideStubMover::apply(), core::pack::task::operation::NoRepackDisulfides::apply(), core::conformation::Residue::copy_residue_connections(), core::scoring::disulfides::FullatomDisulfideEnergy::defines_score_for_residue_pair(), core::conformation::Conformation::detect_disulfides(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::disulfides_changed(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::disulfides_changed(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::disulfides_changed(), core::pose::carbohydrates::find_seqpos_of_saccharides_parent_residue(), core::conformation::Conformation::fix_disulfides(), and core::conformation::Conformation::insert_residue_by_bond().

bool core::chemical::ResidueType::residue_connection_is_polymeric ( Size const resconn_id ) const

inline

References lower_connect_id_, and upper_connect_id_.

utility::vector1< Size > const& core::chemical::ResidueType::residue_connections_for_atom ( Size const atomid ) const

inline

References atom_2_residue_connection_map_.

Referenced by core::conformation::Residue::copy_residue_connections(), core::scoring::methods::MMBondLengthEnergy::eval_atom_derivative(), core::scoring::methods::MMBondAngleEnergy::eval_atom_derivative(), core::scoring::methods::MMTorsionEnergy::eval_atom_derivative(), core::scoring::methods::LK_PolarNonPolarEnergy::get_base_vector(), and core::scoring::methods::LK_hack::residue_pair_energy().

ResidueTypeSetCOP core::chemical::ResidueType::residue_type_set ( ) const

Return an owning pointer to the ResidueTypeSet that this ResidueType belongs to; it will return a null pointer if this ResidueType does not belong to any ResidueTypeSet.

References residue_type_set_.

Referenced by protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::add_aa_virt_rsd_as_root(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::add_aa_virt_rsd_as_root(), protocols::toolbox::sample_around::add_another_virtual_res(), protocols::toolbox::sample_around::add_virtual_res(), protocols::stepwise::monte_carlo::mover::AddMover::append_residue(), protocols::farna::setup::RNA_DeNovoPoseSetup::append_virtual_anchor(), protocols::comparative_modeling::ThreadingMover::apply(), core::pack::rotamer_set::build_fixed_O_water_rotamers_independent(), core::pack::rotamer_set::build_moving_O_water_rotamers_dependent(), core::pack::rotamer_set::build_moving_O_water_rotamers_independent(), core::conformation::change_cys_state(), core::scoring::motif::ResPairMotif::fill_pose_with_motif(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::find_disulfides(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::find_disulfides(), protocols::simple_moves::chiral::get_chiral_residue_type(), protocols::toolbox::AtomID_Mapper::initialize(), core::conformation::Conformation::is_residue_typeset(), protocols::enzdes::ResidueConformerFilter::parse_my_tag(), protocols::stepwise::monte_carlo::mover::AddMover::prepend_residue(), protocols::comparative_modeling::rebuild_loops_until_closed(), protocols::stepwise::monte_carlo::mover::DeleteMover::remove_singletons_and_update_pose_focus(), protocols::features::ResidueTypesFeatures::report_features(), core::conformation::Residue::residue_type_set(), protocols::constraints_additional::BindingSiteConstraint::setup_for_scoring(), protocols::constraints_additional::COMCoordinateConstraint::setup_for_scoring(), and core::io::serialization::write_binary().

void core::chemical::ResidueType::residue_type_set ( ResidueTypeSetCAP set_in )

set the residue type set of origin.

References residue_type_set_.

AtomIndices const& core::chemical::ResidueType::ring_atoms ( uint const ring_num ) const

inline

Return list of indices of the atoms within this residue's nth cycle, not counting virtual atoms.

References ring_atoms_indices_.

Referenced by core::scoring::methods::carbohydrates::SugarBackboneEnergy::eval_residue_dof_derivative(), core::conformation::Residue::ring_conformer(), core::pose::Pose::set_ring_conformation(), and core::conformation::Residue::show().

utility::vector1< AtomIndices > const& core::chemical::ResidueType::ring_atoms ( ) const

inline

Return list of indices of the atoms within this residue's cycles, not counting virtual atoms.

References ring_atoms_indices_.

core::chemical::rings::RingConformerSetCOP core::chemical::ResidueType::ring_conformer_set ( core::uint ring_num ) const

Return a pointer to the object containing the set of ring conformers possible for this residue's nth cycle.

References conformer_sets_.

Referenced by core::conformation::Residue::ring_conformer().

std::list<utility::vector1<ED> > const& core::chemical::ResidueType::rings ( )

inline

References rings_and_their_edges_.

core::chemical::rna::RNA_ResidueType const & core::chemical::ResidueType::RNA_type ( ) const

References rna_residue_type_.

Referenced by protocols::stepwise::modeler::packer::check_o2prime_contact(), core::scoring::rna::RNA_TorsionPotential::eval_atom_derivative(), core::scoring::rna::RNA_TorsionPotential::eval_intrares_energy(), core::scoring::methods::FreeDOF_Energy::get_hbond_energy(), core::pose::rna::is_rna_chainbreak(), and core::conformation::Residue::RNA_type().

VD core::chemical::ResidueType::root_atom ( ) const

inline

get root_atom used as the base of the icoor tree.

References root_atom_.

Referenced by core::conformation::get_root_atomno(), and core::chemical::pretty_print_atomicoor().

void core::chemical::ResidueType::rotamer_aa ( std::string const & type )

inline

AA to use for rotamer scoring.

References core::chemical::aa_from_name(), and rotamer_aa_.

void core::chemical::ResidueType::rotamer_library_specification ( rotamers::RotamerLibrarySpecificationOP rotlibspec )

References rotamer_library_specification_.

Referenced by core::chemical::NCAARotLibPath::apply(), core::pack::rotamers::StoredRotamerLibraryCreator::create(), core::pack::rotamers::SingleResiduePeptoidLibraryCreator::create(), core::pack::dunbrack::SingleResidueDunbrackLibraryCreator::create(), core::pack::rotamers::SingleLigandRotamerLibraryCreator::create(), core::pack::rotamers::SingleNCAARotamerLibraryCreator::create(), core::pack::dunbrack::cenrot::SingleResidueCenrotLibraryCreator::create(), core::pack::rotamers::SingleResidueRotamerLibraryFactory::get_cachetag(), core::chemical::ResidueDatabaseIO::read_residue_type(), core::chemical::ResidueDatabaseIO::report_residue_type(), and core::pack::rotamers::SingleResidueRotamerLibraryFactory::type_for_residuetype().

rotamers::RotamerLibrarySpecificationCOP core::chemical::ResidueType::rotamer_library_specification ( ) const

References rotamer_library_specification_.

void core::chemical::ResidueType::select_orient_atoms	(	Size &	center,
		Size &	nbr1,
		Size &	nbr2
	)		const

Selects three atoms for orienting this residue type.

References atom_base(), atom_index(), atom_is_backbone(), bonded_neighbor(), first_sidechain_atom(), force_nbr_atom_orient(), name(), natoms(), protocols::sic_dock::scores::nbr, nbr_atom(), nbrs(), and nheavyatoms().

Referenced by core::conformation::Residue::select_orient_atoms().

void core::chemical::ResidueType::set_adduct_flag ( bool adduct_in )

References core::chemical::ADDUCT, and properties_.

void core::chemical::ResidueType::set_atom_base	(	std::string const &	atom_name1,
		std::string const &	atom_name2
	)

sets atom_base[ atom1 ] = atom2

sets atom_base_[atom1] = atom2 resize atom_base_ vector as necessary

References atom_name_to_vd_, has(), name(), and core::chemical::tr().

Referenced by core::chemical::AddConnectAndTrackingVirt::apply(), and set_icoor_private().

void core::chemical::ResidueType::set_atom_base	(	VD const &	atom1,
		VD const &	atom2
	)

sets atom_base[ atom1 ] = atom2, vertex descriptor version

sets atom_base_[atom1] = atom2 resize atom_base_ vector as necessary

References atom_base_, atom_name(), cut_bond_neighbor_, finalized_, graph_, has(), and core::chemical::tr().

void core::chemical::ResidueType::set_atom_type	(	std::string const &	atom_name,
		std::string const &	atom_type_name
	)

inline

set atom type

References atom_name_to_vd_.

Referenced by add_atom(), core::chemical::SetAtomType::apply(), core::chemical::SetAllAtomsRepulsive::apply(), core::chemical::ConnectSulfurAndMakeVirtualProton::apply(), core::chemical::rosetta_retype_fullatom(), and core::chemical::sdf::MolFileIOMolecule::set_from_extra_data().

void core::chemical::ResidueType::set_atom_type	(	VD	atom,
		std::string const &	atom_type_name
	)

set atom type

Set atom type, correctly updating internal state.

Note: This method also sets/updates the atom's element and the residue's mass.

void core::chemical::ResidueType::set_backbone_heavyatom ( std::string const & name )

set an atom as backbone heavy atom

backbone stuff is a little tricky if we want to allow newly added atoms, eg in patching, to be backbone atoms. We move any exsiting backbone heavy atoms back into force_bb_ list and add the new one. Afterwards, the new backbone heavy atom list will be generated in finalize() using info from force_bb_.

References atom_name_to_vd_, finalized_, force_bb_, and has().

Referenced by core::chemical::SetBackboneHeavyatom::apply().

void core::chemical::ResidueType::set_base_type_cop ( ResidueTypeCOP new_base_type )

Set the base type COP. This implies that this ResidueType is NOT a base type.

References base_type_cop_.

void core::chemical::ResidueType::set_disulfide_atom_name ( std::string n )

inline

Sets disulfide atom name.

Author: Andrew M. Watkins (amw57.nosp@m.9@ny.nosp@m.u.edu).

References disulfide_atom_name_.

void core::chemical::ResidueType::set_gasteiger_atom_type	(	std::string const &	atom_name,
		std::string const &	gasteiger_atom_type_name
	)

set gasteiger atom type

References atom_name_to_vd_.

void core::chemical::ResidueType::set_gasteiger_atom_type	(	VD	atom,
		std::string const &	gasteiger_atom_type_name
	)

set gasteiger atom type

References core::pose::motif::a(), atom(), core::chemical::Atom::gasteiger_atom_type(), gasteiger_atom_types_, and graph_.

void core::chemical::ResidueType::set_gasteiger_typeset ( gasteiger::GasteigerAtomTypeSetCOP gasteiger_atom_types )

Manually set the gasteiger typeset - will use the default set otherwise.

References gasteiger_atom_types_.

Referenced by core::chemical::gasteiger::assign_gasteiger_atom_types().

void core::chemical::ResidueType::set_icoor	(	std::string const &	atm,
		Real const	phi,
		Real const	theta,
		Real const	d,
		std::string const &	stub_atom1,
		std::string const &	stub_atom2,
		std::string const &	stub_atom3,
		bool const	update_xyz = `false`
	)

set AtomICoor for an atom

phi and theta are in radians

set AtomICoor for an atom

will update the xyz coords as well if desired, useful inside a patching operation where new atoms are being added.

References set_icoor_private().

void core::chemical::ResidueType::set_icoor	(	VD const &	atm,
		Real const	phi,
		Real const	theta,
		Real const	d,
		VD const &	stub_atom1,
		VD const &	stub_atom2,
		VD const &	stub_atom3,
		bool const	update_xyz = `false`
	)

set AtomICoor for an atom, vertex descriptor version

phi and theta are in radians

References graph_, has(), core::chemical::ICoorAtomID::INTERNAL, name(), and set_icoor_private().

void core::chemical::ResidueType::set_icoor	(	std::string const &	atm,
		Real const	phi,
		Real const	theta,
		Real const	d,
		ICoorAtomID const &	stub_atom1,
		ICoorAtomID const &	stub_atom2,
		ICoorAtomID const &	stub_atom3,
		bool const	update_xyz = `false`
	)

set AtomICoor for an atom

phi and theta are in radians

References set_icoor_private().

void core::chemical::ResidueType::set_icoor_private	(	std::string const &	atm,
		ICoorAtomID const &	id,
		AtomICoor const &	ic,
		bool	update_xyz
	)

private

void core::chemical::ResidueType::set_ideal_xyz	(	std::string const &	atm,
		Vector const &	xyz_in
	)

References atom_index().

Referenced by core::chemical::fill_ideal_xyz_from_icoor(), and set_icoor_private().

void core::chemical::ResidueType::set_ideal_xyz	(	Size	index,
		Vector const &	xyz_in
	)

References core::pose::motif::a(), graph_, core::chemical::Atom::ideal_xyz(), and ordered_atoms_.

void core::chemical::ResidueType::set_ideal_xyz	(	VD	atm,
		Vector const &	xyz_in
	)

References core::pose::motif::a(), graph_, has(), and core::chemical::Atom::ideal_xyz().

void core::chemical::ResidueType::set_low_energy_ring_conformers	(	core::uint const	ring_num,
		utility::vector1< std::string > const &	conformers
	)

Set this cyclic residue's low-energy ring conformers for the nth ring by IUPAC name.

References finalized_, and low_ring_conformers_.

void core::chemical::ResidueType::set_lower_connect_atom ( std::string const & atm_name )

set the atom which connects to the lower connection

References atom_index(), finalized_, lower_connect_id_, n_polymeric_residue_connections_, ordered_atoms_, residue_connections_, core::chemical::tr(), update_residue_connection_mapping(), and upper_connect_id_.

Referenced by core::chemical::SetPolymerConnectAtom::apply(), and core::chemical::ResidueDatabaseIO::read_residue_type().

void core::chemical::ResidueType::set_lowest_energy_ring_conformer	(	core::uint const	ring_num,
		std::string const &	conformer
	)

Set this cyclic residue's lowest-energy ring conformer for the nth ring by IUPAC name.

References finalized_, and lowest_ring_conformer_.

void core::chemical::ResidueType::set_mainchain_atoms ( AtomIndices const & mainchain )

set indices of all mainchain atoms

References mainchain_atoms_, and ordered_atoms_.

Referenced by core::chemical::PrependMainchainAtom::apply(), core::chemical::AppendMainchainAtom::apply(), and core::chemical::ReplaceMainchainAtom::apply().

void core::chemical::ResidueType::set_mm_atom_type	(	std::string const &	atom_name,
		std::string const &	mm_atom_type_name
	)

set mm atom type

References core::pose::motif::a(), atom_name(), atom_name_to_vd_, graph_, core::chemical::Atom::mm_atom_type_index(), mm_atom_types_, and core::chemical::Atom::mm_name().

Referenced by core::chemical::SetMMAtomType::apply(), and core::chemical::ConnectSulfurAndMakeVirtualProton::apply().

void core::chemical::ResidueType::set_orbital_icoor_id	(	std::string const &	orbital,
		Real const	phi,
		Real const	theta,
		Real const	d,
		std::string const &	stub_atom1,
		std::string const &	stub_atom2,
		std::string const &	stub_atom3
	)

set OrbitalICoor for an orbital

References atom_index(), orbital_index(), orbitals_, and ordered_atoms_.

void core::chemical::ResidueType::set_properties ( ResiduePropertiesOP properties )

Set the collection of properties for this ResidueType.

References properties(), and properties_.

void core::chemical::ResidueType::set_proton_chi	(	Size	chino,
		utility::vector1< Real > const &	dihedral_samples,
		utility::vector1< Real > const &	extra_samples
	)

Annotate a given chi as a proton chi, and set the sampling behavior If the chi is already listed as a proton chi, change the sampling behavior.

Describe proton behavior for residue type; where should rotamer samples be considered, and if expanded rotamers are desired, what deviations from the original rotamer samples should be included. E.g. dihedral_samples of 60, -60, and 180 could have an extra_sample of 20 which would produce rotamers at 40 60 & 80, -40 -60 & -80, and -160, 180 & 160. Extra_samples at 10 and 20 would produce 15 different rotamer samples.

References chi_2_proton_chi_, is_proton_chi_, nchi(), proton_chi_extra_samples_, proton_chi_samples_, and proton_chis_.

Referenced by core::chemical::AddProtonChi::apply(), core::chemical::ReplaceProtonWithHydroxyl::apply(), and autodetermine_chi_bonds().

void core::chemical::ResidueType::set_shadowing_atom	(	std::string const &	atom,
		std::string const &	atom_being_shadowed
	)

References atom_index(), atom_shadowed_, and ordered_atoms_.

void core::chemical::ResidueType::set_upper_connect_atom ( std::string const & atm_name )

set the atom which connects to the upper connection

References atom_index(), finalized_, lower_connect_id_, n_polymeric_residue_connections_, ordered_atoms_, residue_connections_, core::chemical::tr(), update_residue_connection_mapping(), and upper_connect_id_.

Referenced by core::chemical::SetPolymerConnectAtom::apply(), and core::chemical::ResidueDatabaseIO::read_residue_type().

void core::chemical::ResidueType::setup_atom_ordering ( )

private

set up atom ordering map old2new, called by finalize()

Because some new heavy atoms are added and removed by patching we need to reorder the atoms. The atoms are reordered with the backbone atoms coming first, sidechain atoms second, and finaly hydrogens last.

The graph is iterated over, where bb atoms are defined by the force_bb_ map. If a hydrogen is encountered, it is pushed into the hydrogen vector. If the backbone is not found in the force_bb_ map, then the atom is a side chain atom, if not a hydrogen.

During this process, the attached_H_end and attached_H_begin vectors are filled out.

In order to keep the bb hydrogen atoms first in the hydrogen vector, only the heavy sidechain atoms are assigned to the sidechain vector while bb hydorgens atoms are pushed into the hydrogen vectors.

After the bb and sidechain vectors are assigned, the sidechains are iterated over and their hydrogens are pushed into the hydrogen vector.

Finally, the ordered_atoms_ vector is filled out with the bb atoms, sidechain, and hydrogen atoms.

Derived data set in this method: ordered_atoms_ - (Reset from graph.) n_backbone_heavyatoms_ nheavyatoms_ attached_H_begin_ attached_H_end_

References attached_H_begin_, attached_H_end_, force_bb_, graph_, hydrogens(), n_backbone_heavyatoms_, nheavyatoms_, and ordered_atoms_.

Referenced by finalize().

void core::chemical::ResidueType::show	(	std::ostream &	output = `std::cout`,
		bool	output_atomic_details = `false`
	)		const

Generate string representation of ResidueType for debugging purposes.

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

References all_bb_atoms_, all_sc_atoms_, atom(), atom_name(), base_name_, branch_connect_atom_names(), core::chemical::CARBOHYDRATE, carbohydrate_info_, is_branch_point(), is_cyclic(), mainchain_atoms_indices_, n_rings(), name1_, name3_, name_, natoms(), properties_, ring_atoms_indices_, and core::chemical::Atom::show().

Referenced by core::chemical::operator<<(), and core::conformation::Residue::show().

void core::chemical::ResidueType::show_all_atom_names ( std::ostream & out ) const

References core::pose::motif::a(), graph_, and core::chemical::Atom::name().

Referenced by atom_index(), and atom_vertex().

core::Size core::chemical::ResidueType::smallest_ring_size	(	VD const &	atom,
		core::Size const &	max_size = `999999`
	)		const

A graph-based function to determine the size of the smallest ring that involves a given atom.

References graph_.

Referenced by core::chemical::rosetta_retype_fullatom().

void core::chemical::ResidueType::update_actcoord ( conformation::Residue & rot ) const

update actcoord

average geometrical center of the set of actcoord_atoms_

References core::conformation::Residue::actcoord(), actcoord_atoms_, core::conformation::Residue::atoms(), and vd_to_index_.

Referenced by core::conformation::Residue::update_actcoord().

void core::chemical::ResidueType::update_derived_data ( )

private

update derived data in ResidueType, called by finalize()

update derived data in ResidueType, called by finalize() after primary data have been reordered, update derived data accordingly.

Derived data updated by this method: first_sidechain_hydrogen_ accpt_pos_ accpt_pos_sc_ Haro_index_ Hpol_index_ atoms_with_orb_index_ Hpos_polar_ Hpos_apolar_ Hpos_polar_sc_ all_bb_atoms_ all_sc_atoms_ abase2_ path_distance_ dihedral_atom_sets_ dihedrals_for_atom_ bondangle_atom_sets_ bondangles_for_atom_ atoms_within_one_bond_of_a_residue_connection_ within1bonds_sets_for_atom_ atoms_within_two_bonds_of_a_residue_connection_ within2bonds_sets_for_atom_ last_controlling_chi_ atoms_last_controlled_by_chi_

Atom.heavyatom_has_polar_hydrogens_ - for all atoms. Some AtomProperties: AROMATIC_CARBON_WITH_FREE_VALENCE

rna_residue_type_ – Will be reset based on other ResidueType data carbohydrate_info_ – Will be reset based on other ResidueType data

References abase2_, abase2_indices_, accpt_pos_, accpt_pos_sc_, all_bb_atoms_, all_sc_atoms_, core::chemical::AROMATIC_CARBON_WITH_FREE_VALENCE, atom(), atom_base(), atoms_last_controlled_by_chi_, atoms_with_orb_index_, atoms_within_one_bond_of_a_residue_connection_, atoms_within_two_bonds_of_a_residue_connection_, attached_H_begin_, attached_H_end_, bondangle_atom_sets_, bondangles_for_atom_, bonded_neighbor(), core::chemical::CARBOHYDRATE, carbohydrate_info_, conformer_sets_, core::chemical::CYCLIC, dihedral_atom_sets_, dihedrals_for_atom_, first_sidechain_hydrogen_, core::chemical::get_residue_path_distances(), get_self_weak_ptr(), graph_, Haro_index_, core::chemical::Atom::has_orbitals(), Hpol_index_, Hpos_apolar_, Hpos_polar_, Hpos_polar_sc_, improper_dihedral_atom_sets_, improper_dihedrals_for_atom_, core::chemical::Atom::is_acceptor(), core::chemical::Atom::is_haro(), core::chemical::Atom::is_hydrogen(), core::chemical::Atom::is_polar_hydrogen(), core::chemical::Atom::is_virtual(), last_controlling_chi_, low_ring_conformers_, lowest_ring_conformer_, n_backbone_heavyatoms_, n_rings(), natoms(), nheavyatoms_, ordered_atoms_, path_distance_, path_distances(), properties_, residue_connections_, ring_atoms_, core::chemical::RNA, rna_residue_type_, core::chemical::Atom::set_property(), update_last_controlling_chi(), vd_to_index_, within1bonds_sets_for_atom_, and within2bonds_sets_for_atom_.

Referenced by finalize().

void core::chemical::ResidueType::update_last_controlling_chi ( )

private

compute the last controlling chi for an atom during the update_derived_data() stage. The last controlling chi is the furthest chi downstream of the mainchain which can change the location of an atom.

References atom_base(), atoms_last_controlled_by_chi_, bonded_neighbor(), chi_atoms(), last_controlling_chi_, natoms(), nchi(), and note_chi_controls_atom().

Referenced by update_derived_data().

void core::chemical::ResidueType::update_residue_connection_mapping ( )

private

References atom_2_residue_connection_map_, natoms(), residue_connections_, and vd_to_index_.

Referenced by add_residue_connection(), generate_atom_indices(), set_lower_connect_atom(), and set_upper_connect_atom().

ResidueConnection const & core::chemical::ResidueType::upper_connect ( ) const

References core::chemical::POLYMER, properties_, residue_connections_, and upper_connect_id_.

