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

#include <Conformation.hh>

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 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

Public Member Functions
	Conformation ()
	constructor More...

virtual	~Conformation ()
	default destructor More...

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

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

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

void	clear ()
	clear data More...

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 recurse) 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...

bool	is_residue_typeset (std::string tag) const
	convenience test for residue_type_set ( based on two middle residue – to avoid hitting on ligands or pseudos ) More...

bool	is_fullatom () const
	convenience test for residue_type_set ( based on two middle residue – to avoid hitting on ligands or pseudos ) More...

bool	is_centroid () const
	convenience test for residue_type_set ( based on two middle residue – to avoid hitting on ligands or pseudos ) 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 const setting)
	Set whether this conformation contains any carbohydrate residues. More...

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

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

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

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

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

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

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

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

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

char	secstruct (Size const 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	setup_membrane (utility::vector1< std::pair< int, int > > embres_map, int membrane)
	Setup a Membrane Info Object inside the conformation. More...

membrane::MembraneInfoOP	membrane ()
	Returns a Membrane Info Object in the conformation. 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 const seqpos) const
	Returns the AA enum for position <seqpos> More...

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

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

ResidueCAPs	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 const 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	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...

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...

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...

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...

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...

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

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

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 ()

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 (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 const seqpos, Size const connid)

AtomID	inter_residue_connection_partner (Size const seqpos, int const 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...

utility::vector1 < core::id::AtomID >	bonded_neighbor_all_res (core::id::AtomID atomid, bool virt=false) const
	get all atoms bonded to another More...

void	fill_missing_atoms (id::AtomID_Mask missing)

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

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

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

void	update_polymeric_connection (Size const lower_seqpos)
	Update the polymer connection status between lower_seqpos and lower_seqpos+1 based on chainID's and termini. More...

virtual void	detect_disulfides ()
	Detect existing disulfides from the protein structure. More...

void	fix_disulfides (utility::vector1< std::pair< Size, Size > > disulf_bonds)
	Assigns disulfide bonds based on a pre-determined list. 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 const size, Conformation const &src, Size const begin, Size const src_begin)
	copy a stretch of coordinates/torsions from another Conformation More...

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
	Returns the torsion angle <id> More...

virtual void	set_torsion (TorsionID const &id, Real const setting)
	Sets the AtomTree DOF and the torsion in the corresponding Residue. 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]> 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]> 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> 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...

const Jump &	jump (int const 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

void	insert_ideal_geometry_at_polymer_bond (Size const seqpos)

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)

DOF_ID	dof_id_from_torsion_id (TorsionID const &id) const

id::AtomID	jump_atom_id (int const 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...

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...

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

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

virtual void	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 const 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...

Protected Attributes
ResidueOPs	residues_
	container of Residues More...

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

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

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

void	residues_append (Residue const &new_rsd, bool const start_new_chain, bool const by_jump=false)

void	residues_delete (Size const 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 (TorsionID const &id, AtomID &id1, AtomID &id2, AtomID &id3, AtomID &id4) const
	get four backbone atoms which define this backbone torsion 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 const seqpos, bool const 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 const seqpos, bool const 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 const fire_general=true) const
	notify IdentityEvent observers More...

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

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

Private Attributes
utility::vector1< Size >	chain_endings_
	ResidueCOPs const_residues_; // mirrors residues_ allowing const access – this will be reinstated soon. More...

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

FoldTreeOP	fold_tree_
	fold tree for the kinematics More...

AtomTreeOP	atom_tree_
	atom tree for the kinematics 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...

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

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

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_.

Referenced by clone().

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

virtual

default destructor

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

copy constructor

References atom_tree_, chain_endings_, basic::CONFORMATION_COPY, contains_carbohydrate_residues_, dof_moved_, fold_tree_, residue_coordinates_need_updating_, residue_torsions_need_updating_, residues_, secstruct_, size(), structure_moved_, and xyz_moved_.

Member Function Documentation

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

inline

Returns the AA enum for position <seqpos>

References residues_, and size().

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

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::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

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

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 core::pose::Pose::append_polymer_residue_after_seqpos(), 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.

References core::id::NamedAtomID::atom(), core::conformation::Residue::atom_index(), atom_tree_, const_residues(), fold_tree_, core::conformation::insert_residue_into_atom_tree(), core::conformation::Residue::is_ligand(), core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::lower_connect_atom(), core::conformation::Residue::name(), notify_length_obs(), pre_nresidue_change(), core::conformation::signals::LengthEvent::RESIDUE_APPEND, residue_torsions_need_updating_, residues_, residues_append(), core::id::NamedAtomID::rsd(), setup_atom_tree(), size(), and core::conformation::TR.

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 core::pose::Pose::append_residue_by_bond(), 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.

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

Referenced by core::pose::Pose::append_residue_by_jump(), and core::conformation::symmetry::setup_symmetric_conformation().

bool core::conformation::Conformation::atom_is_backbone_norefold	(	Size const	pos,
		Size const	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 core::pose::Pose::atom_tree(), core::scoring::constraints::AtomPairConstraint::dist(), core::scoring::methods::LinearChainbreakEnergy::do_score_ovp(), core::pose::Pose::has_dof(), core::optimization::CartesianMinimizerMap::setup(), core::optimization::MinimizerMap::setup(), and core::optimization::symmetry::SymMinimizerMap::SymMinimizerMap().

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_, numeric::conversions::degrees(), degrees(), dof_id_from_torsion_id(), get_torsion_angle_atom_ids(), core::id::JUMP, and core::id::TorsionID::type().

Referenced by debug_residue_torsions(), and update_residue_torsions().

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	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(), and core::scoring::constraints::ConstraintSet::attach_to_conformation().

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	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	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	pointer to observer object

Returns: Link that can be used to manage the connection

References length_obs_hub_.

Referenced by core::pose::datacache::LengthEventCollector::attach_impl(), core::pose::datacache::SpecialSegmentsObserver::attach_impl(), core::pose::PDBInfo::attach_to(), and core::scoring::constraints::ConstraintSet::attach_to_conformation().

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	pointer to observer object

Returns: Link that can be used to manage the connection

References xyz_obs_hub_.

Referenced by core::pose::Pose::init(), core::pose::Pose::operator=(), and core::pose::Pose::set_new_conformation().

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

private

get four backbone atoms which define this backbone torsion

Note: Returns TRUE to signal FAILURE; returns TRUE for FAILURE

References core::chemical::ACETYLATED_NTERMINUS, core::conformation::Residue::atom_index(), core::id::AtomID::atomno(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, fold_tree_, core::conformation::Residue::has_variant_type(), core::conformation::Residue::mainchain_atom(), core::conformation::Residue::mainchain_atoms(), core::chemical::METHYLATED_CTERMINUS, residue_(), residues_, core::id::AtomID::rsd(), and torsion().

Referenced by get_torsion_angle_atom_ids().

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

virtual

References xyz().

Referenced by core::pose::Pose::batch_get_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_, runtime_assert, and set_xyz_moved().

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

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]>

References atom_tree_.

Referenced by 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>

References atom_tree_.

Referenced by core::io::pdb::FileData::init_from_pose().

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

get all atoms bonded to another

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::conformation::Residue::is_virtual(), core::conformation::Residue::n_residue_connections(), neighbors, residue(), core::conformation::Residue::residue_connect_atom_index(), and core::id::AtomID::rsd().

Referenced by core::io::pdb::dump_connect_info().

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_.

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

are signals being blocked and buffered?

References general_obs_hub_.

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

inline

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

References chain_endings_.

Referenced by core::conformation::membrane::MembraneInfo::build_membrane_foldtree(), core::pose::Pose::chain_sequence(), core::membrane::geometry::EmbeddingFactory::create_and_add_embedding(), core::pose::metrics::simple_calculators::InterfaceDefinitionCalculator::fill_in_chain_terminii(), core::pack::task::operation::util::find_neighbors_within_CB_cutoff(), core::conformation::symmetry::get_chain2range(), core::pose::get_chain_from_chain_id(), core::pose::get_chain_residues(), core::pose::get_hash_from_chain(), core::scoring::methods::NMerSVMEnergy::get_residue_energy_by_svm(), core::scoring::methods::NMerPSSMEnergy::residue_energy(), core::pack::task::residue_selector::ChainSelector::select_chain_by_index(), core::scoring::constraints::SiteConstraint::setup_csts(), core::scoring::constraints::FabConstraint::setup_csts(), and core::conformation::symmetry::setup_symmetric_conformation().

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

inline

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

References chain_endings_, and size().

Referenced by core::conformation::membrane::MembraneInfo::build_membrane_foldtree(), core::pose::Pose::chain_sequence(), core::pose::metrics::simple_calculators::InterfaceDefinitionCalculator::fill_in_chain_terminii(), core::pack::task::operation::util::find_neighbors_within_CB_cutoff(), core::conformation::symmetry::get_chain2range(), core::pose::get_chain_residues(), core::pose::get_hash_from_chain(), core::scoring::methods::NMerSVMEnergy::get_residue_energy_by_svm(), insert_conformation_by_jump(), core::scoring::methods::NMerPSSMEnergy::residue_energy(), core::pack::task::residue_selector::ChainSelector::select_chain_by_index(), core::scoring::constraints::SiteConstraint::setup_csts(), core::scoring::constraints::FabConstraint::setup_csts(), and core::conformation::symmetry::setup_symmetric_conformation().

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

Returns the list of chain endings.

References chain_endings_.

Referenced by 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(), core::io::pdb::FileData::get_residue_information(), core::pose::renumber_pdbinfo_based_on_conf_chains(), and core::pose::Pose::update_pose_chains_from_pdb_chains().

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

Sets the list of chain endings.

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.

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

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

Rederive the chains from the termini/polymer status.

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

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

clear data

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

Referenced by core::pose::Pose::clear(), operator=(), and core::conformation::symmetry::SymmetricConformation::~SymmetricConformation().

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_.

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

virtual

clone the conformation

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

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

References Conformation().

Referenced by core::pose::Pose::operator=(), and core::pose::Pose::set_new_conformation().

ResidueCAPs 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_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::io::pdb::build_pose_as_is1(), core::import_pose::build_pose_as_is2(), and core::pose::make_pose_from_saccharide_sequence().

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

inline

Set whether this conformation contains any carbohydrate residues.

References contains_carbohydrate_residues_.

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

Referenced by core::pose::Pose::copy_segment().

void core::conformation::Conformation::debug_pause ( bool const 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 ASSERT_ONLY, atom_tree_, atom_tree_torsion(), core::id::AtomID::atomno(), core::id::BB, core::id::CHI, core::conformation::Residue::chi(), numeric::dihedral(), fold_tree_, get_torsion_angle_atom_ids(), j, 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(), basic::subtract_degree_angles(), subtract_degree_angles(), basic::t_warning, torsion(), type, 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
	)

Declare that a chemical bond exists between two residues.

References core::conformation::Residue::atom_index(), core::chemical::ResidueConnection::atomno(), core::conformation::Residue::n_residue_connections(), core::conformation::Residue::name(), core::conformation::Residue::residue_connection(), core::conformation::Residue::residue_connection_partner(), residues_, and utility_exit_with_message.

Referenced by core::util::add_covalent_linkage(), and core::conformation::form_disulfide().

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

Deletes <seqpos> from the list of chain endings.

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

References chain_endings_, rederive_chain_ids(), and utility_exit_with_message.

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

Delete polymer residue at the given sequence position.

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

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 core::pose::Pose::delete_polymer_residue().

void core::conformation::Conformation::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.

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

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().

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

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

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 core::pose::remove_ligand_canonical_residues(), core::pose::remove_nonprotein_residues(), and core::pose::remove_virtual_residues().

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	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_.

Referenced by core::pose::PDBInfo::detach_from(), and core::scoring::constraints::ConstraintSet::detach_from_conformation().

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	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	pointer to observer object

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

References identity_obs_hub_.

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

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	pointer to observer object

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

References length_obs_hub_.

Referenced by core::pose::PDBInfo::detach_from(), and core::scoring::constraints::ConstraintSet::detach_from_conformation().

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	pointer to observer object

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

References xyz_obs_hub_.

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

Referenced by core::io::pdb::build_pose_as_is1(), and core::pose::symmetry::make_symmetric_pose().

void core::conformation::Conformation::detect_disulfides ( )

virtual

Detect existing disulfides from the protein structure.

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.

Referenced by core::pose::symmetry::extract_asymmetric_unit(), core::pose::initialize_disulfide_bonds(), and core::pose::symmetry::make_symmetric_pose().

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

Referenced by core::io::pdb::build_pose_as_is1().

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

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

References atom_tree_.

Referenced by core::pose::Pose::dof(), and core::conformation::symmetry::SymmetricConformation::set_dof().

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

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

Referenced by atom_tree_torsion(), core::optimization::symmetry::SymAtomTreeMinimizer::make_assymetric_movemap(), core::optimization::symmetry::SymAtomTreeMinimizer::make_semisymmetric_movemap(), core::pose::symmetry::make_symmetric_movemap(), 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 const 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 core::pose::Pose::empty().

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

Referenced by core::io::pdb::build_pose_as_is1().

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

Assigns disulfide bonds based on a pre-determined list.

Note: works in centroid and full-atom modes

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

Referenced by core::pose::initialize_disulfide_bonds(), and core::io::raw_data::DisulfideFile::read_in_and_set_disulfides().

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.

References core::kinematics::FoldTree::nres(), setup_atom_tree(), size(), update_residue_coordinates(), and utility_exit_with_message.

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 nres, and 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.

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

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 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::CHI, core::conformation::Residue::chi_atoms(), core::id::JUMP, core::id::NU, core::conformation::Residue::nu_atoms(), residue_(), core::id::AtomID::rsd(), core::id::TorsionID::rsd(), core::id::TorsionID::torsion(), torsion(), core::conformation::TR, core::id::TorsionID::type(), and utility_exit.

Referenced by core::optimization::CartesianMinimizerMap::assign_rosetta_torsions_and_trim(), atom_tree_torsion(), core::optimization::cartesian_collect_torsional_deriv(), core::scoring::rna::RNA_TorsionPotential::check_intra_residue(), debug_residue_torsions(), dof_id_from_torsion_id(), core::pose::rna::RNA_IdealCoord::is_torsion_exists(), core::scoring::rna::RNA_TorsionPotential::print_torsion_info(), set_torsion(), and core::scoring::rna::RNA_TorsionPotential::should_score_torsion().

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

inlinevirtual

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, chain_endings_, dof_moved_, fold_tree_, residue_coordinates_need_updating_, residue_torsions_need_updating_, residues_, runtime_assert, secstruct_, size(), structure_moved_, type, and xyz_moved_.

Referenced by operator=().

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

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

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.

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

Referenced by core::io::pdb::build_pose_as_is1(), core::pose::create_subpose(), core::fragment::make_pose_from_frags(), and core::io::serialization::read_binary().

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.

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

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

References chain_end(), chain_endings_, core::id::AtomID_Map< T >::clear(), core::conformation::Residue::clone(), dof_moved_, fold_tree(), fold_tree_, notify_length_obs(), num_chains(), pre_nresidue_change(), rederive_chain_ids(), residue(), core::conformation::signals::LengthEvent::RESIDUE_APPEND, residue_torsions_need_updating_, residues_, core::id::AtomID_Map< T >::resize(), secstruct_, setup_atom_tree(), size(), update_sequence_numbering(), core::conformation::Residue::update_sequence_numbering(), utility_exit_with_message, and xyz_moved_.

Referenced by core::pose::Pose::append_pose_by_jump(), core::conformation::symmetry::SymmetricConformation::insert_conformation_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
	)

References atom_tree_, and set_dof_moved().

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

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

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

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

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

References numeric::constants::d::pi, 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(), fold_tree_, core::conformation::insert_residue_into_atom_tree(), 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(), and size().

Referenced by append_polymer_residue_after_seqpos(), and prepend_polymer_residue_before_seqpos().

void core::conformation::Conformation::insert_residue_by_jump	(	Residue const &	new_rsd_in,
		Size const	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 ASSERT_ONLY, 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(), runtime_assert, core::conformation::Residue::seqpos(), and size().

Referenced by core::conformation::symmetry::SymmetricConformation::append_residue_by_jump(), and core::pose::Pose::insert_residue_by_jump().

id::AtomID core::conformation::Conformation::inter_residue_connection_partner	(	Size const	seqpos,
		int const	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 core::chemical::ResidueConnection::atomno(), core::conformation::Residue::residue_connection(), core::conformation::Residue::residue_connection_partner(), and residues_.

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

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

convenience test for residue_type_set ( based on two middle residue – to avoid hitting on ligands or pseudos )

Note: this is not a good test –Doug

References core::chemical::CENTROID, and is_residue_typeset().

Referenced by core::pose::Pose::is_centroid().

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

convenience test for residue_type_set ( based on two middle residue – to avoid hitting on ligands or pseudos )

Note: this is not a good test –Doug

References core::chemical::FA_STANDARD, and is_residue_typeset().

Referenced by core::conformation::membrane::MembraneInfo::conformation_changed(), core::conformation::form_disulfide(), core::conformation::membrane::MembraneInfo::init(), and core::pose::Pose::is_fullatom().

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

inline

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

References membrane_info_.

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

inlinevirtual

bool core::conformation::Conformation::is_residue_typeset ( std::string tag ) const

convenience test for residue_type_set ( based on two middle residue – to avoid hitting on ligands or pseudos )

Note: this is not a good test –Doug

References correct, core::chemical::ResidueTypeSet::name(), residue_type(), core::chemical::ResidueType::residue_type_set(), size(), and core::conformation::TR.

Referenced by is_centroid(), and is_fullatom().

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

Returns the Jump with jump number <jump_number>

References atom_tree_, and jump_atom_id().

Referenced by core::pose::Pose::jump(), and core::conformation::symmetry::setup_symmetric_conformation().

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 const jump_number ) const

References core::kinematics::dir_jump, fold_tree_, core::conformation::get_root_atomno(), residue_(), and residues_.

Referenced by dof_id_from_torsion_id(), downstream_jump_stub(), jump(), core::conformation::symmetry::SymmetricConformation::set_jump(), set_jump(), and upstream_jump_stub().

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

Returns a Membrane Info Object in the conformation.

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_.

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 const	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 const	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_jump(), and operator=().

void core::conformation::Conformation::notify_xyz_obs	(	XYZEvent const &	e,
		bool const	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.

References chain_endings_.

Referenced by core::conformation::membrane::MembraneInfo::build_membrane_foldtree(), core::pose::conf2pdb_chain(), core::pose::conf2pdb_chain_default_map(), core::conformation::symmetry::get_chain2range(), core::pose::get_chain_ids_from_chain(), core::pose::has_chain(), insert_conformation_by_jump(), core::conformation::membrane::MembraneInfo::is_membrane(), core::conformation::membrane::MembraneInfo::num_polymer_chains(), core::pack::task::residue_selector::ChainSelector::select_chain_by_index(), core::conformation::symmetry::setup_symmetric_conformation(), core::pose::Pose::split_by_chain(), and core::conformation::membrane::MembraneInfo::total_polymer_residue().

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.

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

Referenced by core::conformation::symmetry::SymmetricConformation::operator=().

virtual void core::conformation::Conformation::pop_passport ( )

inlinevirtual

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_jump(), prepend_polymer_residue_before_seqpos(), and safely_append_polymer_residue_after_seqpos().

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

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

inlinevirtual

void core::conformation::Conformation::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.

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

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(), and prepend_polymer_residue_before_seqpos().

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_name(), core::chemical::AtomICoor::build(), core::chemical::AtomICoor::depends_on_polymer_lower(), core::chemical::AtomICoor::depends_on_polymer_upper(), core::conformation::Residue::icoor(), core::conformation::Residue::natoms(), residue_(), set_xyz(), and update_residue_coordinates().

void core::conformation::Conformation::rebuild_residue_connection_dependent_atoms	(	Size const	seqpos,
		Size const	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::chemical::AtomICoor::depends_on_residue_connection(), core::conformation::Residue::icoor(), core::conformation::Residue::natoms(), residue_(), set_xyz(), and update_residue_coordinates().

Referenced by insert_ideal_geometry_at_residue_connection().

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.

Referenced by core::pose::Pose::operator=().

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

private

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

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

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

private

References chain, 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.

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 core::conformation::change_cys_state(), copy_segment(), core::conformation::form_disulfide(), core::conformation::idealize_position(), core::conformation::replace_conformation_residue_copying_existing_coordinates(), core::conformation::symmetry::SymmetricConformation::replace_residue(), replace_residue(), and core::pose::Pose::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.

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

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

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

References chain_endings_, and rederive_chain_ids().

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

forget all the structure modifications

called after domain map information is transferred to the Energies class

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

Referenced by core::pose::Pose::update_residue_neighbors().

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

inline

reset the structure_moved_ bool

References structure_moved_.

Referenced by core::pose::Pose::scoring_begin(), and core::pose::Pose::update_residue_neighbors().

Residue const& core::conformation::Conformation::residue ( Size const 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_, runtime_assert, size(), update_residue_coordinates(), and update_residue_torsions().

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

inlineprivate

Returns a residue 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 append_polymer_residue_after_seqpos(), append_residue_by_bond(), backbone_torsion_angle_atoms(), detect_pseudobonds(), fill_missing_atoms(), get_torsion_angle_atom_ids(), insert_polymer_residue(), insert_residue_by_jump(), jump_atom_id(), prepend_polymer_residue_before_seqpos(), rebuild_polymer_bond_dependent_atoms(), rebuild_residue_connection_dependent_atoms(), and set_polymeric_connection().

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

inline

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

References residues_, and size().

Referenced by core::conformation::annotated_atom_graph_from_conformation(), core::conformation::atom_graph_from_conformation(), core::chemical::ICoorAtomID::atom_id(), core::conformation::symmetry::SymmetricConformation::detect_disulfides(), detect_disulfides(), core::conformation::form_disulfide(), core::pose::initialize_atomid_map(), core::pose::initialize_atomid_map_heavy_only(), insert_ideal_geometry_at_polymer_bond(), is_residue_typeset(), core::scoring::mm::MMBondAngleResidueTypeParamSet::lookup(), core::conformation::symmetry::recenter(), core::pose::Pose::residue_type(), and core::chemical::ICoorAtomID::xyz().

void core::conformation::Conformation::residues_append	(	Residue const &	new_rsd,
		bool const	start_new_chain,
		bool const	by_jump = `false`
	)

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 chain, core::conformation::Residue::clone(), dof_moved_, core::conformation::Residue::natoms(), nres, rederive_chain_endings(), rederive_chain_ids(), residues_, core::id::AtomID_Map< T >::resize(), secstruct_, structure_moved_, core::conformation::TR, update_polymeric_connection(), and xyz_moved_.

Referenced by append_residue().

void core::conformation::Conformation::residues_delete ( Size const 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 const	seqpos,
		Residue const &	new_rsd,
		bool const	use_lower_chain = `false`,
		bool const	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 chain, 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(), and insert_residue_by_jump().

void core::conformation::Conformation::residues_replace	(	Size const	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
	)

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

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

void core::conformation::Conformation::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

Fires a LengthEvent::RESIDUE_PREPEND signal.

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

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

virtual

determine the type of the ConformationOP

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

References same_type_as_me().

Referenced by core::pose::Pose::operator=(), core::import_pose::pose_from_pdb(), core::conformation::symmetry::SymmetricConformation::same_type_as_me(), and same_type_as_me().

char core::conformation::Conformation::secstruct ( Size const 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 core::pose::Pose::dump_scored_pdb(), core::scoring::MembranePotential::non_helix_in_membrane_penalty(), core::scoring::methods::EnvEnergy::residue_energy(), core::scoring::methods::CenPairEnergy::residue_pair_energy(), and core::pose::Pose::secstruct().

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=().

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.

References atom_tree_, and set_dof_moved().

Referenced by core::fragment::BBTorsionAndAnglesSRFD::apply(), 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(), core::conformation::symmetry::SymmetricConformation::set_bond_angle(), and core::pose::Pose::set_ring_conformation().

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.

References atom_tree_, and set_dof_moved().

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

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 core::conformation::symmetry::SymmetricConformation.

References atom_tree_, residue_torsions_need_updating_, and set_dof_moved().

Referenced by core::conformation::symmetry::SymmetricConformation::set_dof(), and core::pose::Pose::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.

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

Referenced by core::conformation::symmetry::SymmetricConformation::set_jump(), and core::pose::Pose::set_jump().

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

virtual

set a jump

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

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_polymeric_connection	(	Size	res_id_lower,
		Size	res_id_upper
	)

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

References residue_(), residues_, and type.

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.

References secstruct_.

Referenced by core::conformation::symmetry::SymmetricConformation::set_secstruct(), and core::pose::Pose::set_secstruct().

void core::conformation::Conformation::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.

References atom_tree_, and set_dof_moved().

Referenced by core::fragment::DownJumpSRFD::apply(), core::io::silent::BinarySilentStruct::fill_pose(), core::io::silent::ProteinSilentStruct_Template< T >::fill_pose(), and core::pose::swap_transform().

void core::conformation::Conformation::set_torsion	(	TorsionID const &	id,
		Real const	setting
	)

virtual

Sets the AtomTree DOF and the torsion in the corresponding Residue.

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

References atom_tree_, core::id::BB, core::id::CHI, dof_id_from_torsion_id(), get_torsion_angle_atom_ids(), core::id::JUMP, core::id::NU, numeric::conversions::radians(), radians(), residues_, core::id::TorsionID::rsd(), set_dof_moved(), core::id::TorsionID::torsion(), core::conformation::TR, and core::id::TorsionID::type().

Referenced by core::pose::Pose::set_alpha(), core::pose::Pose::set_beta(), core::pose::Pose::set_chi(), core::pose::Pose::set_delta(), core::pose::Pose::set_epsilon(), core::pose::Pose::set_gamma(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), core::conformation::symmetry::SymmetricConformation::set_torsion(), core::pose::Pose::set_torsion(), and core::pose::Pose::set_zeta().

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.

References atom_tree_, residue_torsions_need_updating_, set_dof_moved(), and core::conformation::TR.

Referenced by core::pose::carbohydrates::set_glycosidic_torsion(), and core::conformation::symmetry::SymmetricConformation::set_torsion_angle().

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::pose::carbohydrates::align_virtual_atoms_in_carbohydrate_residue(), fill_missing_atoms(), core::conformation::symmetry::SymmetricConformation::insert_conformation_by_jump(), rebuild_polymer_bond_dependent_atoms(), rebuild_residue_connection_dependent_atoms(), core::conformation::symmetry::recenter(), core::conformation::symmetry::SymmetricConformation::set_xyz(), and core::pose::Pose::set_xyz().

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_membrane	(	utility::vector1< std::pair< int, int > >	embres_map,
		int	membrane
	)

Setup a Membrane Info Object inside the conformation.

Given Embedding and Membrane Positions, Setup a Membrane Info Object.

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

References membrane_info_.

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(), j, core::conformation::Residue::n_non_polymeric_residue_connections(), core::conformation::Residue::n_polymeric_residue_connections(), core::conformation::Residue::n_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(), core::pose::Pose::scoring_begin(), and core::pose::Pose::update_residue_neighbors().

kinematics::Stub core::conformation::Conformation::stub_from_id ( id::StubID const & id ) const

References atom_tree_.

Referenced by core::pose::Pose::stub_from_id().

Real core::conformation::Conformation::torsion ( TorsionID const & id ) const

Returns the torsion angle <id>

References atom_tree_, core::id::BB, numeric::conversions::degrees(), dof_id_from_torsion_id(), core::id::JUMP, residue(), core::id::TorsionID::rsd(), core::id::TorsionID::torsion(), and core::id::TorsionID::type().

Referenced by backbone_torsion_angle_atoms(), debug_residue_torsions(), get_torsion_angle_atom_ids(), core::conformation::symmetry::SymmetricConformation::set_torsion(), and core::pose::Pose::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]>

References atom_tree_.

Referenced by core::pose::carbohydrates::get_glycosidic_torsion().

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_.

void core::conformation::Conformation::update_actcoord ( Size resid )

References residues_.

Referenced by core::pose::Pose::update_actcoord().

void core::conformation::Conformation::update_actcoords ( )

References residues_, and size().

Referenced by core::pose::Pose::update_actcoords().

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 core::pose::Pose::update_residue_neighbors().

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 core::pose::Pose::update_orbital_coords(), 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 const lower_seqpos )

Update the polymer connection status between lower_seqpos and lower_seqpos+1 based on chainID's and termini.

References core::conformation::Residue::chain(), core::conformation::Residue::has_variant_type(), core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_polymer(), residues_, set_polymeric_connection(), and size().

Referenced by 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(), PROF_START, PROF_STOP, residue_coordinates_need_updating_, and basic::UPDATE_RESIDUE_COORDINATES.

Referenced by append_polymer_residue_after_seqpos(), append_residue_by_bond(), debug_residue_torsions(), fill_missing_atoms(), fold_tree(), pre_nresidue_change(), prepend_polymer_residue_before_seqpos(), rebuild_polymer_bond_dependent_atoms(), rebuild_residue_connection_dependent_atoms(), and residue().

void core::conformation::Conformation::update_residue_coordinates	(	Size const	seqpos,
		bool const	fire_signal = `true`
	)		const

private

References atom_tree_, j, 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(), PROF_START, PROF_STOP, residue_torsions_need_updating_, residues_, size(), and basic::UPDATE_RESIDUE_TORSIONS.

Referenced by debug_residue_torsions(), residue(), and setup_atom_tree().

void core::conformation::Conformation::update_residue_torsions	(	Size const	seqpos,
		bool const	fire_signal = `true`
	)		const

private

References atom_tree_torsion(), core::id::BB, core::chemical::rna::CHI, core::id::CHI, core::conformation::Residue::chi(), j, core::conformation::Residue::mainchain_torsions(), core::conformation::Residue::nchi(), notify_xyz_obs(), residues_, and update_orbital_coords().

void core::conformation::Conformation::update_sequence_numbering	(	Size const	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 const 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().

Referenced by core::scoring::DockingScoreFunction::operator()(), and core::pose::symmetry::rotate_anchor_to_x_axis().

PointPosition const & core::conformation::Conformation::xyz ( AtomID const & id ) const

access xyz coordinates of an atom

References atom_tree_.

Referenced by core::pose::carbohydrates::align_virtual_atoms_in_carbohydrate_residue(), batch_get_xyz(), debug_residue_torsions(), core::conformation::symmetry::SymmetricConformation::detect_disulfides(), detect_disulfides(), core::scoring::constraints::AtomPairConstraint::dist(), 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_chain(), core::scoring::func::ConformationXYZ::operator()(), core::conformation::symmetry::recenter(), core::scoring::constraints::DistancePairConstraint::score(), core::scoring::constraints::DihedralPairConstraint::score(), core::scoring::constraints::DihedralConstraint::score(), core::chemical::ICoorAtomID::xyz(), and core::pose::Pose::xyz().

Member Data Documentation

AtomTreeOP core::conformation::Conformation::atom_tree_

private

utility::vector1< Size > core::conformation::Conformation::chain_endings_

private

ResidueCOPs const_residues_; // mirrors residues_ allowing const access – this will be reinstated soon.

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().