A container of Residues and the kinematics to manage them. More...

#include <Conformation.hh>

Inheritance diagram for core::conformation::Conformation:

Public Types
typedef kinematics::Jump	Jump

typedef kinematics::FoldTree	FoldTree

typedef kinematics::FoldTreeOP	FoldTreeOP

typedef kinematics::AtomTree	AtomTree

typedef kinematics::AtomTreeOP	AtomTreeOP

typedef id::AtomID	AtomID

typedef core::conformation::parametric::ParametersSet	ParametersSet

typedef core::conformation::parametric::ParametersSetOP	ParametersSetOP

typedef core::conformation::parametric::ParametersSetCOP	ParametersSetCOP

typedef core::conformation::parametric::Parameters	Parameters

typedef core::conformation::parametric::ParametersOP	ParametersOP

typedef core::conformation::parametric::ParametersOP	ParametersCOP

typedef id::AtomID_Mask	AtomID_Mask

typedef id::DOF_ID	DOF_ID

typedef id::TorsionID	TorsionID

typedef kinematics::DomainMap	DomainMap

typedef core::conformation::signals::ConnectionEvent	ConnectionEvent

typedef core::conformation::signals::GeneralEvent	GeneralEvent

typedef core::conformation::signals::IdentityEvent	IdentityEvent

typedef core::conformation::signals::LengthEvent	LengthEvent

typedef core::conformation::signals::XYZEvent	XYZEvent

typedef std::map< id::AtomID, Vector >	FragXYZ

typedef std::map< id::StubID, kinematics::RT >	FragRT

typedef Size	size_type

typedef ptrdiff_t	difference_type

typedef boost::indirect_iterator < ResidueOPs::const_iterator, Residue const >	const_iterator

typedef boost::indirect_iterator < ResidueOPs::iterator, Residue const >	iterator

Public Member Functions
iterator	begin () noexcept

const_iterator	begin () const noexcept

iterator	end () noexcept

const_iterator	end () const noexcept

	Conformation ()
	constructor More...

	~Conformation () override
	default destructor More...

	Conformation (Conformation const &src)
	copy constructor More...

virtual Conformation &	operator= (Conformation const &src)
	equals operator More...

virtual void	detached_copy (Conformation const &src)
	copy the other conformation into this, but make sure that the two share no possibly-non-bitwise-const data nor do they refer to each other (as the AtomTree does with its topological observer system). More...

virtual ConformationOP	clone () const
	clone the conformation More...

void	clear ()
	clear data More...

ConformationCOP	get_self_ptr () const
	self pointers More...

ConformationOP	get_self_ptr ()

ConformationCAP	get_self_weak_ptr () const

ConformationAP	get_self_weak_ptr ()

void	debug_residue_torsions (bool verbose=false) const
	debugging More...

void	show_residue_connections () const
	Show residue connections for debugging purposes. More...

void	show_residue_connections (std::ostream &os) const
	Show residue connections for debugging purposes. More...

virtual bool	same_type_as_me (Conformation const &other, bool const recurse=true) const
	determine the type of the ConformationOP More...

bool	sequence_matches (Conformation const &other) const
	do the names of all residues in this and src match? More...

Size	size () const
	Returns the number of residues in the Conformation. More...

bool	empty () const
	Returns true if this conformation does not have any residues. More...

core::chemical::ResidueTypeSetCOP	residue_type_set_for_conf (core::chemical::TypeSetMode mode=core::chemical::INVALID_t) const
	Return the appropriate ResidueTypeSet for the Conformation If mode is INVALID_t (the default), then return the typeset for the majority mode of the Conformation. Note: This may be a GlobalResidueTypeSet, if the Conformation doesn't have a specific PoseResidueTypeSet. More...

core::chemical::PoseResidueTypeSetOP	modifiable_residue_type_set_for_conf (core::chemical::TypeSetMode mode=core::chemical::INVALID_t) const
	Return a clone of the Conformation-specific PoseResidueTypeSet (note this is const) Modifications to this RTS won't be seen in the Conformation unless you pass it back in with reset_residue_type_set_for_conf() Should always return a non-null pointer: will create a new PoseResidueTypeSet if the Conformation doesn't have it already. More...

void	reset_residue_type_set_for_conf (core::chemical::PoseResidueTypeSetCOP new_set, core::chemical::TypeSetMode mode=core::chemical::INVALID_t)
	Reset the Conformation-specific PoseResidueTypeSet for the appropriate mode to the given RTS. (If the given mode is INVALID_t (the recommended default) the mode will be auto-determined from the RTS.) More...

core::chemical::TypeSetMode	residue_typeset_mode (bool majority=true) const
	What mode of ResidueTypeSet is this Conformation made of? If majority is true, it will be the mode of the ResidueTypes for most residues in the pose. If majority is false, core::chemical::MIXED_t will be returned for conformations with ResidueTypes of multiple modes. More...

bool	is_fullatom () const
	convenience test for residue_type_set mode More...

bool	is_centroid () const
	convenience test for residue_type_set mode More...

bool	is_mixed_mode () const
	convenience test for residue_type_set mode More...

bool	is_membrane () const
	convenience test for if the conformation contains information for a membrane protein More...

bool	contains_carbohydrate_residues () const
	Return true if this conformation contains any carbohydrate residues. More...

void	contains_carbohydrate_residues (bool setting)
	Set whether this conformation contains any carbohydrate residues. More...

Size	chain_end (Size chain) const
	Returns the position number of the last residue in chain number <chain> More...

Size	chain_begin (Size chain) const
	Returns the position number of the first residue in chain number <chain> More...

Size	num_chains () const
	Returns the number of chains. More...

utility::vector1< Size > const &	chain_endings () const
	Returns the list of (chain number) chain endings. More...

virtual void	chain_endings (utility::vector1< Size > const &endings)
	Sets the list of (chain number) chain endings. More...

virtual void	insert_chain_ending (Size const seqpos)
	Marks <seqpos> as the end of a new (chain number) chain. More...

virtual void	delete_chain_ending (Size const seqpos)
	Deletes <seqpos> from the list of (chain number) chain endings. More...

virtual void	reset_chain_endings ()
	Resets chain data so that the Conformation is marked as a single (chain number) chain. More...

virtual void	chains_from_termini ()
	Rederive the (chain number) chains from the termini/polymer status. More...

char	secstruct (Size seqpos) const
	Returns the secondary structure the position <seqpos> More...

virtual void	set_secstruct (Size const seqpos, char const setting)
	Sets the secondary structure of the position <seqpos> to <setting> More...

void	set_membrane_info (membrane::MembraneInfoOP mem_info)
	Setup a Membrane Info object in Conformation - pos & topology. More...

membrane::MembraneInfoOP	membrane_info ()
	Returns the const MembraneInfo object in conformation. More...

membrane::MembraneInfoOP	membrane_info () const
	Returns the const MembraneInfo object in conformation. More...

void	update_membrane_position (Vector center, Vector normal)
	Update Normal, Center in the Membrane. More...

void	check_valid_membrane () const
	Check that a new membrane position is valid. More...

carbohydrates::GlycanTreeSetCOP	glycan_tree_set () const
	Get the glycan tree set. Nullptr if not present. More...

void	setup_glycan_trees ()
	Setup glycan trees and attach length observer. More...

void	clear_glycan_trees ()
	Safely detaches any tree observers and clears it to null. More...

virtual FoldTree const &	fold_tree () const
	Returns the conformation's FoldTree. More...

virtual void	fold_tree (FoldTree const &fold_tree_in)
	Sets the FoldTree to <fold_tree_in> More...

AtomTree const &	atom_tree () const
	Returns the conformation's AtomTree. More...

chemical::AA const &	aa (Size seqpos) const
	Returns the AA enum for position <seqpos> More...

std::string	annotated_sequence (bool show_all_variants) const
	Returns the variant-tagged string representing the residue types that make up a conformation; e.g. M[MET:N-Terminus-Variant]CDH[HIS_D]LLR[ARG:C-Terminus-Variant]. More...

Residue const &	residue (Size seqpos) const
	access one of the residues More...

basic::datacache::BasicDataCache const &	residue_data (Size seqpos) const
	Read access to the datacache array stored inside a Residue object. Also accessible to the user by calling residue( seqpos ).data_ptr() directly. More...

basic::datacache::BasicDataCache &	residue_data (Size seqpos)
	Write access to the datacache array stored inside a Residue object. Although the Conformation very deliberately does not grant users write access to the whole of its Residue objects, it will grant users access to the Residue objects data cache. So while the coordinates and dihedrals of the Residue will not be changable e.g. during the setup-for-scoring phase, data derived from those coordinates and dihedrals and which ends up living in the Residue will be changable. More...

ResidueCOP	residue_cop (Size seqpos) const
	access one of the residues, using COP More...

chemical::ResidueType const &	residue_type (Size seqpos) const
	access one of the residue's types – avoids coord/torsion update More...

chemical::ResidueTypeCOP	residue_type_ptr (Size seqpos) const
	access one of the residue's types as a COP – avoids coord/torsion update More...

ResidueCOPs	const_residues () const
	Inefficient – constructs copy of residues_. More...

virtual void	append_residue_by_jump (conformation::Residue const &new_rsd, Size const anchor_residue, std::string const &anchor_atom="", std::string const &root_atom="", bool const start_new_chain=false)
	Append a new residue by a jump. More...

void	insert_residue_by_jump (Residue const &new_rsd_in, Size seqpos, Size anchor_pos, std::string const &anchor_atom="", std::string const &root_atom="", bool new_chain=false)
	Insert a new residue by jump. If new_chain is "true", then seqpos must be the last residue of one chain (i.e. residue(seqpos).chain() != residue(seqpos+1).chain() ) More...

void	insert_residue_by_bond (Residue const &new_rsd_in, Size const seqpos, Size anchor_pos, bool const build_ideal_geometry=false, std::string const &anchor_atom="", std::string const &root_atom="", bool new_chain=false, bool const lookup_bond_length=false)
	Insert a new residue by jump. If new_chain is "true", then seqpos must be the last residue of one chain (i.e. residue(seqpos).chain() != residue(seqpos+1).chain() ) More...

void	append_residue_by_bond (conformation::Residue const &new_rsd, bool const build_ideal_geometry=false, int connection_index=0, Size anchor_residue=0, int anchor_connection_index=0, bool const start_new_chain=false, bool const lookup_bond_length=false)
	Append a new residue by a bond. More...

virtual void	append_polymer_residue_after_seqpos (Residue const &new_rsd, Size const seqpos, bool const build_ideal_geometry)
	glues to seqpos and perhaps also seqpos+1 More...

virtual void	safely_append_polymer_residue_after_seqpos (Residue const &new_rsd, Size const seqpos, bool const build_ideal_geometry)
	glues to seqpos and perhaps also seqpos+1, removes termini variants if necessary More...

virtual void	prepend_polymer_residue_before_seqpos (Residue const &new_rsd, Size const seqpos, bool const build_ideal_geometry)
	glues to seqpos and perhaps also seqpos-1 More...

virtual void	safely_prepend_polymer_residue_before_seqpos (Residue const &new_rsd, Size const seqpos, bool const build_ideal_geometry)
	glues to seqpos and perhaps also seqpos-1, removes termini variants if necessary More...

virtual void	replace_residue (Size const seqpos, Residue const &new_rsd, bool const orient_backbone)
	replace residue More...

virtual void	replace_residue (Size const seqpos, Residue const &new_rsd, utility::vector1< std::pair< std::string, std::string > > const &atom_pairs)
	function to replace a residue based on superposition on the specified input atom pairs More...

virtual void	delete_polymer_residue (Size const seqpos)
	Delete polymer residue at the given sequence position. More...

virtual void	delete_residue_slow (Size const seqpos)
	Slow method that relies on FoldTree::delete_seqpos, rebuilds atomtree, can handle jumps/root residue. More...

virtual void	delete_residue_range_slow (Size const range_begin, Size const range_end)
	Slow method that relies on FoldTree::delete_seqpos, rebuilds atomtree, can handle jumps/root residue. More...

virtual utility::vector1< bool >	get_residue_mask () const
	returns a mask of residues to be used in scoring More...

virtual Real	get_residue_weight (core::Size, core::Size) const
	returns a residue-pair weight More...

void	detect_bonds ()

void	detect_pseudobonds ()

virtual void	sever_chemical_bond (Size seqpos1, Size res1_resconn_index, Size seqpos2, Size res2_resconn_index)
	Sever the chemical bond between two residues by stating that the connections for those residues are "incomplete" (i.e. in a state where these residues are not ready to be scored). More...

virtual void	declare_chemical_bond (Size const seqpos1, std::string const &atom_name1, Size const seqpos2, std::string const &atom_name2)
	Declare that a chemical bond exists between two residues. More...

void	rebuild_polymer_bond_dependent_atoms_this_residue_only (Size const seqpos)
	Rebuilds the atoms that are dependent on polymer bonds for the specified residue only. More...

virtual void	rebuild_polymer_bond_dependent_atoms (Size const seqpos)
	Rebuild the atoms ( like HN(seqpos), OC(seqpos+1) ) that are dependent on the polymer bond between seqpos and seqpos+1. More...

void	rebuild_residue_connection_dependent_atoms (Size seqpos, Size connid)

AtomID	inter_residue_connection_partner (Size seqpos, int connection_index) const
	This returns the AtomID of the atom in the other residue to which the "connection_index"-th connection of residue seqpos is connected to. More...

bool	is_bonded (core::id::AtomID const &atomid1, core::id::AtomID const &atomid2, bool virt=false, bool skip_canonical_and_solvent=false) const
	Returns a boolean for two atomIDs to be bonded. More...

utility::vector1 < core::id::AtomID >	bonded_neighbor_all_res (core::id::AtomID const &atomid, bool virt=false, bool skip_canonical_and_solvent=false, bool intra_res=true, bool inter_res=true) const
	Get all atoms bonded to another. More...

virtual void	fill_missing_atoms (id::AtomID_Mask missing)

bool	atom_is_backbone_norefold (Size pos, Size atomno) const
	returns true if atom is part of backbone. More...

virtual void	set_stub_transform (id::StubID const &stub_id1, id::StubID const &stub_id2, kinematics::RT const &target_rt)
	Set the transform between two stubs – only works if there's a jump between the two sets of stubatoms. More...

kinematics::RT	get_stub_transform (id::StubID const &stub_id1, id::StubID const &stub_id2) const
	get the transform between two stubs More...

void	set_jump_atom_stub_id (id::StubID const &id)

kinematics::Stub	stub_from_id (id::StubID const &id) const

kinematics::Stub	upstream_jump_stub (int jump_number) const
	The upstream and downstream Stubs are the coordinate frames between which this jump is transforming. More...

kinematics::Stub	downstream_jump_stub (int jump_number) const
	The upstream and downstream Stubs are the coordinate frames between which this jump is transforming. More...

virtual void	set_polymeric_connection (Size res_id_lower, Size res_id_upper)
	identify polymeric connections More...

void	set_noncanonical_connection (Size res_id_lower, Size lr_conn_id, Size res_id_upper, Size ur_conn_id)
	Create an arbitrary covalent connection between two residues. More...

void	update_polymeric_connection (Size lower_seqpos, bool update_connection_dep_atoms=false)
	Update the polymer connection status between lower_seqpos and lower_seqpos+1 based on chainID's and termini. If update_connection_dep_atoms is true, positions of atoms dependent on the polymer connection are updated. More...

virtual void	update_noncanonical_connection (Size lower_seqpos, Size lr_conn_id, Size upper_seqpos, Size ur_conn_id)
	Update the connection status between the lower_seqpos residue's lr_conn_id connection ID and the upper_seqpos residue's ur_conn_id connection ID. More...

virtual void	detect_disulfides (utility::vector1< Size > const &disulf_one=utility::vector1< core::Size >(), utility::vector1< Size > const &disulf_two=utility::vector1< core::Size >())
	Detect existing disulfides from the protein structure using suggestions from the FileData (or not!) More...

virtual void	fix_disulfides (utility::vector1< std::pair< Size, Size > > const &disulf_bonds)
	Assigns disulfide bonds based on a pre-determined list. More...

void	create_new_parameters_set ()
	Create a new (empty) ParametersSet object and add its owning pointer to the current Conformation object. More...

void	add_parameters_set (ParametersSetOP newset)
	Add a (predefined) ParametersSet object (via its owning pointer) to the current Conformation object. More...

core::Size	n_parameters_sets () const
	Get the number of parameters sets defined for this Conformation. More...

void	clear_parameters_set_list ()
	Delete the list of ParametersSetOP objects. More...

ParametersSetOP	parameters_set (core::Size const index)
	Access one of the ParametersSets objects linked to this Conformation. More...

ParametersSetCOP	parameters_set (core::Size const index) const
	Const access to one of the ParametersSets objects linked to this Conformation. More...

virtual void	insert_conformation_by_jump (Conformation const &conf, Size const insert_seqpos, Size const insert_jumppos, Size const anchor_pos, Size const anchor_jump_number=0, std::string const &anchor_atom="", std::string const &root_atom="")
	Insert one conformation into another. See FoldTree::insert_fold_tree_by_jump. More...

void	copy_segment (Size size, Conformation const &src, Size begin, Size src_begin)
	copy a stretch of coordinates/torsions from another Conformation More...

virtual void	insert_fragment (id::StubID const &instub_id, FragRT const &outstub_transforms, FragXYZ const &frag_xyz)

Real	dof (DOF_ID const &id) const
	Returns the AtomTree degree of freedom (DOF) <id> More...

virtual void	set_dof (DOF_ID const &id, Real const setting)
	Sets the AtomTree degree of freedom (DOF) <id> to <setting> More...

Real	torsion (TorsionID const &id) const
	Return the torsion angle OR rigid-body offset for <id> More...

virtual void	set_torsion (TorsionID const &id, Real const setting)
	Sets the AtomTree DOF and the torsion OR rigid-body offset in the corresponding Residue or Jump. More...

Real	torsion_angle (AtomID const &atom1, AtomID const &atom2, AtomID const &atom3, AtomID const &atom4) const
	Returns the torsion angle defined by <atom[1-4]> in Radians. More...

virtual void	set_torsion_angle (AtomID const &atom1, AtomID const &atom2, AtomID const &atom3, AtomID const &atom4, Real const setting, bool const quiet=false)
	Sets the torsion angle defined by <atom[1-4]> to <setting> More...

Real	bond_angle (AtomID const &atom1, AtomID const &atom2, AtomID const &atom3) const
	Returns the bond angle defined by <atom[1-3]> through the AtomTree. More...

virtual void	set_bond_angle (AtomID const &atom1, AtomID const &atom2, AtomID const &atom3, Real const setting)
	Sets the bond angle defined by <atom[1-3]> to <setting> More...

Real	bond_length (AtomID const &atom1, AtomID const &atom2) const
	Returns the bond length between <atom1> and <atom2> through the AtomTree. More...

virtual void	set_bond_length (AtomID const &atom1, AtomID const &atom2, Real const setting)
	Sets the cond length between <atom1> and <atom2> to <setting> More...

core::Vector	bond_orientation (AtomID const &atom1, AtomID const &atom2) const
	Return the normalized vector of the bond between these two atoms. More...

core::Vector	bond_orientation (core::id::TorsionID const torsion) const
	Return the normalized vector of the bond about which this torsion angle twists. More...

const Jump &	jump (int jump_number) const
	Returns the Jump with jump number <jump_number> More...

const Jump &	jump (AtomID const &id) const
	access a jump More...

virtual void	set_jump (int const jump_number, Jump const &new_jump)
	Sets the jump <jump_number> to <new_jump> More...

virtual void	set_jump (AtomID const &id, Jump const &new_jump)
	set a jump More...

PointPosition const &	xyz (AtomID const &id) const
	access xyz coordinates of an atom More...

virtual void	set_xyz (AtomID const &id, PointPosition const &position)

virtual void	batch_set_xyz (utility::vector1< AtomID > const &id, utility::vector1< PointPosition > const &position)

virtual void	batch_get_xyz (utility::vector1< AtomID > const &id, utility::vector1< PointPosition > &position) const

virtual void	apply_transform_Rx_plus_v (numeric::xyzMatrix< Real > const &R, Vector const &v)

virtual void	insert_ideal_geometry_at_polymer_bond (Size const seqpos)

virtual void	insert_ideal_geometry_at_residue_connection (Size const pos1, Size const connid1)

void	update_actcoords ()

void	update_actcoord (Size resid)

void	update_orbital_coords (Residue &rsd) const

void	update_orbital_coords (Size resid)

id::DOF_ID	dof_id_from_atom_ids (id::AtomID const &id1, id::AtomID const &id2, id::AtomID const &id3, id::AtomID const &id4) const
	Get the DOF_ID corresponding to the torsion angle defined by these four atoms. More...

id::DOF_ID	dof_id_from_atom_ids (id::AtomID const &id1, id::AtomID const &id2, id::AtomID const &id3) const
	Get the DOF_ID corresponding to the bond angle defined by these three atoms. More...

id::DOF_ID	dof_id_from_atom_ids (id::AtomID const &id1, id::AtomID const &id2) const
	Get the DOF_ID corresponding to the bond distance defined by these two atoms. More...

id::DOF_ID	dof_id_from_atom_ids (utility::vector1< id::AtomID > const &ids) const
	Get the DOF_ID defined by these atoms. More...

DOF_ID	dof_id_from_torsion_id (TorsionID const &id) const
	Get the DOF_ID corresponding to this TorsionID. More...

id::AtomID	jump_atom_id (int jump_number) const

bool	get_torsion_angle_atom_ids (TorsionID const &tor_id, AtomID &id1, AtomID &id2, AtomID &id3, AtomID &id4) const
	get four atoms which defined this torsion More...

bool	get_jump_atom_ids (core::Size jump_number, AtomID &upstream_id, AtomID &downstream_id) const
	get two atoms connect by jump More...

bool	atoms_are_bonded (AtomID const &id1, AtomID const &id2) const
	Helper method to determine whether two atoms have a chemical bond linking them. More...

void	update_domain_map (DomainMap &domain_map) const
	Generate a domain_map from the current dof/xyz moved data. More...

bool	structure_moved () const
	has the structure moved since the last call to reset_move_data or reset_structure_moved More...

void	reset_structure_moved () const
	reset the structure_moved_ bool More...

virtual void	reset_move_data ()
	forget all the structure modifications More...

void	align_virtual_atoms_in_carbohydrate_residue (uint const sequence_position)
	Set coordinates of virtual atoms (used as angle reference points) within a saccharide residue of this conformation. More...

virtual void	push_passport (core::environment::DofPassportCOP)

virtual core::environment::DofPassportCOP	pop_passport ()

virtual bool	has_passport () const

virtual bool	is_protected () const

template<typename MemFn , typename Ptr >
utility::signals::Link	attach_connection_obs (MemFn fn, Ptr ptr) const
	attach ConnectionEvent observer function More...

template<typename MemFn , typename Ptr >
bool	detach_connection_obs (MemFn fn, Ptr ptr) const
	detach ConnectionEvent observer function More...

template<typename MemFn , typename Ptr >
utility::signals::Link	attach_general_obs (MemFn fn, Ptr ptr) const
	attach GeneralEvent observer function More...

template<typename MemFn , typename Ptr >
bool	detach_general_obs (MemFn fn, Ptr ptr) const
	detach GeneralEvent observer function More...

template<typename MemFn , typename Ptr >
utility::signals::Link	attach_identity_obs (MemFn fn, Ptr ptr) const
	attach IdentityEvent observer function More...

template<typename MemFn , typename Ptr >
bool	detach_identity_obs (MemFn fn, Ptr ptr) const
	detach IdentityEvent observer function More...

template<typename MemFn , typename Ptr >
utility::signals::Link	attach_length_obs (MemFn fn, Ptr ptr) const
	attach LengthEvent observer function More...

template<typename MemFn , typename Ptr >
bool	detach_length_obs (MemFn fn, Ptr ptr) const
	detach LengthEvent observer function More...

template<typename MemFn , typename Ptr >
utility::signals::Link	attach_xyz_obs (MemFn fn, Ptr ptr) const
	attach XYZEvent observer function More...

template<typename MemFn , typename Ptr >
bool	detach_xyz_obs (MemFn fn, Ptr ptr) const
	detach XYZEvent observer function More...

void	clear_observers ()
	clear all observers More...

void	receive_observers_from (Conformation const &src)
	fire a ConnectionEvent::TRANSFER to transfer observers from some source Conformation More...

void	debug_pause (bool flag) const
	wait for stdin after sending a GeneralEvent signal More...

bool	debug_pause () const
	waiting for stdin after sending a GeneralEvent signal? More...

void	buffer_signals ()
	block signals from being sent and buffer them to be sent after unblocking More...

void	block_signals ()
	block signals from being sent More...

void	unblock_signals ()
	allow signals to be sent More...

bool	buffering_signals () const
	are signals being blocked and buffered? More...

bool	blocking_signals () const
	are signals being blocked? More...

bool	backbone_torsion_angle_atoms (TorsionID const &id, AtomID &id1, AtomID &id2, AtomID &id3, AtomID &id4) const
	get four backbone atoms which define this backbone torsion More...

Protected Member Functions
Residue const &	const_residue_ (Size seqpos) const
	Returns a constant residue reference without triggering coordinate/torsion update. More...

void	force_update_residue_torsions () const
	Force updating of residue torsions. More...

void	force_update_residue_coordinates () const
	Force updating of residue coordinates. More...

Private Member Functions
Residue &	residue_ (Size seqpos)
	Returns a non-constant residue reference without triggering coordinate/torsion update. More...

void	update_sequence_numbering (Size new_size, utility::vector1< Size > const &old2new)
	remap *_moved arrays, sequence numbering in the residues_ arrays, etc, after insertion or deletion of rsds More...

void	rebuild_polymer_bond_dependent_atoms (Size const seqpos, int const upper_lower)
	rebuild atoms in residue seqpos dependent on either the lower (-1) or upper(1) polymer residue More...

void	insert_polymer_residue (Residue const &new_rsd_in, Size const seqpos, bool const join_lower, bool const join_upper)

void	append_residue (Residue const &new_rsd_in, bool const attach_by_jump, std::string const &root_atom, id::NamedAtomID anchor_id, bool const start_new_chain)
	Now a private method public interface: append_residue_by_bond or append_residue_by_jump. More...

void	residues_replace (Size seqpos, Residue const &new_rsd)
	wrap direct access to the Residues container More...

void	residues_insert (Size seqpos, Residue const &new_rsd, bool use_lower_chain=false, bool new_chain=false)

void	residues_append (Residue const &new_rsd, bool start_new_chain, bool by_jump=false, std::string const &root_atom="", id::NamedAtomID anchor_id=id::NamedAtomID::BOGUS_NAMED_ATOM_ID())

void	residues_delete (Size seqpos)

void	setup_atom_tree ()
	(re-)builds the AtomTree using the FoldTree and the Residues More...

Real	atom_tree_torsion (TorsionID const &tor_id) const
	access a torsion from the atom_tree More...

bool	backbone_torsion_angle_atoms_oligourea (TorsionID const &id, AtomID &id1, AtomID &id2, AtomID &id3, AtomID &id4) const
	Get four backbone atoms which define this backbone torsion, if this residue is an oligourea. More...

bool	backbone_torsion_angle_atoms_ortho_aramid (TorsionID const &id, AtomID &id1, AtomID &id2, AtomID &id3, AtomID &id4) const
	Get four backbone atoms which define this backbone torsion, if this residue is an aramid. More...

bool	backbone_torsion_angle_atoms_meta_aramid (TorsionID const &id, AtomID &id1, AtomID &id2, AtomID &id3, AtomID &id4) const
	Get four backbone atoms which define this backbone torsion, if this residue is an aramid. More...

bool	backbone_torsion_angle_atoms_para_aramid (TorsionID const &id, AtomID &id1, AtomID &id2, AtomID &id3, AtomID &id4) const
	Get four backbone atoms which define this backbone torsion, if this residue is an aramid. More...

bool	branch_connection_torsion_angle_atoms (TorsionID const &torsion, AtomID &id1, AtomID &id2, AtomID &id3, AtomID &id4) const
	Find the four atoms that define the torsion angle of this branch connection. More...

void	set_xyz_moved (AtomID const &id)
	notify of xyz-change More...

void	set_xyz_moved (utility::vector1< AtomID > const &ids)
	notify of mutiple-xyz-change More...

void	set_dof_moved (AtomID const &id)
	notify of dof-change More...

void	set_dof_moved (DOF_ID const &id)
	notify of dof-change More...

void	update_residue_coordinates () const
	Will (if necessary) copy the xyz coordinates from the AtomTree to the Residues being managed. More...

void	update_residue_coordinates (Size seqpos, bool fire_signal=true) const

void	rederive_chain_endings ()

void	rederive_chain_ids ()

void	update_residue_torsions () const
	Will (if necessary) copy the torsion angles (mainchain/chi) from the AtomTree to the Residues being managed. More...

void	update_residue_torsions (Size seqpos, bool fire_signal=true) const

void	add_pseudobond (Size lr, Size lr_connid, Size ur, Size ur_connid, Size nbonds)

void	in_place_copy (Conformation const &src)
	Optimizing the common case of assigning a conformation to another with the same sequence. More...

void	pre_nresidue_change ()
	The Conformation must transfer lazily accumulated "moved" data from the AtomTree before changing the number of residues. More...

void	notify_connection_obs (ConnectionEvent const &e) const
	notify ConnectionEvent observers More...

void	notify_general_obs (GeneralEvent const &e) const
	notify GeneralEvent observers More...

void	notify_identity_obs (IdentityEvent const &e, bool fire_general=true) const
	notify IdentityEvent observers More...

void	notify_length_obs (LengthEvent const &e, bool fire_general=true) const
	notify LengthEvent observers More...

void	notify_xyz_obs (XYZEvent const &e, bool fire_general=true) const
	notify XYZEvent observers More...

Private Attributes
ResidueOPs	residues_
	container of Residues More...

core::chemical::CacheableResidueTypeSets	residue_type_sets_
	Any Conformation-specific ResidueTypes are stored here. Note: The ResidueTypeSets contained herein can be shared by multiple Conformations, and should have copy-on-write semantics. More...

utility::vector1< Size >	chain_endings_
	chain number for each position More...

FoldTreeOP	fold_tree_
	fold tree for the kinematics More...

AtomTreeOP	atom_tree_
	atom tree for the kinematics More...

membrane::MembraneInfoOP	membrane_info_
	Membrane Info object. More...

carbohydrates::GlycanTreeSetObserverOP	tree_set_observer_ = nullptr
	GlycanTreeSetObserver Object. More...

utility::vector1< ParametersSetOP >	parameters_set_
	Parameter sets for parametric conformation generation. More...

bool	contains_carbohydrate_residues_

bool	residue_coordinates_need_updating_
	do we need to update the coordinates in the Residues? More...

bool	residue_torsions_need_updating_
	do we need to update the torsion angles in the Residues? More...

AtomID_Mask	dof_moved_
	book-keeping array for energy evaluations More...

AtomID_Mask	xyz_moved_
	book-keeping array for energy evaluations More...

bool	structure_moved_
	has the structure moved since the last call to reset_move_data? More...

utility::vector1< char >	secstruct_

utility::signals::BufferedSignalHub < void, ConnectionEvent >	connection_obs_hub_
	ConnectionEvent observers. More...

utility::signals::PausableSignalHub < void, GeneralEvent >	general_obs_hub_
	GeneralEvent observers. More...

utility::signals::BufferedSignalHub < void, IdentityEvent >	identity_obs_hub_
	IdentityEvent observers. More...

utility::signals::BufferedSignalHub < void, LengthEvent >	length_obs_hub_
	LengthEvent observers. More...

utility::signals::BufferedSignalHub < void, XYZEvent >	xyz_obs_hub_
	LengthEvent observers. More...

Friends
class	::ConformationTests

Detailed Description

A container of Residues and the kinematics to manage them.

Member Typedef Documentation

typedef id::AtomID core::conformation::Conformation::AtomID

typedef id::AtomID_Mask core::conformation::Conformation::AtomID_Mask

typedef kinematics::AtomTree core::conformation::Conformation::AtomTree

typedef kinematics::AtomTreeOP core::conformation::Conformation::AtomTreeOP

typedef core::conformation::signals::ConnectionEvent core::conformation::Conformation::ConnectionEvent

typedef boost::indirect_iterator< ResidueOPs::const_iterator, Residue const > core::conformation::Conformation::const_iterator

typedef ptrdiff_t core::conformation::Conformation::difference_type

typedef id::DOF_ID core::conformation::Conformation::DOF_ID

typedef kinematics::DomainMap core::conformation::Conformation::DomainMap

typedef kinematics::FoldTree core::conformation::Conformation::FoldTree

typedef kinematics::FoldTreeOP core::conformation::Conformation::FoldTreeOP

typedef std::map< id::StubID, kinematics::RT > core::conformation::Conformation::FragRT

typedef std::map< id::AtomID, Vector > core::conformation::Conformation::FragXYZ

typedef core::conformation::signals::GeneralEvent core::conformation::Conformation::GeneralEvent

typedef core::conformation::signals::IdentityEvent core::conformation::Conformation::IdentityEvent

typedef boost::indirect_iterator< ResidueOPs::iterator, Residue const > core::conformation::Conformation::iterator

typedef kinematics::Jump core::conformation::Conformation::Jump

typedef core::conformation::signals::LengthEvent core::conformation::Conformation::LengthEvent

typedef core::conformation::parametric::Parameters core::conformation::Conformation::Parameters

typedef core::conformation::parametric::ParametersOP core::conformation::Conformation::ParametersCOP

typedef core::conformation::parametric::ParametersOP core::conformation::Conformation::ParametersOP

typedef core::conformation::parametric::ParametersSet core::conformation::Conformation::ParametersSet

typedef core::conformation::parametric::ParametersSetCOP core::conformation::Conformation::ParametersSetCOP

typedef core::conformation::parametric::ParametersSetOP core::conformation::Conformation::ParametersSetOP

typedef Size core::conformation::Conformation::size_type

typedef id::TorsionID core::conformation::Conformation::TorsionID

typedef core::conformation::signals::XYZEvent core::conformation::Conformation::XYZEvent

Constructor & Destructor Documentation

core::conformation::Conformation::Conformation ( )

constructor

Note: If you are using PyRosetta, you should NOT BE HERE!

References atom_tree_.

core::conformation::Conformation::~Conformation ( )

override

default destructor

core::conformation::Conformation::Conformation ( Conformation const & src )

copy constructor

References atom_tree_, chain_endings_, contains_carbohydrate_residues_, dof_moved_, fold_tree_, membrane_info_, parameters_set_, residue_coordinates_need_updating_, residue_torsions_need_updating_, residue_type_sets_, residues_, secstruct_, size(), structure_moved_, tree_set_observer_, and xyz_moved_.

Member Function Documentation

chemical::AA const& core::conformation::Conformation::aa ( Size seqpos ) const

inline

Returns the AA enum for position <seqpos>

References residues_, and size().

Referenced by core::conformation::symmetry::SymmetricConformation::get_upstream_vrt(), and core::conformation::symmetry::SymmetricConformation::recalculate_transforms().

void core::conformation::Conformation::add_parameters_set ( ParametersSetOP newset )

Add a (predefined) ParametersSet object (via its owning pointer) to the current Conformation object.

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

References parameters_set_.

Referenced by protocols::helical_bundle::MakeBundleHelix::add_parameter_info_to_pose(), protocols::helical_bundle::MakeBundle::apply(), and insert_conformation_by_jump().

void core::conformation::Conformation::add_pseudobond	(	Size	lr,
		Size	lr_connid,
		Size	ur,
		Size	ur_connid,
		Size	nbonds
	)

private

References core::conformation::PseudoBond::lr(), core::conformation::PseudoBond::lr_conn_id(), core::conformation::PseudoBond::nbonds(), residues_, core::conformation::PseudoBond::ur(), and core::conformation::PseudoBond::ur_conn_id().

Referenced by detect_pseudobonds().

void core::conformation::Conformation::align_virtual_atoms_in_carbohydrate_residue ( uint const sequence_position )

Set coordinates of virtual atoms (used as angle reference points) within a saccharide residue of this conformation.

This method aligns virtual atom VOX, where X is the position of the cyclic oxygen, OY and HOY, where Y is the position of the anomeric carbon, (provided the residue is not the reducing end, where OY and HOY would be real atoms), and HOZ, where Z is the mainchain glycosidic bond location. OY and HOY are aligned with the last two "main chain" atoms of the parent residue. This ensures that torsion angles with duplicate names, e.g., chi1 and phi for internal linked aldoses, will always return the same values. The same concept applies for HOZ, which aligns with the anomeric carbon of the downstream residue. This method should be called after any coordinate change for a sac- charide residue and after loading a saccharide residue from a file or sequence for the first time.

Note: Do I need to worry about aligning the virtual atoms left over from modified sugar patches? Can such virtual atoms be deleted?

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

Referenced by set_bond_angle(), set_bond_length(), and set_torsion_angle().

std::string core::conformation::Conformation::annotated_sequence ( bool show_all_variants ) const

Returns the variant-tagged string representing the residue types that make up a conformation; e.g. M[MET:N-Terminus-Variant]CDH[HIS_D]LLR[ARG:C-Terminus-Variant].

References core::conformation::Residue::annotated_name(), residue(), and size().

Referenced by fold_tree().

void core::conformation::Conformation::append_polymer_residue_after_seqpos	(	Residue const &	new_rsd,
		Size const	seqpos,
		bool const	build_ideal_geometry
	)

virtual

glues to seqpos and perhaps also seqpos+1

Fires a LengthEvent::RESIDUE_PREPEND signal at seqpos + 1 due to insert_polymer_residue() call.

Reimplemented in core::conformation::symmetry::SymmetricConformation, and protocols::environment::ProtectedConformation.

References core::conformation::Residue::clone(), dof_moved_, fold_tree_, insert_polymer_residue(), core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_upper_terminus(), core::conformation::Residue::lower_connect(), core::conformation::Residue::natoms(), core::conformation::orient_residue_for_ideal_bond(), pre_nresidue_change(), rebuild_polymer_bond_dependent_atoms(), residue_(), residue_coordinates_need_updating_, size(), core::id::AtomID_Map< T >::size(), update_residue_coordinates(), core::conformation::Residue::upper_connect(), and xyz_moved_.

Referenced by protocols::chemically_conjugated_docking::add_extra_bodies(), core::conformation::symmetry::SymmetricConformation::append_polymer_residue_after_seqpos(), protocols::protein_interface_design::movers::LoopLengthChange::apply(), protocols::rna::movers::RNAThreadAndMinimizeMover::process_insertions(), and safely_append_polymer_residue_after_seqpos().

void core::conformation::Conformation::append_residue	(	conformation::Residue const &	new_rsd_in,
		bool const	attach_by_jump,
		std::string const &	root_atom,
		id::NamedAtomID	anchor_id,
		bool const	start_new_chain
	)

private

Now a private method public interface: append_residue_by_bond or append_residue_by_jump.

add a residue into residues_ container, update its seqpos, chainid as well fold tree and atoms. private now – this is our internal routine with everything determined ahead of time root_atomno and anchor_id.atomno() may not be filled in yet Fires a LengthEvent::RESIDUE_APPEND signal.

Referenced by append_residue_by_bond(), and append_residue_by_jump().

void core::conformation::Conformation::append_residue_by_bond	(	conformation::Residue const &	new_rsd,
		bool const	build_ideal_geometry = `false`,
		int	residue_connection_index = `0`,
		Size	anchor_pos = `0`,
		int	anchor_residue_connection_index = `0`,
		bool const	start_new_chain = `false`,
		bool const	lookup_bond_length = `false`
	)

Append a new residue by a bond.

The default behavior is to append by a polymeric connection to the preceding residue If we want to connect via a non-polymer connection, we give the connection number, anchor residue and the connection number for the anchor residue. These connection numbers are wrt the connections_ arrays in Residue and ResidueType If build_ideal_bond is TRUE it will transform the coordinates of the new residue so that the bond geometry of the new bond is ideal according to the icoor_internal data in the residues. Otherwise the incoming coordinates of new_rsd are preserved. Fires a LengthEvent::RESIDUE_APPEND signal.

Referenced by protocols::comparative_modeling::ExtraThreadingMover::apply(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::apply(), and core::conformation::is_ideal_position().

void core::conformation::Conformation::append_residue_by_jump	(	conformation::Residue const &	new_rsd,
		Size const	anchor_pos,
		std::string const &	anchor_atom = `""`,
		std::string const &	root_atom = `""`,
		bool const	start_new_chain = `false`
	)

virtual

Append a new residue by a jump.

add a residue into residues_ container, update its seqpos, chainid as well fold tree and atoms. Fires a LengthEvent::RESIDUE_APPEND signal.

Reimplemented in core::conformation::symmetry::SymmetricConformation, core::conformation::symmetry::MirrorSymmetricConformation, and protocols::environment::ProtectedConformation.

References append_residue(), core::id::NamedAtomID::BOGUS_NAMED_ATOM_ID(), pre_nresidue_change(), and size().

Referenced by protocols::chemically_conjugated_docking::add_extra_bodies(), protocols::loop_grower::LoopPartialSolution::add_sheets(), protocols::environment::EnvClaimBroker::add_virtual_residues(), protocols::comparative_modeling::ExtraThreadingMover::apply(), protocols::loop_grower::SheetSampler::apply(), and core::conformation::symmetry::setup_symmetric_conformation().

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

virtual

Reimplemented in core::conformation::symmetry::SymmetricConformation.

References batch_set_xyz(), core::conformation::Residue::natoms(), residue_(), size(), and xyz().

bool core::conformation::Conformation::atom_is_backbone_norefold	(	Size	pos,
		Size	atomno
	)		const

returns true if atom is part of backbone.

There is a version of this in Residue.hh. The problem with that function is that accessing a residue in the pose triggers a refold which is really slow. We do not need a correctly folded residue to makethis check

References residues_.

Referenced by core::conformation::symmetry::guess_torsion_type_of_dof_id().

AtomTree const& core::conformation::Conformation::atom_tree ( ) const

inline

Returns the conformation's AtomTree.

References atom_tree_.

Referenced by protocols::simple_filters::JumpEvaluator::apply(), protocols::environment::collect_dofs(), protocols::simple_filters::SimpleHbondsToAtomFilter::compute(), core::scoring::methods::LinearChainbreakEnergy::do_score_ovp(), protocols::topology_broker::fix_internal_coords_of_siblings(), protocols::abinitio::abscript::fix_internal_coords_of_siblings(), protocols::simple_filters::JumpEvaluator::JumpEvaluator(), core::optimization::CartesianMinimizerMap::setup(), core::optimization::MinimizerMap::setup(), core::optimization::symmetry::SymMinimizerMap::SymMinimizerMap(), core::kinematics::jacobian::ModuleType1::update_screw_vectors(), and protocols::environment::claims::XYZClaim::yield_elements().

Real core::conformation::Conformation::atom_tree_torsion ( TorsionID const & tor_id ) const

private

access a torsion from the atom_tree

used when we want to copy torsions from the atomtree to the residues used when updating the torsion angles stashed in the Residues other torsion access calls look inside the residues since this will be faster than getting from the atomtree, at least in the current implementation of this routine

References atom_tree_, core::id::AtomID::atomno(), atoms_are_bonded(), const_residue_(), dof_id_from_torsion_id(), get_torsion_angle_atom_ids(), core::id::JUMP, core::id::AtomID::rsd(), core::id::TorsionID::type(), and xyz().

Referenced by debug_residue_torsions(), and update_residue_torsions().

bool core::conformation::Conformation::atoms_are_bonded	(	AtomID const &	id1,
		AtomID const &	id2
	)		const

Helper method to determine whether two atoms have a chemical bond linking them.

Helper function to determine whether two atoms have a chemical bond linking them.

Intended for internal use, but there's really no reason not to make this a public method. This works for atoms within the same residue or in different residues. AMW went and made this a public method.

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

References core::id::AtomID::atomno(), const_residue_(), is_bonded(), and core::id::AtomID::rsd().

Referenced by atom_tree_torsion(), protocols::rna::movers::atoms_have_bond_to_bonded_atoms(), protocols::rna::movers::atoms_have_mutual_bond_to_atom(), core::import_pose::build_pose_as_is2(), protocols::rna::movers::bump_check(), and torsion_angle().

template<typename MemFn , typename Ptr >

utility::signals::Link core::conformation::Conformation::attach_connection_obs	(	MemFn	fn,
		Ptr	ptr
	)		const

inline

attach ConnectionEvent observer function

Parameters

fn	pointer to observer's unary member function with signature void( ConnectionEvent const & )
ptr	RAW pointer to observer object

Returns: Link that can be used to manage the connection

Remarks: ConnectionEvent observers will only be notified upon a change in the state of the connection with the Conformation, e.g. if the Conformation is destroyed or if the connection is being transferred. SUGGESTION: Try to use the Link objects that are returned when attaching observers instead of attaching via this function and watching for ConnectionEvents, as it typically makes connection management easier.

References connection_obs_hub_.

Referenced by core::pose::PDBInfo::attach_to().

template<typename MemFn , typename Ptr >

utility::signals::Link core::conformation::Conformation::attach_general_obs	(	MemFn	fn,
		Ptr	ptr
	)		const

inline

attach GeneralEvent observer function

Parameters

fn	pointer to observer's unary member function with signature void( GeneralEvent const & )
ptr	RAW pointer to observer object

Returns: Link that can be used to manage the connection

Remarks: GeneralEvent observers will be notified whenever any signal derived from GeneralEvent occurs.

References general_obs_hub_.

template<typename MemFn , typename Ptr >

utility::signals::Link core::conformation::Conformation::attach_identity_obs	(	MemFn	fn,
		Ptr	ptr
	)		const

inline

attach IdentityEvent observer function

Parameters

fn	pointer to observer's unary member function with signature void( IdentityEvent const & )
ptr	RAW pointer to observer object

Returns: Link that can be used to manage the connection

References identity_obs_hub_.

Referenced by core::pose::PDBInfo::attach_to().

template<typename MemFn , typename Ptr >

utility::signals::Link core::conformation::Conformation::attach_length_obs	(	MemFn	fn,
		Ptr	ptr
	)		const

inline

attach LengthEvent observer function

Parameters

fn	pointer to observer's unary member function with signature void( LengthEvent const & )
ptr	RAW pointer to observer object

Returns: Link that can be used to manage the connection

References length_obs_hub_.

Referenced by core::conformation::carbohydrates::GlycanTreeSetObserver::attach_impl(), protocols::denovo_design::components::StructureDataObserver::attach_impl(), protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver::attach_impl(), core::pose::datacache::LengthEventCollector::attach_impl(), core::pose::datacache::SpecialSegmentsObserver::attach_impl(), protocols::forge::build::BuildInstruction::attach_to(), and core::pose::PDBInfo::attach_to().

template<typename MemFn , typename Ptr >

utility::signals::Link core::conformation::Conformation::attach_xyz_obs	(	MemFn	fn,
		Ptr	ptr
	)		const

inline

attach XYZEvent observer function

Parameters

fn	pointer to observer's unary member function with signature void( XYZEvent const & )
ptr	RAW pointer to observer object

Returns: Link that can be used to manage the connection

References xyz_obs_hub_.

bool core::conformation::Conformation::backbone_torsion_angle_atoms	(	TorsionID const &	id,
		AtomID &	id1,
		AtomID &	id2,
		AtomID &	id3,
		AtomID &	id4
	)		const

get four backbone atoms which define this backbone torsion

Note: Returns TRUE to signal FAILURE

messy... could perhaps keep this cached if speed is an issue but then have to keep sync'ed with changes in the residues

I don't think this is going to be performance critical

consider that in current rosetta we routinely re-evaluate all the backbone and sidechain torsion angles from the xyz coordinates...

This was hacky to begin with, but I feel that I have made it more hacky now. I am currently working on a more elegent method to handle residue types that have a a non-standard number of backbone torsions (ie. beta-peptides, beta-peptoids, and the dipeptides ACE-X-NME I use for making rotamers) –Doug

Dear 2010 Doug, Sorry, I have completely forgoton what we were talking about in your comment. Very Fermat of you. I have a few vauge ideas about what this miraculous solution could possibly be but we probably had more brain cells then so who knows. Basically defining the atoms that comprise the backbone torsions in the params files themselves and storing that in the ResidueType, like is currently done for the chi angles. I guess it is just the cacheing idea in the comments before mine. That way, patches could modify which atoms make up backbone torsions and we would not need special if checks to look at varient types if we want to have 4 backbone torsions. Until then however I am just going to make this function more hacky, sorry. Love, 2012 Doug

Dear all Dougs, I am making this somewhat more elegant, maybe, at least for the ACE-X-NME case, because unless torsion is 1, ntorsions, or ntorsions-1 all the atoms are part of the mainchain Best, Andy

Dear Dougs & Andy, Thank you for a most enjoyable dialog. Sincerely, Labonte

Dear Dougs, Andy, and Jason:

It's 2018, now, and this is STILL a mess. We really should clean this up and have ResidueTypes properly cache their torsion IDs at some point. It's becoming more and more of a headache as we add more noncanonical types.

Sincerely, 2018 Vikram

P.S. 2017 Vikram: why didn't you insist on cleaning this up at the noncanonicals XRW? Head injury is no excuse!

Note: returns TRUE for FAILURE

Referenced by get_torsion_angle_atom_ids(), and protocols::helical_bundle_predict::HBPHelix::get_torsions_for_helix().

bool core::conformation::Conformation::backbone_torsion_angle_atoms_meta_aramid	(	TorsionID const &	id,
		AtomID &	id1,
		AtomID &	id2,
		AtomID &	id3,
		AtomID &	id4
	)		const

private

Get four backbone atoms which define this backbone torsion, if this residue is an aramid.

Author: Andy Watkins (amw57.nosp@m.9@st.nosp@m.anfor.nosp@m.d.ed.nosp@m.u)

References core::chemical::ACETYLATED_NTERMINUS_VARIANT, core::id::AtomID::atomno(), const_residue_(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::conformation::get_second_atom_from_connection(), core::chemical::METHYLATED_CTERMINUS_VARIANT, core::chemical::N_ACETYLATION, core::conformation::Residue::residue_connection_conn_id(), residues_, core::id::AtomID::rsd(), and torsion().

Referenced by backbone_torsion_angle_atoms().

bool core::conformation::Conformation::backbone_torsion_angle_atoms_oligourea	(	TorsionID const &	id,
		AtomID &	id1,
		AtomID &	id2,
		AtomID &	id3,
		AtomID &	id4
	)		const

private

Get four backbone atoms which define this backbone torsion, if this residue is an oligourea.

I'm adding this function because backbone_torsion_angle_atoms() is an Escherian labyrinth.

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

References core::id::AtomID::atomno(), const_residue_(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::conformation::get_second_atom_from_connection(), core::chemical::METHYLATED_CTERMINUS_VARIANT, core::chemical::N_ACETYLATION, core::conformation::Residue::residue_connection_conn_id(), residues_, core::id::AtomID::rsd(), and torsion().

Referenced by backbone_torsion_angle_atoms().

bool core::conformation::Conformation::backbone_torsion_angle_atoms_ortho_aramid	(	TorsionID const &	id,
		AtomID &	id1,
		AtomID &	id2,
		AtomID &	id3,
		AtomID &	id4
	)		const

private

Get four backbone atoms which define this backbone torsion, if this residue is an aramid.

Author: Andy Watkins (amw57.nosp@m.9@st.nosp@m.anfor.nosp@m.d.ed.nosp@m.u)

References core::id::AtomID::atomno(), const_residue_(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::conformation::get_second_atom_from_connection(), core::chemical::METHYLATED_CTERMINUS_VARIANT, core::chemical::N_ACETYLATION, core::conformation::Residue::residue_connection_conn_id(), residues_, core::id::AtomID::rsd(), and torsion().

Referenced by backbone_torsion_angle_atoms().

bool core::conformation::Conformation::backbone_torsion_angle_atoms_para_aramid	(	TorsionID const &	id,
		AtomID &	id1,
		AtomID &	id2,
		AtomID &	id3,
		AtomID &	id4
	)		const

private

Get four backbone atoms which define this backbone torsion, if this residue is an aramid.

Author: Andy Watkins (amw57.nosp@m.9@st.nosp@m.anfor.nosp@m.d.ed.nosp@m.u)

References core::id::AtomID::atomno(), const_residue_(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::conformation::get_second_atom_from_connection(), core::chemical::METHYLATED_CTERMINUS_VARIANT, core::chemical::N_ACETYLATION, core::conformation::Residue::residue_connection_conn_id(), residues_, core::id::AtomID::rsd(), and torsion().

Referenced by backbone_torsion_angle_atoms().

void core::conformation::Conformation::batch_get_xyz	(	utility::vector1< AtomID > const &	id,
		utility::vector1< PointPosition > &	position
	)		const

virtual

References xyz().

void core::conformation::Conformation::batch_set_xyz	(	utility::vector1< AtomID > const &	id,
		utility::vector1< PointPosition > const &	position
	)

virtual

Reimplemented in core::conformation::symmetry::SymmetricConformation.

References atom_tree_, residues_, and set_xyz_moved().

Referenced by core::conformation::symmetry::SymmetricConformation::apply_transform_Rx_plus_v(), apply_transform_Rx_plus_v(), core::conformation::symmetry::SymmetricConformation::batch_set_xyz(), and core::conformation::UltraLightResidue::update_conformation().

iterator core::conformation::Conformation::begin ( )

inlinenoexcept

References residues_.

Referenced by core::conformation::symmetry::SymmetricConformation::batch_set_xyz(), core::conformation::symmetry::MirrorSymmetricConformation::replace_residue(), and core::conformation::symmetry::SymmetricConformation::set_xyz().

const_iterator core::conformation::Conformation::begin ( ) const

inlinenoexcept

References residues_.

void core::conformation::Conformation::block_signals ( )

block signals from being sent

Warning: for safety, ConnectionEvents are never blocked

References general_obs_hub_, identity_obs_hub_, length_obs_hub_, and xyz_obs_hub_.

bool core::conformation::Conformation::blocking_signals ( ) const

are signals being blocked?

References general_obs_hub_.

Real core::conformation::Conformation::bond_angle	(	AtomID const &	atom1,
		AtomID const &	atom2,
		AtomID const &	atom3
	)		const

Returns the bond angle defined by <atom[1-3]> through the AtomTree.

References atom_tree_.

Referenced by protocols::simple_moves::RepeatPropagationMover::copy_phi_psi_omega(), protocols::topology_broker::fix_mainchain_connect(), protocols::abinitio::abscript::fix_mainchain_connect(), and core::fragment::BBTorsionAndAnglesSRFD::steal().

Real core::conformation::Conformation::bond_length	(	AtomID const &	atom1,
		AtomID const &	atom2
	)		const

Returns the bond length between <atom1> and <atom2> through the AtomTree.

References atom_tree_.

Referenced by protocols::simple_moves::RepeatPropagationMover::copy_phi_psi_omega(), protocols::topology_broker::fix_mainchain_connect(), and protocols::abinitio::abscript::fix_mainchain_connect().

core::Vector core::conformation::Conformation::bond_orientation	(	AtomID const &	atom1,
		AtomID const &	atom2
	)		const

Return the normalized vector of the bond between these two atoms.

This function assumes a bond and will return an orientation even if the atoms are not technically bonded.

References xyz().

Referenced by bond_orientation(), and core::conformation::find_bond_torsion_with_nearest_orientation().

core::Vector core::conformation::Conformation::bond_orientation ( core::id::TorsionID const torsion ) const

Return the normalized vector of the bond about which this torsion angle twists.

This function will only work properly if all the reference atoms for <torsion> are defined. If they are not defined, the function will return a zero vector.

References bond_orientation(), and get_torsion_angle_atom_ids().

utility::vector1< id::AtomID > core::conformation::Conformation::bonded_neighbor_all_res	(	core::id::AtomID const &	atomid,
		bool	virt = `false`,
		bool	skip_canonical_and_solvent = `false`,
		bool	intra_res = `true`,
		bool	inter_res = `true`
	)		const

Get all atoms bonded to another.

If intra_res is false, we only find inter - residue neighbors

virtual atoms are excluded by default

References core::conformation::Residue::actual_residue_connection(), core::id::AtomID::atomno(), core::conformation::Residue::bonded_neighbor(), core::conformation::Residue::connection_incomplete(), core::chemical::ResidueType::is_canonical(), core::chemical::ResidueType::is_solvent(), core::conformation::Residue::is_virtual(), core::conformation::Residue::n_possible_residue_connections(), residue(), core::conformation::Residue::residue_connect_atom_index(), core::id::AtomID::rsd(), and core::conformation::Residue::type().

Referenced by protocols::sewing::hashing::AlignmentFileGeneratorMover::add_pose_segments_to_segment_vector(), core::select::residue_selector::BondedResidueSelector::apply(), protocols::branch_angle::branching_atomid1(), protocols::branch_angle::branching_atomids2(), protocols::rna::movers::RNAIdealizeMover::constrain_to_ideal(), core::scoring::MultipoleElecPotential::determine_polarization_groups(), core::scoring::MultipoleElecPotential::find_params_and_neighbors(), core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_conect_records_for_atom(), is_bonded(), and protocols::simple_moves::ConstrainToIdealMover::vary_bond_geometry().

bool core::conformation::Conformation::branch_connection_torsion_angle_atoms	(	TorsionID const &	torsion,
		AtomID &	id1,
		AtomID &	id2,
		AtomID &	id3,
		AtomID &	id4
	)		const

private

Find the four atoms that define the torsion angle of this branch connection.

This method figures out which four atoms define the torsion angle about the given branch connection point and sets the four AtomIDs passed to it.

Parameters

<torsion>	the TorsionID for this branch connection, which must have the BRANCH TorsionType
<id1>	through <id2>: AtomID variables that will be filled with the found atoms

Returns: TRUE to signal FAILURE. (That wasn't my idea! ~Labonte)

Note: This method was written to model the behavior of the backbone_torsion_angle_atoms() method and is used like it within the more general get_torsion_angle_atom_ids() method.

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

References core::id::BRANCH, core::conformation::Residue::connect_atom(), const_residue_(), core::conformation::Residue::first_adjacent_heavy_atom(), core::conformation::Residue::is_branch_point(), core::conformation::Residue::n_non_polymeric_residue_connections(), core::conformation::Residue::n_polymeric_residue_connections(), core::conformation::Residue::residue_connection_partner(), residues_, core::id::TorsionID::rsd(), core::conformation::Residue::seqpos(), core::id::TorsionID::torsion(), core::conformation::TR(), and core::id::TorsionID::type().

Referenced by get_torsion_angle_atom_ids().

void core::conformation::Conformation::buffer_signals ( )

block signals from being sent and buffer them to be sent after unblocking

References general_obs_hub_, identity_obs_hub_, length_obs_hub_, and xyz_obs_hub_.

Referenced by protocols::denovo_design::add_residues_to_pose().

bool core::conformation::Conformation::buffering_signals ( ) const

are signals being blocked and buffered?

References general_obs_hub_.

Size core::conformation::Conformation::chain_begin ( Size chain ) const

inline

Returns the position number of the first residue in chain number <chain>

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

References chain_endings_, and num_chains().

Size core::conformation::Conformation::chain_end ( Size chain ) const

inline

Returns the position number of the last residue in chain number <chain>

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

References chain_endings_, and size().

utility::vector1< Size > const & core::conformation::Conformation::chain_endings ( ) const

Returns the list of (chain number) chain endings.

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

References chain_endings_.

Referenced by protocols::protein_interface_design::movers::AddChainBreak::apply(), protocols::grafting::simple_movers::DeleteRegionMover::apply(), protocols::indexed_structure_store::apply_residue_entries_to_pose(), core::pose::chain_end_res(), protocols::denovo_design::components::StructureData::check_chains(), protocols::denovo_design::components::compute_chain_beginnings(), protocols::denovo_design::components::RemodelLoopMoverPoseFolder::create_remodel_loop_mover(), core::io::silent::BinarySilentStruct::fill_pose(), core::io::silent::ProteinSilentStruct_Template< T >::fill_pose(), core::io::silent::BinarySilentStruct::fill_struct(), core::io::silent::ProteinSilentStruct_Template< T >::fill_struct(), protocols::seeded_abinitio::DefineMovableLoops::find_loops(), protocols::seeded_abinitio::CloseFold::find_loops(), protocols::denovo_design::components::Picker::fragments_for_permutation_take_X_from_pose(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_residue_information(), protocols::denovo_design::components::StructureDataFactory::infer_from_pose(), protocols::features::PoseConformationFeatures::load_chain_endings(), protocols::forge::build::SegmentRebuild::modify_impl(), protocols::chemically_conjugated_docking::pack_extra_bodies(), core::pose::renumber_pdbinfo_based_on_conf_chains(), protocols::features::LoopAnchorFeatures::report_features(), protocols::features::PoseConformationFeatures::report_features_implementation(), protocols::legacy_sewing::Assembly::to_multichain_pose(), and protocols::surface_docking::SurfaceDockingProtocol::valid_surface_pose().

void core::conformation::Conformation::chain_endings ( utility::vector1< Size > const & endings )

virtual

Sets the list of (chain number) chain endings.

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

Remarks: All positions must be strictly less than the number of residues in the Conformation, otherwise the routine will fail fast. Note that the last residue position is not counted as a chain end.

Reimplemented in protocols::environment::ProtectedConformation.

References chain_endings_, rederive_chain_ids(), and size().

void core::conformation::Conformation::chains_from_termini ( )

virtual

Rederive the (chain number) chains from the termini/polymer status.

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

Reimplemented in protocols::environment::ProtectedConformation.

References chain_endings_, rederive_chain_ids(), residues_, and size().

void core::conformation::Conformation::check_valid_membrane ( ) const

Check that a new membrane position is valid.

Given a new membrane normal/center pair, check that the newly constructed stub represents an orthogonal coordinate frame

References downstream_jump_stub(), jump(), and membrane_info_.

Referenced by update_membrane_position().

void core::conformation::Conformation::clear ( )

clear data

References atom_tree_, chain_endings_, core::chemical::CacheableResidueTypeSets::clear(), core::id::AtomID_Map< T >::clear(), clear_glycan_trees(), dof_moved_, fold_tree_, parameters_set_, pre_nresidue_change(), residue_type_sets_, residues_, and xyz_moved_.

Referenced by operator=(), protocols::stepwise::modeler::slice(), core::conformation::symmetry::MirrorSymmetricConformation::~MirrorSymmetricConformation(), and core::conformation::symmetry::SymmetricConformation::~SymmetricConformation().

void core::conformation::Conformation::clear_glycan_trees ( )

Safely detaches any tree observers and clears it to null.

References tree_set_observer_.

Referenced by clear(), core::pose::symmetry::extract_asymmetric_unit(), core::pose::symmetry::get_asymmetric_pose_copy_from_symmetric_pose(), insert_conformation_by_jump(), core::pose::symmetry::make_asymmetric_pose(), and core::pose::symmetry::make_symmetric_pose().

void core::conformation::Conformation::clear_observers ( )

clear all observers

Remarks: ConnectionEvent::DISCONNECT will be sent to all observers

References connection_obs_hub_, core::conformation::signals::ConnectionEvent::DISCONNECT, general_obs_hub_, identity_obs_hub_, length_obs_hub_, notify_connection_obs(), and xyz_obs_hub_.

void core::conformation::Conformation::clear_parameters_set_list ( )

Delete the list of ParametersSetOP objects.

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

References parameters_set_.

Referenced by protocols::helical_bundle::MakeBundle::apply().

ConformationOP core::conformation::Conformation::clone ( ) const

virtual

clone the conformation

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

Reimplemented in protocols::environment::ProtectedConformation, core::conformation::symmetry::SymmetricConformation, and core::conformation::symmetry::MirrorSymmetricConformation.

Referenced by protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList::apply(), core::conformation::symmetry::MirrorSymmetricConformation::insert_conformation_by_jump(), core::conformation::symmetry::SymmetricConformation::insert_conformation_by_jump(), and core::conformation::symmetry::setup_symmetric_conformation().

Residue const& core::conformation::Conformation::const_residue_ ( Size seqpos ) const

inlineprotected

Returns a constant residue reference without triggering coordinate/torsion update.

Use with care. Useful inside torsion/coordinate setters where we want chemical info about a given residue but don't want to trigger the coordinate/torsion updates that go along with a call to residue(seqpos).

References residues_, and size().

Referenced by atom_tree_torsion(), atoms_are_bonded(), backbone_torsion_angle_atoms(), backbone_torsion_angle_atoms_meta_aramid(), backbone_torsion_angle_atoms_oligourea(), backbone_torsion_angle_atoms_ortho_aramid(), backbone_torsion_angle_atoms_para_aramid(), branch_connection_torsion_angle_atoms(), core::conformation::symmetry::SymmetricConformation::detect_disulfides(), get_torsion_angle_atom_ids(), jump_atom_id(), and core::conformation::symmetry::SymmetricConformation::prepend_polymer_residue_before_seqpos().

ResidueCOPs core::conformation::Conformation::const_residues ( ) const

Inefficient – constructs copy of residues_.

References residues_, and size().

Referenced by append_residue(), insert_polymer_residue(), insert_residue_by_bond(), insert_residue_by_jump(), replace_residue(), and setup_atom_tree().

bool core::conformation::Conformation::contains_carbohydrate_residues ( ) const

inline

Return true if this conformation contains any carbohydrate residues.

References contains_carbohydrate_residues_.

Referenced by core::pose::Pose::append_pose_by_jump(), core::io::pose_from_sfr::PoseFromSFRBuilder::build_initial_pose(), core::import_pose::build_pose_as_is2(), core::scoring::electron_density::calculate_rama(), core::pose::carbohydrates::delete_carbohydrate_branch(), core::pose::symmetry::extract_asymmetric_unit(), core::pose::symmetry::get_asymmetric_pose_copy_from_symmetric_pose(), core::pose::carbohydrates::glycosylate_pose(), insert_conformation_by_jump(), core::pose::symmetry::make_asymmetric_pose(), core::pose::make_pose_from_saccharide_sequence(), core::pose::symmetry::make_symmetric_pose(), and core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose().

void core::conformation::Conformation::contains_carbohydrate_residues ( bool setting )

inline

Set whether this conformation contains any carbohydrate residues.

References contains_carbohydrate_residues_.

void core::conformation::Conformation::copy_segment	(	Size	size,
		Conformation const &	src,
		Size	begin,
		Size	src_begin
	)

copy a stretch of coordinates/torsions from another Conformation

copy a stretch of coordinates/torsions from another pose Fires IdentityEvent signals as residues are replaced.

References replace_residue(), residue(), and size().

void core::conformation::Conformation::create_new_parameters_set ( )

Create a new (empty) ParametersSet object and add its owning pointer to the current Conformation object.

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

References parameters_set_.

void core::conformation::Conformation::debug_pause ( bool flag ) const

wait for stdin after sending a GeneralEvent signal

References general_obs_hub_.

bool core::conformation::Conformation::debug_pause ( ) const

waiting for stdin after sending a GeneralEvent signal?

References general_obs_hub_.

void core::conformation::Conformation::debug_residue_torsions ( bool verbose = false ) const

debugging

check that the residue torsions are in sync with the residue coords and atomtree coords

References protocols::comparative_modeling::features::A, atom_tree_, atom_tree_torsion(), core::id::AtomID::atomno(), core::id::BB, core::id::CHI, core::conformation::Residue::chi(), core::chemical::element::F, fold_tree_, get_torsion_angle_atom_ids(), core::conformation::Residue::mainchain_atoms(), core::conformation::Residue::mainchain_torsion(), core::conformation::Residue::nchi(), core::io::raw_data::precision(), residue(), core::id::AtomID::rsd(), size(), torsion(), update_residue_coordinates(), update_residue_torsions(), and xyz().

void core::conformation::Conformation::declare_chemical_bond	(	Size const	seqpos1,
		std::string const &	atom_name1,
		Size const	seqpos2,
		std::string const &	atom_name2
	)

virtual

Declare that a chemical bond exists between two residues.

Reimplemented in core::conformation::symmetry::SymmetricConformation, and protocols::environment::ProtectedConformation.

References core::conformation::Residue::atom_index(), core::chemical::ResidueConnection::atomno(), core::conformation::Residue::n_possible_residue_connections(), core::conformation::Residue::name(), residue(), core::conformation::Residue::residue_connection(), core::conformation::Residue::residue_connection_partner(), residue_torsions_need_updating_, residues_, core::conformation::update_cutpoint_virtual_atoms_if_connected(), and update_residue_torsions().

Referenced by core::util::add_covalent_linkage(), protocols::forge::methods::add_cutpoint_variants(), protocols::denovo_design::add_cutpoints(), protocols::loops::add_single_cutpoint_variant(), protocols::cyclic_peptide::DeclareBond::apply(), protocols::simple_moves::a3b_hbs::A3BHbsPatcher::apply(), protocols::indel::IndelOptimizationMover::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::loop_grower::LoopGrower::apply(), protocols::LoopRebuild::build_loop_with_ccd_closure(), core::pose::correctly_add_2prime_connection_variants(), protocols::relax::cyclize_pose(), core::conformation::symmetry::SymmetricConformation::declare_chemical_bond(), core::pose::declare_cutpoint_chemical_bond(), core::io::silent::BinarySilentStruct::fill_pose(), protocols::protein_interface_design::movers::DisulfideMover::form_disulfide(), core::conformation::form_disulfide(), protocols::grafting::insert_pose_into_pose(), protocols::toolbox::match_enzdes_util::EnzConstraintParameters::make_constraint_covalent(), protocols::forge::methods::make_star_foldtree(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_Moves::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::model_loop(), protocols::denovo_design::movers::new_jump_and_cutpoint(), core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose(), protocols::loops::set_loop_cutpoint_in_pose_fold_tree(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_chainbreak_variants(), protocols::loop_grower::LoopGrower::single_grow(), and protocols::loop_grower::LoopGrower::update_to_stored().

void core::conformation::Conformation::delete_chain_ending ( Size const seqpos )

virtual

Deletes <seqpos> from the list of (chain number) chain endings.

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

Remarks: The last residue position is not counted as a chain ending.

Reimplemented in protocols::environment::ProtectedConformation.

References chain_endings_, and rederive_chain_ids().

Referenced by protocols::forge::build::SegmentRebuild::modify_impl().

void core::conformation::Conformation::delete_polymer_residue ( Size const seqpos )

virtual

Delete polymer residue at the given sequence position.

delete a polymer residues Fires a LengthEvent::RESIDUE_DELETE signal.

Reimplemented in protocols::environment::ProtectedConformation.

References atom_tree_, fold_tree_, notify_length_obs(), pre_nresidue_change(), core::conformation::signals::LengthEvent::RESIDUE_DELETE, residue_torsions_need_updating_, residues_delete(), and size().

Referenced by protocols::protein_interface_design::movers::LoopLengthChange::apply().

void core::conformation::Conformation::delete_residue_range_slow	(	Size const	range_begin,
		Size const	range_end
	)

virtual

Slow method that relies on FoldTree::delete_seqpos, rebuilds atomtree, can handle jumps/root residue.

Like above but only one call to setup_atom_tree Fires a LengthEvent::RESIDUE_DELETE signal.

Reimplemented in protocols::environment::ProtectedConformation.

References atom_tree_, fold_tree_, notify_length_obs(), pre_nresidue_change(), core::conformation::signals::LengthEvent::RESIDUE_DELETE, residue_torsions_need_updating_, residues_delete(), setup_atom_tree(), and size().

Referenced by protocols::cutoutdomain::CutOutDomain::apply(), protocols::protein_interface_design::movers::TopologyBrokerMover::apply(), protocols::simple_moves::DeleteChainsMover::apply(), protocols::indel::IndelOptimizationMover::apply(), protocols::moves::StructureRestrictor::apply(), protocols::loop_grower::SheetSampler::apply(), protocols::antibody_legacy::GraftOneMover::apply(), protocols::fldsgn::CircularPermutation::apply(), protocols::protein_interface_design::filters::AtomicContactCountFilter::compute(), protocols::pose_creation::MakeJunctionsMover::generate_start_pose(), protocols::hotspot_hashing::HotspotStubSet::get_residue_score_(), protocols::loop_grower::LoopGrower::modifiedscore(), protocols::forge::build::SegmentSwap::modify_impl(), protocols::forge::build::SegmentRebuild::modify_impl(), protocols::forge::build::SegmentInsert::modify_impl(), protocols::environment::Environment::remove_nonpermenant_features(), protocols::hybridization::HybridizeFoldtreeDynamic::reset(), protocols::loop_grower::LoopGrower::sheetscore(), protocols::simple_moves::RepeatPropagationMover::trim_back_repeat_to_repair_scar(), and protocols::pose_creation::MakeJunctionsMover::trim_pose().

void core::conformation::Conformation::delete_residue_slow ( Size const seqpos )

virtual

Slow method that relies on FoldTree::delete_seqpos, rebuilds atomtree, can handle jumps/root residue.

Delete a residue from the Conformation the slow way – triggers a rebuild of the atomtree Fires a LengthEvent::RESIDUE_DELETE signal.

Note: Could be upstream and/or downstream of a jump or chemical edge, or the root of the tree; Not well-tested. Expect funny behavior in new or different situations (email pbrad.nosp@m.ley@.nosp@m.fhcrc.nosp@m..org)

LOGIC: uses fold_tree.delete_seqpos to handle shifting the topology around if necessary, then calls setup_atom_tree

Reimplemented in protocols::environment::ProtectedConformation.

References atom_tree_, fold_tree_, notify_length_obs(), pre_nresidue_change(), core::conformation::signals::LengthEvent::RESIDUE_DELETE, residue_torsions_need_updating_, residues_delete(), setup_atom_tree(), size(), unblock_signals(), and xyz_obs_hub_.

template<typename MemFn , typename Ptr >

bool core::conformation::Conformation::detach_connection_obs	(	MemFn	fn,
		Ptr	ptr
	)		const

inline

detach ConnectionEvent observer function

Parameters

fn	pointer to observer's unary member function with signature void( ConnectionEvent const & )
ptr	RAW pointer to observer object

Returns: true if disconnect successful, false if connection does not exist

Remarks: ConnectionEvent observers will only be notified upon a change in the state of the connection with the Conformation, e.g. if the Conformation is destroyed or if the connection is being transferred. SUGGESTION: Try to use the Link objects that are returned when attaching observers instead of attaching via this function and watching for ConnectionEvents, as it typically makes connection management easier.

References connection_obs_hub_.

template<typename MemFn , typename Ptr >

bool core::conformation::Conformation::detach_general_obs	(	MemFn	fn,
		Ptr	ptr
	)		const

inline

detach GeneralEvent observer function

Parameters

fn	pointer to observer's unary member function with signature void( GeneralEvent const & )
ptr	RAW pointer to observer object

Returns: true if disconnect successful, false if connection does not exist

Remarks: GeneralEvent observers will be notified whenever any signal derived from GeneralEvent occurs.

References general_obs_hub_.

template<typename MemFn , typename Ptr >

bool core::conformation::Conformation::detach_identity_obs	(	MemFn	fn,
		Ptr	ptr
	)		const

inline

detach IdentityEvent observer function

Parameters

fn	pointer to observer's unary member function with signature void( IdentityEvent const & )
ptr	RAW pointer to observer object

Returns: true if disconnect successful, false if connection does not exist

References identity_obs_hub_.

template<typename MemFn , typename Ptr >

bool core::conformation::Conformation::detach_length_obs	(	MemFn	fn,
		Ptr	ptr
	)		const

inline

detach LengthEvent observer function

Parameters

fn	pointer to observer's unary member function with signature void( LengthEvent const & )
ptr	RAW pointer to observer object

Returns: true if disconnect successful, false if connection does not exist

References length_obs_hub_.

template<typename MemFn , typename Ptr >

bool core::conformation::Conformation::detach_xyz_obs	(	MemFn	fn,
		Ptr	ptr
	)		const

inline

detach XYZEvent observer function

Parameters

fn	pointer to observer's unary member function with signature void( XYZEvent const & )
ptr	RAW pointer to observer object

Returns: true if disconnect successful, false if connection does not exist

References xyz_obs_hub_.

void core::conformation::Conformation::detached_copy ( Conformation const & src )

virtual

copy the other conformation into this, but make sure that the two share no possibly-non-bitwise-const data nor do they refer to each other (as the AtomTree does with its topological observer system).

Reimplemented in core::conformation::symmetry::SymmetricConformation, and core::conformation::symmetry::MirrorSymmetricConformation.

References atom_tree_.

Referenced by core::conformation::symmetry::SymmetricConformation::detached_copy().

void core::conformation::Conformation::detect_bonds ( )

Referenced by protocols::simple_moves::PeptideStapleMover::apply(), protocols::abinitio::ResolutionSwitcher::apply(), protocols::simple_moves::DeleteChainsMover::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::ncbb::oop::OopCreatorMover::apply(), core::pose::symmetry::make_symmetric_pose(), protocols::frag_picker::FragmentCandidate::output_silent(), core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose(), protocols::simple_moves::CyclizationMover::setup_connections(), and protocols::topology_broker::TopologyBroker::switch_to_fullatom().

void core::conformation::Conformation::detect_disulfides	(	utility::vector1< Size > const &	disulf_one = `utility::vector1< core::Size >()`,
		utility::vector1< Size > const &	disulf_two = `utility::vector1< core::Size >()`
	)

virtual

Detect existing disulfides from the protein structure using suggestions from the FileData (or not!)

For full atom confomations, looks at SG-SG distance. If the SG-SG are about 2.02 A apart, calls it a disulfide bond. For centroid and other conformations, the less accurate CB-CB distance is used instead. In this case a CB-CB distance of 3.72 A is optimal.

Note: Assumes full atom

Reimplemented in core::conformation::symmetry::SymmetricConformation, and core::conformation::symmetry::MirrorSymmetricConformation.

void core::conformation::Conformation::detect_pseudobonds ( )

Referenced by protocols::simple_moves::DeleteChainsMover::apply(), protocols::ncbb::oop::OopCreatorMover::apply(), and core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose().

Real core::conformation::Conformation::dof ( DOF_ID const & id ) const

Returns the AtomTree degree of freedom (DOF) <id>

References atom_tree_.

Referenced by protocols::rna::movers::RNAIdealizeMover::apply(), protocols::environment::collect_dofs(), core::conformation::symmetry::MirrorSymmetricConformation::set_dof(), and core::conformation::symmetry::SymmetricConformation::set_dof().

id::DOF_ID core::conformation::Conformation::dof_id_from_atom_ids	(	id::AtomID const &	id1,
		id::AtomID const &	id2,
		id::AtomID const &	id3,
		id::AtomID const &	id4
	)		const

Get the DOF_ID corresponding to the torsion angle defined by these four atoms.

References atom_tree_.

Referenced by dof_id_from_atom_ids(), and dof_id_from_torsion_id().

id::DOF_ID core::conformation::Conformation::dof_id_from_atom_ids	(	id::AtomID const &	id1,
		id::AtomID const &	id2,
		id::AtomID const &	id3
	)		const

Get the DOF_ID corresponding to the bond angle defined by these three atoms.

References atom_tree_.

id::DOF_ID core::conformation::Conformation::dof_id_from_atom_ids	(	id::AtomID const &	id1,
		id::AtomID const &	id2
	)		const

Get the DOF_ID corresponding to the bond distance defined by these two atoms.

References atom_tree_.

id::DOF_ID core::conformation::Conformation::dof_id_from_atom_ids ( utility::vector1< id::AtomID > const & ids ) const

Get the DOF_ID defined by these atoms.

References dof_id_from_atom_ids(), and core::id::GLOBAL_BOGUS_DOF_ID.

id::DOF_ID core::conformation::Conformation::dof_id_from_torsion_id ( TorsionID const & id ) const

Get the DOF_ID corresponding to this TorsionID.

References dof_id_from_atom_ids(), core::id::get_rb_type(), get_torsion_angle_atom_ids(), core::id::GLOBAL_BOGUS_DOF_ID, core::id::JUMP, jump_atom_id(), core::id::TorsionID::rsd(), core::id::TorsionID::torsion(), and core::id::TorsionID::type().

Referenced by atom_tree_torsion(), protocols::simple_moves::sidechain_moves::SidechainMoverBase::dof_id_ranges(), protocols::simple_moves::sidechain_moves::SidechainMover::dof_id_ranges(), protocols::simple_moves::SmallMover::dof_id_ranges(), protocols::simple_moves::ShearMover::dof_id_ranges(), protocols::environment::claims::TorsionClaim::insert_dof_element(), core::optimization::symmetry::SymAtomTreeMinimizer::make_semisymmetric_movemap(), core::pose::symmetry::make_symmetric_movemap(), protocols::environment::ProtectedConformation::set_secstruct(), protocols::environment::ProtectedConformation::set_torsion(), set_torsion(), core::pose::setup_dof_mask_from_move_map(), core::pose::setup_dof_to_torsion_map(), and torsion().

kinematics::Stub core::conformation::Conformation::downstream_jump_stub ( int jump_number ) const

The upstream and downstream Stubs are the coordinate frames between which this jump is transforming.

References atom_tree_, and jump_atom_id().

bool core::conformation::Conformation::empty ( ) const

inline

Returns true if this conformation does not have any residues.

References residues_.

Referenced by residue_typeset_mode().

iterator core::conformation::Conformation::end ( )

inlinenoexcept

References residues_.

Referenced by core::conformation::symmetry::SymmetricConformation::batch_set_xyz(), core::conformation::symmetry::MirrorSymmetricConformation::replace_residue(), and core::conformation::symmetry::SymmetricConformation::set_xyz().

const_iterator core::conformation::Conformation::end ( ) const

inlinenoexcept

References residues_.

void core::conformation::Conformation::fill_missing_atoms ( id::AtomID_Mask missing )

virtual

Reimplemented in protocols::environment::ProtectedConformation.

Referenced by protocols::antibody::GraftOneCDRLoop::apply(), protocols::antibody_legacy::GraftOneMover::apply(), protocols::indexed_structure_store::apply_residue_entries_to_pose(), core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose(), and protocols::toolbox::match_enzdes_util::replace_residue_keeping_all_atom_positions().

void core::conformation::Conformation::fix_disulfides ( utility::vector1< std::pair< Size, Size > > const & disulf_bonds )

virtual

Assigns disulfide bonds based on a pre-determined list.

Note: works in centroid and full-atom modes

Reimplemented in protocols::environment::ProtectedConformation.

References core::conformation::Residue::atom_index(), core::conformation::change_cys_state(), core::chemical::DISULFIDE, core::chemical::ResidueTypeBase::get_disulfide_atom_name(), residue(), core::chemical::ResidueType::residue_connection_id_for_atom(), residues_, size(), core::conformation::TR(), and core::conformation::Residue::type().

Referenced by protocols::calc_taskop_movers::ForceDisulfidesMover::apply(), protocols::hybridization::MRMover::apply(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::topology_broker::TopologyBroker::apply(), protocols::abinitio::AbrelaxApplication::do_distributed_rerun(), protocols::abinitio::AbrelaxApplication::generate_extended_pose(), core::pose::initialize_disulfide_bonds(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::make_disulfides(), core::io::raw_data::DisulfideFile::read_in_and_set_disulfides(), protocols::fold_from_loops::NubInitioMover::repack_minimize_disulfides(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::setup_disulfides(), protocols::abinitio::AbrelaxApplication::setup_fold(), protocols::topology_broker::TopologyBroker::switch_to_fullatom(), protocols::fold_from_loops::utils::Nub::transfer_unfolded_conformation(), and core::pose::full_model_info::update_disulfides_from_full_model_info().

virtual FoldTree const& core::conformation::Conformation::fold_tree ( ) const

inlinevirtual

Returns the conformation's FoldTree.

Reimplemented in core::conformation::symmetry::SymmetricConformation.

References fold_tree_.

void core::conformation::Conformation::fold_tree ( FoldTree const & fold_tree_in )

virtual

Sets the FoldTree to <fold_tree_in>

setup atom tree as well from the fold tree

Reimplemented in core::conformation::symmetry::SymmetricConformation, core::conformation::symmetry::MirrorSymmetricConformation, and protocols::environment::ProtectedConformation.

References annotated_sequence(), core::kinematics::FoldTree::nres(), setup_atom_tree(), size(), core::conformation::TR(), and update_residue_coordinates().

void core::conformation::Conformation::force_update_residue_coordinates ( ) const

protected

Force updating of residue coordinates.

Needed by derived classes (particularly MirrorSymmetricConformation).

Needed by derived classes

References residue_coordinates_need_updating_, and update_residue_coordinates().

void core::conformation::Conformation::force_update_residue_torsions ( ) const

protected

Force updating of residue torsions.

Needed by derived classes (particularly MirrorSymmetricConformation).

Needed by derived classes

References residue_torsions_need_updating_, and update_residue_torsions().

bool core::conformation::Conformation::get_jump_atom_ids	(	core::Size	jump_number,
		AtomID &	upstream_id,
		AtomID &	downstream_id
	)		const

get two atoms connect by jump

References atom_tree_, and jump_atom_id().

Referenced by core::pose::toolbox::AtomLevelDomainMap::get_jump().

utility::vector1< bool > core::conformation::Conformation::get_residue_mask ( ) const

virtual

returns a mask of residues to be used in scoring

Returns a mask of residues over which scoring is restricted. Only these residues will be used in constructing the neighbor list.

Reimplemented in core::conformation::symmetry::SymmetricConformation.

References residues_.

Referenced by core::scoring::NeighborList::setup().

Real core::conformation::Conformation::get_residue_weight	(	core::Size	,
		core::Size
	)		const

virtual

returns a residue-pair weight

Returns a weight to be used when scoring this residue.

Reimplemented in core::conformation::symmetry::SymmetricConformation, and core::conformation::symmetry::MirrorSymmetricConformation.

Referenced by core::scoring::NeighborList::setup().

ConformationCOP core::conformation::Conformation::get_self_ptr ( ) const

inline

self pointers

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

ConformationOP core::conformation::Conformation::get_self_ptr ( )

inline

ConformationCAP core::conformation::Conformation::get_self_weak_ptr ( ) const

inline

Referenced by core::pose::PDBInfo::attach_to().

ConformationAP core::conformation::Conformation::get_self_weak_ptr ( )

inline

kinematics::RT core::conformation::Conformation::get_stub_transform	(	id::StubID const &	stub_id1,
		id::StubID const &	stub_id2
	)		const

get the transform between two stubs

References atom_tree_.

Referenced by protocols::forge::build::ConnectRight::extract_rt(), protocols::loophash::get_rt_over_leap_without_foldtree_bs(), and core::fragment::DownJumpSRFD::steal().

bool core::conformation::Conformation::get_torsion_angle_atom_ids	(	TorsionID const &	tor_id,
		AtomID &	id1,
		AtomID &	id2,
		AtomID &	id3,
		AtomID &	id4
	)		const

get four atoms which defined this torsion

Note: Returns TRUE to signal FAILURE.

References core::id::AtomID::atomno(), backbone_torsion_angle_atoms(), core::id::BB, core::id::BRANCH, branch_connection_torsion_angle_atoms(), core::id::CHI, core::conformation::Residue::chi_atoms(), const_residue_(), core::id::JUMP, core::id::NU, core::conformation::Residue::nu_atoms(), core::id::AtomID::rsd(), core::id::TorsionID::rsd(), core::id::TorsionID::torsion(), torsion(), core::conformation::TR(), and core::id::TorsionID::type().

Referenced by core::pose::rna::add_chi_constraints(), protocols::constraint_generator::DihedralConstraintGenerator::apply(), protocols::rna::movers::RNAIdealizeMover::apply(), protocols::ncbb::oop::OopCreatorMover::apply(), protocols::symmetry::SetupNCSMover::apply(), core::optimization::CartesianMinimizerMap::assign_rosetta_torsions_and_trim(), atom_tree_torsion(), bond_orientation(), core::optimization::cartesian_collect_torsional_deriv(), core::scoring::rna::RNA_TorsionPotential::check_intra_residue(), debug_residue_torsions(), dof_id_from_torsion_id(), core::pose::toolbox::AtomLevelDomainMap::get(), core::pose::rna::RNA_IdealCoord::is_torsion_exists(), core::pose::rna::is_torsion_valid(), protocols::stepwise::modeler::rna::print_torsion_info(), core::pose::rna::print_torsion_info(), set_torsion(), and update_residue_torsions().

carbohydrates::GlycanTreeSetCOP core::conformation::Conformation::glycan_tree_set ( ) const

Get the glycan tree set. Nullptr if not present.

Get the glycan tree set. Null if not present.

Rosetta Carbohydrate Data /// Core data for interacting with glycan trees in Rosetta /// /// ///

Rosetta Carbohydrate Data /// Core data for interacting with glycan trees in Rosetta /// ///

References tree_set_observer_.

Referenced by core::conformation::carbohydrates::get_glycosidic_bond_residues(), core::conformation::carbohydrates::get_reference_atoms_for_1st_omega(), core::conformation::carbohydrates::get_reference_atoms_for_2nd_omega(), and insert_conformation_by_jump().

virtual bool core::conformation::Conformation::has_passport ( ) const

inlinevirtual

Reimplemented in protocols::environment::ProtectedConformation.

void core::conformation::Conformation::in_place_copy ( Conformation const & src )

private

Optimizing the common case of assigning a conformation to another with the same sequence.

References atom_tree_, chain_endings_, dof_moved_, fold_tree_, parameters_set_, residue_coordinates_need_updating_, residue_torsions_need_updating_, residue_type_sets_, residues_, secstruct_, size(), structure_moved_, and xyz_moved_.

Referenced by operator=().

void core::conformation::Conformation::insert_chain_ending ( Size const seqpos )

virtual

Marks <seqpos> as the end of a new (chain number) chain.

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

Remarks: The last residue position is not counted as a chain ending. Also increases the chain ID number by 1 for all residues upstream from seqpos.

Reimplemented in protocols::environment::ProtectedConformation.

References chain_endings_, rederive_chain_ids(), and size().

Referenced by protocols::cryst::MakeLatticeMover::add_monomers_to_lattice(), protocols::cryst::MakeLayerMover::add_monomers_to_layer(), protocols::protein_interface_design::movers::AddChainBreak::apply(), protocols::simple_moves::ChainSplitMover::apply(), protocols::grafting::simple_movers::DeleteRegionMover::apply(), protocols::metal_interface::MatchGrafter::build_combined_pose_with_zinc_overlay(), core::io::pose_from_sfr::PoseFromSFRBuilder::build_initial_pose(), core::pose::create_subpose(), core::pose::symmetry::extract_asymmetric_unit(), protocols::splice::RBOutMover::get_disulf_jump(), core::fragment::make_pose_from_frags(), core::io::serialization::read_binary(), protocols::relax::RepeatProteinRelax::setup_repeat_pose(), protocols::relax::RepeatProteinRelax::setup_repeat_pose_jumping(), and protocols::fldsgn::CircularPermutation::split_chains().

void core::conformation::Conformation::insert_conformation_by_jump	(	Conformation const &	conf,
		Size const	insert_seqpos,
		Size const	insert_jumppos,
		Size const	anchor_pos,
		Size const	anchor_jump_number = `0`,
		std::string const &	anchor_atom = `""`,
		std::string const &	root_atom = `""`
	)

virtual

Insert one conformation into another. See FoldTree::insert_fold_tree_by_jump.

Calls residue append observers AFTER addition of all residues

Insert one conformation into another. Some tricky issues: (1) residue connections: assume all residue connections within conf carry over, after renumbering residues positions (2) jump numbers: see FoldTree::insert_fold_tree_by_jump (3) chains: chain endings are inserted before insert_seqpos, and after insert_seqpos+conf.size()-1 ie. at the beginning and ending of the inserted conformation; all internal chain endings from conf are used (4) atom_tree: setup_atom_tree is called to rebuild from scratch using the fold_tree (5) Residue append observers are notified AFTER addition of ALL residues into the conformation)

Reimplemented in core::conformation::symmetry::SymmetricConformation, protocols::environment::ProtectedConformation, and core::conformation::symmetry::MirrorSymmetricConformation.

References add_parameters_set(), chain_end(), chain_endings_, core::id::AtomID_Map< T >::clear(), clear_glycan_trees(), core::conformation::Residue::clone(), contains_carbohydrate_residues(), contains_carbohydrate_residues_, dof_moved_, fold_tree(), fold_tree_, glycan_tree_set(), n_parameters_sets(), notify_length_obs(), num_chains(), parameters_set(), pre_nresidue_change(), rederive_chain_ids(), residue(), core::conformation::signals::LengthEvent::RESIDUE_APPEND, residue_cop(), residue_torsions_need_updating_, residues_, core::id::AtomID_Map< T >::resize(), secstruct_, setup_atom_tree(), setup_glycan_trees(), size(), update_sequence_numbering(), and xyz_moved_.

Referenced by protocols::denovo_design::add_residues_to_pose(), protocols::denovo_design::components::append_new_chain_from_template_segment(), core::pose::Pose::append_pose_by_jump(), core::conformation::symmetry::MirrorSymmetricConformation::insert_conformation_by_jump(), core::conformation::symmetry::SymmetricConformation::insert_conformation_by_jump(), protocols::motif_grafting::movers::MotifGraftMover::join_two_poses_by_jump(), and core::conformation::symmetry::setup_symmetric_conformation().

void core::conformation::Conformation::insert_fragment	(	id::StubID const &	instub_id,
		FragRT const &	outstub_transforms,
		FragXYZ const &	frag_xyz
	)

virtual

Reimplemented in protocols::environment::ProtectedConformation.

References atom_tree_, and set_dof_moved().

void core::conformation::Conformation::insert_ideal_geometry_at_polymer_bond ( Size const seqpos )

virtual

Set two bond angles and a bond length. DOES NOT DO ANY DIHEDRALS – NOT EVEN OMEGA IF IT'S A PROTEIN

Reimplemented in protocols::environment::ProtectedConformation.

References core::chemical::ResidueType::lower_connect(), core::chemical::ResidueType::mainchain_atom(), core::chemical::ResidueType::mainchain_atoms(), rebuild_polymer_bond_dependent_atoms(), residue_type(), set_bond_angle(), set_bond_length(), and core::chemical::ResidueType::upper_connect().

Referenced by protocols::forge::remodel::RemodelMover::apply(), protocols::forge::components::VarLengthBuild::apply(), protocols::grafting::idealize_combined_pose(), protocols::forge::build::SegmentInsert::modify_impl(), protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue(), and protocols::forge::remodel::RemodelLoopMover::repeat_propagation().

void core::conformation::Conformation::insert_ideal_geometry_at_residue_connection	(	Size const	pos1,
		Size const	connid1
	)

virtual

Set two bond angles and a bond length. DOES NOT DO ANY DIHEDRALS – NOT EVEN OMEGA IF IT'S A PROTEIN

Reimplemented in protocols::environment::ProtectedConformation.

References rebuild_residue_connection_dependent_atoms(), residues_, set_bond_angle(), and set_bond_length().

void core::conformation::Conformation::insert_polymer_residue	(	Residue const &	new_rsd_in,
		Size const	seqpos,
		bool const	join_lower,
		bool const	join_upper
	)

private

insert a polymer residue Fires a LengthEvent::RESIDUE_PREPEND signal.

References atom_tree_, const_residues(), contains_carbohydrate_residues_, fold_tree_, core::conformation::insert_residue_into_atom_tree(), core::chemical::ResidueType::is_carbohydrate(), core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_upper_terminus(), notify_length_obs(), pre_nresidue_change(), residue_(), core::conformation::signals::LengthEvent::RESIDUE_PREPEND, residue_torsions_need_updating_, residues_insert(), size(), and core::conformation::Residue::type().

Referenced by append_polymer_residue_after_seqpos(), and prepend_polymer_residue_before_seqpos().

void core::conformation::Conformation::insert_residue_by_bond	(	Residue const &	new_rsd_in,
		Size const	seqpos,
		Size	anchor_pos,
		bool const	build_ideal_geometry = `false`,
		std::string const &	anchor_atom = `""`,
		std::string const &	root_atom = `""`,
		bool	new_chain = `false`,
		bool const	lookup_bond_length = `false`
	)

Insert a new residue by jump. If new_chain is "true", then seqpos must be the last residue of one chain (i.e. residue(seqpos).chain() != residue(seqpos+1).chain() )

insert a residue by bond Fires a LengthEvent::RESIDUE_PREPEND signal.

References core::chemical::ResidueType::atom_index(), atom_tree_, core::conformation::Residue::clone(), const_residues(), fold_tree_, core::conformation::insert_residue_into_atom_tree(), notify_length_obs(), core::conformation::orient_residue_for_ideal_bond(), pre_nresidue_change(), residue_(), core::conformation::Residue::residue_connection(), core::chemical::ResidueType::residue_connection_id_for_atom(), residue_coordinates_need_updating_, core::conformation::signals::LengthEvent::RESIDUE_PREPEND, residue_torsions_need_updating_, residues_, residues_insert(), core::conformation::Residue::seqpos(), size(), core::conformation::Residue::type(), and update_residue_coordinates().

void core::conformation::Conformation::insert_residue_by_jump	(	Residue const &	new_rsd_in,
		Size	seqpos,
		Size	anchor_pos,
		std::string const &	anchor_atom = `""`,
		std::string const &	root_atom = `""`,
		bool	new_chain = `false`
	)

Insert a new residue by jump. If new_chain is "true", then seqpos must be the last residue of one chain (i.e. residue(seqpos).chain() != residue(seqpos+1).chain() )

insert a residue by jump Fires a LengthEvent::RESIDUE_PREPEND signal.

References atom_tree_, const_residues(), fold_tree_, core::conformation::insert_residue_into_atom_tree(), notify_length_obs(), pre_nresidue_change(), residue_(), core::conformation::signals::LengthEvent::RESIDUE_PREPEND, residue_torsions_need_updating_, residues_insert(), core::conformation::Residue::seqpos(), and size().

Referenced by protocols::membrane::symmetry::SymmetricAddMembraneMover::add_membrane_virtual(), and core::conformation::symmetry::SymmetricConformation::append_residue_by_jump().

id::AtomID core::conformation::Conformation::inter_residue_connection_partner	(	Size	seqpos,
		int	connection_index
	)		const

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

References residues_.

bool core::conformation::Conformation::is_bonded	(	core::id::AtomID const &	atomid1,
		core::id::AtomID const &	atomid2,
		bool	virt = `false`,
		bool	skip_canonical_and_solvent = `false`
	)		const

Returns a boolean for two atomIDs to be bonded.

Uses bonded_neighbor_all_res, which iterates through residue connections. To speed up, we would need to turn the connects into a proper bonded graph

References bonded_neighbor_all_res(), and core::id::AtomID::rsd().

Referenced by atoms_are_bonded(), and core::simple_metrics::per_residue_metrics::PerResidueClashMetric::calculate().

bool core::conformation::Conformation::is_centroid ( ) const

convenience test for residue_type_set mode

References core::chemical::CENTROID_t, and residue_typeset_mode().

Referenced by protocols::environment::EnvClaimBroker::broker_dofs(), and protocols::loop_grower::LoopGrower::get_resrange_hbond_energy().

bool core::conformation::Conformation::is_fullatom ( ) const

convenience test for residue_type_set mode

References core::chemical::FULL_ATOM_t, and residue_typeset_mode().

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

bool core::conformation::Conformation::is_membrane ( ) const

inline

convenience test for if the conformation contains information for a membrane protein

References membrane_info_.

bool core::conformation::Conformation::is_mixed_mode ( ) const

convenience test for residue_type_set mode

References core::chemical::MIXED_t, and residue_typeset_mode().

virtual bool core::conformation::Conformation::is_protected ( ) const

inlinevirtual

Reimplemented in protocols::environment::ProtectedConformation.

Referenced by protocols::abinitio::abscript::FragmentCM::apply(), and protocols::environment::DofUnlock::~DofUnlock().

Conformation::Jump const & core::conformation::Conformation::jump ( int jump_number ) const

Returns the Jump with jump number <jump_number>

References atom_tree_, and jump_atom_id().

Referenced by check_valid_membrane(), core::conformation::symmetry::setup_symmetric_conformation(), and core::conformation::symmetry::MirrorSymmetricConformation::synch_mirror_jumps_with_atomtree().

Conformation::Jump const & core::conformation::Conformation::jump ( AtomID const & id ) const

access a jump

References atom_tree_.

id::AtomID core::conformation::Conformation::jump_atom_id ( int jump_number ) const

References const_residue_(), core::kinematics::dir_jump, fold_tree_, core::conformation::get_root_atomno(), core::chemical::has(), and residues_.

Referenced by dof_id_from_torsion_id(), downstream_jump_stub(), get_jump_atom_ids(), jump(), protocols::environment::ProtectedConformation::set_jump(), core::conformation::symmetry::MirrorSymmetricConformation::set_jump(), core::conformation::symmetry::SymmetricConformation::set_jump(), set_jump(), upstream_jump_stub(), protocols::environment::claims::JumpClaim::yield_elements(), and protocols::environment::claims::VirtResClaim::yield_elements().

membrane::MembraneInfoOP core::conformation::Conformation::membrane_info ( )

Returns the const MembraneInfo object in conformation.

Returns the MembraneInfo object in conformation.

Membrane Info contains information describing location of the membrane virtual residue in the pose sequence, membrane spanning region definitions and lipid exposure/burial data

References membrane_info_.

membrane::MembraneInfoOP core::conformation::Conformation::membrane_info ( ) const

Returns the const MembraneInfo object in conformation.

Returns a Membrane Info Object in the conformation.

Membrane Info contains information describing location of the membrane virtual residue in the pose sequence, membrane spanning region definitions and lipid exposure/burial data

Membrane Info contains information regarding membrane residues, foldtree modifications, fullatom vs. centroid embedding parameters for scoring and the spanning topology/lipids accessibility data

References membrane_info_.

core::chemical::PoseResidueTypeSetOP core::conformation::Conformation::modifiable_residue_type_set_for_conf ( core::chemical::TypeSetMode mode = core::chemical::INVALID_t ) const

Return a clone of the Conformation-specific PoseResidueTypeSet (note this is const) Modifications to this RTS won't be seen in the Conformation unless you pass it back in with reset_residue_type_set_for_conf() Should always return a non-null pointer: will create a new PoseResidueTypeSet if the Conformation doesn't have it already.

Return a clone of the Conformation-specific PoseResidueTypeSet. Modifications to this RTS won't be seen in the Conformation unless you pass it back in with reset_residue_type_set_for_conf() Should always return a non-null pointer: will create a new PoseResidueTypeSet if the Conformation doesn't have it already.

References core::chemical::FULL_ATOM_t, core::chemical::CacheableResidueTypeSets::get_res_type_set(), core::chemical::INVALID_t, core::chemical::MIXED_t, residue_type_sets_, residue_typeset_mode(), and core::conformation::TR().

Referenced by protocols::ligand_docking::AddHydrogen::apply(), protocols::jd2::ScreeningJobInputter::pose_from_job(), protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::ROT2res(), and core::util::switch_to_residue_type_set().

core::Size core::conformation::Conformation::n_parameters_sets ( ) const

Get the number of parameters sets defined for this Conformation.

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

References parameters_set_.

Referenced by protocols::helical_bundle::MakeBundle::apply(), protocols::helical_bundle::PerturbBundleHelix::apply(), protocols::helical_bundle::PerturbBundle::apply(), protocols::helical_bundle::BundleParametrizationCalculator::copy_params_from_previous_helices_makebundlehelix_style(), protocols::helical_bundle::BundleReporterFilter::generate_full_tracer_report(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_parametric_info(), and insert_conformation_by_jump().

void core::conformation::Conformation::notify_connection_obs ( ConnectionEvent const & e ) const

private

notify ConnectionEvent observers

work in progress void insert_chemical_chainbreak_between_polymer_residues( Size const lower_seqpos ) { ResidueOP lower_rsd( residues_[ lower_seqpos ] );

the type of the desired variant residue ResidueTypeSet const & rsd_set( lower_rsd->residue_type_set() );

ResidueType const & new_lower_rsd_type ( rsd_set.get_residue_type_with_variant_removed( lower_rsd.type(), UPPER_TERMINUS ) ); ResidueOP new_lower_rsd( ResidueFactory::create_residue( new_lower_rsd_type ) ); }

Remarks: called upon a change in the state of connection between the Conformation and the observer (e.g. destruction of Conformation or transfer of connection)

References connection_obs_hub_.

Referenced by clear_observers(), and receive_observers_from().

void core::conformation::Conformation::notify_general_obs ( GeneralEvent const & e ) const

private

notify GeneralEvent observers

Remarks: should only be called when there are no other suitable event types since specific event notifications will automatically fire a GeneralEvent signal

References general_obs_hub_.

Referenced by notify_identity_obs(), notify_length_obs(), and notify_xyz_obs().

void core::conformation::Conformation::notify_identity_obs	(	IdentityEvent const &	e,
		bool	fire_general = `true`
	)		const

private

notify IdentityEvent observers

Parameters

e	the event
fire_general	fire a GeneralEvent afterwards? default true

References identity_obs_hub_, and notify_general_obs().

Referenced by operator=(), and replace_residue().

void core::conformation::Conformation::notify_length_obs	(	LengthEvent const &	e,
		bool	fire_general = `true`
	)		const

private

notify LengthEvent observers

Parameters

e	the event
fire_general	fire a GeneralEvent afterwards? default true

References length_obs_hub_, and notify_general_obs().

Referenced by append_residue(), delete_polymer_residue(), delete_residue_range_slow(), delete_residue_slow(), insert_conformation_by_jump(), insert_polymer_residue(), insert_residue_by_bond(), insert_residue_by_jump(), and operator=().

void core::conformation::Conformation::notify_xyz_obs	(	XYZEvent const &	e,
		bool	fire_general = `true`
	)		const

private

notify XYZEvent observers

Parameters

e	the event
fire_general	fire a GeneralEvent afterwards? default true

References notify_general_obs(), and xyz_obs_hub_.

Referenced by operator=(), update_residue_coordinates(), and update_residue_torsions().

Size core::conformation::Conformation::num_chains ( ) const

inline

Returns the number of chains.

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

References chain_endings_.

Conformation & core::conformation::Conformation::operator= ( Conformation const & src )

virtual

equals operator

If lengths & sequence of source and target are different, will fire a LengthEvent::INVALIDATE signal and then an IdentityEvent::INVALIDATE signal.

Reimplemented in protocols::environment::ProtectedConformation, core::conformation::symmetry::SymmetricConformation, and core::conformation::symmetry::MirrorSymmetricConformation.

References atom_tree_, chain_endings_, clear(), contains_carbohydrate_residues_, dof_moved_, fold_tree_, in_place_copy(), core::conformation::signals::LengthEvent::INVALIDATE, core::conformation::signals::IdentityEvent::INVALIDATE, membrane_info_, notify_identity_obs(), notify_length_obs(), notify_xyz_obs(), parameters_set_, residue_coordinates_need_updating_, residue_torsions_need_updating_, residue_type_sets_, residues_, secstruct_, sequence_matches(), size(), structure_moved_, tree_set_observer_, and xyz_moved_.

Referenced by protocols::environment::ProtectedConformation::operator=().

core::conformation::parametric::ParametersSetOP core::conformation::Conformation::parameters_set ( core::Size const index )

Access one of the ParametersSets objects linked to this Conformation.

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

References parameters_set_.

Referenced by protocols::helical_bundle::MakeBundle::apply(), protocols::helical_bundle::PerturbBundleHelix::apply(), protocols::helical_bundle::PerturbBundle::apply(), protocols::helical_bundle::BundleParametrizationCalculator::copy_params_from_previous_helices_makebundlehelix_style(), protocols::helical_bundle::BundleReporterFilter::generate_full_tracer_report(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_parametric_info(), and insert_conformation_by_jump().

core::conformation::parametric::ParametersSetCOP core::conformation::Conformation::parameters_set ( core::Size const index ) const

Const access to one of the ParametersSets objects linked to this Conformation.

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

References parameters_set_.

virtual core::environment::DofPassportCOP core::conformation::Conformation::pop_passport ( )

inlinevirtual

Reimplemented in protocols::environment::ProtectedConformation.

Referenced by protocols::environment::DofUnlock::~DofUnlock().

void core::conformation::Conformation::pre_nresidue_change ( )

private

The Conformation must transfer lazily accumulated "moved" data from the AtomTree before changing the number of residues.

Copy any un-registered coordinate or DOF changes into the existing residues. For now, the AtomTree only tracks which Residues need external coordinate changes, and not internal coordinate changes. When internal coordinates go out-of-date in the atom tree, the "update_internal_coordinates" recursion begins at the root. Moreover, the Conformation updates internal coordinates for all residues when it updates. However, when this changes and the AtomTree starts tracking which residues need to have their internal coordinates updated, then it will be necessary to add a call to update_residue_torsions() here.

References update_residue_coordinates().

Referenced by append_polymer_residue_after_seqpos(), append_residue(), append_residue_by_bond(), append_residue_by_jump(), clear(), delete_polymer_residue(), delete_residue_range_slow(), delete_residue_slow(), insert_conformation_by_jump(), insert_polymer_residue(), insert_residue_by_bond(), insert_residue_by_jump(), prepend_polymer_residue_before_seqpos(), safely_append_polymer_residue_after_seqpos(), and safely_prepend_polymer_residue_before_seqpos().

void core::conformation::Conformation::prepend_polymer_residue_before_seqpos	(	Residue const &	new_rsd,
		Size const	seqpos,
		bool const	build_ideal_geometry
	)

virtual

glues to seqpos and perhaps also seqpos-1

Fires a LengthEvent::RESIDUE_PREPEND signal.

Reimplemented in core::conformation::symmetry::SymmetricConformation, and protocols::environment::ProtectedConformation.

References core::conformation::Residue::clone(), dof_moved_, fold_tree_, insert_polymer_residue(), core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_upper_terminus(), core::conformation::Residue::lower_connect(), core::conformation::Residue::natoms(), core::conformation::orient_residue_for_ideal_bond(), pre_nresidue_change(), rebuild_polymer_bond_dependent_atoms(), residue_(), size(), core::id::AtomID_Map< T >::size(), core::conformation::Residue::upper_connect(), and xyz_moved_.

Referenced by protocols::protein_interface_design::movers::LoopLengthChange::apply(), core::conformation::symmetry::SymmetricConformation::prepend_polymer_residue_before_seqpos(), and safely_prepend_polymer_residue_before_seqpos().

virtual void core::conformation::Conformation::push_passport ( core::environment::DofPassportCOP )

inlinevirtual

Reimplemented in protocols::environment::ProtectedConformation.

Referenced by protocols::environment::DofUnlock::DofUnlock().

void core::conformation::Conformation::rebuild_polymer_bond_dependent_atoms ( Size const seqpos )

virtual

Rebuild the atoms ( like HN(seqpos), OC(seqpos+1) ) that are dependent on the polymer bond between seqpos and seqpos+1.

rebuilds the atoms that are dependent on the bond between seqpos and seqpos+1 for their torsion offset

Reimplemented in protocols::environment::ProtectedConformation.

Referenced by append_polymer_residue_after_seqpos(), append_residue_by_bond(), core::conformation::insert_ideal_bonds_at_polymer_junction(), insert_ideal_geometry_at_polymer_bond(), core::conformation::symmetry::SymmetricConformation::prepend_polymer_residue_before_seqpos(), prepend_polymer_residue_before_seqpos(), rebuild_polymer_bond_dependent_atoms_this_residue_only(), and update_polymeric_connection().

void core::conformation::Conformation::rebuild_polymer_bond_dependent_atoms	(	Size const	seqpos,
		int const	upper_lower
	)

private

rebuild atoms in residue seqpos dependent on either the lower (-1) or upper(1) polymer residue

References core::conformation::Residue::atom_depends_on_lower(), core::conformation::Residue::atom_depends_on_upper(), core::conformation::Residue::atom_name(), core::chemical::AtomICoor::build(), core::conformation::Residue::connected_residue_at_lower(), core::conformation::Residue::connected_residue_at_upper(), core::conformation::Residue::icoor(), core::conformation::Residue::is_RNA(), core::conformation::Residue::natoms(), residue_(), set_xyz(), and update_residue_coordinates().

void core::conformation::Conformation::rebuild_polymer_bond_dependent_atoms_this_residue_only ( Size const seqpos )

Rebuilds the atoms that are dependent on polymer bonds for the specified residue only.

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

References rebuild_polymer_bond_dependent_atoms().

Referenced by protocols::cyclic_peptide::DeclareBond::apply(), protocols::simple_moves::ModifyVariantTypeMover::apply(), protocols::relax::fixH(), and protocols::simple_moves::MutateResidue::make_mutation().

void core::conformation::Conformation::rebuild_residue_connection_dependent_atoms	(	Size	seqpos,
		Size	connid
	)

Note: This could be rewritten to avoid a refold using set_bond_angle, etc might be safer since by-xyz ignores possibility of propagating dependencies from the moving atoms...

References core::chemical::AtomICoor::build(), core::conformation::Residue::connected_residue_at_resconn(), core::conformation::Residue::icoor(), core::conformation::Residue::natoms(), residue_(), set_xyz(), core::conformation::Residue::type(), and update_residue_coordinates().

Referenced by protocols::cyclic_peptide::DeclareBond::apply(), protocols::generalized_kinematic_closure::correct_polymer_dependent_atoms_in_pose_segment(), insert_ideal_geometry_at_residue_connection(), protocols::simple_moves::CyclizationMover::minimize_rebuild(), protocols::simple_moves::CyclizationMover::setup_connections(), protocols::cyclic_peptide::crosslinker::TMA_Helper::update_tma_amide_bond_dependent_atoms_asymmetric(), and protocols::cyclic_peptide::crosslinker::TMA_Helper::update_tma_amide_bond_dependent_atoms_symmetric().

void core::conformation::Conformation::receive_observers_from ( Conformation const & src )

fire a ConnectionEvent::TRANSFER to transfer observers from some source Conformation

Parameters

src	Take observers from this source Conformation.

Remarks: Only observers that properly honor the TRANSFER event by re-attaching themselves to 'this' Conformation will be transferred.

References notify_connection_obs(), and core::conformation::signals::ConnectionEvent::TRANSFER.

void core::conformation::Conformation::rederive_chain_endings ( )

private

References chain_endings_, residues_, and size().

Referenced by residues_append(), residues_delete(), and residues_insert().

void core::conformation::Conformation::rederive_chain_ids ( )

private

References chain_endings_, residues_, and size().

Referenced by chain_endings(), chains_from_termini(), delete_chain_ending(), insert_chain_ending(), insert_conformation_by_jump(), reset_chain_endings(), residues_append(), and residues_delete().

void core::conformation::Conformation::replace_residue	(	Size const	seqpos,
		Residue const &	new_rsd_in,
		bool const	orient_backbone
	)

virtual

replace residue

replace a residue Fires an IdentityEvent signal.

Reimplemented in core::conformation::symmetry::SymmetricConformation, core::conformation::symmetry::MirrorSymmetricConformation, and protocols::environment::ProtectedConformation.

References atom_tree_, const_residues(), fold_tree_, notify_identity_obs(), core::conformation::replace_residue_in_atom_tree(), core::conformation::signals::IdentityEvent::RESIDUE, residue_torsions_need_updating_, residues_, and residues_replace().

Referenced by protocols::environment::EnvClaimBroker::add_chainbreak_variants(), protocols::stepwise::modeler::packer::SideChainCopier::apply(), core::conformation::change_cys_state(), copy_segment(), core::conformation::form_disulfide_helper(), protocols::residue_optimization::MetapatchEnumeration::generate_derived_types(), core::conformation::idealize_position(), protocols::denovo_design::rebuild_missing_atoms(), core::conformation::replace_conformation_residue_copying_existing_coordinates(), protocols::grafting::replace_region(), core::conformation::symmetry::MirrorSymmetricConformation::replace_residue(), core::conformation::symmetry::SymmetricConformation::replace_residue(), and replace_residue().

void core::conformation::Conformation::replace_residue	(	Size const	seqpos,
		Residue const &	new_rsd_in,
		utility::vector1< std::pair< std::string, std::string > > const &	atom_pairs
	)

virtual

function to replace a residue based on superposition on the specified input atom pairs

Note: NOTE: at the moment, only superposition on 3 atoms works Fires an IdentityEvent signal.

Reimplemented in core::conformation::symmetry::SymmetricConformation, core::conformation::symmetry::MirrorSymmetricConformation, and protocols::environment::ProtectedConformation.

References core::conformation::Residue::orient_onto_residue(), replace_residue(), and residues_.

void core::conformation::Conformation::reset_chain_endings ( )

virtual

Resets chain data so that the Conformation is marked as a single (chain number) chain.

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

Reimplemented in protocols::environment::ProtectedConformation.

References chain_endings_, and rederive_chain_ids().

Referenced by protocols::domain_assembly::AssembleLinkerMover::apply(), protocols::loop_grower::FragmentExtension::apply(), and protocols::fldsgn::CircularPermutation::apply().

void core::conformation::Conformation::reset_move_data ( )

virtual

forget all the structure modifications

called after domain map information is transferred to the Energies class

Reimplemented in protocols::environment::ProtectedConformation.

References dof_moved_, core::id::AtomID_Map< T >::fill_with(), structure_moved_, and xyz_moved_.

void core::conformation::Conformation::reset_residue_type_set_for_conf	(	core::chemical::PoseResidueTypeSetCOP	new_set,
		core::chemical::TypeSetMode	mode = `core::chemical::INVALID_t`
	)

Reset the Conformation-specific PoseResidueTypeSet for the appropriate mode to the given RTS. (If the given mode is INVALID_t (the recommended default) the mode will be auto-determined from the RTS.)

Reset the Conformation-specific PoseResidueTypeSet for the appropriat mode to the given RTS.

NOTE: You're potentially in for a bunch of trouble if the passed in set isn't a modified version of the value returned by modifiable_residue_type_set_for_conf() from this conformation. Also, a clone of the RTS is made, so subsequent edits to the RTS will not be reflected in the Conformation's RTS

References core::chemical::INVALID_t, residue_type_set_for_conf(), residue_type_sets_, core::chemical::CacheableResidueTypeSets::set_res_type_set(), and core::conformation::TR().

Referenced by protocols::ligand_docking::AddHydrogen::apply(), core::io::pose_from_sfr::PoseFromSFRBuilder::build_pose(), protocols::jd2::ScreeningJobInputter::pose_from_job(), and core::util::switch_to_residue_type_set().

void core::conformation::Conformation::reset_structure_moved ( ) const

inline

reset the structure_moved_ bool

References structure_moved_.

Residue const& core::conformation::Conformation::residue ( Size seqpos ) const

inline

access one of the residues

Note: this access is inlined, since otherwise it shows up in the profiler. This will call non-inlined refold methods if necessary.

update coordinates and torsions for this and all other residues before allowing read access

References residue_coordinates_need_updating_, residue_torsions_need_updating_, residues_, size(), update_residue_coordinates(), and update_residue_torsions().

Residue& core::conformation::Conformation::residue_ ( Size seqpos )

inlineprivate

Returns a non-constant residue reference without triggering coordinate/torsion update.

Use with care. Useful inside torsion/coordinate setters where we want chemical info about a given residue but don't want to trigger the coordinate/torsion updates that go along with a call to residue(seqpos).

Note: APL – Conformation should not give out non-const access to its residues even to derived classes. This function should not be called by derived classes.

References residues_, and size().

Referenced by append_polymer_residue_after_seqpos(), append_residue_by_bond(), apply_transform_Rx_plus_v(), detect_pseudobonds(), fill_missing_atoms(), insert_polymer_residue(), insert_residue_by_bond(), insert_residue_by_jump(), prepend_polymer_residue_before_seqpos(), rebuild_polymer_bond_dependent_atoms(), rebuild_residue_connection_dependent_atoms(), residue_data(), set_polymeric_connection(), and sever_chemical_bond().

ResidueCOP core::conformation::Conformation::residue_cop ( Size seqpos ) const

inline

access one of the residues, using COP

References residue_coordinates_need_updating_, residue_torsions_need_updating_, residues_, size(), update_residue_coordinates(), and update_residue_torsions().

Referenced by protocols::helical_bundle::MakeBundleHelix::add_parameter_info_to_pose(), core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid::compute_total_volume_of_current_residues(), core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid::compute_volumes_of_buried_rotamers(), core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::detect_intra_residue_hydrogen_bonds_symmetric(), core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy::finalize_total_energy(), core::pack::interaction_graph::generate_rotamers_from_packer_solution_description(), core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::initialize_graph_for_packing(), insert_conformation_by_jump(), core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid::prune_voxels_for_fixed_residues(), protocols::loop_grower::transform_to_closest_symmunit(), and core::conformation::parametric::ParametersSet::update_residue_links().

basic::datacache::BasicDataCache const& core::conformation::Conformation::residue_data ( Size seqpos ) const

inline

Read access to the datacache array stored inside a Residue object. Also accessible to the user by calling residue( seqpos ).data_ptr() directly.

The purpose of the residue-level data cache is so that scoring terms may store coordinate-derived information in a Residue (perhaps a Residue that does not belong to a Conformation) so that it can be used during scoring evaluation.

References core::conformation::Residue::data_ptr(), and residue().

basic::datacache::BasicDataCache& core::conformation::Conformation::residue_data ( Size seqpos )

inline

Write access to the datacache array stored inside a Residue object. Although the Conformation very deliberately does not grant users write access to the whole of its Residue objects, it will grant users access to the Residue objects data cache. So while the coordinates and dihedrals of the Residue will not be changable e.g. during the setup-for-scoring phase, data derived from those coordinates and dihedrals and which ends up living in the Residue will be changable.

The purpose of the residue-level data cache is so that scoring terms may store coordinate-derived information in a Residue (perhaps a Residue that does not belong to a Conformation) so that it can be used during scoring evaluation. Accessing the residue_data will trigger a coordinate (or torsion) update.

References core::conformation::Residue::nonconst_data_ptr(), residue_(), residue_coordinates_need_updating_, residue_torsions_need_updating_, size(), update_residue_coordinates(), and update_residue_torsions().

chemical::ResidueType const& core::conformation::Conformation::residue_type ( Size seqpos ) const

inline

access one of the residue's types – avoids coord/torsion update

References residues_, and size().

chemical::ResidueTypeCOP core::conformation::Conformation::residue_type_ptr ( Size seqpos ) const

inline

access one of the residue's types as a COP – avoids coord/torsion update

References residues_, and size().

core::chemical::ResidueTypeSetCOP core::conformation::Conformation::residue_type_set_for_conf ( core::chemical::TypeSetMode mode = core::chemical::INVALID_t ) const

Return the appropriate ResidueTypeSet for the Conformation If mode is INVALID_t (the default), then return the typeset for the majority mode of the Conformation. Note: This may be a GlobalResidueTypeSet, if the Conformation doesn't have a specific PoseResidueTypeSet.

Return the appropriate ResidueTypeSet for the Conformation If mode is INVALID_t (the default), then return the typeset for the majority mode of the Conformation.

References core::chemical::FULL_ATOM_t, core::chemical::CacheableResidueTypeSets::get_res_type_set(), core::chemical::INVALID_t, core::chemical::MIXED_t, residue_type_sets_, residue_typeset_mode(), and core::conformation::TR().

Referenced by protocols::environment::EnvClaimBroker::add_chainbreak_variants(), core::conformation::add_variant_type_to_conformation_residue(), core::conformation::change_cys_state(), core::scoring::RamaPrePro::eval_rpp_rama_derivatives(), core::scoring::RamaPrePro::eval_rpp_rama_score(), core::conformation::symmetry::MirrorSymmetricConformation::flip_chirality(), core::conformation::form_disulfide(), core::scoring::RamaPrePro::get_mainchain_torsions_covered(), core::conformation::inv_virtual_type_for_conf(), core::scoring::RamaPrePro::random_mainchain_torsions(), core::conformation::remove_variant_type_from_conformation_residue(), reset_residue_type_set_for_conf(), core::pose::Pose::residue_type_set_for_pose(), core::conformation::symmetry::setup_symmetric_conformation(), and core::conformation::virtual_type_for_conf().

core::chemical::TypeSetMode core::conformation::Conformation::residue_typeset_mode ( bool majority = true ) const

What mode of ResidueTypeSet is this Conformation made of? If majority is true, it will be the mode of the ResidueTypes for most residues in the pose. If majority is false, core::chemical::MIXED_t will be returned for conformations with ResidueTypes of multiple modes.

References empty(), core::chemical::INVALID_t, core::chemical::MIXED_t, residue_type(), size(), core::conformation::TR(), and core::chemical::TYPE_SET_MODES_LENGTH.

Referenced by protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover::apply(), protocols::comparative_modeling::ThreadingMover::apply(), protocols::loop_grower::LoopPartialSolution::apply(), protocols::forge::components::VarLengthBuild::apply(), protocols::loop_grower::LoopPartialSolution::apply_sheets(), protocols::forge::remodel::RemodelMover::centroid_build(), protocols::loop_grower::LoopGrower::get_resrange_hbond_energy(), core::pose::get_restype_for_pose(), core::conformation::inv_virtual_type_for_conf(), is_centroid(), is_fullatom(), is_mixed_mode(), modifiable_residue_type_set_for_conf(), protocols::loop_grower::LoopGrower::nton3_hbond_score(), protocols::comparative_modeling::rebuild_loops_until_closed(), residue_type_set_for_conf(), and core::conformation::virtual_type_for_conf().

void core::conformation::Conformation::residues_append	(	Residue const &	new_rsd,
		bool	start_new_chain,
		bool	by_jump = `false`,
		std::string const &	root_atom = `""`,
		id::NamedAtomID	anchor_id = `id::NamedAtomID::BOGUS_NAMED_ATOM_ID()`
	)

private

PRIVATE: wrap direct access to the Residues container for appending

Warning: Since this is the innermost routine when replacing a residue, it does not fire any signals to ensure that observer access to the residues container does not trigger an atom tree refold prematurely.

References core::id::NamedAtomID::atom(), core::id::NamedAtomID::BOGUS_NAMED_ATOM_ID(), core::conformation::Residue::clone(), dof_moved_, core::conformation::Residue::natoms(), rederive_chain_endings(), rederive_chain_ids(), residues_, core::id::AtomID_Map< T >::resize(), core::id::NamedAtomID::rsd(), secstruct_, structure_moved_, core::conformation::TR(), update_noncanonical_connection(), update_polymeric_connection(), and xyz_moved_.

Referenced by append_residue().

void core::conformation::Conformation::residues_delete ( Size seqpos )

private

PRIVATE: wrap direct access to the Residues container for replacement also handles redimensioning and setting of the _moved arrays and updating of sequence numbers

Warning: Since this is the innermost routine when replacing a residue, it does not fire any signals to ensure that observer access to the residues container does not trigger an atom tree refold prematurely.

References rederive_chain_endings(), rederive_chain_ids(), residues_, secstruct_, update_polymeric_connection(), and update_sequence_numbering().

Referenced by delete_polymer_residue(), delete_residue_range_slow(), and delete_residue_slow().

void core::conformation::Conformation::residues_insert	(	Size	seqpos,
		Residue const &	new_rsd,
		bool	use_lower_chain = `false`,
		bool	new_chain = `false`
	)

private

PRIVATE: wrap direct access to the Residues container for replacement also handles redimensioning and setting of the _moved arrays and updating of sequence numbers

Warning: Since this is the innermost routine when replacing a residue, it does not fire any signals to ensure that observer access to the residues container does not trigger an atom tree refold prematurely.

References core::conformation::Residue::clone(), dof_moved_, core::conformation::Residue::name(), core::conformation::Residue::natoms(), rederive_chain_endings(), residues_, secstruct_, structure_moved_, update_polymeric_connection(), update_sequence_numbering(), and xyz_moved_.

Referenced by insert_polymer_residue(), insert_residue_by_bond(), and insert_residue_by_jump().

void core::conformation::Conformation::residues_replace	(	Size	seqpos,
		Residue const &	new_rsd
	)

private

wrap direct access to the Residues container

PRIVATE: wrap direct access to the Residues container for replacement also handles redimensioning and setting of the _moved arrays

Warning: Since this is the innermost routine when replacing a residue, it does not fire any signals to ensure that observer access to the residues container does not trigger an atom tree refold prematurely.

References core::conformation::Residue::clone(), dof_moved_, core::conformation::Residue::natoms(), residues_, structure_moved_, and xyz_moved_.

Referenced by replace_residue().

void core::conformation::Conformation::safely_append_polymer_residue_after_seqpos	(	Residue const &	new_rsd,
		Size const	seqpos,
		bool const	build_ideal_geometry
	)

virtual

glues to seqpos and perhaps also seqpos+1, removes termini variants if necessary

Reimplemented in core::conformation::symmetry::SymmetricConformation, and protocols::environment::ProtectedConformation.

References append_polymer_residue_after_seqpos(), pre_nresidue_change(), and core::conformation::remove_upper_terminus_type_from_conformation_residue().

Referenced by protocols::loop_grower::LoopPartialSolution::add_sheets(), protocols::seeded_abinitio::GrowPeptides::append_residues_cterminally(), protocols::ncbb::oop::OopCreatorMover::apply(), protocols::loop_grower::SheetSampler::apply(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::apply(), protocols::fldsgn::CircularPermutation::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::forge::components::VarLengthBuild::apply(), protocols::loops::apply_sequence_mapping(), protocols::fold_from_loops::utils::attach_unfolded_pose_to_pose_c_term(), protocols::loop_grower::LoopComparator::fill_pose(), protocols::forge::methods::grow_right_r(), protocols::protein_interface_design::movers::PlaceOnLoop::loop_length(), protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue(), protocols::ub_e2c::ubi_e2c_modeler::restore_cter(), protocols::loop_grower::LoopGrower::single_grow(), and protocols::loop_grower::LoopGrower::update_to_stored().

void core::conformation::Conformation::safely_prepend_polymer_residue_before_seqpos	(	Residue const &	new_rsd,
		Size const	seqpos,
		bool const	build_ideal_geometry
	)

virtual

glues to seqpos and perhaps also seqpos-1, removes termini variants if necessary

Fires a LengthEvent::RESIDUE_PREPEND signal.

Reimplemented in core::conformation::symmetry::SymmetricConformation, and protocols::environment::ProtectedConformation.

References pre_nresidue_change(), prepend_polymer_residue_before_seqpos(), and core::conformation::remove_lower_terminus_type_from_conformation_residue().

Referenced by protocols::loop_grower::LoopPartialSolution::add_sheets(), protocols::seeded_abinitio::GrowPeptides::append_residues_nterminally(), protocols::protein_interface_design::movers::LoopLengthChange::apply(), protocols::ncbb::oop::OopCreatorMover::apply(), protocols::loop_grower::SheetSampler::apply(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::apply(), protocols::loops::apply_sequence_mapping(), protocols::fold_from_loops::utils::attach_unfolded_pose_to_pose_n_term(), protocols::splice::SpliceOutTail::build_ideal_segment(), protocols::splice::SpliceInTail::build_ideal_segment(), protocols::splice::SpliceIn::build_ideal_segment(), protocols::splice::SpliceOut::build_ideal_segment(), protocols::loop_grower::LoopComparator::fill_pose(), protocols::forge::methods::grow_left_r(), protocols::loop_grower::LoopGrower::single_grow(), and protocols::loop_grower::LoopGrower::update_to_stored().

bool core::conformation::Conformation::same_type_as_me	(	Conformation const &	other,
		bool const	recurse = `true`
	)		const

virtual

determine the type of the ConformationOP

Reimplemented in protocols::environment::ProtectedConformation, core::conformation::symmetry::SymmetricConformation, and core::conformation::symmetry::MirrorSymmetricConformation.

References same_type_as_me().

Referenced by core::import_pose::pose_from_file(), core::conformation::symmetry::MirrorSymmetricConformation::same_type_as_me(), core::conformation::symmetry::SymmetricConformation::same_type_as_me(), same_type_as_me(), and protocols::environment::ProtectedConformation::same_type_as_me().

char core::conformation::Conformation::secstruct ( Size seqpos ) const

inline

Returns the secondary structure the position <seqpos>

Returns: character representing secondary structure; returns 'L' if the requested sequence position is larger than the length in the secondary structure array

References secstruct_.

Referenced by protocols::loophash::LoopHashDiversifier::apply(), protocols::LoopRebuild::fast_ccd_close_loops(), protocols::loops::loop_mover::perturb::fast_ccd_close_loops(), protocols::membrane::get_secstruct(), core::scoring::MembranePotential::non_helix_in_membrane_penalty(), core::scoring::methods::EnvEnergy::residue_energy(), core::scoring::membrane::MPNonHelixPenalty::residue_energy(), and core::scoring::methods::CenPairEnergy::residue_pair_energy().

bool core::conformation::Conformation::sequence_matches ( Conformation const & other ) const

do the names of all residues in this and src match?

Am I composed of the same sequence of ResidueType objects as other? DANGER! Fails, unexpectedly, if a histidine pair has a different tautomerization. tex, 9/12/08 The above comment points out that this method isn't a clearly defined idea, because there are many ways that someone could imagine comparing the a sequence, including:

cutpoint variants
tautomers
disulfides For some applications, it's probably to get strings of the one-letter names of the sequence and compare those instead.

References core::conformation::Residue::chain(), core::conformation::Residue::connections_match(), residue(), size(), and core::conformation::Residue::type().

Referenced by operator=(), protocols::design_opt::GreedyOptMutationMover::pose_coords_are_same(), and protocols::matdes::MatDesGreedyOptMutationMover::pose_coords_are_same().

void core::conformation::Conformation::set_bond_angle	(	AtomID const &	atom1,
		AtomID const &	atom2,
		AtomID const &	atom3,
		Real const	setting
	)

virtual

Sets the bond angle defined by <atom[1-3]> to <setting>

Note: in radians!!

Reimplemented in core::conformation::symmetry::SymmetricConformation, and protocols::environment::ProtectedConformation.

References align_virtual_atoms_in_carbohydrate_residue(), atom_tree_, residues_, core::id::AtomID::rsd(), and set_dof_moved().

Referenced by core::fragment::BBTorsionAndAnglesSRFD::apply(), protocols::farnesyl::InstallFarnesylMover::apply(), protocols::helical_bundle::copy_helix_bondangles(), protocols::simple_moves::RepeatPropagationMover::copy_phi_psi_omega(), protocols::topology_broker::fix_internal_coords_of_siblings(), protocols::abinitio::abscript::fix_internal_coords_of_siblings(), protocols::topology_broker::fix_mainchain_connect(), protocols::abinitio::abscript::fix_mainchain_connect(), core::conformation::idealize_position(), core::conformation::insert_ideal_bonds_at_polymer_junction(), insert_ideal_geometry_at_polymer_bond(), insert_ideal_geometry_at_residue_connection(), core::conformation::insert_ideal_mainchain_bonds(), protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::semiexpl_water_hbgeom_score(), core::conformation::symmetry::SymmetricConformation::set_bond_angle(), and protocols::generalized_kinematic_closure::set_loop_pose().

void core::conformation::Conformation::set_bond_length	(	AtomID const &	atom1,
		AtomID const &	atom2,
		Real const	setting
	)

virtual

Sets the cond length between <atom1> and <atom2> to <setting>

Reimplemented in core::conformation::symmetry::SymmetricConformation, and protocols::environment::ProtectedConformation.

References align_virtual_atoms_in_carbohydrate_residue(), atom_tree_, residues_, core::id::AtomID::rsd(), and set_dof_moved().

Referenced by protocols::farnesyl::InstallFarnesylMover::apply(), protocols::backbone_moves::local_backbone_mover::Residue::apply_to_pose(), protocols::helical_bundle::copy_helix_bondlengths(), protocols::simple_moves::RepeatPropagationMover::copy_phi_psi_omega(), protocols::topology_broker::fix_mainchain_connect(), protocols::abinitio::abscript::fix_mainchain_connect(), core::conformation::idealize_position(), core::conformation::insert_ideal_bonds_at_polymer_junction(), insert_ideal_geometry_at_polymer_bond(), insert_ideal_geometry_at_residue_connection(), core::conformation::insert_ideal_mainchain_bonds(), protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::semiexpl_water_hbgeom_score(), core::conformation::symmetry::SymmetricConformation::set_bond_length(), and protocols::generalized_kinematic_closure::set_loop_pose().

void core::conformation::Conformation::set_dof	(	DOF_ID const &	id,
		Real const	setting
	)

virtual

Sets the AtomTree degree of freedom (DOF) <id> to <setting>

Reimplemented in protocols::environment::ProtectedConformation, core::conformation::symmetry::SymmetricConformation, and core::conformation::symmetry::MirrorSymmetricConformation.

References atom_tree_, residue_torsions_need_updating_, and set_dof_moved().

Referenced by protocols::rna::movers::RNAIdealizeMover::apply(), protocols::topology_broker::fix_internal_coords_of_siblings(), protocols::abinitio::abscript::fix_internal_coords_of_siblings(), core::conformation::symmetry::MirrorSymmetricConformation::set_dof(), and core::conformation::symmetry::SymmetricConformation::set_dof().

void core::conformation::Conformation::set_dof_moved ( AtomID const & id )

inlineprivate

notify of dof-change

References dof_moved_, residue_coordinates_need_updating_, and structure_moved_.

Referenced by insert_fragment(), set_bond_angle(), set_bond_length(), set_dof(), set_jump(), set_stub_transform(), set_torsion(), and set_torsion_angle().

void core::conformation::Conformation::set_dof_moved ( DOF_ID const & id )

inlineprivate

notify of dof-change

References dof_moved_, residue_coordinates_need_updating_, and structure_moved_.

void core::conformation::Conformation::set_jump	(	int const	jump_number,
		Jump const &	new_jump
	)

virtual

Sets the jump <jump_number> to <new_jump>

Reimplemented in core::conformation::symmetry::SymmetricConformation, core::conformation::symmetry::MirrorSymmetricConformation, and protocols::environment::ProtectedConformation.

References atom_tree_, jump_atom_id(), core::kinematics::Jump::ortho_check(), and set_dof_moved().

Referenced by protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue(), protocols::environment::ProtectedConformation::set_jump(), core::conformation::symmetry::MirrorSymmetricConformation::set_jump(), core::conformation::symmetry::SymmetricConformation::set_jump(), and core::conformation::symmetry::MirrorSymmetricConformation::synch_mirror_jumps_with_atomtree().

void core::conformation::Conformation::set_jump	(	AtomID const &	id,
		Jump const &	new_jump
	)

virtual

set a jump

Reimplemented in core::conformation::symmetry::SymmetricConformation, core::conformation::symmetry::MirrorSymmetricConformation, and protocols::environment::ProtectedConformation.

References atom_tree_, core::kinematics::Jump::ortho_check(), and set_dof_moved().

void core::conformation::Conformation::set_jump_atom_stub_id ( id::StubID const & id )

References atom_tree_.

void core::conformation::Conformation::set_membrane_info ( membrane::MembraneInfoOP mem_info )

Setup a Membrane Info object in Conformation - pos & topology.

Rosetta Membrane Framework /// Core data for interacting with membrane proteins in Rosetta /// /// Authors: ///

Rebecca Alford (rfalf.nosp@m.ord1.nosp@m.2@gma.nosp@m.il.c.nosp@m.om) ///
Julia Koehler Leman (julia.nosp@m..koe.nosp@m.hler1.nosp@m.982@.nosp@m.gmail.nosp@m..com) ///
Jeff Gray (jgray.nosp@m.@jhu.nosp@m..edu) ///

Add a MembraneInfo object - describes the position of the membrane virtual residue, information on membrane spanning regions, lipid exposure/burial of residues in the pose, and fullatom steepness and thickness parameters. At construction, specify membrane position and list of spanning topology objects by chain.

References membrane_info_.

Referenced by protocols::membrane::AddMembraneMover::apply().

void core::conformation::Conformation::set_noncanonical_connection	(	Size	res_id_lower,
		Size	lr_conn_id,
		Size	res_id_upper,
		Size	ur_conn_id
	)

Create an arbitrary covalent connection between two residues.

References residues_.

Referenced by protocols::cyclic_peptide::DeclareBond::apply(), core::conformation::symmetry::SymmetricConformation::update_noncanonical_connection(), and update_noncanonical_connection().

void core::conformation::Conformation::set_polymeric_connection	(	Size	res_id_lower,
		Size	res_id_upper
	)

virtual

identify polymeric connections

The lower residue connects to the upper residue through its upper_connect connection The upper residue connects to the lower residue through its lower_connect connection

Reimplemented in protocols::environment::ProtectedConformation.

References residue_(), and residues_.

Referenced by update_polymeric_connection().

virtual void core::conformation::Conformation::set_secstruct	(	Size const	seqpos,
		char const	setting
	)

inlinevirtual

Sets the secondary structure of the position <seqpos> to <setting>

Sets secondary structure character of a sequence position. Will resize the secondary structure array if the requested sequence position is larger than the length of the array.

Reimplemented in core::conformation::symmetry::SymmetricConformation, and protocols::environment::ProtectedConformation.

References secstruct_.

Referenced by protocols::environment::ProtectedConformation::set_secstruct(), and core::conformation::symmetry::SymmetricConformation::set_secstruct().

void core::conformation::Conformation::set_stub_transform	(	id::StubID const &	stub_id1,
		id::StubID const &	stub_id2,
		kinematics::RT const &	target_rt
	)

virtual

Set the transform between two stubs – only works if there's a jump between the two sets of stubatoms.

Reimplemented in protocols::environment::ProtectedConformation.

References atom_tree_, and set_dof_moved().

Referenced by protocols::denovo_design::movers::AlignResiduesMover::align_residues(), core::fragment::DownJumpSRFD::apply(), core::io::silent::BinarySilentStruct::fill_pose(), core::io::silent::ProteinSilentStruct_Template< T >::fill_pose(), protocols::forge::build::ConnectRight::modify_impl(), protocols::jumping::MembraneJump::rt_templates(), protocols::jumping::PairingLibrary::set_tmh_jump(), and core::pose::swap_transform().

void core::conformation::Conformation::set_torsion	(	TorsionID const &	tor_id,
		Real const	setting
	)

virtual

Sets the AtomTree DOF and the torsion OR rigid-body offset in the corresponding Residue or Jump.

Remarks: This is a poorly named method, as it can also be used to set jump rigid-body offsets. ~Labonte

Reimplemented in core::conformation::symmetry::SymmetricConformation, core::conformation::symmetry::MirrorSymmetricConformation, and protocols::environment::ProtectedConformation.

References atom_tree_, core::id::BB, core::id::BRANCH, core::id::CHI, dof_id_from_torsion_id(), get_torsion_angle_atom_ids(), core::id::JUMP, core::conformation::Residue::mainchain_atom(), core::conformation::Residue::mainchain_atoms(), core::conformation::Residue::mainchain_torsions(), core::id::NU, core::id::PHI, residues_, core::id::TorsionID::rsd(), set_dof_moved(), core::id::TorsionID::torsion(), core::conformation::TR(), core::id::TorsionID::type(), and core::id::DOF_ID::valid().

Referenced by protocols::simple_moves::RandomOmegaFlipMover::apply(), protocols::simple_moves::RandomTorsionMover::apply(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::apply(), core::kinematics::jacobian::ModuleType1::apply_delta_torsions_angles(), protocols::helical_bundle::copy_helix_dihedrals(), protocols::environment::ProtectedConformation::set_torsion(), core::conformation::symmetry::MirrorSymmetricConformation::set_torsion(), and core::conformation::symmetry::SymmetricConformation::set_torsion().

void core::conformation::Conformation::set_torsion_angle	(	AtomID const &	atom1,
		AtomID const &	atom2,
		AtomID const &	atom3,
		AtomID const &	atom4,
		Real const	setting,
		bool const	quiet = `false`
	)

virtual

Sets the torsion angle defined by <atom[1-4]> to <setting>

Reimplemented in core::conformation::symmetry::SymmetricConformation, protocols::environment::ProtectedConformation, and core::conformation::symmetry::MirrorSymmetricConformation.

References align_virtual_atoms_in_carbohydrate_residue(), atom_tree_, residue_torsions_need_updating_, residues_, core::id::AtomID::rsd(), set_dof_moved(), and core::conformation::TR().

Referenced by protocols::simple_moves::oop::OopMover::apply(), protocols::simple_moves::triazolamer::TriazolamerMover::apply(), protocols::simple_moves::chiral::ChiralMover::apply(), protocols::simple_moves::TorsionDOFMover::apply(), protocols::simple_moves::SetTorsion::apply(), protocols::topology_broker::fix_mainchain_connect(), protocols::abinitio::abscript::fix_mainchain_connect(), protocols::generalized_kinematic_closure::general_set_phi(), protocols::generalized_kinematic_closure::general_set_psi(), protocols::frags::TorsionFragment::insert(), protocols::cyclic_peptide::PeptideStubMover::preserve_old_mainchain_torsions(), protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::semiexpl_water_hbgeom_score(), core::conformation::carbohydrates::set_glycosidic_torsion(), protocols::generalized_kinematic_closure::set_loop_pose(), core::conformation::symmetry::MirrorSymmetricConformation::set_torsion_angle(), core::conformation::symmetry::SymmetricConformation::set_torsion_angle(), protocols::simple_moves::oop::OopMover::update_hydrogens_(), and protocols::simple_moves::triazolamer::TriazolamerMover::update_hydrogens_().

void core::conformation::Conformation::set_xyz	(	AtomID const &	id,
		PointPosition const &	position
	)

virtual

Reimplemented in core::conformation::symmetry::SymmetricConformation.

References atom_tree_, residues_, and set_xyz_moved().

Referenced by core::conformation::carbohydrates::align_virtual_atoms_in_carbohydrate_residue(), align_virtual_atoms_in_carbohydrate_residue(), protocols::carbohydrates::IdealizeAnomericHydrogens::apply(), fill_missing_atoms(), protocols::rna::movers::RNAIdealizeMover::perturb_pose(), protocols::cyclic_peptide::PeptideStubMover::rebuild_atoms(), rebuild_polymer_bond_dependent_atoms(), rebuild_residue_connection_dependent_atoms(), core::conformation::symmetry::recenter(), core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose(), protocols::fibril::reorient_extended_fibril(), core::conformation::symmetry::SymmetricConformation::set_xyz(), and core::conformation::update_cutpoint_virtual_atoms_if_connected().

void core::conformation::Conformation::set_xyz_moved ( AtomID const & id )

inlineprivate

notify of xyz-change

References residue_torsions_need_updating_, structure_moved_, and xyz_moved_.

Referenced by batch_set_xyz(), and set_xyz().

void core::conformation::Conformation::set_xyz_moved ( utility::vector1< AtomID > const & ids )

inlineprivate

notify of mutiple-xyz-change

References residue_torsions_need_updating_, structure_moved_, and xyz_moved_.

void core::conformation::Conformation::setup_atom_tree ( )

private

(re-)builds the AtomTree using the FoldTree and the Residues

References atom_tree_, core::conformation::build_tree(), const_residues(), fold_tree_, residue_coordinates_need_updating_, residue_torsions_need_updating_, and update_residue_torsions().

Referenced by append_residue(), delete_residue_range_slow(), delete_residue_slow(), fold_tree(), and insert_conformation_by_jump().

void core::conformation::Conformation::setup_glycan_trees ( )

Setup glycan trees and attach length observer.

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

Referenced by core::pose::symmetry::extract_asymmetric_unit(), core::pose::symmetry::get_asymmetric_pose_copy_from_symmetric_pose(), core::pose::carbohydrates::glycosylate_pose(), insert_conformation_by_jump(), core::pose::symmetry::make_asymmetric_pose(), core::pose::make_pose_from_saccharide_sequence(), core::pose::symmetry::make_symmetric_pose(), and core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose().

void core::conformation::Conformation::sever_chemical_bond	(	Size	seqpos1,
		Size	res1_resconn_index,
		Size	seqpos2,
		Size	res2_resconn_index
	)

virtual

Sever the chemical bond between two residues by stating that the connections for those residues are "incomplete" (i.e. in a state where these residues are not ready to be scored).

References core::conformation::Residue::mark_connect_incomplete(), and residue_().

Referenced by core::pose::correctly_add_2prime_connection_variants(), and core::pose::declare_cutpoint_chemical_bond().

void core::conformation::Conformation::show_residue_connections ( ) const

Show residue connections for debugging purposes.

References core::conformation::TR().

Referenced by core::conformation::operator<<().

void core::conformation::Conformation::show_residue_connections ( std::ostream & os ) const

Show residue connections for debugging purposes.

Note: This method is a rewrite of an earlier version to include an argument for desired output stream. This is to be more consistent with typical show() methods and allows for simple << operator overloading for use in PyRosetta. ~ Labonte

References core::conformation::Residue::connect_map(), core::chemical::ResConnID::connid(), core::conformation::Residue::n_non_polymeric_residue_connections(), core::conformation::Residue::n_polymeric_residue_connections(), core::conformation::Residue::n_possible_residue_connections(), core::conformation::Residue::name(), core::chemical::ResConnID::resid(), core::conformation::Residue::residue_connect_atom_index(), residues_, and size().

Size core::conformation::Conformation::size ( ) const

inline

Returns the number of residues in the Conformation.

References residues_.

bool core::conformation::Conformation::structure_moved ( ) const

inline

has the structure moved since the last call to reset_move_data or reset_structure_moved

References structure_moved_.

Referenced by core::pack::create_packer_graph(), protocols::features::AtomInResidueAtomInResiduePairFeatures::report_atom_pairs(), protocols::features::AtomAtomPairFeatures::report_atom_pairs(), protocols::features::TaskOperationFeatures::report_features(), protocols::features::HBondFeatures::report_features(), and protocols::features::PairFeatures::report_residue_pairs().

kinematics::Stub core::conformation::Conformation::stub_from_id ( id::StubID const & id ) const

References atom_tree_.

Real core::conformation::Conformation::torsion ( TorsionID const & tor_id ) const

Return the torsion angle OR rigid-body offset for <id>

Remarks: This is a poorly named method, as it can also be used to access jump rigid-body offsets. ~Labonte

References atom_tree_, core::id::BB, core::id::BRANCH, core::id::CHI, dof_id_from_torsion_id(), core::id::JUMP, core::id::NU, residue(), residue_coordinates_need_updating_, residue_torsions_need_updating_, core::id::TorsionID::rsd(), core::id::TorsionID::torsion(), core::id::TorsionID::type(), update_residue_coordinates(), and update_residue_torsions().

Referenced by protocols::simple_moves::RandomOmegaFlipMover::apply(), protocols::simple_moves::RandomTorsionMover::apply(), core::kinematics::jacobian::ModuleType1::apply_delta_torsions_angles(), backbone_torsion_angle_atoms(), backbone_torsion_angle_atoms_meta_aramid(), backbone_torsion_angle_atoms_oligourea(), backbone_torsion_angle_atoms_ortho_aramid(), backbone_torsion_angle_atoms_para_aramid(), protocols::helical_bundle::copy_helix_dihedrals(), debug_residue_torsions(), get_torsion_angle_atom_ids(), core::conformation::symmetry::MirrorSymmetricConformation::set_torsion(), and core::conformation::symmetry::SymmetricConformation::set_torsion().

Real core::conformation::Conformation::torsion_angle	(	AtomID const &	atom1,
		AtomID const &	atom2,
		AtomID const &	atom3,
		AtomID const &	atom4
	)		const

Returns the torsion angle defined by <atom[1-4]> in Radians.

References atom_tree_, atoms_are_bonded(), core::id::DOF_ID::BOGUS_DOF_ID(), core::conformation::TR(), update_residue_coordinates(), and xyz().

Referenced by protocols::simple_moves::oop::OopRandomSmallMover::apply(), protocols::simple_moves::triazolamer::TriazolamerRandomSmallMover::apply(), protocols::simple_moves::chiral::ChiralMover::apply(), protocols::constraint_generator::DihedralConstraintGenerator::apply(), protocols::simple_moves::SetTorsion::apply(), protocols::generalized_kinematic_closure::selector::GeneralizedKICselector::apply_lowest_delta_torsion_selector(), protocols::topology_broker::fix_mainchain_connect(), protocols::abinitio::abscript::fix_mainchain_connect(), core::conformation::carbohydrates::get_glycosidic_torsion(), protocols::cyclic_peptide::PeptideStubMover::handle_lower_terminus(), protocols::simple_moves::oop::OopMover::update_hydrogens_(), and protocols::simple_moves::triazolamer::TriazolamerMover::update_hydrogens_().

void core::conformation::Conformation::unblock_signals ( )

allow signals to be sent

If unblocking after buffering, buffered/held signals will be sent.

References general_obs_hub_, identity_obs_hub_, length_obs_hub_, and xyz_obs_hub_.

Referenced by protocols::denovo_design::add_residues_to_pose(), and delete_residue_slow().

void core::conformation::Conformation::update_actcoord ( Size resid )

References residues_.

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

void core::conformation::Conformation::update_actcoords ( )

References residues_, and size().

void core::conformation::Conformation::update_domain_map ( DomainMap & domain_map ) const

Generate a domain_map from the current dof/xyz moved data.

References atom_tree_, dof_moved_, size(), and xyz_moved_.

Referenced by protocols::rna::movers::RNA_LoopCloser::passes_fast_scan().

void core::conformation::Conformation::update_membrane_position	(	Vector	center,
		Vector	normal
	)

Update Normal, Center in the Membrane.

Sets the center and normal coordinates to the appropriate parameters and checks for a valid stub prior to returning.

References core::conformation::membrane::center, check_valid_membrane(), membrane_info_, core::conformation::membrane::normal, and residues_.

Referenced by protocols::membrane::SetMembranePositionMover::apply(), protocols::membrane::MembranePositionFromTopologyMover::apply(), protocols::membrane::SetMembraneNormalMover::apply(), protocols::membrane::SetMembraneCenterMover::apply(), and protocols::membrane::membrane_normal_to_length_15().

void core::conformation::Conformation::update_noncanonical_connection	(	Size	lower_seqpos,
		Size	lr_conn_id,
		Size	upper_seqpos,
		Size	ur_conn_id
	)

virtual

Update the connection status between the lower_seqpos residue's lr_conn_id connection ID and the upper_seqpos residue's ur_conn_id connection ID.

Reimplemented in core::conformation::symmetry::SymmetricConformation.

References residues_, set_noncanonical_connection(), size(), and core::conformation::TR().

Referenced by core::pose::add_custom_variant_type_to_pose_residue(), core::pose::add_variant_type_to_pose_residue(), core::pose::Pose::real_to_virtual(), core::pose::remove_variant_type_from_pose_residue(), residues_append(), and core::pose::Pose::virtual_to_real().

void core::conformation::Conformation::update_orbital_coords ( Residue & rsd ) const

References core::conformation::Residue::atoms_with_orb_index(), core::conformation::Residue::bonded_orbitals(), core::conformation::Residue::build_orbital_xyz(), and core::conformation::Residue::set_orbital_xyz().

Referenced by update_residue_coordinates(), and update_residue_torsions().

void core::conformation::Conformation::update_orbital_coords ( Size resid )

References residues_.

void core::conformation::Conformation::update_polymeric_connection	(	Size	lower_seqpos,
		bool	update_connection_dep_atoms = `false`
	)

Update the polymer connection status between lower_seqpos and lower_seqpos+1 based on chainID's and termini. If update_connection_dep_atoms is true, positions of atoms dependent on the polymer connection are updated.

References core::chemical::C_METHYLAMIDATION, core::conformation::Residue::chain(), core::conformation::Residue::has_variant_type(), core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_polymer(), core::chemical::N_ACETYLATION, rebuild_polymer_bond_dependent_atoms(), residues_, set_polymeric_connection(), and size().

Referenced by protocols::simple_moves::hbs::HbsPatcher::apply(), protocols::simple_moves::a3b_hbs::A3BHbsPatcher::apply(), protocols::ncbb::oop::OopCreatorMover::apply(), protocols::protein_interface_design::movers::copy_hotspot_to_pose(), protocols::relax::cyclize_pose(), protocols::metal_interface::MatchGrafter::graft(), protocols::protein_interface_design::movers::PlaceStubMover::place_stub(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::place_stubs(), residues_append(), residues_delete(), and residues_insert().

void core::conformation::Conformation::update_residue_coordinates ( ) const

private

Will (if necessary) copy the xyz coordinates from the AtomTree to the Residues being managed.

The AtomTree is responsible for tracking the set of residues whose coordinates need updating, and informs the Conformation object of these residues. The Conformation only updates coordinates for this subset of residues.

Note: Always safe to call. Nothing will happen unless coords_need_updating_ is true.

References atom_tree_, notify_xyz_obs(), and residue_coordinates_need_updating_.

Referenced by append_polymer_residue_after_seqpos(), append_residue_by_bond(), debug_residue_torsions(), fill_missing_atoms(), fold_tree(), force_update_residue_coordinates(), insert_residue_by_bond(), pre_nresidue_change(), rebuild_polymer_bond_dependent_atoms(), rebuild_residue_connection_dependent_atoms(), residue(), residue_cop(), residue_data(), torsion(), and torsion_angle().

void core::conformation::Conformation::update_residue_coordinates	(	Size	seqpos,
		bool	fire_signal = `true`
	)		const

private

References atom_tree_, core::conformation::Residue::natoms(), notify_xyz_obs(), residues_, core::conformation::Residue::set_xyz(), core::conformation::Residue::update_actcoord(), and update_orbital_coords().

void core::conformation::Conformation::update_residue_torsions ( ) const

private

Will (if necessary) copy the torsion angles (mainchain/chi) from the AtomTree to the Residues being managed.

Note: Always safe to call. Nothing will happen unless torsions_need_updating_ is true.

References notify_xyz_obs(), residue_torsions_need_updating_, residues_, and size().

Referenced by debug_residue_torsions(), declare_chemical_bond(), force_update_residue_torsions(), residue(), residue_cop(), residue_data(), setup_atom_tree(), and torsion().

void core::conformation::Conformation::update_residue_torsions	(	Size	seqpos,
		bool	fire_signal = `true`
	)		const

private

References core::chemical::ACETYLATED_NTERMINUS_VARIANT, atom_tree_torsion(), core::id::BB, core::chemical::rna::CHI, core::id::CHI, core::conformation::Residue::chi(), get_torsion_angle_atom_ids(), core::conformation::Residue::has_variant_type(), core::conformation::Residue::mainchain_torsions(), core::chemical::METHYLATED_CTERMINUS_VARIANT, core::conformation::Residue::n_nus(), core::conformation::Residue::nchi(), notify_xyz_obs(), core::id::NU, core::conformation::Residue::nus(), residues_, and update_orbital_coords().

void core::conformation::Conformation::update_sequence_numbering	(	Size	new_size,
		utility::vector1< Size > const &	old2new
	)

private

remap *_moved arrays, sequence numbering in the residues_ arrays, etc, after insertion or deletion of rsds

private need to update:

seqpos of Residues, residue_connection_partners_ info in Residues
xyz_moved, dof_moved

References dof_moved_, residues_, size(), core::id::AtomID_Map< T >::update_sequence_numbering(), and xyz_moved_.

Referenced by insert_conformation_by_jump(), residues_delete(), and residues_insert().

kinematics::Stub core::conformation::Conformation::upstream_jump_stub ( int jump_number ) const

The upstream and downstream Stubs are the coordinate frames between which this jump is transforming.

References atom_tree_, and jump_atom_id().

PointPosition const & core::conformation::Conformation::xyz ( AtomID const & id ) const

access xyz coordinates of an atom

References atom_tree_.

Referenced by core::conformation::carbohydrates::align_virtual_atoms_in_carbohydrate_residue(), align_virtual_atoms_in_carbohydrate_residue(), core::conformation::symmetry::SymmetricConformation::apply_transform_Rx_plus_v(), apply_transform_Rx_plus_v(), atom_tree_torsion(), batch_get_xyz(), bond_orientation(), protocols::ligand_docking::ComputeLigandRDF::compute_rdf(), core::membrane::concave_shell(), debug_residue_torsions(), core::conformation::symmetry::SymmetricConformation::declare_chemical_bond(), core::scoring::methods::CustomAtomPairEnergy::eval_atom_derivative(), fill_missing_atoms(), core::pose::get_hash_excluding_chain(), core::pose::get_hash_from_chain(), core::pose::get_sha1_hash_excluding_chains(), core::pose::get_sha1_hash_from_chains(), core::scoring::func::ConformationXYZ::operator()(), protocols::rna::movers::RNAIdealizeMover::perturb_pose(), core::conformation::symmetry::recenter(), protocols::fibril::reorient_extended_fibril(), core::scoring::constraints::DistancePairConstraint::score(), core::scoring::constraints::DihedralPairConstraint::score(), core::scoring::constraints::DihedralConstraint::score(), core::scoring::constraints::AngleConstraint::score(), torsion_angle(), and core::chemical::ICoorAtomID::xyz().

Friends And Related Function Documentation

friend class ::ConformationTests

friend

Member Data Documentation

AtomTreeOP core::conformation::Conformation::atom_tree_

private

atom tree for the kinematics

Referenced by append_residue(), atom_tree(), atom_tree_torsion(), batch_set_xyz(), bond_angle(), bond_length(), clear(), Conformation(), debug_residue_torsions(), delete_polymer_residue(), delete_residue_range_slow(), delete_residue_slow(), detached_copy(), dof(), dof_id_from_atom_ids(), downstream_jump_stub(), get_jump_atom_ids(), get_stub_transform(), in_place_copy(), insert_fragment(), insert_polymer_residue(), insert_residue_by_bond(), insert_residue_by_jump(), jump(), operator=(), replace_residue(), set_bond_angle(), set_bond_length(), set_dof(), set_jump(), set_jump_atom_stub_id(), set_stub_transform(), set_torsion(), set_torsion_angle(), set_xyz(), setup_atom_tree(), stub_from_id(), torsion(), torsion_angle(), update_domain_map(), update_residue_coordinates(), upstream_jump_stub(), and xyz().

utility::vector1< Size > core::conformation::Conformation::chain_endings_

private

chain number for each position

conformation is in charge of making sure that the Residue chain ID's and the chain_endings_ vector stay in sync.

Referenced by chain_begin(), chain_end(), chain_endings(), chains_from_termini(), clear(), Conformation(), delete_chain_ending(), in_place_copy(), insert_chain_ending(), insert_conformation_by_jump(), num_chains(), operator=(), rederive_chain_endings(), rederive_chain_ids(), and reset_chain_endings().

utility::signals::BufferedSignalHub< void, ConnectionEvent > core::conformation::Conformation::connection_obs_hub_

mutableprivate

ConnectionEvent observers.

Remarks: Notification only occurs when there is a change in the state of the connection between observers and the Conformation object, e.g. destruction or transfer of the connection.

Referenced by attach_connection_obs(), clear_observers(), detach_connection_obs(), and notify_connection_obs().

bool core::conformation::Conformation::contains_carbohydrate_residues_

private

Referenced by append_residue(), Conformation(), contains_carbohydrate_residues(), insert_conformation_by_jump(), insert_polymer_residue(), and operator=().

AtomID_Mask core::conformation::Conformation::dof_moved_

private

book-keeping array for energy evaluations

store which DOF's have changed since the last call to reset_move_data note that we are not currently differentiating dof's from the same atom

Referenced by append_polymer_residue_after_seqpos(), clear(), Conformation(), in_place_copy(), insert_conformation_by_jump(), operator=(), prepend_polymer_residue_before_seqpos(), reset_move_data(), residues_append(), residues_insert(), residues_replace(), set_dof_moved(), update_domain_map(), and update_sequence_numbering().

FoldTreeOP core::conformation::Conformation::fold_tree_

private

utility::signals::PausableSignalHub< void, GeneralEvent > core::conformation::Conformation::general_obs_hub_

mutableprivate

GeneralEvent observers.

Remarks: GeneralEvent observers will be notified whenever any signal derived from GeneralEvent occurs.

Referenced by attach_general_obs(), block_signals(), blocking_signals(), buffer_signals(), buffering_signals(), clear_observers(), debug_pause(), detach_general_obs(), notify_general_obs(), and unblock_signals().

utility::signals::BufferedSignalHub< void, IdentityEvent > core::conformation::Conformation::identity_obs_hub_

mutableprivate

IdentityEvent observers.

Referenced by attach_identity_obs(), block_signals(), buffer_signals(), clear_observers(), detach_identity_obs(), notify_identity_obs(), and unblock_signals().

utility::signals::BufferedSignalHub< void, LengthEvent > core::conformation::Conformation::length_obs_hub_

mutableprivate

LengthEvent observers.

Referenced by attach_length_obs(), block_signals(), buffer_signals(), clear_observers(), detach_length_obs(), notify_length_obs(), and unblock_signals().

membrane::MembraneInfoOP core::conformation::Conformation::membrane_info_

private

Membrane Info object.

Referenced by check_valid_membrane(), Conformation(), is_membrane(), membrane_info(), operator=(), set_membrane_info(), and update_membrane_position().

utility::vector1< ParametersSetOP > core::conformation::Conformation::parameters_set_

private

Parameter sets for parametric conformation generation.

This is a list of pointers to parameter set objects. The list is empty by default; the list only contains anything if the conformation has parametrically-generated bits. Each ParametersSet is intended to describe an assemblage of secondary structure (e.g. a helical bundle); each Parameters object in a ParametersSet is intended to describe a single piece of (likely contiguous) structure (e.g. a single helix in a helical bundle).

Referenced by add_parameters_set(), clear(), clear_parameters_set_list(), Conformation(), create_new_parameters_set(), in_place_copy(), n_parameters_sets(), operator=(), and parameters_set().

bool core::conformation::Conformation::residue_coordinates_need_updating_

mutableprivate

do we need to update the coordinates in the Residues?

Referenced by append_polymer_residue_after_seqpos(), append_residue_by_bond(), Conformation(), force_update_residue_coordinates(), in_place_copy(), insert_residue_by_bond(), operator=(), residue(), residue_cop(), residue_data(), set_dof_moved(), setup_atom_tree(), torsion(), and update_residue_coordinates().

bool core::conformation::Conformation::residue_torsions_need_updating_

mutableprivate

do we need to update the torsion angles in the Residues?

Referenced by append_residue(), Conformation(), declare_chemical_bond(), delete_polymer_residue(), delete_residue_range_slow(), delete_residue_slow(), force_update_residue_torsions(), in_place_copy(), insert_conformation_by_jump(), insert_polymer_residue(), insert_residue_by_bond(), insert_residue_by_jump(), operator=(), replace_residue(), residue(), residue_cop(), residue_data(), set_dof(), set_torsion_angle(), set_xyz_moved(), setup_atom_tree(), torsion(), and update_residue_torsions().

core::chemical::CacheableResidueTypeSets core::conformation::Conformation::residue_type_sets_

private

Any Conformation-specific ResidueTypes are stored here. Note: The ResidueTypeSets contained herein can be shared by multiple Conformations, and should have copy-on-write semantics.

Referenced by clear(), Conformation(), in_place_copy(), modifiable_residue_type_set_for_conf(), operator=(), reset_residue_type_set_for_conf(), and residue_type_set_for_conf().