Referenced by core::scoring::methods::CartesianBondedEnergy::eval_intraresidue_dof_derivative(), core::chemical::has_assigned_coords(), core::conformation::Conformation::insert_ideal_geometry_at_polymer_bond(), core::conformation::Residue::upper_connect(), core::chemical::write_topology_file(), and core::chemical::ICoorAtomID::xyz().

Size core::chemical::ResidueType::upper_connect_atom ( ) const

index number of the atom which connects to the upper connection

References core::chemical::POLYMER, properties_, residue_connections_, upper_connect_id_, and vd_to_index_.

Referenced by protocols::denovo_design::components::StructureData::are_connectable(), core::chemical::ICoorAtomID::atom_id(), core::chemical::ResidueDatabaseIO::report_residue_type(), and core::conformation::Residue::upper_connect_atom().

Size core::chemical::ResidueType::upper_connect_id ( ) const

inline

References upper_connect_id_.

Referenced by core::conformation::Conformation::append_residue_by_bond(), protocols::cyclic_peptide::DeclareBond::apply(), protocols::cyclic_peptide::PeptideStubMover::apply(), core::scoring::bin_transitions::BinTransitionCalculator::are_normally_bonded(), core::conformation::Conformation::backbone_torsion_angle_atoms(), core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), core::io::silent::BinarySilentStruct::fill_struct(), core::conformation::Residue::has_upper_connect(), core::conformation::Residue::is_polymer_bonded(), and core::chemical::ICoorAtomID::xyz().

utility::vector1< VariantType > core::chemical::ResidueType::variant_type_enums ( ) const

Get a vector of VariantType enums for this ResidueType.

This ONLY includes standard, enum-based variants, not on-the-fly custom variants.

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

References properties_.

utility::vector1< std::string > core::chemical::ResidueType::variant_types ( ) const

get all the variant types for this ResidueType

This will include both on-the-fly custom variants defined by string AND string equivalents of standard, enumerated variants. – rhiju (merging roccomoretti/restypeset_fiddle)

References properties_.

Referenced by protocols::loops::apply_sequence_mapping(), core::pose::rna::mutate_position(), and core::pack::task::ResidueLevelTask_::ResidueLevelTask_().

utility::vector1< std::pair< Size, Size > > const& core::chemical::ResidueType::within1bonds_sets_for_atom ( Size atomid ) const

inline

Returns a list of pairs for atom# atomid where first == the residue_connection id that lists atomid as being within one bond of a residue connection, and second == the index of the entry containing this atom in the atoms_within_one_bond_of_a_residue_connection_[ first ] array. Useful for calculating the derivatives for an atom.

References within1bonds_sets_for_atom_.

Referenced by core::scoring::methods::MMBondAngleEnergy::eval_atom_derivative(), and core::scoring::methods::MMTorsionEnergy::eval_atom_derivative().

utility::vector1< std::pair< Size, Size > > core::chemical::ResidueType::within2bonds_sets_for_atom ( Size atomid ) const

inline

Returns a list of pairs for atom # atomid where first == the residue_connection id that lists this atom as being within two bonds of a residue connection, and second == the index of the entry containing this atom in the atoms_within_two_bonds_of_a_residue_connection_[ first ] array. Useful for calculating the derivatives for an atom.

References within2bonds_sets_for_atom_.

Referenced by core::scoring::methods::MMTorsionEnergy::eval_atom_derivative().

Member Data Documentation

AA core::chemical::ResidueType::aa_

private

standard rosetta aa-type for knowledge-based potentials, may be aa_unk – Primary

Referenced by aa(), backbone_aa(), and operator=().

std::map<VD, VD> core::chemical::ResidueType::abase2_

private

The base of the atom base – Derived.

Referenced by operator=(), and update_derived_data().

utility::vector1<Size> core::chemical::ResidueType::abase2_indices_

private

Index version of abase2_ – Derived.

Referenced by abase2(), operator=(), and update_derived_data().

AtomIndices core::chemical::ResidueType::accpt_pos_

private

indices of Hbond acceptor positions – Derived

Referenced by accpt_pos(), operator=(), and update_derived_data().

AtomIndices core::chemical::ResidueType::accpt_pos_sc_

private

indices of Hbond acceptor positions that are part of the sidechain – Derived must be a subset of the atoms listed in the accpt_pos_ array

Referenced by accpt_pos_sc(), operator=(), and update_derived_data().

utility::vector1< VD > core::chemical::ResidueType::actcoord_atoms_

private

indices of action coordinate centers – Primary

the geometric center of the atoms listed defined the residue's "action coordinate"

Referenced by add_actcoord_atom(), delete_act_coord_atom(), generate_atom_indices(), operator=(), requires_actcoord(), and update_actcoord().

AtomIndices core::chemical::ResidueType::actcoord_atoms_indices_

private

Index version of actcoord_atoms_ – Derived.

Referenced by actcoord_atoms(), delete_act_coord_atom(), generate_atom_indices(), and operator=().

AtomIndices core::chemical::ResidueType::all_bb_atoms_

private

Indices of all backbone atoms, hydrogens and heavyatoms – Derived.

Referenced by all_bb_atoms(), operator=(), show(), and update_derived_data().

AtomIndices core::chemical::ResidueType::all_sc_atoms_

private

Indices of all sidechain atoms, hydrogens and heavyatoms – Derived.

Referenced by all_sc_atoms(), operator=(), show(), and update_derived_data().

utility::vector1< utility::vector1< Size > > core::chemical::ResidueType::atom_2_residue_connection_map_

private

Mapping of atom indicies to residue connections – Derived.

Referenced by add_atom(), atom_forms_residue_connection(), generate_atom_indices(), n_residue_connections_for_atom(), operator=(), residue_connection_id_for_atom(), residue_connections_for_atom(), and update_residue_connection_mapping().

std::map< std::string, std::string > core::chemical::ResidueType::atom_aliases_

private

A mapping of alias atom names to canonical atom names – Primary Will be added to atom_name_to_vd_ during finalization.

Referenced by add_atom_alias(), delete_atom_alias(), generate_atom_indices(), and operator=().

std::map<VD, VD> core::chemical::ResidueType::atom_base_

private

The atom "one up" in the atom tree. – Derived, valid during Mutable. Updated in set_icoor. (also set_atom_base - TODO: Fix redundancy issue.

Referenced by add_atom(), atom_base(), generate_atom_indices(), operator=(), set_atom_base(), and set_icoor_private().

utility::vector1<Size> core::chemical::ResidueType::atom_base_indices_

private

Index version of atom_base_ – Derived.

Referenced by atom_base(), generate_atom_indices(), and operator=().

std::map< std::string, VD > core::chemical::ResidueType::atom_name_to_vd_

private

atom index lookup by atom name string – Derived, valid during Mutable, with caveats

Note that during the Mutable stage not all atoms will necessarily have names or unique names. This map will merely map those which do,

Referenced by add_atom(), add_bond(), add_cut_bond(), add_orbital_bond(), atom(), atom_index(), atom_vertex(), change_bond_type(), delete_act_coord_atom(), generate_atom_indices(), has(), operator=(), set_atom_base(), set_atom_type(), set_backbone_heavyatom(), set_gasteiger_atom_type(), and set_mm_atom_type().

std::map<VD, VD> core::chemical::ResidueType::atom_shadowed_

private

Data to describe virtual atoms that should shadow other atoms for the sake of keeping intraresidue cycles closed when working with an atom tree, e.g. NV shadows N on proline. For each atom, the following vector lists the index of the atom it is shadowing. – Primary.

Referenced by generate_atom_indices(), has_shadow_atoms(), operator=(), and set_shadowing_atom().

utility::vector1< Size > core::chemical::ResidueType::atom_shadowed_indices_

private

Index version of atom_shadowed_ – Derived.

Referenced by atom_being_shadowed(), generate_atom_indices(), and operator=().

AtomTypeSetCOP core::chemical::ResidueType::atom_types_

private

The type set for Rosetta Atom types. – Primary used to define the set of allowed atomtypes for this residue and their properties Needs to be non-null by the time finalize() is called.

ResidueType Data Organization

These notes apply to ResidueType and associated subsidiary types. (Atom, Bond, AtomICoor, ICoorAtomID ...)

Data stored here is in one of two classes. Primary and Derived:

Primary data cannot be deduced from any of the other data in the ResidueType
Derived data can be deduced from Primary data, and is stored separately mainly for access efficiency reasons.

A ResidueType also has three stages of its existence:

Mutable - In this stage only the Primary data and selected Derived data are valid. All other Derived data may be in an inconsistent state with itself or the Primary data. If you're creating or modifying residue types, you'll be in this stage.
Finalized - In this stage the all Derived data is self consistent with primary data. To go from Building to Finalized, call the finalize() method. You can go back to the Building stage by calling a function which modifies the ResidueType.
Fixed - A conceptual stage at this point. The ResidueType is completely finished. Only Fixed ResidueTypes should be placed into ResidueTypeSets and be used to construct Residues. Do not call any modification methods on Fixed ResidueTypes. There may be programmatic enforcement of this in the future.

Documentation requirements:

Data: All data stored in ResidueType should be annotated with it's Primary/Derived state. For derived data, it should also annotate whether it's valid during the Mutable stage. (If not mentioned it's valid during mutability, it should be assumed it's not.)

Methods: Methods which return/use derived data should note whether it's valid during the Mutable stage. Non-const methods should mention if they're meant to be called during the Mutable stage. (Such methods can be called from the Finalized stage, but will turn the ResidueType into a mutable one.

N.B. For typical ResidueType usage pretty much all of the levels/category distinctions can be ignored. For a constant, finalized ResidueType such as one gets as a COP from a ResidueTypeSet or a Residue, all data and methods which are allowed are valid.

Referenced by acceptor_atoms(), apolar_hydrogens(), aromatic_atoms(), atom_type(), atom_type_set(), atom_type_set_ptr(), heavy_atom_with_hydrogens(), heavy_atom_with_polar_hydrogens(), heavy_atoms(), hydrogens(), operator=(), polar_hydrogens(), and set_atom_type().

utility::vector1< AtomIndices > core::chemical::ResidueType::atoms_last_controlled_by_chi_

private

for chi i, the list of atoms last controlled by i – Derived E.g. chi2 on LEU list cd1, 1hd1, 1hd2, 1hd3, cd2, 2hd1, 2hd2, 2hd3, and hg1

Referenced by atoms_last_controlled_by_chi(), operator=(), update_derived_data(), and update_last_controlling_chi().

AtomIndices core::chemical::ResidueType::atoms_with_orb_index_

private

indices of atoms with orbitals – Derived

Referenced by atoms_with_orb_index(), operator=(), and update_derived_data().

utility::vector1< utility::vector1< two_atom_set > > core::chemical::ResidueType::atoms_within_one_bond_of_a_residue_connection_

private

For calculating inter-residue bond angle and bond torsion energies, it is useful to have a list of those atoms within one bond of a residue connection atom. For residue connection i, its position in this array is a list of pairs of atom-id's, the first of which is always the id for the atom forming residue connection i. – Derived.

Referenced by atoms_within_one_bond_of_a_residue_connection(), operator=(), and update_derived_data().

utility::vector1< utility::vector1< three_atom_set > > core::chemical::ResidueType::atoms_within_two_bonds_of_a_residue_connection_

private

For calculating inter-residue bond torsion energies, it is useful to have a list of those atoms within two bonds of a residue connection atom. For residue connection i, its position in this array is a list of triples of atom-id's, the first of which is always the id for the atom forming residue connection i. – Derived.

Referenced by atoms_within_two_bonds_of_a_residue_connection(), operator=(), and update_derived_data().

utility::vector1< Size > core::chemical::ResidueType::attached_H_begin_

private

indices of each heavyatom's first attached hydrogen – Derived.

Referenced by attached_H_begin(), number_bonded_hydrogens(), operator=(), setup_atom_ordering(), and update_derived_data().

utility::vector1< Size > core::chemical::ResidueType::attached_H_end_

private

indices of each heavyatom's last attached hydrogen – Derived.

Referenced by attached_H_end(), number_bonded_hydrogens(), operator=(), setup_atom_ordering(), and update_derived_data().

AA core::chemical::ResidueType::backbone_aa_

private

Referenced by backbone_aa(), operator=(), and perform_checks().

std::string core::chemical::ResidueType::base_name_

private

Residue id for the base type (i.e. sans variants).

Does not accumulate VariantType names (e.g. "ALA").

Referenced by base_name(), operator=(), and show().

ResidueTypeCOP core::chemical::ResidueType::base_type_cop_

private

Const-access owning pointer to the base residue type.

NULL if this ResidueType is a base type. If this ResidueType is cloned or copied from a base type, this will point to the base type. If this ResidueType is cloned or copied from a non-base type, this will point to the non-base type's base type. The test for whether something is a base type is whether this owning pointer is NULL.

Note: The base type must not hold an owning pointer to itself!

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

Referenced by get_base_type_cop(), is_base_type(), operator=(), reset_base_type_cop(), and set_base_type_cop().

utility::vector1< bondangle_atom_set > core::chemical::ResidueType::bondangle_atom_sets_

private

vector of sets of atoms that make up bond angles in the residue – Derived

Referenced by bondangle(), num_bondangles(), operator=(), print_bondangles(), and update_derived_data().

utility::vector1< utility::vector1< Size > > core::chemical::ResidueType::bondangles_for_atom_

private

??? – Derived

Referenced by bondangles_for_atom(), operator=(), and update_derived_data().

utility::vector1< AtomIndices > core::chemical::ResidueType::bonded_neighbor_

private

indices of the atoms psuedo bonded atoms. Used in orbital code – Derived

Referenced by add_atom(), add_bond(), bonded_neighbor(), generate_atom_indices(), and operator=().

utility::vector1<utility::vector1<BondName> > core::chemical::ResidueType::bonded_neighbor_type_

private

??? – Derived

Referenced by add_atom(), add_bond(), bonded_neighbor_types(), change_bond_type(), generate_atom_indices(), and operator=().

core::chemical::carbohydrates::CarbohydrateInfoOP core::chemical::ResidueType::carbohydrate_info_

private

A container for residue properties unique to carbohydrates. – Derived, can be null.

Referenced by carbohydrate_info(), operator=(), show(), and update_derived_data().

utility::vector1< Size > core::chemical::ResidueType::chi_2_proton_chi_

private

A "map" of chi indices to proteon_chi indices – Derived, valid during Mutable.

Referenced by add_chi(), autodetermine_chi_bonds(), chi_2_proton_chi(), delete_terminal_chi(), operator=(), redefine_chi(), and set_proton_chi().

utility::vector1<utility::vector1<VD> > core::chemical::ResidueType::chi_atoms_

private

the four atoms to build each chi angle – Primary.

Referenced by add_chi(), autodetermine_chi_bonds(), chi_atom_vds(), delete_terminal_chi(), generate_atom_indices(), nchi(), operator=(), and redefine_chi().

utility::vector1< AtomIndices > core::chemical::ResidueType::chi_atoms_indices_

private

Index version of chi_atoms_ – Derived.

Referenced by chi_atoms(), generate_atom_indices(), and operator=().

utility::vector1< utility::vector1< std::pair< Real, Real > > > core::chemical::ResidueType::chi_rotamers_

private

Additional non-Dunbrack rotamer bins – Primary.

pair<Real,Real> ==> mean,sdev for each chi angle i and rotamer j: chi_rotamers_[i][j]

Referenced by add_chi(), add_chi_rotamer(), autodetermine_chi_bonds(), chi_rotamers(), clear_chi_rotamers(), delete_terminal_chi(), and operator=().

utility::vector1< rings::RingConformerSetOP > core::chemical::ResidueType::conformer_sets_

private

The sets of all possible ring conformers, one per ring – Derived, can be null.

Referenced by operator=(), ring_conformer_set(), and update_derived_data().

std::map<VD, utility::vector1<VD> > core::chemical::ResidueType::cut_bond_neighbor_

private

??? – Derived

Referenced by add_cut_bond(), generate_atom_indices(), operator=(), and set_atom_base().

utility::vector1< AtomIndices > core::chemical::ResidueType::cut_bond_neighbor_indices_

private

Index version of cut_bond_neighbor_ – Primary - will be converted to derived (from Bond.cut_bond())

Referenced by cut_bond_neighbor(), generate_atom_indices(), and operator=().

utility::vector1< Adduct > core::chemical::ResidueType::defined_adducts_

private

Adducts defined for this residue – Primary.

Referenced by add_adduct(), defined_adducts(), operator=(), and report_adducts().

utility::vector1< dihedral_atom_set > core::chemical::ResidueType::dihedral_atom_sets_

private

Data for the mm potentials. – Derived List all of the intra-residue dihedral angles and bond angles. vector of sets of atoms that make up dihedral angles in the residue Data for the mm potentials.

Referenced by dihedral(), ndihe(), operator=(), print_dihedrals(), and update_derived_data().

utility::vector1< utility::vector1< Size > > core::chemical::ResidueType::dihedrals_for_atom_

private

all intra-residue dihedral angles that each atom "participates" in – Derived

Referenced by dihedrals_for_atom(), operator=(), and update_derived_data().

std::string core::chemical::ResidueType::disulfide_atom_name_

private

Name of the disulfide-forming atom, if any.

Referenced by get_disulfide_atom_name(), operator=(), and set_disulfide_atom_name().

ElementSetCOP core::chemical::ResidueType::elements_

private

The set for element objects. – Primary, can be null.

Referenced by element_set(), element_set_ptr(), operator=(), and set_atom_type().

bool core::chemical::ResidueType::finalized_

private

Size core::chemical::ResidueType::first_sidechain_hydrogen_

private

the index of first sidechain hydrogen atom – Derived.

Referenced by atom_is_backbone(), first_sidechain_hydrogen(), operator=(), and update_derived_data().

utility::vector1<VD> core::chemical::ResidueType::force_bb_

private

atom indices forced to be considered backbone – Primary

Referenced by operator=(), set_backbone_heavyatom(), and setup_atom_ordering().

bool core::chemical::ResidueType::force_nbr_atom_orient_

private

Controls which atoms are selected by "select_orient_atoms", used to overlay residues during packing. – Primary

Referenced by force_nbr_atom_orient(), and operator=().

gasteiger::GasteigerAtomTypeSetCOP core::chemical::ResidueType::gasteiger_atom_types_

private

The set for GasteigerAtomTypes. – Primary, can be null.

Referenced by gasteiger_atom_typeset(), operator=(), set_gasteiger_atom_type(), and set_gasteiger_typeset().

ResidueGraph core::chemical::ResidueType::graph_

private

The Atoms and Bonds of the ResidueType, stored as Nodes and Edges. – Primary.

Referenced by acceptor_atoms(), add_atom(), add_bond(), add_cut_bond(), add_orbital_bond(), apolar_hydrogens(), aromatic_atoms(), assign_internal_coordinates(), assign_neighbor_atom(), atom(), atom_index(), atom_is_polar_hydrogen(), atom_iterators(), atom_name(), atom_type(), bond(), bond_iterators(), bonded_neighbor_iterators(), bonded_orbitals(), change_bond_type(), clear_orbitals(), delete_atom(), dump_vd_info(), fill_ideal_xyz_from_icoor(), gasteiger_atom_type(), generate_atom_indices(), graph(), has(), heavy_atom_with_hydrogens(), heavy_atom_with_polar_hydrogens(), heavy_atoms(), heavyatom_has_polar_hydrogens(), heavyatom_is_an_acceptor(), hydrogens(), mm_atom_type(), natoms(), nbonds(), operator=(), polar_hydrogens(), print_bondangles(), print_dihedrals(), print_pretty_path_distances(), set_atom_base(), set_atom_type(), set_gasteiger_atom_type(), set_icoor(), set_ideal_xyz(), set_mm_atom_type(), setup_atom_ordering(), show_all_atom_names(), smallest_ring_size(), and update_derived_data().

AtomIndices core::chemical::ResidueType::Haro_index_

private

indices of haro hydrogens – Derived

Referenced by Haro_index(), operator=(), and update_derived_data().

AtomIndices core::chemical::ResidueType::Hpol_index_

private

indices of hpolar hydrogens – Derived

Referenced by Hpol_index(), operator=(), perform_checks(), and update_derived_data().

AtomIndices core::chemical::ResidueType::Hpos_apolar_

private

indices of apolar hydrogens – Derived

Referenced by Hpos_apolar(), operator=(), and update_derived_data().

AtomIndices core::chemical::ResidueType::Hpos_polar_

private

indices of polar Hydrogens for Hbond donors – Derived

Referenced by Hpos_polar(), operator=(), perform_checks(), and update_derived_data().

AtomIndices core::chemical::ResidueType::Hpos_polar_sc_

private

indices of polar Hydrogens for Hbond donors that are part of the sidechain – Derived must be a subset of the atoms listed in the Hpos_polar_ array

Referenced by Hpos_polar_sc(), operator=(), and update_derived_data().

std::map< VD, AtomICoor > core::chemical::ResidueType::icoor_

private

Internal coordinates on how to build the given atom – Primary.

Referenced by add_atom(), fill_ideal_xyz_from_icoor(), generate_atom_indices(), icoor(), operator=(), and set_icoor_private().

utility::vector1< dihedral_atom_set > core::chemical::ResidueType::improper_dihedral_atom_sets_

private

Referenced by improper_dihedral(), operator=(), and update_derived_data().

utility::vector1< utility::vector1< Size > > core::chemical::ResidueType::improper_dihedrals_for_atom_

private

Referenced by improper_dihedrals_for_atom(), operator=(), and update_derived_data().

std::string core::chemical::ResidueType::interchangeability_group_

private

interchangeability group lets a ResidueType claim to be functionally interchangeable with any other ResidueType in the same group. This is used by the packer to decide which ResidueType from a desired group has the right set of variants to be placed at a particular position. E.g. if the interchangeability group is "ALA" and the packer is building rotamers for residue 1, (the N-terminal residue) then, the packer will select the "ALA:NTermProteinFull" ResidueType and build rotamers for it. Primary.

Referenced by interchangeability_group(), and operator=().

utility::vector1< bool > core::chemical::ResidueType::is_proton_chi_

private

Is the corresponding chi in chi_atoms_ a proton chi? – Primary.

Referenced by add_chi(), autodetermine_chi_bonds(), delete_terminal_chi(), operator=(), redefine_chi(), and set_proton_chi().

utility::vector1< Size > core::chemical::ResidueType::last_controlling_chi_

private

Data for controlling chi. – Derived. Computed in update_last_controlling_chi() for each atom 0 means an atom whose location is not determined by any chi.

Referenced by last_controlling_chi(), note_chi_controls_atom(), operator=(), update_derived_data(), and update_last_controlling_chi().

utility::vector1< utility::vector1< std::string > > core::chemical::ResidueType::low_ring_conformers_

private

Low-energy ring conformers for each ring – Primary.

used for setting up the RingConformerSets

Referenced by add_ring(), operator=(), set_low_energy_ring_conformers(), and update_derived_data().

Size core::chemical::ResidueType::lower_connect_id_

private

Polymer lower connections – Derived, valid during Mutable Updated in set_lower_connect_atom()

Note: ResidueConnection objects store the ideal internal coordinates for the connected atom

Referenced by branch_connect_atoms(), lower_connect(), lower_connect_atom(), lower_connect_id(), operator=(), residue_connection_is_polymeric(), set_icoor_private(), set_lower_connect_atom(), and set_upper_connect_atom().

utility::vector1< std::string > core::chemical::ResidueType::lowest_ring_conformer_

private

Lowest-energy ring conformer for each ring – Primary.

used for setting up the RingConformerSets

Referenced by add_ring(), operator=(), set_lowest_energy_ring_conformer(), and update_derived_data().

utility::vector1<VD> core::chemical::ResidueType::mainchain_atoms_

private

Verticies of all mainchain atoms – Primary.

mainchain_atoms are those atoms on a path from polymer lower_connect to upper_connect. For protein, this will be N, CA and C.

Referenced by generate_atom_indices(), operator=(), and set_mainchain_atoms().

AtomIndices core::chemical::ResidueType::mainchain_atoms_indices_

private

Index version of mainchain_atoms_ – Derived.

Referenced by generate_atom_indices(), mainchain_atom(), mainchain_atoms(), operator=(), and show().

Real core::chemical::ResidueType::mass_

private

The isotopically averaged mass of the residue – Derived.

Referenced by mass(), operator=(), and set_atom_type().

utility::vector1< std::string > core::chemical::ResidueType::metal_binding_atoms_

private

Names of all of the atoms that are able to make a bond to a metal, for metal-binding residue types.

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

Referenced by add_metalbinding_atom(), delete_metalbinding_atom(), get_metal_binding_atoms(), operator=(), and perform_checks().

MMAtomTypeSetCOP core::chemical::ResidueType::mm_atom_types_

private

The set for MMAtomTypes. – Primary, can be null.

Referenced by add_atom(), mm_atom_type(), mm_atom_types_ptr(), operator=(), and set_mm_atom_type().

Size core::chemical::ResidueType::n_backbone_heavyatoms_

private

number of backbone heavy atoms – Derived.

Referenced by atom_is_backbone(), first_sidechain_atom(), last_backbone_atom(), operator=(), setup_atom_ordering(), and update_derived_data().

Size core::chemical::ResidueType::n_hbond_acceptors_

private

The number of hbond_acceptors – Derived.

Referenced by n_hbond_acceptors(), operator=(), and set_atom_type().

Size core::chemical::ResidueType::n_hbond_donors_

private

number of hbond_donors – Derived.

Referenced by n_hbond_donors(), operator=(), and set_atom_type().

Size core::chemical::ResidueType::n_non_polymeric_residue_connections_

private

Number of non-polymeric residue connections – Derived.

Referenced by add_residue_connection(), branch_connect_atoms(), n_non_polymeric_residue_connections(), and operator=().

Size core::chemical::ResidueType::n_polymeric_residue_connections_

private

Number of polymeric residue connections – Derived.

Referenced by n_polymeric_residue_connections(), operator=(), set_lower_connect_atom(), and set_upper_connect_atom().

char core::chemical::ResidueType::name1_

private

one-letter code, also not necessarily unique – Primary

Referenced by name1(), operator=(), and show().

std::string core::chemical::ResidueType::name3_

private

PDB-file id, need not be unique – Primary NOTE: The "name3" is not necessarily three characters long. e.g. Metal ions may be only two characters.

Referenced by get_numeric_property(), get_string_property(), name3(), operator=(), and show().

std::string core::chemical::ResidueType::name_

private

Residue id – Primary, should be unique.

Accumulates VariantType names (e.g. "ALA:NtermProteinFull").

Referenced by add_actcoord_atom(), name(), operator=(), and show().

VD core::chemical::ResidueType::nbr_atom_

private

atom used for calculating residue-level neighbors – Primary

Referenced by assign_internal_coordinates(), generate_atom_indices(), nbr_atom(), nbr_vertex(), and operator=().

Size core::chemical::ResidueType::nbr_atom_indices_

private

Index version of nbr_atom_ – Derived.

Referenced by generate_atom_indices(), nbr_atom(), and operator=().

Real core::chemical::ResidueType::nbr_radius_

private

radius cutoff to define neighbors – Primary

Should be the maximum distance from the nbr_atom_ to any heavy atom in any valid rotamer.

Referenced by nbr_radius(), and operator=().

Size core::chemical::ResidueType::nheavyatoms_

private

The number of heavy atoms – Derived.

Referenced by atom_is_backbone(), atom_is_hydrogen(), first_sidechain_atom(), nheavyatoms(), operator=(), perform_checks(), setup_atom_ordering(), and update_derived_data().

bool core::chemical::ResidueType::nondefault_

private

Referenced by nondefault(), and operator=().

utility::vector1< utility::vector1< VD > > core::chemical::ResidueType::nu_atoms_

private

VDs of four atoms to build each nu angle – Primary.

Referenced by add_nu(), generate_atom_indices(), n_nus(), and operator=().

utility::vector1< AtomIndices > core::chemical::ResidueType::nu_atoms_indices_

private

Index version of nu_atoms_ – Derived.

Referenced by generate_atom_indices(), nu_atoms(), and operator=().

VD const core::chemical::ResidueType::null_vertex = boost::graph_traits<ResidueGraph>::null_vertex()

static

Referenced by core::chemical::gasteiger::assign_gasteiger_atom_types(), assign_internal_coordinates(), core::chemical::AtomICoor::AtomICoor(), core::chemical::sdf::MolFileIOMolecule::convert_to_ResidueType(), core::chemical::find_nbr_dist(), core::chemical::ICoorAtomID::ICoorAtomID(), operator=(), core::chemical::pretty_print_atomicoor(), and set_icoor_private().

orbitals::OrbitalTypeSetCOP core::chemical::ResidueType::orbital_types_

private

The set for OrbitalTypes. – Primary, can be null.

Referenced by add_orbital(), operator=(), orbital_type(), and orbital_types_ptr().

utility::vector1< Orbital > core::chemical::ResidueType::orbitals_

private

The orbitals on the ResidueType, if any. – Primary.

Referenced by add_orbital(), clear_orbitals(), generate_atom_indices(), n_orbitals(), new_orbital_icoor_data(), operator=(), orbital(), orbital_icoor_data(), orbital_type(), and set_orbital_icoor_id().

std::map< std::string, int > core::chemical::ResidueType::orbitals_index_

private

index lookup for orbitals based on atom name – Derived, valid during Mutable Updated in add_orbital()

Referenced by add_orbital(), add_orbital_bond(), clear_orbitals(), has_orbital(), operator=(), and orbital_index().

VDs core::chemical::ResidueType::ordered_atoms_

private

Vector of atoms for index->vd mapping.

Atom order rules: (1) heavyatoms before hydrogens (2) backbone heavyatoms before sidechain heavyatoms (3) hydrogens are grouped by the heavyatom they are attached to and come in the order of those heavyatoms (4) as a consequence of (2)+(3) –> backbone hydrogens come before sidechain hydrogens (5) atom order in the residue file is preserved subject to rules 1-4 see finalize() for the logic to determine the atom order

WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING

If you add new properties that are associated with atoms, You need to make sure that you iterate over the VDs! Then in the generate indices function, associate your VDs to atom ordering.

There is no more old2new ordering!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING

Derived - During the Mutable stage all atoms will be present in the vector, but the ordering guarantees above will not be valid.

Referenced by abase2(), add_actcoord_atom(), add_atom(), add_nu(), add_orbital_bond(), add_residue_connection(), add_ring(), assign_internal_coordinates(), assign_neighbor_atom(), atom(), atom_base(), atom_index(), atom_is_polar_hydrogen(), atom_name(), atom_type(), atom_vertex(), bonded_orbitals(), clear_orbitals(), delete_atom(), dump_vd_info(), gasteiger_atom_type(), generate_atom_indices(), heavyatom_has_polar_hydrogens(), heavyatom_is_an_acceptor(), icoor(), mm_atom_type(), nbonds(), nbr_atom(), operator=(), print_bondangles(), print_dihedrals(), print_pretty_path_distances(), redefine_chi(), set_ideal_xyz(), set_lower_connect_atom(), set_mainchain_atoms(), set_orbital_icoor_id(), set_shadowing_atom(), set_upper_connect_atom(), setup_atom_ordering(), and update_derived_data().

utility::vector1< utility::vector1< int > > core::chemical::ResidueType::path_distance_

private

number of bonds separated between any pair of atoms in this residue – Derived.

Referenced by operator=(), path_distance(), path_distances(), print_pretty_path_distances(), and update_derived_data().

ResiduePropertiesOP core::chemical::ResidueType::properties_

private

Residue properties as defined in the residue topology (.params) files – Primary.

Referenced by add_numeric_property(), add_property(), add_string_property(), add_variant_type(), custom_variant_types(), delete_property(), enable_custom_variant_types(), get_numeric_property(), get_string_property(), has_property(), has_sc_orbitals(), has_variant_type(), is_acetylated_nterminus(), is_achiral_backbone(), is_adduct(), is_alpha_aa(), is_aromatic(), is_beta_aa(), is_branch_lower_terminus(), is_branch_point(), is_canonical_aa(), is_canonical_nucleic(), is_carbohydrate(), is_charged(), is_coarse(), is_cyclic(), is_d_aa(), is_disulfide_bonded(), is_DNA(), is_gamma_aa(), is_inverted_virtual_residue(), is_l_aa(), is_ligand(), is_lipid(), is_lower_terminus(), is_membrane(), is_metal(), is_metalbinding(), is_methylated_cterminus(), is_peptoid(), is_polar(), is_polymer(), is_protein(), is_RNA(), is_sidechain_amine(), is_sidechain_thiol(), is_solvent(), is_sri(), is_surface(), is_triazolemer(), is_upper_terminus(), is_virtual_residue(), lower_connect(), lower_connect_atom(), operator=(), perform_checks(), placeholder_clone(), properties(), remove_variant_type(), requires_actcoord(), set_adduct_flag(), set_properties(), show(), update_derived_data(), upper_connect(), upper_connect_atom(), variant_type_enums(), and variant_types().

utility::vector1< utility::vector1< Real > > core::chemical::ResidueType::proton_chi_extra_samples_

private

For a proton chi, how to handle extra ex_ levels – Primary.

Referenced by autodetermine_chi_bonds(), operator=(), proton_chi_extra_samples(), and set_proton_chi().

utility::vector1< utility::vector1< Real > > core::chemical::ResidueType::proton_chi_samples_

private

For a proton chi, the primary samples to diversify the rotamer library with – Primary.

Referenced by autodetermine_chi_bonds(), operator=(), proton_chi_samples(), and set_proton_chi().

utility::vector1< Size > core::chemical::ResidueType::proton_chis_

private

Indices of the chi_atoms_ vector for proton chis – Derived, valid during Mutable.

Referenced by autodetermine_chi_bonds(), delete_terminal_chi(), is_proton_chi(), n_proton_chi(), operator=(), proton_chi_2_chi(), and set_proton_chi().

bool core::chemical::ResidueType::remap_pdb_atom_names_

private

Should we attempt to rename atoms for this residue type when we read in PDB files? – Primary.

Referenced by operator=(), and remap_pdb_atom_names().

utility::vector1< ResidueConnection > core::chemical::ResidueType::residue_connections_

private

Vector of inter-residue connections expected for this residuetype – Primary NOW includes the polymer connections, as well as disulf-type connections.

Note: ResidueConnection objects store the ideal internal coordinates for the connected atom; Much of the code assumes at most one residue connection per atom. The pseudobond code has been partially written to handle cases where multiple connections to a single atom can exist, but much of the standard residue connection code assumes a simple correspondence between atoms and residue connections. That code will have to be updated to support single-atom "backbones."

Referenced by add_residue_connection(), generate_atom_indices(), lower_connect(), lower_connect_atom(), n_possible_residue_connections(), operator=(), residue_connect_atom_index(), residue_connection(), set_icoor_private(), set_lower_connect_atom(), set_upper_connect_atom(), update_derived_data(), update_residue_connection_mapping(), upper_connect(), and upper_connect_atom().

ResidueTypeSetCAP core::chemical::ResidueType::residue_type_set_

private

The owning ResidueTypeSet, if any. – Primary, can be null.

Once added to a ResidueTypeSet, the ResidueType should be considered Fixed.

Referenced by in_residue_type_set(), operator=(), and residue_type_set().

utility::vector1< utility::vector1< VD > > core::chemical::ResidueType::ring_atoms_

private

VDs of all ring atoms, not counting virtual atoms – Primary.

Referenced by add_ring(), generate_atom_indices(), n_rings(), operator=(), and update_derived_data().

utility::vector1< AtomIndices > core::chemical::ResidueType::ring_atoms_indices_

private

Index version of ring_atoms_ – Derived.

Referenced by generate_atom_indices(), operator=(), ring_atoms(), and show().

utility::vector1< Size > core::chemical::ResidueType::ring_sizes_

private

The size of each ring in this residue – Primary.

std::list<utility::vector1< ED > > core::chemical::ResidueType::rings_and_their_edges_

private

All the rings and the edges. Defaulted to null until defined – Derived.

Referenced by operator=(), and rings().

core::chemical::rna::RNA_ResidueTypeOP core::chemical::ResidueType::rna_residue_type_

private

A container for properties unique to RNA. – Derived, can be null.

Referenced by operator=(), RNA_type(), and update_derived_data().

VD core::chemical::ResidueType::root_atom_

private

Atom at the nominal root of the ICOOR tree.

Referenced by assign_internal_coordinates(), operator=(), root_atom(), and set_icoor_private().

AA core::chemical::ResidueType::rotamer_aa_

private

Referenced by operator=(), and rotamer_aa().

rotamers::RotamerLibrarySpecificationOP core::chemical::ResidueType::rotamer_library_specification_

private

How to construct a rotamer library for this ResidueType – Primary.

Referenced by operator=(), and rotamer_library_specification().

Size core::chemical::ResidueType::upper_connect_id_

private

Polymer upper connections – Derived valid during Mutable Updated in set_upper_connect_atom()

Note: ResidueConnection objects store the ideal internal coordinates for the connected atom

Referenced by branch_connect_atoms(), operator=(), residue_connection_is_polymeric(), set_icoor_private(), set_lower_connect_atom(), set_upper_connect_atom(), upper_connect(), upper_connect_atom(), and upper_connect_id().

std::map<VD, Size> core::chemical::ResidueType::vd_to_index_

private

A map of graph VDs to vector indexes. – Derived, valid during Mutable.

Referenced by add_atom(), atom_index(), generate_atom_indices(), lower_connect_atom(), operator=(), residue_connect_atom_index(), update_actcoord(), update_derived_data(), update_residue_connection_mapping(), and upper_connect_atom().

utility::vector1< utility::vector1< std::pair< Size, Size > > > core::chemical::ResidueType::within1bonds_sets_for_atom_

private

For atom i, its position in this vector is a list of pairs where first == the residue_connection id that lists this atom as being within one bond of a residue connection, and second == the index of the entry containing this atom in the atoms_within_one_bond_of_a_residue_connection_[ first ] array. – Derived.

Referenced by operator=(), update_derived_data(), and within1bonds_sets_for_atom().

utility::vector1< utility::vector1< std::pair< Size, Size > > > core::chemical::ResidueType::within2bonds_sets_for_atom_

private

For atom i, its position in this vector is a list of pairs where first == the residue_connection id that lists this atom as being within two bonds of a residue connection, and second == the index of the entry containing this atom in the atoms_within_two_bonds_of_a_residue_connection_[ first ] array. – Derived.

Referenced by operator=(), update_derived_data(), and within2bonds_sets_for_atom().

The documentation for this class was generated from the following files:

src/core/chemical/ResidueType.hh
src/core/chemical/ResidueType.cc

Public Member Functions

Static Public Attributes

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation