A molecular system including residues, kinematics, and energies. More...

#include <Pose.hh>

Inheritance diagram for core::pose::Pose:

Public Types
typedef id::AtomID	AtomID

typedef id::NamedAtomID	NamedAtomID

typedef id::TorsionID	TorsionID

typedef id::DOF_ID	DOF_ID

typedef conformation::Residue	Residue

typedef conformation::Conformation	Conformation

typedef conformation::ConformationOP	ConformationOP

typedef conformation::ConformationCOP	ConformationCOP

typedef pose::datacache::ObserverCache	ObserverCache

typedef pose::datacache::ObserverCacheOP	ObserverCacheOP

typedef pose::signals::ConformationEvent	ConformationEvent

typedef pose::signals::DestructionEvent	DestructionEvent

typedef pose::signals::EnergyEvent	EnergyEvent

typedef pose::signals::GeneralEvent	GeneralEvent

typedef scoring::constraints::ConstraintSetOP	ConstraintSetOP

typedef scoring::constraints::ConstraintSetCOP	ConstraintSetCOP

typedef basic::datacache::BasicDataCache	BasicDataCache

typedef basic::datacache::BasicDataCacheOP	BasicDataCacheOP

typedef basic::datacache::ConstDataMap	ConstDataMap

typedef basic::datacache::ConstDataMapOP	ConstDataMapOP

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

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

Public Member Functions
iterator	begin () noexcept

const_iterator	begin () const noexcept

iterator	end () noexcept

const_iterator	end () const noexcept

	Pose ()
	default constructor, builds an empty pose More...

	~Pose () override
	destructor – > kill data on the heap More...

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

	Pose (Pose const &src, Size residue_begin, Size residue_end)
	partial copy constructor More...

Pose &	operator= (Pose const &src)
	Construct pose from pdb file. More...

void	detached_copy (Pose const &src)
	Performs a deep copy of the src Pose into this Pose in a way that guarantees that no non-bitwise-constant data is shared between them (such as the AtomTree's observer system) – this Pose will be effectively detached from any data that lives in other objects. More...

PoseOP	clone () const
	clone the conformation More...

PoseCOP	get_self_ptr () const
	self pointers More...

PoseOP	get_self_ptr ()

PoseCAP	get_self_weak_ptr () const

PoseAP	get_self_weak_ptr ()

Conformation const &	conformation () const
	Returns the pose Conformation (const-access) More...

Conformation &	conformation ()
	Returns the pose Conformation (non-const access) More...

ConformationCOP	conformation_ptr () const
	Returns the pose Conformation pointer (const access) More...

ConformationOP &	conformation_ptr ()
	Returns the pose Conformation pointer (nonconst access) More...

kinematics::FoldTree const &	fold_tree () const
	Returns the pose FoldTree. More...

void	fold_tree (kinematics::FoldTree const &fold_tree_in)
	Sets the pose FoldTree to <fold_tree_in> More...

void	set_new_conformation (conformation::ConformationCOP new_conformation)
	Now that the conformation_ member data is an owning pointer, and we have derived classes of Conformation. More...

void	set_new_energies_object (scoring::EnergiesOP energies)
	Now that the energies_ member data is an owning pointer, and we have derived classes of Energies. More...

kinematics::AtomTree const &	atom_tree () const
	Returns the pose AtomTree. More...

scoring::Energies const &	energies () const
	Returns the pose Energies (const-access) More...

scoring::Energies &	energies ()
	Returns the pose Energies (non-const access) More...

ConstraintSetCOP	constraint_set () const

scoring::constraints::ConstraintCOP	add_constraint (scoring::constraints::ConstraintCOP cst)
	adding a constraint is done by cloning the input constraint. A const copy is then returned More...

scoring::constraints::ConstraintCOPs	add_constraints (scoring::constraints::ConstraintCOPs csts)

bool	remove_constraint (scoring::constraints::ConstraintCOP cst, bool object_comparison=false)
	re object_comparison see comment for ConstraintSet::remove_constraint function More...

bool	remove_constraints (scoring::constraints::ConstraintCOPs csts, bool object_comparison=false)
	re object_comparison see comment for ConstraintSet::remove_constraint function More...

bool	remove_constraints ()

void	clear_sequence_constraints ()
	Remove all sequence constraints from this pose. More...

void	constraint_set (ConstraintSetOP)

void	transfer_constraint_set (const pose::Pose &pose)

void	reference_pose_from_current (std::string const &ref_pose_name, bool override_current=false)
	Create a new reference pose from the current state of the pose. More...

core::pose::reference_pose::ReferencePoseSetOP	reference_pose_set ()
	Access the ReferencePoseSet object (non-const). More...

core::pose::reference_pose::ReferencePoseSetCOP	reference_pose_set_cop () const
	Const-access the ReferencePoseSet object. More...

core::Size	corresponding_residue_in_current (core::Size const ref_residue_index, std::string const &ref_pose_name) const
	Returns the index of a residue in this pose corresponding to a residue in a reference pose. More...

void	increment_reference_pose_mapping_after_seqpos (core::Size const seqpos)
	Find all mappings in the new pose after seqpos in all ReferencePose objects, and increment them by 1. More...

void	decrement_reference_pose_mapping_after_seqpos (core::Size const seqpos)
	Find all mappings in the new pose after seqpos in all ReferencePose objects, and decrement them by 1. More...

void	zero_reference_pose_mapping_at_seqpos (core::Size const seqpos)
	Find all mappings in the new pose to seqpos in all ReferencePose objects, and set them to point to residue 0 (deletion signal). More...

bool	has_reference_pose () const
	Returns true if a pose has at least one reference pose, false otherwise. More...

PDBInfoCOP	pdb_info () const
	Returns the pose PDBInfo (const) More...

PDBInfoOP	pdb_info ()
	Returns the pose PDBInfo. More...

PDBInfoOP	pdb_info (PDBInfoOP new_info)
	Sets pose PDBInfo to <new_info> More...

void	metric (std::string const &calculator_name, std::string const &key, basic::MetricValueBase &val) const

std::string	print_metric (std::string const &calculator_name, std::string const &key) const

void	append_residue_by_jump (conformation::Residue const &new_rsd, Size const jump_anchor_residue, std::string const &jump_anchor_atom="", std::string const &jump_root_atom="", bool const start_new_chain=false)
	Appends <new_rsd> (a residue) to pose by a new jump. More...

void	append_residue_by_bond (conformation::Residue const &new_rsd, bool const build_ideal_geometry=false, int const connection=0, Size const anchor_residue=0, int const anchor_connection=0, bool const start_new_chain=false, bool const lookup_bond_length=false)
	Appends <new_rsd> (a residue) to pose by a new bond. More...

void	append_residue_by_atoms (conformation::Residue const &new_rsd, bool const build_ideal_geometry, std::string const &connect_atom, Size const anchor_rsd_seqpos, std::string const &anchor_connect_atom, bool const start_new_chain=false, bool const lookup_bond_length=false)
	Appends <new_rsd> (a residue) to pose by a new bond to a given atom. More...

void	insert_residue_by_jump (Residue const &new_rsd_in, Size const seqpos, Size anchor_pos, std::string const &anchor_atomno="", std::string const &root_atomno="")
	Adds <new_rsd_in> to pose at <seqpos> More...

void	insert_residue_by_bond (Residue const &new_rsd_in, Size const seqpos, Size anchor_pos, bool const build_ideal_geometry=false, std::string const &anchor_atom="", std::string const &root_atom="", bool new_chain=false, bool const lookup_bond_length=false)
	Adds <new_rsd_in> to pose at <seqpos> More...

void	replace_residue (Size const seqpos, Residue const &new_rsd_in, bool const orient_backbone)
	Replaces the residue at <seqpos> with <new_rsd_in> More...

void	replace_residue (int const seqpos, Residue const &new_rsd_in, utility::vector1< std::pair< std::string, std::string > > const &atom_pairs)
	Replaces the residue at <seqpos> with <new_rsd> based on superposition on the specified input atom pairs NOTE: at the moment, only superposition on 3 atoms works This code sorely belongs in Pose.cc. 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	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	append_pose_by_jump (Pose const &src, Size const jump_anchor_residue, std::string const &jump_anchor_atom="", std::string const &jump_root_atom="")
	Appends source pose conformation to pose by a new jump. More...

void	delete_polymer_residue (Size const seqpos)
	Delete a residue in the pose. Update Observers. Update any Reference Poses. More...

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

void	delete_residue_range_slow (Size const start, Size const end)
	Delete a range of residues in the pose. More...

void	copy_segment (Size const size, Pose const &src, Size const begin, Size const src_begin)
	Copy a stretch of coordinates/torsions from <src> to pose. More...

BasicDataCache const &	data () const
	BasicDataCache indexed by enum in core/pose/datacache/CacheableDataType.hh. More...

BasicDataCache &	data ()
	BasicDataCache indexed by enum in core/pose/datacache/CacheableDataType.hh. More...

template<class T >
void	set_const_data (std::string const &category, std::string const &name, T const &original)
	Controlled method for adding an object to the Pose's constant data cache; this function is the only way to add data to the Pose's data cache. An object, identified by two strings, is freshly constructed and inserted into the ConstDataCache. Objects inserted into the ConstDataCache must remain bitwise const for thread-safety reasons. The ConstDataCache has shallow-copy semantics, meaning that two poses would point to the same object if one were copied into the other. If these two Poses were then handed to separate threads, and the data they were both pointing at were to change, that would create race conditions. For this reason, the Pose attempts to prevent non-constant pointers to the data held in the ConstDataCache from existing. Objects placed in the ConstDataCache must have a copy constructor (either implicit or explicit). More...

basic::datacache::ConstDataMap const &	const_data_cache () const
	Read access to the const data cache. More...

ObserverCache const &	observer_cache () const
	ObserverCache indexed by enum in core/pose/datacache/CacheableObserverType.hh. More...

ObserverCache &	observer_cache ()
	ObserverCache indexed by enum in core/pose/datacache/CacheableObserverType.hh. More...

Size	total_residue () const
	Returns the number of residues in the pose conformation. More...

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

Size	total_atoms () const
	Returns the total number of atoms in the pose conformation example: pose.total_atoms() More...

bool	empty () const
	Returns true if there are no residues in the conformation. More...

Size	num_jump () const
	Returns the number of jumps in the pose FoldTree. More...

chemical::AA	aa (Size const seqpos) const
	Returns the chemical::AA of the residue at <seqpos> More...

char	secstruct (Size const seqpos) const
	Returns the secondary structure of residue <seqpos> this usually comes from fragments. The conformation object will not invoke DSSP to determine the secondary structure if e.g. it has not been made from fragments. 'H' = helical 'E' = strand or sheet 'L' = loop. More...

std::string	secstruct () const
	Returns a string representing pose secondary structure. More...

void	set_secstruct (Size const seqpos, char const setting)
	Assign the secondary structure of residue <seqpos> to <setting> More...

std::string	sequence () const
	Returns a string representing the 1-letter-coded sequence of the pose conformation. More...

std::string	sequence (core::Size resnum_start, core::Size resnum_end) const
	Returns a string representing the 1-letter-coded sequence of the pose conformation. From start to end. More...

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

std::string	chain_sequence (core::Size const chain_in) const
	Returns the sequence for the chain number <chain_in> More...

std::string	glycan_tree_branch_sequence (core::uint const start_residue) const
	Return the IUPAC sequence of a single branch of a glycan tree, Beginning with residue number <start_residue>. More...

std::string	glycan_tree_sequence (core::uint const residue_in_tree) const
	Return the IUPAC sequence of the entire glycan tree encompassing residue number <residue_in_tree>. More...

Residue const &	residue (Size const seqpos) const
	Returns the Residue at position <seqpos> (read access) Note: this method will trigger a refold if either the torsions or the coordinates are out-of-date. More...

basic::datacache::BasicDataCache &	residue_data (Size const seqpos)
	Returns the DataCache held by Residue at position <seqpos> (read/write access) Note: this method will trigger a refold if either the torsions or the coordinates are out-of-date. More...

basic::datacache::BasicDataCache const &	residue_data (Size const seqpos) const
	Returns the DataCache held by Residue at position <seqpos> (read access) Note: this method will trigger a refold if either the torsions or the coordinates are out-of-date. More...

chemical::ResidueType const &	residue_type (Size const seqpos) const
	Returns the ResidueType at position <seqpos> (read access) Note: this method NOT will trigger a refold if either the torsions or the coordinates are out-of-date. More...

chemical::ResidueTypeCOP	residue_type_ptr (Size const seqpos) const
	Returns the ResidueTypeCOP for position <seqpos> (read access) Note: this method NOT will trigger a refold if either the torsions or the coordinates are out-of-date. More...

bool	is_fullatom () const
	Returns true if pose is ResidueType fullatom. More...

bool	is_centroid () const
	Returns true if pose is ResidueType centroid. More...

core::chemical::ResidueTypeSetCOP	residue_type_set_for_pose (core::chemical::TypeSetMode mode=core::chemical::INVALID_t) const
	Return the custom ResidueTypeSet for the Pose, if any. Otherwise will return the appropriate global ResidueTypeSet. More...

Real	phi (Size const seqpos) const
	Returns the phi torsion angle of residue <seqpos> in degrees. More...

void	set_phi (Size const seqpos, Real const setting)
	Sets the phi torsion angle of residue <seqpos> to <setting> More...

Real	psi (Size const seqpos) const
	Returns the psi torsion angle of residue <seqpos> in degrees Note: assumes the residue is an amino acid or monosaccharide. More...

void	set_psi (Size const seqpos, Real const setting)
	Sets the psi torsion angle of residue <seqpos> to <setting> More...

