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
	~Pose ()
	destructor -- > kill data on the heap
	Pose (Pose const &src)
	copy constructor
	Pose (Pose const &src, Size residue_begin, Size residue_end)
	partial copy constructor
Pose &	operator= (Pose const &src)
	Construct pose from pdb file.
Conformation const &	conformation () const
	Returns the pose Conformation (const-access)
Conformation &	conformation ()
	Returns the pose Conformation (non-const access)
kinematics::FoldTree const &	fold_tree () const
	Returns the pose FoldTree.
void	fold_tree (kinematics::FoldTree const &fold_tree_in)
	Sets the pose FoldTree to <fold_tree_in>
void	set_new_conformation (ConformationOP new_conformation)
	Now that the conformation_ member data is an owning pointer, and we have derived classes of Conformation.
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.
kinematics::AtomTree const &	atom_tree () const
	Returns the pose AtomTree.
int	chain (Size const seqpos) const
	Returns the chain number of residue <seqpos>
utility::vector1< PoseOP >	split_by_chain () const
	Returns a vector of poses with one element per chain of the original pose.
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.
scoring::Energies const &	energies () const
	Returns the pose Energies (const-access)
scoring::Energies &	energies ()
	Returns the pose Energies (non-const access)
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
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
bool	remove_constraints (scoring::constraints::ConstraintCOPs csts, bool object_comparison=false)
	re object_comparison see comment for ConstraintSet::remove_constraint function
bool	remove_constraints ()
void	constraint_set (ConstraintSetOP)
void	transfer_constraint_set (const pose::Pose &pose)
PDBInfoCOP	pdb_info () const
	Returns the pose PDBInfo (const)
PDBInfoOP	pdb_info ()
	Returns the pose PDBInfo.
PDBInfoOP	pdb_info (PDBInfoOP new_info)
	Sets pose PDBInfo to <new_info>
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.
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)
	Appends <new_rsd> (a residue) to pose by a new bond.
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>
void	replace_residue (Size const seqpos, Residue const &new_rsd_in, bool const orient_backbone)
	Replaces the residue at <seqpos> with <new_rsd_in>
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.
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
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
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.
BasicDataCache const &	data () const
	BasicDataCache indexed by enum in core/pose/datacache/CacheableDataType.hh.
BasicDataCache &	data ()
	BasicDataCache indexed by enum in core/pose/datacache/CacheableDataType.hh.
ObserverCache const &	observer_cache () const
	ObserverCache indexed by enum in core/pose/datacache/CacheableObserverType.hh.
ObserverCache &	observer_cache ()
	ObserverCache indexed by enum in core/pose/datacache/CacheableObserverType.hh.
Size	total_residue () const
	Returns the number of residues in the pose conformation.
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.
bool	empty () const
	Returns true if there are no residues in the conformation.
Size	num_jump () const
	Returns the number of jumps in the pose FoldTree.
chemical::AA	aa (Size const seqpos) const
	Returns the chemical::AA of the residue at <seqpos>
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.
std::string	secstruct () const
	Returns a string representing pose secondary structure.
void	set_secstruct (Size const seqpos, char const setting)
	Assign the secondary structure of residue <seqpos> to <setting>
std::string	sequence () const
	Returns a string representing the 1-leter-coded sequence of the pose conformation.
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].
std::string	chain_sequence (core::Size const chain_in) const
	Returns the sequence for the chain <chain_in>
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.
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.
bool	is_fullatom () const
	Returns true if pose is ResidueType fullatom.
bool	is_centroid () const
	Returns true if pose is ResidueType centroid.
Real	phi (Size const seqpos) const
	Returns the phi torsion angle of residue <seqpos>
void	set_phi (Size const seqpos, Real const setting)
	Sets the phi torsion angle of residue <seqpos> to <setting>
Real	psi (Size const seqpos) const
	Returns the psi torsion angle of residue <seqpos> Note: assumes the residue is an amino acid.
void	set_psi (Size const seqpos, Real const setting)
	Sets the psi torsion angle of residue <seqpos> to <setting>
Real	omega (Size const seqpos) const
	Returns the omega torsion angle of residue <seqpos>
void	set_omega (Size const seqpos, Real const setting)
	Sets the omega torsion angle of residue <seqpos> to <setting>
Real	alpha (Size const pos) const
	Returns the alpha torsion angle of residue <seqpos>
void	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.
Real	beta (Size const seqpos) const
	Returns the beta torsion angle of residue <seqpos>
void	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.
Real	gamma (Size const seqpos) const
	Returns the gamma torsion angle of residue <seqpos>
void	set_gamma (Size const seqpos, Real const setting)
	Sets the gamma torsion angle of residue <seqpos> to <setting> Note: <setting> must be in degrees, assumes residue is an nucleic acid.
Real	delta (Size const pos) const
	Returns the delta torsion angle of residue <seqpos>
void	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.
Real	epsilon (Size const seqpos) const
	Returns the epsilon torsion angle of residue <seqpos>
void	set_epsilon (Size const seqpos, Real const setting)
	Sets the epsilon torsion angle of residue <seqpos> to <setting> Note: <setting> must be in degrees, assumes residue is an nucleic acid.
Real	zeta (Size const seqpos) const
	Returns the zeta torsion angle of residue <seqpos>
void	set_zeta (Size const seqpos, Real const setting)
	Sets the zeta torsion angle of residue <seqpos> to <setting> Note: <setting> must be in degrees, assumes residue is an nucleic acid.
Real	chi (Size const seqpos) const
	Returns the chi torsion angle of residue <seqpos>
void	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.
void	set_jump (int const jump_number, const kinematics::Jump &new_jump)
	Sets the pose FoldTree Jump <jump_number> to <new_jump>
void	set_jump_now (int const jump_number, const kinematics::Jump &new_jump)
	Sets the pose FoldTree Jump <jump_number> to <new_jump>
kinematics::Jump const &	jump (int const jump_number) const
	Returns the pose FoldTree Jump <jump_number>
void	set_jump (AtomID const &id, const kinematics::Jump &new_jump)
	Sets the pose FoldTree Jump <id> to <new_jump>
kinematics::Jump const &	jump (AtomID const &id) const
	Returns the pose FoldTree Jump <id>
Real	chi (int const chino, Size const seqpos) const
	Returns the <chino> chi torsion angle of residue <seqpos>
void	set_chi (int const chino, Size const seqpos, Real const setting)
	Sets the <chino> chi torsion angle of residue <seqpos> to <setting>
Real	torsion (TorsionID const &id) const
	Returns the Conformation torsion angle identified by <id>
void	set_torsion (TorsionID const &id, Real const setting)
	Sets the Conformation torsion angle identified by <id> to <setting>
Real	dof (DOF_ID const &id) const
	Returns the value of the AtomTree DOF <id>
void	set_dof (DOF_ID const &id, Real const setting)
	Sets the value of the AtomTree DOF <id>
bool	has_dof (DOF_ID const &id) const
	Returns true if pose has DOF <id>
PointPosition const &	xyz (AtomID const &id) const
	Returns the location (xyz) of pose AtomID <id>
PointPosition const &	xyz (NamedAtomID const &id) const
	Returns the location (xyz) of pose NamedAtomID <id>
void	set_xyz (AtomID const &id, PointPosition const &point)
	Sets the location (xyz) of pose AtomID <id> to the PointPosition <point>
void	set_xyz (NamedAtomID const &id, PointPosition const &point)
	Sets the location (xyz) of pose NamedAtomID <id> to the PointPosition <point>
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>
void	batch_get_xyz (utility::vector1< AtomID > const &ids, utility::vector1< PointPosition > &points) const
	Gets the locations (xyz) of pose AtomIDs in <ids>
kinematics::Stub	stub_from_id (id::NamedStubID const &id)
void	center ()
	Sets pose coordinates such that the pose center is at the Euclidean origin.
void	update_residue_neighbors ()
	Updates neighbor links in the pose Energies object.
void	scoring_begin (scoring::ScoreFunction const &info)
	Called by ScoreFunction at the beginning of scoring.
void	scoring_end (scoring::ScoreFunction const &scorefxn)
	Called by ScoreFunction at the end of scoring.
void	update_actcoords ()
	Called by PairEPotential to update the action coordinates for all residues.
void	update_actcoord (Size resid)
	Updates the action coordinates for pose residue <resid>
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.
void	clear ()
	Empty the pose contents.
bool	dump_pdb (std::string const &file_name, std::string const &tag="1") const
	Export pose data to the PDB file <file_name>
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
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.
template<typename MemFn , typename Ptr >
utility::signals::Link	attach_destruction_obs (MemFn fn, Ptr ptr)
	attach DestructionEvent observer function
template<typename MemFn , typename Ptr >
bool	detach_destruction_obs (MemFn fn, Ptr ptr) const
	detach DestructionEvent observer function
template<typename MemFn , typename Ptr >
utility::signals::Link	attach_general_obs (MemFn fn, Ptr ptr)
	attach GeneralEvent observer function
template<typename MemFn , typename Ptr >
bool	detach_general_obs (MemFn fn, Ptr ptr) const
	detach GeneralEvent observer function
template<typename MemFn , typename Ptr >
utility::signals::Link	attach_energy_obs (MemFn fn, Ptr ptr)
	attach EnergyEvent observer function
template<typename MemFn , typename Ptr >
bool	detach_energy_obs (MemFn fn, Ptr ptr) const
	detach EnergyEvent observer function
template<typename MemFn , typename Ptr >
utility::signals::Link	attach_conformation_obs (MemFn fn, Ptr ptr)
	attach ConformationEvent observer function
template<typename MemFn , typename Ptr >
bool	detach_conformation_obs (MemFn fn, Ptr ptr) const
	detach ConformationEvent observer function

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

Member Typedef Documentation

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Constructor & Destructor Documentation

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

default constructor, builds an empty pose

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

default constructor

Referenced by split_by_chain().

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

destructor -- > kill data on the heap

construc pose using info from PDB file

destructor -- > kill data on the heap

References clear().

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

copy constructor

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

partial copy constructor

References make_table_of_pilot_apps::begin, core::sequence::end, 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

References total_residue().

Referenced by protocols::toolbox::task_operations::JointSequenceOperation::apply(), protocols::flxbb::FilterStructs_TotalCharge::apply(), protocols::loops::loop_closure::ccd::ccd_moves(), protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter::compute(), protocols::fldsgn::filters::InterlockingAromaFilter::compute(), protocols::fldsgn::filters::CoreDunbrackFilter::compute(), protocols::loops::loop_closure::ccd::fast_ccd_loop_closure(), protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturber::perturb_chain(), protocols::fldsgn::potentials::AACompositionEnergy::residue_energy(), protocols::loops::set_secstruct_from_dssp(), and core::scoring::methods::MembraneEnvSmoothEnergy::setup_for_derivatives().

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

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::comparative_modeling::hybridize::FoldTreeHybridize::add_gap_constraints_to_pose(), protocols::toolbox::match_enzdes_util::EnzConstraintIO::add_pregenerated_constraints_to_pose(), protocols::simple_moves::AddCavitiesMover::add_suckers(), protocols::anchored_design::AnchorMoversData::anchor_noise_constraints_setup(), protocols::simple_moves::symmetry::SetupNCSMover::apply(), protocols::simple_moves::SequenceProfileMover::apply(), protocols::simple_moves::FavorSequenceProfile::apply(), protocols::simple_moves::AddConstraintsToCurrentConformationMover::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::comparative_modeling::hybridize::HybridizeProtocol::apply(), protocols::forge::methods::cyclize_pose(), protocols::relax::derive_sc_sc_restraints(), protocols::loops::fix_with_coord_cst(), 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::LigandBaseProtocol::restrain_protein_Calphas(), 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::star::setup_constraints(), and protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver::setup_favor_native_constraints().

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

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::seeded_abinitio::add_coordinate_constraints(), protocols::protein_interface_design::movers::add_coordinate_constraints(), protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_pose(), protocols::forge::remodel::RemodelConstraintGenerator::add_remodel_constraints_to_pose(), protocols::simple_moves::ConsensusDesignMover::apply(), protocols::protein_interface_design::movers::TaskAwareCsts::apply(), protocols::protein_interface_design::movers::PlacementAuctionMover::apply(), protocols::flxbb::FlxbbDesign::apply(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::design(), protocols::protein_interface_design::movers::PlacementMinimizationMover::refresh_bbstub_constraints(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::refresh_coordinate_constraints(), and protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver::setup_favor_native_constraints().

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

Returns the alpha torsion angle of residue <seqpos>

Note:: assumes the residue is an nucleic acid

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

References core::id::BB, residue_type(), 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

References core::chemical::aa_from_oneletter_code(), core::pack::dunbrack::c, core::conformation::Residue::name(), make_table_of_pilot_apps::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::comparative_modeling::LoopRelaxMover::apply(), protocols::topology_broker::TopologyBroker::check_chainbreak_variants(), protocols::swa::InputStreamWithResidueInfo::copy_next_pose_segment(), core::io::silent::BinaryProteinSilentStruct::fill_pose(), core::io::silent::ProteinSilentStruct_Template< T >::fill_struct(), core::io::silent::BinaryRNASilentStruct::fill_struct(), core::io::silent::BinaryProteinSilentStruct::fill_struct(), protocols::topology_broker::SequenceClaimer::initialize_residues(), core::pose::make_pose_from_sequence(), protocols::topology_broker::SequenceClaimer::set_sequence(), 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

References total_residue().

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`
	)

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.

Referenced by protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::apply(), protocols::ligand_docking::LigandDesign::apply(), protocols::ligand_docking::GrowLigand::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::rna::create_rna_vall_torsions(), core::pose::symmetry::extract_asymmetric_unit(), core::pose::symmetry::get_asymmetric_pose_copy_from_symmetric_pose(), protocols::forge::methods::grow_right_r(), core::scoring::methods::TorsionDatabase::lookup(), core::pose::make_pose_from_sequence(), core::fragment::make_pose_from_sequence_(), protocols::swa::pdbslice(), core::io::serialization::read_binary(), 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.

Referenced by 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::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::apply(), protocols::match::MatcherMover::apply(), protocols::idealize::IdealizeMover::apply(), protocols::comparative_modeling::LoopRelaxMover::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(), core::pose::create_subpose(), protocols::motifs::MotifHit::dump_motif_hit(), core::pose::symmetry::extract_asymmetric_unit(), for(), core::pose::symmetry::get_asymmetric_pose_copy_from_symmetric_pose(), protocols::motifs::MotifSearch::incorporate_motifs(), protocols::motifs::LigandMotifSearch::incorporate_motifs(), protocols::match::output::PoseMatchOutputWriter::insert_match_into_pose(), 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(), 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::relax::RelaxProtocolBase::set_up_constraints(), 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.

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

Referenced by protocols::pockets::PlaidFingerprint::dump_oriented_pose_and_fp_to_pdb(), protocols::pockets::PlaidFingerprint::get_oriented_pose(), and protocols::pockets::PlaidFingerprint::PlaidFingerprint().

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

Returns the pose AtomTree.

get the atom_tree

Referenced by protocols::simple_moves::TorsionDOFMover::apply(), core::optimization::symmetry::atom_tree_dfunc(), core::optimization::atom_tree_dfunc(), protocols::backrub::BackrubSegment::bond_angle_atoms(), 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(), core::scoring::rna::fix_sugar_coords(), core::scoring::rna::fix_sugar_coords_WORKS_BUT_SLOW(), protocols::forge::constraints::InverseRotamersRCG::generate_remodel_constraints(), core::scoring::rna::initialize_atoms_for_which_we_need_new_dofs(), protocols::simple_moves::DOFHistogramRecorder::insert_dofs_by_residue(), core::scoring::methods::TorsionDatabase::lookup(), 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::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(), core::optimization::MinimizerMap::setup(), core::optimization::CartesianMinimizerMap::setup(), protocols::backrub::BackrubSegment::start_atoms1(), protocols::backrub::BackrubSegment::start_atoms2(), and core::optimization::symmetry::SymMinimizerMap::SymMinimizerMap().

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.

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

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.

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.

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

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

Referenced by protocols::rbsegment_relax::SequenceShiftMover::apply(), protocols::loophash::LoopHashMoverWrapper::apply(), protocols::comparative_modeling::hybridize::InsertChunkMover::apply_transform(), protocols::rbsegment_relax::RBSegmentMover::applyRotation(), protocols::rbsegment_relax::RBSegmentMover::applyTransformation(), protocols::rbsegment_relax::RBSegmentMover::applyTranslation(), protocols::comparative_modeling::hybridize::InsertChunkMover::check_overlap(), core::optimization::CartesianMinimizerMap::copy_dofs_to_pose(), core::io::silent::BinaryProteinSilentStruct::fill_pose(), protocols::comparative_modeling::hybridize::InsertChunkMover::set_bb_xyz_aligned(), and protocols::comparative_modeling::hybridize::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

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.

References 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

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

Referenced by protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_pose(), protocols::loops::add_loop(), protocols::ligand_docking::append_multi_residue_ligand_RMSD(), protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::apply(), protocols::ligand_docking::LigandDesign::apply(), protocols::fldsgn::CircularPermutation::apply(), protocols::dna::RestrictDesignToProteinDNAInterface::apply(), protocols::ddg::ddGMover::apply(), protocols::loops::apply_sequence_mapping(), core::pose::metrics::simple_calculators::InterfaceDefinitionCalculator::chain_letter_to_number(), protocols::enzdes::LigDSasaFilter::compute(), core::pose::conf2pdb_chain(), protocols::dna::DnaInterfacePacker::dna_seq_tag(), protocols::enzdes::EnzdesFlexBBProtocol::generate_ensemble_for_region(), core::pose::get_chain_id_from_jump_id(), core::pose::get_jump_id_from_chain_id(), protocols::features::HBondFeatures::insert_site_row(), protocols::loops::Loop::is_terminal(), protocols::loops::loops_around_residues(), protocols::analysis::InterfaceAnalyzerMover::make_multichain_interface_set(), protocols::toolbox::pose_metric_calculators::ResidueDecompositionByChainCalculator::recompute(), core::pose::renumber_pdbinfo_based_on_conf_chains(), protocols::dna::DnaInterfacePacker::reversion_scan(), protocols::dna::seq_pdb_str(), core::scoring::constraints::SiteConstraint::setup_csts(), and protocols::docking::setup_foldtree().

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

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

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

Returns the chi torsion angle of residue <seqpos>

Note:: assumes the residue is an nucleic acid

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

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

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

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

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

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

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

Empty the pose contents.

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

References pdb_info().

Referenced by protocols::topology_broker::TopologyBroker::apply(), protocols::simple_moves::ExtendedPoseMover::apply(), core::io::pdb::build_pose_as_is1(), core::coarse::TranslatorSet::coarsify(), 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_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::SilentFileJobInputter::pose_from_job(), protocols::jd2::PoseInputStreamJobInputter::pose_from_job(), protocols::jd2::LazySilentFileJobInputter::pose_from_job(), protocols::jd2::AtomTreeDiffJobInputter::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

Conformation& core::pose::Pose::conformation ( ) [inline]

Returns the pose Conformation (non-const access)

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

References constraint_set().

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

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

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

References make_table_of_pilot_apps::begin, and conformation().

Referenced by protocols::surface_docking::SurfaceDockingProtocol::apply(), protocols::protein_interface_design::Revert::apply(), protocols::loops::loop_closure::ccd::ShortLoopClosure::apply(), protocols::simple_moves::AddCavitiesMover::clear_suckers(), 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.

BasicDataCache& core::pose::Pose::data ( ) [inline]

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

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

References total_residue().

Referenced by protocols::protein_interface_design::movers::LoopLengthChange::apply(), protocols::swa::rna::Correctly_position_cutpoint_phosphate_torsions(), 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

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

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

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

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

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.

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

References core::id::DOF_ID::atom_id(), core::id::DOF_ID::atomno(), 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(), and protocols::comparative_modeling::hybridize::InsertChunkMover::steal_torsion_and_bonds_from_template().

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

Adds <new_rsd_in> to pose at <seqpos>

This code sorely belongs in Pose.cc

References total_residue().

Referenced by protocols::toolbox::pose_manipulation::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

Referenced by 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

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

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

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 (); }

Referenced by protocols::simple_filters::PoseMetricEvaluator< T >::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::forge::components::BDR::apply(), protocols::flexpep_docking::FlexPepDockingPoseMetrics::calc_interface_metrics(), protocols::simple_filters::InterfaceSasaFilter::compute(), protocols::protein_interface_design::InterfaceSasaFilter::compute(), protocols::fldsgn::filters::FragQualFilter::compute(), protocols::enzdes::DiffAtomSasaFilter::compute(), protocols::enzdes::LigDSasaFilter::compute(), protocols::analysis::InterfaceAnalyzerMover::compute_interface_delta_hbond_unsat(), protocols::analysis::InterfaceAnalyzerMover::compute_interface_energy(), protocols::analysis::InterfaceAnalyzerMover::compute_separated_sasa(), protocols::abinitio::AbrelaxApplication::do_rerun(), protocols::multistate_design::MetricCalculatorFitnessFunction::evaluate(), protocols::anchored_design::AnchoredDesignMover::filter(), protocols::toolbox::pose_metric_calculators::MetricValueGetter::get(), protocols::analysis::InterfaceAnalyzerMover::make_interface_set(), protocols::analysis::InterfaceAnalyzerMover::make_multichain_interface_set(), protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::recompute(), protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator::recompute(), protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::recompute(), core::pose::metrics::simple_calculators::InterfaceDeltaEnergeticsCalculator::recompute(), protocols::forge::remodel::RemodelDesignMover::reduce_task(), protocols::toolbox::task_operations::RestrictOperationsBase::run_calculator(), and protocols::forge::remodel::run_calculator().

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.

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

ObserverCache const& core::pose::Pose::observer_cache ( ) const [inline]

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

Referenced by protocols::enzdes::DetectProteinLigandInterface::add_observer_cache_segments_to_set(), protocols::seeded_abinitio::adjust_mm_to_length(), protocols::forge::remodel::RemodelMover::apply(), core::pack::task::operation::ReadResfileAndObeyLengthEvents::apply(), protocols::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(), and protocols::loops::loop_mover::LoopMover::set_loops_from_pose_observer_cache().

ObserverCache& core::pose::Pose::observer_cache ( ) [inline]

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

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

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

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

Referenced by protocols::loophash::BackboneDB::add_pose(), protocols::protein_interface_design::filters::Torsion::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::fldsgn::filters::SecondaryStructureFilter::apply(), protocols::analysis::LoopAnalyzerMover::apply(), protocols::forge::remodel::RemodelLoopMover::boost_closure_stage(), protocols::protein_interface_design::filters::Torsion::compute(), 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::build::SegmentRebuild::modify_impl(), protocols::forge::build::SegmentInsert::modify_impl(), OPT_1GRP_KEY(), protocols::loophash::BackboneSegment::read_from_pose(), protocols::forge::remodel::RemodelLoopMover::repeat_propagation(), protocols::abinitio::run_boinc_debug(), protocols::forge::remodel::RemodelLoopMover::simultaneous_stage(), core::pose::transfer_phi_psi(), and core::io::pdb::write_additional_pdb_data().

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

References core::pose::datacache::CacheableObserverType::num_cacheable_data_types, core::pose::datacache::CacheableDataType::num_cacheable_data_types, 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

References 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

References 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

References 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

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

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

Referenced by protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_pose(), protocols::loophash::BackboneDB::add_pose(), protocols::simple_moves::sidechain_moves::SidechainMover::apply(), protocols::protein_interface_design::filters::Torsion::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::fldsgn::filters::SecondaryStructureFilter::apply(), protocols::analysis::LoopAnalyzerMover::apply(), protocols::abinitio::ResolutionSwitcher::apply(), protocols::forge::remodel::RemodelLoopMover::boost_closure_stage(), core::pack::rotamer_set::ContinuousRotamerSet::build_rotamers(), protocols::flexpep_docking::FlexPepDockingPoseMetrics::calc_phipsi_RMSD(), protocols::protein_interface_design::filters::Torsion::compute(), protocols::enzdes::EnzdesFlexibleRegion::examine_new_loopconf(), protocols::swa::protein::fix_end_phi_psi(), protocols::abinitio::AbrelaxApplication::fold(), protocols::canonical_sampling::CanonicalSamplingMover::get_ABGEO_string(), protocols::simple_moves::BBG8T3AMover::get_L_move(), core::util::ABEGOManager::get_symbols(), protocols::forge::remodel::RemodelLoopMover::independent_stage(), protocols::topology_broker::StartStructClaimer::initialize_dofs(), protocols::simple_moves::ShearMover::make_move(), protocols::simple_moves::SmallMover::make_move(), protocols::forge::build::SegmentRebuild::modify_impl(), protocols::forge::build::SegmentInsert::modify_impl(), protocols::abinitio::AllResiduesChanged::operator()(), OPT_1GRP_KEY(), protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturber::perturb_chain(), protocols::simple_moves::BBGaussianMover::pivot_range_randomly(), protocols::loophash::BackboneSegment::read_from_pose(), protocols::forge::remodel::RemodelLoopMover::repeat_propagation(), protocols::abinitio::run_boinc_debug(), core::pose::set_ss_from_phipsi(), protocols::abinitio::AllResiduesChanged::show_unmoved(), protocols::forge::remodel::RemodelLoopMover::simultaneous_stage(), protocols::comparative_modeling::hybridize::InsertChunkMover::steal_torsion_from_template(), core::pose::transfer_phi_psi(), and core::io::pdb::write_additional_pdb_data().

void core::pose::Pose::prepend_polymer_residue_before_seqpos	(	Residue const &	new_rsd,
		Size const	seqpos,
		bool const	build_ideal_geometry
	)

glues to seqpos and perhaps also seqpos-1

References total_residue().

Referenced by 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

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.

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

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

Referenced by protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_pose(), protocols::loophash::BackboneDB::add_pose(), protocols::simple_moves::sidechain_moves::SidechainMover::apply(), protocols::protein_interface_design::filters::Torsion::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::fldsgn::filters::SecondaryStructureFilter::apply(), protocols::analysis::LoopAnalyzerMover::apply(), protocols::abinitio::ResolutionSwitcher::apply(), protocols::forge::remodel::RemodelLoopMover::boost_closure_stage(), core::pack::rotamer_set::ContinuousRotamerSet::build_rotamers(), protocols::flexpep_docking::FlexPepDockingPoseMetrics::calc_phipsi_RMSD(), protocols::protein_interface_design::filters::Torsion::compute(), protocols::enzdes::EnzdesFlexibleRegion::examine_new_loopconf(), protocols::swa::protein::fix_end_phi_psi(), protocols::abinitio::AbrelaxApplication::fold(), protocols::canonical_sampling::CanonicalSamplingMover::get_ABGEO_string(), protocols::simple_moves::BBG8T3AMover::get_L_move(), core::util::ABEGOManager::get_symbols(), protocols::forge::remodel::RemodelLoopMover::independent_stage(), protocols::topology_broker::StartStructClaimer::initialize_dofs(), protocols::simple_moves::ShearMover::make_move(), protocols::simple_moves::SmallMover::make_move(), protocols::forge::build::SegmentRebuild::modify_impl(), protocols::forge::build::SegmentInsert::modify_impl(), protocols::abinitio::AllResiduesChanged::operator()(), OPT_1GRP_KEY(), protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturber::perturb_chain(), protocols::simple_moves::BBGaussianMover::pivot_range_randomly(), protocols::loophash::BackboneSegment::read_from_pose(), protocols::forge::remodel::RemodelLoopMover::repeat_propagation(), protocols::abinitio::run_boinc_debug(), core::pose::set_ss_from_phipsi(), protocols::abinitio::AllResiduesChanged::show_unmoved(), protocols::forge::remodel::RemodelLoopMover::simultaneous_stage(), protocols::comparative_modeling::hybridize::InsertChunkMover::steal_torsion_from_template(), 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

Referenced by 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

Referenced by protocols::ligand_docking::append_multi_residue_ligand_RMSD(), protocols::simple_moves::ConsensusDesignMover::apply(), protocols::simple_moves::ClearConstraintsMover::apply(), protocols::medal::MedalExchangeMover::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::flxbb::FlxbbDesign::apply(), protocols::ddg::ddGMover::apply(), protocols::comparative_modeling::hybridize::FoldTreeHybridize::apply(), protocols::canonical_sampling::CanonicalSamplingMover::apply(), protocols::anchored_design::AnchoredDesignMover::apply(), protocols::forge::components::VarLengthBuild::centroid_build(), OPT_1GRP_KEY(), protocols::hotspot_hashing::HotspotStubSet::remove_all_hotspot_constraints(), protocols::toolbox::match_enzdes_util::EnzConstraintIO::remove_constraints_from_pose_for_block(), protocols::protein_interface_design::remove_coordinate_constraints_from_pose(), protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver::remove_favor_native_constraints(), protocols::hotspot_hashing::remove_hotspot_constraints_from_pose(), protocols::forge::remodel::RemodelConstraintGenerator::remove_remodel_constraints_from_pose(), protocols::simple_moves::symmetry::SymShakeStructureMover::run_mc(), protocols::simple_moves::ShakeStructureMover::run_mc(), protocols::motifs::IRCollection::successful_loop_closure(), and protocols::star::tear_down_constraints().

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

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

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

References total_residue().

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

Replaces the residue at <seqpos> with <new_rsd_in>

References 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.

Residue at position seqpos.

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

References 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

References 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.

References total_residue(), and update_residue_neighbors().

Referenced by 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.

Referenced by 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

References 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

References total_residue().

Referenced by dump_scored_pdb().

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

Returns a string representing the 1-leter-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

References 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

References core::id::BB, 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

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

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

Sets the chi torsion angle of residue <seqpos> to <setting> Note: <setting> must be in degrees, assumes residue is an nucleic acid.

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

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

Referenced by protocols::simple_moves::sidechain_moves::SidechainMoverBase::apply(), protocols::simple_moves::sidechain_moves::SidechainMover::apply(), core::io::silent::ProteinSilentStruct_Template< T >::fill_pose(), core::io::raw_data::DecoyStruct::fill_pose(), protocols::simple_moves::sidechain_moves::SidechainMoverBase::idealize_sidechains(), protocols::simple_moves::sidechain_moves::SidechainMover::idealize_sidechains(), protocols::features::ResidueConformationFeatures::load_conformation(), and protocols::swa::protein::reinstate_side_chain_angles().

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

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

References core::id::CHI, residue(), 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

References core::id::BB, 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)

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
	)

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

bool core::pose::Pose::dump_pdb	(	std::string const &	file_name,
		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	(	NamedAtomID const &	id,
		PointPosition const &	point
	)

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

Public Types

Public Member Functions

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation