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core::pose::Pose Class Reference

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

#include <Pose.hh>

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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...
 
Poseoperator= (Pose const &src)
 Construct pose from pdb file. More...
 
Conformation const & conformation () const
 Returns the pose Conformation (const-access) More...
 
Conformationconformation ()
 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< PoseOPsplit_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::Energiesenergies ()
 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...
 
BasicDataCachedata ()
 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...
 
ObserverCacheobserver_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:

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

Constructor & Destructor Documentation

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

default constructor, builds an empty pose

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

default constructor

References init().

Referenced by split_by_chain().

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

destructor – > kill data on the heap

construc pose using info from PDB file

destructor – > kill data on the heap

References clear(), and notify_destruction_obs().

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

copy constructor

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

partial copy constructor

References 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

References conformation_, and total_residue().

Referenced by protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), 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::CoreDunbrackFilter::compute(), protocols::toolbox::SelectResiduesByLayer::compute(), protocols::fldsgn::filters::InterlockingAromaFilter::compute(), protocols::design_opt::GreedyOptMutationMover::dump_scoring_table(), protocols::loops::loop_closure::ccd::fast_ccd_loop_closure(), protocols::swa::StepWiseScreener::get_main_chain_torsion_set_list_c_terminus(), protocols::swa::protein::StepWiseProteinScreener::get_main_chain_torsion_set_list_c_terminus(), protocols::swa::StepWiseScreener::get_main_chain_torsion_set_list_coarse(), protocols::swa::protein::StepWiseProteinScreener::get_main_chain_torsion_set_list_coarse(), protocols::swa::StepWiseScreener::get_main_chain_torsion_set_list_full(), protocols::swa::protein::StepWiseProteinScreener::get_main_chain_torsion_set_list_full(), protocols::swa::StepWiseScreener::get_main_chain_torsion_set_list_n_terminus(), protocols::swa::protein::StepWiseProteinScreener::get_main_chain_torsion_set_list_n_terminus(), 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::swa::StepWiseScreener::get_main_chain_torsion_set_list_sample_psi_only(), protocols::swa::protein::StepWiseProteinScreener::get_main_chain_torsion_set_list_sample_psi_only(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::model_loop(), protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturber::perturb_chain(), protocols::loops::loop_closure::kinematic_closure::NeighborDependentTorsionSamplingKinematicPerturber::perturb_chain(), protocols::loops::loop_closure::kinematic_closure::TorsionRestrictedKinematicPerturber::perturb_chain(), protocols::loops::loop_closure::kinematic_closure::TabooSamplingKinematicPerturber::perturb_chain(), protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturber::perturb_chain(), protocols::fldsgn::potentials::AACompositionEnergy::residue_energy(), protocols::loops::set_secstruct_from_dssp(), and core::scoring::methods::MembraneEnvSmoothEnergy::setup_for_derivatives().

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

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().

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

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

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

The default behavior is to append by a polymeric connection to the preceding residue If we want to connect via a non-polymer connection, we give the connection number, anchor residue and the connection number for the anchor residue. These connection numbers are wrt the connections_ arrays in Residue and ResidueType

If build_ideal_bond is TRUE it will transform the coordinates of the new residue so that the bond geometry of the new bond is ideal according to the icoor_internal data in the residues.

Otherwise the incoming coordinates of new_rsd are preserved.

References conformation_, and energies_.

Referenced by protocols::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.

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

Returns the pose AtomTree.

get the atom_tree

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
fnpointer to observer's unary member function with signature void( ConformationEvent const & )
ptrpointer to observer object
Returns
Link that can be used to manage the connection.

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
fnpointer to observer's unary member function with signature void( DestructionEvent const & )
ptrpointer to observer object
Returns
Link that can be used to manage the connection.
Remarks
DestructionEvent observers will only be notified upon destruction of the Pose

References destruction_obs_hub_.

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

template<typename MemFn , typename Ptr >
utility::signals::Link core::pose::Pose::attach_energy_obs ( MemFn  fn,
Ptr  ptr 
)
inline

attach EnergyEvent observer function

Parameters
fnpointer to observer's unary member function with signature void( EnergyEvent const & )
ptrpointer to observer object
Returns
Link that can be used to manage the connection.

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
fnpointer to observer's unary member function with signature void( GeneralEvent const & )
ptrpointer to observer object
Returns
Link that can be used to manage the connection.
Remarks
GeneralEvent observers will be notified whenever any signal derived from GeneralEvent occurs.

References general_obs_hub_.

Referenced by protocols::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

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 
)
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::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

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

Referenced by protocols::dna::DnaInterfaceMultiStateDesign::add_dna_states(), protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_pose(), protocols::loops::add_loop(), protocols::ligand_docking::append_multi_residue_ligand_RMSD(), protocols::ligand_docking::LigandDesign::apply(), protocols::dna::RestrictDesignToProteinDNAInterface::apply(), protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::apply(), protocols::ddg::ddGMover::apply(), protocols::fldsgn::CircularPermutation::apply(), protocols::loops::apply_sequence_mapping(), protocols::analysis::InterfaceAnalyzerMover::calc_hbond_sasaE(), protocols::dna::DnaInterfacePacker::calculate_specificity(), core::pose::metrics::simple_calculators::InterfaceDefinitionCalculator::chain_letter_to_number(), protocols::simple_filters::ResidueSetChainEnergyFilter::compute(), protocols::enzdes::LigDSasaFilter::compute(), protocols::protein_interface_design::filters::AtomicContactCountFilter::compute(), protocols::analysis::InterfaceAnalyzerMover::compute_interface_sc(), core::pose::conf2pdb_chain(), protocols::dna::DnaInterfacePacker::dna_seq_tag(), protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMover::generate_csts(), protocols::enzdes::EnzdesFlexBBProtocol::generate_ensemble_for_region(), core::pose::get_chain_id_from_jump_id(), protocols::antibody2::AntibodyInfo::get_FoldTree_L_HA(), protocols::antibody2::AntibodyInfo::get_FoldTree_LA_H(), protocols::antibody2::AntibodyInfo::get_FoldTree_LH_A(), core::pose::get_hash_excluding_chain(), core::pose::get_jump_id_from_chain_id(), core::pose::get_sha1_hash_excluding_chain(), protocols::dna::DnaInterfacePacker::init_standard(), protocols::features::HBondFeatures::insert_site_row(), protocols::loops::Loop::is_terminal(), protocols::loops::loops_around_residues(), protocols::analysis::InterfaceAnalyzerMover::make_multichain_interface_set(), protocols::analysis::InterfaceAnalyzerMover::parse_my_tag(), protocols::dna::DnaInterfacePacker::protein_scan(), protocols::toolbox::pose_metric_calculators::ResidueDecompositionByChainCalculator::recompute(), protocols::ddg::ddGMover::relax_wildtype_structure(), core::pose::renumber_pdbinfo_based_on_conf_chains(), core::scoring::methods::NMerPSSMEnergy::residue_energy(), protocols::simple_filters::NonSequentialNeighborsFilter::residue_neighbors(), protocols::dna::DnaInterfacePacker::reversion_scan(), protocols::dna::seq_pdb_str(), protocols::dna::DesignProteinBackboneAroundDNA::set_loop_info(), core::scoring::constraints::FabConstraint::setup_csts(), protocols::docking::setup_foldtree(), and protocols::enzdes::EnzdesScorefileFilter::setup_pose_metric_calculators().

std::string core::pose::Pose::chain_sequence ( core::Size const  chain_in) const
Real core::pose::Pose::chi ( int const  chino,
Size const  seqpos 
) const
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().

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

Empty the pose contents.

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

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

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

References conformation_.

Referenced by protocols::simple_moves::HelicalPeptideLengthMover::add_residue_(), protocols::protein_interface_design::movers::Splice::add_sequence_constraints(), core::optimization::symmetry::SymMinimizerMap::add_torsion(), core::pose::add_variant_type_to_residue(), core::pack::rotamer_set::UnboundRotamersOperation::alter_rotamer_set(), protocols::anchored_design::AnchorMoversData::anchor_noise_constraints_setup(), protocols::ligand_docking::append_ligand_RMSD(), core::io::pdb::FileData::append_residue(), protocols::seeded_abinitio::GrowPeptides::append_residues_cterminally(), protocols::seeded_abinitio::GrowPeptides::append_residues_nterminally(), protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspots::apply(), protocols::seeded_abinitio::DefineMovableLoops::apply(), protocols::seeded_abinitio::SwapSegment::apply(), protocols::protein_interface_design::movers::LoopLengthChange::apply(), protocols::qsar::qsarMover::apply(), protocols::simple_moves::ForceDisulfidesMover::apply(), protocols::seeded_abinitio::CAcstGenerator::apply(), protocols::simple_moves::SwitchChainOrderMover::apply(), protocols::simple_filters::EnergyPerResidueFilter::apply(), protocols::simple_moves::oop::OopMover::apply(), protocols::protein_interface_design::movers::SetAtomTree::apply(), protocols::seeded_abinitio::PlaceFragments::apply(), protocols::protein_interface_design::movers::PrepackMover::apply(), protocols::protein_interface_design::movers::SpinMover::apply(), protocols::seeded_abinitio::CloseFold::apply(), protocols::simple_moves::PeptideStapleMover::apply(), protocols::seeded_abinitio::SeedFoldTree::apply(), protocols::simple_moves::hbs::HbsPatcher::apply(), protocols::simple_moves::oop::OopPatcher::apply(), protocols::ligand_docking::LigandDesign::apply(), protocols::ligand_docking::RigidSearchMover::apply(), protocols::antibody2::GraftOneCDRLoop::apply(), protocols::seeded_abinitio::SegmentHybridizer::apply(), protocols::ligand_docking::MinimizeLigand::apply(), protocols::ligand_docking::RandomConformers::apply(), protocols::simple_moves::oop::OopRandomSmallMover::apply(), protocols::toolbox::task_operations::SelectBySASAOperation::apply(), protocols::ligand_docking::AddHydrogens::apply(), protocols::ligand_docking::GrowLigand::apply(), protocols::filters::HeavyAtomFilter::apply(), protocols::ligand_docking::TetherLigand::apply(), protocols::symmetric_docking::SymFoldandDockSlideTrialMover::apply(), protocols::protein_interface_design::filters::FilterScanFilter::apply(), protocols::abinitio::ResolutionSwitcher::apply(), protocols::dna::SeparateDnaFromNonDna::apply(), protocols::simple_moves::symmetry::SymmetricRMSMover::apply(), protocols::rigid::RotateJumpAxisMover::apply(), protocols::nonlocal::SheetTranslate::apply(), protocols::domain_assembly::AssembleLinkerMover::apply(), protocols::simple_moves::FavorSequenceProfile::apply(), protocols::swa::protein::StepWiseProteinPoseMinimizer::apply(), protocols::toolbox::task_operations::RestrictNonSurfaceToRepackingOperation::apply(), protocols::ligand_docking::CompleteConnectionsFilter::apply(), protocols::protein_interface_design::movers::BackrubDDMover::apply(), protocols::nonlocal::HelixRotate::apply(), protocols::comparative_modeling::PartialThreadingMover::apply(), protocols::ligand_docking::HBondDonorFilter::apply(), protocols::simple_moves::chiral::ChiralMover::apply(), protocols::toolbox::task_operations::PreventChainFromRepackingOperation::apply(), protocols::toolbox::task_operations::RestrictToAlignedSegmentsOperation::apply(), protocols::toolbox::task_operations::RestrictChainToRepackingOperation::apply(), protocols::ligand_docking::HeavyAtomFilter::apply(), protocols::ligand_docking::AtomCountFilter::apply(), protocols::ligand_docking::HBondAcceptorFilter::apply(), protocols::ligand_docking::MolarMassFilter::apply(), protocols::ligand_docking::MolecularMassFilter::apply(), protocols::abinitio::AbrelaxMover::apply(), protocols::protein_interface_design::movers::SaveAndRetrieveSidechains::apply(), protocols::simple_moves::ReturnSidechainMover::apply(), protocols::simple_filters::JumpEvaluator::apply(), protocols::simple_moves::MutateResidue::apply(), protocols::symmetric_docking::SymFoldandDockRbTrialMover::apply(), protocols::toolbox::task_operations::RestrictToTerminiOperation::apply(), protocols::protein_interface_design::movers::PlacementAuctionMover::apply(), protocols::simple_moves::symmetry::SetupNCSMover::apply(), protocols::simple_moves::TorsionDOFMover::apply(), protocols::toolbox::task_operations::RestrictNativeResiduesOperation::apply(), protocols::toolbox::task_operations::ProteinInterfaceDesignOperation::apply(), protocols::loophash::LoopHashDiversifier::apply(), protocols::protein_interface_design::movers::LoopMoverFromCommandLine::apply(), protocols::simple_moves::symmetry::SymDockingInitialPerturbation::apply(), protocols::flexpep_docking::FlexPepDockingProtocol::apply(), protocols::comparative_modeling::ExtraThreadingMover::apply(), protocols::toolbox::task_operations::SeqprofConsensusOperation::apply(), protocols::ligand_docking::Transform::apply(), core::fragment::BBTorsionAndAnglesSRFD::apply(), protocols::toolbox::task_operations::JointSequenceOperation::apply(), protocols::rbsegment_relax::FragInsertAndAlignMover::apply(), protocols::moves::StructureRestrictor::apply(), protocols::ligand_docking::Translate::apply(), protocols::rigid::WholeBodyTranslationMover::apply(), protocols::protein_interface_design::movers::PlaceStubMover::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::match::MatcherMover::apply(), protocols::analysis::InterfaceAnalyzerMover::apply(), protocols::relax::ClassicRelax::apply(), protocols::canonical_sampling::CanonicalSamplingMover::apply(), protocols::rigid::WholeBodyRotationMover::apply(), protocols::enzdes::DetectProteinLigandInterface::apply(), protocols::simple_moves::symmetry::SymDockingSlideIntoContact::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::idealize::IdealizeMover::apply(), protocols::protein_interface_design::movers::Splice::apply(), protocols::comparative_modeling::ThreadingMover::apply(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::apply(), protocols::enzdes::LigInterfaceEnergyFilter::apply(), protocols::simple_moves::symmetry::FaSymDockingSlideTogether::apply(), protocols::symmetric_docking::SymDockProtocol::apply(), protocols::relax::FastRelax::apply(), protocols::antibody::GraftOneMover::apply(), protocols::fldsgn::CircularPermutation::apply(), protocols::grafting::AnchoredGraftMover::apply(), protocols::fldsgn::potentials::SetSecStructEnergies::apply(), protocols::topology_broker::TopologyBroker::apply(), protocols::abinitio::MembraneAbinitio::apply(), protocols::enzdes::PredesignPerturbMover::apply(), core::fragment::DownJumpSRFD::apply(), protocols::rigid::RigidBodyPerturbMover::apply(), protocols::enzdes::RepackLigandSiteWithoutLigandMover::apply(), protocols::rigid::RigidBodyRandomizeMover::apply(), protocols::rigid::RigidBodySpinMover::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::rigid::RigidBodyDeterministicSpinMover::apply(), protocols::rigid::RigidBodyTransMover::apply(), protocols::forge::components::VarLengthBuild::apply(), protocols::seeded_abinitio::SegmentHybridizer::apply_frame(), protocols::hybridization::CartesianSampler::apply_frame(), protocols::hybridization::CartesianHybridize::apply_frame(), protocols::pockets::PlaidFingerprint::apply_rotation_offset_to_pose_(), protocols::loops::apply_sequence_mapping(), core::optimization::CartesianMinimizerMap::assign_rosetta_torsions_and_trim(), core::optimization::symmetry::SymMinimizerMap::asymmetric_dof(), core::optimization::symmetry::atom_tree_dfunc(), core::optimization::symmetry::atom_tree_get_atompairE_deriv(), core::pack::scmin::AtomTreeCollection::AtomTreeCollection(), protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver::attach_impl(), core::pose::datacache::LengthEventCollector::attach_impl(), core::pose::datacache::SpecialSegmentsObserver::attach_impl(), protocols::forge::build::BuildInstruction::attach_to(), protocols::pockets::PocketGrid::autoexpanding_pocket_eval(), protocols::idealize::basic_idealize(), protocols::branch_angle::branching_atomid1(), protocols::branch_angle::branching_atomids2(), core::pack::rotamer_set::build_lib_dna_rotamers(), core::pack::rotamer_set::RotamerSet_::build_optimize_H_rotamers(), core::scoring::GenBornPotential::build_placeholders(), core::scoring::FACTSPotential::build_placeholders(), core::io::pdb::build_pose_as_is1(), core::pack::rotamer_set::build_random_dna_rotamers(), core::pack::rotamer_set::build_rna_chi_rotamers(), core::pack::rotamer_set::RotamerSets::build_rotamers(), core::pack::rotamer_set::RotamerSet_::build_rotamers_for_concrete(), core::scoring::CA_rmsd_symmetric(), core::pack::task::operation::util::calc_interacting_vector(), protocols::symmetric_docking::SymDockProtocol::calc_interaction_energy(), protocols::symmetric_docking::SymDockProtocol::calc_rms(), protocols::pockets::PlaidFingerprint::calculate_ligand_CoM(), protocols::pmut_scan::PointMutScanDriver::calculate_neighbor_table(), protocols::anchored_design::AnchoredDesignMover::calculate_rmsd(), core::optimization::cartesian_collect_torsional_deriv(), core::optimization::cartesian_dfunc(), protocols::simple_moves::CutChainMover::chain_cut(), protocols::ligand_docking::Transform::change_conformer(), protocols::hybridization::HybridizeProtocol::check_and_create_fragments(), core::scoring::rna::RNA_TorsionPotential::check_intra_residue(), protocols::simple_filters::ResidueBurialFilter::compute(), protocols::simple_filters::SidechainRmsdFilter::compute(), protocols::simple_filters::ResidueDistanceFilter::compute(), protocols::simple_filters::NeighborTypeFilter::compute(), protocols::simple_filters::TerminusDistanceFilter::compute(), protocols::protein_interface_design::filters::AverageDegreeFilter::compute(), protocols::protein_interface_design::filters::SequenceRecoveryFilter::compute(), protocols::simple_filters::ResidueIEFilter::compute(), protocols::protein_interface_design::filters::SpecificResiduesNearInterfaceFilter::compute(), protocols::protein_interface_design::filters::AtomicContactCountFilter::compute(), protocols::protein_interface_design::filters::HbondsToResidueFilter::compute(), protocols::enzdes::LigBurialFilter::compute(), protocols::toolbox::task_operations::LayerOperations::compute(), protocols::simple_filters::SymmetricMotifFilter::compute_d2(), protocols::hybridization::CartesianSampler::compute_fragment_bias(), protocols::pockets::PlaidFingerprint::compute_ligand_natoms(), core::scoring::disulfides::DisulfideMatchingPotential::compute_matching_energy(), core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::compute_one_body_energies(), core::pack::interaction_graph::SurfacePotential::compute_pose_hpatch_score(), core::pack::interaction_graph::SurfacePotential::compute_pose_surface_energy(), core::pose::conf2pdb_chain(), protocols::protein_interface_design::movers::copy_hotspot_to_pose(), protocols::star::copy_residues(), copy_segment(), core::scoring::symmetry::SymmetricScoreFunction::correct_finalize_score(), protocols::protein_interface_design::movers::SetAtomTree::create_atom_tree(), protocols::floppy_tail::create_extra_output(), core::pack::create_packer_graph(), protocols::ligand_docking::Rotate::create_random_rotations(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::create_rotamers_from_chisets(), protocols::simple_moves::CutChainMover::create_subpose(), core::pose::create_subpose(), protocols::forge::methods::cyclize_pose(), protocols::pockets::PocketGrid::DARC_autoexpanding_pocket_eval(), protocols::pockets::PocketGrid::DARC_pocket_eval(), protocols::seeded_abinitio::define_movemap_chains(), protocols::grafting::GraftMoverBase::delete_overhang_residues(), protocols::grafting::delete_region(), protocols::relax::delete_virtual_residues(), core::scoring::constraints::ConstraintSet::deprecated_eval_atom_derivative(), core::scoring::constraints::ConstraintSet::deprecated_eval_atom_derivative_for_residue_pairs(), core::scoring::constraints::AmbiguousNMRConstraint::dist(), core::scoring::constraints::CoordinateConstraint::dist(), core::scoring::constraints::AtomPairConstraint::dist(), core::scoring::constraints::AmbiguousNMRDistanceConstraint::dist(), core::scoring::constraints::LocalCoordinateConstraint::dist(), protocols::abinitio::AbrelaxApplication::do_distributed_rerun(), core::scoring::methods::LinearChainbreakEnergy::do_score_ovp(), protocols::simple_moves::sidechain_moves::SidechainMoverBase::dof_id_ranges(), protocols::simple_moves::sidechain_moves::SidechainMover::dof_id_ranges(), protocols::simple_moves::SmallMover::dof_id_ranges(), protocols::simple_moves::ShearMover::dof_id_ranges(), core::import_pose::atom_tree_diffs::dump_atom_tree_diff(), core::io::pdb::dump_connect_info(), protocols::pockets::PlaidFingerprint::dump_oriented_pose_and_fp_to_pdb(), protocols::viewer::dump_pose_kinemage(), protocols::ligand_docking::InterfaceBuilder::enforce_minimum_length(), core::scoring::disulfides::FullatomDisulfideEnergy::ensure_lrenergy_container_is_up_to_date(), protocols::rigid::MovePoseToMembraneCenterMover::estimate_membrane_center(), core::scoring::methods::ChainbreakEnergy::eval_atom_derivative(), core::scoring::methods::CustomAtomPairEnergy::eval_atom_derivative(), core::scoring::methods::MMBondAngleEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensCenEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensEnergy::eval_atom_derivative(), core::scoring::electron_density::FastDensEnergy::eval_atom_derivative(), core::scoring::symmetry::SymmetricScoreFunction::eval_long_range_twobody_energies(), core::scoring::constraints::ConstraintSet::eval_multibody_atom_derivative(), protocols::constraints_additional::MaxSeqSepConstraintSet::eval_non_residue_pair_energy(), core::scoring::constraints::ConstraintSet::eval_non_residue_pair_energy(), core::scoring::symmetry::SymmetricScoreFunction::eval_onebody_energies(), core::scoring::symmetry::SymmetricScoreFunction::eval_twobody_neighbor_energies(), protocols::star::Extender::extend_unaligned(), core::pose::symmetry::extract_asymmetric_unit(), core::pose::symmetry::extract_asymmetric_unit_pdb_info(), protocols::forge::build::ConnectRight::extract_rt(), protocols::LoopRebuild::fast_ccd_close_loops(), protocols::loops::loop_mover::perturb::fast_ccd_close_loops(), protocols::swa::rna::StepWiseRNA_Minimizer::Figure_out_moving_residues(), protocols::swa::Figure_out_moving_residues(), core::pose::metrics::simple_calculators::InterfaceDefinitionCalculator::fill_in_chain_terminii(), protocols::toolbox::pose_metric_calculators::SequenceComparison::fill_num_neighbors(), core::scoring::symmetry::SymmetricEnergies::fill_point_graph(), core::scoring::solid_surface::SurfaceEnergies::fill_point_graph(), core::scoring::Energies::fill_point_graph(), core::io::silent::BinaryProteinSilentStruct::fill_pose(), core::io::silent::ProteinSilentStruct_Template< T >::fill_pose(), core::pack::dunbrack::SingleLigandRotamerLibrary::fill_rotamer_vector(), core::io::silent::BinaryProteinSilentStruct::fill_struct(), core::io::silent::ProteinSilentStruct_Template< T >::fill_struct(), protocols::coarse_rna::CoarseRNA_LoopCloser::filter_path(), core::pack::rotamer_set::symmetry::SymmetricRotamerSets::final_visit_to_edge(), core::scoring::methods::MetalloPlacementEnergy::finalize_total_energy(), core::scoring::methods::MembraneLipo::finalize_total_energy(), core::scoring::methods::ChainbreakEnergy::finalize_total_energy(), protocols::ligand_docking::InterfaceBuilder::find_interface_residues(), core::pack::task::operation::util::find_jump_partners_within_CB_cutoff(), protocols::seeded_abinitio::DefineMovableLoops::find_loops(), protocols::seeded_abinitio::CloseFold::find_loops(), protocols::protein_interface_design::find_lowest_constraint_energy_residue(), protocols::protein_interface_design::find_nearest_residue(), protocols::protein_interface_design::movers::find_nearest_residue_to_coord(), core::pack::task::operation::util::find_neighbors_within_CB_cutoff(), protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockMoveRbJumpMover::find_new_jump_residue(), core::pose::symmetry::find_new_symmetric_jump_residues(), core::pose::symmetry::find_symmetric_basejump_anchor(), protocols::topology_broker::fix_internal_coords_of_siblings(), protocols::topology_broker::fix_mainchain_connect(), protocols::protein_interface_design::movers::Splice::fold_tree(), protocols::forge::methods::fold_tree_from_loops(), protocols::loops::fold_tree_from_loops(), protocols::forge::methods::fold_tree_from_pose(), protocols::simple_moves::CutChainMover::foldTree(), protocols::rosetta_scripts::foreach_movemap_tag(), protocols::protein_interface_design::movers::DisulfideMover::form_disulfide(), protocols::topology_broker::FoldandDockClaimer::generate_claims(), protocols::topology_broker::AsymFoldandDockClaimer::generate_claims(), protocols::topology_broker::FibrilModelingClaimer::generate_claims(), protocols::abinitio::AbrelaxApplication::generate_extended_pose(), protocols::protein_interface_design::movers::MapHotspot::GenerateMap(), core::pose::get_chain_from_chain_id(), core::pose::get_chain_ids_from_chain(), core::pose::get_chain_residues(), protocols::pockets::DelphiElectrostatics::get_electrostatics_energy(), core::scoring::rna::RNA_TorsionPotential::get_f1_f2(), protocols::antibody2::AntibodyInfo::get_FoldTree_L_HA(), protocols::antibody2::AntibodyInfo::get_FoldTree_LA_H(), protocols::antibody2::AntibodyInfo::get_FoldTree_LH_A(), core::pose::get_hash_excluding_chain(), core::pose::get_hash_from_chain(), protocols::hotspot_hashing::HotspotStub::get_nearest_residue(), protocols::hybridization::get_num_residues_nonvirt(), protocols::hotspot_hashing::HotspotStubSet::get_residue_score_(), protocols::loophash::get_rt_over_leap_without_foldtree_bs(), core::pose::get_sha1_hash_excluding_chain(), core::pose::symmetry::get_symm_axis(), protocols::pockets::PocketGrid::getRelaxResidues(), protocols::forge::methods::grow_left_r(), protocols::forge::methods::grow_right_r(), core::pose::has_chain(), core::scoring::SecondaryStructurePotential::hspair(), protocols::loops::idealize_loop(), protocols::simple_moves::sidechain_moves::SidechainMoverBase::idealize_sidechains(), protocols::simple_moves::sidechain_moves::SidechainMover::idealize_sidechains(), protocols::antibody2::AntibodyInfo::identify_antibody(), core::scoring::SecondaryStructurePotential::identify_ss(), protocols::forge::build::SegmentSwap::init(), protocols::forge::build::SegmentInsert::init(), protocols::ub_e2c::ubi_e2c_modeler::initial_cter_perturbation(), protocols::hybridization::HybridizeFoldtreeDynamic::initialize(), protocols::hybridization::HybridizeProtocol::initialize_and_sample_loops(), core::pose::initialize_disulfide_bonds(), protocols::features::ReportToDB::initialize_pose(), protocols::rna::FullAtomRNA_Fragments::insert_fragment(), core::scoring::symmetry::SymmetricScoreFunction::intersubunit_hbond_energy(), core::pose::is_ideal_position(), core::pose::symmetry::is_symmetric(), protocols::rna::RNA_IdealCoord::is_torsion_exists(), protocols::simple_filters::JumpEvaluator::JumpEvaluator(), protocols::features::PoseConformationFeatures::load_chain_endings(), protocols::protein_interface_design::movers::PlaceOnLoop::loop_length(), protocols::loops::loopfinder(), protocols::loops::loops_around_residues(), core::optimization::symmetry::SymAtomTreeMinimizer::make_assymetric_movemap(), core::pose::symmetry::make_asymmetric_pose(), protocols::motifs::make_base_pair_mutation(), protocols::toolbox::match_enzdes_util::EnzConstraintParameters::make_constraint_covalent(), protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover::make_disjointed_foldtree(), protocols::forge::remodel::RemodelDesignMover::make_disulfide(), protocols::protein_interface_design::make_hotspot_foldtree(), protocols::loophash::LocalInserter_SimpleMin::make_local_bb_change_close_gaps(), core::pack::make_new_symmetric_PackerTask_by_intersection(), core::pack::make_new_symmetric_PackerTask_by_union(), core::fragment::make_pose_from_frags(), core::pose::symmetry::make_residue_mask_symmetric(), core::optimization::symmetry::SymAtomTreeMinimizer::make_semisymmetric_movemap(), protocols::fibril::make_symmetric_fibril(), core::pose::symmetry::make_symmetric_movemap(), core::pack::make_symmetric_PackerTask_by_truncation(), core::pose::symmetry::make_symmetric_pdb_info(), core::pose::symmetry::make_symmetric_pose(), protocols::simple_moves::symmetry::SymPackRotamersMover::make_symmetric_task(), protocols::simple_moves::symmetry::SymRotamerTrialsMover::make_symmetric_task(), protocols::simple_moves::symmetry::SymEnergyCutRotamerTrialsMover::make_symmetric_task(), protocols::rotamer_recovery::RRComparerAutomorphicRMSD::measure_rotamer_recovery(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::minimize_all(), MinimizeInterface(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_Moves::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::model_loop(), protocols::forge::build::SegmentSwap::modify_impl(), protocols::forge::build::Bridge::modify_impl(), protocols::forge::build::SegmentRebuild::modify_impl(), protocols::forge::build::ConnectRight::modify_impl(), protocols::forge::build::SegmentInsert::modify_impl(), protocols::ub_e2c::ubi_e2c_modeler::monoub_initial_cter_perturbation(), protocols::pockets::PlaidFingerprint::move_ligand_(), protocols::pockets::PocketGrid::move_pose_to_standard_orie(), core::scoring::MembranePotential::non_helix_in_membrane_penalty(), core::scoring::DockingScoreFunction::operator()(), protocols::ligand_docking::LigandDockProtocol::optimize_orientation3(), protocols::protein_interface_design::movers::MapHotspot::output_pose(), protocols::frag_picker::FragmentCandidate::output_silent(), protocols::branch_angle::BranchAngleOptimizer::param1(), protocols::branch_angle::BranchAngleOptimizer::param2(), protocols::seeded_abinitio::DefineMovableLoops::parse_my_tag(), protocols::seeded_abinitio::CloseFold::parse_my_tag(), protocols::protein_interface_design::movers::PlaceOnLoop::parse_my_tag(), protocols::simple_moves::DesignRepackMover::parse_my_tag(), protocols::ligand_docking::Rotate::parse_my_tag(), protocols::protein_interface_design::movers::PlaceStubMover::parse_my_tag(), protocols::contact_map::ContactMap::parse_region_string(), protocols::rna::RNA_LoopCloser::passes_fast_scan(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::perform_bump_check(), protocols::anchored_design::AnchoredDesignMover::perturb_anchor(), protocols::comparative_modeling::pick_loops_chainbreak(), protocols::protein_interface_design::movers::PlaceStubMover::place_stub(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::place_stubs(), protocols::hotspot_hashing::StubGenerator::placeResidueOnPose(), protocols::pockets::PlaidFingerprint::PlaidFingerprint(), protocols::pockets::PocketConstraint::PocketConstraint(), protocols::design_opt::GreedyOptMutationMover::pose_coords_are_same(), core::import_pose::atom_tree_diffs::pose_from_atom_tree_diff(), core::import_pose::pose_from_pdb(), core::pack::rotamer_set::symmetry::SymmetricRotamerSets::precompute_two_body_energies(), protocols::hotspot_hashing::HotspotStubSet::prepare_hashing_packer_task_(), core::scoring::rna::prepare_scratch_residue(), core::pack::rotamer_set::symmetry::SymmetricRotamerSets::prepare_symm_otf_interaction_graph(), protocols::swa::rna::Print_torsion_info(), core::scoring::rna::RNA_TorsionPotential::print_torsion_info(), protocols::anchored_design::AnchoredDesignMover::randomize_input_sequence(), core::io::serialization::read_binary(), core::io::raw_data::DisulfideFile::read_in_and_set_disulfides(), core::util::rebuild_disulfide(), core::pose::metrics::simple_calculators::InterfaceNeighborDefinitionCalculator::recompute(), protocols::toolbox::pose_metric_calculators::NeighborsByDistanceCalculator::recompute(), protocols::toolbox::pose_metric_calculators::NeighborhoodByDistanceCalculator::recompute(), protocols::toolbox::pose_metric_calculators::ResidueDecompositionByChainCalculator::recompute(), protocols::toolbox::pose_metric_calculators::InterGroupNeighborsCalculator::recompute(), protocols::protein_interface_design::movers::PlacementMinimizationMover::refresh_bbstub_constraints(), protocols::abinitio::AbrelaxApplication::relax(), protocols::jumping::remove_cut(), core::pose::remove_ligand_canonical_residues(), protocols::toolbox::pose_manipulation::remove_non_protein_residues(), core::pose::remove_nonprotein_residues(), protocols::hybridization::remove_residues(), core::pose::remove_variant_type_from_residue(), core::pose::remove_virtual_residues(), core::pose::renumber_pdbinfo_based_on_conf_chains(), protocols::analysis::InterfaceAnalyzerMover::reorder_foldtree_find_jump(), protocols::forge::remodel::RemodelLoopMover::repeat_generation(), protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue(), protocols::forge::remodel::RemodelLoopMover::repeat_propagation(), core::pose::replace_pose_residue_copying_existing_coordinates(), protocols::grafting::replace_region(), protocols::simple_filters::AlaScan::report(), protocols::features::AtomInResidueAtomInResiduePairFeatures::report_atom_pairs(), protocols::features::AtomAtomPairFeatures::report_atom_pairs(), protocols::features::ResidueGridScoresFeatures::report_features(), protocols::features::ResidueConformationFeatures::report_features(), protocols::features::ProteinResidueConformationFeatures::report_features(), protocols::features::LoopAnchorFeatures::report_features(), protocols::features::HBondFeatures::report_features(), protocols::features::PoseConformationFeatures::report_features_implementation(), protocols::features::PairFeatures::report_residue_pairs(), protocols::simple_filters::AlaScan::report_symmetry(), protocols::hybridization::HybridizeFoldtreeDynamic::reset(), core::scoring::methods::EnvEnergy::residue_energy(), core::scoring::methods::NMerPSSMEnergy::residue_energy(), protocols::simple_filters::NonSequentialNeighborsFilter::residue_neighbors(), core::scoring::methods::MembraneCenPairEnergy::residue_pair_energy(), core::scoring::methods::CenPairEnergy::residue_pair_energy(), core::scoring::methods::MMBondAngleEnergy::residue_pair_energy(), core::scoring::electron_density::ElecDensEnergy::residue_pair_energy(), core::scoring::electron_density::FastDensEnergy::residue_pair_energy(), protocols::ub_e2c::ubi_e2c_modeler::restore_cter(), protocols::forge::methods::restore_residues(), protocols::ligand_docking::Transform::revert_conformer(), protocols::pockets::PlaidFingerprint::rmsd(), core::pose::symmetry::rotate_anchor_to_x_axis(), protocols::ligand_docking::Rotate::rotate_ligand(), core::optimization::symmetry::SymAtomTreeMinimizer::run(), protocols::hybridization::DomainAssembly::run(), protocols::swa::rna::sample_user_specified_virtual_riboses(), protocols::pmut_scan::AlterSpecDisruptionDriver::score(), core::scoring::MembranePotential::score_normal_center(), core::pose::symmetry::scorefxn_is_symmetric(), core::pose::symmetry::sealed_symmetric_fold_tree(), protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::semiexpl_water_hbgeom_score(), protocols::ligand_docking::MoveMapBuilder::set_all_chi(), core::pose::symmetry::set_asymm_unit_fold_tree(), protocols::hybridization::InsertChunkMover::set_bb_xyz_aligned(), protocols::symmetric_docking::SymDockingLowRes::set_default_protocol(), protocols::symmetric_docking::SymDockingHiRes::set_dock_mcm_protocol(), protocols::symmetric_docking::SymDockingHiRes::set_dock_ppk_protocol(), protocols::abinitio::KinematicTaskControl::set_extended_torsions_and_idealize_loops(), protocols::loops::set_extended_torsions_and_idealize_loops(), protocols::anchored_design::AnchoredDesignMover::set_fold_tree_and_cutpoints(), protocols::hybridization::FoldTreeHybridize::set_loops_to_virt_ala(), protocols::seeded_abinitio::SeedSetupMover::set_packerTasks_target_and_seeds(), protocols::analysis::InterfaceAnalyzerMover::set_pose_info(), protocols::flexpep_docking::FlexPepDockingProtocol::set_receptor_constraints(), protocols::loops::set_single_loop_fold_tree(), core::scoring::symmetry::SymmetricScoreFunction::set_symmetric_cenlist(), protocols::scoring::Interface::set_symmetric_pack(), core::scoring::symmetry::SymmetricScoreFunction::set_symmetric_residue_neighbors_hbonds(), protocols::pockets::PocketConstraint::set_target_res(), protocols::pockets::PocketConstraint::set_target_res_pdb(), protocols::jumping::PairingLibrary::set_tmh_jump(), core::scoring::constraints::LocalCoordinateConstraint::set_xyz_target(), core::optimization::CartesianMinimizerMap::setup(), core::optimization::MinimizerMap::setup(), protocols::simple_moves::symmetry::SymmetrySlider::setup(), core::scoring::NeighborList::setup(), protocols::qsar::scoring_grid::ChargeGrid::setup_charge_atoms(), protocols::star::setup_constraints(), protocols::medal::setup_coordinate_constraints(), core::scoring::constraints::SiteConstraint::setup_csts(), core::scoring::constraints::FabConstraint::setup_csts(), protocols::swa::StepWisePoseSetup::setup_disulfides(), protocols::simple_moves::setup_dme_point_graph(), core::pose::setup_dof_mask_from_move_map(), core::pose::setup_dof_to_torsion_map(), protocols::abinitio::AbrelaxApplication::setup_fold(), protocols::jumping::MembraneJump::setup_fold_tree(), protocols::hybridization::FoldTreeHybridize::setup_foldtree(), protocols::docking::setup_foldtree(), core::scoring::electron_density::ElecDensEnergy::setup_for_derivatives(), core::scoring::electron_density::FastDensEnergy::setup_for_derivatives(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::setup_for_derivatives(), core::scoring::electron_density::ElecDensCenEnergy::setup_for_derivatives(), core::scoring::symmetry::SymmetricScoreFunction::setup_for_derivatives(), core::scoring::constraints::ConstraintSet::setup_for_derivatives(), core::scoring::symmetry::SymmetricScoreFunction::setup_for_minimizing(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::setup_for_scoring(), core::scoring::electron_density::ElecDensCenEnergy::setup_for_scoring(), core::scoring::constraints::ConstraintSet::setup_for_scoring(), protocols::idealize::IdealizeMover::setup_idealize_constraints(), protocols::rna::RNA_Minimizer::setup_movemap(), protocols::swa::rna::StepWiseRNA_PoseSetup::setup_native_pose(), core::scoring::SecondaryStructurePotential::sheets_from_dimers(), core::scoring::rna::RNA_TorsionPotential::Should_score_torsion(), core::scoring::constraints::DihedralConstraint::show_violations(), core::scoring::constraints::AngleConstraint::show_violations(), core::scoring::constraints::AtomPairConstraint::show_violations(), protocols::simple_moves::symmetry::SymmetrySlider::slide(), protocols::simple_moves::symmetry::SymmetrySlider::slide_away(), protocols::rna::MultipleDomainMover::slide_back_to_origin(), split_by_chain(), protocols::fldsgn::CircularPermutation::split_chains(), core::scoring::SecondaryStructurePotential::sspair(), protocols::protein_interface_design::star_fold_tree(), core::fragment::BBTorsionAndAnglesSRFD::steal(), core::fragment::DownJumpSRFD::steal(), core::scoring::constraints::CoordinateConstraint::steal_def(), core::scoring::constraints::LocalCoordinateConstraint::steal_def(), protocols::protein_interface_design::movers::PlaceStubMover::StubMinimize(), protocols::dna::substitute_residue(), protocols::seeded_abinitio::SwapSegment::swap_chain(), core::pose::swap_transform(), protocols::topology_broker::TopologyBroker::switch_to_fullatom(), core::util::switch_to_residue_type_set(), core::scoring::sym_rmsd_with_super_subset(), core::pack::symmetric_pack_rotamers_run(), protocols::scoring::Interface::symmetric_protein_calculate(), core::pack::symmetric_repackable_residues(), core::pack::symmetric_rotamer_trials(), core::pack::task::operation::RestrictToInterface::symmetric_task(), core::scoring::symmetry::SymmetricScoreFunction::symmetrical_allow_hbonds(), core::pose::symmetry::symmetrize_fold_tree(), core::pose::symmetry::symmetry_info(), core::optimization::symmetry::SymMinimizerMap::SymMinimizerMap(), protocols::nonlocal::StarTreeBuilder::tear_down(), protocols::star::StarAbinitio::tear_down_kinematics(), core::scoring::MembranePotential::termini_penalty(), protocols::simple_filters::RelativePoseFilter::thread_seq(), protocols::protein_interface_design::transform_pose(), protocols::rna::MultipleDomainMover::try_to_slide_into_contact(), protocols::hybridization::HybridizeFoldtreeDynamic::update(), protocols::simple_moves::oop::OopMover::update_hydrogens_(), core::scoring::symmetry::SymmetricEnergies::update_neighbor_links(), protocols::simple_moves::ConstrainToIdealMover::vary_bond_geometry(), protocols::simple_moves::symmetry::SymmetrySlider::very_far_away(), protocols::fldsgn::CircularPermutation::which_chain(), and core::scoring::constraints::LocalCoordinateConstraint::xyz_target().

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

Returns the pose Conformation (non-const access)

References conformation_.

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

References constraint_set_.

Referenced by protocols::topology_broker::TopologyBroker::add_chainbreak_variants(), protocols::topology_broker::ConstraintClaimer::add_constraints(), protocols::abinitio::AbrelaxApplication::add_constraints(), protocols::topology_broker::TopologyBroker::add_constraints(), core::scoring::constraints::add_constraints_from_cmdline_to_pose(), protocols::dna::add_constraints_from_file(), core::scoring::constraints::add_coordinate_constraints(), protocols::loops::add_cutpoint_variants(), core::scoring::constraints::add_fa_constraints_from_cmdline_to_pose(), protocols::swa::rna::Add_harmonic_chainbreak_constraint(), protocols::toolbox::match_enzdes_util::EnzConstraintIO::add_pregenerated_constraints_to_pose(), protocols::protein_interface_design::movers::Splice::add_sequence_constraints(), protocols::loops::add_single_cutpoint_variant(), protocols::swa::rna::StepWiseRNA_PoseSetup::add_terminal_res_repulsion(), protocols::swa::StepWisePoseSetup::add_terminal_res_repulsion(), protocols::anchored_design::AnchorMoversData::anchor_noise_constraints_setup(), protocols::relax::MiniRelax::apply(), protocols::seeded_abinitio::CAcstGenerator::apply(), protocols::medal::MedalExchangeMover::apply(), protocols::domain_assembly::AddAssemblyConstraints::apply(), protocols::rna::RNA_Minimizer::apply(), protocols::abinitio::ResolutionSwitcher::apply(), protocols::simple_moves::ConstraintSetMover::apply(), protocols::swa::protein::StepWiseProteinPoseMinimizer::apply(), protocols::dna::RestrictDesignToProteinDNAInterface::apply(), protocols::protein_interface_design::movers::SetupHotspotConstraintsMover::apply(), protocols::anchored_design::AnchoredDesignMover::apply(), protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMover::apply(), protocols::abinitio::AbrelaxMover::apply(), protocols::forge::constraints::RemoveCsts::apply(), protocols::rna::RNA_Relaxer::apply(), protocols::enzdes::EnzRepackMinimize::apply(), protocols::simple_filters::TruncatedScoreEvaluator::apply(), protocols::protein_interface_design::movers::PlaceStubMover::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::abinitio::KinematicAbinitio::apply(), protocols::idealize::IdealizeMover::apply(), protocols::abinitio::FoldConstraints::apply(), protocols::ddg::ddGMover::apply(), protocols::abinitio::ConstraintFragmentSampler::apply(), protocols::relax::FastRelax::apply(), protocols::abinitio::ClassicAbinitio::apply(), protocols::abinitio::ShowViolation::apply(), protocols::abinitio::ComputeTotalDistCst::apply(), protocols::relax::FastRelax::batch_apply(), core::pack::rotamer_set::build_lib_dna_rotamers(), protocols::LoopRebuild::build_loop_with_ccd_closure(), protocols::fldsgn::BluePrintBDR::centroid_build(), protocols::swa::check_scorefxn_has_constraint_terms_if_pose_has_constraints(), protocols::abinitio::FragmentSampler::checkpointed_cycle_block(), protocols::abinitio::AbrelaxApplication::close_loops(), protocols::enzdes::EnzScoreFilter::compute(), protocols::ligand_docking::constrain_ligand_torsions(), constraint_set(), protocols::enzdes::EnzdesBaseProtocol::cst_minimize(), core::scoring::constraints::CstEnergyContainer::CstEnergyContainer(), core::scoring::constraints::ConstraintsEnergy::defines_high_order_terms(), core::scoring::constraints::ConstraintsEnergy::defines_residue_pair_energy(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::design(), protocols::forge::remodel::RemodelMover::design_refine_seq_relax(), protocols::toolbox::match_enzdes_util::EnzConstraintParameters::determine_best_constraint(), protocols::ligand_docking::ResidueTorsionRestraints::disable(), protocols::abinitio::AbrelaxApplication::do_distributed_rerun(), protocols::abinitio::ConstraintFragmentSampler::do_stage1_cycles(), protocols::abinitio::FoldConstraints::do_stage1_cycles(), protocols::ligand_docking::ResidueTorsionRestraints::enable(), core::scoring::constraints::ConstraintsEnergy::eval_atom_derivative(), core::scoring::constraints::ConstraintsEnergy::eval_intrares_energy(), protocols::forge::methods::fill_non_loop_cst_set(), core::scoring::constraints::ConstraintsEnergy::finalize_total_energy(), protocols::enzdes::EnzdesConstraintReporter::find_constraints_to_ligand(), protocols::swa::rna::floating_base_chain_closure_post_process(), protocols::swa::rna::floating_base_chain_closure_setup(), protocols::abinitio::AbrelaxApplication::fold(), protocols::rna::RNA_LoopCloser::get_extra_cutpoints(), protocols::simple_filters::ConstraintScoreCutoffFilter::get_score(), protocols::motifs::MotifSearch::incorporate_motifs(), protocols::motifs::LigandMotifSearch::incorporate_motifs(), protocols::coarse_rna::CoarseRNA_DeNovoProtocol::initialize_constraints(), protocols::rna::RNA_DeNovoProtocol::initialize_constraints(), protocols::loophash::MPI_LoopHashRefine::load_structures_from_cmdline_into_library(), protocols::rna::RNA_Relaxer::lores_monte_carlo(), protocols::abinitio::FoldConstraints::min_trial(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::minimize_all(), protocols::swa::rna::minimize_with_constraints(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_Moves::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::model_loop(), core::scoring::constraints::ConstraintsEnergy::prepare_constraints_energy_container(), protocols::abinitio::FoldConstraints::prepare_loop_in_stage3(), protocols::abinitio::ConstraintFragmentSampler::prepare_loop_in_stage3(), protocols::abinitio::FoldConstraints::prepare_loop_in_stage4(), protocols::abinitio::ConstraintFragmentSampler::prepare_loop_in_stage4(), protocols::constraints_additional::ConstraintEvaluator::prepare_pose(), protocols::abinitio::FoldConstraints::prepare_stage2(), protocols::abinitio::ConstraintFragmentSampler::prepare_stage2(), protocols::abinitio::FoldConstraints::prepare_stage4(), protocols::rna::RNA_HelixAssembler::put_constraints_on_base_step(), protocols::abinitio::AbrelaxApplication::relax(), protocols::ddg::ddGMover::relax_wildtype_structure(), protocols::protein_interface_design::remove_coordinate_constraints_from_pose(), protocols::loops::remove_cutpoint_variants(), protocols::hotspot_hashing::remove_hotspot_constraints_from_pose(), core::scoring::constraints::ConstraintsEnergy::residue_pair_energy(), protocols::canonical_sampling::SilentTrajectoryRecorder::restart_simulation(), protocols::simple_moves::symmetry::SymShakeStructureMover::run_mc(), protocols::simple_moves::ShakeStructureMover::run_mc(), protocols::rbsegment_relax::set_constraints(), protocols::abinitio::FoldConstraints::set_max_seq_sep(), protocols::abinitio::ConstraintFragmentSampler::set_max_seq_sep(), protocols::rbsegment_relax::set_rb_constraints(), protocols::flexpep_docking::FlexPepDockingProtocol::set_receptor_constraints(), protocols::enzdes::EnzdesBaseProtocol::setup_bbmin_ft_and_csts(), protocols::hybridization::setup_centroid_constraints(), protocols::ligand_docking::ResidueTorsionRestraints::setup_constraints(), protocols::swa::StepWisePoseSetup::setup_constraints(), protocols::ddg::ddGMover::setup_constraints(), protocols::docking::DockingProtocol::setup_constraints(), protocols::abinitio::AbrelaxApplication::setup_fold(), core::scoring::constraints::ConstraintsEnergy::setup_for_derivatives(), core::scoring::constraints::ConstraintsEnergy::setup_for_minimizing_for_residue(), core::scoring::constraints::ConstraintsEnergy::setup_for_minimizing_for_residue_pair(), core::scoring::constraints::ConstraintsEnergy::setup_for_scoring(), protocols::hybridization::setup_fullatom_constraints(), protocols::protein_interface_design::movers::PlaceStubMover::StubMinimize(), protocols::motifs::IRCollection::successful_loop_closure(), protocols::topology_broker::TopologyBroker::switch_to_fullatom(), protocols::rna::RNA_LoopCloser::tight_minimize(), protocols::coarse_rna::CoarseRNA_DeNovoProtocol::update_pose_constraints(), protocols::rna::RNA_DeNovoProtocol::update_pose_constraints(), protocols::star::update_sequence_separation(), and protocols::simple_moves::ConstrainToIdealMover::vary_bond_geometry().

void core::pose::Pose::constraint_set ( ConstraintSetOP  constraint_set)
void core::pose::Pose::copy_segment ( Size const  size,
Pose const &  src,
Size const  begin,
Size const  src_begin 
)
BasicDataCache const& core::pose::Pose::data ( ) const
inline

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

References data_cache_.

Referenced by core::pose::add_comment(), core::pose::add_score_line_string(), protocols::simple_moves::AddCavitiesMover::add_suckers(), protocols::ub_e2c::ubi_e2c_modeler::apply(), protocols::simple_moves::symmetry::SymmetricRMSMover::apply(), protocols::simple_moves::MembraneTopology::apply(), protocols::antibody::AntibodyModeler::apply(), protocols::enzdes::SecondaryMatchProtocol::apply(), protocols::abinitio::AbrelaxMover::apply(), protocols::pb_potential::SetupPoissonBoltzmannPotential::apply(), protocols::surface_docking::SurfaceOrientMover::apply(), protocols::simple_moves::ddG::apply(), protocols::surface_docking::SlideIntoSurface::apply(), protocols::docking::ConformerSwitchMover::apply(), protocols::hybridization::CartesianHybridize::apply(), protocols::surface_docking::SurfaceDockingProtocol::apply(), protocols::simple_moves::ScoreMover::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::surface_docking::FaSlideIntoSurface::apply(), protocols::relax::ClassicRelax::apply(), protocols::surface_docking::FaSlideAwayFromSurface::apply(), protocols::symmetric_docking::SymDockProtocol::apply(), core::pack::rotamer_set::build_dependent_water_rotamers(), core::pack::rotamer_set::build_independent_water_rotamers(), core::scoring::EnvPairPotential::cenlist_from_pose(), core::scoring::SmoothEnvPairPotential::cenlist_from_pose(), protocols::ub_e2c::ubi_e2c_modeler::centroid_mode_perturbation(), protocols::simple_moves::AddCavitiesMover::clear_suckers(), core::pose::clearPoseExtraScore(), core::pose::clearPoseExtraScores(), core::scoring::methods::compute_and_store_pose_waters(), protocols::swa::monte_carlo::const_sub_to_full_info_from_pose(), protocols::enzdes::PoseFoundResiduesCombination::construct_and_dump_outpose(), core::scoring::symmetry::SymmetricScoreFunction::correct_arrays_for_symmetry(), core::scoring::SmoothEnvPairPotential::dcenlist_from_pose(), core::pose::delete_comment(), core::io::silent::SilentStruct::energies_from_pose(), core::io::silent::SilentStruct::energies_into_pose(), core::scoring::packing::SurfVolEnergy::eval_atom_derivative(), core::scoring::packing::SurfEnergy::eval_atom_derivative(), core::scoring::packing::HolesEnergy::eval_atom_derivative(), core::scoring::packing::HolesEnergyRes::eval_atom_derivative(), core::scoring::GenBornPotential::eval_atom_derivative(), core::scoring::FACTSPotential::eval_atom_nonpolar_derivative(), core::scoring::FACTSPotential::eval_atom_polar_derivative(), core::scoring::methods::FACTSEnergy::eval_intrares_energy(), core::scoring::methods::GenBornEnergy::eval_intrares_energy(), protocols::ub_e2c::ubi_e2c_modeler::evaluate_native(), core::scoring::methods::FACTSEnergy::evaluate_rotamer_background_energies(), core::scoring::methods::GenBornEnergy::evaluate_rotamer_background_energies(), core::scoring::methods::FACTSEnergy::evaluate_rotamer_background_energy_maps(), core::scoring::methods::GenBornEnergy::evaluate_rotamer_background_energy_maps(), core::scoring::methods::FACTSEnergy::evaluate_rotamer_intrares_energies(), core::pose::extract_tag_from_pose(), core::import_pose::pose_stream::LazySilentFilePoseInputStream::fill_pose(), core::import_pose::pose_stream::PDBPoseInputStream::fill_pose(), core::import_pose::pose_stream::SilentFilePoseInputStream::fill_pose(), core::scoring::methods::MembraneLipo::finalize_total_energy(), protocols::scoring::methods::EnsembleEnergy::finalize_total_energy(), protocols::features::FeaturesReporter::find_tag(), protocols::abinitio::AbrelaxApplication::fold(), core::scoring::GenBornPotential::get_all_born_radii(), core::pose::get_all_comments(), core::pose::get_all_score_line_strings(), protocols::jobdist::get_output_tag(), protocols::enzdes::enzutil::get_pdb_code_from_pose_tag(), protocols::rna::get_rna_secstruct(), core::scoring::FACTSPotential::get_rotamers_born_radii(), core::scoring::GenBornPotential::get_rotamers_born_radii(), protocols::jobdist::get_score_map(), core::pose::getPoseExtraScores(), core::scoring::SecondaryStructurePotential::hairpin_killing_score(), protocols::ub_e2c::ubi_e2c_modeler::init_k48r_perturbation(), protocols::ub_e2c::ubi_e2c_modeler::initial_perturbation(), protocols::topology_broker::MembraneTopologyClaimer::initialize_dofs(), protocols::scoring::InterchainPotential::interface_from_pose(), core::pose::is_position_conserved_residue(), core::scoring::methods::Fa_MbenvEnergy::Membrane_FAEmbed_from_pose(), core::scoring::methods::Fa_MbsolvEnergy::Membrane_FAEmbed_from_pose(), core::scoring::Membrane_FAEmbed_from_pose(), core::scoring::methods::Fa_MbenvEnergy::MembraneEmbed_from_pose(), protocols::abinitio::MembraneAbinitio::MembraneEmbed_from_pose(), core::scoring::MembraneEmbed_from_pose(), core::scoring::methods::MembraneCbetaEnergy::MembraneTopology_from_pose(), core::scoring::methods::Fa_MbenvEnergy::MembraneTopology_from_pose(), core::scoring::methods::MembraneEnvEnergy::MembraneTopology_from_pose(), core::scoring::methods::MembraneCenPairEnergy::MembraneTopology_from_pose(), core::scoring::methods::Fa_MbsolvEnergy::MembraneTopology_from_pose(), core::scoring::MembraneTopology_from_pose(), protocols::abinitio::MembraneAbinitio::MembraneTopology_from_pose(), core::scoring::methods::RG_Energy_Fast::mindata_from_pose(), protocols::ub_e2c::ubi_e2c_modeler::monoub_apply(), protocols::ub_e2c::ubi_e2c_modeler::monoub_first_perturbation(), protocols::ub_e2c::ubi_e2c_modeler::monoub_initial_perturbation(), core::scoring::EnvPairPotential::nonconst_cenlist_from_pose(), core::scoring::SmoothEnvPairPotential::nonconst_cenlist_from_pose(), core::scoring::SmoothEnvPairPotential::nonconst_dcenlist_from_pose(), protocols::scoring::InterchainPotential::nonconst_interface_from_pose(), core::scoring::nonconst_Membrane_FAEmbed_from_pose(), protocols::abinitio::MembraneAbinitio::nonconst_MembraneEmbed_from_pose(), core::scoring::nonconst_MembraneEmbed_from_pose(), core::scoring::nonconst_MembraneTopology_from_pose(), protocols::abinitio::MembraneAbinitio::nonconst_MembraneTopology_from_pose(), core::scoring::methods::RG_Energy_Fast::nonconst_mindata_from_pose(), core::scoring::rna::nonconst_rna_scoring_info_from_pose(), protocols::swa::monte_carlo::nonconst_sub_to_full_info_from_pose(), protocols::ub_e2c::ubi_e2c_modeler::optimize_cov_bond(), protocols::frag_picker::FragmentCandidate::output_silent(), protocols::scoring::methods::pcs::PCS_Energy::PCS_data_from_pose(), protocols::scoring::methods::pcs2::PcsEnergy::PCS_multi_data_from_pose(), protocols::moves::StructureRestrictor::pose_name(), protocols::abinitio::AbrelaxApplication::process_decoy(), protocols::docking::DockingEnsemble::recover_conformer_sidechains(), protocols::simple_filters::PoseInfoFilter::report(), protocols::rotamer_recovery::RRReporterSQLite::report_rotamer_recovery_full(), core::scoring::methods::FACTSEnergy::residue_pair_energy(), core::scoring::methods::GenBornEnergy::residue_pair_energy(), protocols::canonical_sampling::SilentTrajectoryRecorder::restart_simulation(), core::scoring::dna::retrieve_base_partner_from_pose(), core::scoring::methods::retrieve_base_partner_from_pose_inline(), core::scoring::retrieve_const_ss_info_from_pose(), core::scoring::retrieve_CSA_from_pose(), core::scoring::retrieve_DC_from_pose(), core::scoring::methods::retrieve_nonconst_residue_info(), core::scoring::retrieve_nonconst_ss_info_from_pose(), core::scoring::retrieve_RDC_from_pose(), core::scoring::retrieve_RDC_ROHL_from_pose(), protocols::scoring::retrieve_RDC_segments_from_pose(), core::scoring::methods::retrieve_residue_info(), core::scoring::rna::rna_scoring_info_from_pose(), core::scoring::dna::set_base_partner(), protocols::hybridization::InsertChunkMover::set_bb_xyz_aligned(), protocols::rna::set_rna_secstruct(), core::scoring::symmetry::SymmetricScoreFunction::set_symmetric_cenlist(), core::io::silent::SilentStruct::set_tag_from_pose(), core::pose::setPoseExtraScores(), protocols::jumping::MembraneJump::setup_fold_tree(), protocols::docking::setup_foldtree(), core::scoring::packing::SurfVolEnergy::setup_for_derivatives(), core::scoring::packing::SurfEnergy::setup_for_derivatives(), core::scoring::packing::HolesEnergy::setup_for_derivatives(), core::scoring::packing::HolesEnergyRes::setup_for_derivatives(), core::scoring::FACTSPotential::setup_for_derivatives(), core::scoring::FACTSPotential::setup_for_packing(), core::scoring::GenBornPotential::setup_for_packing(), core::scoring::methods::PoissonBoltzmannEnergy::setup_for_scoring(), core::scoring::FACTSPotential::setup_for_scoring(), protocols::relax::setup_membrane_topology(), protocols::abinitio::AbrelaxApplication::setup_membrane_topology(), core::scoring::SecondaryStructurePotential::sspair(), core::scoring::store_CSA_in_pose(), core::scoring::store_DC_in_pose(), core::scoring::store_RDC_in_pose(), core::scoring::store_RDC_ROHL_in_pose(), protocols::scoring::store_RDC_segments_in_pose(), core::pose::tag_from_pose(), core::pose::tag_into_pose(), core::scoring::FACTSPotential::update_residue_for_packing(), and core::scoring::GenBornPotential::update_residue_for_packing().

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

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

References data_cache_.

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

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
fnpointer to observer's unary member function with signature void( ConformationEvent const & )
ptrpointer to observer object
Returns
true if disconnect successful, false if connection does not exist

References conformation_obs_hub_.

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

template<typename MemFn , typename Ptr >
bool core::pose::Pose::detach_destruction_obs ( MemFn  fn,
Ptr  ptr 
) const
inline

detach DestructionEvent observer function

Parameters
fnpointer to observer's unary member function with signature void( DestructionEvent const & )
ptrpointer to observer object
Returns
true if disconnect successful, false if connection does not exist
Remarks
DestructionEvent observers will only be notified upon destruction of the Pose

References destruction_obs_hub_.

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

template<typename MemFn , typename Ptr >
bool core::pose::Pose::detach_energy_obs ( MemFn  fn,
Ptr  ptr 
) const
inline

detach EnergyEvent observer function

Parameters
fnpointer to observer's unary member function with signature void( EnergyEvent const & )
ptrpointer to observer object
Returns
true if disconnect successful, false if connection does not exist

References energy_obs_hub_.

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

template<typename MemFn , typename Ptr >
bool core::pose::Pose::detach_general_obs ( MemFn  fn,
Ptr  ptr 
) const
inline

detach GeneralEvent observer function

Parameters
fnpointer to observer's unary member function with signature void( GeneralEvent const & )
ptrpointer to observer object
Returns
true if disconnect successful, false if connection does not exist
Remarks
GeneralEvent observers will be notified whenever any signal derived from GeneralEvent occurs.

References general_obs_hub_.

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

Real core::pose::Pose::dof ( DOF_ID const &  id) const
bool core::pose::Pose::dump_pdb ( std::string const &  file_name,
std::string const &  tag = "1" 
) const

Export pose data to the PDB file <file_name>

example(s): pose.dump_pdb('new_01.pdb') See also: Pose pose_from_pdb

save pose data to file with supplied file_name

References core::io::pdb::FileData::dump_pdb().

Referenced by protocols::topology_broker::ConstraintClaimer::add_constraints(), protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::align_VDW_rep_screen_pose(), protocols::comparative_modeling::AlignmentClustering::AlignmentClustering(), protocols::simple_moves::DumpPdb::apply(), protocols::medal::MedalExchangeMover::apply(), protocols::simple_moves::PDBReloadMover::apply(), protocols::rna::RNA_Minimizer::apply(), protocols::simple_filters::ExternalEvaluator::apply(), protocols::swa::protein::StepWiseProteinPoseSetup::apply(), protocols::swa::rna::StepWiseRNA_PoseSetup::apply(), protocols::loops::loop_mover::IndependentLoopMover::apply(), protocols::enzdes::SecondaryMatchProtocol::apply(), protocols::coarse_rna::CoarseRNA_DeNovoProtocol::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::rna::RNA_DeNovoProtocol::apply(), protocols::flxbb::InterlockAroma::apply(), protocols::simple_moves::sidechain_moves::SidechainMCMover::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::ddg::ddGMover::apply(), protocols::relax::FastRelax::apply(), protocols::simple_moves::GenericMonteCarloMover::apply(), protocols::fldsgn::BluePrintBDR::apply(), protocols::moves::PyMolMover::apply(), protocols::swa::rna::RNA_AnalyticLoopCloser::apply_solutions(), protocols::coarse_rna::CoarseRNA_LoopCloser::apply_solutions(), protocols::simple_moves::GenericMonteCarloMover::boltzmann(), protocols::docking::DockingEnsemble::calculate_highres_ref_energy(), core::scoring::packstat::cavity_distance_constraint(), protocols::rna::MultipleDomainMover::close_all_loops(), protocols::abinitio::AbrelaxApplication::close_loops(), protocols::optimize_weights::IterativeOptEDriver::collect_ddG_of_binding_data(), protocols::optimize_weights::IterativeOptEDriver::collect_ddG_of_mutation_data(), core::pack::compare_mingraph_and_energy_graph(), core::pack::compare_simple_inteaction_graph_alt_state_and_energy_graph(), core::scoring::ResidualDipolarCoupling::compute_dipscore(), protocols::enzdes::PoseFoundResiduesCombination::construct_and_dump_outpose(), protocols::swa::rna::StepWiseRNA_PoseSetup::correctly_copy_HO2star_positions(), protocols::loops::loop_mover::refine::SmallMinCCDTrial::debug_five(), protocols::loops::loop_mover::refine::SmallMinCCDTrial::debug_four(), protocols::loops::loop_mover::refine::SmallMinCCDTrial::debug_one(), protocols::loops::loop_mover::refine::SmallMinCCDTrial::debug_three(), protocols::loops::loop_mover::refine::SmallMinCCDTrial::debug_two(), protocols::loops::loop_mover::refine::SmallMinCCDTrial::debug_zero(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::debugging_output(), protocols::rna::RNA_DeNovoProtocol::do_random_moves(), core::optimization::AtomTreeMultifunc::dump(), core::optimization::CartesianMultifunc::dump(), core::optimization::symmetry::SymAtomTreeMultifunc::dump(), protocols::sic_dock::dump_loophash_linkers(), core::io::pdb::dump_pdb(), protocols::vip::VIP_Mover::dump_pdb_to_file(), protocols::rna::export_packer_results(), protocols::abinitio::AbrelaxApplication::fold(), protocols::swa::rna::RNA_AnalyticLoopCloser::get_all_solutions(), protocols::coarse_rna::CoarseRNA_LoopCloser::get_all_solutions(), protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::get_base_atr_rep_score(), protocols::swa::rna::StepWiseRNA_ResidueSampler::get_base_atr_rep_score(), protocols::vip::VIP_Mover::get_neighbors(), protocols::motifs::IRCollection::incorporate_motifs(), protocols::swa::StepWisePoseSetup::initialize_pose_from_streams(), protocols::rna::RNA_ChunkLibrary::initialize_random_chunks(), protocols::sparta::PDB::loadPDB(), protocols::toolbox::match_enzdes_util::EnzConstraintParameters::make_constraint_covalent(), protocols::swa::rna::StepWiseRNA_PoseSetup::make_pose(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::model_loop(), protocols::forge::build::SegmentRebuild::modify_impl(), protocols::abinitio::MembraneAbinitio::output_debug_structure(), protocols::abinitio::ClassicAbinitio::output_debug_structure(), protocols::protein_interface_design::movers::MapHotspot::output_pose(), core::pose::partition_pose_by_jump(), protocols::cluster::ClusterBase::print_cluster_PDBs(), protocols::rna::MultipleDomainMover::randomize_orientations(), protocols::swa::rna::StepWiseRNA_PoseSetup::read_input_pose_and_copy_dofs(), protocols::ddg::ddGMover::relax_wildtype_structure(), protocols::rna::RNA_LoopCloser::rna_ccd_close(), protocols::swa::protein::StepWiseProteinLoopBridger::sample_omega_recursively(), protocols::sic_dock::LinkerScore::score(), protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure::select_final_loop(), protocols::swa::rna::StepWiseRNA_PoseSetup::setup_native_pose(), core::io::pdb::traced_dump_pdb(), protocols::rna::MultipleDomainMover::try_to_slide_into_contact(), protocols::outputter::PDBOutputter::write(), protocols::dna::write_checkpoint(), protocols::canonical_sampling::PDBTrajectoryRecorder::write_model(), and protocols::flxbb::LayerDesignOperation::write_pymol_script().

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

References core::io::pdb::FileData::dump_pdb().

void core::pose::Pose::dump_scored_pdb ( std::string const &  file_name,
scoring::ScoreFunction const &  scorefxn,
std::string const &  tag = "1" 
)
bool core::pose::Pose::empty ( ) const

Returns true if there are no residues in the conformation.

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

References conformation_.

Referenced by protocols::design_opt::GreedyOptMutationMover::apply().

scoring::Energies const& core::pose::Pose::energies ( ) const
inline

Returns the pose Energies (const-access)

APL Removing illegal non-const accessors to residues which otherwise violate the data-integrity guarantees provided by class Conformation. accessors for iteration over residues THIS MUST BE REMOVED ASAP! example(s): pose.energies() See also: Pose Energies PDBInfo ScoreFunction create_score_function

References energies_.

Referenced by protocols::enzdes::SecondaryMatchProtocol::add_enz_cst_interaction_to_pose(), protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_pose(), protocols::ligand_docking::InterfaceScoreCalculator::add_scores_to_job(), core::scoring::geometric_solvation::add_to_individual_sol_energies(), protocols::toolbox::rotamer_set_operations::RigidBodyMoveBaseRSO::alter_rotamer_set(), protocols::rbsegment_relax::AutoRBMover::apply(), protocols::medal::MedalExchangeMover::apply(), protocols::cluster::GatherPosesMover::apply(), protocols::flexpack::FlexPacker::apply(), protocols::analysis::LoopAnalyzerMover::apply(), protocols::antibody2::AntibodyModelerProtocol::apply(), protocols::simple_moves::ReturnSidechainMover::apply(), protocols::surface_docking::SlideIntoSurface::apply(), protocols::moves::JumpOutMover::apply(), protocols::simple_filters::EvaluatedTrialMover::apply(), protocols::simple_moves::ScoreMover::apply(), protocols::antibody2::RefineOneCDRLoop::apply(), protocols::surface_docking::FaSlideIntoSurface::apply(), protocols::flxbb::InterlockAroma::apply(), protocols::simple_moves::symmetry::SymDockingSlideIntoContact::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::moves::MCShowMover::apply(), protocols::fldsgn::filters::HelixKinkFilter::apply(), protocols::ddg::ddGMover::apply(), protocols::simple_moves::symmetry::FaSymDockingSlideTogether::apply(), protocols::docking::DockingSlideIntoContact::apply(), protocols::moves::TrialMover::apply(), protocols::docking::DockingProtocol::apply(), protocols::docking::FaDockingSlideIntoContact::apply(), protocols::forge::remodel::RemodelLoopMover::apply(), protocols::abinitio::ComputeTotalDistCst::apply(), core::optimization::symmetry::atom_tree_get_atompairE_deriv(), core::optimization::atom_tree_get_atompairE_deriv(), core::scoring::hbonds::HBondEnergy::backbone_backbone_energy(), core::scoring::etable::BaseEtableEnergy< Derived >::backbone_backbone_energy(), core::scoring::hbonds::HBondEnergy::backbone_sidechain_energy(), core::scoring::etable::BaseEtableEnergy< Derived >::backbone_sidechain_energy(), protocols::moves::MonteCarlo::boltzmann(), core::pack::rotamer_set::RotamerSet_::build_rotamers_for_concrete(), protocols::features::helixAssembly::HelixBundleFeatures::calc_fa_energy(), protocols::flexpep_docking::FlexPepDockingPoseMetrics::calc_pep_scores(), protocols::analysis::InterfaceAnalyzerMover::calc_per_residue_energy(), protocols::scoring::Interface::calculate(), core::scoring::methods::LK_hack::calculate_derivatives_for_atoms_and_pseudo_base_atoms(), core::optimization::cartesian_collect_atompairE_deriv(), protocols::fldsgn::BluePrintBDR::centroid_build(), protocols::forge::components::BDR::centroid_build(), protocols::forge::remodel::RemodelMover::centroid_build(), protocols::forge::components::VarLengthBuild::centroid_build(), protocols::ub_e2c::ubi_e2c_modeler::centroid_filter(), protocols::swa::rna::StepWiseRNA_ResidueSampler::Chain_break_screening_general(), protocols::swa::rna::RNA_LoopCloseSampler::check_clash(), protocols::fldsgn::topology::check_internal_hbonds(), protocols::fldsgn::topology::check_kink_helix(), protocols::enzdes::PackRotamersMoverPartGreedy::choose_n_best(), core::scoring::rna::RNA_PairwiseLowResolutionEnergy::clean_up_rna_two_body_energy_tables(), protocols::optimize_weights::IterativeOptEDriver::collect_ddG_of_binding_data(), protocols::optimize_weights::IterativeOptEDriver::collect_ddG_of_mutation_data(), core::pack::compare_mingraph_and_energy_graph(), core::pack::compare_simple_inteaction_graph_alt_state_and_energy_graph(), protocols::simple_filters::ResidueSetChainEnergyFilter::compute(), protocols::fldsgn::filters::CoreDunbrackFilter::compute(), protocols::fldsgn::filters::InterlockingAromaFilter::compute(), protocols::enzdes::RepackWithoutLigandFilter::compute(), protocols::simple_moves::GreenPacker::compute_absent_energies(), protocols::sasa_scores::compute_avge_scores(), core::scoring::EnvPairPotential::compute_centroid_environment(), core::scoring::SmoothEnvPairPotential::compute_centroid_environment(), core::scoring::SmoothEnvPairPotential::compute_dcentroid_environment(), protocols::features::StructureScoresFeatures::compute_energies(), protocols::hybridization::CartesianSampler::compute_fragment_bias(), protocols::toolbox::pose_metric_calculators::NumberHBondsCalculator::compute_Hbonds_for_residue(), protocols::analysis::InterfaceAnalyzerMover::compute_interface_energy(), protocols::enzdes::EnzdesScorefileFilter::compute_metrics_for_residue_subset(), core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::compute_one_body_energies(), core::pack::rotamer_set::RotamerSet_::compute_one_body_energies(), protocols::flexpack::rotamer_set::FlexbbRotamerSets::compute_one_body_energies_for_otf_ig(), core::pack::rotamer_set::RotamerSet_::compute_one_body_energy_maps(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_polar_group_sol_energy(), core::pack::interaction_graph::SurfacePotential::compute_pose_surface_energy(), core::pack::interaction_graph::SurfacePotential::compute_residue_surface_energy(), protocols::enzdes::LigInterfaceEnergyFilter::constraint_energy(), core::scoring::symmetry::SymmetricScoreFunction::correct_finalize_score(), core::pack::create_minimization_graph(), core::pack::create_packer_graph(), core::scoring::hbonds::HBondEnergy::create_rotamer_trie(), protocols::loops::loop_mover::refine::SmallMinCCDTrial::debug_five(), protocols::loops::loop_mover::refine::SmallMinCCDTrial::debug_four(), protocols::loops::loop_mover::refine::SmallMinCCDTrial::debug_one(), protocols::loops::loop_mover::refine::SmallMinCCDTrial::debug_three(), protocols::loops::loop_mover::refine::SmallMinCCDTrial::debug_two(), protocols::loops::loop_mover::refine::SmallMinCCDTrial::debug_zero(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::debugging_output(), core::scoring::disulfides::DisulfideMatchingEnergy::defines_residue_pair_energy(), core::scoring::disulfides::CentroidDisulfideEnergy::defines_residue_pair_energy(), core::scoring::disulfides::FullatomDisulfideEnergy::defines_residue_pair_energy(), protocols::forge::components::BDR::design_refine(), protocols::forge::remodel::RemodelMover::design_refine(), protocols::forge::remodel::RemodelMover::design_refine_seq_relax(), protocols::enzdes::EnzdesBaseProtocol::design_targets_score(), protocols::toolbox::match_enzdes_util::EnzConstraintParameters::determine_best_constraint(), protocols::toolbox::pose_metric_calculators::NumberHBondsCalculator::determine_res_to_recompute(), protocols::symmetric_docking::SymDockProtocol::docking_highres_filter(), protocols::symmetric_docking::SymDockProtocol::docking_lowres_filter(), core::optimization::AtomTreeMultifunc::dump(), core::optimization::CartesianMultifunc::dump(), core::optimization::symmetry::SymAtomTreeMultifunc::dump(), dump_scored_pdb(), protocols::jobdist::PlainPdbJobDistributor::dump_scores(), core::io::silent::SilentStruct::energies_from_pose(), core::io::silent::SilentStruct::energies_into_pose(), core::pose::energy_from_pose(), core::scoring::disulfides::FullatomDisulfideEnergy::ensure_lrenergy_container_is_up_to_date(), core::scoring::methods::Fa_MbsolvEnergy::eval_atom_derivative(), core::scoring::rna::RNA_LJ_BaseEnergy::eval_atom_derivative(), core::scoring::methods::MMLJEnergyIntra::eval_atom_derivative(), core::scoring::methods::EnvSmoothEnergy::eval_atom_derivative(), core::scoring::hackaro::HackAroEnergy::eval_atom_derivative(), core::scoring::methods::MembraneEnvSmoothEnergy::eval_atom_derivative(), core::scoring::methods::LK_CosThetaEnergy::eval_atom_derivative(), core::scoring::rna::RNA_FullAtomStackingEnergy::eval_atom_derivative(), core::scoring::methods::HybridVDW_Energy::eval_atom_derivative(), core::scoring::methods::VDW_Energy::eval_atom_derivative(), core::scoring::rna::RNA_DataBackboneEnergy::eval_atom_derivative(), core::scoring::rna::RNA_VDW_Energy::eval_atom_derivative(), core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy::eval_atom_derivative(), core::scoring::methods::WaterAdductHBondEnergy::eval_atom_derivative(), core::scoring::geometric_solvation::GeometricSolEnergy::eval_atom_derivative(), core::scoring::methods::MMLJEnergyInter::eval_atom_derivative(), core::scoring::hackelec::HackElecEnergyAroAll::eval_atom_derivative(), core::scoring::hackelec::HackElecEnergyAroAro::eval_atom_derivative(), core::scoring::hackelec::RNAHackElecEnergy::eval_atom_derivative(), core::scoring::etable::BaseEtableEnergy< Derived >::eval_atom_derivative(), core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_base_base(), core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_rna_backbone_backbone(), core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_rna_base_backbone(), core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_rna_repulsive(), core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy::eval_atom_energy(), core::scoring::geometric_solvation::GeometricSolEnergy::eval_atom_energy(), core::scoring::symmetry::SymmetricScoreFunction::eval_dof_derivative(), core::scoring::ScoreFunction::eval_dof_derivative(), core::scoring::hbonds::HBondEnergy::eval_intrares_derivatives(), core::scoring::etable::BaseEtableEnergy< Derived >::eval_intrares_derivatives(), core::scoring::etable::TableLookupEtableEnergy::eval_intrares_energy(), core::scoring::etable::AnalyticEtableEnergy::eval_intrares_energy(), core::scoring::etable::BaseEtableEnergy< Derived >::eval_intrares_energy_ext(), core::scoring::symmetry::SymmetricScoreFunction::eval_long_range_twobody_energies(), core::scoring::ScoreFunction::eval_long_range_twobody_energies(), core::scoring::symmetry::SymmetricScoreFunction::eval_npd_atom_derivative(), core::scoring::ScoreFunction::eval_npd_atom_derivative(), core::scoring::OmegaTether::eval_omega_score_all(), core::scoring::symmetry::SymmetricScoreFunction::eval_onebody_energies(), core::scoring::ScoreFunction::eval_onebody_energies(), core::scoring::Ramachandran::eval_rama_score_all(), core::scoring::Ramachandran2B::eval_rama_score_all(), core::scoring::methods::PairEnergy::eval_residue_pair_derivatives(), core::scoring::hbonds::HBondEnergy::eval_residue_pair_derivatives(), core::scoring::etable::BaseEtableEnergy< Derived >::eval_residue_pair_derivatives(), core::scoring::symmetry::SymmetricScoreFunction::eval_twobody_neighbor_energies(), core::scoring::ScoreFunction::eval_twobody_neighbor_energies(), protocols::multistate_design::SingleStateFitnessFunction::evaluate(), protocols::abinitio::ConstraintFragmentSampler::evaluate_constraint_energy(), protocols::abinitio::FoldConstraints::evaluate_constraint_energy(), core::scoring::methods::MMLJEnergyInter::evaluate_rotamer_background_energies(), core::scoring::hackelec::HackElecEnergy::evaluate_rotamer_background_energies(), core::scoring::hbonds::HBondEnergy::evaluate_rotamer_background_energies(), core::scoring::etable::BaseEtableEnergy< Derived >::evaluate_rotamer_background_energies(), core::scoring::hbonds::HBondEnergy::evaluate_rotamer_pair_energies(), protocols::enzdes::EnzdesScorefileFilter::examine_pose(), protocols::LoopRebuild::extend_barcode_regions_if_chain_break(), protocols::enzdes::EnzdesFlexibleRegion::extract_lig_designability_score(), core::io::pdb::extract_scores(), protocols::swa::protein::StepWiseProteinPacker::figure_out_neighbors(), protocols::swa::protein::StepWiseProteinResidueSampler::figure_out_neighbors(), protocols::simple_moves::ddG::fill_energy_vector(), core::scoring::WaterAdductHBondPotential::fill_h2o_hbond_set(), core::scoring::hbonds::fill_hbond_set(), core::scoring::hbonds::fill_hbond_set_by_AHdist_threshold(), protocols::simple_moves::ddG::fill_per_residue_energy_vector(), core::io::silent::BinaryProteinSilentStruct::fill_pose(), protocols::swa::protein::StepWiseProteinFilterer::filter(), protocols::swa::StepWiseFilterer::filter(), core::pack::interaction_graph::SurfaceEnergy::finalize_total_energy(), core::pack::interaction_graph::HPatchEnergy::finalize_total_energy(), core::scoring::hackelec::HackElecEnergy::finalize_total_energy(), core::scoring::hbonds::HBondEnergy::finalize_total_energy(), core::scoring::etable::BaseEtableEnergy< Derived >::finalize_total_energy(), protocols::swa::rna::floating_base_chain_break_screening(), protocols::swa::rna::floating_base_chain_closure_setup(), protocols::swa::rna::floating_base_full_atom_van_der_Waals_screening(), protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::Full_atom_van_der_Waals_screening(), protocols::swa::rna::StepWiseRNA_ResidueSampler::Full_atom_van_der_Waals_screening(), protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::Full_atom_van_der_Waals_screening_REPLICATE(), protocols::swa::rna::StepWiseRNA_ResidueSampler::Full_atom_van_der_Waals_screening_REPLICATE(), protocols::ub_e2c::ubi_e2c_modeler::fullatom_filter(), protocols::enzdes::EnzdesFlexBBProtocol::generate_alc_ensemble_for_region(), protocols::enzdes::EnzdesFlexibleRegion::get_12A_neighbors(), core::scoring::geometric_solvation::GeometricSolEnergy::get_atom_atom_geometric_solvation_for_acceptor(), core::scoring::geometric_solvation::GeometricSolEnergy::get_atom_atom_geometric_solvation_for_donor(), protocols::features::get_current_model_score(), protocols::vip::VIP_Report::get_GOE_relaxed_report(), protocols::vip::VIP_Report::get_GOE_repack_report(), protocols::optimize_weights::IterativeOptEDriver::get_nat_aa_opte_data(), protocols::ligand_docking::LigandBaseProtocol::get_non_bb_clashing_rotamers(), protocols::nonlocal::get_per_residue_score(), protocols::relax::get_per_residue_scores(), protocols::swa::monte_carlo::RNA_O2StarMover::get_random_o2star_residue_near_moving_residue(), protocols::enzdes::EnzdesFlexibleRegion::get_region_mm_bend_score(), protocols::enzdes::EnzdesFlexibleRegion::get_region_total_score(), protocols::simple_filters::ScoreCutoffFilter::get_score(), core::scoring::ScoreFunction::get_sub_score(), core::scoring::ScoreFunction::get_sub_score_exclude_res(), protocols::enzdes::EnzdesFlexBBProtocol::get_tenA_neighbor_residues(), protocols::loops::get_tenA_neighbor_residues(), protocols::enzdes::PackRotamersMoverPartGreedy::greedy_around(), core::scoring::SecondaryStructurePotential::hspair(), protocols::motifs::MotifSearch::incorporate_motifs(), protocols::motifs::LigandMotifSearch::incorporate_motifs(), protocols::features::HBondFeatures::insert_hbond_dehydron_row(), protocols::features::ResidueTotalScoresFeatures::insert_residue_total_scores_rows(), protocols::features::ResidueScoresFeatures::insert_two_body_long_range_residue_score_rows(), protocols::features::ResidueScoresFeatures::insert_two_body_residue_score_rows(), protocols::simple_filters::RotamerBoltzmannWeight::interface_interaction_energy(), core::scoring::symmetry::SymmetricScoreFunction::intersubunit_hbond_energy(), protocols::swa::protein::StepWiseProteinPoseMinimizer::let_neighboring_chis_minimize(), core::pose::symmetry::make_asymmetric_pose(), core::pose::symmetry::make_symmetric_pose(), core::import_pose::atom_tree_diffs::map_of_weighted_scores(), core::scoring::electron_density::ElectronDensity::matchPoseToPatterson(), core::scoring::electron_density::ElectronDensity::matchRes(), core::pack::min_pack(), core::scoring::etable::BaseEtableEnergy< Derived >::minimize_in_whole_structure_context(), core::scoring::hackelec::HackElecEnergy::minimize_in_whole_structure_context(), protocols::enzdes::EnzdesFlexibleRegion::minimize_region(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_Moves::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::model_loop(), protocols::loop_build::LoopMover_SlidingWindow::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::model_loop(), protocols::match::NumNeighborsMPM::modified_match_positions(), protocols::forge::build::BuildInstruction::modify(), protocols::ub_e2c::ubi_e2c_modeler::monoub_centroid_filter(), protocols::ub_e2c::ubi_e2c_modeler::monoub_fullatom_filter(), core::scoring::disulfides::FullatomDisulfideEnergy::old_eval_atom_derivative(), core::optimization::SingleResidueMultifunc::operator()(), core::scoring::DockingScoreFunction::operator()(), core::scoring::MinScoreScoreFunction::operator()(), core::scoring::symmetry::SymmetricScoreFunction::operator()(), core::scoring::ScoreFunction::operator()(), protocols::simple_filters::ScoreCutoffFilter::output_residue_pair_energies(), protocols::frag_picker::FragmentCandidate::output_silent(), core::pack::rotamer_set::symmetry::SymmetricRotamerSets::precompute_two_body_energies(), core::pack::rotamer_set::RotamerSets::precompute_two_body_energies(), core::scoring::constraints::ConstraintsEnergy::prepare_constraints_energy_container(), core::pack::rotamer_set::RotamerSets::prepare_otf_graph(), core::pack::rotamer_set::symmetry::SymmetricRotamerSets::prepare_symm_otf_interaction_graph(), protocols::optimize_weights::IterativeOptEDriver::print_energies(), protocols::scoring::Interface::protein_calculate(), core::pose::metrics::simple_calculators::InterfaceDeltaEnergeticsCalculator::recompute(), protocols::toolbox::pose_metric_calculators::NonlocalContactsCalculator::recompute(), protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator::recompute(), protocols::vip::VIP_Mover::relax_favorable_poses(), protocols::ddg::ddGMover::relax_wildtype_structure(), protocols::toolbox::pose_manipulation::remove_non_protein_residues(), protocols::simple_filters::EnergyPerResidueFilter::report(), protocols::simple_filters::ScoreCutoffFilter::report(), protocols::features::AtomInResidueAtomInResiduePairFeatures::report_atom_pairs(), protocols::features::AtomAtomPairFeatures::report_atom_pairs(), protocols::features::ResidueBurialFeatures::report_features(), protocols::features::ProteinBackboneAtomAtomPairFeatures::report_features(), protocols::features::HBondFeatures::report_features(), protocols::features::PairFeatures::report_residue_pairs(), core::scoring::methods::BurialEnergy::residue_energy(), core::scoring::nv::NVscore::residue_energy(), core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::residue_energy(), core::scoring::methods::EnvSmoothEnergy::residue_energy(), core::scoring::methods::MembraneEnvSmoothEnergy::residue_energy(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::residue_energy(), protocols::optimize_weights::IterativeOptEDriver::residue_has_unacceptably_bad_dunbrack_energy(), core::scoring::disulfides::DisulfideMatchingEnergy::residue_pair_energy(), core::scoring::disulfides::CentroidDisulfideEnergy::residue_pair_energy(), core::scoring::methods::PairEnergy::residue_pair_energy(), core::scoring::hbonds::HBondEnergy::residue_pair_energy(), core::scoring::hackelec::HackElecEnergy::residue_pair_energy(), core::scoring::disulfides::FullatomDisulfideEnergy::residue_pair_energy(), core::scoring::etable::BaseEtableEnergy< Derived >::residue_pair_energy(), core::scoring::etable::BaseEtableEnergy< Derived >::residue_pair_energy_ext(), protocols::forge::methods::restore_residues(), core::pack::RTMin::rtmin(), core::optimization::symmetry::SymAtomTreeMinimizer::run(), core::optimization::CartesianMinimizer::run(), core::optimization::AtomTreeMinimizer::run(), protocols::fldsgn::potentials::sspot::HSPairPotential::score(), protocols::fldsgn::potentials::sspot::SSPairPotential::score(), protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential::score(), protocols::moves::MonteCarlo::score_function(), protocols::optimize_weights::IterativeOptEDriver::score_ligand_interface(), protocols::jd2::ScoreMap::score_map_from_scored_pose(), protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::semiexpl_water_hbgeom_score(), protocols::moves::PyMolMover::send_energy(), protocols::vip::set_local_movemap(), core::scoring::symmetry::SymmetricScoreFunction::set_symmetric_residue_neighbors_hbonds(), core::io::sequence_comparation::DesignContrast::setNeighbors(), protocols::simple_moves::symmetry::SymEnergyCutRotamerTrialsMover::setup_energycut_task(), protocols::simple_moves::EnergyCutRotamerTrialsMover::setup_energycut_task(), protocols::simple_moves::EnergyCutRotamerTrialsMinMover::setup_energycut_task(), core::scoring::methods::WaterAdductHBondEnergy::setup_for_derivatives(), core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy::setup_for_derivatives(), core::scoring::methods::EnvSmoothEnergy::setup_for_derivatives(), core::scoring::geometric_solvation::GeometricSolEnergy::setup_for_derivatives(), core::scoring::methods::MembraneEnvSmoothEnergy::setup_for_derivatives(), core::scoring::symmetry::SymmetricScoreFunction::setup_for_derivatives(), core::scoring::etable::BaseEtableEnergy< Derived >::setup_for_derivatives(), core::scoring::ScoreFunction::setup_for_derivatives(), core::scoring::methods::MMLJEnergyIntra::setup_for_minimizing(), core::scoring::methods::MMLJEnergyInter::setup_for_minimizing(), core::scoring::symmetry::SymmetricScoreFunction::setup_for_minimizing(), core::scoring::hackelec::HackElecEnergy::setup_for_minimizing(), core::scoring::etable::BaseEtableEnergy< Derived >::setup_for_minimizing(), core::scoring::ScoreFunction::setup_for_minimizing(), core::scoring::ScoreFunction::setup_for_minimizing_for_node(), core::scoring::hbonds::HBondEnergy::setup_for_minimizing_for_residue(), core::scoring::etable::BaseEtableEnergy< Derived >::setup_for_minimizing_for_residue(), core::scoring::etable::BaseEtableEnergy< Derived >::setup_for_minimizing_for_residue_pair(), core::scoring::methods::MMLJEnergyInter::setup_for_packing(), core::scoring::hbonds::HBondEnergy::setup_for_packing(), core::scoring::hackelec::HackElecEnergy::setup_for_packing(), core::scoring::etable::BaseEtableEnergy< Derived >::setup_for_packing(), core::scoring::hbonds::HBondSet::setup_for_residue_pair_energies(), core::scoring::sym_e::symEnergy::setup_for_scoring(), core::scoring::disulfides::DisulfideMatchingEnergy::setup_for_scoring(), core::scoring::disulfides::CentroidDisulfideEnergy::setup_for_scoring(), core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy::setup_for_scoring(), core::scoring::electron_density::PattersonCorrEnergy::setup_for_scoring(), core::scoring::geometric_solvation::GeometricSolEnergy::setup_for_scoring(), core::scoring::electron_density::ElecDensEnergy::setup_for_scoring(), core::scoring::methods::dfire::DFIRE_Energy::setup_for_scoring(), core::scoring::electron_density::FastDensEnergy::setup_for_scoring(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::setup_for_scoring(), core::scoring::electron_density::ElecDensCenEnergy::setup_for_scoring(), core::scoring::methods::FACTSEnergy::setup_for_scoring(), core::scoring::hackelec::HackElecEnergy::setup_for_scoring(), core::scoring::methods::GenBornEnergy::setup_for_scoring(), core::scoring::methods::PoissonBoltzmannEnergy::setup_for_scoring(), core::scoring::hbonds::HBondEnergy::setup_for_scoring(), core::scoring::electron_density_atomwise::ElecDensAtomwiseEnergy::setup_for_scoring(), core::scoring::etable::BaseEtableEnergy< Derived >::setup_for_scoring(), core::scoring::FACTSPotential::setup_for_scoring(), core::scoring::methods::CartesianBondedEnergy::setup_for_scoring(), core::scoring::ScoreFunction::setup_for_scoring(), core::scoring::ScoreFunction::show(), core::scoring::ScoreFunction::show_line(), core::scoring::hbonds::HBondEnergy::sidechain_sidechain_energy(), core::scoring::etable::BaseEtableEnergy< Derived >::sidechain_sidechain_energy(), protocols::optimize_weights::IterativeOptEDriver::single_structure_data_for_pose(), protocols::simple_moves::symmetry::SymmetrySlider::slide_score(), protocols::vip::VIP_Mover::sort_fill_energies(), core::scoring::SecondaryStructurePotential::sspair(), protocols::ddg::ddGMover::store_energies(), protocols::motifs::IRCollection::successful_loop_closure(), protocols::enzdes::enzutil::sum_constraint_scoreterms(), protocols::protein_interface_design::sum_total_residue_energy(), core::util::switch_to_residue_type_set(), protocols::scoring::Interface::symmetric_protein_calculate(), core::scoring::symmetry::SymmetricScoreFunction::symmetrical_allow_hbonds(), protocols::simple_moves::symmetry::SymmetrySlider::SymmetrySlider(), core::optimization::symmetry::SymMinimizerMap::SymMinimizerMap(), core::pose::total_energy_from_pose(), protocols::vip::VIP_Mover::try_point_mutants(), protocols::canonical_sampling::MetricRecorder::update_after_boltzmann(), core::scoring::methods::MMLJEnergyInter::update_residue_for_packing(), core::scoring::hbonds::HBondEnergy::update_residue_for_packing(), core::scoring::hackelec::HackElecEnergy::update_residue_for_packing(), core::scoring::etable::BaseEtableEnergy< Derived >::update_residue_for_packing(), core::scoring::rna::RNA_LowResolutionPotential::update_rna_base_base_interactions(), protocols::features::ProteinSilentReport::write_full_report(), and protocols::canonical_sampling::PDBTrajectoryRecorder::write_model().

scoring::Energies& core::pose::Pose::energies ( )
inline

Returns the pose Energies (non-const access)

References energies_.

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

Returns the epsilon torsion angle of residue <seqpos>

Note
assumes the residue is an nucleic acid

example(s): pose.epsilon(5) See also: Pose Pose.residue Pose.set_epsilon Residue

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

kinematics::FoldTree const & core::pose::Pose::fold_tree ( ) const

Returns the pose FoldTree.

example(s): pose.fold_tree() See also: Pose FoldTree

References conformation_.

Referenced by protocols::swa::rna::StepWiseRNA_PoseSetup::add_aa_virt_rsd_as_root(), protocols::abinitio::KinematicControl::add_chainbreak_variants(), protocols::topology_broker::TopologyBroker::add_chainbreak_variants(), protocols::toolbox::pose_manipulation::add_chainbreaks_according_to_jumps(), protocols::topology_broker::ConstraintClaimer::add_constraints(), protocols::relax::add_coordinate_constraints_to_pose(), protocols::loops::add_coordinate_constraints_to_pose(), core::util::add_cutpoint_variants(), protocols::forge::methods::add_cutpoint_variants(), protocols::loops::add_cutpoint_variants(), protocols::rna::RNA_StructureParameters::add_new_RNA_jump(), protocols::abinitio::MembraneAbinitio::add_spanning_region(), protocols::swa::rna::StepWiseRNA_PoseSetup::add_terminal_res_repulsion(), protocols::swa::StepWisePoseSetup::add_terminal_res_repulsion(), core::pose::addVirtualResAsRoot(), protocols::topology_broker::MembraneTopologyClaimer::addVirtualResAsRootMembrane(), protocols::antibody::Antibody::all_cdr_fold_tree(), protocols::antibody::AntibodyModeler::all_cdr_VL_VH_fold_tree(), protocols::antibody::CDRH3Modeler::antibody_modeling_insert_ter(), protocols::ligand_docking::LigandDockProtocol::append_ligand_docking_scores(), protocols::ligand_docking::append_multi_residue_ligand_RMSD(), protocols::ligand_docking::append_radius_of_gyration(), protocols::toolbox::pose_metric_calculators::append_rsd_by_jump_near_atom(), protocols::RBSegmentRelaxImpl::apply(), protocols::loops::FoldTreeFromLoops::apply(), protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspots::apply(), protocols::seeded_abinitio::CoordinateCst::apply(), protocols::seeded_abinitio::DefineMovableLoops::apply(), protocols::protein_interface_design::movers::AddChainBreak::apply(), protocols::seeded_abinitio::CAcstGenerator::apply(), protocols::seeded_abinitio::GrowPeptides::apply(), protocols::simple_moves::SwitchChainOrderMover::apply(), protocols::star::StarAbinitio::apply(), protocols::medal::MedalExchangeMover::apply(), protocols::protein_interface_design::movers::DockAndRetrieveSidechains::apply(), protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover::apply(), protocols::rigid::RigidBodyMotionMover::apply(), protocols::antibody2::CloseOneCDRLoop::apply(), protocols::protein_interface_design::movers::SetAtomTree::apply(), protocols::protein_interface_design::movers::SpinMover::apply(), protocols::seeded_abinitio::CloseFold::apply(), protocols::simple_moves::PeptideStapleMover::apply(), protocols::seeded_abinitio::SeedFoldTree::apply(), protocols::loops::loop_closure::ccd::ShortLoopClosure::apply(), protocols::medal::MedalMover::apply(), protocols::enzdes::BackboneSampler::apply(), protocols::dna::SeparateDnaFromNonDna::apply(), protocols::simple_moves::MissingDensityToJumpMover::apply(), protocols::dna::DesignProteinBackboneAroundDNA::apply(), protocols::rigid::RotateJumpAxisMover::apply(), protocols::nonlocal::SheetTranslate::apply(), protocols::domain_assembly::AssembleLinkerMover::apply(), protocols::protein_interface_design::movers::BackrubDDMover::apply(), protocols::ligand_docking::FinalMinimizer::apply(), protocols::nonlocal::HelixRotate::apply(), protocols::ligand_docking::MinimizeBackbone::apply(), protocols::loops::loop_mover::IndependentLoopMover::apply(), protocols::swa::rna::StepWiseRNA_PoseSetup::apply(), protocols::antibody2::AntibodyModelerProtocol::apply(), protocols::antibody2::SnugDockProtocol::apply(), protocols::rna::RNA_HelixAssembler::apply(), protocols::protein_interface_design::movers::DesignMinimizeHbonds::apply(), protocols::abinitio::AbrelaxMover::apply(), protocols::coarse_rna::CoarseRNA_LoopCloser::apply(), protocols::antibody2::H3CterInsert::apply(), protocols::moves::ChangeFoldTreeMover::apply(), protocols::antibody2::SnugDock::apply(), protocols::floppy_tail::FloppyTailMover::apply(), protocols::enzdes::EnzRepackMinimize::apply(), protocols::coarse_rna::CoarseRNA_DeNovoProtocol::apply(), protocols::antibody2::H3PerturbCCD::apply(), protocols::nonlocal::BiasedFragmentMover::apply(), protocols::rbsegment_relax::RBSegmentRelax::apply(), protocols::protein_interface_design::movers::LoopMoverFromCommandLine::apply(), protocols::hybridization::CartesianHybridize::apply(), protocols::ligand_docking::LigandDockProtocol::apply(), protocols::protein_interface_design::movers::LoopRemodel::apply(), protocols::hybridization::DomainAssembly::apply(), protocols::protein_interface_design::movers::TryRotamers::apply(), core::pack::task::operation::DockingNoRepack1::apply(), protocols::protein_interface_design::movers::PlaceStubMover::apply(), protocols::abinitio::KinematicTaskControl::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::apply(), protocols::docking::DockMCMProtocol::apply(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::apply(), protocols::backrub::BackrubMover::apply(), protocols::abinitio::KinematicAbinitio::apply(), protocols::nonlocal::SingleFragmentMover::apply(), protocols::enzdes::DetectProteinLigandInterface::apply(), protocols::backrub::BackrubSidechainMover::apply(), protocols::docking::InterfaceSidechainMinMover::apply(), core::pack::task::operation::DockingNoRepack2::apply(), protocols::docking::TemperedDocking::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::protein_interface_design::movers::Splice::apply(), protocols::idealize::IdealizeMover::apply(), protocols::abinitio::FoldConstraints::apply(), protocols::abinitio::ConstraintFragmentSampler::apply(), protocols::relax::FastRelax::apply(), protocols::fldsgn::CircularPermutation::apply(), protocols::grafting::AnchoredGraftMover::apply(), protocols::topology_broker::TopologyBroker::apply(), protocols::docking::DockingProtocol::apply(), core::fragment::DownJumpSRFD::apply(), protocols::abinitio::JumpingFoldConstraintsWrapper::apply(), protocols::antibody::LoopRlxMover::apply(), protocols::LoopRefine::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::forge::remodel::RemodelLoopMover::apply(), protocols::forge::components::VarLengthBuild::apply(), protocols::coarse_rna::CoarseRNA_LoopCloser::apply_after_jump_change(), protocols::simple_moves::WobbleMover::apply_fragment(), protocols::hybridization::CartesianSampler::apply_frame(), protocols::loops::apply_sequence_mapping(), protocols::loophash::BackboneSegment::apply_to_pose(), protocols::swa::rna::apply_virtual_rna_residue_variant_type(), core::optimization::symmetry::atom_tree_get_atompairE_deriv(), protocols::idealize::basic_idealize(), protocols::forge::remodel::RemodelLoopMover::boost_closure_stage(), protocols::ligand_docking::MoveMapBuilder::build(), protocols::LoopRebuild::build_random_loops(), core::scoring::sc::MolecularSurfaceCalculator::Calc(), protocols::docking::calc_Fnat(), protocols::docking::calc_Irmsd(), protocols::docking::calc_Lrmsd(), protocols::scoring::Interface::calculate(), protocols::analysis::LoopAnalyzerMover::calculate_all_chainbreaks(), protocols::geometry::centroids_by_jump(), protocols::geometry::centroids_by_jump_int(), protocols::topology_broker::TopologyBroker::check_chainbreak_variants(), protocols::rna::RNA_ChunkLibrary::check_connections(), protocols::rna::ChunkSet::check_fold_tree_OK(), protocols::rna::RNA_ChunkLibrary::check_jump_match(), protocols::coarse_rna::CoarseRNA_DeNovoProtocol::check_new_pairing_dists(), protocols::swa::StepWisePoseSetup::check_superimpose_res(), protocols::jumping::close_chainbreaks(), protocols::antibody::CloseOneMover::close_one_loop_stem(), protocols::abinitio::AbrelaxMover::close_with_idealization(), core::coarse::TranslatorSet::coarsify(), protocols::protein_interface_design::filters::AtomicContactCountFilter::compute(), protocols::simple_filters::ShapeComplementarityFilter::compute(), core::scoring::ResidualDipolarCoupling::compute_dipscore(), core::scoring::ResidualDipolarCoupling::compute_dipscore_nls(), core::scoring::ResidualDipolarCoupling::compute_dipscore_nlsDa(), core::scoring::ResidualDipolarCoupling::compute_dipscore_nlsDaR(), core::scoring::ResidualDipolarCoupling::compute_dipscore_nlsR(), core::scoring::compute_jump_rmsd(), protocols::optimize_weights::IterativeOptEDriver::compute_rotamers_around_ligands(), core::scoring::electron_density::ElectronDensity::compute_symm_rotations(), protocols::forge::remodel::RemodelMover::confirm_sequence(), protocols::protein_interface_design::movers::copy_hotspot_to_pose(), protocols::topology_broker::copy_internal_coords(), protocols::protein_interface_design::movers::copy_stretch(), protocols::swa::rna::copy_torsions_FROM_TO(), protocols::forge::methods::count_cutpoints(), protocols::docking::DockTaskFactory::create_and_attach_task_factory(), protocols::enzdes::EnzdesBaseProtocol::create_enzdes_movemap(), protocols::ligand_docking::MinimizeBackbone::create_fold_tree_with_ligand_jumps_from_attach_pts(), protocols::medal::MedalMover::create_fragment_and_rigid_mover(), protocols::hybridization::create_fragment_set(), protocols::rna::create_rna_vall_torsions(), core::pose::create_subpose(), protocols::enzdes::EnzdesBaseProtocol::cst_minimize(), protocols::forge::components::BDR::design_refine(), protocols::forge::remodel::RemodelMover::design_refine(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::determine_loop(), protocols::enzdes::DiversifyStoredRBConfs::diversify_all_confs(), protocols::medal::MedalMover::do_loop_closure(), protocols::toolbox::pose_metric_calculators::dock_waters_to_atom(), protocols::topology_broker::AsymFoldandDockClaimer::docking_jump(), protocols::electron_density::dockPoseIntoMap(), protocols::hybridization::downstream_residues_from_jump(), core::import_pose::atom_tree_diffs::dump_atom_tree_diff(), protocols::anchored_design::dump_cutpoint_info(), protocols::abinitio::KinematicAbinitio::dump_jump_log(), protocols::viewer::dump_pose_kinemage(), core::import_pose::atom_tree_diffs::dump_reference_pose(), protocols::simple_moves::ClassicFragmentMover::end_bias_check(), core::scoring::methods::ChainbreakEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensCenEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensEnergy::eval_atom_derivative(), core::scoring::electron_density::FastDensEnergy::eval_atom_derivative(), core::scoring::methods::CartesianBondedEnergy::eval_intraresidue_dof_derivative(), core::scoring::methods::CartesianBondedEnergy::eval_residue_pair_derivatives(), protocols::LoopRebuild::extend_barcode_regions_if_chain_break(), protocols::star::Extender::extend_unaligned(), core::pose::symmetry::extract_asymmetric_unit(), protocols::loophash::LoopHashLibrary::extract_data_from_pose(), protocols::seeded_abinitio::CloseFold::fast_loopclose(), protocols::coarse_rna::CoarseRNA_LoopCloser::figure_out_dof_ids_and_offsets(), protocols::swa::protein::StepWiseProteinLoopBridger::figure_out_loop(), protocols::swa::rna::StepWiseRNA_Minimizer::Figure_out_moving_residues(), protocols::swa::Figure_out_moving_residues(), protocols::swa::StepWisePoseSetup::figure_out_partition_definition(), protocols::swa::StepWisePoseSetup::figure_out_Prepend_Internal(), protocols::rna::figure_out_reasonable_rna_fold_tree(), protocols::coarse_rna::CoarseRNA_LoopCloser::figure_out_which_cutpoints_were_affected(), protocols::hotspot_hashing::HotspotStubSet::fill(), core::io::silent::BinaryRNASilentStruct::fill_pose(), core::io::silent::BinaryProteinSilentStruct::fill_pose(), core::io::silent::ProteinSilentStruct_Template< T >::fill_pose(), core::io::silent::RNA_SilentStruct::fill_pose(), core::io::silent::BinaryRNASilentStruct::fill_struct(), core::io::silent::BinaryProteinSilentStruct::fill_struct(), core::io::silent::ProteinSilentStruct_Template< T >::fill_struct(), core::io::silent::RNA_SilentStruct::fill_struct(), protocols::docking::DockingEnsemblePrepackProtocol::finalize_setup(), protocols::antibody2::CDRsMinPackMin::finalize_setup(), protocols::antibody2::RefineBetaBarrel::finalize_setup(), protocols::antibody2::H3RefineCCD::finalize_setup(), protocols::docking::TemperedDocking::finalize_setup(), protocols::antibody2::AntibodyModelerProtocol::finalize_setup(), protocols::docking::DockingProtocol::finalize_setup(), core::scoring::methods::ChainbreakEnergy::finalize_total_energy(), core::scoring::methods::DistanceChainbreakEnergy::finalize_total_energy(), core::scoring::methods::LinearChainbreakEnergy::finalize_total_energy(), protocols::enzdes::SecondaryMatchProtocol::find_all_allowed_positions(), protocols::ligand_docking::find_attach_pt(), protocols::forge::methods::find_cutpoint(), protocols::ligand_docking::LigandBaseProtocol::find_interface_backbone(), protocols::ligand_docking::LigandBaseProtocol::find_interface_rsds(), core::pack::task::operation::util::find_jump_partners_within_CB_cutoff(), protocols::seeded_abinitio::DefineMovableLoops::find_loops(), protocols::seeded_abinitio::CloseFold::find_loops(), protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockMoveRbJumpMover::find_new_jump_residue(), protocols::loophash::FastGapMover::find_next_gap(), protocols::electron_density::findLoopFromDensity(), protocols::electron_density::findLoopFromPatterson(), protocols::swa::rna::floating_base_chain_closure_setup(), protocols::abinitio::AbrelaxApplication::fold(), protocols::protein_interface_design::movers::Splice::fold_tree(), protocols::forge::methods::fold_tree_from_loops(), protocols::loops::fold_tree_from_loops(), protocols::simple_moves::CutChainMover::foldTree(), protocols::topology_broker::AsymFoldandDockClaimer::generate_claims(), protocols::enzdes::EnzdesFlexBBProtocol::generate_ensemble_for_region(), protocols::swa::protein::StepWiseBetaAntiParallelJumpSampleGenerator::get_antiparallel_beta_jumps(), core::pose::get_chain_id_from_jump_id(), protocols::rna::RNA_ChunkLibrary::get_component_sequences(), protocols::swa::rna::get_default_allowed_bulge_res(), protocols::rna::RNA_LoopCloser::get_extra_cutpoints(), protocols::fldsgn::potentials::sspot::get_foldtree_seqsep(), core::scoring::SecondaryStructurePotential::get_foldtree_seqsep(), core::pose::get_jump_id_from_chain_id(), protocols::ligand_docking::LigandBaseProtocol::get_ligand_id(), protocols::hybridization::InsertChunkMover::get_local_sequence_mapping(), protocols::swa::monte_carlo::get_moving_residue_case(), protocols::swa::monte_carlo::get_potential_add_residues(), protocols::swa::monte_carlo::get_potential_delete_residues(), protocols::rna::RNA_HelixAssembler::get_rid_of_capping_base_pairs(), protocols::rna::get_rigid_body_jumps(), protocols::loophash::get_rt_over_leap(), protocols::loophash::get_rt_over_leap_fast(), core::pose::symmetry::get_symdof_subunits(), protocols::swa::StepWisePoseSetup::get_working_pose(), protocols::seeded_abinitio::GrowPeptides::grow_from_verteces(), protocols::loops::Loops::grow_loop(), protocols::loops::Loops::grow_loop_away_from_sheets(), protocols::seeded_abinitio::SegmentHybridizer::hybridize(), protocols::forge::remodel::RemodelLoopMover::independent_stage(), protocols::topology_broker::JumpClaimer::init_jumps(), protocols::floppy_tail::FloppyTailMover::init_on_new_input(), protocols::hybridization::HybridizeProtocol::initialize_and_sample_loops(), protocols::topology_broker::TopologyBroker::initialize_cuts(), protocols::topology_broker::FragmentClaimer::initialize_dofs(), protocols::topology_broker::AsymFoldandDockClaimer::initialize_dofs(), protocols::topology_broker::TopologyBroker::initialize_dofs(), protocols::swa::rna::StepWiseRNA_ResidueSampler::initialize_o2star_green_packer(), protocols::backrub::BackrubMover::initialize_simulation(), protocols::backrub::BackrubSidechainMover::initialize_simulation(), protocols::rna::RNA_StructureParameters::insert_base_pair_jumps(), protocols::grafting::insert_pose_into_pose(), protocols::forge::remodel::RemodelLoopMover::insert_random_smallestmer_per_loop(), core::scoring::rna::is_cutpoint_open(), core::scoring::methods::is_lower_cutpoint(), core::scoring::methods::is_upper_cutpoint(), protocols::simple_filters::JumpEvaluator::JumpEvaluator(), protocols::forge::methods::jumps_and_cuts_from_pose(), protocols::forge::methods::linear_chainbreak(), protocols::features::PoseConformationFeatures::load_fold_tree(), protocols::rna::RNA_LoopCloser::local_minimize_at_chainbreaks(), protocols::antibody2::RefineOneCDRLoopCentroid::loop_centroid_relax(), protocols::antibody::CDRH3Modeler::loop_centroid_relax(), protocols::antibody::CDRH3Modeler::loop_fa_relax(), protocols::forge::remodel::RemodelLoopMover::loophash_stage(), protocols::rna::make_coarse_pose(), protocols::swa::make_cut_at_moving_suite(), protocols::swa::rna::make_cut_at_moving_suite(), protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover::make_disjointed_foldtree(), protocols::ligand_docking::LigandBaseProtocol::make_movemap(), protocols::swa::StepWisePoseSetup::make_pose(), core::fragment::make_pose_from_frags(), protocols::forge::methods::make_star_foldtree(), protocols::fibril::make_symmetric_fibril(), core::pose::symmetry::make_symmetric_movemap(), core::scoring::electron_density::ElectronDensity::matchRes(), protocols::enzdes::EnzdesFlexibleRegion::minimize_region(), protocols::protein_interface_design::movers::PlaceOnLoop::minimize_toward_stub(), protocols::protein_interface_design::movers::MapHotspot::MinimizeHotspots(), MinimizeInterface(), core::pose::MiniPose::MiniPose(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_Moves::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::model_loop(), protocols::loop_build::LoopMover_SlidingWindow::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::model_loop(), protocols::forge::build::BuildManager::modify(), protocols::forge::build::SegmentSwap::modify_impl(), protocols::forge::build::Bridge::modify_impl(), protocols::forge::build::SegmentRebuild::modify_impl(), protocols::forge::build::ConnectRight::modify_impl(), protocols::forge::build::SegmentInsert::modify_impl(), protocols::ub_e2c::ubi_e2c_modeler::monoub_fold_tree(), protocols::abinitio::DoubleLayerKinematicAbinitio::new_kinematics(), protocols::abinitio::LoopJumpFoldCst::new_kinematics(), core::pose::operator<<(), protocols::swa::rna::Output_fold_tree_info(), protocols::swa::rna::Output_movemap(), protocols::swa::monte_carlo::RNA_SWA_MonteCarloMover::output_silent_file(), protocols::forge::methods::overlap_chainbreak(), protocols::enzdes::PredesignPerturbMover::parse_my_tag(), core::pose::partition_pose_by_jump(), protocols::swa::pdbslice(), protocols::hybridization::ChunkTrialMover::pick_random_chunk(), protocols::protein_interface_design::movers::PlaceStubMover::place_stub(), core::import_pose::atom_tree_diffs::pose_from_atom_tree_diff(), protocols::constraints_additional::ConstraintEvaluator::prepare_pose(), protocols::abinitio::KinematicControl::prepare_pose_for_sampling(), protocols::abinitio::AbrelaxApplication::process_decoy(), protocols::forge::methods::quadratic_chainbreak(), protocols::seeded_abinitio::CloseFold::quick_closure(), protocols::rna::RNA_StructureParameters::random_jump_change(), protocols::forge::remodel::RemodelLoopMover::randomize_stage(), protocols::flexpep_docking::FlexPepDockingProtocol::randomlySlidePeptideJump(), protocols::enzdes::MinimizeStoredRBConfs::rb_minimize_all_confs(), core::import_pose::read_additional_pdb_data(), core::io::serialization::read_binary(), protocols::swa::rna::StepWiseRNA_PoseSetup::read_input_pose_and_copy_dofs(), protocols::protein_interface_design::PatchdockReader::read_poses(), protocols::protein_interface_design::movers::PlacementMinimizationMover::refresh_bbstub_constraints(), protocols::antibody::AntibodyModeler::relax_cdrs(), protocols::swa::rna::remove_chain_break_jump_point(), protocols::toolbox::pose_manipulation::remove_chainbreaks_according_to_jumps(), protocols::jumping::remove_cut(), protocols::rna::remove_cutpoint_closed(), core::util::remove_cutpoint_variants(), protocols::forge::methods::remove_cutpoint_variants(), protocols::loops::remove_cutpoint_variants(), protocols::rna::remove_cutpoints_closed(), protocols::ligand_docking::MinimizeBackbone::reorder_foldtree_around_mobile_regions(), protocols::ligand_docking::LigandBaseProtocol::reorder_foldtree_around_mobile_regions(), protocols::analysis::InterfaceAnalyzerMover::reorder_foldtree_find_jump(), protocols::forge::remodel::RemodelLoopMover::repeat_generation(), protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue(), protocols::forge::remodel::RemodelLoopMover::repeat_propagation(), protocols::simple_filters::PoseInfoFilter::report(), protocols::simple_filters::EnergyPerResidueFilter::report(), protocols::enzdes::LigInterfaceEnergyFilter::report(), protocols::features::ProteinBondGeometryFeatures::report_interres_angles(), protocols::features::ProteinBondGeometryFeatures::report_interres_lengths(), protocols::simple_filters::ShapeComplementarityFilter::report_sm(), protocols::swa::StepWisePoseSetup::reroot_fold_tree(), core::scoring::methods::CartesianBondedEnergy::residue_pair_energy_sorted(), protocols::rbsegment_relax::restore_pose_from_rbsegs(), core::import_pose::atom_tree_diffs::rms_error_with_noise(), core::pose::symmetry::rotate_anchor_to_x_axis(), protocols::jumping::JumpSample::safe_secstruct(), protocols::jumping::safe_secstruct(), protocols::rna::RNA_StructureParameters::sample_alternative_chain_connection(), protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure::sample_loops(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::sample_loops(), protocols::antibody::CDRH3Modeler::scored_frag_close(), core::pose::symmetry::sealed_symmetric_fold_tree(), protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure::select_final_loop(), protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::semiexpl_water_hbgeom_score(), protocols::enzdes::RepackLigandSiteWithoutLigandMover::separate_protein_and_ligand(), protocols::hybridization::InsertChunkMover::set_bb_xyz_aligned(), protocols::docking::DockingHighResLegacy::set_dock_mcm_protocol(), protocols::ub_e2c::ubi_e2c_modeler::set_e2g2_diubi_fold_tree(), protocols::anchored_design::AnchoredDesignMover::set_fold_tree_and_cutpoints(), protocols::jumping::JumpSample::set_fold_tree_in_pose(), protocols::loops::set_loop_cutpoint_in_pose_fold_tree(), protocols::scoring::Interface::set_pack(), protocols::analysis::InterfaceAnalyzerMover::set_pose_info(), core::import_pose::set_reasonable_fold_tree(), protocols::forge::methods::set_single_loop_fold_tree(), protocols::loops::set_single_loop_fold_tree(), protocols::antibody::AntibodyModeler::set_snugdock_foldtree(), protocols::nonlocal::SimpleTreeBuilder::set_up(), protocols::nonlocal::StarTreeBuilder::set_up(), protocols::relax::RelaxProtocolBase::set_up_constraints(), protocols::swa::rna::setup_bulge_jump_point(), protocols::rna::RNA_StructureParameters::setup_chainbreak_variants(), protocols::ub_e2c::ubi_e2c_modeler::setup_complex_fold_tree(), protocols::star::setup_constraints(), protocols::abinitio::AbrelaxApplication::setup_fold(), protocols::jumping::MembraneJump::setup_fold_tree(), protocols::rna::RNA_StructureParameters::setup_fold_tree_and_jumps_and_variants(), protocols::flexpep_docking::FlexPepDockingProtocol::setup_foldtree(), protocols::hybridization::FoldTreeHybridize::setup_foldtree(), protocols::docking::setup_foldtree(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::setup_foldtree_and_add_cutpoint_variants(), protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover::setup_foldtree_around_anchor_invrot(), core::scoring::electron_density::PattersonCorrEnergy::setup_for_scoring(), core::scoring::electron_density::ElecDensEnergy::setup_for_scoring(), core::scoring::electron_density::FastDensEnergy::setup_for_scoring(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::setup_for_scoring(), core::scoring::electron_density::ElecDensCenEnergy::setup_for_scoring(), core::scoring::electron_density_atomwise::ElecDensAtomwiseEnergy::setup_for_scoring(), protocols::hotspot_hashing::HotspotStubSet::setup_hotspot_foldtree_(), protocols::rna::MultipleDomainMover::setup_jump_numbers_and_partner(), protocols::rna::RNA_StructureParameters::setup_jumps(), protocols::star::StarAbinitio::setup_kinematics(), protocols::rna::RNA_Minimizer::setup_movemap(), protocols::swa::rna::StepWiseRNA_PoseSetup::setup_native_pose(), protocols::simple_moves::DesignRepackMover::setup_packer_and_movemap(), protocols::docking::DockingHighResLegacy::setup_packing(), protocols::rbsegment_relax::setup_pose_from_rbsegs(), protocols::rbsegment_relax::setup_pose_rbsegs_keep_loops(), protocols::ub_e2c::ubi_e2c_modeler::setup_simple_fold_tree(), protocols::antibody::AntibodyModeler::setup_simple_fold_tree(), protocols::swa::rna::setup_simple_fold_tree(), protocols::grafting::GraftMoverBase::setup_single_loop_double_arm_remodeling_foldtree(), protocols::grafting::GraftMoverBase::setup_single_loop_single_arm_remodeling_foldtree(), protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::setup_using_user_input_VDW_pose(), protocols::rna::RNA_StructureParameters::setup_virtual_phosphate_variants_OLD(), protocols::surface_docking::SurfaceDockingProtocol::setupFoldTree(), protocols::star::simple_fold_tree(), protocols::antibody2::simple_fold_tree(), protocols::antibody::simple_fold_tree(), protocols::antibody2::simple_one_loop_fold_tree(), protocols::antibody::simple_one_loop_fold_tree(), protocols::forge::remodel::RemodelLoopMover::simultaneous_stage(), protocols::fldsgn::CircularPermutation::split_chains(), protocols::protein_interface_design::star_fold_tree(), core::fragment::steal_constant_length_frag_set_from_pose(), protocols::comparative_modeling::steal_ligands(), protocols::protein_interface_design::movers::PlaceStubMover::stub_based_atom_tree(), protocols::hybridization::FoldTreeHybridize::superimpose_strand_pairings_to_templates(), core::pose::swap_transform(), protocols::loophash::LoopHashLibrary::test_loop_sample(), protocols::jumping::JumpSample::transfer_jumps(), core::pose::transfer_jumps(), protocols::rna::translate_virtual_anchor_to_first_rigid_body(), protocols::rna::MultipleDomainMover::try_to_slide_into_contact(), protocols::rna::RNA_Minimizer::update_allow_insert_with_extra_minimize_res(), protocols::noesy_assign::CrossPeakList::update_decoy_compatibility_score(), protocols::coarse_rna::CoarseRNA_DeNovoProtocol::update_pose_constraints(), protocols::rna::RNA_DeNovoProtocol::update_pose_constraints(), protocols::backrub::BackrubSidechainMover::update_segments(), protocols::star::update_sequence_separation(), protocols::rna::virtualize_5prime_phosphates(), core::io::pdb::write_additional_pdb_data(), and core::io::serialization::write_binary().

void core::pose::Pose::fold_tree ( kinematics::FoldTree const &  fold_tree_in)

Sets the pose FoldTree to <fold_tree_in>

example(s): pose.fold_tree( foldtree ) See also: Pose pose.fold_tree FoldTree

References conformation_.

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

Returns the gamma torsion angle of residue <seqpos>

Note
assumes the residue is an nucleic acid

example(s): pose.gamma(3) See also: Pose Pose.residue Pose.set_gamma Residue

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

bool core::pose::Pose::has_dof ( DOF_ID const &  id) const
void core::pose::Pose::init ( void  )
private

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

default init function

References 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

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

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

References conformation_.

Referenced by protocols::topology_broker::CoordConstraintClaimer::add_constraints(), protocols::topology_broker::ConstraintClaimer::add_constraints(), core::pose::addVirtualResAsRoot(), protocols::topology_broker::MembraneTopologyClaimer::addVirtualResAsRootMembrane(), protocols::simple_filters::PalesEvaluator::applicable(), protocols::simple_filters::CamShiftEvaluator::applicable(), protocols::sparta::ChemicalShiftEvaluator::applicable(), protocols::simple_filters::ScoreEvaluator::applicable(), protocols::simple_filters::RPF_ScoreEvaluator::applicable(), protocols::relax::MiniRelax::apply(), protocols::simple_moves::symmetry::SetupForSymmetryMover::apply(), protocols::simple_filters::SAXSScoreFilter::apply(), protocols::abinitio::ResolutionSwitcher::apply(), protocols::simple_moves::ConstraintSetMover::apply(), protocols::swa::protein::StepWiseProteinPacker::apply(), protocols::loops::loop_mover::IndependentLoopMover::apply(), protocols::hybridization::CartesianSampler::apply(), protocols::rbsegment_relax::RBSegmentRelax::apply(), protocols::simple_filters::TruncatedScoreEvaluator::apply(), protocols::antibody2::H3RefineCCD::apply(), protocols::antibody2::RefineOneCDRLoop::apply(), protocols::flxbb::InterlockAroma::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::idealize::IdealizeMover::apply(), protocols::symmetric_docking::SymDockProtocol::apply(), protocols::relax::FastRelax::apply(), protocols::flxbb::FlxbbDesign::apply(), protocols::docking::DockingProtocol::apply(), protocols::antibody::LoopRlxMover::apply(), protocols::docking::DockingInitialPerturbation::apply_body(), protocols::docking::calc_Fnat(), protocols::ub_e2c::ubi_e2c_modeler::calc_interaction_energy(), protocols::docking::calc_Irmsd(), protocols::checkpoint::CheckPointer::checkpoint(), protocols::abinitio::AbrelaxApplication::close_loops(), protocols::simple_filters::ResidueSetChainEnergyFilter::compute(), protocols::hybridization::CartesianSampler::compute_fragment_bias(), protocols::abinitio::AbrelaxApplication::do_distributed_rerun(), protocols::abinitio::AbrelaxApplication::do_rerun(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::eval_atom_derivative(), core::scoring::electron_density::PattersonCorrEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensCenEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensEnergy::eval_atom_derivative(), core::scoring::electron_density::FastDensEnergy::eval_atom_derivative(), core::pose::symmetry::extract_asymmetric_unit(), core::io::silent::BinaryProteinSilentStruct::fill_pose(), core::io::silent::BinaryProteinSilentStruct::fill_struct(), core::io::silent::ProteinSilentStruct_Template< T >::fill_struct(), protocols::abinitio::AbrelaxApplication::fold(), core::scoring::gdtsc(), protocols::topology_broker::RigidChunkClaimer::init_after_reading(), core::pose::initialize_disulfide_bonds(), protocols::topology_broker::RigidChunkClaimer::initialize_dofs(), protocols::features::HBondFeatures::insert_site_environment_row(), protocols::features::ProteinResidueConformationFeatures::load_conformation(), protocols::features::ResidueConformationFeatures::load_conformation(), protocols::antibody::CDRH3Modeler::loop_fa_relax(), protocols::loophash::LoopHashRelaxProtocol::manual_call(), protocols::ub_e2c::ubi_e2c_modeler::monoub_calc_interaction_energy(), protocols::topology_broker::RigidChunkClaimer::new_decoy(), protocols::frag_picker::FragmentCandidate::output_silent(), core::scoring::constraints::parse_NMR_name(), core::scoring::constraints::parse_NMR_name_old(), protocols::constraints_additional::ConstraintEvaluator::prepare_pose(), core::scoring::constraints::AtomPairConstraint::read_def(), protocols::abinitio::IterativeAbrelax::read_structures(), protocols::topology_broker::FibrilModelingClaimer::read_tag(), protocols::topology_broker::RigidChunkClaimer::read_tag(), protocols::toolbox::pose_metric_calculators::ClashCountCalculator::recompute(), protocols::checkpoint::CheckPointer::recover_checkpoint(), protocols::abinitio::IterativeBase::replace_noesy_filter_constraints(), protocols::features::ProteinResidueConformationFeatures::report_features(), protocols::features::HBondFeatures::report_features(), protocols::features::PoseConformationFeatures::report_features_implementation(), protocols::relax::WorkUnit_BatchRelax_and_PostRescore::rescore_all_decoys(), protocols::abinitio::IterativeBase::rescore_nonlocal_archive(), protocols::forge::methods::restore_residues(), protocols::topology_broker::RigidChunkClaimer::RigidChunkClaimer(), protocols::swa::protein::StepWiseProteinPacker::sample_residues(), protocols::jd2::archive::DebugArchive::score(), protocols::relax::WorkUnit_BatchRelax_and_PostRescore::set_defaults(), protocols::abinitio::AbrelaxApplication::setup_fold(), core::scoring::electron_density::PattersonCorrEnergy::setup_for_derivatives(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::setup_for_derivatives(), core::scoring::electron_density::ElecDensCenEnergy::setup_for_derivatives(), protocols::topology_broker::TopologyBroker::switch_to_fullatom(), core::util::switch_to_residue_type_set(), protocols::flexpep_docking::FlexPepDockingLowRes::to_allatom(), protocols::flexpep_docking::FlexPepDockingAbInitio::to_allatom(), protocols::flexpep_docking::FlexPepDockingLowRes::to_centroid(), protocols::flexpep_docking::FlexPepDockingAbInitio::to_centroid(), protocols::nonlocal::SingleFragmentMover::to_centroid(), protocols::protein_interface_design::transform_pose(), and protocols::jobdist::universal_main().

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

References conformation_.

Referenced by protocols::toolbox::pose_metric_calculators::append_rsd_by_jump_near_atom(), protocols::rigid::RigidBodyMotionMover::apply(), protocols::protein_interface_design::movers::SpinMover::apply(), protocols::ligand_docking::RigidSearchMover::apply(), protocols::dna::SeparateDnaFromNonDna::apply(), protocols::nonlocal::SheetTranslate::apply(), protocols::nonlocal::HelixRotate::apply(), protocols::protein_interface_design::movers::SaveAndRetrieveSidechains::apply(), protocols::ligand_docking::Transform::apply(), protocols::protein_interface_design::movers::TryRotamers::apply(), protocols::rigid::WholeBodyTranslationMover::apply(), protocols::rigid::WholeBodyRotationMover::apply(), protocols::enzdes::PredesignPerturbMover::apply(), protocols::rigid::RigidBodyPerturbMover::apply(), protocols::rigid::RigidBodyPerturbNoCenterMover::apply(), protocols::rigid::RigidBodyRandomizeMover::apply(), protocols::rigid::RigidBodySpinMover::apply(), protocols::rigid::RigidBodyDeterministicSpinMover::apply(), protocols::rigid::RigidBodyTransMover::apply(), protocols::rigid::RigidBodyDofRandomizeMover::apply(), protocols::rigid::RigidBodyDofTransMover::apply(), protocols::rigid::RigidBodyDofPerturbMover::apply(), core::pose::copy_dofs(), protocols::protein_interface_design::movers::copy_hotspot_to_pose(), protocols::ligand_docking::Rotate::create_random_rotation(), protocols::toolbox::pose_metric_calculators::dock_waters_to_atom(), protocols::electron_density::dockPoseIntoMap(), core::import_pose::atom_tree_diffs::dump_atom_tree_diff(), core::io::silent::BinaryRNASilentStruct::fill_struct(), core::io::silent::BinaryProteinSilentStruct::fill_struct(), core::io::silent::ProteinSilentStruct_Template< T >::fill_struct(), core::io::silent::RNA_SilentStruct::fill_struct(), protocols::rigid::gaussian_jump_move(), protocols::loophash::get_rt_over_leap_fast(), core::scoring::DockingScoreFunction::operator()(), protocols::ligand_docking::LigandDockProtocol::optimize_orientation3(), protocols::hotspot_hashing::StubGenerator::placeResidueOnPose(), protocols::rna::RNA_DeNovoProtocol::randomize_rigid_body_orientations(), protocols::forge::remodel::RemodelLoopMover::repeat_generation(), protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue(), protocols::features::PoseConformationFeatures::report_features_implementation(), core::optimization::symmetry::SymMinimizerMap::reset_jump_rb_deltas(), core::optimization::MinimizerMap::reset_jump_rb_deltas(), core::pose::symmetry::rotate_anchor_to_x_axis(), protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::semiexpl_water_hbgeom_score(), protocols::simple_moves::symmetry::SymmetrySlider::setup(), protocols::rna::MultipleDomainMover::slide_back_to_origin(), protocols::comparative_modeling::steal_ligands(), protocols::jumping::JumpSample::transfer_jumps(), core::pose::transfer_jumps(), protocols::ligand_docking::Transform::transform_ligand(), protocols::rna::MultipleDomainMover::try_to_slide_into_contact(), and core::io::serialization::write_binary().

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

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 (); }

References metrics_.

Referenced by protocols::simple_filters::PoseMetricEvaluator< T >::apply(), protocols::forge::components::BDR::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::flexpep_docking::FlexPepDockingPoseMetrics::calc_interface_metrics(), protocols::simple_filters::InterfaceSasaFilter::compute(), protocols::enzdes::LigDSasaFilter::compute(), protocols::fldsgn::filters::FragQualFilter::compute(), protocols::enzdes::DiffAtomSasaFilter::compute(), protocols::analysis::InterfaceAnalyzerMover::compute_interface_delta_hbond_unsat(), protocols::analysis::InterfaceAnalyzerMover::compute_interface_energy(), protocols::enzdes::EnzdesScorefileFilter::compute_metrics_for_residue_subset(), 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::pmut_scan::PointMutScanDriver::make_mutant_structure(), core::pose::metrics::simple_calculators::InterfaceDeltaEnergeticsCalculator::recompute(), protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::recompute(), protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::recompute(), protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator::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.

References conformation_.

Referenced by protocols::forge::methods::add_cutpoint_variants(), protocols::kinmatch::alapose(), protocols::ligand_docking::LigandDesign::apply(), protocols::enzdes::BackboneSampler::apply(), protocols::toolbox::task_operations::SelectBySASAOperation::apply(), protocols::simple_moves::RepulsiveOnlyMover::apply(), protocols::simple_moves::ModifyVariantTypeMover::apply(), protocols::simple_moves::ddG::apply(), protocols::simple_moves::MakePolyXMover::apply(), core::pack::task::operation::OptCysHG::apply(), protocols::forge::remodel::RemodelMover::apply(), core::scoring::orbitals::OrbitalsStatistics::bb_stats(), core::io::pdb::build_pose_as_is1(), core::scoring::sc::MolecularSurfaceCalculator::Calc(), protocols::analysis::InterfaceAnalyzerMover::calc_hbond_sasaE(), core::scoring::calc_per_res_hydrophobic_sasa(), protocols::pmut_scan::PointMutScanDriver::calculate_neighbor_table(), core::scoring::packstat::cavity_distance_constraint(), protocols::sic_dock::cb_weight_map_from_pose(), protocols::sic_dock::cb_weights_from_pose(), protocols::fldsgn::BluePrintBDR::centroid_build(), protocols::forge::components::BDR::centroid_build(), protocols::forge::components::VarLengthBuild::centroid_build(), protocols::simple_filters::AtomicDistanceFilter::compute(), protocols::protein_interface_design::filters::AtomicContactCountFilter::compute(), protocols::analysis::InterfaceAnalyzerMover::compute_interface_sc(), core::pack::rotamer_set::RotamerSet_::compute_one_body_energy_maps(), core::pack::interaction_graph::SurfacePotential::compute_pose_surface_energy(), core::pose::conf2pdb_chain(), protocols::sic_dock::count_CBs(), protocols::forge::methods::count_cutpoints(), protocols::forge::methods::cyclize_pose(), protocols::forge::components::BDR::design_refine(), protocols::forge::remodel::RemodelMover::design_refine_seq_relax(), protocols::sic_dock::dump_loophash_linkers(), core::scoring::methods::ChainbreakEnergy::eval_atom_derivative(), protocols::forge::build::ConnectRight::extract_rt(), protocols::pmut_scan::PointMutScanDriver::fill_mutations_list(), protocols::toolbox::pose_metric_calculators::SequenceComparison::fill_num_neighbors(), core::scoring::orbitals::OrbitalsScore::finalize_after_derivatives(), core::scoring::methods::ChainbreakEnergy::finalize_total_energy(), core::scoring::orbitals::OrbitalsScore::finalize_total_energy(), protocols::forge::methods::find_cutpoint(), protocols::forge::methods::fixH(), protocols::forge::methods::fold_tree_from_loops(), protocols::forge::methods::fold_tree_from_pose(), protocols::sic_dock::get_CB_Vecs(), protocols::ligand_docking::FinalMinimizer::get_final_min_mover(), core::pose::get_hash_excluding_chain(), core::pose::get_sha1_hash_excluding_chain(), protocols::sic_dock::get_termini_from_pose(), protocols::sic_dock::SICFast::init(), protocols::forge::build::SegmentSwap::init(), protocols::forge::build::SegmentInsert::init(), protocols::sic_dock::xyzStripeHashPoseWithMeta::init_with_pose(), protocols::sic_dock::xyzStripeHashPose::init_with_pose(), core::pose::initialize_atomid_map(), core::pose::initialize_atomid_map_heavy_only(), core::pose::initialize_dof_id_map(), protocols::forge::build::SegmentInsert::insert_pose_torsion_override_movemap(), protocols::features::PdbDataFeatures::insert_residue_pdb_confidence_rows(), protocols::features::PdbDataFeatures::insert_residue_pdb_identification_rows(), protocols::forge::build::SegmentInsert::insertion_end_residue(), protocols::forge::methods::linear_chainbreak(), protocols::simple_moves::BBConRotMover::make_move(), protocols::pmut_scan::PointMutScanDriver::make_mutant_structure(), protocols::ligand_docking::HighResDocker::make_packer_task(), protocols::fibril::make_symmetric_fibril(), core::pose::symmetry::make_symmetric_pose(), protocols::forge::build::BuildManager::modify(), protocols::forge::build::SegmentSwap::modify_impl(), protocols::forge::build::Bridge::modify_impl(), protocols::forge::build::SegmentRebuild::modify_impl(), protocols::forge::build::ConnectRight::modify_impl(), protocols::forge::build::SegmentInsert::modify_impl(), protocols::sic_dock::neighbor_count(), protocols::forge::methods::overlap_chainbreak(), protocols::contact_map::ContactMap::parse_my_tag(), protocols::contact_map::ContactMap::parse_region_string(), core::pose::parse_selection_block(), core::scoring::packing::PoseBalls::PoseBalls(), protocols::forge::methods::quadratic_chainbreak(), protocols::forge::remodel::RemodelLoopMover::randomize_stage(), protocols::toolbox::pose_metric_calculators::SaltBridgeCalculator::recompute(), protocols::toolbox::pose_metric_calculators::CatPiCalculator::recompute(), protocols::toolbox::pose_metric_calculators::PiPiCalculator::recompute(), protocols::forge::remodel::RemodelAccumulator::recover_checkpoint(), protocols::qsar::scoring_grid::VdwGrid::refresh(), protocols::forge::methods::remove_cutpoint_variants(), core::pose::renumber_pdbinfo_based_on_conf_chains(), protocols::ligand_docking::reorder_with_first_non_mobile_as_root(), protocols::forge::remodel::RemodelLoopMover::repeat_generation(), protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue(), protocols::forge::remodel::RemodelLoopMover::repeat_propagation(), protocols::forge::remodel::RemodelLoopMover::repeat_sync(), protocols::features::PoseConformationFeatures::report_features(), protocols::features::ResidueTypesFeatures::report_features(), protocols::features::ProteinResidueConformationFeatures::report_features(), protocols::features::ResidueConformationFeatures::report_features(), protocols::features::HBondFeatures::report_features(), protocols::features::OrbitalsFeatures::report_hpol_orbital_interactions(), protocols::forge::build::ConnectRight::reset_accounting_impl(), core::pose::PDBInfo::resize_atom_records(), protocols::forge::methods::restore_residues(), core::scoring::orbitals::OrbitalsStatistics::sc_H_orbital(), protocols::sic_dock::XfoxmScore::score(), core::scoring::hackelec::HackElecEnergy::set_nres_mono(), core::optimization::CartesianMinimizerMap::setup(), core::pose::setup_dof_mask_from_move_map(), core::pose::setup_dof_to_torsion_map(), core::scoring::orbitals::OrbitalsScore::setup_for_derivatives(), core::scoring::orbitals::OrbitalsScore::setup_for_minimizing(), protocols::simple_moves::BBGaussianMover::setup_list(), protocols::forge::remodel::RemodelLoopMover::simultaneous_stage(), core::io::pdb::write_additional_pdb_data(), protocols::sic_dock::xform_pose(), core::fragment::xform_pose(), and protocols::sic_dock::xform_pose_rev().

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

notify ConformationEvent observers

Parameters
ethe event
fire_generalfire a GeneralEvent afterwards? default true

References conformation_obs_hub_, and notify_general_obs().

Referenced by on_conf_xyz_change().

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

notify DestructionEvent observers

Remarks
called only upon destruction of the Pose

References destruction_obs_hub_.

Referenced by ~Pose().

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

notify EnergyEvent observers

Parameters
ethe event
fire_generalfire a GeneralEvent afterwards? default true

References energy_obs_hub_, and notify_general_obs().

Referenced by scoring_end().

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

notify GeneralEvent observers

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

References general_obs_hub_.

Referenced by notify_conformation_obs(), and notify_energy_obs().

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

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

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

References observer_cache_.

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

Returns the omega torsion angle of residue <seqpos>

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!)

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

Returns the pose PDBInfo (const)

get pdb info (const)

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

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

References pdb_info_, and total_residue().

Referenced by protocols::dna::DnaInterfaceMultiStateDesign::add_dna_states(), protocols::loops::add_loop(), protocols::toolbox::task_operations::JointSequenceOperation::add_pose(), core::pose::addVirtualResAsRoot(), protocols::hybridization::HybridizeProtocol::align_by_domain(), protocols::antibody::AntibodyModeler::all_cdr_VL_VH_fold_tree(), protocols::antibody::Antibody::Antibody(), protocols::ligand_docking::append_automorphic_rmsd(), core::io::pdb::FileData::append_residue(), protocols::protein_interface_design::movers::LoopLengthChange::apply(), protocols::protein_interface_design::movers::SetTemperatureFactor::apply(), protocols::analysis::PackStatMover::apply(), protocols::dna::WatsonCrickRotamerCouplings::apply(), protocols::simple_moves::SwitchChainOrderMover::apply(), protocols::simple_filters::EnergyPerResidueFilter::apply(), protocols::protein_interface_design::movers::SetAtomTree::apply(), protocols::domain_assembly::AddAssemblyConstraints::apply(), protocols::protein_interface_design::filters::Torsion::apply(), protocols::frag_picker::nonlocal::NonlocalFrags::apply(), protocols::domain_assembly::PostDockAssemblyScorer::apply(), protocols::protein_interface_design::filters::FilterScanFilter::apply(), protocols::dna::SeparateDnaFromNonDna::apply(), protocols::dna::RestrictDesignToProteinDNAInterface::apply(), protocols::domain_assembly::AssembleLinkerMover::apply(), protocols::comparative_modeling::PartialThreadingMover::apply(), protocols::motifs::MotifDnaPacker::apply(), protocols::enzdes::EnzdesFlexBBProtocol::apply(), protocols::antibody2::ModelCDRH3::apply(), protocols::surface_docking::SurfaceDockingProtocol::apply(), protocols::comparative_modeling::ExtraThreadingMover::apply(), protocols::toolbox::task_operations::JointSequenceOperation::apply(), protocols::moves::StructureRestrictor::apply(), protocols::comparative_modeling::ThreadingMover::apply(), protocols::fldsgn::BluePrintBDR::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::hybridization::CartesianHybridize::apply_frag(), protocols::motifs::MotifDnaPacker::aromatic_motifs(), protocols::match::output::PDBWriter::assemble_remark_lines(), protocols::ub_e2c::ubi_e2c_modeler::assign_CSPs(), protocols::ub_e2c::ubi_e2c_modeler::assign_non_CSPs(), protocols::idealize::basic_idealize(), core::scoring::orbitals::OrbitalsStatistics::bb_stats(), protocols::motifs::bpdefs2map(), core::io::pdb::build_pose_as_is1(), core::import_pose::build_pose_as_is2(), core::scoring::calc_per_atom_sasa(), protocols::dna::DnaInterfacePacker::calculate_specificity(), protocols::antibody::CDRH3Modeler::CDR_H3_filter(), protocols::antibody2::CDR_H3_filter_legacy_code_with_old_rule(), core::pose::metrics::simple_calculators::InterfaceDefinitionCalculator::chain_letter_to_number(), clear(), protocols::protein_interface_design::filters::DesignableResiduesFilter::compute(), protocols::hybridization::CartesianSampler::compute_fragment_bias(), protocols::simple_filters::RotamerBoltzmannWeight::compute_modified_ddG(), core::pack::interaction_graph::SurfacePotential::compute_pose_hpatch_score(), core::pose::conf2pdb_chain(), protocols::forge::remodel::RemodelMover::confirm_sequence(), protocols::enzdes::PoseFoundResiduesCombination::construct_and_dump_outpose(), protocols::docking::DockTaskFactory::create_and_attach_task_factory(), protocols::floppy_tail::create_extra_output(), protocols::enzdes::enzutil::create_remark_headers_from_cstcache(), protocols::docking::DockingHighResLegacy::define_loops(), protocols::motifs::defs2allowedtypes(), protocols::motifs::defs2map(), protocols::motifs::defs2vector(), protocols::antibody2::AntibodyInfo::detect_and_set_regular_CDR_H3_stem_type(), protocols::antibody2::AntibodyInfo::detect_and_set_regular_CDR_H3_stem_type_new_rule(), protocols::antibody::Antibody::detect_regular_CDR_H3_stem_type(), protocols::enzdes::EnzdesFlexBBProtocol::determine_flexible_regions(), protocols::antibody::AntibodyModeler::display_constraint_residues(), protocols::antibody2::GraftCDRLoopsProtocol::display_constraint_residues(), protocols::antibody2::AntibodyModelerProtocol::display_constraint_residues(), protocols::dna::DnaInterfacePacker::dna_seq_tag(), protocols::design_opt::GreedyOptMutationMover::dump_scoring_table(), core::scoring::methods::CartesianBondedEnergy::eval_improper_torsions(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd1(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd2(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_bond_energy(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_angle_energies(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_improper_torsion_energies(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_length_energies(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_torsion_energies(), protocols::enzdes::EnzdesBaseProtocol::exchange_ligands_in_pose(), protocols::motifs::MotifDnaPacker::expand_motifs(), core::pose::symmetry::extract_asymmetric_unit(), protocols::pmut_scan::PointMutScanDriver::fill_mutations_list(), core::fragment::fill_template_frames_from_pdb(), protocols::dna::find_basepairs(), protocols::features::FeaturesReporter::find_tag(), protocols::hybridization::find_uncovered_residues(), core::io::silent::SilentStruct::finish_pose(), protocols::match::BfactorMPM::get_ca_bfactors(), core::pose::get_chain_from_chain_id(), protocols::antibody2::AntibodyInfo::get_FoldTree_AllCDRs_LHDock(), protocols::antibody2::AntibodyInfo::get_FoldTree_L_HA(), protocols::antibody2::AntibodyInfo::get_FoldTree_LA_H(), protocols::antibody2::AntibodyInfo::get_FoldTree_LH_A(), protocols::optimize_weights::IterativeOptEDriver::get_nat_aa_opte_data(), protocols::optimize_weights::IterativeOptEDriver::get_nat_rot_opte_data(), protocols::moves::PyMolMover::get_PyMol_model_name(), core::pose::get_resnum(), protocols::pockets::PocketGrid::getRelaxResidues(), protocols::antibody2::AntibodyInfo::identify_antibody(), protocols::motifs::MotifSearch::incorporate_motifs(), protocols::motifs::LigandMotifSearch::incorporate_motifs(), core::io::pdb::FileData::init_from_pose(), protocols::floppy_tail::FloppyTailMover::init_on_new_input(), protocols::dna::DnaInterfacePacker::init_standard(), protocols::topology_broker::AsymFoldandDockClaimer::initialize_dofs(), protocols::match::output::PoseMatchOutputWriter::insert_match_into_pose(), protocols::features::PdbDataFeatures::insert_residue_pdb_confidence_rows(), protocols::features::PdbDataFeatures::insert_residue_pdb_identification_rows(), protocols::features::HBondFeatures::insert_site_pdb_row(), protocols::features::UnrecognizedAtomFeatures::insert_unrecognized_atoms_rows(), protocols::features::UnrecognizedAtomFeatures::insert_unrecognized_neighbors_rows(), protocols::features::UnrecognizedAtomFeatures::insert_unrecognized_residues_rows(), protocols::features::PdbDataFeatures::load_residue_pdb_confidence(), protocols::features::PdbDataFeatures::load_residue_pdb_identification(), core::pack::task::ResfileContents::locate_resid(), protocols::dna::make_base_pair_aware_fold_tree(), protocols::motifs::make_dna_mutations(), protocols::motifs::IRCollection::make_motif_filename(), core::pose::symmetry::make_symmetric_pose(), protocols::hybridization::FoldTreeHybridize::map_pdb_info_number(), protocols::forge::build::SegmentSwap::modify_impl(), protocols::forge::build::SegmentRebuild::modify_impl(), protocols::forge::build::ConnectRight::modify_impl(), protocols::forge::build::SegmentInsert::modify_impl(), protocols::ub_e2c::ubi_e2c_modeler::monoub_assign_CSPs(), protocols::ub_e2c::ubi_e2c_modeler::monoub_setup_key_residues(), protocols::dna::not_already_connected(), protocols::simple_moves::PackRotamersMover::note_packertask_settings(), core::pack::task::operation::ResiduePDBIndexIs::operator()(), core::pack::task::operation::ChainIs::operator()(), core::pose::operator<<(), operator=(), OPT_1GRP_KEY(), core::io::sequence_comparation::DesignContrast::output_sqc_file(), core::pack::task::ResfileContents::parse_body_line(), protocols::simple_filters::RelativePoseFilter::parse_my_tag(), protocols::protein_interface_design::movers::BestHotspotCstMover::parse_my_tag(), protocols::analysis::InterfaceAnalyzerMover::parse_my_tag(), protocols::forge::methods::parse_resfile_string_with_no_lockdown(), core::scoring::constraints::ConstraintIO::parse_residue(), core::pose::parse_resnum(), protocols::pockets::PocketConstraint::PocketConstraint(), protocols::moves::StructureRestrictor::pose_name(), core::scoring::constraints::FabConstraint::pose_res_no(), core::scoring::packing::PoseBalls::PoseBalls(), core::scoring::packing::PoseBallsLite::PoseBallsLite(), protocols::dna::DnaChains::print(), protocols::analysis::InterfaceAnalyzerMover::print_pymol_selection_of_hbond_unsat(), protocols::analysis::InterfaceAnalyzerMover::print_pymol_selection_of_interface_residues(), protocols::analysis::InterfaceAnalyzerMover::print_pymol_selection_of_packing(), protocols::toolbox::match_enzdes_util::EnzConstraintIO::process_pdb_header(), protocols::dna::DnaInterfacePacker::protein_scan(), protocols::anchored_design::Anchor::read_anchorfile(), protocols::pmut_scan::PointMutScanDriver::read_mutants_list_file(), protocols::hybridization::TMalign::read_pose(), protocols::toolbox::pose_metric_calculators::ResidueDecompositionByChainCalculator::recompute(), protocols::enzdes::EnzdesFlexBBProtocol::recover_loops_from_file(), protocols::enzdes::enzutil::remove_remark_header_for_geomcst(), protocols::hybridization::remove_residues(), core::pose::renumber_pdbinfo_based_on_conf_chains(), protocols::simple_filters::PoseInfoFilter::report(), protocols::simple_filters::RotamerBoltzmannWeight::report(), protocols::simple_filters::EnergyPerResidueFilter::report(), protocols::simple_filters::AlaScan::report(), protocols::rotamer_recovery::RRReporterSQLite::report_rotamer_recovery_full(), protocols::simple_filters::AlaScan::report_symmetry(), protocols::optimize_weights::IterativeOptEDriver::residue_has_bad_bfactor(), protocols::toolbox::task_operations::RestrictToCDRH3Loop::residue_is_in_h3_loop(), core::io::raw_data::DisulfideFile::resnum_to_rosetta_num(), protocols::loops::ResidueIndexDescription::resolve_index(), protocols::loops::ResidueIndexDescriptionFromFile::resolve_index(), protocols::dna::DnaInterfacePacker::reversion_scan(), core::scoring::orbitals::OrbitalsStatistics::sc_H_orbital(), protocols::moves::PyMolMover::send_energy(), protocols::moves::PyMolMover::send_RAW_Energies(), protocols::dna::seq_pdb_str(), core::sequence::Sequence::Sequence(), core::pose::sequence_map_from_pdbinfo(), protocols::dna::set_base_segment_chainbreak_constraints(), protocols::antibody::Antibody::set_defaults(), protocols::vip::VIP_Mover::set_excluded_positions(), protocols::dna::DesignProteinBackboneAroundDNA::set_loop_info(), protocols::analysis::InterfaceAnalyzerMover::set_pose_info(), protocols::pockets::PocketConstraint::set_target_res_pdb(), protocols::match::MatcherTask::set_upstream_pose(), protocols::antibody2::AntibodyInfo::setup_CDRsInfo(), core::scoring::constraints::FabConstraint::setup_csts(), protocols::flexpep_docking::FlexPepDockingProtocol::setup_foldtree(), protocols::docking::setup_foldtree(), protocols::antibody2::AntibodyInfo::setup_FrameWorkInfo(), protocols::ub_e2c::ubi_e2c_modeler::setup_key_residues(), protocols::antibody2::AntibodyInfo::setup_VL_VH_packing_angle(), core::scoring::hbonds::HBond::show(), protocols::loops::split_by_resSeq(), core::pack::task::PackerTask_::task_string(), protocols::toolbox::match_enzdes_util::EnzConstraintParameters::update_pdb_remarks(), protocols::flexpep_docking::FlexPepDockingFlags::updateChains(), protocols::outputter::ResFileOutputter::write(), and core::io::pdb::write_additional_pdb_data().

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

Returns the pose PDBInfo.

get pdb info

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

References pdb_info_, and 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_infothe new pdb info to copy, pass NULL if you want to zero the existence of pdb info inside this Pose
Returns
the prior pdb info instance

References conformation_, pdb_info_, and 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...

References core::pose::carbohydrates::calculate_carbohydrate_phi(), core::conformation::Residue::mainchain_torsion(), core::id::phi_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::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::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::remodel::RemodelLoopMover::apply(), protocols::forge::components::VarLengthBuild::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::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_psi_only(), protocols::swa::protein::StepWiseProteinScreener::get_main_chain_torsion_set_list_sample_psi_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().

void core::pose::Pose::prepend_polymer_residue_before_seqpos ( Residue const &  new_rsd,
Size const  seqpos,
bool const  build_ideal_geometry 
)
std::string core::pose::Pose::print_metric ( std::string const &  calculator_name,
std::string const &  key 
) const

References metrics_.

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

Returns the psi torsion angle of residue <seqpos> 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.

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

re object_comparison see comment for ConstraintSet::remove_constraint function

References constraint_set_, and energies_.

Referenced by protocols::ligand_docking::append_multi_residue_ligand_RMSD(), protocols::simple_moves::ClearConstraintsMover::apply(), protocols::medal::MedalExchangeMover::apply(), protocols::anchored_design::AnchoredDesignMover::apply(), protocols::forge::constraints::RemoveCsts::apply(), protocols::floppy_tail::FloppyTailMover::apply(), protocols::simple_moves::ConsensusDesignMover::apply(), protocols::canonical_sampling::CanonicalSamplingMover::apply(), protocols::ddg::ddGMover::apply(), protocols::hybridization::FoldTreeHybridize::apply(), protocols::flxbb::FlxbbDesign::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::forge::components::VarLengthBuild::centroid_build(), protocols::ligand_docking::Rotate::create_random_rotations(), protocols::protein_interface_design::movers::PlaceStubMover::cst_cleanup(), protocols::hybridization::generate_centroid_constraints(), OPT_1GRP_KEY(), protocols::ddg::ddGMover::relax_wildtype_structure(), 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::canonical_sampling::CanonicalSamplingMover::setup_constraints(), protocols::ddg::ddGMover::setup_constraints(), protocols::ddg::ddGMover::setup_repack_constraints(), protocols::protein_interface_design::movers::PlaceStubMover::StubMinimize(), protocols::motifs::IRCollection::successful_loop_closure(), and protocols::star::tear_down_constraints().

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

References constraint_set_, and energies_.

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

Replaces the residue at <seqpos> with <new_rsd_in>

References conformation_, and total_residue().

Referenced by protocols::enzdes::SecondaryMatchProtocol::add_enz_cst_interaction_to_pose(), protocols::comparative_modeling::StealSideChainsMover::apply(), protocols::ligand_docking::RandomConformerMover::apply(), protocols::simple_moves::PeptideStapleMover::apply(), protocols::simple_moves::hbs::HbsPatcher::apply(), protocols::simple_moves::oop::OopPatcher::apply(), protocols::frag_picker::nonlocal::NonlocalFrags::apply(), protocols::ligand_docking::AddHydrogen::apply(), protocols::flexpack::FlexPacker::apply(), protocols::simple_moves::chiral::ChiralMover::apply(), protocols::canonical_sampling::SidechainMetropolisHastingsMover::apply(), protocols::simple_moves::ReturnSidechainMover::apply(), protocols::protein_interface_design::movers::SaveAndRetrieveSidechains::apply(), protocols::simple_moves::MutateResidue::apply(), protocols::simple_moves::symmetry::SetupNCSMover::apply(), protocols::enzdes::PackRotamersMoverPartGreedy::apply(), protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover::apply(), protocols::protein_interface_design::movers::TryRotamers::apply(), protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::apply(), protocols::flxbb::InterlockAroma::apply(), protocols::simple_moves::sidechain_moves::SidechainMCMover::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::idealize::IdealizeMover::apply(), protocols::simple_moves::sidechain_moves::SidechainMover::apply(), protocols::simple_moves::sidechain_moves::SidechainMoverBase::apply(), protocols::comparative_modeling::ThreadingMover::apply(), protocols::loops::apply_sequence_mapping(), protocols::pack_daemon::PackDaemon::assign_last_rotamers_to_pose(), core::pack::interaction_graph::LinearMemNode::assign_state(), core::pack::interaction_graph::LinearMemNode::commit_considered_substitution(), protocols::simple_filters::RotamerBoltzmannWeight::compute_Boltzmann_weight(), protocols::enzdes::PoseFoundResiduesCombination::construct_and_dump_outpose(), protocols::toolbox::pose_manipulation::construct_poly_uniq_restype_pose(), protocols::toolbox::pose_manipulation::construct_poly_XXX_pose(), protocols::flexpep_docking::FlexPepDockingAbInitio::convertPSERtoASP(), protocols::flexpep_docking::FlexPepDockingAbInitio::convertPSERtoGLU(), protocols::topology_broker::copy_internal_coords(), protocols::abinitio::copy_side_chains(), protocols::seeded_abinitio::SwapSegment::copying_side_chains(), protocols::enzdes::EnzdesBaseProtocol::cst_minimize(), core::import_pose::atom_tree_diffs::dump_atom_tree_diff(), protocols::enzdes::EnzdesBaseProtocol::exchange_ligands_in_pose(), protocols::protein_interface_design::movers::DisulfideMover::form_disulfide(), protocols::protein_interface_design::movers::MapHotspot::GenerateMap(), protocols::ligand_docking::grid_rotamer_trials(), protocols::ligand_docking::grid_rotamer_trials_atr_rep(), protocols::simple_moves::sidechain_moves::SidechainMoverBase::idealize_sidechains(), protocols::simple_moves::sidechain_moves::SidechainMover::idealize_sidechains(), protocols::motifs::MotifSearch::incorporate_motifs(), protocols::motifs::LigandMotifSearch::incorporate_motifs(), protocols::match::downstream::LigandConformerBuilder::initialize_conformers(), protocols::match::output::PoseMatchOutputWriter::insert_match_into_pose(), protocols::motifs::make_base_pair_mutation(), core::pack::min_pack(), protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::output_alternative_states(), core::pack::pack_rotamers_run(), protocols::protein_interface_design::movers::PlaceStubMover::place_stub(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::place_stubs(), protocols::flexpep_docking::FlexPepDockingProtocol::polyAla(), core::import_pose::atom_tree_diffs::pose_from_atom_tree_diff(), protocols::match::output::PoseInserter::process_hit(), protocols::anchored_design::AnchoredDesignMover::randomize_input_sequence(), protocols::enzdes::PredesignPerturbMover::reinstate_pose(), protocols::vip::VIP_Mover::relax_favorable_poses(), core::pose::replace_pose_residue_copying_existing_coordinates(), protocols::toolbox::match_enzdes_util::replace_residue_keeping_all_atom_positions(), protocols::forge::methods::restore_residues(), protocols::flexpep_docking::FlexPepDockingAbInitio::restorePSER(), core::pack::rotamer_trials(), protocols::ligand_docking::Rotate::rotate_ligand(), core::pack::RTMin::rtmin(), protocols::rotamer_recovery::RRProtocolRTMin::run(), protocols::hybridization::FoldTreeHybridize::set_loops_to_virt_ala(), protocols::vip::VIP_Mover::skip_relax(), protocols::vip::VIP_Mover::sort_fill_energies(), core::pack::stochastic_pack(), protocols::dna::substitute_residue(), protocols::motifs::IRCollection::successful_loop_closure(), protocols::seeded_abinitio::SwapSegment::swap_chain(), protocols::seeded_abinitio::SwapSegment::swap_segment(), protocols::topology_broker::RigidChunkClaimer::switch_to_fullatom(), core::util::switch_to_residue_type_set(), core::pack::symmetric_pack_rotamers_run(), and core::pack::symmetric_rotamer_trials().

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

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

References conformation_, and 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

References conformation_, and total_residue().

Referenced by protocols::LoopRebuild::acceptable_rmsd_change(), protocols::swa::rna::StepWiseRNA_PoseSetup::add_aa_virt_rsd_as_root(), protocols::protein_interface_design::movers::PlaceOnLoop::add_bb_csts_to_loop(), protocols::simple_moves::ConstrainToIdealMover::add_bond_angle_constraint(), protocols::simple_moves::ConstrainToIdealMover::add_bond_constraint(), protocols::jumping::JumpSample::add_chainbreaks(), protocols::jumping::JumpSample::add_chainbreaks_as_distance_constraint(), protocols::protein_interface_design::movers::add_coordinate_constraints(), protocols::seeded_abinitio::add_coordinate_constraints(), core::scoring::constraints::add_coordinate_constraints(), protocols::relax::add_coordinate_constraints_to_pose(), protocols::loops::add_coordinate_constraints_to_pose(), protocols::ligand_docking::MinimizeBackbone::add_cut_points(), protocols::forge::methods::add_cutpoint_variants(), protocols::loops::add_cutpoint_variants(), protocols::seeded_abinitio::add_dist_constraints(), core::scoring::dna::DNATorsionPotential::add_dna_base_distance_constraints(), protocols::dna::DnaInterfaceMultiStateDesign::add_dna_states(), core::scoring::dna::DNATorsionPotential::add_DNA_torsion_constraint(), core::scoring::dna::DNATorsionPotential::add_dna_torsion_tethers(), protocols::enzdes::SecondaryMatchProtocol::add_enz_cst_interaction_to_pose(), protocols::swa::rna::Add_harmonic_chainbreak_constraint(), protocols::simple_moves::hbs::add_hbs_constraint(), protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_pose(), protocols::motifs::add_motif_bb_constraints(), protocols::motifs::add_motif_sc_constraints(), protocols::rna::RNA_StructureParameters::add_new_RNA_jump(), protocols::hybridization::add_non_protein_cst(), protocols::rna::RNA_DeNovoProtocol::add_number_base_pairs(), protocols::rna::RNA_DeNovoProtocol::add_number_native_base_pairs(), protocols::simple_moves::oop::add_oop_constraint(), protocols::loops::add_single_cutpoint_variant(), protocols::hybridization::add_strand_pairs_cst(), protocols::simple_moves::AddCavitiesMover::add_suckers(), core::scoring::dna::DNATorsionPotential::add_sugar_ring_closure_constraints(), protocols::swa::rna::StepWiseRNA_PoseSetup::add_terminal_res_repulsion(), protocols::swa::StepWisePoseSetup::add_terminal_res_repulsion(), core::scoring::geometric_solvation::add_to_individual_sol_energies(), core::pose::add_variant_type_to_pose_residue(), protocols::swa::rna::Add_virtual_O2Star_hydrogen(), protocols::relax::add_virtual_residue_to_cterm(), protocols::loops::addScoresForLoopParts(), core::pose::addVirtualResAsRoot(), protocols::kinmatch::alapose(), protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::align_all_pose(), protocols::swa::rna::align_poses(), protocols::hybridization::TMalign::alignment2AtomMap(), protocols::features::BetaTurnDetectionFeatures::all_turn_residues_are_on_the_same_chain(), core::scoring::methods::LK_hack::allocate_appropriate_memory(), core::scoring::Membrane_FAEmbed::allocate_appropriate_memory(), core::pack::rotamer_set::UnboundRotamersOperation::alter_rotamer_set(), protocols::toolbox::rotamer_set_operations::RigidBodyMoveBaseRSO::alter_rotamer_set(), annotated_sequence(), core::scoring::APBSConfig::APBSConfig(), protocols::ligand_docking::append_automorphic_rmsd(), protocols::ligand_docking::LigandDockProtocol::append_ligand_docking_scores(), protocols::ligand_docking::append_radius_of_gyration(), protocols::toolbox::AllowInsert::append_residue(), protocols::seeded_abinitio::GrowPeptides::append_residues_cterminally(), protocols::seeded_abinitio::GrowPeptides::append_residues_nterminally(), protocols::toolbox::pose_metric_calculators::append_rsd_by_jump_near_atom(), protocols::rna::RNA_StructureParameters::append_virtual_anchor(), protocols::RBSegmentRelaxImpl::apply(), protocols::simple_moves::AddConstraintsToCurrentConformationMover::apply(), protocols::simple_filters::ResidueBurialFilter::apply(), protocols::protein_interface_design::movers::TaskAwareCsts::apply(), protocols::simple_filters::ResidueDistanceFilter::apply(), protocols::protein_interface_design::movers::LoopLengthChange::apply(), protocols::qsar::qsarMover::apply(), protocols::simple_filters::PredictedBurialEvaluator::apply(), protocols::comparative_modeling::StealSideChainsMover::apply(), protocols::protein_interface_design::movers::AddChainBreak::apply(), protocols::protein_interface_design::movers::SetTemperatureFactor::apply(), protocols::simple_filters::NeighborTypeFilter::apply(), protocols::simple_filters::EnergyPerResidueFilter::apply(), protocols::simple_moves::oop::OopMover::apply(), protocols::ligand_docking::RandomConformerMover::apply(), protocols::protein_interface_design::movers::RandomMutation::apply(), protocols::antibody2::CloseOneCDRLoop::apply(), protocols::protein_interface_design::movers::SetAtomTree::apply(), protocols::simple_moves::PeptideStapleMover::apply(), protocols::protein_interface_design::filters::Torsion::apply(), protocols::protein_interface_design::movers::SpinMover::apply(), protocols::protein_interface_design::movers::PrepackMover::apply(), protocols::simple_moves::hbs::HbsPatcher::apply(), protocols::simple_moves::oop::OopPatcher::apply(), protocols::simple_moves::oop::OopRandomPuckMover::apply(), protocols::antibody2::GraftOneCDRLoop::apply(), protocols::comparative_modeling::Align_RotamerEvaluator::apply(), protocols::simple_moves::sidechain_moves::SetChiMover::apply(), protocols::frag_picker::nonlocal::NonlocalFrags::apply(), protocols::ligand_docking::LigandDesign::apply(), protocols::ligand_docking::RigidSearchMover::apply(), protocols::simple_moves::oop::OopRandomSmallMover::apply(), protocols::abinitio::DomainAssembly::apply(), protocols::domain_assembly::PostDockAssemblyScorer::apply(), protocols::enzdes::BackboneSampler::apply(), protocols::toolbox::task_operations::SelectBySASAOperation::apply(), protocols::ligand_docking::AddHydrogen::apply(), protocols::ligand_docking::GrowLigand::apply(), protocols::ligand_docking::AddHydrogens::apply(), protocols::rna::RNA_IdealCoord::apply(), protocols::simple_moves::MissingDensityToJumpMover::apply(), protocols::protein_interface_design::filters::FilterScanFilter::apply(), protocols::protein_interface_design::movers::BestHotspotCstMover::apply(), protocols::rigid::RotateJumpAxisMover::apply(), protocols::dna::RestrictDesignToProteinDNAInterface::apply(), protocols::simple_moves::RepulsiveOnlyMover::apply(), protocols::ligand_docking::CompleteConnectionsFilter::apply(), protocols::protein_interface_design::movers::BackrubDDMover::apply(), protocols::toolbox::task_operations::RestrictIdentitiesAtAlignedPositionsOperation::apply(), protocols::simple_moves::ModifyVariantTypeMover::apply(), protocols::swa::protein::StepWiseProteinPoseSetup::apply(), protocols::rigid::RollMover::apply(), protocols::rna::RNA_LoopCloser::apply(), protocols::simple_moves::chiral::ChiralMover::apply(), protocols::rna::RNA_HelixAssembler::apply(), protocols::analysis::LoopAnalyzerMover::apply(), protocols::canonical_sampling::SidechainMetropolisHastingsMover::apply(), protocols::protein_interface_design::movers::DesignMinimizeHbonds::apply(), protocols::simple_filters::ChiWellRmsdEvaluator::apply(), protocols::simple_moves::ReturnSidechainMover::apply(), protocols::protein_interface_design::movers::SaveAndRetrieveSidechains::apply(), protocols::simple_moves::MutateResidue::apply(), protocols::enzdes::EnzdesFlexBBProtocol::apply(), protocols::toolbox::task_operations::DesignAroundOperation::apply(), protocols::motifs::MotifDnaPacker::apply(), protocols::simple_moves::symmetry::SetupNCSMover::apply(), protocols::protein_interface_design::movers::PlacementAuctionMover::apply(), protocols::protein_interface_design::movers::LoopFinder::apply(), protocols::simple_moves::MakePolyXMover::apply(), protocols::design_opt::GreedyOptMutationMover::apply(), protocols::contact_map::ContactMap::apply(), protocols::antibody2::H3PerturbCCD::apply(), protocols::toolbox::task_operations::RestrictNativeResiduesOperation::apply(), protocols::hybridization::CartesianSampler::apply(), protocols::toolbox::task_operations::ProteinInterfaceDesignOperation::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_Backrub::apply(), protocols::rbsegment_relax::RBSegmentRelax::apply(), protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover::apply(), protocols::simple_filters::SheetFilter::apply(), protocols::hybridization::CartesianHybridize::apply(), protocols::comparative_modeling::ExtraThreadingMover::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::ligand_docking::Transform::apply(), protocols::rbsegment_relax::FragInsertAndAlignMover::apply(), protocols::protein_interface_design::movers::TryRotamers::apply(), core::pack::task::operation::NoRepackDisulfides::apply(), core::pack::task::operation::OptCysHG::apply(), protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::apply(), protocols::protein_interface_design::movers::PlaceStubMover::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::antibody::GraftMover::apply(), protocols::flxbb::InterlockAroma::apply(), protocols::simple_moves::carbohydrates::RingConformationMover::apply(), protocols::simple_moves::sidechain_moves::SidechainMCMover::apply(), protocols::comparative_modeling::MultiThreadingMover::apply(), protocols::relax::ClassicRelax::apply(), protocols::enzdes::DetectProteinLigandInterface::apply(), protocols::protein_interface_design::Revert::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::idealize::IdealizeMover::apply(), protocols::protein_interface_design::movers::Splice::apply(), protocols::simple_moves::sidechain_moves::SidechainMover::apply(), protocols::simple_moves::sidechain_moves::SidechainMoverBase::apply(), protocols::comparative_modeling::ThreadingMover::apply(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::apply(), protocols::enzdes::GenerateStoredRBConfs::apply(), protocols::antibody::GraftOneMover::apply(), protocols::fldsgn::CircularPermutation::apply(), protocols::hybridization::FoldTreeHybridize::apply(), protocols::flxbb::LayerDesignOperation::apply(), protocols::antibody::CloseOneMover::apply(), protocols::anchored_design::AnchoredPerturbMover::apply(), protocols::enzdes::ProteinLigandInterfaceUpweighter::apply(), protocols::antibody::LoopRlxMover::apply(), protocols::enzdes::RepackLigandSiteWithoutLigandMover::apply(), protocols::rbsegment_relax::SequenceShiftMover::apply(), protocols::anchored_design::AnchoredRefineMover::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::forge::components::VarLengthBuild::apply(), protocols::hybridization::TMalign::apply(), protocols::swa::rna::StepWiseRNA_ResidueSampler::apply_bulge_variant(), protocols::motifs::Motif::apply_check(), protocols::swa::StepWisePoseSetup::apply_cutpoint_variants(), protocols::hybridization::CartesianHybridize::apply_frag(), protocols::seeded_abinitio::SegmentHybridizer::apply_frame(), protocols::seeded_abinitio::PlaceFragments::apply_frame(), protocols::hybridization::CartesianSampler::apply_frame(), protocols::hybridization::CartesianHybridize::apply_frame(), protocols::simple_moves::apply_ideal_coordinates_for_alternative_pucker(), protocols::swa::StepWisePoseSetup::apply_peptide_plane_variants(), protocols::swa::rna::apply_protonated_H1_adenosine_variant_type(), protocols::swa::monte_carlo::RNA_TorsionMover::apply_random_nucleoside_torsion(), protocols::swa::protein::StepWiseProteinPacker::apply_regular_packer(), protocols::swa::protein::StepWiseProteinResidueSampler::apply_regular_packer(), protocols::loops::apply_sequence_mapping(), protocols::swa::StepWisePoseSetup::apply_terminus_variants_at_protein_rna_boundaries(), protocols::swa::rna::StepWiseRNA_PoseSetup::apply_virtual_phosphate_variants(), protocols::swa::StepWisePoseSetup::apply_virtual_phosphate_variants(), protocols::swa::rna::apply_virtual_rna_residue_variant_type(), protocols::rbsegment_relax::RBSegmentMover::applyRotation(), protocols::rbsegment_relax::RBSegmentMover::applyTransformation(), protocols::rbsegment_relax::RBSegmentMover::applyTranslation(), protocols::vip::are_seqs_different(), core::scoring::ScoreFunction::are_they_neighbors(), core::scoring::methods::ResidualDipolarCouplingEnergy_Rohl::assemble_datamatrix(), protocols::rna::assert_phosphate_nomenclature_matches_mini(), core::scoring::electron_density_atomwise::ElectronDensityAtomwise::atom_gradient(), core::pose::atom_id_to_named_atom_id(), protocols::hybridization::atom_map_valid_size(), core::optimization::symmetry::atom_tree_get_atompairE_deriv(), core::optimization::atom_tree_get_atompairE_deriv(), core::pack::scmin::AtomTreeCollection::AtomTreeCollection(), core::scoring::constraints::BackboneStubConstraint::BackboneStubConstraint(), protocols::LoopRebuild::barcode_extend_stems(), protocols::swa::rna::base_atoms_square_deviation(), protocols::rna::bases_form_a_hydrogen_bond(), protocols::idealize::basic_idealize(), protocols::toolbox::pose_metric_calculators::RotamerRecovery::bb_bins_from_pose(), core::pack::rotamer_set::bb_independent_rotamers(), core::scoring::orbitals::OrbitalsStatistics::bb_stats(), protocols::seeded_abinitio::SeedFoldTree::best_by_ala_scan(), protocols::features::BetaTurnDetectionFeatures::beta_turn_present(), core::scoring::biggest_residue_deviation_no_super(), core::scoring::biggest_residue_deviation_no_super_subset(), protocols::ligand_docking::MoveMapBuilder::build(), core::pack::rotamer_set::RotamerSet_::build_dependent_rotamers(), core::pack::rotamer_set::build_dna_rotamers(), core::pack::rotamer_set::build_fixed_O_water_rotamers_independent(), protocols::motifs::Motif::build_inverted_rotamers(), core::pack::rotamer_set::build_lib_dna_rotamers(), protocols::LoopRebuild::build_loop_with_ccd_closure(), core::pack::rotamer_set::build_moving_O_water_rotamers_dependent(), core::pack::rotamer_set::build_moving_O_water_rotamers_independent(), core::pack::rotamer_set::RotamerSet_::build_optimize_H_rotamers(), core::scoring::GenBornPotential::build_placeholders(), core::scoring::FACTSPotential::build_placeholders(), core::io::pdb::build_pose_as_is1(), core::pack::rotamer_set::build_random_dna_rotamers(), protocols::flexpack::rotamer_set::FlexbbRotamerSets::build_residue_vector_from_fragment(), core::pack::rotamer_set::build_rna_chi_rotamers(), core::pack::rotamer_set::build_rna_rotamers(), core::pack::rotamer_set::ContinuousRotamerSet::build_rotamers(), core::pack::rotamer_set::RotamerSet_::build_rotamers(), core::pack::rotamer_set::RotamerSets::build_rotamers(), protocols::motifs::Motif::build_rotamers(), core::pack::rotamer_set::RotamerSet_::build_rotamers_for_concrete_virt(), protocols::motifs::build_rotamers_lite(), protocols::motifs::MotifSearch::BuildPosition_from_Size(), protocols::flexpack::rotamer_set::FlexbbRotamerSet::bump_check(), core::pack::rotamer_set::RotamerSet_::bump_check(), protocols::match::bump_grid_to_enclose_pose(), core::scoring::sc::MolecularSurfaceCalculator::Calc(), protocols::features::helixAssembly::HelixBundleFeatures::calc_crossing_angles(), protocols::docking::calc_Fnat(), protocols::flexpep_docking::FlexPepDockingPoseMetrics::calc_frac_atoms_kA_to_native(), protocols::flexpep_docking::FlexPepDockingPoseMetrics::calc_frac_native_contacts(), protocols::features::helixAssembly::HelixBundleFeatures::calc_pc_and_com(), core::scoring::calc_per_atom_sasa(), core::scoring::calc_per_res_hydrophobic_sasa(), protocols::protein_interface_design::ReportPSSMDifferences::calculate(), protocols::protein_interface_design::ReportSequenceDifferences::calculate(), protocols::scoring::Interface::calculate(), protocols::dna::DNAParameters::calculate(), core::pose::carbohydrates::calculate_carbohydrate_phi(), core::scoring::methods::ContactOrderEnergy::calculate_contact_order(), core::scoring::methods::LK_hack::calculate_derivatives_for_residue_pair(), protocols::pmut_scan::PointMutScanDriver::calculate_neighbor_table(), core::scoring::methods::LK_hack::calculate_orientation_vectors_and_pseudo_base_atoms(), protocols::pockets::NonPlaidFingerprint::calculate_protein_CoM(), core::scoring::methods::RG_Energy_Fast::calculate_rg_score(), protocols::scoring::methods::pcs::PCS_Energy::calculate_scores_and_tensors_from_pose_and_PCS_data(), core::scoring::calpha_superimpose_pose(), core::sequence::calpha_superimpose_with_mapping(), core::pose::canonical_atom_count(), core::pose::canonical_residue_count(), core::optimization::cartesian_collect_atompairE_deriv(), core::scoring::packstat::cavity_distance_constraint(), protocols::sic_dock::cb_weight_map_from_pose(), protocols::sic_dock::cb_weights_from_pose(), protocols::loops::loop_closure::ccd::ccd_moves(), protocols::antibody2::CDR_H3_cter_filter(), protocols::antibody::CDRH3Modeler::CDR_H3_filter(), protocols::antibody2::CDR_H3_filter_legacy_code_with_old_rule(), protocols::scoring::Interface::center(), center(), protocols::hybridization::FoldTreeHybridize::center_of_mass(), protocols::geometry::center_of_mass(), protocols::fldsgn::BluePrintBDR::centroid_build(), protocols::forge::components::BDR::centroid_build(), protocols::forge::components::VarLengthBuild::centroid_build(), protocols::ub_e2c::ubi_e2c_modeler::centroid_mode_perturbation(), protocols::geometry::centroids_by_jump(), protocols::geometry::centroids_by_jump_int(), chain(), protocols::swa::rna::StepWiseRNA_ResidueSampler::Chain_break_screening_general(), protocols::simple_moves::CutChainMover::chain_cut(), chain_sequence(), protocols::hybridization::HybridizeProtocol::check_and_create_fragments(), protocols::rna::check_base_pair(), protocols::features::helixAssembly::HelixBundleFeatures::check_cap_distances(), protocols::swa::rna::Check_chain_closable(), protocols::swa::rna::Check_chain_closable_floating_base(), protocols::topology_broker::TopologyBroker::check_chainbreak_variants(), core::scoring::rna::RNA_LowResolutionPotential::check_clear_for_stacking(), protocols::rna::RNA_LoopCloser::check_closure(), protocols::swa::rna::check_floating_base_chain_closable(), protocols::swa::rna::check_for_messed_up_structure(), core::scoring::rna::RNA_LowResolutionPotential::check_forming_base_pair(), protocols::rna::RNA_StructureParameters::check_forward_backward(), protocols::swa::RigidBodySampler::check_o2star_needs_optimization(), protocols::hybridization::InsertChunkMover::check_overlap(), protocols::rna::RNA_ChunkLibrary::check_res_map(), protocols::features::strand_assembly::StrandBundleFeatures::check_sheet_dis_antiparallel(), protocols::features::strand_assembly::StrandBundleFeatures::check_sheet_dis_parallel(), core::scoring::MembranePotential::check_spanning(), chi(), protocols::toolbox::pose_metric_calculators::RotamerRecovery::chis_from_pose(), protocols::loops::Loop::choose_cutpoint(), protocols::enzdes::PackRotamersMoverPartGreedy::choose_n_best(), protocols::scoring::ImplicitFastClashCheck::clash_check_trimer(), core::scoring::electron_density::ElectronDensity::clear_dCCdx_res_cache(), protocols::antibody::CloseOneMover::close_one_loop_stem(), protocols::scoring::Interface::closest_interface_residue(), protocols::enzdes::ModifyStoredRBConfs::closest_orient_atoms_msd(), core::coarse::TranslatorSet::coarsify(), core::scoring::constraints::combine_NMR_atom_string(), protocols::seeded_abinitio::combine_two_poses(), core::pose::compare_atom_coordinates(), protocols::simple_moves::GreenPacker::compare_input_pose_geometry_to_reference(), core::pack::compare_mingraph_and_energy_graph(), protocols::simple_filters::ResidueBurialFilter::compute(), protocols::simple_filters::InterfaceSasaFilter::compute(), protocols::simple_filters::NeighborTypeFilter::compute(), protocols::simple_filters::AtomicDistanceFilter::compute(), protocols::simple_filters::AtomicContactFilter::compute(), protocols::simple_filters::TerminusDistanceFilter::compute(), protocols::protein_interface_design::filters::AverageDegreeFilter::compute(), protocols::protein_interface_design::filters::DesignableResiduesFilter::compute(), protocols::simple_filters::RotamerBoltzmannWeight::compute(), protocols::simple_filters::ResidueIEFilter::compute(), protocols::protein_interface_design::filters::AtomicContactCountFilter::compute(), protocols::simple_filters::ResidueCountFilter::compute(), core::scoring::dssp::Dssp::compute(), protocols::enzdes::LigBurialFilter::compute(), protocols::simple_filters::ShapeComplementarityFilter::compute(), protocols::fldsgn::filters::InterlockingAromaFilter::compute(), protocols::enzdes::DiffAtomSasaFilter::compute(), protocols::enzdes::RepackWithoutLigandFilter::compute(), protocols::features::LoopAnchorFeatures::compute_anchor_transform(), core::scoring::methods::compute_and_store_pose_waters(), protocols::features::LoopAnchorFeatures::compute_atom_angles(), core::scoring::packstat::compute_atom_packing_scores(), protocols::noesy_assign::FragsToAtomDist::compute_average_distances(), protocols::sasa_scores::compute_avge_scores(), protocols::simple_filters::RotamerBoltzmannWeight::compute_Boltzmann_weight(), core::scoring::EnvPairPotential::compute_centroid_environment(), core::scoring::SmoothEnvPairPotential::compute_centroid_environment(), core::scoring::ChemicalShiftAnisotropy::compute_csascore(), protocols::simple_filters::SymmetricMotifFilter::compute_d2(), core::scoring::SmoothEnvPairPotential::compute_dcentroid_environment(), core::scoring::DipolarCoupling::compute_dcscore(), protocols::enzdes::PackRotamersMoverPartGreedy::compute_designable_neighbors(), core::scoring::ResidualDipolarCoupling::compute_dipscore(), core::scoring::ResidualDipolarCoupling::compute_dipscore_nls(), core::scoring::ResidualDipolarCoupling::compute_dipscore_nlsDa(), core::scoring::ResidualDipolarCoupling::compute_dipscore_nlsDaR(), core::scoring::ResidualDipolarCoupling::compute_dipscore_nlsR(), core::scoring::saxs::SAXSEnergy::compute_distance_histogram(), protocols::features::StructureScoresFeatures::compute_energies(), core::scoring::geometric_solvation::compute_exact_geosol(), protocols::hybridization::CartesianSampler::compute_fragment_bias(), protocols::toolbox::pose_metric_calculators::NumberHBondsCalculator::compute_Hbonds_for_residue(), core::scoring::packing::compute_holes_deriv_res(), core::scoring::packing::compute_holes_score_res(), protocols::analysis::InterfaceAnalyzerMover::compute_interface_sc(), protocols::pockets::PlaidFingerprint::compute_ligand_resnum(), core::scoring::disulfides::DisulfideMatchingPotential::compute_matching_energy(), core::scoring::MembranePotential::compute_membrane_embedding(), protocols::simple_filters::RotamerBoltzmannWeight::compute_modified_ddG(), core::scoring::electron_density_atomwise::ElectronDensityAtomwise::compute_normalization(), protocols::vip::VIP_Mover::compute_number_cavities(), core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::compute_one_body_energies(), core::pack::rotamer_set::RotamerSet_::compute_one_body_energies(), core::pack::rotamer_set::RotamerSet_::compute_one_body_energy_maps(), protocols::scoring::methods::saxs::PDDFEnergy::compute_pddf(), protocols::scoring::methods::saxs::PDDFEnergy::compute_pddf_without_ff(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_polar_group_sol_energy(), core::pack::interaction_graph::SurfacePotential::compute_pose_hpatch_score(), core::pack::interaction_graph::SurfacePotential::compute_pose_surface_energy(), protocols::simple_filters::NMerPSSMEnergyFilter::compute_residue(), core::pack::interaction_graph::SurfacePotential::compute_residue_surface_energy(), protocols::optimize_weights::IterativeOptEDriver::compute_rotamers_around_ligands(), protocols::sasa_scores::compute_sasapack_scores(), core::scoring::electron_density::ElectronDensity::compute_symm_rotations(), protocols::forge::remodel::RemodelMover::confirm_sequence(), protocols::backrub::connected_mainchain_atomids(), protocols::toolbox::match_enzdes_util::constrain_pose_res_to_invrots(), protocols::flxbb::constraints_sheet(), protocols::relax::coordinate_constrain_selection(), protocols::swa::rna::copy_all_o2star_torsions(), protocols::swa::rna::StepWiseRNA_ResidueSampler::Copy_CCD_torsions_general(), protocols::swa::StepWiseScreener::copy_coords(), protocols::swa::protein::StepWiseProteinScreener::copy_coords(), core::pose::copy_dofs(), protocols::topology_broker::copy_internal_coords(), protocols::swa::StepWisePoseSetup::copy_rna_chi(), protocols::abinitio::copy_side_chains(), protocols::abinitio::AbrelaxApplication::copy_structure(), protocols::swa::rna::copy_torsions_FROM_TO(), core::scoring::APBSWrapper::count_atoms(), protocols::sic_dock::count_CBs(), protocols::forge::methods::count_cutpoints(), protocols::swa::create_alignment_id_map(), protocols::swa::rna::create_alignment_id_map(), protocols::protein_interface_design::movers::SetAtomTree::create_atom_tree(), protocols::enzdes::EnzdesBaseProtocol::create_enzdes_movemap(), protocols::floppy_tail::create_extra_output(), protocols::hotspot_hashing::HotspotStubSet::create_hotspot_after_pose(), core::pack::create_minimization_graph(), protocols::enzdes::enzutil::create_remark_headers_from_cstcache(), protocols::rna::create_rna_vall_torsions(), protocols::protein_interface_design::movers::MapHotspot::create_rotamer_set(), protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::create_rotamer_string(), protocols::swa::rna::StepWiseRNA_ResidueSampler::create_rotamer_string(), core::pack::create_scmin_minimizer_map(), protocols::swa::rna::create_standard_o2star_pack_task(), protocols::simple_moves::CutChainMover::create_subpose(), core::pose::create_subpose(), protocols::toolbox::DecoySetEvaluation::create_xyz_constraints_median(), protocols::enzdes::EnzdesBaseProtocol::cst_minimize(), protocols::toolbox::match_enzdes_util::cst_residue_in_pose(), protocols::vip::VIP_Mover::cull_mutatable_residues(), protocols::dna::DnaInterfacePacker::current_working_sequence(), protocols::antibody::CDRH3Modeler::cutpoint_separation(), protocols::antibody2::cutpoint_separation(), protocols::forge::methods::cyclize_pose(), core::scoring::electron_density::ElectronDensity::dCCdx_fastRes(), protocols::simple_filters::AlaScan::ddG_for_single_residue(), core::io::raw_data::DecoyStruct::DecoyStruct(), core::scoring::electron_density::PattersonCorrEnergy::defines_residue_pair_energy(), core::scoring::electron_density::ElecDensEnergy::defines_residue_pair_energy(), core::scoring::electron_density::FastDensEnergy::defines_residue_pair_energy(), core::scoring::electron_density_atomwise::ElecDensAtomwiseEnergy::defines_residue_pair_energy(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::defines_residue_pair_energy(), core::scoring::electron_density::ElecDensCenEnergy::defines_residue_pair_energy(), protocols::relax::derive_sc_sc_restraints(), protocols::simple_moves::PeptideStapleMover::derive_staple_constraints_(), core::scoring::etable::CoarseEtableEnergy::derived_prepare_for_residue_pair(), protocols::forge::remodel::RemodelMover::design_refine(), protocols::antibody2::AntibodyInfo::detect_and_set_regular_CDR_H3_stem_type(), protocols::antibody2::AntibodyInfo::detect_and_set_regular_CDR_H3_stem_type_new_rule(), core::pack::interaction_graph::SurfaceNode< V, E, G >::detect_neighborship_with_node(), protocols::antibody::Antibody::detect_regular_CDR_H3_stem_type(), protocols::dna::DnaInterfaceFinder::determine_dna_interface(), protocols::enzdes::EnzdesFlexBBProtocol::determine_flexible_regions(), protocols::dna::DnaInterfaceFinder::determine_protein_interface(), protocols::flexpack::rotamer_set::FlexbbRotamerSets::determine_res_cb_deviation(), protocols::idealize::dihedral_distance(), protocols::ligand_docking::ResidueTorsionRestraints::disable(), protocols::hybridization::discontinued_lower(), protocols::hybridization::discontinued_upper(), protocols::antibody::AntibodyModeler::display_constraint_residues(), protocols::antibody2::GraftCDRLoopsProtocol::display_constraint_residues(), protocols::antibody2::AntibodyModelerProtocol::display_constraint_residues(), core::scoring::methods::LK_hack::distribute_pseudo_base_atom_derivatives(), protocols::protein_interface_design::movers::DisulfideMover::disulfide_list(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::disulfides_changed(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::disulfides_changed(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::disulfides_changed(), protocols::enzdes::DiversifyStoredRBConfs::diversify_all_confs(), protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::diversify_backbone_only_rotamers(), core::scoring::methods::LinearChainbreakEnergy::do_score_ovp(), core::scoring::dssp::Dssp::Dssp(), core::import_pose::atom_tree_diffs::dump_atom_tree_diff(), core::io::pdb::dump_bfactor_pdb(), core::io::pdb::dump_connect_info(), protocols::anchored_design::dump_cutpoint_info(), core::fragment::dump_frames_as_pdb(), core::pack::rotamer_set::RotamerSets::dump_pdb(), core::io::pdb::dump_pdb(), protocols::flexpack::rotamer_set::FlexbbRotamerSets::dump_pdbs(), protocols::jobdist::PlainPdbJobDistributor::dump_scores(), core::scoring::electron_density::ElectronDensity::ElectronDensity(), protocols::ligand_docking::ResidueTorsionRestraints::enable(), protocols::ligand_docking::HighResDocker::enable_ligand_rotamer_packing(), protocols::ligand_docking::InterfaceBuilder::enforce_minimum_length(), protocols::rna::ensure_phosphate_nomenclature_matches_mini(), protocols::rigid::MovePoseToMembraneCenterMover::estimate_membrane_center(), core::scoring::methods::Fa_MbsolvEnergy::eval_atom_derivative(), core::scoring::rna::RNA_TorsionPotential::eval_atom_derivative(), core::scoring::saxs::FastSAXSEnergy::eval_atom_derivative(), core::scoring::rna::RNA_LJ_BaseEnergy::eval_atom_derivative(), core::scoring::methods::Fa_MbenvEnergy::eval_atom_derivative(), core::scoring::methods::LK_hack::eval_atom_derivative(), core::scoring::methods::ChainbreakEnergy::eval_atom_derivative(), core::scoring::methods::SymmetricLigandEnergy::eval_atom_derivative(), core::scoring::methods::MMLJEnergyIntra::eval_atom_derivative(), core::scoring::methods::SuckerEnergy::eval_atom_derivative(), core::scoring::rna::RG_Energy_RNA::eval_atom_derivative(), core::scoring::hackaro::HackAroEnergy::eval_atom_derivative(), core::scoring::methods::EnvSmoothEnergy::eval_atom_derivative(), core::scoring::methods::MembraneEnvSmoothEnergy::eval_atom_derivative(), core::scoring::methods::LK_CosThetaEnergy::eval_atom_derivative(), core::scoring::rna::RNA_FullAtomVDW_BasePhosphate::eval_atom_derivative(), core::scoring::methods::LinearChainbreakEnergy::eval_atom_derivative(), core::scoring::rna::RNA_FullAtomStackingEnergy::eval_atom_derivative(), core::scoring::methods::ResidualDipolarCouplingEnergy::eval_atom_derivative(), core::scoring::methods::ChemicalShiftAnisotropyEnergy::eval_atom_derivative(), core::scoring::methods::DipolarCouplingEnergy::eval_atom_derivative(), core::scoring::methods::HybridVDW_Energy::eval_atom_derivative(), core::scoring::methods::RG_Energy_Fast::eval_atom_derivative(), core::scoring::methods::DNA_BaseEnergy::eval_atom_derivative(), core::scoring::methods::VDW_Energy::eval_atom_derivative(), core::scoring::rna::RNA_DataBackboneEnergy::eval_atom_derivative(), core::scoring::rna::RNA_VDW_Energy::eval_atom_derivative(), core::scoring::methods::MMTorsionEnergy::eval_atom_derivative(), core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy::eval_atom_derivative(), core::scoring::methods::MMBondLengthEnergy::eval_atom_derivative(), core::scoring::geometric_solvation::GeometricSolEnergy::eval_atom_derivative(), core::scoring::methods::MMBondAngleEnergy::eval_atom_derivative(), core::scoring::methods::MMLJEnergyInter::eval_atom_derivative(), core::scoring::methods::ResidualDipolarCouplingEnergyRigidSegments::eval_atom_derivative(), core::scoring::electron_density_atomwise::ElecDensAtomwiseEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::eval_atom_derivative(), core::scoring::electron_density::PattersonCorrEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensCenEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensEnergy::eval_atom_derivative(), core::scoring::electron_density::FastDensEnergy::eval_atom_derivative(), core::scoring::hackelec::HackElecEnergyAroAll::eval_atom_derivative(), core::scoring::hackelec::HackElecEnergyAroAro::eval_atom_derivative(), core::scoring::hackelec::RNAHackElecEnergy::eval_atom_derivative(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::eval_atom_derivative(), core::scoring::GenBornPotential::eval_atom_derivative(), core::scoring::etable::BaseEtableEnergy< Derived >::eval_atom_derivative(), core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_base_base(), core::scoring::methods::LK_CosThetaEnergy::eval_atom_derivative_intra_RNA(), core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy::eval_atom_derivative_intra_RNA(), core::scoring::geometric_solvation::GeometricSolEnergy::eval_atom_derivative_intra_RNA(), core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_rna_backbone_backbone(), core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_rna_base_backbone(), core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_rna_repulsive(), core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy::eval_atom_energy(), core::scoring::geometric_solvation::GeometricSolEnergy::eval_atom_energy(), core::scoring::rna::RNA_LJ_BaseEnergy::eval_atom_energy(), core::scoring::FACTSPotential::eval_atom_nonpolar_derivative(), core::scoring::FACTSPotential::eval_atom_polar_derivative(), core::scoring::dna::DNAChiEnergy::eval_dof_derivative(), core::scoring::methods::RamachandranEnergy2B::eval_dof_derivative(), core::scoring::methods::RamachandranEnergy::eval_dof_derivative(), core::scoring::methods::P_AA_pp_Energy::eval_dof_derivative(), core::pack::dunbrack::DunbrackEnergy::eval_dof_derivative(), core::scoring::symmetry::SymmetricScoreFunction::eval_dof_derivative(), core::scoring::ScoreFunction::eval_dof_derivative(), core::scoring::methods::CartesianBondedEnergy::eval_intraresidue_dof_derivative(), core::scoring::symmetry::SymmetricScoreFunction::eval_long_range_twobody_energies(), core::scoring::ScoreFunction::eval_long_range_twobody_energies(), core::scoring::OmegaTether::eval_omega_score_all(), core::scoring::symmetry::SymmetricScoreFunction::eval_onebody_energies(), core::scoring::ScoreFunction::eval_onebody_energies(), core::scoring::Ramachandran::eval_rama_score_all(), core::scoring::Ramachandran2B::eval_rama_score_all(), core::scoring::symmetry::SymmetricScoreFunction::eval_twobody_neighbor_energies(), core::scoring::ScoreFunction::eval_twobody_neighbor_energies(), core::scoring::MembranePotential::evaluate_env(), core::scoring::methods::MMLJEnergyInter::evaluate_rotamer_background_energies(), core::scoring::methods::FACTSEnergy::evaluate_rotamer_background_energies(), core::scoring::hackelec::HackElecEnergy::evaluate_rotamer_background_energies(), core::scoring::hbonds::HBondEnergy::evaluate_rotamer_background_energies(), core::scoring::etable::BaseEtableEnergy< Derived >::evaluate_rotamer_background_energies(), core::scoring::methods::FACTSEnergy::evaluate_rotamer_background_energy_maps(), core::scoring::methods::FACTSEnergy::evaluate_rotamer_intrares_energies(), core::scoring::methods::GenBornEnergy::evaluate_rotamer_intrares_energies(), core::scoring::methods::FACTSEnergy::evaluate_rotamer_intrares_energy_maps(), core::scoring::methods::GenBornEnergy::evaluate_rotamer_intrares_energy_maps(), core::scoring::methods::FACTSEnergy::evaluate_rotamer_pair_energies(), core::scoring::methods::GenBornEnergy::evaluate_rotamer_pair_energies(), core::scoring::hackelec::HackElecEnergy::evaluate_rotamer_pair_energies(), core::scoring::hbonds::HBondEnergy::evaluate_rotamer_pair_energies(), protocols::hotspot_hashing::HotspotStubSet::evaluate_stub_bumps_(), protocols::hotspot_hashing::HotspotStubSet::evaluate_stub_self_energy_(), protocols::enzdes::EnzdesFlexibleRegion::examine_new_loopconf(), protocols::enzdes::EnzdesBaseProtocol::exchange_ligands_in_pose(), protocols::hotspot_hashing::movers::PlaceProbeMover::execute_one_search(), protocols::loops::extend_sequence_mapping(), core::pose::symmetry::extract_asymmetric_unit(), core::pose::symmetry::extract_asymmetric_unit_pdb_info(), core::io::pdb::extract_scores(), core::scoring::Membrane_FAPotential::fa_projection(), protocols::electron_density::fast2DRotAlignPose(), protocols::loops::loop_closure::ccd::fast_ccd_loop_closure(), protocols::toolbox::pose_metric_calculators::fast_clash_check(), protocols::forge::remodel::fast_clash_check(), protocols::swa::rna::fast_full_atom_VDW_repulsion_screen(), protocols::electron_density::fastTransAlignPose(), protocols::swa::rna::StepWiseRNA_Minimizer::figure_out_actual_five_prime_chain_break_res(), protocols::swa::rna::RNA_AnalyticLoopCloser::figure_out_dof_ids_and_offsets(), protocols::swa::rna::StepWiseRNA_Minimizer::Figure_out_moving_residues(), protocols::swa::Figure_out_moving_residues(), protocols::rna::figure_out_reasonable_rna_fold_tree(), protocols::hotspot_hashing::HotspotStubSet::fill(), protocols::frag_picker::scores::FragmentDME::fill_CA_coords(), protocols::frag_picker::scores::FragmentCrmsd::fill_CA_coords(), protocols::frag_picker::scores::FragmentCrmsdResDepth::fill_CA_coords(), protocols::swa::protein::StepWiseProteinLoopBridger::fill_chainTORS_info(), protocols::contact_map::ContactMap::fill_contacts(), protocols::frag_picker::scores::FragmentAllAtomCrmsd::fill_coords(), core::scoring::WaterAdductHBondPotential::fill_h2o_hbond_set(), core::scoring::dssp::fill_hbond_bb_pair_score_dssp(), core::scoring::hbonds::fill_hbond_set(), core::scoring::hbonds::fill_hbond_set_by_AHdist_threshold(), protocols::rna::RNA_StructureParameters::fill_in_default_jump_atoms(), core::scoring::hbonds::fill_intra_res_hbond_set(), protocols::pmut_scan::PointMutScanDriver::fill_mutations_list(), protocols::forge::methods::fill_non_loop_cst_set(), core::io::raw_data::DecoyStruct::fill_pose(), core::io::silent::BinaryProteinSilentStruct::fill_pose(), core::io::silent::RNA_SilentStruct::fill_pose(), core::scoring::fill_rmsd_coordinates(), core::io::silent::BinaryRNASilentStruct::fill_struct(), core::io::silent::BinaryProteinSilentStruct::fill_struct(), core::io::silent::ProteinSilentStruct_Template< T >::fill_struct(), core::io::silent::RNA_SilentStruct::fill_struct(), protocols::anchored_design::AnchoredDesignMover::filter(), protocols::loops::filter_loop_neighbors_by_distance(), core::scoring::methods::RG_Energy::finalize_total_energy(), core::scoring::methods::MembraneLipo::finalize_total_energy(), core::scoring::methods::ChainbreakEnergy::finalize_total_energy(), core::scoring::methods::DistanceChainbreakEnergy::finalize_total_energy(), core::scoring::methods::DirectReadoutEnergy::finalize_total_energy(), core::scoring::methods::LinearChainbreakEnergy::finalize_total_energy(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::finalize_total_energy(), core::scoring::hackelec::HackElecEnergy::finalize_total_energy(), core::scoring::etable::BaseEtableEnergy< Derived >::finalize_total_energy(), protocols::features::strand_assembly::StrandBundleFeatures::find_antiparallel(), protocols::ligand_docking::find_attach_pt(), core::scoring::dna::find_basepairs(), protocols::dna::find_basepairs(), protocols::motifs::IRCollection::find_closest_backbone(), protocols::forge::methods::find_cutpoint(), protocols::enzdes::DetectProteinLigandInterface::find_design_interface(), protocols::enzdes::DetectProteinLigandInterface::find_design_interface_arg_sweep(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::find_disulfides(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::find_disulfides(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::find_disulfides(), protocols::forge::remodel::RemodelDesignMover::find_disulfides_in_the_neighborhood(), protocols::enzdes::PredesignPerturbMover::find_geometric_center_for_constrained_lig_atoms(), protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::find_in_pose_if_missing_from_header(), protocols::ligand_docking::LigandBaseProtocol::find_interface_backbone(), core::pack::task::operation::util::find_interface_pointing_residues_from_neighbs(), protocols::ligand_docking::LigandBaseProtocol::find_interface_rsds(), protocols::flxbb::find_ligands(), protocols::ddg::ddGMover::find_nbrs(), protocols::rosetta_scripts::find_nearest_res(), protocols::protein_interface_design::find_nearest_residue(), protocols::protein_interface_design::movers::find_nearest_residue_to_coord(), protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockMoveRbJumpMover::find_new_jump_residue(), core::pose::symmetry::find_new_symmetric_jump_residues(), protocols::loophash::FastGapMover::find_next_gap(), protocols::features::strand_assembly::StrandBundleFeatures::find_parallel(), protocols::analysis::LoopAnalyzerMover::find_positions(), protocols::ligand_docking::InterfaceBuilder::find_protein_residues(), protocols::toolbox::pose_metric_calculators::find_res_unsat_polars(), core::pack::find_residue_max_radii(), protocols::enzdes::PredesignPerturbMover::find_rotation_center(), core::pose::symmetry::find_symmetric_basejump_anchor(), protocols::ligand_docking::find_unconnected_residues(), protocols::electron_density::findLoopFromDensity(), protocols::electron_density::findLoopFromPatterson(), protocols::simple_filters::RotamerBoltzmannWeight::first_pass_ala_scan(), protocols::topology_broker::fix_internal_coords_of_siblings(), protocols::topology_broker::fix_mainchain_connect(), protocols::swa::StepWisePoseSetup::fix_phi_psi_offsets(), core::scoring::rna::fix_sugar_coords(), core::scoring::rna::fix_sugar_coords_WORKS_BUT_SLOW(), protocols::loops::fix_with_coord_cst(), protocols::forge::methods::fixH(), protocols::swa::rna::floating_base_chain_closure_sampling(), protocols::swa::rna::floating_base_chain_closure_setup(), protocols::swa::rna::StepWiseRNA_ResidueSampler::floating_base_sampling(), protocols::protein_interface_design::movers::Splice::fold_tree(), protocols::forge::methods::fold_tree_from_loops(), protocols::loops::fold_tree_from_loops(), protocols::forge::methods::fold_tree_from_pose(), protocols::swa::rna::full_length_rmsd_over_residue_list(), protocols::ub_e2c::ubi_e2c_modeler::fullatom_mode_perturbation(), protocols::comparative_modeling::gather_coords(), core::scoring::gdtha(), core::scoring::gdtsc(), protocols::toolbox::match_enzdes_util::EnzConstraintParameters::generate_active_pose_constraints(), protocols::enzdes::EnzdesFlexBBProtocol::generate_alc_ensemble_for_region(), protocols::enzdes::EnzdesFlexBBProtocol::generate_backrub_ensemble_for_region(), protocols::relax::generate_bb_coordinate_constraints(), protocols::topology_broker::CoordConstraintClaimer::generate_constraints(), protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMover::generate_csts(), protocols::enzdes::EnzdesBaseProtocol::generate_explicit_ligand_rotamer_poses(), protocols::abinitio::AbrelaxApplication::generate_extended_pose(), protocols::fldsgn::SheetConstraintsRCG::generate_remodel_constraints(), protocols::protein_interface_design::movers::MapHotspot::GenerateMap(), core::scoring::GenBornPotential::get_all_born_radii(), core::pose::symmetry::get_asymmetric_pose_copy_from_symmetric_pose(), core::scoring::dna::DNATorsionPotential::get_atom_ids_by_torsion(), protocols::swa::get_base_centroid_and_rotation_matrix(), protocols::rna::get_base_pairing_info(), protocols::rna::get_base_pairing_list(), core::scoring::methods::LK_CosThetaEnergy::get_base_vector(), protocols::swa::rna::get_binary_rna_silent_struct_safe(), protocols::match::BfactorMPM::get_ca_bfactors(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_calc_chem_shift_value(), protocols::vip::VIP_Mover::get_cav_approx(), protocols::vip::VIP_Mover::get_cavity_positions(), protocols::sic_dock::get_CB_Vecs(), core::pose::get_chain_residues(), protocols::rna::RNA_LoopCloser::get_chainbreak_xyz(), protocols::simple_moves::AddCavitiesMover::get_closest_heavy_atom(), protocols::rna::RNA_ChunkLibrary::get_component_sequences(), protocols::simple_filters::get_contact_features(), core::scoring::methods::MMLJEnergyIntra::get_count_pair_function(), core::scoring::etable::BaseEtableEnergy< Derived >::get_count_pair_function(), core::scoring::methods::MMLJEnergyInter::get_count_pair_function(), core::scoring::hackelec::HackElecEnergy::get_count_pair_function(), core::scoring::methods::MMLJEnergyInter::get_count_pair_function_trie(), core::scoring::hackelec::HackElecEnergy::get_count_pair_function_trie(), core::scoring::etable::BaseEtableEnergy< Derived >::get_count_pair_function_trie(), core::io::silent::BinaryRNASilentStruct::get_debug_rmsd(), core::io::silent::BinaryProteinSilentStruct::get_debug_rmsd(), core::io::silent::RNA_SilentStruct::get_debug_rmsd(), core::io::silent::ProteinSilentStruct_Template< T >::get_debug_rmsd(), protocols::swa::rna::get_default_allowed_bulge_res(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_deriv_for_chemical_shift_data_atom(), protocols::cluster::GatherPosesMover::get_distance_measure(), protocols::toolbox::IGLigandDesignEdgeUpweighter::get_edge_reweight(), protocols::pockets::DelphiElectrostatics::get_electrostatics_energy(), protocols::rna::RNA_LoopCloser::get_extra_cutpoints(), protocols::toolbox::match_enzdes_util::get_first_protein_residue(), protocols::toolbox::match_enzdes_util::InvrotTreeNode::get_fixed_pt(), protocols::rna::RNA_LoopCloser::get_gap_distance(), protocols::vip::VIP_Report::get_GOE_packstat_report(), protocols::vip::VIP_Report::get_GOE_relaxed_report(), protocols::vip::VIP_Report::get_GOE_repack_report(), protocols::features::helixAssembly::HelixBundleFeatures::get_helix_pairs(), protocols::simple_moves::BBConRotMover::get_L_move(), protocols::toolbox::match_enzdes_util::get_last_protein_residue(), protocols::sic_dock::get_leap_lower_stub(), protocols::sic_dock::get_leap_upper_stub(), protocols::ligand_docking::LigandBaseProtocol::get_ligand_id(), protocols::ligand_docking::get_ligand_torsion_constraints(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_magnetic_anisotropy_deriv_for_src_atom(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_magnetic_anisotropy_deriv_for_src_base(), protocols::swa::StepWiseScreener::get_main_chain_torsion_set_list(), protocols::swa::protein::StepWiseProteinScreener::get_main_chain_torsion_set_list(), protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::get_matching_res_in_VDW_rep_screen_pose(), protocols::optimize_weights::IterativeOptEDriver::get_nat_aa_opte_data(), protocols::optimize_weights::IterativeOptEDriver::get_nat_rot_opte_data(), protocols::swa::rna::StepWiseRNA_PoseSetup::get_nearest_dist_to_O2star(), protocols::hotspot_hashing::HotspotStub::get_nearest_residue(), protocols::vip::VIP_Mover::get_neighbors(), protocols::ligand_docking::LigandBaseProtocol::get_non_bb_clashing_rotamers(), protocols::hybridization::get_num_residues_nonvirt(), protocols::rna::get_o1p_o2p_sign(), protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::get_pose_data(), protocols::swa::protein::get_pretend_phi_explicit(), protocols::swa::rna::StepWiseRNA_JobParameters_Setup::get_previously_closed_cutpoint_from_imported_silent_file(), protocols::simple_filters::AbinitioBaseFilter::get_protein_sstype(), protocols::swa::monte_carlo::RNA_O2StarMover::get_random_o2star_residue_near_moving_residue(), protocols::swa::rna::StepWiseRNA_ResidueSampler::get_reference_stub(), protocols::swa::rna::Get_residue_base_state(), protocols::swa::rna::Get_residue_pucker_state(), protocols::hotspot_hashing::HotspotStubSet::get_residue_score_(), protocols::rna::RNA_HelixAssembler::get_rid_of_capping_base_pairs(), protocols::hotspot_hashing::SearchPatternRotSetOp::get_rigid_body_confs(), protocols::enzdes::ModifyStoredRBConfs::get_rigid_body_confs(), protocols::rna::get_rigid_body_jumps(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_ring_current_deriv_for_src_base(), protocols::loophash::get_rt_over_leap_without_foldtree_bs(), core::scoring::FACTSPotential::get_single_rotamer_born_radii(), core::scoring::GenBornPotential::get_single_rotamer_born_radii(), protocols::motifs::LigandMotifSearch::get_sphere_aa(), protocols::rna::RNA_StructureParameters::get_stem_residues(), protocols::hybridization::get_superposition_transformation(), protocols::swa::rna::get_surrounding_O2star_hydrogen(), core::pose::symmetry::get_symm_axis(), core::scoring::GenBornPotential::get_template_born_radii(), core::scoring::FACTSPotential::get_template_born_radii(), protocols::enzdes::EnzdesFlexBBProtocol::get_tenA_neighbor_residues(), protocols::loops::get_tenA_neighbor_residues(), protocols::sic_dock::get_termini_from_pose(), protocols::simple_moves::BBConRotMover::get_VdRdPhi(), protocols::simple_moves::BBG8T3AMover::get_VdRdPhi(), protocols::rbsegment_relax::RBSegmentMover::getCoM(), protocols::rbsegment_relax::HelicalGaussianMover::getCoordinateTransformation(), protocols::rbsegment_relax::StrandTwistingMover::getCoordinateTransformation(), protocols::ligand_docking::grid_rotamer_trials_atr_rep(), protocols::simple_moves::ChainGroupDiscriminator::group_id(), protocols::forge::methods::grow_left_r(), protocols::forge::methods::grow_right_r(), protocols::rbsegment_relax::guess_rbsegs_from_pose(), has_dof(), protocols::ligand_docking::has_incomplete_connections(), protocols::swa::rna::has_virtual_rna_residue_variant_type(), hbonded(), protocols::seeded_abinitio::SegmentHybridizer::hybridize(), protocols::simple_moves::ConstrainToIdealMover::i_want_this_atom_to_move(), protocols::simple_moves::sidechain_moves::SidechainMoverBase::idealize_sidechains(), protocols::simple_moves::sidechain_moves::SidechainMover::idealize_sidechains(), protocols::antibody2::AntibodyInfo::identify_antibody(), protocols::motifs::MotifSearch::identify_motif_BuildPositions(), core::scoring::SecondaryStructurePotential::identify_ss(), protocols::motifs::MotifSearch::incorporate_motifs(), protocols::motifs::LigandMotifSearch::incorporate_motifs(), protocols::hotspot_hashing::SearchPatternRotSetOp::increase_packer_residue_radius(), protocols::toolbox::rotamer_set_operations::RigidBodyMoveBaseRSO::increase_packer_residue_radius(), protocols::sic_dock::SICFast::init(), protocols::constraints_additional::BindingSiteConstraint::init(), protocols::forge::build::SegmentSwap::init(), protocols::forge::build::SegmentInsert::init(), core::io::pdb::FileData::init_from_pose(), core::scoring::MembranePotential::init_membrane_center_normal(), protocols::toolbox::pose_metric_calculators::RotamerBoltzCalculator::init_task(), protocols::sic_dock::xyzStripeHashPoseWithMeta::init_with_pose(), protocols::sic_dock::xyzStripeHashPose::init_with_pose(), protocols::ub_e2c::ubi_e2c_modeler::initial_perturbation(), protocols::hybridization::HybridizeFoldtreeDynamic::initialize(), protocols::motifs::MotifSearch::initialize(), core::scoring::GenBornPoseInfo::initialize(), core::scoring::FACTSPoseInfo::initialize(), protocols::hybridization::HybridizeProtocol::initialize_and_sample_loops(), core::scoring::rna::initialize_atoms_for_which_we_need_new_dofs(), core::scoring::rna::RNA_CentroidInfo::initialize_base_centroids_and_stubs(), protocols::swa::rna::StepWiseRNA_BaseCentroidScreener::Initialize_base_stub_list(), protocols::match::downstream::LigandConformerBuilder::initialize_conformers(), core::pose::initialize_dof_id_map(), protocols::topology_broker::RigidChunkClaimer::initialize_dofs(), protocols::swa::protein::StepWiseProteinPacker::initialize_for_regular_packer(), protocols::swa::protein::StepWiseProteinResidueSampler::initialize_for_regular_packer(), protocols::swa::rna::StepWiseRNA_BaseCentroidScreener::Initialize_is_virtual_base(), protocols::relax::RelaxProtocolBase::initialize_movemap(), protocols::swa::rna::StepWiseRNA_ResidueSampler::initialize_o2star_green_packer(), protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::initialize_o2star_packer_task(), protocols::swa::StepWisePoseSetup::initialize_phi_psi_offsets(), protocols::features::ReportToDB::initialize_pose(), protocols::rbsegment_relax::FragInsertAndAlignMover::initialize_rb_fragments(), protocols::topology_broker::SequenceClaimer::initialize_residues(), protocols::rna::RNA_ChunkLibrary::initialize_rna_chunk_library(), protocols::swa::rna::StepWiseRNA_RotamerGenerator::initialize_sample_base_states(), protocols::rna::RNA_StructureParameters::initialize_secstruct(), protocols::rna::FullAtomRNA_Fragments::insert_fragment(), protocols::features::HBondFeatures::insert_hbond_dehydron_row(), protocols::features::HBondFeatures::insert_hbond_geom_coords(), protocols::features::HBondFeatures::insert_hbond_lennard_jones_row(), protocols::features::ResidueScoresFeatures::insert_one_body_residue_score_rows(), protocols::grafting::insert_pose_into_pose(), protocols::features::PdbDataFeatures::insert_residue_pdb_confidence_rows(), protocols::features::ResidueFeatures::insert_residue_rows(), protocols::features::ResidueScoresFeatures::insert_residue_scores_rows(), protocols::features::HBondFeatures::insert_site_atoms_row(), protocols::features::HBondFeatures::insert_site_row(), protocols::features::ResidueScoresFeatures::insert_two_body_residue_score_rows(), protocols::features::UnrecognizedAtomFeatures::insert_unrecognized_neighbors_rows(), protocols::simple_filters::RotamerBoltzmannWeight::interface_interaction_energy(), protocols::swa::Is_close_chain_break(), protocols::swa::rna::Is_close_chain_break(), core::scoring::rna::RNA_TorsionPotential::Is_cutpoint_closed_torsion(), core::scoring::is_heavyatom(), core::scoring::is_ligand_heavyatom(), core::scoring::methods::is_lower_cutpoint(), core::scoring::is_nbr_atom(), protocols::swa::rna::StepWiseRNA_Clusterer::Is_old_individual_suite_cluster(), core::scoring::is_polymer_heavyatom(), core::scoring::is_protein_backbone(), core::scoring::is_protein_backbone_including_O(), core::scoring::is_protein_CA(), core::scoring::is_protein_CA_or_CB(), protocols::swa::rna::Is_residues_in_contact(), protocols::swa::rna::Is_ribose_virtual(), core::scoring::rna::is_rna_chainbreak(), protocols::loops::Loop::is_terminal(), core::scoring::methods::is_upper_cutpoint(), protocols::swa::protein::StepWiseProteinLoopBridger::KIC_loop_close(), core::scoring::packstat::LeeRichards::LeeRichards(), protocols::swa::protein::StepWiseProteinPoseMinimizer::let_neighboring_chis_minimize(), protocols::scoring::Interface::ligand_calculate(), protocols::motifs::load_build_position_data(), protocols::loops::loop_closure::ccd::load_coords_and_torsions(), protocols::features::PdbDataFeatures::load_residue_pdb_confidence(), protocols::rna::RNA_LoopCloser::local_minimize_at_chainbreaks(), protocols::antibody2::RefineOneCDRLoopCentroid::loop_centroid_relax(), protocols::antibody::CDRH3Modeler::loop_centroid_relax(), protocols::antibody::CDRH3Modeler::loop_fa_relax(), protocols::protein_interface_design::movers::PlaceOnLoop::loop_length(), protocols::loops::loop_local_rmsd(), protocols::loops::loop_rmsd(), protocols::loops::loop_rmsd_with_superimpose_core(), protocols::loops::loopfinder(), protocols::ligand_docking::make_atr_rep_grid(), protocols::ligand_docking::make_atr_rep_grid_without_ligands(), protocols::dna::make_base_pair_aware_fold_tree(), protocols::motifs::make_base_pair_mutation(), protocols::rna::make_coarse_pose(), protocols::toolbox::match_enzdes_util::EnzConstraintParameters::make_constraint_covalent(), protocols::toolbox::match_enzdes_util::EnzConstraintParameters::make_constraint_covalent_helper(), protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover::make_disjointed_foldtree(), protocols::motifs::make_dna_mutations(), protocols::relax::make_dna_rigid(), protocols::protein_interface_design::make_hotspot_foldtree(), protocols::simple_moves::BBConRotMover::make_move(), protocols::simple_moves::SmallMover::make_move(), protocols::simple_moves::ShearMover::make_move(), protocols::ligand_docking::LigandBaseProtocol::make_movemap(), protocols::ligand_docking::HighResDocker::make_packer_task_from_vector(), protocols::ligand_docking::LigandBaseProtocol::make_packer_task_ligand_only(), protocols::rna::make_phosphate_nomenclature_matches_mini(), protocols::swa::StepWisePoseSetup::make_pose(), core::fragment::make_pose_from_frags(), core::pose::symmetry::make_symmetric_movemap(), protocols::simple_moves::symmetry::SymPackRotamersMover::make_symmetric_task(), protocols::relax::FastRelax::makeDnaRigid(), protocols::swa::protein::StepWiseProteinPoseSetup::match_specific_variants(), core::scoring::electron_density::ElectronDensity::matchCentroidPose(), core::scoring::electron_density::ElectronDensity::matchPose(), core::scoring::electron_density::ElectronDensity::matchPoseToPatterson(), core::scoring::electron_density::ElectronDensity::matchRes(), protocols::optimize_weights::IterativeOptEDriver::measure_rotamer_recovery(), protocols::toolbox::pose_metric_calculators::SequenceComparison::measure_sequence_recovery(), protocols::optimize_weights::IterativeOptEDriver::measure_sequence_recovery(), core::pack::min_pack(), protocols::swa::rna::minimize_all_sampled_floating_bases(), MinimizeInterface(), core::pose::MiniPose::MiniPose(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_Moves::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::model_loop(), protocols::loop_build::LoopMover_SlidingWindow::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::model_loop(), protocols::match::NumNeighborsMPM::modified_match_positions(), protocols::enzdes::EnzdesFlexBBProtocol::modified_task(), protocols::forge::build::BuildManager::modify(), protocols::forge::build::SegmentSwap::modify_impl(), protocols::forge::build::Bridge::modify_impl(), protocols::forge::build::SegmentRebuild::modify_impl(), protocols::forge::build::ConnectRight::modify_impl(), protocols::forge::build::SegmentInsert::modify_impl(), core::pose::molar_mass(), core::pose::molecular_mass(), protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::moving_res_contact_filter(), protocols::motifs::mutate_loops_for_search(), protocols::ddg::ddGMover::mutation_label(), protocols::hybridization::natom_aligned(), protocols::sic_dock::neighbor_count(), protocols::ddg::ddGMover::neighborhood_of_mutations(), core::scoring::MembranePotential::non_helix_in_membrane_penalty(), core::pose::noncanonical_atom_count(), core::pose::noncanonical_chi_count(), core::pose::noncanonical_residue_count(), protocols::frag_picker::FragmentPicker::nonlocal_pairs(), core::pose::num_atoms(), core::pose::num_chi_angles(), core::pose::num_hbond_acceptors(), core::pose::num_hbond_donors(), core::pose::num_heavy_atoms(), protocols::swa::rna::o2star_minimize(), protocols::rna::RNA_Minimizer::o2star_trials(), core::scoring::disulfides::FullatomDisulfideEnergy::old_eval_atom_derivative(), core::scoring::methods::OmegaTetherEnergy::old_eval_dof_derivative(), omega(), protocols::dna::RotamerDNAHBondFilter::operator()(), core::optimization::SingleResidueMultifunc::operator()(), core::scoring::symmetry::SymmetricScoreFunction::operator()(), protocols::hybridization::AllResiduesChanged::operator()(), core::pack::task::operation::ResidueTypeFilter::operator()(), protocols::abinitio::AllResiduesChanged::operator()(), core::scoring::ScoreFunction::operator()(), OPT_1GRP_KEY(), protocols::branch_angle::BranchAngleOptimizer::optimize_angles(), protocols::ub_e2c::ubi_e2c_modeler::optimize_cov_bond(), core::pack::optimize_H_and_notify(), protocols::ligand_docking::LigandDockProtocol::optimize_orientation3(), core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::orient_rotamer_set_to_symmetric_partner(), core::pack::rotamer_set::symmetry::SymmetricRotamerSets::orient_rotamer_set_to_symmetric_partner(), protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::output_alternative_states(), protocols::protein_interface_design::movers::MapHotspot::output_pose(), protocols::swa::monte_carlo::RNA_SWA_MonteCarloMover::output_silent_file(), core::io::sequence_comparation::DesignContrast::output_sqc_file(), protocols::branch_angle::BranchAngleOptimizer::overall_params(), core::pack::pack_rotamers_loop(), core::pack::task::PackerTask_::PackerTask_(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::pair_sets_with_positions(), protocols::protein_interface_design::filters::RmsdFilter::parse_my_tag(), protocols::simple_filters::ResidueCountFilter::parse_my_tag(), protocols::protein_interface_design::movers::PlaceStubMover::parse_my_tag(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::parse_my_tag(), protocols::protein_interface_design::movers::Splice::parse_my_tag(), protocols::enzdes::DiffAtomSasaFilter::parse_my_tag(), protocols::forge::remodel::RemodelLoopMover::parse_my_tag(), core::pose::parse_selection_block(), protocols::protein_interface_design::movers::parse_stub_sets(), protocols::hybridization::partial_align(), protocols::swa::rna::StepWiseRNA_Minimizer::pass_all_pose_screens(), protocols::match::NumNeighborsMPM::passes_com_vector_criterion(), core::pose::PDBInfo::PDBInfo(), protocols::swa::pdbslice(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::perform_rama_check(), phi(), protocols::swa::rna::phosphate_base_phosphate_square_deviation(), protocols::swa::rna::phosphate_square_deviation(), protocols::comparative_modeling::pick_loops_chainbreak(), protocols::hybridization::ChunkTrialMover::pick_random_chunk(), protocols::protein_interface_design::movers::PlaceStubMover::place_stub(), protocols::hotspot_hashing::StubGenerator::placeResidueAtTransform(), protocols::hotspot_hashing::StubGenerator::placeResidueOnPose(), protocols::simple_moves::point_graph_dme(), protocols::design_opt::GreedyOptMutationMover::pose_coords_are_same(), core::import_pose::atom_tree_diffs::pose_from_atom_tree_diff(), core::pose::pose_max_nbr_radius(), core::scoring::UnfoldedStatePotential::pose_raw_unfolded_state_energymap(), core::scoring::packing::PoseBalls::PoseBalls(), core::scoring::packing::PoseBallsLite::PoseBallsLite(), core::scoring::PQR::PQR(), core::scoring::NeighborList::prepare_for_scoring(), protocols::hotspot_hashing::HotspotStubSet::prepare_hashing_packer_task_(), protocols::swa::rna::print_atom_info(),