Real	omega (Size const seqpos) const
	Returns the omega torsion angle of residue <seqpos> in degrees. More...

void	set_omega (Size const seqpos, Real const setting)
	Sets the omega torsion angle of residue <seqpos> to <setting> More...

Real	theta (Size const seqpos) const
	Returns the theta torsion angle of beta-amino acid residue or oligourea residue <seqpos>. More...

void	set_theta (Size const seqpos, Real const setting)
	Sets the theta torsion angle of beta-amino acid residue or oligourea residue <seqpos> to <setting>. More...

Real	mu (Size const seqpos) const
	Returns the mu torsion angle of oligourea residue <seqpos>. More...

void	set_mu (Size const seqpos, Real const setting)
	Sets the mu torsion angle of oligourea residue <seqpos> to <setting>. More...

Real	alpha (Size const pos) const
	Returns the alpha torsion angle of residue <seqpos> More...

void	set_alpha (Size const seqpos, Real const setting)
	Sets the alpha torsion angle of residue <seqpos> to <setting> More...

Real	beta (Size const seqpos) const
	Returns the beta torsion angle of residue <seqpos> More...

void	set_beta (Size const seqpos, Real const setting)
	Sets the beta torsion angle of residue <seqpos> to <setting> More...

Real	gamma (Size const seqpos) const
	Returns the gamma torsion angle of residue <seqpos> More...

void	set_gamma (Size const seqpos, Real const setting)
	Sets the gamma torsion angle of residue <seqpos> to <setting> More...

Real	delta (Size const pos) const
	Returns the delta torsion angle of residue <seqpos> More...

void	set_delta (Size const seqpos, Real const setting)
	Sets the delta torsion angle of residue <seqpos> to <setting> More...

Real	epsilon (Size const seqpos) const
	Returns the epsilon torsion angle of residue <seqpos> More...

void	set_epsilon (Size const seqpos, Real const setting)
	Sets the epsilon torsion angle of residue <seqpos> to <setting> More...

Real	zeta (Size const seqpos) const
	Returns the zeta torsion angle of residue <seqpos> More...

void	set_zeta (Size const seqpos, Real const setting)
	Sets the zeta torsion angle of residue <seqpos> to <setting> More...

Real	chi (int const chino, Size const seqpos) const
	Returns the <chino> chi torsion angle of residue <seqpos> More...

void	set_chi (int const chino, Size const seqpos, Real const setting)
	Sets the <chino> chi torsion angle of residue <seqpos> to <setting> More...

Real	chi (Size const seqpos) const
	Returns the chi torsion angle of residue <seqpos> More...

void	set_chi (Size const seqpos, Real const setting)
	Sets the chi torsion angle of residue <seqpos> to <setting> More...

core::Size	num_chains () const
	Returns the total number of (chain ID) chains in the pose. More...

core::Size	chain (Size const seqpos) const
	Returns the chain number of residue <seqpos> More...

core::Size	chain_begin (Size const chain_num) const
	Returns the sequence position of the beginning of chain <chain_num>. More...

core::Size	chain_end (Size const chain_num) const
	Returns the sequence position of the end of chain <chain_num>. More...

utility::vector1< PoseOP >	split_by_chain () const
	Returns a vector of poses with one element per (chain number) chain of the original pose. More...

PoseOP	split_by_chain (Size chain_id) const
	Return a new pose with just the residues from the specified (chain number) chain. More...

void	update_pose_chains_from_pdb_chains ()
	Updates the pose chain IDs to match the pdb chain letters. More...

void	set_jump (int const jump_number, const kinematics::Jump &new_jump)
	Sets the pose FoldTree Jump <jump_number> to <new_jump> More...

kinematics::Jump const &	jump (int const jump_number) const
	Returns the pose FoldTree Jump <jump_number> More...

void	set_jump (AtomID const &id, const kinematics::Jump &new_jump)
	Sets the pose FoldTree Jump <id> to <new_jump> More...

kinematics::Jump const &	jump (AtomID const &id) const
	Returns the pose FoldTree Jump <id> More...

void	set_ring_conformation (uint const seqpos, uint const ring_num, core::chemical::rings::RingConformer const &conformer)
	Set the given residue and ring's ring conformation, if appropriate. More...

Real	torsion (TorsionID const &id) const
	Returns the Conformation torsion angle identified by <id> More...

void	set_torsion (TorsionID const &id, Real const setting)
	Sets the Conformation torsion angle identified by <id> to <setting> More...

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

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

bool	has_dof (DOF_ID const &id) const
	Returns true if pose has DOF <id> More...

PointPosition const &	xyz (AtomID const &id) const
	Returns the location (xyz) of pose AtomID <id> More...

PointPosition const &	xyz (NamedAtomID const &id) const
	Returns the location (xyz) of pose NamedAtomID <id> More...

void	set_xyz (AtomID const &id, PointPosition const &point)
	Sets the location (xyz) of pose AtomID <id> to the PointPosition <point> More...

void	set_xyz (NamedAtomID const &id, PointPosition const &point)
	Sets the location (xyz) of pose NamedAtomID <id> to the PointPosition <point> More...

void	batch_set_xyz (utility::vector1< AtomID > const &ids, utility::vector1< PointPosition > const &points)
	Sets the locations (xyz) of pose AtomIDs in <ids> to mathcing PointPositions in <points> More...

void	batch_get_xyz (utility::vector1< AtomID > const &ids, utility::vector1< PointPosition > &points) const
	Gets the locations (xyz) of pose AtomIDs in <ids> More...

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

void	center ()
	Sets pose coordinates such that the pose center is at the Euclidean origin. More...

void	update_residue_neighbors ()
	Updates neighbor links in the pose Energies object. More...

void	scoring_begin (scoring::ScoreFunction const &info)
	Called by ScoreFunction at the beginning of scoring. More...

void	scoring_end (scoring::ScoreFunction const &scorefxn)
	Called by ScoreFunction at the end of scoring. More...

void	update_actcoords ()
	Called by PairEPotential to update the action coordinates for all residues. More...

void	update_actcoord (Size resid)
	Updates the action coordinates for pose residue <resid> More...

void	update_orbital_coords (Size resid)

void	apply_transform_Rx_plus_v (numeric::xyzMatrix< Real > const &R, Vector const &v)
	Apply a transform of the Rx + v form, where R is a rotation matrix and v is a translation vector. More...

void	real_to_virtual (core::Size seqpos)
	Switch residues to VIRTUAL. More...

void	virtual_to_real (core::Size seqpos)
	Switch residues from VIRTUAL to a REAL residue. More...

conformation::carbohydrates::GlycanTreeSetCOP	glycan_tree_set () const
	Get information on any glycan trees within this pose. If this is not setup, will return a nullptr due to the const nature of the function. More...

conformation::membrane::MembraneInfoOP	membrane_info () const
	Get information about the membrane orientaiton, geometry, and lipid composition within this pose. More...

conformation::membrane::MembraneInfoOP	membrane_info ()
	Get information about the membrane orientaiton, geometry, and lipid composition within this pose. More...

void	clear ()
	Empty the pose contents. More...

void	dump_file (std::string const &file_name) const
	Export pose data to a file, <file_name>, determining which type of file format to write based on the file extension. More...

void	dump_cif (std::string const &file_name) const
	Export pose data to the mmCIF file <file_name> More...

void	dump_mmtf (std::string const &file_name) const
	Export pose data to the mmtf file <file_name> More...

bool	dump_pdb (std::string const &file_name) const
	Export pose data to the PDB file <file_name> More...

void	dump_pdb (std::ostream &out) const

void	dump_pdb (std::ostream &out, utility::vector1< core::Size > const &residue_indices) const
	for writing a specified subset of residues in pdb format More...

void	dump_scored_pdb (std::string const &file_name, scoring::ScoreFunction const &scorefxn)
	Export pose data to the PDB file <file_name>, add some score output. More...

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

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

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

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

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

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

template<>
void	set_const_data (std::string const &category, std::string const &name, Pose const &original)

Private Member Functions
void	init (void)
	initialize internal for a freshly build pose object. Use this function when you need to create new constructor. More...

void	store_const_data (std::string const &category, std::string const &name, utility::pointer::ReferenceCountCOP)
	Internal method for storing a shared pointer to some constant object in the ConstantDataCache. More...

void	notify_destruction_obs (DestructionEvent const &e)
	notify DestructionEvent observers More...

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

void	notify_energy_obs (EnergyEvent const &e, bool const fire_general=true)
	notify EnergyEvent observers More...

void	notify_conformation_obs (ConformationEvent const &e, bool const fire_general=true)
	notify ConformationEvent observers More...

void	buffer_observers () const
	Temporarily turn off observer notification Used for places where the Pose is in a temporarily inconsistent state. More...

void	unbuffer_observers () const
	Turn back on observer notification Used for places where the Pose is in a temporarily inconsistent state. More...

void	on_conf_xyz_change (core::conformation::signals::XYZEvent const &event)
	upon receiving a conformation::signals::XYZEvent More...

Private Attributes
ConformationOP	conformation_

scoring::EnergiesOP	energies_

metrics::PoseMetricContainerOP	metrics_

BasicDataCacheOP	data_cache_
	BasicDataCache indexed by enum in core/pose/datacache/CacheableDataType.hh. More...

ConstDataMapOP	constant_cache_
	The DataMap is a way to store arbitrarily complicated, constant data. The contents of the datamap are copied by value – the pointers are copied – meaning that two poses can point to the same data. For thread safety reasons, it is essential that the data inside this map is bitwise const (i.e. no mutable data is used or changes state). Poses may be placed inside the constant datamap, but it is important that ownership cycles are not created (e.g. A –> B; B–>C; C–>A) or memory will be leaked. Care must be taken that the this never happens. One way to avoid this possibility is to only cache freshly cloned Poses. The other way is to first call Pose::purge_cached_poses. More...

ObserverCacheOP	observer_cache_
	ObserverCache indexed by enum in core/pose/datacache/CacheableObserverType.hh. More...

PDBInfoOP	pdb_info_
	pdb info More...

ConstraintSetOP	constraint_set_

core::pose::reference_pose::ReferencePoseSetOP	reference_pose_set_
	The set of ReferencePose objects that this pose stores. More...

utility::signals::BufferedSignalHub < void, DestructionEvent >	destruction_obs_hub_
	DestructionEvent observers. More...

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

utility::signals::BufferedSignalHub < void, EnergyEvent >	energy_obs_hub_
	EnergyEvent observers. More...

utility::signals::BufferedSignalHub < void, ConformationEvent >	conformation_obs_hub_
	ConformationEvent observers. More...

Detailed Description

A molecular system including residues, kinematics, and energies.

The Pose class represents a molecular system (protein-dna-ligand...) as a container of Rosetta Residue objects together with a Conformation object that defines how internal coordinate changes propagate through the system and an Energies object that stores information from the last energy evaluation.

The main responsibilities of the pose are:

Kinematic: (a) to update the xyz coordinates in response to changes to internal degrees of freedom, and (b) to update internal coordinates when the user modifes the xyz (Cartesian) coords,

Scoring: (a) to keep track of what parts of the structure have changed since the last score evaluation, and (b) to cache residue and residue-pair energies for efficient re-use

As a container: The pose provides a single object for passing a molecular system and for copying of entire molecules or stretches of molecules from one Pose object into another.

Output Methods: Common Methods: Pose.assign Pose.atom_tree Pose.conformation Pose.dump_pdb Pose.dump_cif Pose.dump_mmtf Pose.dump_file Pose.energies Pose.fold_tree Pose.pdb_info Pose.residue Pose.sequence Pose.size

Member Typedef Documentation

typedef id::AtomID core::pose::Pose::AtomID

typedef basic::datacache::BasicDataCache core::pose::Pose::BasicDataCache

typedef basic::datacache::BasicDataCacheOP core::pose::Pose::BasicDataCacheOP

typedef conformation::Conformation core::pose::Pose::Conformation

typedef conformation::ConformationCOP core::pose::Pose::ConformationCOP

typedef pose::signals::ConformationEvent core::pose::Pose::ConformationEvent

typedef conformation::ConformationOP core::pose::Pose::ConformationOP

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

typedef basic::datacache::ConstDataMap core::pose::Pose::ConstDataMap

typedef basic::datacache::ConstDataMapOP core::pose::Pose::ConstDataMapOP

typedef scoring::constraints::ConstraintSetCOP core::pose::Pose::ConstraintSetCOP

typedef scoring::constraints::ConstraintSetOP core::pose::Pose::ConstraintSetOP

typedef pose::signals::DestructionEvent core::pose::Pose::DestructionEvent

typedef id::DOF_ID core::pose::Pose::DOF_ID

typedef pose::signals::EnergyEvent core::pose::Pose::EnergyEvent

typedef pose::signals::GeneralEvent core::pose::Pose::GeneralEvent

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

typedef id::NamedAtomID core::pose::Pose::NamedAtomID

typedef pose::datacache::ObserverCache core::pose::Pose::ObserverCache

typedef pose::datacache::ObserverCacheOP core::pose::Pose::ObserverCacheOP

typedef conformation::Residue core::pose::Pose::Residue

typedef id::TorsionID core::pose::Pose::TorsionID

Constructor & Destructor Documentation

core::pose::Pose::Pose ( )

default constructor, builds an empty pose

AtomTree default /bonding information Conformation default /change propagation Energies default /contains pose energy information FoldTree default /directs building of Pose Residue default /container of individual Residue objects

default constructor

References init().

Referenced by split_by_chain().

core::pose::Pose::~Pose ( )

override

destructor – > kill data on the heap

References clear(), and notify_destruction_obs().

core::pose::Pose::Pose ( Pose const & src )

copy constructor

core::pose::Pose::Pose	(	Pose const &	src,
		Size	residue_begin,
		Size	residue_end
	)

partial copy constructor

References begin(), end(), init(), and core::io::pose_from_pose().

Member Function Documentation

chemical::AA core::pose::Pose::aa ( Size const seqpos ) const

Returns the chemical::AA of the residue at <seqpos>

example(s): pose.aa(17) See also: Pose Pose.Residue Pose.sequence Residue

References conformation_, and size().

scoring::constraints::ConstraintCOP core::pose::Pose::add_constraint ( scoring::constraints::ConstraintCOP cst )

adding a constraint is done by cloning the input constraint. A const copy is then returned

References conformation_, constraint_set_, and energies_.

scoring::constraints::ConstraintCOPs core::pose::Pose::add_constraints ( scoring::constraints::ConstraintCOPs csts )

References conformation_, constraint_set_, and energies_.

Real core::pose::Pose::alpha ( Size const pos ) const

Returns the alpha torsion angle of residue <seqpos>

Note: assumes the residue is an nucleic acid

example(s): pose.alpha(1) See also: Pose Pose.residue Pose.set_alpha Residue

References core::id::BB, residue_type(), size(), and torsion().

std::string core::pose::Pose::annotated_sequence ( bool show_all_variants = false ) const

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

example(s): pose.annotated_sequence() See also: Pose Pose.sequence Pose.size Residue

References conformation_.

void core::pose::Pose::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

References conformation_, energies_, increment_reference_pose_mapping_after_seqpos(), and size().

Referenced by protocols::cryst::MakeLatticeMover::add_monomers_to_lattice(), protocols::cryst::MakeLayerMover::add_monomers_to_layer(), protocols::denovo_design::add_residues_to_pose(), protocols::denovo_design::components::add_to_pose(), core::import_pose::RNA_HelixAssembler::append_Aform_residue(), protocols::denovo_design::components::append_new_chain_from_template_segment(), protocols::denovo_design::components::append_new_residues(), protocols::stepwise::monte_carlo::mover::AddMover::append_residue(), protocols::denovo_design::components::append_residues_from_template_segment(), protocols::cyclic_peptide::PeptideStubMover::apply(), protocols::splice::SpliceOutTail::build_ideal_segment(), protocols::splice::SpliceInTail::build_ideal_segment(), protocols::splice::SpliceIn::build_ideal_segment(), protocols::splice::SpliceOut::build_ideal_segment(), and core::scoring::motif::Xfrag::insert().

void core::pose::Pose::append_pose_by_jump	(	Pose const &	src,
		Size const	jump_anchor_residue,
		std::string const &	jump_anchor_atom = `""`,
		std::string const &	jump_root_atom = `""`
	)

Appends source pose conformation to pose by a new jump.

References conformation(), conformation_, core::conformation::Conformation::contains_carbohydrate_residues(), energies_, glycan_tree_set(), core::conformation::Conformation::insert_conformation_by_jump(), num_jump(), pdb_info(), and size().

Referenced by protocols::simple_moves::LoadPDBMover::apply(), protocols::simple_moves::DeleteChainMover::apply(), protocols::helical_bundle::MakeBundle::apply(), protocols::helical_bundle::MakeBundleHelix::apply(), and protocols::tcr::TCRmodel::build_graft_model().

void core::pose::Pose::append_residue_by_atoms	(	conformation::Residue const &	new_rsd,
		bool const	build_ideal_geometry,
		std::string const &	connect_atom,
		Size const	anchor_rsd_seqpos,
		std::string const &	anchor_connect_atom,
		bool const	start_new_chain = `false`,
		bool const	lookup_bond_length = `false`
	)

Appends <new_rsd> (a residue) to pose by a new bond to a given atom.

This function effectively wraps append_residue_by_bond for an easier syntax. Instead of having to know what the connection, anchor residue, and anchor connection are, we give the atoms and query the ResidueType for the remaining information.

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.

References core::conformation::Residue::atom_index(), conformation_, energies_, core::conformation::Residue::has(), core::conformation::Residue::n_possible_residue_connections(), residue(), and core::conformation::Residue::residue_connect_atom_index().

Referenced by core::pose::append_pose_with_glycan_residues(), and protocols::farnesyl::InstallFarnesylMover::apply().

void core::pose::Pose::append_residue_by_bond	(	conformation::Residue const &	new_rsd,
		bool const	build_ideal_geometry = `false`,
		int const	connection = `0`,
		Size const	anchor_residue = `0`,
		int const	anchor_connection = `0`,
		bool const	start_new_chain = `false`,
		bool const	lookup_bond_length = `false`
	)

Appends <new_rsd> (a residue) to pose by a new 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.

References conformation_, and energies_.

Referenced by protocols::generalized_kinematic_closure::GeneralizedKIC::addloopgeometry(), protocols::generalized_kinematic_closure::GeneralizedKIC::addtailgeometry(), protocols::generalized_kinematic_closure::GeneralizedKIC::addupperanchor(), core::pose::append_pose_with_glycan_residues(), core::pose::append_subpose_to_pose(), protocols::cyclic_peptide::DeclareBond::apply(), protocols::cyclic_peptide::PeptideStubMover::apply(), protocols::ligand_docking::LigandDesign::apply(), protocols::ligand_docking::GrowLigand::apply(), protocols::rbsegment_relax::IdealizeHelicesMover::apply(), protocols::simple_moves::ReportEffectivePKA::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::hybridization::CartesianSampler::apply_frame(), protocols::pockets::PocketGrid::autoexpanding_pocket_eval(), protocols::metal_interface::MatchGrafter::build_combined_pose_with_zinc_overlay(), core::io::pose_from_sfr::PoseFromSFRBuilder::build_initial_pose(), protocols::cryst::MakeLatticeMover::build_lattice_of_virtuals(), protocols::cryst::MakeLayerMover::build_layer_of_virtuals(), core::pack::rotamer_set::build_lib_dna_rotamers(), core::pack::rotamer_set::build_random_dna_rotamers(), core::scoring::util_methods::DumpTrajectoryEnergy::calculate_energy(), protocols::hotspot_hashing::HotspotStubSet::create_hotspot_after_pose(), protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::create_random_fragments(), protocols::rna::denovo::create_rna_vall_torsions(), protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::create_sequence_match_fragments(), protocols::simple_moves::CutChainMover::create_subpose(), core::pose::create_subpose(), protocols::cyclic_peptide::SymmetricCycpepAlign::do_trim_to_single_repeat(), protocols::sic_dock::dump_loophash_linkers(), protocols::simple_moves::RepeatPropagationMover::duplicate_residues_by_type(), core::pose::symmetry::extract_asymmetric_unit(), core::pose::symmetry::get_asymmetric_pose_copy_from_symmetric_pose(), core::pose::symmetry::get_buildingblock_and_neighbor_subs(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::get_working_pose(), protocols::forge::methods::grow_right_r(), protocols::chemically_conjugated_docking::UBQ_GTPaseMover::initialize(), protocols::ncbb::SecStructFinder::initialize_pose(), core::scoring::methods::IdealParametersDatabase::lookup_torsion_legacy(), protocols::sic_dock::make_Cx(), protocols::ncbb::ResidueReplacementRebuildMover::make_new_pose(), core::pose::make_pose_from_sequence(), core::fragment::make_pose_from_sequence_(), protocols::stepwise::modeler::merge_two_poses(), protocols::forge::build::ConnectRight::modify_impl(), core::pose::pdbslice(), protocols::make_rot_lib::MakeRotLibJobInputter::pose_from_job(), core::io::serialization::read_binary(), protocols::sic_dock::read_biounit(), protocols::stepwise::monte_carlo::mover::DeleteMover::remove_singletons_and_update_pose_focus(), protocols::rna::movers::RNA_LoopCloser::rna_ccd_close(), protocols::rbsegment_relax::setup_pose_from_rbsegs(), protocols::relax::RepeatProteinRelax::setup_repeat_pose(), protocols::stepwise::modeler::slice(), protocols::motif_grafting::movers::MotifGraftMover::stich_motif_in_scaffold_by_indexes_rotation_and_translation(), and protocols::motif_grafting::movers::MotifGraftMover::test_epigraft_and_contextStructure_clashes().

void core::pose::Pose::append_residue_by_jump	(	conformation::Residue const &	new_rsd,
		Size const	jump_anchor_residue,
		std::string const &	jump_anchor_atom = `""`,
		std::string const &	jump_root_atom = `""`,
		bool const	start_new_chain = `false`
	)

Appends <new_rsd> (a residue) to pose by a new jump.

References conformation_, and energies_.

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

Apply a transform of the Rx + v form, where R is a rotation matrix and v is a translation vector.

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

References conformation_.

Referenced by protocols::cyclic_peptide::SymmetricCycpepAlign::align_to_origin(), protocols::cyclic_peptide::SymmetricCycpepAlign::align_to_zaxis(), protocols::symmetry::DetectSymmetry::apply(), protocols::cryst::UpdateCrystInfo::apply(), protocols::dna_dock::PropagateClashCheckFilter::apply(), protocols::pockets::PlaidFingerprint::apply_rotation_offset_to_pose_(), protocols::pockets::PlaidFingerprint::dump_oriented_pose_and_fp_to_pdb(), protocols::electron_density::VoxelSpacingMultifunc::foldInChanges(), protocols::pockets::PlaidFingerprint::get_oriented_pose(), protocols::cryst::DockLatticeMover::initialize(), protocols::pockets::PocketGrid::move_pose_to_standard_orie(), protocols::cryst::MakeLayerMover::place_near_origin(), protocols::cryst::MakeLatticeMover::place_near_origin(), protocols::pockets::PlaidFingerprint::PlaidFingerprint(), and protocols::simple_moves::PeriodicBoxMover::setup_pose().

kinematics::AtomTree const & core::pose::Pose::atom_tree ( ) const

Returns the pose AtomTree.

get the atom_tree

References conformation_.

Referenced by core::scoring::MultipoleElecPotential::align_residue_multipole_axes(), protocols::chemically_conjugated_docking::UBQ_GTPaseMover::analyze_and_filter(), protocols::simple_moves::TorsionDOFMover::apply(), protocols::rna::movers::RNAIdealizeMover::apply(), core::optimization::atom_tree_dfunc(), core::optimization::symmetry::atom_tree_dfunc(), protocols::backrub::BackrubSegment::bond_angle_atoms(), protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::calculate_jump(), core::import_pose::RNA_JumpMover::check_forward_backward(), protocols::simple_moves::ConstrainToIdealMover::check_if_really_connected(), protocols::rna::movers::connected_in_atom_tree(), protocols::toolbox::match_enzdes_util::constrain_pose_res_to_invrots(), protocols::ligand_docking::ga_ligand_dock::GriddedAtomTreeMultifunc::dfunc(), core::scoring::constraints::AtomPairConstraint::dist(), protocols::backrub::BackrubMover::dof_id_ranges(), core::import_pose::atom_tree_diffs::dump_atom_tree_diff(), protocols::viewer::dump_pose_kinemage(), protocols::backrub::BackrubSegment::end_atoms1(), protocols::stepwise::sampler::rna::RNA_KinematicCloser::figure_out_dof_ids_and_offsets(), protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::figure_out_dof_ids_and_offsets(), protocols::rna::denovo::coarse::CoarseRNA_LoopCloser::figure_out_dof_ids_and_offsets(), core::pose::copydofs::CopyDofs::figure_out_dofs(), protocols::rna::denovo::coarse::CoarseRNA_LoopCloser::figure_out_forward_backward_res_by_backtracking(), core::pose::rna::fix_sugar_coords(), protocols::stepwise::modeler::align::StepWisePoseAligner::get_root_triad_atom_id_map(), core::pose::rna::initialize_atoms_for_which_we_need_new_dofs(), protocols::simple_moves::DOFHistogramRecorder::insert_dofs_by_residue(), protocols::branch_angle::BranchAngleOptimizer::optimize_angles(), protocols::branch_angle::BranchAngleOptimizer::overall_params(), protocols::rna::denovo::print_internal_coords(), protocols::backrub::BackrubMover::random_angle(), protocols::ligand_docking::restrain_ligand_nbr_atom(), protocols::ligand_docking::LigandBaseProtocol::restrain_ligand_nbr_atom(), protocols::ligand_docking::LigandBaseProtocol::restrain_protein_Calphas(), protocols::ligand_docking::MinimizeBackbone::restrain_protein_Calphas(), core::import_pose::atom_tree_diffs::rms_error_with_noise(), protocols::backrub::BackrubMover::rotate_segment(), protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturber::set_pose_after_closure(), protocols::loops::loop_closure::kinematic_closure::VicinitySamplingKinematicPerturber::set_pose_after_closure(), protocols::loops::loop_closure::kinematic_closure::NeighborDependentTorsionSamplingKinematicPerturber::set_pose_after_closure(), protocols::loops::loop_closure::kinematic_closure::TorsionRestrictedKinematicPerturber::set_pose_after_closure(), protocols::loops::loop_closure::kinematic_closure::BaseTabooPerturber::set_pose_after_closure(), core::optimization::CartesianMinimizerMap::setup(), core::optimization::MinimizerMap::setup(), protocols::backrub::BackrubSegment::start_atoms1(), protocols::backrub::BackrubSegment::start_atoms2(), protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::store_target_icoors(), core::optimization::symmetry::SymMinimizerMap::SymMinimizerMap(), protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::update_current(), protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::update_target(), protocols::simple_moves::ConstrainToIdealMover::vary_bond_geometry(), and protocols::rna::movers::ErraserMinimizerMover::vary_bond_geometry().

template<typename MemFn , typename Ptr >

utility::signals::Link core::pose::Pose::attach_conformation_obs	(	MemFn	fn,
		Ptr	ptr
	)

inline

attach ConformationEvent observer function

Parameters

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

Returns: Link that can be used to manage the connection.

References conformation_obs_hub_.

