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

#include <Pose.hh>

Inheritance diagram for core::pose::Pose:

Collaboration 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 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

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

virtual	~Pose ()
	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...

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

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

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

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

Pose	split_by_chain (Size chain_id) const

void	update_pose_chains_from_pdb_chains ()
	Updates the pose chain IDs to match the pdb chain IDs. 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	constraint_set (ConstraintSetOP)

void	transfer_constraint_set (const pose::Pose &pose)

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	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	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	delete_polymer_residue (Size const seqpos)

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...

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	n_residue () const
	Returns the number of residues in the pose conformation example(s): pose.n_residue() See also: Pose Pose.sequence Pose.total_residue. 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 'S' = strand or sheet 'E' = 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	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 <chain_in> 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...

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...

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

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

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

void	set_omega (Size const seqpos, Real const setting)
	Sets the omega torsion angle of 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...

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

void	set_jump_now (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...

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

bool	dump_pdb (std::string const &file_name, std::string const &tag="1") const
	Export pose data to the PDB file <file_name> More...

void	dump_pdb (std::ostream &out, std::string const &tag="1") const

void	dump_pdb (std::ostream &out, utility::vector1< core::Size > const &residue_indices, std::string const &tag="1") 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, std::string const &tag="1")
	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...

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

Private Attributes
ConformationOP	conformation_
	the kinematics object, wraps a fold_tree and an atom_tree More...

scoring::EnergiesOP	energies_
	the cached energies object, stores total,rsd,and rsd-pair energies and neighbor info More...

metrics::PoseMetricContainerOP	metrics_

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

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

PDBInfoOP	pdb_info_
	pdb info More...

ConstraintSetOP	constraint_set_

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.energies Pose.fold_tree Pose.pdb_info Pose.residue Pose.sequence Pose.total_residue

Definition at line 188 of file Pose.hh.

Member Typedef Documentation

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

Definition at line 191 of file Pose.hh.

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

Definition at line 206 of file Pose.hh.

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

Definition at line 207 of file Pose.hh.

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

Definition at line 196 of file Pose.hh.

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

Definition at line 200 of file Pose.hh.

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

Definition at line 197 of file Pose.hh.

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

Definition at line 205 of file Pose.hh.

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

Definition at line 204 of file Pose.hh.

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

Definition at line 201 of file Pose.hh.

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

Definition at line 194 of file Pose.hh.

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

Definition at line 202 of file Pose.hh.

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

Definition at line 203 of file Pose.hh.

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

Definition at line 192 of file Pose.hh.

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

Definition at line 198 of file Pose.hh.

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

Definition at line 199 of file Pose.hh.

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

Definition at line 195 of file Pose.hh.

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

Definition at line 193 of file Pose.hh.

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

Definition at line 110 of file Pose.cc.

References init().

Referenced by split_by_chain().

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

virtual

destructor – > kill data on the heap

construc pose using info from PDB file

destructor – > kill data on the heap

Definition at line 129 of file Pose.cc.

References clear(), and notify_destruction_obs().

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

copy constructor

Definition at line 137 of file Pose.cc.

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

partial copy constructor

Definition at line 144 of file Pose.cc.

References core::sequence::end, init(), and core::io::pdb::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

Definition at line 552 of file Pose.cc.

References conformation_, and total_residue().

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

Definition at line 1348 of file Pose.cc.

References conformation_, constraint_set_, and energies_.

Referenced by protocols::jumping::JumpSample::add_chainbreaks_as_distance_constraint(), protocols::relax::add_coordinate_constraints_to_pose(), protocols::loops::add_coordinate_constraints_to_pose(), protocols::hybridization::FoldTreeHybridize::add_gap_constraints_to_pose(), protocols::simple_moves::hbs::add_hbs_constraint(), protocols::hybridization::add_non_protein_cst(), protocols::simple_moves::oop::add_oop_constraint(), protocols::toolbox::match_enzdes_util::EnzConstraintIO::add_pregenerated_constraints_to_pose(), protocols::protein_interface_design::FavorNativeResidue::add_residue_constraints(), protocols::protein_interface_design::FavorNonNativeResidue::add_residue_constraints(), protocols::protein_interface_design::movers::Splice::add_sequence_constraints(), protocols::hybridization::add_strand_pairs_cst(), protocols::simple_moves::AddCavitiesMover::add_suckers(), protocols::anchored_design::AnchorMoversData::anchor_noise_constraints_setup(), protocols::simple_moves::AddConstraintsToCurrentConformationMover::apply(), protocols::simple_moves::SequenceProfileMover::apply(), protocols::simple_moves::FavorSequenceProfile::apply(), protocols::simple_moves::symmetry::SetupNCSMover::apply(), protocols::hybridization::CartesianHybridize::apply(), protocols::hybridization::DomainAssembly::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::forge::methods::cyclize_pose(), protocols::relax::derive_sc_sc_restraints(), protocols::simple_moves::PeptideStapleMover::derive_staple_constraints_(), protocols::loops::fix_with_coord_cst(), protocols::hybridization::generate_centroid_constraints(), core::pack::dunbrack::load_unboundrot(), OPT_1GRP_KEY(), protocols::forge::remodel::RemodelAccumulator::recover_checkpoint(), protocols::ligand_docking::restrain_ligand_nbr_atom(), protocols::ligand_docking::LigandBaseProtocol::restrain_ligand_nbr_atom(), protocols::ligand_docking::MinimizeBackbone::restrain_protein_Calpha(), protocols::ligand_docking::LigandBaseProtocol::restrain_protein_Calphas(), protocols::dna::set_base_segment_chainbreak_constraints(), protocols::relax::RelaxProtocolBase::set_up_constraints(), protocols::rna::setup_base_pair_constraints(), protocols::simple_moves::ShakeStructureMover::setup_ca_constraints(), protocols::rna::setup_coarse_chainbreak_constraints(), protocols::canonical_sampling::CanonicalSamplingMover::setup_constraints(), protocols::star::setup_constraints(), protocols::ddg::ddGMover::setup_constraints(), protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver::setup_favor_native_constraints(), and protocols::idealize::IdealizeMover::setup_idealize_constraints().

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

Definition at line 1361 of file Pose.cc.

References conformation_, constraint_set_, and energies_.

Referenced by protocols::topology_broker::CoordConstraintClaimer::add_constraints(), protocols::topology_broker::ConstraintClaimer::add_constraints(), protocols::abinitio::AbrelaxApplication::add_constraints(), protocols::toolbox::match_enzdes_util::EnzConstraintIO::add_constraints_to_pose_for_block_without_clearing_and_header_processing(), protocols::protein_interface_design::movers::add_coordinate_constraints(), protocols::seeded_abinitio::add_coordinate_constraints(), protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_pose(), protocols::forge::remodel::RemodelConstraintGenerator::add_remodel_constraints_to_pose(), protocols::protein_interface_design::movers::TaskAwareCsts::apply(), protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMover::apply(), protocols::protein_interface_design::movers::PlacementAuctionMover::apply(), protocols::simple_moves::ConsensusDesignMover::apply(), protocols::flxbb::FlxbbDesign::apply(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::design(), protocols::protein_interface_design::movers::PlaceStubMover::final_cleanup(), protocols::simple_filters::ConstraintScoreCutoffFilter::get_score(), protocols::protein_interface_design::movers::PlacementMinimizationMover::refresh_bbstub_constraints(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::refresh_coordinate_constraints(), protocols::canonical_sampling::SilentTrajectoryRecorder::restart_simulation(), protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver::setup_favor_native_constraints(), and protocols::protein_interface_design::movers::PlaceStubMover::StubMinimize().

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

Definition at line 838 of file Pose.cc.

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

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.total_residue Residue

Definition at line 595 of file Pose.cc.

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

Referenced by protocols::topology_broker::CoordConstraintClaimer::add_constraints(), protocols::topology_broker::ConstraintClaimer::add_constraints(), protocols::rna::RNA_StructureParameters::append_virtual_anchor(), protocols::loop_build::LoopBuildMover::apply(), protocols::swa::monte_carlo::RNA_AddOrDeleteMover::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::topology_broker::TopologyBroker::check_chainbreak_variants(), protocols::swa::InputStreamWithResidueInfo::check_sequence(), protocols::swa::InputStreamWithResidueInfo::copy_next_pose_segment(), protocols::swa::protein::StepWiseProteinLoopBridger::figure_out_loop(), core::io::silent::BinaryProteinSilentStruct::fill_pose(), core::io::silent::BinaryRNASilentStruct::fill_struct(), core::io::silent::BinaryProteinSilentStruct::fill_struct(), core::io::silent::ProteinSilentStruct_Template< T >::fill_struct(), protocols::rna::RNA_DeNovoProtocol::initialize_movers(), protocols::topology_broker::SequenceClaimer::initialize_residues(), protocols::swa::StepWisePoseSetup::make_full_pose(), core::pose::make_pose_from_sequence(), protocols::features::PoseConformationFeatures::report_features_implementation(), protocols::topology_broker::SequenceClaimer::set_sequence(), core::scoring::rna::RNA_VDW_Energy::setup_atom_numbers_for_vdw_calculation(), protocols::swa::StepWisePoseSetup::setup_disulfides(), protocols::rna::RNA_StructureParameters::setup_fold_tree_and_jumps_and_variants(), core::scoring::rna::RNA_Mg_KnowledgeBasedPotential::setup_info_for_mg_calculation(), and protocols::topology_broker::TopologyBroker::switch_to_fullatom().

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

Definition at line 480 of file Pose.cc.

References conformation_, energies_, and total_residue().

Referenced by protocols::swa::monte_carlo::RNA_AddMover::apply(), and protocols::rna::RNA_HelixAssembler::build_on_base_pair().

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.

Definition at line 426 of file Pose.cc.

References conformation_, and energies_.

Referenced by protocols::ligand_docking::LigandDesign::apply(), protocols::ligand_docking::GrowLigand::apply(), protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::apply(), protocols::hybridization::HybridizeProtocol::apply(), core::pack::rotamer_set::build_lib_dna_rotamers(), core::io::pdb::build_pose_as_is1(), core::pack::rotamer_set::build_random_dna_rotamers(), core::coarse::TranslatorSet::coarsify(), protocols::hotspot_hashing::HotspotStubSet::create_hotspot_after_pose(), protocols::rna::create_rna_vall_torsions(), protocols::simple_moves::CutChainMover::create_subpose(), protocols::sic_dock::dump_loophash_linkers(), core::pose::symmetry::extract_asymmetric_unit(), core::pose::symmetry::get_asymmetric_pose_copy_from_symmetric_pose(), protocols::swa::StepWisePoseSetup::get_working_pose(), protocols::forge::methods::grow_right_r(), core::scoring::methods::IdealParametersDatabase::lookup_torsion_legacy(), core::pose::make_pose_from_saccharide_sequence(), core::pose::make_pose_from_sequence(), core::fragment::make_pose_from_sequence_(), protocols::swa::pdbslice(), core::io::serialization::read_binary(), protocols::rna::RNA_LoopCloser::rna_ccd_close(), and protocols::rbsegment_relax::setup_pose_from_rbsegs().

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.

Definition at line 412 of file Pose.cc.

References conformation_, and energies_.

Referenced by protocols::swa::rna::StepWiseRNA_PoseSetup::add_aa_virt_rsd_as_root(), protocols::relax::add_coordinate_constraints_to_pose(), protocols::loops::add_coordinate_constraints_to_pose(), protocols::simple_moves::AddCavitiesMover::add_suckers(), protocols::relax::add_virtual_residue_to_cterm(), core::pose::addVirtualResAsRoot(), protocols::topology_broker::MembraneTopologyClaimer::addVirtualResAsRootMembrane(), protocols::toolbox::pose_metric_calculators::append_rsd_by_jump_near_atom(), protocols::rna::RNA_StructureParameters::append_virtual_anchor(), protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover::apply(), protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::match::MatcherMover::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::idealize::IdealizeMover::apply(), core::pack::rotamer_set::bb_independent_rotamers(), core::pack::rotamer_set::build_lib_dna_rotamers(), core::io::pdb::build_pose_as_is1(), core::pack::rotamer_set::build_random_dna_rotamers(), protocols::relax::coordinate_constrain_selection(), protocols::protein_interface_design::movers::copy_hotspot_to_pose(), protocols::hotspot_hashing::HotspotStubSet::create_hotspot_after_pose(), core::pose::create_subpose(), protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::diversify_backbone_only_rotamers(), protocols::sic_dock::dump_loophash_linkers(), protocols::motifs::MotifHit::dump_motif_hit(), core::pose::symmetry::extract_asymmetric_unit(), for(), core::pose::symmetry::get_asymmetric_pose_copy_from_symmetric_pose(), protocols::hotspot_hashing::HotspotStubSet::get_residue_score_(), protocols::swa::StepWisePoseSetup::get_working_pose(), protocols::motifs::MotifSearch::incorporate_motifs(), protocols::motifs::LigandMotifSearch::incorporate_motifs(), protocols::match::downstream::LigandConformerBuilder::initialize_conformers(), protocols::match::output::PoseMatchOutputWriter::insert_match_into_pose(), core::pose::make_pose_from_saccharide_sequence(), core::pose::make_pose_from_sequence(), core::fragment::make_pose_from_sequence_(), protocols::forge::build::BuildManager::modify(), protocols::forge::build::ConnectRight::modify_impl(), protocols::swa::pdbslice(), protocols::hotspot_hashing::StubGenerator::placeResidueOnPose(), core::io::serialization::read_binary(), protocols::hotspot_hashing::HotspotStubSet::rescore(), protocols::rbsegment_relax::restore_pose_from_rbsegs(), protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::semiexpl_water_hbgeom_score(), protocols::rbsegment_relax::setup_pose_from_rbsegs(), and protocols::comparative_modeling::steal_ligands().

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.

Definition at line 1259 of file Pose.cc.

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

Referenced by protocols::simple_moves::symmetry::DetectSymmetry::apply(), protocols::pockets::PlaidFingerprint::apply_rotation_offset_to_pose_(), protocols::pockets::PlaidFingerprint::dump_oriented_pose_and_fp_to_pdb(), protocols::pockets::PlaidFingerprint::get_oriented_pose(), protocols::pockets::PocketGrid::move_pose_to_standard_orie(), and protocols::pockets::PlaidFingerprint::PlaidFingerprint().

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

Returns the pose AtomTree.

get the atom_tree

Definition at line 224 of file Pose.cc.

References conformation_.

Referenced by protocols::simple_moves::TorsionDOFMover::apply(), core::optimization::symmetry::atom_tree_dfunc(), core::optimization::atom_tree_dfunc(), protocols::backrub::BackrubSegment::bond_angle_atoms(), protocols::rna::RNA_StructureParameters::check_forward_backward(), protocols::simple_moves::ConstrainToIdealMover::check_if_really_connected(), protocols::toolbox::match_enzdes_util::constrain_pose_res_to_invrots(), core::pose::copy_dofs(), protocols::backrub::BackrubMover::dof_id_ranges(), core::import_pose::atom_tree_diffs::dump_atom_tree_diff(), core::io::pdb::dump_connect_info(), protocols::viewer::dump_pose_kinemage(), protocols::backrub::BackrubSegment::end_atoms1(), protocols::swa::rna::RNA_AnalyticLoopCloser::figure_out_dof_ids_and_offsets(), protocols::coarse_rna::CoarseRNA_LoopCloser::figure_out_dof_ids_and_offsets(), protocols::coarse_rna::CoarseRNA_LoopCloser::figure_out_forward_backward_res_by_backtracking(), core::scoring::rna::fix_sugar_coords(), core::scoring::rna::fix_sugar_coords_WORKS_BUT_SLOW(), core::scoring::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::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::MinimizeBackbone::restrain_protein_Calphas(), protocols::ligand_docking::LigandBaseProtocol::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::TabooSamplingKinematicPerturber::set_pose_after_closure(), protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturber::set_pose_after_closure(), core::optimization::CartesianMinimizerMap::setup(), core::optimization::MinimizerMap::setup(), protocols::backrub::BackrubSegment::start_atoms1(), protocols::backrub::BackrubSegment::start_atoms2(), core::optimization::symmetry::SymMinimizerMap::SymMinimizerMap(), and protocols::simple_moves::ConstrainToIdealMover::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	pointer to observer object

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

Definition at line 1425 of file Pose.hh.

References conformation_obs_hub_.

Referenced by 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	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

Definition at line 1347 of file Pose.hh.

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	pointer to observer object

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

Definition at line 1401 of file Pose.hh.

References energy_obs_hub_.

Referenced by 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	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.

Definition at line 1375 of file Pose.hh.

References general_obs_hub_.

Referenced by protocols::moves::AddPyMolObserver(), and protocols::moves::PyMolObserver::attach().

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

Definition at line 1143 of file Pose.cc.

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

Definition at line 1135 of file Pose.cc.

References conformation_.

Referenced by protocols::loophash::LoopHashMoverWrapper::apply(), protocols::rbsegment_relax::SequenceShiftMover::apply(), protocols::hybridization::apply_transformation(), protocols::rbsegment_relax::RBSegmentMover::applyRotation(), 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::BinaryProteinSilentStruct::fill_pose(), protocols::hybridization::InsertChunkMover::set_bb_xyz_aligned(), protocols::features::ProteinResidueConformationFeatures::set_coords_for_residues(), and protocols::hybridization::FoldTreeHybridize::translate_virt_to_CoM().

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

Definition at line 857 of file Pose.cc.

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

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

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

Definition at line 1157 of file Pose.cc.

References core::io::serialization::at(), core::conformation::Residue::natoms(), residue(), set_xyz(), total_residue(), and xyz().

Referenced by protocols::comparative_modeling::LoopRelaxMover::apply().

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

Returns the chain number of residue <seqpos>

example(s): pose.chain(3) See also: Pose Pose.annotated_sequence Pose.chain_sequence Pose.fold_tree Pose.sequence FoldTree

Definition at line 230 of file Pose.cc.

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

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

Returns the sequence for the chain <chain_in>

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

Definition at line 614 of file Pose.cc.

References core::conformation::Residue::carbohydrate_info(), conformation_, core::sequence::end, core::conformation::Residue::name1(), and residue().

Referenced by protocols::simple_moves::symmetry::DetectSymmetry::apply(), protocols::flexpep_docking::FlexPepDockingProtocol::hires_fpdock_protocol(), and core::pose::make_pose_from_saccharide_sequence().

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

Definition at line 955 of file Pose.cc.

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

Referenced by protocols::comparative_modeling::Align_RotamerEvaluator::apply(), protocols::backrub::BackrubSidechainMover::apply(), protocols::comparative_modeling::chis_from_pose(), protocols::toolbox::pose_metric_calculators::RotamerRecovery::chis_from_pose(), protocols::swa::StepWisePoseSetup::copy_rna_chi(), protocols::simple_moves::sidechain_moves::SidechainMoverBase::idealize_sidechains(), protocols::simple_moves::sidechain_moves::SidechainMover::idealize_sidechains(), protocols::swa::protein::StepWiseProteinPacker::reinstate_side_chain_angles(), protocols::swa::protein::StepWiseProteinResidueSampler::reinstate_side_chain_angles(), protocols::swa::protein::reinstate_side_chain_angles(), and protocols::rotamer_recovery::PerNativeRRReporterHuman::set_native().

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

Definition at line 986 of file Pose.cc.

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

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

Empty the pose contents.

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

Definition at line 1273 of file Pose.cc.

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

Referenced by protocols::simple_moves::SwitchChainOrderMover::apply(), protocols::simple_moves::ExtendedPoseMover::apply(), protocols::topology_broker::TopologyBroker::apply(), core::io::pdb::build_pose_as_is1(), protocols::LoopRebuild::build_random_loops(), protocols::design_opt::GreedyOptMutationMover::clear_cached_data(), core::coarse::TranslatorSet::coarsify(), protocols::simple_moves::CutChainMover::create_subpose(), core::pose::create_subpose(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::final_cleanup(), core::fragment::Frame::fragment_as_pose(), protocols::topology_broker::JumpClaimer::init_jumps(), core::fragment::make_pose_from_frags(), core::pose::make_pose_from_saccharide_sequence(), core::pose::make_pose_from_sequence(), core::fragment::make_pose_from_sequence_(), protocols::forge::build::SegmentRebuild::modify_impl(), protocols::topology_broker::JumpClaimer::new_decoy(), protocols::swa::pdbslice(), core::import_pose::atom_tree_diffs::pose_from_atom_tree_diff(), protocols::checkpoint::pose_from_binary_silent_file(), protocols::jd2::LazySilentFileJobInputter::pose_from_job(), protocols::jd2::PoseInputStreamJobInputter::pose_from_job(), protocols::jd2::JD2ResourceManagerJobInputter::pose_from_job(), protocols::jd2::AtomTreeDiffJobInputter::pose_from_job(), protocols::jd2::SilentFileJobInputter::pose_from_job(), protocols::features::DatabaseJobInputter::pose_from_job(), core::io::serialization::read_binary(), protocols::rbsegment_relax::setup_pose_from_rbsegs(), protocols::comparative_modeling::AlignmentCluster::~AlignmentCluster(), and ~Pose().

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

inline

Returns the pose Conformation (const-access)

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

Definition at line 252 of file Pose.hh.

References conformation_.

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

inline

Returns the pose Conformation (non-const access)

Definition at line 259 of file Pose.hh.

References conformation_.

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

Definition at line 1339 of file Pose.cc.

References constraint_set_.

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

Definition at line 1405 of file Pose.cc.

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.

Definition at line 514 of file Pose.cc.

References conformation(), and conformation_.

Referenced by protocols::loops::loop_closure::ccd::ShortLoopClosure::apply(), protocols::surface_docking::SurfaceDockingProtocol::apply(), protocols::hybridization::DomainAssembly::apply(), protocols::protein_interface_design::Revert::apply(), protocols::simple_moves::AddCavitiesMover::clear_suckers(), protocols::protein_interface_design::movers::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::ub_e2c::ubi_e2c_modeler::restore_cter(), protocols::rbsegment_relax::restore_pose_from_rbsegs(), and protocols::docking::ConformerSwitchMover::switch_conformer().

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

inline

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

Definition at line 526 of file Pose.hh.

References data_cache_.

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

inline

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

Definition at line 533 of file Pose.hh.

References data_cache_.

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

Definition at line 505 of file Pose.cc.

References conformation_, energies_, and total_residue().

Referenced by protocols::protein_interface_design::movers::LoopLengthChange::apply(), protocols::swa::monte_carlo::RNA_DeleteMover::apply(), protocols::swa::rna::Correctly_position_cutpoint_phosphate_torsions(), protocols::rna::RNA_HelixAssembler::get_rid_of_capping_base_pairs(), protocols::protein_interface_design::movers::PlaceOnLoop::loop_length(), and protocols::ub_e2c::ubi_e2c_modeler::trim_cter().

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

Definition at line 895 of file Pose.cc.

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

Referenced by protocols::swa::monte_carlo::RNA_TorsionMover::apply_random_suite_torsion().

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	pointer to observer object

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

Definition at line 1437 of file Pose.hh.

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	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

Definition at line 1361 of file Pose.hh.

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	pointer to observer object

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

Definition at line 1413 of file Pose.hh.

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	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.

Definition at line 1389 of file Pose.hh.

References general_obs_hub_.

Referenced by protocols::moves::PyMolObserver::detach().

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

Definition at line 1089 of file Pose.cc.

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(), core::id::THETA, total_residue(), and core::id::DOF_ID::type().

Referenced by core::pose::symmetry::make_symmetric_movemap().

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

Definition at line 87 of file Pose.cc.

References conformation_, data_cache_, energies_, metrics_, core::pose::datacache::CacheableObserverType::num_cacheable_data_types, core::pose::datacache::CacheableDataType::num_cacheable_data_types, observer_cache_, and on_conf_xyz_change().

Referenced by Pose().

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

Definition at line 442 of file Pose.cc.

References conformation_, energies_, and total_residue().

Referenced by protocols::grafting::insert_pose_into_pose(), and protocols::forge::build::SegmentSwap::modify_impl().

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

Returns true if pose is ResidueType centroid.

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

example(s): pose.is_centroid() See also: Pose Pose.is_fullatom Residue ResidueType this is nt a good test –Doug

Definition at line 1481 of file Pose.cc.

References conformation_.

Referenced by protocols::relax::CentroidRelax::apply(), protocols::simple_filters::ResidueSetChainEnergyFilter::compute(), 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 ( based on two middle residue – to avoid hitting on ligands or pseudos )

example(s): pose.is_fullatom() See also: Pose Pose.is_centroid Residue ResidueType this is nt a good test –Doug

Definition at line 1477 of file Pose.cc.

References conformation_.

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

Returns the pose FoldTree Jump <jump_number>

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

Definition at line 1047 of file Pose.cc.

References conformation_.

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

Returns the pose FoldTree Jump <id>

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

Definition at line 1064 of file Pose.cc.

References conformation_.

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

APL Illegal. conformation::ResidueOPs::iterator Pose::res_begin() { return conformation_->res_begin(); } conformation::ResidueOPs::iterator Pose::res_end () { return conformation_->res_end (); }

Definition at line 404 of file Pose.cc.

References metrics_.

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

Returns the number of residues in the pose conformation example(s): pose.n_residue() See also: Pose Pose.sequence Pose.total_residue.

Definition at line 534 of file Pose.cc.

References conformation_.

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

Definition at line 1517 of file Pose.cc.

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

Definition at line 1488 of file Pose.cc.

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

Definition at line 1506 of file Pose.cc.

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

Definition at line 1497 of file Pose.cc.

References general_obs_hub_.

Referenced by notify_conformation_obs(), and notify_energy_obs().

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

Returns the number of jumps in the pose FoldTree.

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

Definition at line 546 of file Pose.cc.

References conformation_.

Referenced by protocols::abinitio::MembraneAbinitio::add_spanning_region(), protocols::ligand_docking::append_ligand_RMSD(), protocols::simple_moves::symmetry::DetectSymmetry::apply(), protocols::simple_moves::HelicalPeptideLengthMover::apply(), protocols::dna::SeparateDnaFromNonDna::apply(), protocols::enzdes::EnzdesFixBBProtocol::apply(), protocols::surface_docking::SurfaceOrientMover::apply(), protocols::surface_docking::SurfaceDockingProtocol::apply(), protocols::simple_filters::JumpNrEvaluator::apply(), protocols::ligand_docking::Transform::apply(), protocols::surface_docking::FullatomRelaxMover::apply(), protocols::hybridization::ChunkTrialMover::apply(), protocols::enzdes::DetectProteinLigandInterface::apply(), protocols::enzdes::PredesignPerturbMover::apply(), protocols::loops::apply_sequence_mapping(), protocols::idealize::basic_idealize(), core::scoring::sc::ShapeComplementarityCalculator::Calc(), core::scoring::sc::MolecularSurfaceCalculator::Calc(), protocols::rna::RNA_ChunkLibrary::check_connections(), protocols::rna::ChunkSet::check_fold_tree_OK(), protocols::rna::RNA_ChunkLibrary::check_jump_match(), protocols::simple_filters::BuriedUnsatHbondFilter::compute(), protocols::simple_filters::TerminusDistanceFilter::compute(), protocols::simple_filters::ResiduesInInterfaceFilter::compute(), protocols::protein_interface_design::filters::AtomicContactCountFilter::compute(), protocols::optimize_weights::IterativeOptEDriver::compute_rotamers_around_ligands(), protocols::docking::DockTaskFactory::create_and_attach_task_factory(), protocols::enzdes::EnzdesBaseProtocol::create_enzdes_movemap(), protocols::hotspot_hashing::HotspotStubSet::create_hotspot_after_pose(), core::import_pose::atom_tree_diffs::dump_atom_tree_diff(), protocols::hotspot_hashing::HotspotStubSet::fill(), protocols::docking::TemperedDocking::finalize_setup(), protocols::surface_docking::FullatomRelaxMover::FinalizeMovers(), protocols::enzdes::SecondaryMatchProtocol::find_all_allowed_positions(), protocols::rigid::gaussian_jump_move(), protocols::protein_interface_design::movers::MapHotspot::GenerateMap(), core::pose::get_jump_id_from_chain_id(), protocols::ligand_docking::LigandBaseProtocol::get_ligand_jump_id(), protocols::topology_broker::TopologyBroker::initialize_cuts(), protocols::topology_broker::TopologyBroker::initialize_dofs(), protocols::rna::RNA_StructureParameters::insert_base_pair_jumps(), core::pose::jumps_from_pose(), protocols::rna::make_coarse_pose(), protocols::protein_interface_design::make_hotspot_foldtree(), protocols::fibril::make_symmetric_fibril(), core::pose::symmetry::make_symmetric_movemap(), core::pose::symmetry::make_symmetric_pose(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::minimize_all(), protocols::protein_interface_design::movers::MapHotspot::MinimizeHotspots(), MinimizeInterface(), protocols::forge::build::SegmentRebuild::modify_impl(), core::scoring::DockingScoreFunction::operator()(), protocols::protein_interface_design::movers::MapHotspot::output_pose(), protocols::protein_interface_design::movers::MapHotspot::parse_my_tag(), protocols::simple_filters::ResidueIEFilter::parse_my_tag(), protocols::protein_interface_design::movers::LoopFinder::parse_my_tag(), protocols::enzdes::LigInterfaceEnergyFilter::parse_my_tag(), protocols::enzdes::PredesignPerturbMover::parse_my_tag(), protocols::hybridization::ChunkTrialMover::pick_random_chunk(), protocols::hotspot_hashing::StubGenerator::placeResidueAtTransform(), protocols::hotspot_hashing::StubGenerator::placeResidueOnPose(), core::import_pose::atom_tree_diffs::pose_from_atom_tree_diff(), protocols::abinitio::AbrelaxApplication::process_decoy(), protocols::rna::RNA_StructureParameters::random_jump_change(), protocols::forge::remodel::RemodelLoopMover::repeat_generation(), protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue(), protocols::ligand_docking::Transform::revert_jumps(), protocols::rigid::RigidBodyPerturbMover::RigidBodyPerturbMover(), protocols::rigid::RigidBodyPerturbNoCenterMover::RigidBodyPerturbNoCenterMover(), protocols::optimize_weights::IterativeOptEDriver::score_ligand_interface(), protocols::relax::RelaxProtocolBase::set_up_constraints(), protocols::surface_docking::SurfaceDockingProtocol::SetSecondayStruct(), core::pose::setup_dof_mask_from_move_map(), core::pose::setup_dof_to_torsion_map(), protocols::hotspot_hashing::HotspotStubSet::setup_hotspot_foldtree_(), protocols::simple_moves::DesignRepackMover::setup_packer_and_movemap(), protocols::docking::DockingHighResLegacy::setup_packing(), protocols::surface_docking::SurfaceDockingProtocol::setupFoldTree(), protocols::forge::remodel::RemodelLoopMover::simultaneous_stage(), protocols::protein_interface_design::movers::PlaceStubMover::StubMinimize(), core::pose::transfer_jumps(), protocols::ligand_docking::Transform::transform_ligand(), and core::io::serialization::write_binary().

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

inline

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

Definition at line 541 of file Pose.hh.

References observer_cache_.

Referenced by protocols::enzdes::DetectProteinLigandInterface::add_observer_cache_segments_to_set(), protocols::seeded_abinitio::adjust_mm_to_length(), core::pack::task::operation::ReadResfileAndObeyLengthEvents::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::forge::components::VarLengthBuild::centroid_build(), protocols::enzdes::EnzdesFlexBBProtocol::determine_flexible_regions(), protocols::enzdes::EnzdesScorefileFilter::examine_pose(), protocols::toolbox::match_enzdes_util::get_enzdes_observer(), protocols::enzdes::EnzdesJobInputter::pose_from_job(), 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.

Definition at line 549 of file Pose.hh.

References observer_cache_.

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

Returns the omega torsion angle of residue <seqpos>

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 carbohydrates glycosylated at an exocyclic position, omega of residue n is defined as OX(n-1)-CX(n-1)-CX-1(n-1)-OX-1(n-1), where X is the position of the glycosidic linkage. (Note that every atom defining this torsion comes from the previous residue!)

Definition at line 777 of file Pose.cc.

References core::chemical::ResidueType::carbohydrate_info(), core::conformation::Residue::mainchain_torsion(), core::id::omega_torsion(), residue(), residue_type(), torsion(), and total_residue().

Referenced by protocols::loophash::BackboneDB::add_pose(), protocols::protein_interface_design::filters::Torsion::apply(), protocols::analysis::LoopAnalyzerMover::apply(), protocols::antibody2::ModelCDRH3::apply(), protocols::protein_interface_design::movers::Splice::apply(), protocols::fldsgn::filters::SecondaryStructureFilter::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::forge::components::VarLengthBuild::apply(), protocols::forge::remodel::RemodelLoopMover::boost_closure_stage(), protocols::antibody::CDRH3Modeler::build_centroid_loop(), protocols::protein_interface_design::filters::Torsion::compute(), protocols::hotspot_hashing::HotspotStubSet::create_hotspot_after_pose(), protocols::features::BetaTurnDetectionFeatures::determine_ramachandran_hash(), protocols::enzdes::EnzdesFlexibleRegion::examine_new_loopconf(), protocols::anchored_design::AnchoredDesignMover::filter(), protocols::abinitio::AbrelaxApplication::fold(), protocols::canonical_sampling::CanonicalSamplingMover::get_ABGEO_string(), core::util::ABEGOManager::get_symbols(), protocols::forge::remodel::RemodelLoopMover::independent_stage(), protocols::forge::remodel::RemodelLoopMover::loophash_stage(), protocols::forge::build::SegmentRebuild::modify_impl(), protocols::forge::build::SegmentInsert::modify_impl(), OPT_1GRP_KEY(), protocols::loophash::BackboneSegment::read_from_pose(), protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue(), protocols::forge::remodel::RemodelLoopMover::repeat_propagation(), protocols::forge::remodel::RemodelLoopMover::repeat_sync(), protocols::abinitio::run_boinc_debug(), protocols::forge::remodel::RemodelLoopMover::simultaneous_stage(), protocols::loops::loop_mover::LoopMover::torsion_features_string(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::torsion_features_string(), core::pose::transfer_phi_psi(), and core::io::pdb::write_additional_pdb_data().

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

private

upon receiving a conformation::signals::XYZEvent

Definition at line 1526 of file Pose.cc.

References notify_conformation_obs().

Referenced by 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

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

Definition at line 158 of file Pose.cc.

References conformation_, constraint_set_, data_cache_, energies_, metrics_, core::pose::datacache::CacheableObserverType::num_cacheable_data_types, core::pose::datacache::CacheableDataType::num_cacheable_data_types, observer_cache_, on_conf_xyz_change(), pdb_info(), and pdb_info_.

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

Definition at line 1437 of file Pose.cc.

References pdb_info_, and total_residue().

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

Definition at line 1446 of file Pose.cc.

References pdb_info_, and total_residue().

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

Definition at line 1457 of file Pose.cc.

References conformation_, pdb_info_, and total_residue().

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

Returns the phi torsion angle of residue <seqpos>

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, phi is defined as C(n-1)-N(n)-CA(n)-C(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...

Definition at line 676 of file Pose.cc.

References core::pose::carbohydrates::calculate_carbohydrate_phi(), core::conformation::Residue::mainchain_torsion(), core::id::phi_torsion(), residue(), residue_type(), and total_residue().

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

Definition at line 493 of file Pose.cc.

References conformation_, energies_, and total_residue().

Referenced by protocols::swa::monte_carlo::RNA_AddMover::apply(), protocols::rna::RNA_HelixAssembler::build_on_base_pair(), and protocols::swa::rna::Correctly_position_cutpoint_phosphate_torsions().

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

Definition at line 408 of file Pose.cc.

References metrics_.

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

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

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 aldoses, psi is defined as C1(n)-OX(n-1)-CX(n-1)-CX-1(n-1), where X is the position of the glycosidic linkage. For 2-ketoses (uloses), replace C1 with C2, etc.

Definition at line 724 of file Pose.cc.

References core::chemical::ResidueType::carbohydrate_info(), core::conformation::Residue::mainchain_torsion(), core::id::psi_torsion(), residue(), residue_type(), torsion(), and total_residue().

Referenced by protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_pose(), protocols::loophash::BackboneDB::add_pose(), protocols::simple_moves::oop::OopMover::apply(), protocols::protein_interface_design::filters::Torsion::apply(), protocols::simple_moves::oop::OopRandomSmallMover::apply(), protocols::abinitio::ResolutionSwitcher::apply(), protocols::simple_moves::chiral::ChiralMover::apply(), protocols::analysis::LoopAnalyzerMover::apply(), protocols::antibody2::ModelCDRH3::apply(), protocols::protein_interface_design::movers::Splice::apply(), protocols::simple_moves::sidechain_moves::SidechainMover::apply(), protocols::fldsgn::filters::SecondaryStructureFilter::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::forge::components::VarLengthBuild::apply(), protocols::forge::remodel::RemodelLoopMover::boost_closure_stage(), protocols::antibody::CDRH3Modeler::build_centroid_loop(), core::pack::rotamer_set::ContinuousRotamerSet::build_rotamers(), protocols::flexpep_docking::FlexPepDockingPoseMetrics::calc_phipsi_RMSD(), protocols::protein_interface_design::filters::Torsion::compute(), protocols::hotspot_hashing::HotspotStubSet::create_hotspot_after_pose(), protocols::features::BetaTurnDetectionFeatures::determine_ramachandran_hash(), protocols::enzdes::EnzdesFlexibleRegion::examine_new_loopconf(), protocols::swa::StepWiseScreener::filter_native_BIG_BINS(), protocols::swa::protein::StepWiseProteinScreener::filter_native_BIG_BINS(), protocols::swa::protein::fix_end_phi_psi(), protocols::swa::StepWisePoseSetup::fix_phi_psi_offsets(), protocols::abinitio::AbrelaxApplication::fold(), protocols::canonical_sampling::CanonicalSamplingMover::get_ABGEO_string(), protocols::simple_moves::BBG8T3AMover::get_L_move(), protocols::swa::StepWiseScreener::get_main_chain_torsion_set_list_sample_phi_only(), protocols::swa::protein::StepWiseProteinScreener::get_main_chain_torsion_set_list_sample_phi_only(), protocols::optimize_weights::IterativeOptEDriver::get_nat_rot_opte_data(), core::util::ABEGOManager::get_symbols(), protocols::forge::remodel::RemodelLoopMover::independent_stage(), protocols::topology_broker::StartStructClaimer::initialize_dofs(), protocols::swa::protein::StepWiseProteinLoopBridger::KIC_loop_close_with_perturbations(), protocols::forge::remodel::RemodelLoopMover::loophash_stage(), protocols::simple_moves::SmallMover::make_move(), protocols::simple_moves::ShearMover::make_move(), protocols::forge::build::SegmentRebuild::modify_impl(), protocols::forge::build::SegmentInsert::modify_impl(), protocols::hybridization::AllResiduesChanged::operator()(), protocols::abinitio::AllResiduesChanged::operator()(), OPT_1GRP_KEY(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::perform_rama_check(), protocols::loops::loop_closure::kinematic_closure::VicinitySamplingKinematicPerturber::perturb_chain(), protocols::simple_moves::BBGaussianMover::pivot_range_randomly(), protocols::flexpep_docking::FlexPepDockingProtocol::random_peptide_phi_psi_perturbation(), protocols::loophash::BackboneSegment::read_from_pose(), protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue(), protocols::forge::remodel::RemodelLoopMover::repeat_propagation(), protocols::forge::remodel::RemodelLoopMover::repeat_sync(), protocols::abinitio::run_boinc_debug(), protocols::hybridization::AllResiduesChanged::set_initial_pose(), protocols::abinitio::AllResiduesChanged::set_initial_pose(), core::pose::set_ss_from_phipsi(), protocols::hybridization::AllResiduesChanged::show_unmoved(), protocols::abinitio::AllResiduesChanged::show_unmoved(), protocols::forge::remodel::RemodelLoopMover::simultaneous_stage(), protocols::loops::loop_mover::LoopMover::torsion_features_string(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::torsion_features_string(), core::pose::transfer_phi_psi(), and core::io::pdb::write_additional_pdb_data().

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

re object_comparison see comment for ConstraintSet::remove_constraint function

Definition at line 1377 of file Pose.cc.

References constraint_set_, and energies_.

Referenced by protocols::protein_interface_design::movers::Splice::add_sequence_constraints(), protocols::ligand_docking::LigandDockProtocol::apply(), and protocols::ligand_docking::TetherLigand::release().

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

re object_comparison see comment for ConstraintSet::remove_constraint function

Definition at line 1387 of file Pose.cc.

References constraint_set_, and energies_.

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

Definition at line 1397 of file Pose.cc.

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>

Definition at line 457 of file Pose.cc.

References conformation_, and total_residue().

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.

Definition at line 469 of file Pose.cc.

References conformation_, and total_residue().

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.total_residue Residue ResidueType

Definition at line 647 of file Pose.cc.

References conformation_, and total_residue().

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.sequence Pose.total_residue Residue ResidueType

Definition at line 656 of file Pose.cc.

References conformation_, and total_residue().

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.

Definition at line 1211 of file Pose.cc.

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

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

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

Called by ScoreFunction at the end of scoring.

Definition at line 1228 of file Pose.cc.

References energies_, and notify_energy_obs().

Referenced by core::optimization::SingleResidueMultifunc::operator()(), core::scoring::symmetry::SymmetricScoreFunction::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 'S' = strand or sheet 'E' = loop.

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

Definition at line 559 of file Pose.cc.

References conformation_, and total_residue().

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

Definition at line 566 of file Pose.cc.

References total_residue().

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.total_residue

Definition at line 585 of file Pose.cc.

References conformation_, core::conformation::Residue::name1(), and residue().

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

Definition at line 847 of file Pose.cc.

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

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

Definition at line 866 of file Pose.cc.

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

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

Definition at line 969 of file Pose.cc.

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

Referenced by protocols::simple_moves::sidechain_moves::SetChiMover::apply(), protocols::simple_moves::sidechain_moves::SidechainMover::apply(), protocols::simple_moves::sidechain_moves::SidechainMoverBase::apply(), protocols::noesy_assign::FragsToAtomDist::compute_average_distances(), protocols::swa::StepWisePoseSetup::copy_rna_chi(), core::io::raw_data::DecoyStruct::fill_pose(), core::io::silent::ProteinSilentStruct_Template< T >::fill_pose(), protocols::simple_moves::sidechain_moves::SidechainMoverBase::idealize_sidechains(), protocols::simple_moves::sidechain_moves::SidechainMover::idealize_sidechains(), protocols::features::ResidueConformationFeatures::load_conformation(), protocols::features::ProteinResidueConformationFeatures::load_conformation(), protocols::swa::protein::StepWiseProteinPacker::reinstate_side_chain_angles(), protocols::swa::protein::StepWiseProteinResidueSampler::reinstate_side_chain_angles(), protocols::swa::protein::reinstate_side_chain_angles(), and protocols::ligand_docking::LigandDockProtocol::shear_min_protocol().

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

Definition at line 995 of file Pose.cc.

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

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

Definition at line 904 of file Pose.cc.

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

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)

See also: Pose TorsionID

Definition at line 1009 of file Pose.cc.

References conformation_.

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

Returns the number of residues in the pose conformation.

example(s): pose.total_residue() See also: Pose Pose.n_residue Pose.sequence

Definition at line 528 of file Pose.cc.

References conformation_.

void core::pose::Pose::transfer_constraint_set ( const pose::Pose & pose)

Definition at line 1418 of file Pose.cc.

References conformation_, constraint_set_, and energies_.

void core::pose::Pose::update_actcoord ( Size resid)

Updates the action coordinates for pose residue <resid>

Definition at line 1244 of file Pose.cc.

References conformation_.

Referenced by core::scoring::methods::CustomAtomPairEnergy::update_residue_for_packing(), and core::scoring::methods::PairEnergy::update_residue_for_packing().

void core::pose::Pose::update_actcoords ( )

Called by PairEPotential to update the action coordinates for all residues.

called by PairEPotential

Definition at line 1238 of file Pose.cc.

References conformation_.

void core::pose::Pose::update_orbital_coords ( Size resid)

Definition at line 1250 of file Pose.cc.

References conformation_.

Referenced by core::scoring::orbitals::OrbitalsScore::finalize_after_derivatives(), core::scoring::orbitals::OrbitalsScore::finalize_total_energy(), core::scoring::orbitals::OrbitalsScore::setup_for_derivatives(), core::scoring::orbitals::OrbitalsScore::setup_for_minimizing(), and core::scoring::orbitals::OrbitalsScore::update_residue_for_packing().

void core::pose::Pose::update_pose_chains_from_pdb_chains ( )

Updates the pose chain IDs to match the pdb chain IDs.

This method updates the pose chain IDs to match the chain IDs found in pdb_info(). In some applications, it is more intuitive to change pdb chain ID letters than it is to change pose chain IDs. This method adds chain endings between pdb chains and redrives the pose chain IDs. Currently, disconnected segments with the same pdb chain ID character are treated as separate pose chains, e.g., it is possible for pose chains 1, 3, and 5 to all be chain X. In the future, I will add a flag to force a one-to-one correspondence between the two chain designations, e.g., if residues 6 through 10 are chain B and residues 1 through 5 AND residues 11 through 15 are chain A, then the pose will be reordered to place all res- idues with the same pdb chain ID into a single pose chain. (This is how it works when a pose is loaded from a pdb file.) I personally have needed use of both functionalities. I have chosen to create this as a separate method, rather than a part of a change_pdb_chain_ID_of_range(), to avoid multiple calls to Conformation.rederive_chain_ids(). Thus, this method should be called once after all modifications to pdb_info() have been made. ~ Labonte

See also: PDBInfo.chain() PDBInfo.set_resinfo() Pose.split_by_chain() Conformation.rederive_chain_IDs() Conformation.rederive_chain_endings()

Definition at line 378 of file Pose.cc.

References conformation_, and pdb_info_.

void core::pose::Pose::update_residue_neighbors ( )

Updates neighbor links in the pose Energies object.

transfers domain map information into the Energies object, and then resets the domain map information from the Conformation object

Definition at line 1186 of file Pose.cc.

References conformation_, energies_, residue(), and total_residue().

PointPosition const & core::pose::Pose::xyz ( AtomID const & id) const

Returns the location (xyz) of pose AtomID <id>

get the location of an atom

example(s): atom = AtomID(1,1) pose.xyz(atom) See also: Pose Pose.residue AtomID Residue Residue.xyz

Definition at line 1104 of file Pose.cc.

References conformation_.

PointPosition const & core::pose::Pose::xyz ( NamedAtomID const & id) const

Returns the location (xyz) of pose NamedAtomID <id>

get the location of an atom

Tutorial soon... See also: Pose Pose.residue NamedAtomID Residue Residue.xyz

Definition at line 1111 of file Pose.cc.

References conformation_.

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

Returns the zeta torsion angle of residue <seqpos>

Note: assumes the residue is an nucleic acid

example(s): pose.zeta(6) See also: Pose Pose.residue Pose.set_zeta Residue

Definition at line 933 of file Pose.cc.

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

Member Data Documentation

ConformationOP core::pose::Pose::conformation_

private

the kinematics object, wraps a fold_tree and an atom_tree

responsible for updating Residue coords in response to changes in the internal coordinates also keeps track of what has changed since last update neighbors call

Definition at line 1622 of file Pose.hh.

Referenced by aa(), add_constraint(), add_constraints(), annotated_sequence(), append_polymer_residue_after_seqpos(), append_residue_by_bond(), append_residue_by_jump(), atom_tree(), batch_get_xyz(), batch_set_xyz(), chain_sequence(), clear(), conformation(), constraint_set(), copy_segment(), delete_polymer_residue(), dof(), dump_scored_pdb(), empty(), fold_tree(), has_dof(), init(), insert_residue_by_jump(), is_centroid(), is_fullatom(), jump(), n_residue(), num_jump(), operator=(), pdb_info(), prepend_polymer_residue_before_seqpos(), replace_residue(), residue(), residue_type(), scoring_begin(), secstruct(), sequence(), set_alpha(), set_beta(), set_chi(), set_delta(), set_dof(), set_epsilon(), set_gamma(), set_jump(), set_jump_now(), set_new_conformation(), set_omega(), set_phi(), set_psi(), set_secstruct(), set_torsion(), set_xyz(), set_zeta(), split_by_chain(), stub_from_id(), torsion(), total_residue(), 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)

Definition at line 1665 of file Pose.hh.

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

ConstraintSetOP core::pose::Pose::constraint_set_

private

Definition at line 1649 of file Pose.hh.

Referenced by add_constraint(), add_constraints(), clear(), constraint_set(), 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 convenience access

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

Definition at line 1638 of file Pose.hh.

Referenced by clear(), data(), init(), 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

Definition at line 1653 of file Pose.hh.

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

scoring::EnergiesOP core::pose::Pose::energies_

private

the cached energies object, stores total,rsd,and rsd-pair energies and neighbor info

stores information from the last energy evaluation handles cacheing rsd and rsd-pair energies

Definition at line 1629 of file Pose.hh.

Referenced by add_constraint(), add_constraints(), append_polymer_residue_after_seqpos(), append_residue_by_bond(), append_residue_by_jump(), clear(), constraint_set(), delete_polymer_residue(), energies(), init(), insert_residue_by_jump(), operator=(), prepend_polymer_residue_before_seqpos(), remove_constraint(), remove_constraints(), scoring_begin(), scoring_end(), set_new_conformation(), set_new_energies_object(), transfer_constraint_set(), and update_residue_neighbors().

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

mutableprivate

EnergyEvent observers.

Definition at line 1661 of file Pose.hh.

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

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.

Definition at line 1658 of file Pose.hh.

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

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

mutableprivate

Definition at line 1632 of file Pose.hh.

Referenced by clear(), init(), 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.

Definition at line 1643 of file Pose.hh.

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

PDBInfoOP core::pose::Pose::pdb_info_

private

pdb info

Definition at line 1646 of file Pose.hh.

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

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::dump_scored_pdb	(	std::string const &	file_name,
		scoring::ScoreFunction const &	scorefxn,
		std::string const &	tag = `"1"`
	)

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

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

bool core::pose::Pose::dump_pdb	(	std::string const &	file_name,
		std::string const &	tag = `"1"`
	)		const

void core::pose::Pose::dump_pdb	(	std::ostream &	out,
		std::string const &	tag = `"1"`
	)		const

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_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_secstruct	(	Size const	seqpos,
		char 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