Referenced by protocols::network::UIObserver::attach_impl(), protocols::moves::PyMOLObserver::attach_impl(), and core::pose::metrics::PoseMetricContainer::attach_to().

template<typename MemFn , typename Ptr >

utility::signals::Link core::pose::Pose::attach_destruction_obs	(	MemFn	fn,
		Ptr	ptr
	)

inline

attach DestructionEvent observer function

Parameters

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

Returns: Link that can be used to manage the connection.

Remarks: DestructionEvent observers will only be notified upon destruction of the Pose

References destruction_obs_hub_.

Referenced by core::pose::metrics::PoseMetricContainer::attach_to().

template<typename MemFn , typename Ptr >

utility::signals::Link core::pose::Pose::attach_energy_obs	(	MemFn	fn,
		Ptr	ptr
	)

inline

attach EnergyEvent observer function

Parameters

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

Returns: Link that can be used to manage the connection.

References energy_obs_hub_.

Referenced by protocols::network::UIObserver::attach_impl(), protocols::moves::PyMOLObserver::attach_impl(), protocols::viewer::SilentObserver::attach_to(), and core::pose::metrics::PoseMetricContainer::attach_to().

template<typename MemFn , typename Ptr >

utility::signals::Link core::pose::Pose::attach_general_obs	(	MemFn	fn,
		Ptr	ptr
	)

inline

attach GeneralEvent observer function

Parameters

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

Returns: Link that can be used to manage the connection.

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

References general_obs_hub_.

Referenced by protocols::network::UIObserver::attach_impl(), and protocols::moves::PyMOLObserver::attach_impl().

void core::pose::Pose::batch_get_xyz	(	utility::vector1< AtomID > const &	ids,
		utility::vector1< PointPosition > &	points
	)		const

Gets the locations (xyz) of pose AtomIDs in <ids>

get the locations of a vector of atoms

References conformation_.

Referenced by core::optimization::CartesianMinimizerMap::copy_dofs_from_pose().

void core::pose::Pose::batch_set_xyz	(	utility::vector1< AtomID > const &	ids,
		utility::vector1< PointPosition > const &	points
	)

Sets the locations (xyz) of pose AtomIDs in <ids> to mathcing PointPositions in <points>

set the locations of a vector of atoms

References conformation_.

Referenced by protocols::loop_grower::LoopGrower::addnativesolution(), protocols::loop_grower::SheetSampler::alignPerfectCA(), protocols::loop_grower::SheetSampler::alignStrand(), protocols::loophash::LoopHashMoverWrapper::apply(), protocols::comparative_modeling::PartialThreadingMover::apply(), protocols::simple_moves::Tumble::apply(), protocols::rbsegment_relax::SequenceShiftMover::apply(), protocols::hybridization::CartesianHybridize::apply_frag(), protocols::hybridization::CartesianHybridize::apply_frame(), protocols::electron_density::DockIntoDensityMover::apply_transform(), protocols::simple_filters::RepeatParameterFilter::apply_transformation(), protocols::forge::methods::apply_transformation(), protocols::hybridization::apply_transformation(), protocols::rbsegment_relax::RBSegmentMover::applyTransformation(), protocols::rbsegment_relax::RBSegmentMover::applyTranslation(), protocols::hybridization::InsertChunkMover::check_overlap(), core::optimization::CartesianMinimizerMap::copy_dofs_to_pose(), core::io::silent::BinarySilentStruct::fill_pose(), protocols::hybridization::InsertChunkMover::set_bb_xyz_aligned(), protocols::loop_grower::LoopPartialSolution::set_coordinates(), protocols::features::ProteinResidueConformationFeatures::set_coords_for_residues(), and protocols::hybridization::FoldTreeHybridize::translate_virt_to_CoM().

iterator core::pose::Pose::begin ( )

noexcept

Referenced by core::pose::canonical_atom_count(), core::pose::canonical_residue_count(), chain_sequence(), copy_segment(), protocols::tcr::graft_framework(), protocols::forge::methods::grow_left_rtype(), protocols::forge::methods::grow_right_rtype(), protocols::forge::build::SegmentInsert::modify_impl(), core::pose::noncanonical_atom_count(), core::pose::noncanonical_chi_count(), core::pose::noncanonical_residue_count(), core::pose::nres_protein(), and Pose().

const_iterator core::pose::Pose::begin ( ) const

noexcept

Real core::pose::Pose::beta ( Size const seqpos ) const

Returns the beta torsion angle of residue <seqpos>

Note: assumes the residue is an nucleic acid

example(s): pose.beta(2) See also: Pose Pose.residue Pose.set_beta Residue

References core::id::BB, residue_type(), size(), and torsion().

void core::pose::Pose::buffer_observers ( ) const

private

Temporarily turn off observer notification Used for places where the Pose is in a temporarily inconsistent state.

References conformation_obs_hub_, destruction_obs_hub_, energy_obs_hub_, and general_obs_hub_.

Referenced by operator=().

void core::pose::Pose::center ( )

Sets pose coordinates such that the pose center is at the Euclidean origin.

References core::conformation::Residue::natoms(), residue(), set_xyz(), size(), and xyz().

Referenced by protocols::simple_moves::AlignChainMover::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), and protocols::features::strand_assembly::SandwichFeatures::report_features().

core::Size core::pose::Pose::chain ( Size const seqpos ) const

Returns the chain number of residue <seqpos>

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

example(s): pose.chain(3) see also: pose pose.num_chains pose.annotated_sequence pose.chain_sequence pose.fold_tree pose.sequence foldtree

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

Referenced by protocols::dna::DnaInterfaceMultiStateDesign::add_dna_states(), protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_pose(), protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_wholepose(), protocols::loops::add_loop(), protocols::denovo_design::components::add_to_pose(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::alignment_atoms_in_res(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::alignment_torsions_in_res(), core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr(), core::io::pose_to_sfr::PoseToStructFileRepConverter::append_residue_to_sfr(), core::pose::append_subpose_to_pose(), protocols::cyclic_peptide::DeclareBond::apply(), protocols::ligand_docking::LigandDesign::apply(), protocols::dna::RestrictDesignToProteinDNAInterface::apply(), protocols::matdes::BuildingBlockInterfaceOperation::apply(), protocols::antibody::AntibodyNumberingConverterMover::apply(), protocols::denovo_design::residue_selectors::NamedSegmentSelector::apply(), protocols::denovo_design::movers::RotateSegmentMover::apply(), protocols::membrane::AddMPLigandMover::apply(), protocols::ddg::ddGMover::apply(), protocols::fldsgn::filters::HelixKinkFilter::apply(), protocols::fldsgn::CircularPermutation::apply(), protocols::loops::apply_sequence_mapping(), protocols::analysis::InterfaceAnalyzerMover::calc_hbond_sasaE(), protocols::analysis::InterfaceAnalyzerMover::calc_interface_to_surface_fraction(), protocols::analysis::InterfaceAnalyzerMover::calc_per_residue_dG(), protocols::analysis::InterfaceAnalyzerMover::calc_per_residue_dSASA(), protocols::analysis::InterfaceAnalyzerMover::calc_per_residue_dSASA_general(), protocols::dna::DnaInterfacePacker::calculate_specificity(), core::pose::metrics::simple_calculators::InterfaceDefinitionCalculator::chain_letter_to_number(), protocols::membrane::chain_tm_com(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::check_backbones_match(), protocols::simple_filters::ResidueSetChainEnergyFilter::compute(), protocols::frag_picker::FragmentScoreFilter::compute(), protocols::enzdes::LigDSasaFilter::compute(), protocols::protein_interface_design::filters::AtomicContactCountFilter::compute(), protocols::protein_interface_design::filters::HbondsToResidueFilter::compute(), protocols::fldsgn::filters::SecondaryStructureHasResidueFilter::compute(), protocols::simple_filters::InterfaceHbondsFilter::compute_hbonds(), protocols::analysis::InterfaceAnalyzerMover::compute_interface_sc(), core::pose::compute_unique_chains(), core::pose::conf2pdb_chain(), protocols::membrane::create_membrane_foldtree_anchor_pose_tmcom(), core::scoring::membrane::MPSpanInsertionEnergy::create_updated_span(), core::pack::hbonds::determine_atom_level_edge_info(), protocols::dna::DnaInterfacePacker::dna_seq_tag(), core::pack::hbonds::HBondGraphInitializerIG::find_symmetric_hbonds(), protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::fragment_check(), protocols::constraint_movers::AddConstraintsToCurrentConformationMover::generate_atom_pair_constraints(), protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMover::generate_csts(), protocols::enzdes::EnzdesFlexBBProtocol::generate_ensemble_for_region(), core::io::pose_to_sfr::PoseToStructFileRepConverter::generate_secondary_structure_informations(), protocols::antibody::AntibodyInfo::get_CDRNameEnum_of_residue(), protocols::membrane::get_chain_and_z(), core::pose::get_chain_id_from_jump_id(), core::pose::get_chain_ids_from_chains(), protocols::toolbox::IGInterfaceEdgeUpweighter::get_edge_reweight(), protocols::antibody::AntibodyInfo::get_FoldTree_L_HA(), protocols::antibody::AntibodyInfo::get_FoldTree_LA_H(), protocols::antibody::AntibodyInfo::get_FoldTree_LH_A(), protocols::simple_filters::HelixHelixAngleFilter::get_helix_start_stop(), core::pack::hbonds::HBondGraphInitializerIG::get_ind_res(), protocols::hbnet::HBNet::get_ind_res(), core::pose::get_jump_ids_from_chain_ids(), core::scoring::motif::MotifHash::get_matching_motifs(), protocols::antibody::AntibodyInfo::get_region_of_residue(), core::scoring::methods::NMerSVMEnergy::get_residue_energy_by_svm(), core::scoring::methods::NMerRefEnergy::get_residue_energy_by_table(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_residue_information(), core::pose::full_model_info::FullModelParameters::get_sequence_with_gaps_filled_with_n(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::get_start_and_end_aa(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::get_start_and_end_indices(), core::pack::hbonds::get_symm_ind_res(), core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_torsion_records(), core::scoring::motif::HACK_dump_helices(), protocols::hbnet::HBNetStapleInterface::has_pH_His(), protocols::analysis::InterfaceAnalyzerMover::init_on_new_input(), protocols::dna::DnaInterfacePacker::init_standard(), protocols::frags::insert_random_fragments_in_flexible_protein_regions(), protocols::features::HBondFeatures::insert_site_row(), core::pose::is_lower_terminus(), protocols::loops::Loop::is_terminal(), core::pose::is_upper_terminus(), protocols::ligand_docking::ComputeLigandRDF::ligand_protein_rdf(), protocols::denovo_design::loop_start_without_overlap(), protocols::denovo_design::loop_stop_without_overlap(), protocols::loops::loops_around_residues(), protocols::analysis::InterfaceAnalyzerMover::make_multichain_interface_set(), protocols::denovo_design::movers::new_jump_and_cutpoint(), protocols::hbnet::HBNetStapleInterface::num_intermolecular_hbonds(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::pose_from_posedata(), protocols::ligand_docking::ComputeLigandRDF::protein_protein_rdf(), protocols::dna::DnaInterfacePacker::protein_scan(), protocols::sic_dock::read_biounit(), protocols::pose_metric_calculators::ResidueDecompositionByChainCalculator::recompute(), protocols::ddg::ddGMover::relax_wildtype_structure(), core::pose::renumber_pdbinfo_based_on_conf_chains(), core::scoring::methods::NMerPSSMEnergy::residue_energy(), protocols::simple_filters::NonSequentialNeighborsFilter::residue_neighbors(), core::scoring::motif::ResPairMotif::ResPairMotif(), protocols::dna::DnaInterfacePacker::reversion_scan(), protocols::membrane::rsd_closest_to_chain_com(), protocols::analysis::InterfaceAnalyzerMover::score_separated_chains(), protocols::antibody::select_epitope_residues(), protocols::interface::select_interface_residues(), protocols::dna::seq_pdb_str(), protocols::dna::DesignProteinBackboneAroundDNA::set_loop_info(), protocols::hbnet::HBNet::set_symmetry(), protocols::antibody::snugdock::SnugDockProtocol::setup_ab_ag_foldtree(), core::scoring::constraints::FabConstraint::setup_csts(), protocols::docking::setup_edges_for_partner(), protocols::docking::setup_foldtree(), protocols::membrane::setup_foldtree_pose_com(), protocols::enzdes::EnzdesScorefileFilter::setup_pose_metric_calculators(), protocols::denovo_design::components::StructureData::specific_enzdes_header(), protocols::membrane::split_topology_by_chain_noshift(), protocols::membrane::split_topology_by_jump_noshift(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::storeposedata(), core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::three_body_approximate_buried_unsat_calculation(), protocols::cyclic_peptide::PeptideStubMover::update_pdb_numbering(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::use_in_rmsd(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::use_in_rmsd_offset(), and protocols::loops::Loops::verify_against().

core::Size core::pose::Pose::chain_begin ( Size const chain_num ) const

Returns the sequence position of the beginning of chain <chain_num>.

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps. This is a pass-through function which returns conformation_->chain_begin( chain_num )

example(s): pose.chain_begin(1) see also: pose pose.num_chains pose.annotated_sequence pose.chain_sequence pose.fold_tree pose.sequence foldtree

References conformation_, and num_chains().

Referenced by protocols::stepwise::monte_carlo::mover::ensure_appropriate_foldtree_for_move(), protocols::constel::get_chain_terms(), protocols::protein_interface_design::movers::SetAtomTree::set_ab_fold_tree(), protocols::splice::SpliceInTail::set_fold_tree_nodes(), protocols::splice::SpliceOutTail::set_fold_tree_nodes(), protocols::splice::SpliceIn::set_fold_tree_nodes(), protocols::splice::SpliceOut::set_fold_tree_nodes(), and split_by_chain().

core::Size core::pose::Pose::chain_end ( Size const chain_num ) const

Returns the sequence position of the end of chain <chain_num>.

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps. This is a pass-through function which returns conformation_->chain_end( chain_num )

example(s): pose.chain_end(1) see also: pose pose.num_chains pose.annotated_sequence pose.chain_sequence pose.fold_tree pose.sequence foldtree

References conformation_, and num_chains().

Referenced by protocols::constel::get_chain_terms(), and split_by_chain().

std::string core::pose::Pose::chain_sequence ( core::Size const chain_in ) const

Returns the sequence for the chain number <chain_in>

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

Example(s): pose.chain_sequence(1) See also: Pose Pose.chain Pose.residue Pose.sequence

References begin(), core::chemical::ResidueType::carbohydrate_info(), conformation_, end(), core::chemical::ResidueTypeBase::name1(), num_chains(), core::conformation::membrane::out, and residue_type().

Referenced by protocols::symmetry::DetectSymmetry::apply(), protocols::evolution::EvolutionaryDynamicsMover::boltzmann(), protocols::monte_carlo::GenericMonteCarloMover::boltzmann(), protocols::evolution::AASynthesisFitnessCost::compute(), protocols::frag_picker::FragmentScoreFilter::compute(), core::pose::compute_unique_chains(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::do_initial_import_and_scoring(), protocols::simple_filters::SecretionPredictionFilter::find_tm_regions(), core::scoring::methods::NMerSVMEnergy::get_residue_energy_by_svm(), core::scoring::methods::NMerRefEnergy::get_residue_energy_by_table(), core::pose::make_pose_from_saccharide_sequence(), core::io::external::PsiPredInterface::run_psipred(), and core::io::external::PsiPredInterface::run_psipred_prob().

Real core::pose::Pose::chi	(	int const	chino,
		Size const	seqpos
	)		const

Returns the <chino> chi torsion angle of residue <seqpos>

Note: assumes the residue is an amino acid or monosaccharide

example(s): pose.chi(1,7) See also: Pose Pose.set_chi Pose.residue Residue

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

Real core::pose::Pose::chi ( Size const seqpos ) const

Returns the chi torsion angle of residue <seqpos>

Note: assumes the residue is an nucleic acid

example(s): pose.chi(7) See also: Pose Pose.residue Pose.set_chi Residue

References core::id::CHI, residue_type(), size(), and torsion().

void core::pose::Pose::clear ( )

Empty the pose contents.

example(s): pose.clear() See also: Pose Pose.assign Pose.empty

References conformation_, constraint_set_, data_cache_, energies_, metrics_, observer_cache_, and pdb_info().

void core::pose::Pose::clear_sequence_constraints ( )

Remove all sequence constraints from this pose.

References constraint_set_.

Referenced by protocols::aa_composition::ClearCompositionConstraintsMover::apply().

PoseOP core::pose::Pose::clone ( ) const

clone the conformation

clone the pose

Conformation const& core::pose::Pose::conformation ( ) const

inline

Returns the pose Conformation (const-access)

example(s): pose.Conformation() See also: Pose Conformation

References conformation_.

Conformation& core::pose::Pose::conformation ( )

inline

Returns the pose Conformation (non-const access)

References conformation_.

ConformationCOP core::pose::Pose::conformation_ptr ( ) const

Returns the pose Conformation pointer (const access)

References conformation_.

Referenced by protocols::cyclic_peptide::crosslinker::Metal_HelperBase::add_linker_constraints_symmetric(), protocols::cyclic_peptide::crosslinker::TBMB_Helper::add_linker_symmetric(), protocols::cyclic_peptide::crosslinker::TMA_Helper::add_linker_symmetric(), protocols::cyclic_peptide::crosslinker::Metal_HelperBase::add_linker_symmetric(), protocols::environment::claims::EnvLabelSelector::apply(), core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::calculate_penalty_once_from_scratch(), core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::detect_intra_residue_hydrogen_bonds_symmetric(), protocols::environment::Environment::end(), core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::initialize_graph_for_packing(), core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy::initialize_graphs(), core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::initialize_node(), core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::initialize_node(), core::pack::interaction_graph::ResidueArrayAnnealingEvaluator::initialize_symmetry_info(), core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::orient_rotamer_set_to_symmetric_partner(), core::pack::rotamer_set::symmetry::SymmetricRotamerSets::orient_rotamer_set_to_symmetric_partner(), core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::orient_rotamer_to_symmetric_partner(), protocols::denovo_design::DisulfidizeMover::prune_symmetric_disulfides(), core::util::rebuild_disulfide(), protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::selection_is_symmetric(), core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyEnergy::set_up_residuearrayannealableenergy_for_packing(), core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::set_up_residuearrayannealableenergy_for_packing(), core::scoring::mhc_epitope_energy::MHCEpitopeEnergy::setup_symmetry(), and protocols::fold_from_loops::movers::SplitAndMixPoseMover::transfer_conformation().

ConformationOP & core::pose::Pose::conformation_ptr ( )

Returns the pose Conformation pointer (nonconst access)

WHOA: This is not cool. The Pose cannot hand out access to the OP directly. Do not use.

References conformation_.

basic::datacache::ConstDataMap const & core::pose::Pose::const_data_cache ( ) const

Read access to the const data cache.

References constant_cache_.

Pose::ConstraintSetCOP core::pose::Pose::constraint_set ( ) const

References constraint_set_.

void core::pose::Pose::constraint_set ( ConstraintSetOP constraint_set )

FIX ME! This function should clone all of the constraints held in the input constraint set instead of allowing the input constraint set to perform a shallow copy of its constraints. Someone may be nefariously holding onto non-const pointers to the constraints in the input constraint set.

References conformation_, constraint_set(), constraint_set_, and energies_.

void core::pose::Pose::copy_segment	(	Size const	size,
		Pose const &	src,
		Size const	begin,
		Size const	src_begin
	)

Copy a stretch of coordinates/torsions from <src> to pose.

References begin(), conformation(), and conformation_.

Referenced by protocols::loops::loop_closure::ccd::ShortLoopClosure::apply(), protocols::hybridization::DomainAssembly::apply(), protocols::protein_interface_design::Revert::apply(), protocols::simple_moves::AddCavitiesMover::clear_suckers(), protocols::splice::Splice::copy_stretch(), core::fragment::fill_template_frames_from_pdb(), protocols::ub_e2c::ubi_e2c_modeler::init_d77_perturbation(), protocols::ub_e2c::ubi_e2c_modeler::init_k48r_perturbation(), protocols::surface_docking::SurfaceDockingProtocol::merge_protein_surface_poses(), protocols::ub_e2c::ubi_e2c_modeler::restore_cter(), protocols::rbsegment_relax::restore_pose_from_rbsegs(), and protocols::docking::ConformerSwitchMover::switch_conformer().

core::Size core::pose::Pose::corresponding_residue_in_current	(	core::Size const	ref_residue_index,
		std::string const &	ref_pose_name
	)		const

Returns the index of a residue in this pose corresponding to a residue in a reference pose.

Throws an error if the reference pose with the given name doesn't exist, or the residue number doesn't exist in that reference pose. Returns zero if no corresponding residue exists in this pose (e.g. if the residue in question has been deleted.

References reference_pose_set_cop().

Referenced by protocols::carbohydrates::SimpleGlycosylateMover::apply(), core::select::residue_selector::GlycanResidueSelector::apply(), core::pose::carbohydrates::delete_carbohydrate_branch(), core::pose::carbohydrates::delete_leaf(), core::pose::get_resnumber_from_reference_pose(), and core::simple_metrics::SimpleMetricData::get_value().

BasicDataCache const& core::pose::Pose::data ( ) const

inline

BasicDataCache indexed by enum in core/pose/datacache/CacheableDataType.hh.

References data_cache_.

BasicDataCache& core::pose::Pose::data ( )

inline

BasicDataCache indexed by enum in core/pose/datacache/CacheableDataType.hh.

References data_cache_.

void core::pose::Pose::decrement_reference_pose_mapping_after_seqpos ( core::Size const seqpos )

Find all mappings in the new pose after seqpos in all ReferencePose objects, and decrement them by 1.

If there is no ReferencePose object, do nothing.

References reference_pose_set_.

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

void core::pose::Pose::delete_polymer_residue ( Size const seqpos )

Delete a residue in the pose. Update Observers. Update any Reference Poses.

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

References conformation_, decrement_reference_pose_mapping_after_seqpos(), energies_, size(), and zero_reference_pose_mapping_at_seqpos().

Referenced by protocols::protein_interface_design::movers::LoopLengthChange::apply(), core::import_pose::RNA_HelixAssembler::get_rid_of_capping_base_pairs(), core::scoring::motif::Xfrag::insert(), protocols::protein_interface_design::movers::PlaceOnLoop::loop_length(), core::pose::rna::position_cutpoint_phosphate_torsions(), protocols::stepwise::modeler::rna::phosphate::position_five_prime_phosphate_SLOW(), protocols::splice::SpliceOut::remove_hairpin(), protocols::splice::Splice::remove_hairpin(), and protocols::ub_e2c::ubi_e2c_modeler::trim_cter().

void core::pose::Pose::delete_residue_range_slow	(	Size const	start,
		Size const	end
	)

Delete a range of residues in the pose.

Calls confromation::delete_residue_range_slow(). Update Observers. Update any Reference Poses

Calls confromation::delete_residue_range_slow(). Also, updates reference poses, if present.

References conformation_, decrement_reference_pose_mapping_after_seqpos(), energies_, size(), and protocols::loops::start.

Referenced by protocols::loop_grower::LoopComparator::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::splice::SpliceOutTail::build_ideal_segment(), protocols::splice::SpliceInTail::build_ideal_segment(), protocols::splice::SpliceIn::build_ideal_segment(), protocols::splice::SpliceOut::build_ideal_segment(), protocols::rna::denovo::delete_non_protein_from_pose(), and protocols::grafting::delete_region().

void core::pose::Pose::delete_residue_slow ( Size const seqpos )

Slow method that relies on FoldTree::delete_seqpos, rebuilds atomtree, can handle jumps/root residue. Update Observers. Update any Reference Poses.

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 conformation_, decrement_reference_pose_mapping_after_seqpos(), energies_, size(), and zero_reference_pose_mapping_at_seqpos().

Referenced by protocols::protein_interface_design::movers::LoopLengthChange::apply(), protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::apply(), protocols::antibody::snugdock::SnugDockProtocol::apply(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::calculate_free_receptor_score(), core::pose::carbohydrates::delete_leaf(), protocols::cyclic_peptide::PeptideStubMover::preserve_old_mainchain_torsions(), and protocols::rna::movers::RNAThreadAndMinimizeMover::process_deletions().

Real core::pose::Pose::delta ( Size const pos ) const

Returns the delta torsion angle of residue <seqpos>

Note: assumes the residue is an nucleic acid

example(s): pose.delta(4) See also: Pose Pose.residue Pose.set_delta Residue

References core::id::BB, residue_type(), size(), and torsion().

Referenced by protocols::stepwise::monte_carlo::rna::RNA_TorsionMover::apply_random_suite_torsion(), and protocols::stepwise::modeler::rna::phosphate::PhosphateMover::screen_three_prime_phosphate().

template<typename MemFn , typename Ptr >

bool core::pose::Pose::detach_conformation_obs	(	MemFn	fn,
		Ptr	ptr
	)		const

inline

detach ConformationEvent observer function

Parameters

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

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

References conformation_obs_hub_.

Referenced by core::pose::metrics::PoseMetricContainer::detach_from().

template<typename MemFn , typename Ptr >

bool core::pose::Pose::detach_destruction_obs	(	MemFn	fn,
		Ptr	ptr
	)		const

inline

detach DestructionEvent observer function

Parameters

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

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

Remarks: DestructionEvent observers will only be notified upon destruction of the Pose

References destruction_obs_hub_.

Referenced by core::pose::metrics::PoseMetricContainer::detach_from().

template<typename MemFn , typename Ptr >

bool core::pose::Pose::detach_energy_obs	(	MemFn	fn,
		Ptr	ptr
	)		const

inline

detach EnergyEvent observer function

Parameters

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

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

References energy_obs_hub_.

Referenced by core::pose::metrics::PoseMetricContainer::detach_from().

template<typename MemFn , typename Ptr >

bool core::pose::Pose::detach_general_obs	(	MemFn	fn,
		Ptr	ptr
	)		const

inline

detach GeneralEvent observer function

Parameters

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

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

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

References general_obs_hub_.

void core::pose::Pose::detached_copy ( Pose const & src )

Performs a deep copy of the src Pose into this Pose in a way that guarantees that no non-bitwise-constant data is shared between them (such as the AtomTree's observer system) – this Pose will be effectively detached from any data that lives in other objects.

This is basically a stub for an actual implementation of detached_copy which would not contain the "receive_observers_from" call that the operator = assignment does.

References conformation_, constraint_set_, and on_conf_xyz_change().

Referenced by protocols::fold_from_loops::utils::Nub::add_binders(), protocols::fold_from_loops::movers::AlignByResidueSelectorMover::apply(), protocols::fold_from_loops::utils::Nub::apply(), protocols::fold_from_loops::filters::ScorePoseSegmentFromResidueSelectorFilter::compute(), protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter::compute(), protocols::fold_from_loops::NubInitioMover::refold_pose(), and protocols::fold_from_loops::NubInitioMover::sanity_check().

Real core::pose::Pose::dof ( DOF_ID const & id ) const

Returns the value of the AtomTree DOF <id>

get the value of the atomtree degree of freedom (DOF)

See also: Pose DOF_ID

References core::id::DOF_ID::atom_id(), core::id::DOF_ID::atomno(), conformation_, core::id::D, core::id::PHI, residue(), core::id::DOF_ID::rsd(), size(), core::id::THETA, and core::id::DOF_ID::type().

Referenced by core::pose::symmetry::make_symmetric_movemap(), protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturber::set_pose_after_closure(), protocols::loops::loop_closure::kinematic_closure::VicinitySamplingKinematicPerturber::set_pose_after_closure(), protocols::loops::loop_closure::kinematic_closure::NeighborDependentTorsionSamplingKinematicPerturber::set_pose_after_closure(), protocols::loops::loop_closure::kinematic_closure::TorsionRestrictedKinematicPerturber::set_pose_after_closure(), and protocols::loops::loop_closure::kinematic_closure::BaseTabooPerturber::set_pose_after_closure().

bool core::pose::Pose::has_reference_pose ( ) const

Returns true if a pose has at least one reference pose, false otherwise.

References reference_pose_set_.

void core::pose::Pose::increment_reference_pose_mapping_after_seqpos ( core::Size const seqpos )

Find all mappings in the new pose after seqpos in all ReferencePose objects, and increment them by 1.

If there is no ReferencePose object, do nothing.

References reference_pose_set_.

Referenced by append_polymer_residue_after_seqpos(), insert_residue_by_bond(), insert_residue_by_jump(), and prepend_polymer_residue_before_seqpos().

void core::pose::Pose::init ( void )

private

initialize internal for a freshly build pose object. Use this function when you need to create new constructor.

default init function

References core::conformation::RotamerSetCacheableDataType::num_cacheable_data_types, core::pose::datacache::CacheableDataType::num_cacheable_data_types, and on_conf_xyz_change().

Referenced by Pose().

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

Adds <new_rsd_in> to pose at <seqpos>

This code sorely belongs in Pose.cc

References conformation_, energies_, increment_reference_pose_mapping_after_seqpos(), and size().

Referenced by protocols::cyclic_peptide::PeptideStubMover::apply(), and protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_fold_tree_through_build_full_model_info().

void core::pose::Pose::insert_residue_by_jump	(	Residue const &	new_rsd_in,
		Size const	seqpos,
		Size	anchor_pos,
		std::string const &	anchor_atomno = `""`,
		std::string const &	root_atomno = `""`
	)

Adds <new_rsd_in> to pose at <seqpos>

This code sorely belongs in Pose.cc

References conformation_, energies_, increment_reference_pose_mapping_after_seqpos(), and size().

Referenced by protocols::cryst::MakeLatticeMover::add_monomers_to_lattice(), protocols::cryst::MakeLayerMover::add_monomers_to_layer(), protocols::stepwise::monte_carlo::mover::AddMover::append_residue(), protocols::grafting::insert_pose_into_pose(), protocols::forge::build::SegmentSwap::modify_impl(), protocols::stepwise::monte_carlo::mover::AddMover::prepend_residue(), and protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_fold_tree_through_build_full_model_info().

bool core::pose::Pose::is_centroid ( ) const

Returns true if pose is ResidueType centroid.

Note: convenience test for residue_type_set

example(s): pose.is_centroid() See also: Pose Pose.is_fullatom Residue ResidueType

References conformation_.

Referenced by protocols::loop_grower::LoopPartialSolution::add_sheets(), protocols::loop_grower::LoopGrower::add_user_csts(), protocols::simple_moves::CombinePoseMover::apply(), protocols::backrub::BackrubProtocol::apply(), protocols::normalmode::NormalModeRelaxMover::apply(), protocols::abinitio::abscript::AbscriptMover::apply(), protocols::docking::membrane::MPFindInterfaceMover::apply(), protocols::relax::CentroidRelax::apply(), protocols::relax::RangeRelaxMover::apply(), protocols::loop_grower::SheetSampler::apply(), protocols::loop_grower::LoopPartialSolution::apply(), protocols::forge::components::VarLengthBuild::apply(), protocols::normalmode::NormalModeRelaxMover::apply_on_pose(), protocols::loop_grower::LoopPartialSolution::apply_sheets(), core::scoring::membrane::MPResidueLipophilicityEnergy::calc_energy(), core::scoring::membrane::MPHelicalityEnergy::calc_residue_burial(), core::scoring::membrane::MPResidueLipophilicityEnergy::calc_residue_burial(), protocols::simple_filters::ResidueSetChainEnergyFilter::compute(), protocols::loop_modeling::utilities::PrepareForCentroid::do_apply(), protocols::loop_grower::LoopComparator::fill_pose(), protocols::backrub::BackrubProtocol::finalize_setup(), protocols::abinitio::AbrelaxApplication::fold(), protocols::constraints_additional::BindingSiteConstraint::init(), protocols::abinitio::abscript::RigidChunkCM::initialize(), protocols::legacy_sewing::Assembly::native_positions(), core::scoring::membrane::MPResidueLipophilicityEnergy::report_ressolv(), protocols::mpi_refinement::WorkUnit_bbGauss::run(), protocols::mpi_refinement::WorkUnit_MD::run(), protocols::mpi_refinement::WorkUnit_FragInsert::run(), protocols::mpi_refinement::WorkUnit_NormalMode::run(), protocols::mpi_refinement::WorkUnit_KicCloser::run(), protocols::star::to_centroid(), and protocols::medal::to_centroid().

bool core::pose::Pose::is_fullatom ( ) const

Returns true if pose is ResidueType fullatom.

Note: convenience test for residue_type_set

example(s): pose.is_fullatom() See also: Pose Pose.is_centroid Residue ResidueType

References conformation_.

kinematics::Jump const & core::pose::Pose::jump ( int const jump_number ) const

Returns the pose FoldTree Jump <jump_number>

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

example(s): pose.jump(1) See also: Pose Pose.fold_tree Pose.set_jump FoldTree FoldTree.jump_edge Jump

References conformation_.

kinematics::Jump const & core::pose::Pose::jump ( AtomID const & id ) const

Returns the pose FoldTree Jump <id>

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

example(s): pose.set_jump(R5N) See also: Pose Pose.fold_tree Pose.set_jump FoldTree FoldTree.jump_edge AtomID

References conformation_.

conformation::membrane::MembraneInfoOP core::pose::Pose::membrane_info ( ) const

Get information about the membrane orientaiton, geometry, and lipid composition within this pose.

MembraneInfo contains all information pertaining to the conformation and composition of a membrane enviornment

example(s): pose.membrane_info() conformation.membrane_info()

References conformation_.

conformation::membrane::MembraneInfoOP core::pose::Pose::membrane_info ( )

Get information about the membrane orientaiton, geometry, and lipid composition within this pose.

MembraneInfo contains all information pertaining to the conformation and composition of a membrane enviornment

example(s): pose.membrane_info() conformation.membrane_info()

References conformation_.

void core::pose::Pose::metric	(	std::string const &	calculator_name,
		std::string const &	key,
		basic::MetricValueBase &	val
	)		const

References metrics_.

Real core::pose::Pose::mu ( Size const seqpos ) const

Returns the mu torsion angle of oligourea residue <seqpos>.

Mu is defined as CM(n)-NU(n)-C(n)-N(n+1) for an oligourea.

Note: Assumes residue is an oligourea.

example(s): pose.mu(21) See also: Pose Pose.set_mu Pose.residue Residue

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

References core::conformation::Residue::mainchain_torsion(), core::id::mu_torsion_oligourea(), residue(), residue_type(), and size().

void core::pose::Pose::notify_conformation_obs	(	ConformationEvent const &	e,
		bool const	fire_general = `true`
	)

private

notify ConformationEvent observers

Parameters

e	the event
fire_general	fire a GeneralEvent afterwards? default true

References conformation_obs_hub_, and notify_general_obs().

Referenced by on_conf_xyz_change().

void core::pose::Pose::notify_destruction_obs ( DestructionEvent const & e )

private

notify DestructionEvent observers

Remarks: called only upon destruction of the Pose

References destruction_obs_hub_.

Referenced by ~Pose().

void core::pose::Pose::notify_energy_obs	(	EnergyEvent const &	e,
		bool const	fire_general = `true`
	)

private

notify EnergyEvent observers

Parameters

e	the event
fire_general	fire a GeneralEvent afterwards? default true

References energy_obs_hub_, and notify_general_obs().

Referenced by scoring_end().

void core::pose::Pose::notify_general_obs ( GeneralEvent const & e )

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_conformation_obs(), and notify_energy_obs().

core::Size core::pose::Pose::num_chains ( ) const

Returns the total number of (chain ID) chains in the pose.

INFORMATION ABOUT CHAIN NUMBERS (chain ids), CHAIN LETTERS and JUMP NUMBERS

Chain numbers/ids, chain letters and jumps all serve very similar purposes in Rosetta, that is, to identify sets of "connected" residue. That said, their purpose and meaning are distinct and not directly interchangable.

Chain numbers (or chain ids) are associated with the Pose's Conformation object. These are sequentially numbered positive integers that represet consecutively (Pose/Rosetta) numbered residues which are chemically connected. Not all chemically connected units will have a single chain ID. It's perfectly acceptable to split a single consecutive covalent peptide chain across muliple chain IDs. Additionally, non-consecutive peptides may be covalently (C->N) connected, yet must by necessity have different chain IDs.
Chain letters are associated with the Pose's PDBInfo object. These are arbitrary single characters given to each residue. While convention is to maintain the same chain letter for a chemically connected entity, that's not always the case. One single protein chain (all a single chain ID, all one peptide edge in the FoldTree) can have more than one chain letter, and different chemical entities (different chain IDs, connected by different jumps) can have the same chain letter. There is also no gurantee about the ordering of chain letters - they may not be consecutive nor alphabetically ordered, and may not start or even include 'A'
Jumps and jump numbers are associated with the Pose's FoldTree object These specify how movement (e.g. backbone movement) propigates. A covalently connected peptide chain may be controlled by multiple jumps - not just connected with internal jumps, but different portions or domains of the protein may be on completely different branches of the FoldTree, only attached at the root of the FoldTree. While a controlling jump for a single residue (except for those at the root) can be assigned, is no gurantee that a single jump can be identified which controls all the residues with a given chain letter or chain id. (Unless the FoldTree has been specifically arranged for that to be the case. example(s): pose.num_chains() see also: pose pose.chain pose.annotated_sequence pose.chain_sequence pose.fold_tree pose.sequence foldtree

References conformation_.

Referenced by protocols::energy_based_clustering::EnergyBasedClusteringProtocol::calc_dist(), chain_begin(), chain_end(), chain_sequence(), protocols::simple_filters::ChainCountFilter::compute(), protocols::simple_filters::BuriedUnsatHbondFilter::compute(), core::pose::get_chain_from_chain_id(), core::pose::get_chain_residues(), protocols::constel::get_chain_terms(), core::pose::get_chains(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_new_chainIDs(), core::pose::get_resnums_for_chain_id(), core::pose::ResidueIndexDescriptionChainEnd::resolve_index(), protocols::fold_from_loops::NubInitioMover::sanity_check(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::swap_alignment_vector(), and protocols::energy_based_clustering::EnergyBasedClusteringProtocol::swap_chains().

Size core::pose::Pose::num_jump ( ) const

Returns the number of jumps in the pose FoldTree.

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

example(s): pose.num_jump() See also: Pose Pose.jump Pose.set_jump FoldTree Jump

References conformation_.

ObserverCache const& core::pose::Pose::observer_cache ( ) const

inline

ObserverCache indexed by enum in core/pose/datacache/CacheableObserverType.hh.

References observer_cache_.

Referenced by protocols::enzdes::DetectProteinLigandInterface::add_observer_cache_segments_to_set(), protocols::seeded_abinitio::adjust_mm_to_length(), protocols::forge::remodel::RemodelMover::apply(), core::pack::task::operation::ReadResfileAndObeyLengthEvents::apply(), protocols::denovo_design::components::StructureDataFactory::attach_observer(), protocols::forge::components::VarLengthBuild::centroid_build(), protocols::denovo_design::components::StructureDataFactory::detach_observer(), protocols::enzdes::EnzdesFlexBBProtocol::determine_flexible_regions(), protocols::enzdes::EnzdesScorefileFilter::examine_pose(), protocols::toolbox::match_enzdes_util::get_enzdes_observer(), protocols::moves::get_pymol_observer(), protocols::network::get_ui_observer(), protocols::denovo_design::components::StructureDataFactory::observer_attached(), protocols::enzdes::EnzdesJobInputter::pose_from_job(), protocols::denovo_design::components::StructureDataFactory::retrieve_observer(), core::pose::datacache::SpecialSegmentsObserver::set_farray_from_sso(), protocols::loops::loop_mover::LoopMover::set_loops_from_pose_observer_cache(), and protocols::seeded_abinitio::GrowPeptides::setup_cached_observers().

ObserverCache& core::pose::Pose::observer_cache ( )

inline

ObserverCache indexed by enum in core/pose/datacache/CacheableObserverType.hh.

References observer_cache_.

Real core::pose::Pose::omega ( Size const seqpos ) const

Returns the omega torsion angle of residue <seqpos> in degrees.

Returns the value of the omega backbone dihedral angle.

Note: assumes the residue is an amino acid or monosaccharide

example(s): pose.omega(3) See also: Pose Pose.residue Pose.set_omega Residue

For proteins, omega is defined as CA(n)-C(n)-N(n+1)-CA(n+1). For beta-amino acids, omega is defined as CM(n)-C(n)-N(n+1)-CA(n+1). For carbohydrates glycosylated at an exocyclic position, omega of residue n is defined as OX(n-1)-CX(n-1)-CX-1(n-1)-CX-2(n-1), where X is the position of the glycosidic linkage. (Note that every atom defining this torsion comes from the previous residue!)

void core::pose::Pose::on_conf_xyz_change ( core::conformation::signals::XYZEvent const & event )

private

upon receiving a conformation::signals::XYZEvent

References notify_conformation_obs().

Referenced by detached_copy(), init(), operator=(), and set_new_conformation().

Pose & core::pose::Pose::operator= ( Pose const & src )

Construct pose from pdb file.

copy assignment

Copies <src> into the pose where it remains possible that two Poses may point to each other in non-const ways or share non-bitwise constant data between them (E.g. the AtomTree observer system).

example(s): test_pose.assign(pose) See also: Pose

References buffer_observers(), conformation_, constant_cache_, constraint_set_, data_cache_, energies_, metrics_, core::conformation::RotamerSetCacheableDataType::num_cacheable_data_types, core::pose::datacache::CacheableDataType::num_cacheable_data_types, observer_cache_, on_conf_xyz_change(), pdb_info(), pdb_info_, core::pose::datacache::PYMOL_OBSERVER, reference_pose_set_, and unbuffer_observers().

PDBInfoCOP core::pose::Pose::pdb_info ( ) const

Returns the pose PDBInfo (const)

get pdb info (const)

example(s): pose.pdb_info() See also: Pose Energies PDBInfo ScoreFunction pose_from_pdb

Returns: NULL if no PDBInfo instance exists, the pdb info instance otherwise; NULL if no PDBInfo instance exists, the pdb info instance otherwise

References pdb_info_, and size().

PDBInfoOP core::pose::Pose::pdb_info ( )

Returns the pose PDBInfo.

get pdb info

Returns: NULL if no PDBInfo instance exists, the PDBInfo instance otherwise; NULL if no PDBInfo instance exists, the pdb info instance otherwise

References pdb_info_, and size().

PDBInfoOP core::pose::Pose::pdb_info ( PDBInfoOP new_info )

Sets pose PDBInfo to <new_info>

copy new pdb info into this Pose

Parameters

[in] <new_info> the new PDBInfo to copy, pass NULL if you want to zero the existence of PDBInfo inside this Pose

Returns: the prior PDBInfo instance

Parameters

[in] new_info the new pdb info to copy, pass NULL if you want to zero the existence of pdb info inside this Pose

Returns: the prior pdb info instance

References conformation_, pdb_info_, and size().

Real core::pose::Pose::phi ( Size const seqpos ) const

Returns the phi torsion angle of residue <seqpos> in degrees.

Returns the value of the phi backbone dihedral angle.

Note: assumes the residue is an amino acid or monosaccharide

example(s): pose.phi(1) See also: Pose Pose.residue Pose.set_phi Residue

For proteins and peptoids, phi is defined as C(n-1)-N(n)-CA(n)-C(n). For beta-amino acids, phi is defined as C(n-1)-N(n)-CA(n)-CM(n). For aldopyranoses, phi is defined as O5(n)-C1(n)-OX(n-1)-CX(n-1), where X is the position of the glycosidic linkage. For aldofuranoses, phi is defined as O4(n)-C1(n)-OX(n-1)-CX(n-1). For 2-ketopyranoses, phi is defined as O6(n)-C2(n)-OX(n-1)-CX(n-1). For 2-ketofuranoses, phi is defined as O5(n)-C2(n)-OX(n-1)-CX(n-1). Et cetera...

void core::pose::Pose::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

References conformation_, energies_, increment_reference_pose_mapping_after_seqpos(), and size().

Referenced by protocols::cryst::MakeLatticeMover::add_monomers_to_lattice(), protocols::cryst::MakeLayerMover::add_monomers_to_layer(), protocols::denovo_design::components::add_to_pose(), protocols::denovo_design::components::append_new_chain_from_template_segment(), protocols::cyclic_peptide::PeptideStubMover::apply(), core::pose::rna::position_cutpoint_phosphate_torsions(), protocols::stepwise::modeler::rna::phosphate::position_five_prime_phosphate_SLOW(), core::import_pose::RNA_HelixAssembler::prepend_Aform_residue(), protocols::denovo_design::components::prepend_new_residues(), and protocols::stepwise::monte_carlo::mover::AddMover::prepend_residue().

std::string core::pose::Pose::print_metric	(	std::string const &	calculator_name,
		std::string const &	key
	)		const

References metrics_.

Real core::pose::Pose::psi ( Size const seqpos ) const

Returns the psi torsion angle of residue <seqpos> in degrees Note: assumes the residue is an amino acid or monosaccharide.

Returns the value of the psi backbone dihedral angle.

example(s): pose.psi(2) See also: Pose Pose.residue Pose.set_psi Residue

For proteins, psi is defined as N(n)-CA(n)-C(n)-N(n+1). For beta-amino acids, psi is defined as CA(n)-CM(n)-C(n)-N(n+1). For saccharides, psi is defined as: C(anomeric)(n)-OX(n-1)-CX(n-1)-CX-1(n-1), where X is the position of the glycosidic linkage.

void core::pose::Pose::real_to_virtual ( core::Size seqpos )

Switch residues to VIRTUAL.

VIRTUAL residues are the same except not SCORED or DUMPED.

example(s): pose.real_to_virtual(3) See also: Pose ResidueType

Author: Sebastian Raemisch raemi.nosp@m.sch@.nosp@m.scrip.nosp@m.ps.e.nosp@m.du; Jared Adolf-Bryfogle jadol.nosp@m.fbr@.nosp@m.gmail.nosp@m..com

References conformation(), core::conformation::Residue::connect_map(), core::conformation::Residue::connected_residue_at_resconn(), core::chemical::ResConnID::connid(), core::chemical::ResidueType::make(), core::chemical::ResidueType::n_possible_residue_connections(), core::chemical::real_to_virtual(), core::pose::replace_pose_residue_copying_existing_coordinates(), core::conformation::Conformation::residue(), residue(), residue_type(), and core::conformation::Conformation::update_noncanonical_connection().

Referenced by protocols::simple_moves::ConvertRealToVirtualMover::apply().

void core::pose::Pose::reference_pose_from_current	(	std::string const &	ref_pose_name,
		bool	override_current = `false`
	)

Create a new reference pose from the current state of the pose.

If a ReferencePoseSet object does not exist, this function will create it. If override_current is set to true, will override any currently set reference pose with the ref_pose_name.

If a ReferencePoseSet object does not exist, this function will create it.

References reference_pose_set_.

Referenced by protocols::simple_moves::StorePoseSnapshot::apply(), protocols::carbohydrates::SimpleGlycosylateMover::apply(), core::pose::carbohydrates::delete_carbohydrate_branch(), and core::simple_metrics::SimpleMetricData::set_value().

core::pose::reference_pose::ReferencePoseSetOP core::pose::Pose::reference_pose_set ( )

Access the ReferencePoseSet object (non-const).

If a ReferencePoseSet object does not exist, this function will create it.

References reference_pose_set_.

core::pose::reference_pose::ReferencePoseSetCOP core::pose::Pose::reference_pose_set_cop ( ) const

Const-access the ReferencePoseSet object.

If a ReferencePoseSet object does not exist, this function will throw an error.

References reference_pose_set_.

Referenced by corresponding_residue_in_current().

bool core::pose::Pose::remove_constraint	(	scoring::constraints::ConstraintCOP	cst,
		bool	object_comparison = `false`
	)

re object_comparison see comment for ConstraintSet::remove_constraint function

References constraint_set_, and energies_.

Referenced by core::pose::ncbb::add_oop_constraint(), protocols::splice::SpliceManager::add_sequence_constraints(), protocols::splice::Splice::add_sequence_constraints(), protocols::magnesium::MgMinimizer::apply(), protocols::ligand_docking::LigandDockProtocol::apply(), protocols::ligand_docking::TetherLigand::release(), protocols::ligand_docking::MinimizeBackbone::remove_constraints(), core::scoring::constraints::remove_constraints_of_type(), and core::scoring::constraints::remove_nonbb_constraints().

bool core::pose::Pose::remove_constraints	(	scoring::constraints::ConstraintCOPs	csts,
		bool	object_comparison = `false`
	)

re object_comparison see comment for ConstraintSet::remove_constraint function

References constraint_set_, and energies_.

bool core::pose::Pose::remove_constraints ( )

References constraint_set_, and energies_.

void core::pose::Pose::replace_residue	(	Size const	seqpos,
		Residue const &	new_rsd_in,
		bool const	orient_backbone
	)

Replaces the residue at <seqpos> with <new_rsd_in>

References conformation_, and size().

void core::pose::Pose::replace_residue	(	int const	seqpos,
		Residue const &	new_rsd_in,
		utility::vector1< std::pair< std::string, std::string > > const &	atom_pairs
	)

Replaces the residue at <seqpos> with <new_rsd> based on superposition on the specified input atom pairs NOTE: at the moment, only superposition on 3 atoms works This code sorely belongs in Pose.cc.

References conformation_, and size().

Pose::Residue const & core::pose::Pose::residue ( Size const seqpos ) const

Returns the Residue at position <seqpos> (read access) Note: this method will trigger a refold if either the torsions or the coordinates are out-of-date.

example(s): pose.residue(4) See also: Pose Pose.sequence Pose.size Residue ResidueType

References conformation_, and size().

basic::datacache::BasicDataCache & core::pose::Pose::residue_data ( Size const seqpos )

Returns the DataCache held by Residue at position <seqpos> (read/write access) Note: this method will trigger a refold if either the torsions or the coordinates are out-of-date.

example(s): pose.residue_data(4) See also: Pose Pose.residue Pose.sequence Pose.size Residue ResidueType

References conformation_, and size().

Referenced by core::scoring::ScoreFunction::asym_setup_for_derivatives(), core::scoring::ScoreFunction::asym_setup_for_minimizing(), core::pack::create_minimization_graph(), protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), protocols::ligand_docking::ga_ligand_dock::GridScorer::dof_derivative(), core::scoring::lkball::LK_BallEnergy::setup_for_packing(), core::scoring::ScoreFunction::setup_for_scoring(), protocols::ncbb::SecStructMinimizeMultiFunc::setup_minimization_graph(), core::scoring::ScoreFunction::sym_setup_for_derivatives(), core::scoring::ScoreFunction::sym_setup_for_minimizing(), and core::scoring::lkball::LK_BallEnergy::update_residue_for_packing().

basic::datacache::BasicDataCache const & core::pose::Pose::residue_data ( Size const seqpos ) const

Returns the DataCache held by Residue at position <seqpos> (read access) Note: this method will trigger a refold if either the torsions or the coordinates are out-of-date.

example(s): pose.residue_data(4) See also: Pose Pose.residue Pose.sequence Pose.size Residue ResidueType

References conformation_, and size().

chemical::ResidueType const & core::pose::Pose::residue_type ( Size const seqpos ) const

Returns the ResidueType at position <seqpos> (read access) Note: this method NOT will trigger a refold if either the torsions or the coordinates are out-of-date.

example(s): pose.residue_type(5) See also: Pose Pose.residue Pose.residue_type_ptr Pose.sequence Pose.size Residue ResidueType

References conformation_, and size().

chemical::ResidueTypeCOP core::pose::Pose::residue_type_ptr ( Size const seqpos ) const

Returns the ResidueTypeCOP for position <seqpos> (read access) Note: this method NOT will trigger a refold if either the torsions or the coordinates are out-of-date.

example(s): pose.residue_type_ptr(5) See also: Pose Pose.residue Pose.residue_type Pose.sequence Pose.size Residue ResidueType

References conformation_, and size().

Referenced by protocols::cyclic_peptide::crosslinker::SquarePlanarMetal_Helper::add_dihedral_constraint_to_stream(), protocols::cyclic_peptide::crosslinker::TrigonalPlanarMetal_Helper::add_dihedral_constraints(), protocols::toolbox::rotamer_set_operations::RigidBodyMoveBaseRSO::alter_rotamer_set(), protocols::ligand_docking::RandomConformerMover::apply(), protocols::simple_moves::ModifyVariantTypeMover::apply(), protocols::backbone_moves::RandomizeBBByRamaPrePro::apply(), protocols::cyclic_peptide::RamaMutationSelector::apply(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_rama_prepro_check(), core::scoring::BB_Pos::bbindices_up_to_date(), protocols::dna::DnaInterfacePacker::current_working_sequence(), protocols::dna::design_residues_list(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::find_disulfides(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::find_disulfides(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::find_disulfides(), protocols::ligand_docking::LigandBaseProtocol::get_non_bb_clashing_rotamers(), protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::get_pose_data(), protocols::dna::DnaInterfacePacker::get_targeted_sequence(), protocols::dna::DnaInterfacePacker::init_standard(), protocols::dna::DnaInterfacePacker::measure_specificities(), protocols::dna::DnaInterfacePacker::protein_scan(), protocols::features::ResidueTypesFeatures::report_features(), protocols::dna::DnaInterfacePacker::reversion_scan(), protocols::ligand_docking::rotamers_for_trials(), protocols::minimization_packing::RotamerizeMover::task_is_valid(), protocols::minimization_packing::MinPackMover::task_is_valid(), protocols::minimization_packing::PackRotamersMover::task_is_valid(), and protocols::hbnet::HBNet::task_is_valid().

core::chemical::ResidueTypeSetCOP core::pose::Pose::residue_type_set_for_pose ( core::chemical::TypeSetMode mode = core::chemical::INVALID_t ) const

Return the custom ResidueTypeSet for the Pose, if any. Otherwise will return the appropriate global ResidueTypeSet.

If mode is INVALID_t (the default), the returned ResidueTypeSet is the one corresponding to the majority of the residues in the Pose. i.e. FULL_ATOM if pose.is_fullatom(); CENTROID if pose.is_centriod()

examples(s): pose.residue_type_set_for_pose() pose.residue_type_set_for_pose( core::chemical::CENTROID_t ) See also: Pose Pose.is_fullatom Pose.is_centroid ResidueTypeSet

References conformation(), and core::conformation::Conformation::residue_type_set_for_conf().

void core::pose::Pose::scoring_begin ( scoring::ScoreFunction const & sfxn )

Called by ScoreFunction at the beginning of scoring.

called by the ScoreFunction at the start of scoring. If the score function has changed since the last round of scoring, then cached energies may have become invalidated – the Energies object makes that decision.

References conformation_, energies_, size(), and update_residue_neighbors().

Referenced by core::optimization::SingleResidueMultifunc::operator()(), and core::scoring::ScoreFunction::operator()().

void core::pose::Pose::scoring_end ( scoring::ScoreFunction const & scorefxn )

Called by ScoreFunction at the end of scoring.

References energies_, and notify_energy_obs().

Referenced by core::optimization::SingleResidueMultifunc::operator()(), and core::scoring::ScoreFunction::operator()().

char core::pose::Pose::secstruct ( Size const seqpos ) const

Returns the secondary structure of residue <seqpos> this usually comes from fragments. The conformation object will not invoke DSSP to determine the secondary structure if e.g. it has not been made from fragments. 'H' = helical 'E' = strand or sheet 'L' = loop.

example(s): pose.secstruct(3) See also: Pose Pose.residue Pose.set_secstruct Residue

References conformation_, and size().

std::string core::pose::Pose::secstruct ( ) const

Returns a string representing pose secondary structure.

example(s): pose.secstruct() See also: Pose Pose.residue Pose.set_secstruct Residue

References size().

Referenced by dump_scored_pdb().

std::string core::pose::Pose::sequence ( ) const

Returns a string representing the 1-letter-coded sequence of the pose conformation.

example(s): pose.sequence() See also: Pose Pose.annotated_sequence Pose.chain Pose.chain_sequence Pose.residue Pose.size

References conformation_, core::chemical::ResidueTypeBase::name1(), and residue_type().

std::string core::pose::Pose::sequence	(	core::Size	resnum_start,
		core::Size	resnum_end
	)		const

Returns a string representing the 1-letter-coded sequence of the pose conformation. From start to end.

example(s): pose.sequence() See also: Pose Pose.annotated_sequence Pose.chain Pose.chain_sequence Pose.residue Pose.size

References sequence(), and size().

void core::pose::Pose::set_alpha	(	Size const	seqpos,
		Real const	setting
	)

Sets the alpha torsion angle of residue <seqpos> to <setting>

Note: <setting> must be in degrees, assumes residue is an nucleic acid

example(s): pose.set_alpha(1) See also: Pose Pose.alpha Pose.residue Residue

References core::id::BB, conformation_, residue_type(), and size().

Referenced by protocols::rpc::JSON_RPC::run().

void core::pose::Pose::set_beta	(	Size const	seqpos,
		Real const	setting
	)

Sets the beta torsion angle of residue <seqpos> to <setting>

Note: <setting> must be in degrees, assumes residue is an nucleic acid

example(s): pose.set_beta(2) See also: Pose Pose.beta Pose.residue Residue

References core::id::BB, conformation_, residue_type(), and size().

Referenced by protocols::rpc::JSON_RPC::run().

void core::pose::Pose::set_chi	(	int const	chino,
		Size const	seqpos,
		Real const	setting
	)

Sets the <chino> chi torsion angle of residue <seqpos> to <setting>

Note: <setting> must be in degrees, assumes residue is an amino acid or monosaccharide

example(s): pose.set_chi(1,7,120) See also: Pose Pose.chi Pose.residue Residue

References core::id::CHI, conformation_, protocols::magnesium::is_ligand(), protocols::stepwise::modeler::is_protein(), residue_type(), and size().

void core::pose::Pose::set_chi	(	Size const	seqpos,
		Real const	setting
	)

Sets the chi torsion angle of residue <seqpos> to <setting>

Note: <setting> must be in degrees, assumes residue is an nucleic acid

example(s): pose.set_chi(7) See also: Pose Pose.chi Pose.residue Residue

References core::id::CHI, conformation_, residue_type(), and size().

template<class T >

void core::pose::Pose::set_const_data	(	std::string const &	category,
		std::string const &	name,
		T const &	original
	)

inline

Controlled method for adding an object to the Pose's constant data cache; this function is the only way to add data to the Pose's data cache. An object, identified by two strings, is freshly constructed and inserted into the ConstDataCache. Objects inserted into the ConstDataCache must remain bitwise const for thread-safety reasons. The ConstDataCache has shallow-copy semantics, meaning that two poses would point to the same object if one were copied into the other. If these two Poses were then handed to separate threads, and the data they were both pointing at were to change, that would create race conditions. For this reason, the Pose attempts to prevent non-constant pointers to the data held in the ConstDataCache from existing. Objects placed in the ConstDataCache must have a copy constructor (either implicit or explicit).

Arbitrary constant data can be stored in the Pose, but the Pose will make a clone of the starting data in an effort to ensure that the data it holds cannot be modified by anyone holding a non-constant pointer to that data. Of course, if the data being held does not perform a deep copy in its copy constructor (e.g. if it itself holds pointers to other data) then this code does not actually succeed in making sure that the data is guaranteed bitwise const.

References store_const_data().

template<>

void core::pose::Pose::set_const_data	(	std::string const &	category,
		std::string const &	name,
		Pose const &	original
	)

inline

template specialization for when storing a Pose inside a Pose. For the sake of thread safety, the Pose that should be stored must represent a deep copy – one that does not contain pointers to any outside objects through which it might "communicate" behind the scenes or which might try to communicate with the starting pose. Therefore, a "detached_copy" of the original pose is created.

References store_const_data().

void core::pose::Pose::set_delta	(	Size const	seqpos,
		Real const	setting
	)

Sets the delta torsion angle of residue <seqpos> to <setting>

Note: <setting> must be in degrees, assumes residue is an nucleic acid

example(s): pose.set_delta(4) See also: Pose Pose.delta Pose.residue Residue

References core::id::BB, conformation_, residue_type(), and size().

Referenced by protocols::rpc::JSON_RPC::run().

void core::pose::Pose::set_dof	(	DOF_ID const &	id,
		Real const	setting
	)

Sets the value of the AtomTree DOF <id>

set the value of the atomtree degree of freedom (DOF)

Member Data Documentation

ConformationOP core::pose::Pose::conformation_

private

Referenced by aa(), add_constraint(), add_constraints(), annotated_sequence(), append_polymer_residue_after_seqpos(), append_pose_by_jump(), append_residue_by_atoms(), append_residue_by_bond(), append_residue_by_jump(), apply_transform_Rx_plus_v(), atom_tree(), batch_get_xyz(), batch_set_xyz(), chain_begin(), chain_end(), chain_sequence(), clear(), conformation(), conformation_ptr(), constraint_set(), copy_segment(), delete_polymer_residue(), delete_residue_range_slow(), delete_residue_slow(), detached_copy(), dof(), dump_scored_pdb(), empty(), fold_tree(), glycan_tree_set(), has_dof(), insert_residue_by_bond(), insert_residue_by_jump(), is_centroid(), is_fullatom(), jump(), membrane_info(), num_chains(), num_jump(), operator=(), pdb_info(), prepend_polymer_residue_before_seqpos(), replace_residue(), residue(), residue_data(), residue_type(), residue_type_ptr(), scoring_begin(), secstruct(), sequence(), set_alpha(), set_beta(), set_chi(), set_delta(), set_dof(), set_epsilon(), set_gamma(), set_jump(), set_mu(), set_new_conformation(), set_omega(), set_phi(), set_psi(), set_ring_conformation(), set_secstruct(), set_theta(), set_torsion(), set_xyz(), set_zeta(), size(), split_by_chain(), stub_from_id(), torsion(), transfer_constraint_set(), update_actcoord(), update_actcoords(), update_orbital_coords(), update_pose_chains_from_pdb_chains(), update_residue_neighbors(), and xyz().

utility::signals::BufferedSignalHub< void, ConformationEvent > core::pose::Pose::conformation_obs_hub_

mutableprivate

ConformationEvent observers.

Remarks: fires when Conformation experiences a coordinate change (conformation::signals::XYZEvent)

Referenced by attach_conformation_obs(), buffer_observers(), detach_conformation_obs(), notify_conformation_obs(), and unbuffer_observers().

ConstDataMapOP core::pose::Pose::constant_cache_

private

The DataMap is a way to store arbitrarily complicated, constant data. The contents of the datamap are copied by value – the pointers are copied – meaning that two poses can point to the same data. For thread safety reasons, it is essential that the data inside this map is bitwise const (i.e. no mutable data is used or changes state). Poses may be placed inside the constant datamap, but it is important that ownership cycles are not created (e.g. A –> B; B–>C; C–>A) or memory will be leaked. Care must be taken that the this never happens. One way to avoid this possibility is to only cache freshly cloned Poses. The other way is to first call Pose::purge_cached_poses.

Referenced by const_data_cache(), operator=(), and store_const_data().

ConstraintSetOP core::pose::Pose::constraint_set_

private

Referenced by add_constraint(), add_constraints(), clear(), clear_sequence_constraints(), constraint_set(), detached_copy(), operator=(), remove_constraint(), remove_constraints(), set_new_conformation(), and transfer_constraint_set().

BasicDataCacheOP core::pose::Pose::data_cache_

private

BasicDataCache indexed by enum in core/pose/datacache/CacheableDataType.hh.

Remarks: contains data we can tuck inside the pose for O(1) time access. Each element cached in the data_cache_ is cloned in the Pose copy operations, and so it is not a good place to store large, unchanging data, as that will be

Warning: DataCache must always be initialized with the number of cacheable data types – see the last enum entry. Data that does not need to be retrieved in O(1) time and does not need to ever change may be cached in either the Pose's const DataMap.

Referenced by clear(), data(), operator=(), and set_new_conformation().

utility::signals::BufferedSignalHub< void, DestructionEvent > core::pose::Pose::destruction_obs_hub_

mutableprivate

DestructionEvent observers.

Remarks: notification only occurs when Pose object is destroyed

Referenced by attach_destruction_obs(), buffer_observers(), detach_destruction_obs(), notify_destruction_obs(), and unbuffer_observers().

utility::signals::BufferedSignalHub< void, EnergyEvent > core::pose::Pose::energy_obs_hub_

mutableprivate

EnergyEvent observers.

Referenced by attach_energy_obs(), buffer_observers(), detach_energy_obs(), notify_energy_obs(), and unbuffer_observers().

utility::signals::BufferedSignalHub< void, GeneralEvent > core::pose::Pose::general_obs_hub_

mutableprivate

GeneralEvent observers.

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

Referenced by attach_general_obs(), buffer_observers(), detach_general_obs(), notify_general_obs(), and unbuffer_observers().

metrics::PoseMetricContainerOP core::pose::Pose::metrics_

mutableprivate

Referenced by clear(), metric(), operator=(), print_metric(), and set_new_conformation().

ObserverCacheOP core::pose::Pose::observer_cache_

private

ObserverCache indexed by enum in core/pose/datacache/CacheableObserverType.hh.

Warning: ObserverCache must always be initialized with the number of cacheable observer types – see the last enum entry.

Referenced by clear(), observer_cache(), operator=(), and set_new_conformation().

PDBInfoOP core::pose::Pose::pdb_info_

private

pdb info

Referenced by operator=(), pdb_info(), set_new_conformation(), and update_pose_chains_from_pdb_chains().

core::pose::reference_pose::ReferencePoseSetOP core::pose::Pose::reference_pose_set_

private

The set of ReferencePose objects that this pose stores.

By default, this owning pointer is null, and there is next to no memory overhead associated with having it here.

Referenced by decrement_reference_pose_mapping_after_seqpos(), has_reference_pose(), increment_reference_pose_mapping_after_seqpos(), operator=(), reference_pose_from_current(), reference_pose_set(), reference_pose_set_cop(), and zero_reference_pose_mapping_at_seqpos().

The documentation for this class was generated from the following files:

src/core/pose/Pose.hh
src/core/pose/Pose.cc

void core::pose::Pose::set_jump	(	int const	jump_number,
		const kinematics::Jump &	new_jump
	)

void core::pose::Pose::dump_pdb	(	std::ostream &	out,
		utility::vector1< core::Size > const &	residue_indices
	)		const

void core::pose::Pose::dump_scored_pdb	(	std::string const &	file_name,
		scoring::ScoreFunction const &	scorefxn
	)

void core::pose::Pose::set_epsilon	(	Size const	seqpos,
		Real const	setting
	)

void core::pose::Pose::set_gamma	(	Size const	seqpos,
		Real const	setting
	)

void core::pose::Pose::set_jump	(	AtomID const &	id,
		const kinematics::Jump &	new_jump
	)

void core::pose::Pose::set_mu	(	Size const	seqpos,
		Real const	setting
	)

void core::pose::Pose::set_omega	(	Size const	seqpos,
		Real const	setting
	)

void core::pose::Pose::set_phi	(	Size const	seqpos,
		Real const	setting
	)

void core::pose::Pose::set_psi	(	Size const	seqpos,
		Real const	setting
	)

void core::pose::Pose::set_ring_conformation	(	uint const	seqpos,
		uint const	ring_num,
		core::chemical::rings::RingConformer const &	conformer
	)

void core::pose::Pose::set_secstruct	(	Size const	seqpos,
		char const	setting
	)

void core::pose::Pose::set_theta	(	Size const	seqpos,
		Real const	setting
	)

void core::pose::Pose::set_torsion	(	TorsionID const &	id,
		Real const	setting
	)

void core::pose::Pose::set_xyz	(	AtomID const &	id,
		PointPosition const &	point
	)

void core::pose::Pose::set_xyz	(	NamedAtomID const &	id,
		PointPosition const &	point
	)

void core::pose::Pose::set_zeta	(	Size const	seqpos,
		Real const	setting
	)

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation