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core::pose::Pose Class Reference

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

#include <Pose.hh>

Inheritance diagram for core::pose::Pose:
Inheritance graph
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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
conformation::ConformationCOP 
ConformationCOP
 
typedef
pose::datacache::ObserverCache 
ObserverCache
 
typedef
pose::datacache::ObserverCacheOP 
ObserverCacheOP
 
typedef
pose::signals::ConformationEvent 
ConformationEvent
 
typedef
pose::signals::DestructionEvent 
DestructionEvent
 
typedef pose::signals::EnergyEvent EnergyEvent
 
typedef pose::signals::GeneralEvent GeneralEvent
 
typedef
scoring::constraints::ConstraintSetOP 
ConstraintSetOP
 
typedef
scoring::constraints::ConstraintSetCOP 
ConstraintSetCOP
 
typedef
basic::datacache::BasicDataCache 
BasicDataCache
 
typedef
basic::datacache::BasicDataCacheOP 
BasicDataCacheOP
 
typedef
basic::datacache::ConstDataMap 
ConstDataMap
 
typedef
basic::datacache::ConstDataMapOP 
ConstDataMapOP
 
typedef
boost::indirect_iterator
< conformation::ResidueOPs::const_iterator,
Residue const > 
const_iterator
 
typedef
boost::indirect_iterator
< conformation::ResidueOPs::iterator,
Residue const > 
iterator
 

Public Member Functions

iterator begin () noexcept
 
const_iterator begin () const noexcept
 
iterator end () noexcept
 
const_iterator end () const noexcept
 
 Pose ()
 default constructor, builds an empty pose More...
 
 ~Pose () override
 destructor – > kill data on the heap More...
 
 Pose (Pose const &src)
 copy constructor More...
 
 Pose (Pose const &src, Size residue_begin, Size residue_end)
 partial copy constructor More...
 
Poseoperator= (Pose const &src)
 Construct pose from pdb file. More...
 
void detached_copy (Pose const &src)
 Performs a deep copy of the src Pose into this Pose in a way that guarantees that no non-bitwise-constant data is shared between them (such as the AtomTree's observer system) – this Pose will be effectively detached from any data that lives in other objects. More...
 
PoseOP clone () const
 clone the conformation More...
 
PoseCOP get_self_ptr () const
 self pointers More...
 
PoseOP get_self_ptr ()
 
PoseCAP get_self_weak_ptr () const
 
PoseAP get_self_weak_ptr ()
 
Conformation const & conformation () const
 Returns the pose Conformation (const-access) More...
 
Conformationconformation ()
 Returns the pose Conformation (non-const access) More...
 
ConformationCOP conformation_ptr () const
 Returns the pose Conformation pointer (const access) More...
 
ConformationOPconformation_ptr ()
 Returns the pose Conformation pointer (nonconst access) More...
 
kinematics::FoldTree const & fold_tree () const
 Returns the pose FoldTree. More...
 
void fold_tree (kinematics::FoldTree const &fold_tree_in)
 Sets the pose FoldTree to <fold_tree_in> More...
 
void set_new_conformation (conformation::ConformationCOP new_conformation)
 Now that the conformation_ member data is an owning pointer, and we have derived classes of Conformation. More...
 
void set_new_energies_object (scoring::EnergiesOP energies)
 Now that the energies_ member data is an owning pointer, and we have derived classes of Energies. More...
 
kinematics::AtomTree const & atom_tree () const
 Returns the pose AtomTree. More...
 
scoring::Energies const & energies () const
 Returns the pose Energies (const-access) More...
 
scoring::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 clear_sequence_constraints ()
 Remove all sequence constraints from this pose. More...
 
void constraint_set (ConstraintSetOP)
 
void transfer_constraint_set (const pose::Pose &pose)
 
void reference_pose_from_current (std::string const &ref_pose_name, bool override_current=false)
 Create a new reference pose from the current state of the pose. More...
 
core::pose::reference_pose::ReferencePoseSetOP reference_pose_set ()
 Access the ReferencePoseSet object (non-const). More...
 
core::pose::reference_pose::ReferencePoseSetCOP reference_pose_set_cop () const
 Const-access the ReferencePoseSet object. More...
 
core::Size corresponding_residue_in_current (core::Size const ref_residue_index, std::string const &ref_pose_name) const
 Returns the index of a residue in this pose corresponding to a residue in a reference pose. More...
 
void increment_reference_pose_mapping_after_seqpos (core::Size const seqpos)
 Find all mappings in the new pose after seqpos in all ReferencePose objects, and increment them by 1. More...
 
void decrement_reference_pose_mapping_after_seqpos (core::Size const seqpos)
 Find all mappings in the new pose after seqpos in all ReferencePose objects, and decrement them by 1. More...
 
void zero_reference_pose_mapping_at_seqpos (core::Size const seqpos)
 Find all mappings in the new pose to seqpos in all ReferencePose objects, and set them to point to residue 0 (deletion signal). More...
 
bool has_reference_pose () const
 Returns true if a pose has at least one reference pose, false otherwise. More...
 
PDBInfoCOP pdb_info () const
 Returns the pose PDBInfo (const) More...
 
PDBInfoOP pdb_info ()
 Returns the pose PDBInfo. More...
 
PDBInfoOP pdb_info (PDBInfoOP new_info)
 Sets pose PDBInfo to <new_info> More...
 
void metric (std::string const &calculator_name, std::string const &key, basic::MetricValueBase &val) const
 
std::string print_metric (std::string const &calculator_name, std::string const &key) const
 
void append_residue_by_jump (conformation::Residue const &new_rsd, Size const jump_anchor_residue, std::string const &jump_anchor_atom="", std::string const &jump_root_atom="", bool const start_new_chain=false)
 Appends <new_rsd> (a residue) to pose by a new jump. More...
 
void append_residue_by_bond (conformation::Residue const &new_rsd, bool const build_ideal_geometry=false, int const connection=0, Size const anchor_residue=0, int const anchor_connection=0, bool const start_new_chain=false, bool const lookup_bond_length=false)
 Appends <new_rsd> (a residue) to pose by a new bond. More...
 
void append_residue_by_atoms (conformation::Residue const &new_rsd, bool const build_ideal_geometry, std::string const &connect_atom, Size const anchor_rsd_seqpos, std::string const &anchor_connect_atom, bool const start_new_chain=false, bool const lookup_bond_length=false)
 Appends <new_rsd> (a residue) to pose by a new bond to a given atom. More...
 
void insert_residue_by_jump (Residue const &new_rsd_in, Size const seqpos, Size anchor_pos, std::string const &anchor_atomno="", std::string const &root_atomno="")
 Adds <new_rsd_in> to pose at <seqpos> More...
 
void insert_residue_by_bond (Residue const &new_rsd_in, Size const seqpos, Size anchor_pos, bool const build_ideal_geometry=false, std::string const &anchor_atom="", std::string const &root_atom="", bool new_chain=false, bool const lookup_bond_length=false)
 Adds <new_rsd_in> to pose at <seqpos> More...
 
void replace_residue (Size const seqpos, Residue const &new_rsd_in, bool const orient_backbone)
 Replaces the residue at <seqpos> with <new_rsd_in> More...
 
void replace_residue (int const seqpos, Residue const &new_rsd_in, utility::vector1< std::pair< std::string, std::string > > const &atom_pairs)
 Replaces the residue at <seqpos> with <new_rsd> based on superposition on the specified input atom pairs NOTE: at the moment, only superposition on 3 atoms works This code sorely belongs in Pose.cc. More...
 
void append_polymer_residue_after_seqpos (Residue const &new_rsd, Size const seqpos, bool const build_ideal_geometry)
 glues to seqpos and perhaps also seqpos+1 More...
 
void prepend_polymer_residue_before_seqpos (Residue const &new_rsd, Size const seqpos, bool const build_ideal_geometry)
 glues to seqpos and perhaps also seqpos-1 More...
 
void append_pose_by_jump (Pose const &src, Size const jump_anchor_residue, std::string const &jump_anchor_atom="", std::string const &jump_root_atom="")
 Appends source pose conformation to pose by a new jump. More...
 
void delete_polymer_residue (Size const seqpos)
 Delete a residue in the pose. Update Observers. Update any Reference Poses. More...
 
void delete_residue_slow (Size const seqpos)
 Slow method that relies on FoldTree::delete_seqpos, rebuilds atomtree, can handle jumps/root residue. Update Observers. Update any Reference Poses. More...
 
void delete_residue_range_slow (Size const start, Size const end)
 Delete a range of residues in the pose. More...
 
void copy_segment (Size const size, Pose const &src, Size const begin, Size const src_begin)
 Copy a stretch of coordinates/torsions from <src> to pose. More...
 
BasicDataCache const & data () const
 BasicDataCache indexed by enum in core/pose/datacache/CacheableDataType.hh. More...
 
BasicDataCachedata ()
 BasicDataCache indexed by enum in core/pose/datacache/CacheableDataType.hh. More...
 
template<class T >
void set_const_data (std::string const &category, std::string const &name, T const &original)
 Controlled method for adding an object to the Pose's constant data cache; this function is the only way to add data to the Pose's data cache. An object, identified by two strings, is freshly constructed and inserted into the ConstDataCache. Objects inserted into the ConstDataCache must remain bitwise const for thread-safety reasons. The ConstDataCache has shallow-copy semantics, meaning that two poses would point to the same object if one were copied into the other. If these two Poses were then handed to separate threads, and the data they were both pointing at were to change, that would create race conditions. For this reason, the Pose attempts to prevent non-constant pointers to the data held in the ConstDataCache from existing. Objects placed in the ConstDataCache must have a copy constructor (either implicit or explicit). More...
 
basic::datacache::ConstDataMap
const & 
const_data_cache () const
 Read access to the const data cache. More...
 
ObserverCache const & observer_cache () const
 ObserverCache indexed by enum in core/pose/datacache/CacheableObserverType.hh. More...
 
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 size () const
 Returns the number of residues in the pose conformation. More...
 
Size total_atoms () const
 Returns the total number of atoms in the pose conformation example: pose.total_atoms() More...
 
bool empty () const
 Returns true if there are no residues in the conformation. More...
 
Size num_jump () const
 Returns the number of jumps in the pose FoldTree. More...
 
chemical::AA aa (Size const seqpos) const
 Returns the chemical::AA of the residue at <seqpos> More...
 
char secstruct (Size const seqpos) const
 Returns the secondary structure of residue <seqpos> this usually comes from fragments. The conformation object will not invoke DSSP to determine the secondary structure if e.g. it has not been made from fragments. 'H' = helical 'E' = strand or sheet 'L' = loop. More...
 
std::string secstruct () const
 Returns a string representing pose secondary structure. More...
 
void set_secstruct (Size const seqpos, char const setting)
 Assign the secondary structure of residue <seqpos> to <setting> More...
 
std::string sequence () const
 Returns a string representing the 1-letter-coded sequence of the pose conformation. More...
 
std::string sequence (core::Size resnum_start, core::Size resnum_end) const
 Returns a string representing the 1-letter-coded sequence of the pose conformation. From start to end. More...
 
std::string annotated_sequence (bool show_all_variants=false) const
 Returns the variant-tagged string representing the residue types that make up a conformation; e.g. M[MET:N-Terminus-Variant]CDH[HIS_D]LLR[ARG:C-Terminus-Variant]. More...
 
std::string chain_sequence (core::Size const chain_in) const
 Returns the sequence for the chain number <chain_in> More...
 
std::string glycan_tree_branch_sequence (core::uint const start_residue) const
 Return the IUPAC sequence of a single branch of a glycan tree, Beginning with residue number <start_residue>. More...
 
std::string glycan_tree_sequence (core::uint const residue_in_tree) const
 Return the IUPAC sequence of the entire glycan tree encompassing residue number <residue_in_tree>. More...
 
Residue const & residue (Size const seqpos) const
 Returns the Residue at position <seqpos> (read access) Note: this method will trigger a refold if either the torsions or the coordinates are out-of-date. More...
 
basic::datacache::BasicDataCache & residue_data (Size const seqpos)
 Returns the DataCache held by Residue at position <seqpos> (read/write access) Note: this method will trigger a refold if either the torsions or the coordinates are out-of-date. More...
 
basic::datacache::BasicDataCache
const & 
residue_data (Size const seqpos) const
 Returns the DataCache held by Residue at position <seqpos> (read access) Note: this method will trigger a refold if either the torsions or the coordinates are out-of-date. More...
 
chemical::ResidueType const & residue_type (Size const seqpos) const
 Returns the ResidueType at position <seqpos> (read access) Note: this method NOT will trigger a refold if either the torsions or the coordinates are out-of-date. More...
 
chemical::ResidueTypeCOP residue_type_ptr (Size const seqpos) const
 Returns the ResidueTypeCOP for position <seqpos> (read access) Note: this method NOT will trigger a refold if either the torsions or the coordinates are out-of-date. More...
 
bool is_fullatom () const
 Returns true if pose is ResidueType fullatom. More...
 
bool is_centroid () const
 Returns true if pose is ResidueType centroid. More...
 
core::chemical::ResidueTypeSetCOP residue_type_set_for_pose (core::chemical::TypeSetMode mode=core::chemical::INVALID_t) const
 Return the custom ResidueTypeSet for the Pose, if any. Otherwise will return the appropriate global ResidueTypeSet. More...
 
Real phi (Size const seqpos) const
 Returns the phi torsion angle of residue <seqpos> in degrees. More...
 
void set_phi (Size const seqpos, Real const setting)
 Sets the phi torsion angle of residue <seqpos> to <setting> More...
 
Real psi (Size const seqpos) const
 Returns the psi torsion angle of residue <seqpos> in degrees Note: assumes the residue is an amino acid or monosaccharide. More...
 
void set_psi (Size const seqpos, Real const setting)
 Sets the psi torsion angle of residue <seqpos> to <setting> More...
 
Real omega (Size const seqpos) const
 Returns the omega torsion angle of residue <seqpos> in degrees. More...
 
void set_omega (Size const seqpos, Real const setting)
 Sets the omega torsion angle of residue <seqpos> to <setting> More...
 
Real theta (Size const seqpos) const
 Returns the theta torsion angle of beta-amino acid residue or oligourea residue <seqpos>. More...
 
void set_theta (Size const seqpos, Real const setting)
 Sets the theta torsion angle of beta-amino acid residue or oligourea residue <seqpos> to <setting>. More...
 
Real mu (Size const seqpos) const
 Returns the mu torsion angle of oligourea residue <seqpos>. More...
 
void set_mu (Size const seqpos, Real const setting)
 Sets the mu torsion angle of oligourea residue <seqpos> to <setting>. More...
 
Real alpha (Size const pos) const
 Returns the alpha torsion angle of residue <seqpos> More...
 
void set_alpha (Size const seqpos, Real const setting)
 Sets the alpha torsion angle of residue <seqpos> to <setting> More...
 
Real beta (Size const seqpos) const
 Returns the beta torsion angle of residue <seqpos> More...
 
void set_beta (Size const seqpos, Real const setting)
 Sets the beta torsion angle of residue <seqpos> to <setting> More...
 
Real gamma (Size const seqpos) const
 Returns the gamma torsion angle of residue <seqpos> More...
 
void set_gamma (Size const seqpos, Real const setting)
 Sets the gamma torsion angle of residue <seqpos> to <setting> More...
 
Real delta (Size const pos) const
 Returns the delta torsion angle of residue <seqpos> More...
 
void set_delta (Size const seqpos, Real const setting)
 Sets the delta torsion angle of residue <seqpos> to <setting> More...
 
Real epsilon (Size const seqpos) const
 Returns the epsilon torsion angle of residue <seqpos> More...
 
void set_epsilon (Size const seqpos, Real const setting)
 Sets the epsilon torsion angle of residue <seqpos> to <setting> More...
 
Real zeta (Size const seqpos) const
 Returns the zeta torsion angle of residue <seqpos> More...
 
void set_zeta (Size const seqpos, Real const setting)
 Sets the zeta torsion angle of residue <seqpos> to <setting> More...
 
Real chi (int const chino, Size const seqpos) const
 Returns the <chino> chi torsion angle of residue <seqpos> More...
 
void set_chi (int const chino, Size const seqpos, Real const setting)
 Sets the <chino> chi torsion angle of residue <seqpos> to <setting> More...
 
Real chi (Size const seqpos) const
 Returns the chi torsion angle of residue <seqpos> More...
 
void set_chi (Size const seqpos, Real const setting)
 Sets the chi torsion angle of residue <seqpos> to <setting> More...
 
core::Size num_chains () const
 Returns the total number of (chain ID) chains in the pose. More...
 
core::Size chain (Size const seqpos) const
 Returns the chain number of residue <seqpos> More...
 
core::Size chain_begin (Size const chain_num) const
 Returns the sequence position of the beginning of chain <chain_num>. More...
 
core::Size chain_end (Size const chain_num) const
 Returns the sequence position of the end of chain <chain_num>. More...
 
utility::vector1< PoseOPsplit_by_chain () const
 Returns a vector of poses with one element per (chain number) chain of the original pose. More...
 
PoseOP split_by_chain (Size chain_id) const
 Return a new pose with just the residues from the specified (chain number) chain. More...
 
void update_pose_chains_from_pdb_chains ()
 Updates the pose chain IDs to match the pdb chain letters. More...
 
void set_jump (int const jump_number, const kinematics::Jump &new_jump)
 Sets the pose FoldTree Jump <jump_number> to <new_jump> More...
 
kinematics::Jump const & jump (int const jump_number) const
 Returns the pose FoldTree Jump <jump_number> More...
 
void set_jump (AtomID const &id, const kinematics::Jump &new_jump)
 Sets the pose FoldTree Jump <id> to <new_jump> More...
 
kinematics::Jump const & jump (AtomID const &id) const
 Returns the pose FoldTree Jump <id> More...
 
void set_ring_conformation (uint const seqpos, uint const ring_num, core::chemical::rings::RingConformer const &conformer)
 Set the given residue and ring's ring conformation, if appropriate. More...
 
Real torsion (TorsionID const &id) const
 Returns the Conformation torsion angle identified by <id> More...
 
void set_torsion (TorsionID const &id, Real const setting)
 Sets the Conformation torsion angle identified by <id> to <setting> More...
 
Real dof (DOF_ID const &id) const
 Returns the value of the AtomTree DOF <id> More...
 
void set_dof (DOF_ID const &id, Real const setting)
 Sets the value of the AtomTree DOF <id> More...
 
bool has_dof (DOF_ID const &id) const
 Returns true if pose has DOF <id> More...
 
PointPosition const & xyz (AtomID const &id) const
 Returns the location (xyz) of pose AtomID <id> More...
 
PointPosition const & xyz (NamedAtomID const &id) const
 Returns the location (xyz) of pose NamedAtomID <id> More...
 
void set_xyz (AtomID const &id, PointPosition const &point)
 Sets the location (xyz) of pose AtomID <id> to the PointPosition <point> More...
 
void set_xyz (NamedAtomID const &id, PointPosition const &point)
 Sets the location (xyz) of pose NamedAtomID <id> to the PointPosition <point> More...
 
void batch_set_xyz (utility::vector1< AtomID > const &ids, utility::vector1< PointPosition > const &points)
 Sets the locations (xyz) of pose AtomIDs in <ids> to mathcing PointPositions in <points> More...
 
void batch_get_xyz (utility::vector1< AtomID > const &ids, utility::vector1< PointPosition > &points) const
 Gets the locations (xyz) of pose AtomIDs in <ids> More...
 
kinematics::Stub stub_from_id (id::NamedStubID const &id)
 
void center ()
 Sets pose coordinates such that the pose center is at the Euclidean origin. More...
 
void update_residue_neighbors ()
 Updates neighbor links in the pose Energies object. More...
 
void scoring_begin (scoring::ScoreFunction const &info)
 Called by ScoreFunction at the beginning of scoring. More...
 
void scoring_end (scoring::ScoreFunction const &scorefxn)
 Called by ScoreFunction at the end of scoring. More...
 
void update_actcoords ()
 Called by PairEPotential to update the action coordinates for all residues. More...
 
void update_actcoord (Size resid)
 Updates the action coordinates for pose residue <resid> More...
 
void update_orbital_coords (Size resid)
 
void apply_transform_Rx_plus_v (numeric::xyzMatrix< Real > const &R, Vector const &v)
 Apply a transform of the Rx + v form, where R is a rotation matrix and v is a translation vector. More...
 
void real_to_virtual (core::Size seqpos)
 Switch residues to VIRTUAL. More...
 
void virtual_to_real (core::Size seqpos)
 Switch residues from VIRTUAL to a REAL residue. More...
 
conformation::carbohydrates::GlycanTreeSetCOP glycan_tree_set () const
 Get information on any glycan trees within this pose. If this is not setup, will return a nullptr due to the const nature of the function. More...
 
conformation::membrane::MembraneInfoOP membrane_info () const
 Get information about the membrane orientaiton, geometry, and lipid composition within this pose. More...
 
conformation::membrane::MembraneInfoOP membrane_info ()
 Get information about the membrane orientaiton, geometry, and lipid composition within this pose. More...
 
void clear ()
 Empty the pose contents. More...
 
void dump_file (std::string const &file_name) const
 Export pose data to a file, <file_name>, determining which type of file format to write based on the file extension. More...
 
void dump_cif (std::string const &file_name) const
 Export pose data to the mmCIF file <file_name> More...
 
bool dump_pdb (std::string const &file_name) const
 Export pose data to the PDB file <file_name> More...
 
void dump_pdb (std::ostream &out) const
 
void dump_pdb (std::ostream &out, utility::vector1< core::Size > const &residue_indices) const
 for writing a specified subset of residues in pdb format More...
 
void dump_scored_pdb (std::string const &file_name, scoring::ScoreFunction const &scorefxn)
 Export pose data to the PDB file <file_name>, add some score output. More...
 
template<typename MemFn , typename Ptr >
utility::signals::Link attach_destruction_obs (MemFn fn, Ptr ptr)
 attach DestructionEvent observer function More...
 
template<typename MemFn , typename Ptr >
bool detach_destruction_obs (MemFn fn, Ptr ptr) const
 detach DestructionEvent observer function More...
 
template<typename MemFn , typename Ptr >
utility::signals::Link attach_general_obs (MemFn fn, Ptr ptr)
 attach GeneralEvent observer function More...
 
template<typename MemFn , typename Ptr >
bool detach_general_obs (MemFn fn, Ptr ptr) const
 detach GeneralEvent observer function More...
 
template<typename MemFn , typename Ptr >
utility::signals::Link attach_energy_obs (MemFn fn, Ptr ptr)
 attach EnergyEvent observer function More...
 
template<typename MemFn , typename Ptr >
bool detach_energy_obs (MemFn fn, Ptr ptr) const
 detach EnergyEvent observer function More...
 
template<typename MemFn , typename Ptr >
utility::signals::Link attach_conformation_obs (MemFn fn, Ptr ptr)
 attach ConformationEvent observer function More...
 
template<typename MemFn , typename Ptr >
bool detach_conformation_obs (MemFn fn, Ptr ptr) const
 detach ConformationEvent observer function More...
 
template<>
void set_const_data (std::string const &category, std::string const &name, Pose const &original)
 

Private Member Functions

void init (void)
 initialize internal for a freshly build pose object. Use this function when you need to create new constructor. More...
 
void store_const_data (std::string const &category, std::string const &name, utility::pointer::ReferenceCountCOP)
 Internal method for storing a shared pointer to some constant object in the ConstantDataCache. More...
 
void notify_destruction_obs (DestructionEvent const &e)
 notify DestructionEvent observers More...
 
void notify_general_obs (GeneralEvent const &e)
 notify GeneralEvent observers More...
 
void notify_energy_obs (EnergyEvent const &e, bool const fire_general=true)
 notify EnergyEvent observers More...
 
void notify_conformation_obs (ConformationEvent const &e, bool const fire_general=true)
 notify ConformationEvent observers More...
 
void buffer_observers () const
 Temporarily turn off observer notification Used for places where the Pose is in a temporarily inconsistent state. More...
 
void unbuffer_observers () const
 Turn back on observer notification Used for places where the Pose is in a temporarily inconsistent state. More...
 
void on_conf_xyz_change (core::conformation::signals::XYZEvent const &event)
 upon receiving a conformation::signals::XYZEvent More...
 

Private Attributes

ConformationOP conformation_
 
scoring::EnergiesOP energies_
 
metrics::PoseMetricContainerOP metrics_
 
BasicDataCacheOP data_cache_
 BasicDataCache indexed by enum in core/pose/datacache/CacheableDataType.hh. More...
 
ConstDataMapOP constant_cache_
 The DataMap is a way to store arbitrarily complicated, constant data. The contents of the datamap are copied by value – the pointers are copied – meaning that two poses can point to the same data. For thread safety reasons, it is essential that the data inside this map is bitwise const (i.e. no mutable data is used or changes state). Poses may be placed inside the constant datamap, but it is important that ownership cycles are not created (e.g. A –> B; B–>C; C–>A) or memory will be leaked. Care must be taken that the this never happens. One way to avoid this possibility is to only cache freshly cloned Poses. The other way is to first call Pose::purge_cached_poses. More...
 
ObserverCacheOP observer_cache_
 ObserverCache indexed by enum in core/pose/datacache/CacheableObserverType.hh. More...
 
PDBInfoOP pdb_info_
 pdb info More...
 
ConstraintSetOP constraint_set_
 
core::pose::reference_pose::ReferencePoseSetOP reference_pose_set_
 The set of ReferencePose objects that this pose stores. More...
 
utility::signals::BufferedSignalHub
< void, DestructionEvent
destruction_obs_hub_
 DestructionEvent observers. More...
 
utility::signals::BufferedSignalHub
< void, GeneralEvent
general_obs_hub_
 GeneralEvent observers. More...
 
utility::signals::BufferedSignalHub
< void, EnergyEvent
energy_obs_hub_
 EnergyEvent observers. More...
 
utility::signals::BufferedSignalHub
< void, ConformationEvent
conformation_obs_hub_
 ConformationEvent observers. More...
 

Detailed Description

A molecular system including residues, kinematics, and energies.

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

The main responsibilities of the pose are:

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

Member Typedef Documentation

typedef basic::datacache::BasicDataCache core::pose::Pose::BasicDataCache
typedef basic::datacache::BasicDataCacheOP core::pose::Pose::BasicDataCacheOP
typedef boost::indirect_iterator< conformation::ResidueOPs::const_iterator, Residue const > core::pose::Pose::const_iterator
typedef basic::datacache::ConstDataMap core::pose::Pose::ConstDataMap
typedef basic::datacache::ConstDataMapOP core::pose::Pose::ConstDataMapOP
typedef boost::indirect_iterator< conformation::ResidueOPs::iterator, Residue const > core::pose::Pose::iterator

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 clone(), and split_by_chain().

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

destructor – > kill data on the heap

destructor – > kill data on the heap

References clear(), and notify_destruction_obs().

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

copy constructor

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

partial copy constructor

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

Member Function Documentation

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

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

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

References conformation_, and size().

Referenced by protocols::splice::Splice::add_coordinate_constraints(), protocols::splice::SpliceManager::add_coordinate_constraints(), protocols::splice::Splice::add_dihedral_constraints(), protocols::splice::SpliceManager::add_dihedral_constraints(), protocols::task_operations::JointSequenceOperation::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::flxbb::FilterStructs_TotalCharge::apply(), protocols::analysis::simple_metrics::SequenceRecoveryMetric::calculate(), protocols::kinematic_closure::ClosureSolution::check_rama(), protocols::simple_filters::NetChargeFilter::compute(), protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter::compute(), protocols::matdes::ClashCheckFilter::compute(), protocols::fldsgn::filters::CoreDunbrackFilter::compute(), protocols::fldsgn::filters::InterlockingAromaFilter::compute(), core::select::util::SelectResiduesByLayer::compute(), protocols::loops::loop_closure::ccd::RamaCheck1B::compute_rama_score(), protocols::loops::loop_closure::ccd::RamaCheck2B::compute_rama_score(), protocols::design_opt::GreedyOptMutationMover::dump_scoring_table(), protocols::matdes::MatDesGreedyOptMutationMover::dump_scoring_table(), protocols::motif_grafting::movers::MotifGraftMover::generate_match_pose(), protocols::motif_grafting::movers::MotifGraftMover::get_fragments_by_CA_distances_and_NCpoints_restrains(), core::scoring::rna::data::RNA_DMS_Potential::get_logL_values(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::get_main_chain_torsion_set_list_coarse(), protocols::antibody::design::NativeAntibodySeq::get_native_sequence_matching_current_length(), protocols::loops::loop_closure::kinematic_closure::TabooSamplingKinematicPerturber::get_random_phi_psi_for_residue(), protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturber::get_random_phi_psi_for_residue(), core::scoring::rna::get_rna_motifs(), protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_useful_info(), core::pose::MiniPose::MiniPose(), 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::BaseTabooPerturber::perturb_chain(), protocols::kinematic_closure::perturbers::OmegaPerturber::perturb_subset(), protocols::kinematic_closure::perturbers::RamaPerturber::perturb_subset(), protocols::kinematic_closure::perturbers::Rama2bPerturber::perturb_subset(), protocols::kinematic_closure::perturbers::RamaPerturber::perturb_subset_with_balance(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::rama_energy(), protocols::fldsgn::potentials::AACompositionEnergy::residue_energy(), protocols::antibody::design::NativeAntibodySeq::set_from_cdr(), protocols::loops::set_secstruct_from_dssp(), protocols::antibody::design::NativeAntibodySeq::set_sequence(), core::scoring::methods::MembraneEnvSmoothEnergy::setup_for_derivatives(), and core::scoring::membrane::FaMPEnvSmoothEnergy::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::rna::movers::RNAThreadAndMinimizeMover::accomodate_length_change(), protocols::rna::movers::RNAIdealizeMover::add_bond_angle_constraint(), protocols::rna::movers::RNAIdealizeMover::add_bond_constraint(), protocols::jumping::JumpSample::add_chainbreaks_as_distance_constraint(), core::pose::rna::add_chi_constraints(), protocols::metal_interface::AddZincSiteConstraints::add_constraints(), protocols::hybridization::add_constraints(), core::util::add_constraints_to_metal(), protocols::relax::add_coordinate_constraints_to_pose(), protocols::loops::add_coordinate_constraints_to_pose(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::add_cyclic_constraints(), protocols::ncbb::SecStructMinimizeMover::add_dihedral_constraints_to_pose(), protocols::hybridization::HybridizeProtocol::add_fragment_csts(), protocols::loop_grower::LoopGrower::add_fragment_csts(), core::pose::ncbb::add_generic_hbs_constraint(), protocols::antibody::constraints::add_harmonic_dihedral_cst_general(), protocols::simple_moves::StructProfileMover::add_MSAcst_to_pose(), protocols::hybridization::add_non_protein_cst(), core::pose::ncbb::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::splice::SampleRotamersFromPDB_RotamerSetOperation::add_rotamer_constraints(), protocols::splice::SpliceManager::add_sequence_constraints(), protocols::splice::Splice::add_sequence_constraints(), protocols::hybridization::add_strand_pairs_cst(), protocols::simple_moves::AddCavitiesMover::add_suckers(), core::pose::ncbb::add_triazole_constraint(), protocols::anchored_design::AnchorMoversData::anchor_noise_constraints_setup(), protocols::cyclic_peptide::CreateAngleConstraint::apply(), protocols::cyclic_peptide::CreateTorsionConstraint::apply(), protocols::cyclic_peptide::CreateDistanceConstraint::apply(), protocols::simple_moves::FavorSymmetricSequence::apply(), protocols::simple_moves::SequenceProfileMover::apply(), protocols::magnesium::MgMinimizer::apply(), protocols::rbsegment_relax::IdealizeHelicesMover::apply(), protocols::simple_moves::FavorSequenceProfile::apply(), protocols::constraint_movers::ResidueTypeConstraintMover::apply(), protocols::antibody::constraints::ParatopeSiteConstraintMover::apply(), protocols::rna::movers::RNAIdealizeMover::apply(), protocols::aa_composition::AddMHCEpitopeConstraintMover::apply(), protocols::aa_composition::AddNetChargeConstraintMover::apply(), protocols::aa_composition::AddCompositionConstraintMover::apply(), protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover::apply(), protocols::hybridization::DomainAssembly::apply(), protocols::membrane::AddMembraneSpanConstraint::apply(), protocols::membrane::AddMembraneSpanTermZConstraint::apply(), protocols::ncbb::oop::OopCreatorMover::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::symmetry::SetupNCSMover::apply(), protocols::legacy_sewing::LegacyAssemblyConstraintsMover::apply(), protocols::loop_grower::LoopGrower::apply(), protocols::hybridization::CartesianSampler::apply_constraints(), protocols::hybridization::CartesianSampler::apply_fragcsts(), protocols::simple_moves::MSDMover::apply_linked_constraints(), protocols::mpi_refinement::constrain_residue(), core::pose::ncbb::constrain_ring_atoms(), protocols::relax::RangeRelaxMover::constrain_to_reference(), protocols::md::CartesianMD::cst_on_pose_dynamic(), protocols::md::CartesianMD::cst_on_pose_simple(), protocols::relax::cyclize_pose(), protocols::relax::derive_sc_sc_restraints(), protocols::simple_moves::PeptideStapleMover::derive_staple_constraints_(), protocols::aa_composition::AddHelixSequenceConstraintsMover::do_overall_or_alanine_constraints(), protocols::aa_composition::AddHelixSequenceConstraintsMover::do_terminal_constraints(), protocols::loops::fix_with_coord_cst(), protocols::normalmode::NormalModeRelaxMover::gen_coord_constraint(), protocols::hybridization::generate_centroid_constraints(), core::pose::get_constraints_from_link_records(), protocols::relax::RangeRelaxMover::idealize_pose(), protocols::antibody::kink_constrain_antibody_H3(), core::pack::dunbrack::load_unboundrot(), protocols::forge::remodel::RemodelAccumulator::recover_checkpoint(), protocols::simple_moves::RepeatPropagationMover::repeat_ligand_constraints(), 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(), core::pose::rna::setup_base_pair_constraints(), protocols::simple_moves::ShakeStructureMover::setup_ca_constraints(), protocols::rna::denovo::setup_coarse_chainbreak_constraints(), protocols::simple_moves::CyclizationMover::setup_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(), protocols::idealize::IdealizeMover::setup_idealize_constraints(), protocols::hybridization::setup_user_coordinate_constraints(), and protocols::loop_grower::LoopGrower::single_grow().

References conformation_, constraint_set_, and energies_.

Referenced by protocols::cyclic_peptide::crosslinker::SquarePlanarMetal_Helper::add_angle_constraints(), protocols::cyclic_peptide::crosslinker::OctahedralMetal_Helper::add_angle_constraints(), protocols::cyclic_peptide::crosslinker::TetrahedralMetal_Helper::add_angle_constraints(), protocols::cyclic_peptide::crosslinker::TrigonalPlanarMetal_Helper::add_angle_constraints(), protocols::cyclic_peptide::crosslinker::TrigonalPyramidalMetal_Helper::add_angle_constraints(), 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::splice::Splice::add_coordinate_constraints(), protocols::splice::SpliceManager::add_coordinate_constraints(), protocols::cyclic_peptide::crosslinker::SquarePyramidalMetal_Helper::add_dihedral_constraints(), protocols::cyclic_peptide::crosslinker::SquarePlanarMetal_Helper::add_dihedral_constraints(), protocols::cyclic_peptide::crosslinker::TrigonalPlanarMetal_Helper::add_dihedral_constraints(), protocols::splice::Splice::add_dihedral_constraints(), protocols::splice::SpliceManager::add_dihedral_constraints(), protocols::antibody::constraints::CDRDihedralConstraintMover::add_harmonic_cluster_constraint(), protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_pose(), protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_wholepose(), protocols::forge::remodel::RemodelConstraintGenerator::add_remodel_constraints_to_pose(), protocols::protein_interface_design::movers::TaskAwareCsts::apply(), protocols::constraint_movers::AddConstraintsToCurrentConformationMover::apply(), protocols::constraint_generator::AddConstraints::apply(), protocols::constraint_movers::ConstraintSetMover::apply(), protocols::relax::AtomCoordinateCstMover::apply(), protocols::protein_interface_design::movers::PlacementAuctionMover::apply(), protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMover::apply(), protocols::calc_taskop_movers::ConsensusDesignMover::apply(), protocols::flxbb::FlxbbDesign::apply(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::design(), protocols::protein_interface_design::movers::PlaceStubMover::final_cleanup(), protocols::constraint_filters::ConstraintScoreCutoffFilter::get_score(), core::scoring::constraints::merge_constraints_from_cmdline_to_pose(), core::scoring::constraints::merge_fa_constraints_from_cmdline_to_pose(), protocols::pose_creation::MergePDBatOverlapMover::minimize_overlap(), protocols::abinitio::abscript::ConstraintPreparer::prepare(), protocols::protein_interface_design::movers::PlacementMinimizationMover::refresh_bbstub_constraints(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::refresh_coordinate_constraints(), protocols::protein_interface_design::movers::PlaceStubMover::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(), size(), and torsion().

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

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

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

References conformation_.

Referenced by protocols::topology_broker::CoordConstraintClaimer::add_constraints(), protocols::topology_broker::ConstraintClaimer::add_constraints(), protocols::loop_build::LoopBuildMover::apply(), protocols::cyclic_peptide::PeptideStubMover::apply(), protocols::fold_from_loops::movers::DisplayPoseLabelsMover::apply(), protocols::stepwise::monte_carlo::mover::AddOrDeleteMover::apply(), protocols::rna::movers::RNAIdealizeMover::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::fold_from_loops::movers::SplitAndMixPoseMover::apply(), protocols::rna::movers::RNAThreadAndMinimizeMover::apply(), core::pose::rna::apply_virtual_rna_residue_variant_type(), protocols::topology_broker::TMHTopologySamplerClaimer::build_fold_tree(), protocols::topology_broker::TopologyBroker::check_chainbreak_variants(), core::pose::full_model_info::check_full_model_info_OK(), protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::check_screen(), protocols::stepwise::modeler::protein::InputStreamWithResidueInfo::check_sequence(), protocols::simple_moves::ConstrainToIdealMover::create_pose_reference(), protocols::environment::Environment::end(), protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger::figure_out_loop(), core::io::silent::BinarySilentStruct::fill_pose(), core::io::silent::RigidBodySilentStruct::fill_struct(), core::io::silent::SilentStruct::fill_struct(), protocols::stepwise::modeler::find_downstream_connection_res(), core::import_pose::libraries::ChunkSet::get_atom_id_domain_map_for_rosetta_library_chunk(), protocols::magnesium::get_bound_water_res(), protocols::stepwise::modeler::align::StepWisePoseAligner::get_rmsd_no_superimpose(), protocols::stepwise::modeler::align::StepWisePoseAligner::initialize(), core::import_pose::libraries::RNA_ChunkLibrary::initialize_rna_chunk_library(), protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::Initialize_terminal_res(), protocols::stepwise::modeler::rna::sugar::look_for_jumps(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::make_full_pose(), core::pose::make_pose_from_sequence(), protocols::topology_broker::SequenceClaimer::make_sequence_claim(), core::scoring::constraints::map_constraints_from_original_pose(), core::pose::rna::mutate_position(), core::sequence::output_fasta_file(), core::scoring::PolymerBondedEnergyContainer::PolymerBondedEnergyContainer(), protocols::rna::movers::RNAThreadAndMinimizeMover::process_insertions(), protocols::environment::Environment::remove_nonpermenant_features(), protocols::simple_filters::PoseInfoFilter::report(), protocols::features::PoseConformationFeatures::report_features_implementation(), protocols::fold_from_loops::utils::report_unfolded(), core::scoring::rna::RNA_VDW_Energy::setup_atom_numbers_for_vdw_calculation(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::setup_disulfides(), core::scoring::electron_density_atomwise::ElecDensAtomwiseEnergy::setup_for_scoring(), core::scoring::magnesium::MgKnowledgeBasedPotential::setup_info_for_mg_calculation(), protocols::stepwise::modeler::rna::phosphate::PhosphateMover::setup_variants_and_free_pose_for_five_prime_phosphate(), protocols::fold_from_loops::movers::NubInitioLoopClosureMover::show_cutpoints(), protocols::topology_broker::TopologyBroker::switch_to_fullatom(), protocols::topology_broker::SymmetryClaimer::symmetry_duplicate(), and core::pose::rna::virtualize_free_rna_moieties().

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_pose_by_jump ( Pose const &  src,
Size const  jump_anchor_residue,
std::string const &  jump_anchor_atom = "",
std::string const &  jump_root_atom = "" 
)
void core::pose::Pose::append_residue_by_atoms ( conformation::Residue const &  new_rsd,
bool const  build_ideal_geometry,
std::string const &  connect_atom,
Size const  anchor_rsd_seqpos,
std::string const &  anchor_connect_atom,
bool const  start_new_chain = false,
bool const  lookup_bond_length = false 
)

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

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

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

Otherwise the incoming coordinates of new_rsd are preserved.

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

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

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

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

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

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

Otherwise the incoming coordinates of new_rsd are preserved.

References conformation_, and energies_.

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

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

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

References conformation_, and energies_.

Referenced by protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::add_aa_virt_rsd_as_root(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::add_aa_virt_rsd_as_root(), protocols::toolbox::sample_around::add_another_virtual_res(), protocols::relax::add_coordinate_constraints_to_pose(), protocols::loops::add_coordinate_constraints_to_pose(), protocols::cyclic_peptide::crosslinker::TBMB_Helper::add_linker_asymmetric(), protocols::cyclic_peptide::crosslinker::TMA_Helper::add_linker_asymmetric(), protocols::cyclic_peptide::crosslinker::TBMB_Helper::add_linker_symmetric(), protocols::cyclic_peptide::crosslinker::TMA_Helper::add_linker_symmetric(), protocols::membrane::AddMembraneMover::add_membrane_virtual(), core::scoring::rna::data::RNA_DMS_Potential::add_probe_to_pose(), protocols::magnesium::add_single_magnesium(), protocols::simple_moves::AddCavitiesMover::add_suckers(), protocols::rna::movers::ErraserMinimizerMover::add_virtual_res(), protocols::toolbox::sample_around::add_virtual_res(), protocols::relax::add_virtual_residue_to_cterm(), protocols::generalized_kinematic_closure::GeneralizedKIC::addloweranchor(), core::pose::addVirtualResAsRoot(), protocols::topology_broker::MembraneTopologyClaimer::addVirtualResAsRootMembrane(), protocols::magnesium::append_mg_bound_water(), protocols::denovo_design::components::append_new_residues(), core::pose::append_pose_with_glycan_residues(), protocols::pose_metric_calculators::append_rsd_by_jump_near_atom(), protocols::hydrate::append_single_far_away_water(), core::pose::append_subpose_to_pose(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::append_virtual_anchor(), protocols::cyclic_peptide::DeclareBond::apply(), protocols::cyclic_peptide::PeptideStubMover::apply(), protocols::magnesium::MgMonteCarlo::apply(), protocols::ncbb::SecStructFinder::apply(), protocols::rna::movers::RNAIdealizeMover::apply(), protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover::apply(), protocols::membrane::visualize::VisualizeEmbeddingMover::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::membrane::visualize::VisualizeMembraneMover::apply(), protocols::idealize::IdealizeMover::apply(), protocols::rna::movers::RNAThreadAndMinimizeMover::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::simple_moves::WaterBoxMover::apply(), protocols::simple_moves::WaterBoxMover::attach_rotamer_clouds_to_pose_and_rotset(), protocols::pockets::PocketGrid::autoexpanding_pocket_eval(), core::pack::rotamer_set::bb_independent_rotamers(), protocols::metal_interface::MatchGrafter::build_combined_pose_with_zinc_overlay(), core::io::pose_from_sfr::PoseFromSFRBuilder::build_initial_pose(), protocols::cryst::MakeLatticeMover::build_lattice_of_virtuals(), protocols::cryst::MakeLayerMover::build_layer_of_virtuals(), core::pack::rotamer_set::build_lib_dna_rotamers(), core::pack::rotamer_set::build_random_dna_rotamers(), protocols::ligand_docking::Transform::convert_to_full_pose(), protocols::relax::coordinate_constrain_selection(), protocols::protein_interface_design::movers::copy_hotspot_to_pose(), protocols::hotspot_hashing::HotspotStubSet::create_hotspot_after_pose(), protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::create_random_fragments(), protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::create_sequence_match_fragments(), core::pose::create_subpose(), protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::diversify_backbone_only_rotamers(), protocols::cyclic_peptide::SymmetricCycpepAlign::do_trim_to_single_repeat(), protocols::sic_dock::dump_loophash_linkers(), protocols::motifs::MotifHit::dump_motif_hit(), core::io::pdb::dump_pdb_residue(), protocols::simple_ddg::ddG::duplicate_waters_across_jump(), core::pose::symmetry::extract_asymmetric_unit(), protocols::pockets::GenPharmacophore::extract_Hbond_atoms_from_protein_rna_complex(), protocols::pockets::GenPharmacophore::extract_rna_rings_from_protein_rna_complex(), core::scoring::motif::ResPairMotif::fill_pose_with_motif(), core::pose::symmetry::get_asymmetric_pose_copy_from_symmetric_pose(), core::pose::symmetry::get_buildingblock_and_neighbor_subs(), protocols::hotspot_hashing::HotspotStubSet::get_residue_score_(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::get_working_pose(), protocols::metal_interface::MatchGrafter::graft(), protocols::hydrate::hydrate_cavities(), protocols::hydrate::hydrate_hyfile(), 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::sic_dock::make_Cx(), core::pose::make_pose_from_sequence(), core::fragment::make_pose_from_sequence_(), protocols::stepwise::modeler::merge_two_poses(), protocols::make_rot_lib::min_rotamers(), protocols::forge::build::BuildManager::modify(), protocols::forge::build::ConnectRight::modify_impl(), protocols::topology_broker::TMHTopologySamplerClaimer::output_membrane_vector(), core::pose::pdbslice(), protocols::cyclic_peptide::crosslinker::TMA_Helper::place_tma_asymmetric(), protocols::cyclic_peptide::crosslinker::TMA_Helper::place_tma_symmetric(), protocols::hotspot_hashing::StubGenerator::placeResidueOnPose(), protocols::make_rot_lib::MakeRotLibJobInputter::pose_from_job(), protocols::ligand_docking::ProtLigEnsemble::prepare_single_ligand_pose(), protocols::denovo_design::components::prepend_new_residues(), protocols::match::MatcherMover::process_pose(), core::io::serialization::read_binary(), protocols::sic_dock::read_biounit(), protocols::simple_moves::RepeatPropagationMover::repeat_ligand(), protocols::hotspot_hashing::HotspotStubSet::rescore(), protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::semiexpl_water_hbgeom_score(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_fold_tree_through_build_full_model_info(), protocols::rbsegment_relax::setup_pose_from_rbsegs(), protocols::relax::RepeatProteinRelax::setup_repeat_pose_jumping(), protocols::stepwise::modeler::slice(), protocols::comparative_modeling::steal_ligands(), protocols::motif_grafting::movers::MotifGraftMover::stich_motif_in_scaffold_by_indexes_rotation_and_translation(), protocols::topology_broker::SymmetryClaimer::symmetry_duplicate(), and protocols::sewing::data_storage::SmartAssembly::to_pose().

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 core::scoring::MultipoleElecPotential::align_residue_multipole_axes(), protocols::chemically_conjugated_docking::UBQ_GTPaseMover::analyze_and_filter(), protocols::simple_moves::TorsionDOFMover::apply(), protocols::rna::movers::RNAIdealizeMover::apply(), core::optimization::atom_tree_dfunc(), core::optimization::symmetry::atom_tree_dfunc(), protocols::backrub::BackrubSegment::bond_angle_atoms(), protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::calculate_jump(), core::import_pose::RNA_JumpMover::check_forward_backward(), protocols::simple_moves::ConstrainToIdealMover::check_if_really_connected(), protocols::rna::movers::connected_in_atom_tree(), protocols::toolbox::match_enzdes_util::constrain_pose_res_to_invrots(), protocols::ligand_docking::ga_ligand_dock::GriddedAtomTreeMultifunc::dfunc(), core::scoring::constraints::AtomPairConstraint::dist(), protocols::backrub::BackrubMover::dof_id_ranges(), core::import_pose::atom_tree_diffs::dump_atom_tree_diff(), protocols::viewer::dump_pose_kinemage(), protocols::backrub::BackrubSegment::end_atoms1(), protocols::stepwise::sampler::rna::RNA_KinematicCloser::figure_out_dof_ids_and_offsets(), protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::figure_out_dof_ids_and_offsets(), protocols::rna::denovo::coarse::CoarseRNA_LoopCloser::figure_out_dof_ids_and_offsets(), core::pose::copydofs::CopyDofs::figure_out_dofs(), protocols::rna::denovo::coarse::CoarseRNA_LoopCloser::figure_out_forward_backward_res_by_backtracking(), core::pose::rna::fix_sugar_coords(), protocols::stepwise::modeler::align::StepWisePoseAligner::get_root_triad_atom_id_map(), core::pose::rna::initialize_atoms_for_which_we_need_new_dofs(), protocols::simple_moves::DOFHistogramRecorder::insert_dofs_by_residue(), protocols::branch_angle::BranchAngleOptimizer::optimize_angles(), protocols::branch_angle::BranchAngleOptimizer::overall_params(), protocols::rna::denovo::print_internal_coords(), protocols::backrub::BackrubMover::random_angle(), protocols::ligand_docking::restrain_ligand_nbr_atom(), protocols::ligand_docking::LigandBaseProtocol::restrain_ligand_nbr_atom(), protocols::ligand_docking::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::BaseTabooPerturber::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(), protocols::simple_moves::ConstrainToIdealMover::vary_bond_geometry(), and protocols::rna::movers::ErraserMinimizerMover::vary_bond_geometry().

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

attach ConformationEvent observer function

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

References conformation_obs_hub_.

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

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

attach DestructionEvent observer function

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

References destruction_obs_hub_.

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

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

attach EnergyEvent observer function

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

References energy_obs_hub_.

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

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

attach GeneralEvent observer function

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

References general_obs_hub_.

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

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

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

get the locations of a vector of atoms

References conformation_.

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

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

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

set the locations of a vector of atoms

References conformation_.

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

iterator core::pose::Pose::begin ( )
noexcept
const_iterator core::pose::Pose::begin ( ) const
noexcept
Real core::pose::Pose::beta ( Size const  seqpos) const

Returns the beta torsion angle of residue <seqpos>

Note
assumes the residue is an nucleic acid

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

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

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

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

References conformation_obs_hub_, destruction_obs_hub_, energy_obs_hub_, and general_obs_hub_.

Referenced by operator=().

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

Returns the chain number of residue <seqpos>

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

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

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

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

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

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

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

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

References conformation_, and num_chains().

Referenced by protocols::protein_interface_design::movers::SetAtomTree::set_ab_fold_tree(), protocols::splice::SpliceInTail::set_fold_tree_nodes(), protocols::splice::SpliceOutTail::set_fold_tree_nodes(), protocols::splice::SpliceIn::set_fold_tree_nodes(), protocols::splice::SpliceOut::set_fold_tree_nodes(), and split_by_chain().

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

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

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

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

References conformation_, and num_chains().

Referenced by split_by_chain().

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

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

Note
assumes the residue is an amino acid or monosaccharide

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

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

Referenced by protocols::simple_moves::RepeatPropagationMover::add_cap_seq(), protocols::splice::Splice::add_coordinate_constraints(), protocols::splice::SpliceManager::add_coordinate_constraints(), protocols::simple_moves::CombinePoseMover::apply(), protocols::comparative_modeling::Align_RotamerEvaluator::apply(), protocols::simple_moves::CopyRotamerMover::apply(), protocols::backrub::BackrubSidechainMover::apply(), protocols::simple_moves::CopyRotamerMover::apply_from_template_pose(), protocols::comparative_modeling::chis_from_pose(), protocols::pose_metric_calculators::RotamerRecovery::chis_from_pose(), protocols::simple_moves::RepeatPropagationMover::copy_phi_psi_omega(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::copy_rna_chi(), core::scoring::rna::data::RNA_DMS_LowResolutionPotential::evaluate(), core::scoring::rna::data::RNA_DMS_Potential::get_features(), protocols::simple_moves::sidechain_moves::SidechainMoverBase::idealize_sidechains(), protocols::simple_moves::sidechain_moves::SidechainMover::idealize_sidechains(), protocols::make_rot_lib::min_rotamers(), protocols::make_rot_lib::MakeRotLibMover::minimize_rotamer(), core::pose::rna::mutate_position(), protocols::cryst::DockLatticeMover::perturb_chis(), protocols::simple_moves::PeriodicBoxMover::perturb_molecule_move(), protocols::loop_grower::ResTorsions::ResTorsions(), protocols::environment::ClientMover::sandboxed_copy(), and protocols::rotamer_recovery::PerNativeRRReporterHuman::set_native().

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

Returns the chi torsion angle of residue <seqpos>

Note
assumes the residue is an nucleic acid

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

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

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

Empty the pose contents.

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

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

Referenced by protocols::generalized_kinematic_closure::GeneralizedKIC::addloweranchor(), protocols::cyclic_peptide::DeclareBond::apply(), protocols::cyclic_peptide::PeptideStubMover::apply(), protocols::simple_moves::SwitchChainOrderMover::apply(), protocols::pose_creation::ExtendedPoseMover::apply(), protocols::helical_bundle::MakeBundle::apply(), protocols::helical_bundle::MakeBundleHelix::apply(), protocols::carbohydrates::GlycanTreeModeler::apply(), protocols::topology_broker::TopologyBroker::apply(), protocols::cryst::MakeLatticeMover::build_lattice_of_virtuals(), protocols::cryst::MakeLayerMover::build_layer_of_virtuals(), core::io::pose_from_sfr::PoseFromSFRBuilder::build_pose(), protocols::LoopRebuild::build_random_loops(), protocols::forge::remodel::RemodelAccumulator::clear(), protocols::design_opt::GreedyOptMutationMover::clear_cached_data(), protocols::matdes::MatDesGreedyOptMutationMover::clear_cached_data(), protocols::loop_modeling::LoopProtocol::clear_movers(), protocols::simple_filters::NetChargeFilter::compute(), protocols::simple_moves::CutChainMover::create_subpose(), core::pose::create_subpose(), protocols::pockets::GenPharmacophore::extract_rna_rings_from_protein_rna_complex(), core::scoring::motif::ResPairMotif::fill_pose_with_motif(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::final_cleanup(), core::fragment::Frame::fragment_as_pose(), protocols::topology_broker::FragmentJumpClaimer::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::FragmentJumpClaimer::new_decoy(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::pair_sets_with_positions(), core::pose::pdbslice(), protocols::cyclic_peptide::crosslinker::TMA_Helper::place_tma_asymmetric(), protocols::cyclic_peptide::crosslinker::TMA_Helper::place_tma_symmetric(), 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::AtomTreeDiffJobInputter::pose_from_job(), protocols::jd2::SilentFileJobInputter::pose_from_job(), protocols::features::DatabaseJobInputter::pose_from_job(), protocols::denovo_design::components::prune_unpaired_residues(), core::io::serialization::read_binary(), protocols::stepwise::monte_carlo::mover::DeleteMover::remove_singletons_and_update_pose_focus(), protocols::rbsegment_relax::setup_pose_from_rbsegs(), protocols::fold_from_loops::movers::SplitAndMixPoseMover::transfer_conformation(), protocols::fold_from_loops::utils::Nub::transfer_unfolded_conformation(), protocols::comparative_modeling::AlignmentCluster::~AlignmentCluster(), and ~Pose().

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

Remove all sequence constraints from this pose.

References constraint_set_.

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

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

clone the conformation

clone the pose

References Pose().

Referenced by protocols::stepwise::modeler::packer::StepWiseMasterPacker::add_packer_screeners(), protocols::stepwise::modeler::add_to_pose_list(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::apply(), protocols::pose_length_moves::InsertResMover::apply(), protocols::pose_length_moves::AnalyzeLoopModeling::apply(), protocols::rna::denovo::RNA_FragmentMonteCarlo::apply(), protocols::cyclic_peptide::TryDisulfPermutations::apply(), protocols::rosetta_scripts::MultiplePoseMover::apply(), protocols::stepwise::modeler::align::StepWiseClusterer::apply(), protocols::residue_selectors::HBondSelector::apply(), protocols::ligand_docking::Transform::apply(), protocols::relax::membrane::MPRangeRelaxMover::apply(), protocols::forge::remodel::RemodelLoopMover::apply(), protocols::cyclic_peptide::CrosslinkerMover::asymmetric_apply(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::bulge_chain_closure_complete(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::bulge_chain_minimize_legacy(), protocols::simple_moves::StructProfileMover::calc_cenlist(), protocols::docking::calc_interaction_energy(), protocols::simple_filters::RepeatParameterFilter::calculate_helical_parameters(), protocols::antibody::cdr_energy(), protocols::stepwise::modeler::StepWiseMinimizer::check_pose_list(), protocols::stepwise::legacy::screener::SimplePoseSelection::check_screen(), protocols::simple_moves::CombinePoseMover::CombinePoseMover(), protocols::stepwise::sampler::copy_dofs::CopyDofStepWiseSampler::CopyDofStepWiseSampler(), protocols::pose_length_moves::NearNativeLoopCloser::create_maximum_length_pose(), protocols::stepwise::modeler::StepWiseMinimizer::do_full_minimizing(), protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::do_prepack(), protocols::stepwise::modeler::StepWiseModeler::do_stepwise_lores(), protocols::generalized_kinematic_closure::GeneralizedKIC::doKIC(), protocols::relax::RangeRelaxMover::finalize_setup(), protocols::pose_creation::MergePDBMover::generate_overlaps(), protocols::relax::AtomCoordinateCstMover::get_constraint_target_pose(), protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::get_sugar_modeling_set(), protocols::jd2::archive::ArchiveBase::init_from_decoy_set(), protocols::rna::setup::RNA_MonteCarloJobDistributor::initialize(), protocols::rna::setup::RNA_CSA_JobDistributor::initialize(), core::scoring::rna::data::RNA_DMS_Potential::initialize(), protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_checkers(), protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_moving_residue_pose_list(), protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_sampler(), protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::instantiate_sugars_recursively(), protocols::pose_creation::MergePDBatOverlapMover::makeJunctions_apply(), protocols::stepwise::modeler::rna::sugar::modeler_starting_pose_data_list(), protocols::constraint_generator::CoordinateConstraintGenerator::prepare_constraint_target_pose(), protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::prepare_from_prior_sampled_sugar_jobs(), protocols::match::MatcherMover::process_pose(), protocols::denovo_design::DisulfidizeMover::process_pose(), protocols::relax::RepeatProteinRelax::relax_pose(), protocols::stepwise::monte_carlo::mover::DeleteMover::remove_singletons_and_update_pose_focus(), protocols::hbnet::HBNetScore::report_sm(), protocols::stepwise::modeler::packer::StepWisePacker::reset(), protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::reset(), protocols::magnesium::MgScanner::scan_magnesiums(), protocols::features::InterfaceDdGMover::set_mut_pose(), core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::set_up_residuearrayannealableenergy_for_packing(), protocols::features::InterfaceDdGMover::set_wt_pose(), protocols::stepwise::modeler::rna::rigid_body::setup_pose_with_moving_residue_alternative_list(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::setup_sugar_conformations(), protocols::stepwise::modeler::rna::phosphate::PhosphateMover::setup_variants_and_free_pose_for_five_prime_phosphate(), protocols::stepwise::modeler::rna::phosphate::PhosphateMover::setup_variants_and_free_pose_for_three_prime_phosphate(), protocols::fold_from_loops::movers::SplitAndMixPoseMover::split_pose(), protocols::stepwise::modeler::switch_focus_to_other_pose(), protocols::cyclic_peptide::CrosslinkerMover::symmetric_apply(), protocols::toolbox::rigid_body::transform_moving_partition_to_origin(), protocols::stepwise::monte_carlo::mover::FromScratchMover::update_full_model_info_and_switch_focus_to_new_pose(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection::update_pose_list(), protocols::stepwise::modeler::align::StepWisePoseAligner::update_reference_pose_local(), and protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::virtualize_distal_partition().

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_filters::SpanTopologyMatchPoseFilter::actual_topology(), core::pose::rna::add_chi_constraints(), protocols::matdes::SymDofMover::add_components_to_pose_if_necessary(), core::util::add_covalent_linkage(), core::pose::add_custom_variant_type_to_pose_residue(), protocols::forge::methods::add_cutpoint_variants(), protocols::denovo_design::add_cutpoints(), protocols::chemically_conjugated_docking::add_extra_bodies(), protocols::membrane::symmetry::SymmetricAddMembraneMover::add_membrane_virtual(), protocols::cryst::MakeLatticeMover::add_monomers_to_lattice(), protocols::cryst::MakeLayerMover::add_monomers_to_layer(), protocols::simple_moves::AddChainMover::add_new_chain(), protocols::hybridization::add_non_protein_cst(), protocols::helical_bundle::MakeBundleHelix::add_parameter_info_to_pose(), protocols::sewing::hashing::AlignmentFileGeneratorMover::add_pose_segments_to_segment_vector(), protocols::denovo_design::add_residues_to_pose(), protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::add_rotamer_to_rotamer_set(), protocols::splice::SpliceManager::add_sequence_constraints(), protocols::splice::Splice::add_sequence_constraints(), protocols::loop_grower::LoopPartialSolution::add_sheets(), protocols::loops::add_single_cutpoint_variant(), protocols::denovo_design::components::add_to_pose(), core::optimization::symmetry::SymMinimizerMap::add_torsion(), core::pose::add_variant_type_to_pose_residue(), core::pose::add_variant_type_to_residue(), protocols::loop_grower::LoopGrower::addnativesolution(), protocols::splice::SpliceManager::adjust_stem_positions_by_template(), protocols::denovo_design::movers::AlignResiduesMover::align_residues(), core::pose::carbohydrates::align_virtual_atoms_in_carbohydrate_residue(), core::pack::rotamer_set::AddResiduesRotamerSetOperation::alter_rotamer_set(), protocols::matdes::MotifHitsRotamersOperation::alter_rotamer_set(), core::pack::rotamer_set::UnboundRotamersOperation::alter_rotamer_set(), protocols::chemically_conjugated_docking::UBQ_GTPaseMover::analyze_and_filter(), protocols::anchored_design::AnchorMoversData::anchor_noise_constraints_setup(), protocols::denovo_design::components::append_new_chain_from_template_segment(), append_pose_by_jump(), protocols::seeded_abinitio::GrowPeptides::append_residues_cterminally(), protocols::seeded_abinitio::GrowPeptides::append_residues_nterminally(), protocols::cyclic_peptide::DeclareBond::apply(), protocols::simple_moves::ReportXYZ::apply(), protocols::simple_moves::AddJobPairData::apply(), protocols::simple_moves::VirtualRootMover::apply(), protocols::cutoutdomain::CutOutDomain::apply(), protocols::simple_moves::AlignChainMover::apply(), protocols::protein_interface_design::movers::AddChainBreak::apply(), protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspots::apply(), protocols::seeded_abinitio::DefineMovableLoops::apply(), protocols::seeded_abinitio::SwapSegment::apply(), protocols::electron_density::ScaleMapIntensities::apply(), protocols::electron_density::ReportFSC::apply(), protocols::protein_interface_design::movers::LoopLengthChange::apply(), protocols::seeded_abinitio::CAcstGenerator::apply(), protocols::calc_taskop_movers::ForceDisulfidesMover::apply(), protocols::simple_moves::ChainSplitMover::apply(), protocols::simple_moves::hbs::HbsPatcher::apply(), protocols::simple_moves::SwitchChainOrderMover::apply(), protocols::simple_moves::oop::OopMover::apply(), protocols::simple_moves::oop::OopPatcher::apply(), protocols::simple_moves::triazolamer::TriazolamerMover::apply(), protocols::protein_interface_design::movers::SetAtomTree::apply(), protocols::protein_interface_design::movers::TopologyBrokerMover::apply(), protocols::simple_moves::WriteSSEMover::apply(), protocols::grafting::simple_movers::DeleteRegionMover::apply(), protocols::protein_interface_design::movers::SpinMover::apply(), protocols::ligand_docking::WriteLigandMolFile::apply(), protocols::simple_moves::PeptideStapleMover::apply(), protocols::protein_interface_design::movers::PrepackMover::apply(), protocols::seeded_abinitio::CloseFold::apply(), protocols::simple_filters::SSMotifFinder::apply(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList::apply(), protocols::simple_moves::a3b_hbs::A3BHbsPatcher::apply(), protocols::seeded_abinitio::SeedFoldTree::apply(), protocols::simple_filters::StemFinder::apply(), protocols::ligand_docking::RandomConformers::apply(), protocols::ligand_docking::RigidSearchMover::apply(), protocols::ligand_docking::AddHydrogens::apply(), protocols::ligand_docking::LigandDesign::apply(), protocols::antibody::GraftOneCDRLoop::apply(), protocols::seeded_abinitio::SegmentHybridizer::apply(), protocols::stepwise::modeler::precomputed::PrecomputedLibraryMover::apply(), protocols::ligand_docking::AddHydrogen::apply(), protocols::ligand_docking::GrowLigand::apply(), protocols::ligand_docking::MinimizeLigand::apply(), protocols::simple_moves::oop::OopRandomSmallMover::apply(), protocols::simple_moves::triazolamer::TriazolamerRandomSmallMover::apply(), protocols::task_operations::SelectBySASAOperation::apply(), protocols::hybridization::MRMover::apply(), protocols::ligand_docking::TetherLigand::apply(), protocols::stepwise::modeler::packer::SideChainCopier::apply(), protocols::symmetric_docking::SymFoldandDockSlideTrialMover::apply(), protocols::task_operations::SelectByDeltaScoreOperation::apply(), protocols::loops::loop_mover::LoopCM::apply(), protocols::abinitio::ResolutionSwitcher::apply(), protocols::symmetry::SymmetricRMSMover::apply(), protocols::ligand_docking::HBondDonorFilter::apply(), protocols::protein_interface_design::filters::FilterScanFilter::apply(), protocols::carbohydrates::IdealizeAnomericHydrogens::apply(), protocols::simple_moves::ModifyVariantTypeMover::apply(), protocols::dna::SeparateDnaFromNonDna::apply(), protocols::metal_interface::ZincHeterodimerMover::apply(), protocols::nonlocal::SheetTranslate::apply(), protocols::rigid::RotateJumpAxisMover::apply(), protocols::simple_moves::CyclizationMover::apply(), protocols::simple_moves::FavorSequenceProfile::apply(), protocols::simple_moves::RandomOmegaFlipMover::apply(), protocols::domain_assembly::AssembleLinkerMover::apply(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::apply(), protocols::fold_from_loops::movers::NubInitioLoopClosureMover::apply(), protocols::task_operations::SelectResiduesWithinChainOperation::apply(), protocols::nonlocal::HelixRotate::apply(), protocols::simple_moves::DeleteChainsMover::apply(), protocols::task_operations::RestrictChainToRepackingOperation::apply(), protocols::task_operations::RestrictNonSurfaceToRepackingOperation::apply(), protocols::ligand_docking::CompleteConnectionsFilter::apply(), core::select::residue_selector::BondedResidueSelector::apply(), protocols::protein_interface_design::movers::BackrubDDMover::apply(), protocols::comparative_modeling::PartialThreadingMover::apply(), protocols::task_operations::RestrictToAlignedSegmentsOperation::apply(), protocols::indel::IndelOptimizationMover::apply(), protocols::abinitio::abscript::StructPerturberCM::apply(), protocols::protein_interface_design::movers::PlacementAuctionMover::apply(), protocols::environment::ScriptCM::apply(), protocols::task_operations::PreventChainFromRepackingOperation::apply(), protocols::abinitio::AbrelaxMover::apply(), protocols::simple_filters::JumpEvaluator::apply(), protocols::simple_moves::chiral::ChiralMover::apply(), protocols::simple_moves::RandomTorsionMover::apply(), protocols::ligand_docking::AtomCountFilter::apply(), protocols::ligand_docking::HBondAcceptorFilter::apply(), protocols::ligand_docking::HeavyAtomFilter::apply(), protocols::ligand_docking::MolarMassFilter::apply(), protocols::ligand_docking::MolecularMassFilter::apply(), protocols::constraint_generator::DihedralConstraintGenerator::apply(), protocols::splice::SpliceOut::apply(), protocols::docking::EllipsoidalRandomizationMover::apply(), protocols::splice::DesignInterfacesOperation::apply(), protocols::matdes::SymDofMover::apply(), protocols::protein_interface_design::movers::SaveAndRetrieveSidechains::apply(), protocols::antibody::ModelCDRH3::apply(), protocols::task_operations::RestrictToTerminiOperation::apply(), core::select::residue_selector::ResidueInMembraneSelector::apply(), protocols::simple_moves::DisulfideInsertionMover::apply(), protocols::simple_moves::TorsionDOFMover::apply(), protocols::farnesyl::InstallFarnesylMover::apply(), core::select::residue_selector::NumNeighborsSelector::apply(), protocols::simple_moves::SetTorsion::apply(), protocols::membrane::benchmark::SampleTiltAngles::apply(), protocols::minimization_packing::DisulfideOptimizationMover::apply(), protocols::rna::movers::RNAIdealizeMover::apply(), protocols::symmetric_docking::SymFoldandDockRbTrialMover::apply(), protocols::flexpep_docking::FlexPepDockingProtocol::apply(), protocols::abinitio::abscript::FragmentCM::apply(), protocols::task_operations::RestrictNativeResiduesOperation::apply(), protocols::environment::CoMTrackerCM::apply(), protocols::hybridization::CartesianSampler::apply(), protocols::simple_moves::ReturnSidechainMover::apply(), protocols::symmetry::SymDockingInitialPerturbation::apply(), protocols::abinitio::abscript::AbscriptLoopCloserCM::apply(), protocols::protein_interface_design::movers::LoopMoverFromCommandLine::apply(), protocols::rigid::UniformRigidBodyCM::apply(), protocols::task_operations::JointSequenceOperation::apply(), protocols::hybridization::CartesianHybridize::apply(), protocols::task_operations::ProteinInterfaceDesignOperation::apply(), protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover::apply(), protocols::rbsegment_relax::FragInsertAndAlignMover::apply(), protocols::rna::movers::ErraserMinimizerMover::apply(), protocols::comparative_modeling::ExtraThreadingMover::apply(), protocols::loop_grower::FragmentExtension::apply(), protocols::cyclic_peptide::RamaMutationSelector::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), core::select::residue_selector::AsymmetricUnitSelector::apply(), core::fragment::BBTorsionAndAnglesSRFD::apply(), protocols::moves::StructureRestrictor::apply(), protocols::task_operations::SeqprofConsensusOperation::apply(), protocols::ligand_docking::Translate::apply(), protocols::ligand_docking::Transform::apply(), protocols::ligand_docking::TransformEnsemble::apply(), protocols::membrane::SetMembranePositionMover::apply(), protocols::simple_moves::UniformRotationMover::apply(), protocols::rigid::WholeBodyTranslationMover::apply(), protocols::simple_moves::ReportEffectivePKA::apply(), protocols::hybridization::BackboneTorsionPerturbation::apply(), protocols::hybridization::BackboneTorsionSampler::apply(), protocols::membrane::RandomPositionRotationMover::apply(), protocols::task_operations::RestrictToInterfaceVectorOperation::apply(), protocols::canonical_sampling::CanonicalSamplingMover::apply(), protocols::ncbb::NcbbDockDesignProtocol::apply(), protocols::cryst::UpdateCrystInfo::apply(), protocols::splice::Splice::apply(), protocols::helical_bundle::MakeBundle::apply(), protocols::membrane::visualize::VisualizeEmbeddingMover::apply(), protocols::ncbb::oop::OopDockDesignProtocol::apply(), protocols::helical_bundle::PerturbBundleHelix::apply(), protocols::helical_bundle::PerturbBundle::apply(), protocols::loophash::LoopHashDiversifier::apply(), core::select::residue_selector::DensityFitResidueSelector::apply(), protocols::cyclic_peptide::CrosslinkerMover::apply(), protocols::simple_moves::bin_transitions::PerturbByBins::apply(), protocols::simple_moves::bin_transitions::InitializeByBins::apply(), protocols::relax::LocalRelax::apply(), protocols::denovo_design::movers::RotateSegmentMover::apply(), protocols::membrane::OptimizeProteinEmbeddingMover::apply(), protocols::symmetry::SymDockingSlideIntoContact::apply(), protocols::membrane::MembranePositionFromTopologyMover::apply(), protocols::relax::ClassicRelax::apply(), protocols::rigid::WholeBodyRotationMover::apply(), protocols::simple_moves::PeriodicBoxMover::apply(), protocols::relax::membrane::MPFastRelaxMover::apply(), protocols::docking::membrane::MPFindInterfaceMover::apply(), protocols::ncbb::oop::OopCreatorMover::apply(), protocols::enzdes::DetectProteinLigandInterface::apply(), protocols::relax::membrane::MPRangeRelaxMover::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::membrane::AddMPLigandMover::apply(), protocols::symmetry::SetupNCSMover::apply(), protocols::symmetric_docking::membrane::MPSymDockMover::apply(), protocols::relax::RangeRelaxMover::apply(), protocols::ligand_docking::ProtLigEnsemble::apply(), protocols::membrane::visualize::VisualizeMembraneMover::apply(), protocols::antibody::design::AntibodyDesignMover::apply(), protocols::protein_interface_design::movers::PlaceStubMover::apply(), protocols::idealize::IdealizeMover::apply(), protocols::loop_grower::SheetSampler::apply(), protocols::comparative_modeling::ThreadingMover::apply(), protocols::symmetry::FaSymDockingSlideTogether::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::membrane::TiltMover::apply(), protocols::membrane::TransformIntoMembraneMover::apply(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::apply(), protocols::membrane::TranslationMover::apply(), protocols::antibody_legacy::GraftOneMover::apply(), protocols::membrane::AddMembraneMover::apply(), protocols::membrane::RandomPositionTranslationMover::apply(), protocols::simple_moves::UniformTranslationMover::apply(), protocols::fldsgn::CircularPermutation::apply(), protocols::cryst::MakeLayerMover::apply(), protocols::relax::FastRelax::apply(), protocols::enzdes::LigInterfaceEnergyFilter::apply(), protocols::enzdes::PredesignPerturbMover::apply(), protocols::abinitio::MembraneAbinitio::apply(), protocols::membrane::SetMembraneNormalMover::apply(), protocols::topology_broker::TopologyBroker::apply(), protocols::symmetric_docking::SymDockProtocol::apply(), protocols::loop_grower::LoopPartialSolution::apply(), core::fragment::DownJumpSRFD::apply(), protocols::rigid::RigidBodyPerturbMover::apply(), protocols::docking::DockingSlideIntoContact::apply(), protocols::membrane::SetMembraneCenterMover::apply(), protocols::enzdes::RepackLigandSiteWithoutLigandMover::apply(), protocols::membrane::RotationMover::apply(), protocols::moves::PyMOLMover::apply(), protocols::rigid::RigidBodyRandomizeMover::apply(), protocols::cryst::MakeLatticeMover::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::membrane::TranslationRotationMover::apply(), protocols::rigid::RigidBodySpinMover::apply(), protocols::rigid::RigidBodyDeterministicSpinMover::apply(), protocols::rigid::RigidBodyTiltMover::apply(), protocols::forge::components::VarLengthBuild::apply(), protocols::loop_grower::LoopGrower::apply(), protocols::rigid::RigidBodyTransMover::apply(), protocols::fold_from_loops::movers::NubInitioLoopClosureMover::apply_closure_trust(), protocols::analysis::InterfaceAnalyzerMover::apply_const(), protocols::hybridization::CartesianSampler::apply_constraints(), protocols::seeded_abinitio::SegmentHybridizer::apply_frame(), protocols::hybridization::CartesianHybridize::apply_frame(), protocols::hybridization::CartesianSampler::apply_frame(), protocols::kinematic_closure::ClosureProblem::apply_internal_coordinates(), protocols::generalized_kinematic_closure::selector::GeneralizedKICselector::apply_lowest_delta_torsion_selector(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_perturb_backbone_by_bins(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_rama_prepro_check(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_randomize_backbone_by_bins(), protocols::indexed_structure_store::apply_residue_entries_to_pose(), protocols::pockets::PlaidFingerprint::apply_rotation_offset_to_pose_(), protocols::loops::apply_sequence_mapping(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_set_backbone_bin(), protocols::loop_grower::LoopPartialSolution::apply_sheets(), protocols::toolbox::apply_superposition_transform_to_jump(), protocols::backbone_moves::local_backbone_mover::Residue::apply_to_pose(), protocols::pockets::ElectrostaticpotentialGrid::assign_esp_for_protein_grid_points(), protocols::splice::SpliceOutAntibody::assign_from_res_to_res(), protocols::splice::SpliceInTail::assign_from_res_to_res(), protocols::splice::SpliceInAntibody::assign_from_res_to_res(), core::optimization::CartesianMinimizerMap::assign_rosetta_torsions_and_trim(), core::optimization::symmetry::SymMinimizerMap::asymmetric_dof(), protocols::simple_filters::atom_distance(), core::optimization::symmetry::atom_tree_dfunc(), core::optimization::symmetry::atom_tree_get_atompairE_deriv(), core::scoring::atomic_depth::atomic_depth(), core::scoring::atomic_depth::atoms_deeper_than(), core::pack::scmin::AtomTreeCollection::AtomTreeCollection(), protocols::denovo_design::components::StructureDataObserver::attach_impl(), 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::fold_from_loops::utils::attach_unfolded_pose_to_pose_c_term(), protocols::fold_from_loops::utils::attach_unfolded_pose_to_pose_n_term(), protocols::sic_dock::auto_trim_floppy_termini(), protocols::pockets::PocketGrid::autoexpanding_pocket_eval(), core::scoring::hbonds::HBondEnergy::backbone_backbone_energy(), core::scoring::hbonds::HBondEnergy::backbone_sidechain_energy(), protocols::idealize::basic_idealize(), protocols::peptide_deriver::PeptideDeriverMarkdownStreamOutputter::begin_structure(), protocols::electron_density::BfactorMultifunc::BfactorMultifunc(), protocols::evolution::EvolutionaryDynamicsMover::boltzmann(), protocols::monte_carlo::GenericMonteCarloMover::boltzmann(), protocols::branch_angle::branching_atomid1(), protocols::branch_angle::branching_atomids2(), protocols::minimization_packing::DisulfideOptimizationMover::break_repack_reform(), protocols::environment::EnvClaimBroker::broker_dofs(), protocols::forge::remodel::build_and_score_disulfide(), protocols::metal_interface::MatchGrafter::build_combined_pose_with_zinc_overlay(), protocols::splice::SpliceOutTail::build_ideal_segment(), protocols::splice::SpliceInTail::build_ideal_segment(), protocols::splice::SpliceIn::build_ideal_segment(), protocols::splice::SpliceOut::build_ideal_segment(), core::io::pose_from_sfr::PoseFromSFRBuilder::build_initial_pose(), core::pack::rotamer_set::build_lib_dna_rotamers(), protocols::LoopRebuild::build_loop_with_ccd_closure(), core::pack::rotamer_set::RotamerSet_::build_optimize_H_rotamers(), core::scoring::GenBornPotential::build_placeholders(), core::import_pose::build_pose_as_is2(), core::pack::rotamer_set::build_random_dna_rotamers(), core::pack::rotamer_set::build_rna_chi_rotamers(), core::pack::rotamer_set::RotamerSets::build_rotamers(), core::scoring::CA_rmsd_symmetric(), core::scoring::membrane::FaMPEnvSmoothEnergy::calc_energy(), core::scoring::membrane::MPHelicalityEnergy::calc_energy(), core::scoring::membrane::MPResidueLipophilicityEnergy::calc_energy(), protocols::flexpep_docking::FlexPepDockingPoseMetrics::calc_frac_atoms_kA_to_native(), protocols::membrane::calc_helix_tilt_angle(), core::select::util::calc_interacting_vector(), protocols::symmetric_docking::SymDockProtocol::calc_interaction_energy(), protocols::denovo_design::components::calc_paired_residues(), protocols::symmetric_docking::SymDockProtocol::calc_rms(), core::scoring::membrane::MPSpanInsertionEnergy::calc_span_score(), protocols::pockets::PlaidFingerprint::calculate_ligand_CoM(), protocols::pmut_scan::PointMutScanDriver::calculate_neighbor_table(), core::scoring::electron_density::calculate_rama(), core::scoring::fiber_diffraction::FiberDiffractionEnergyDens::calculate_rho_fast2(), protocols::anchored_design::AnchoredDesignMover::calculate_rmsd(), core::optimization::cartesian_collect_torsional_deriv(), core::optimization::cartesian_dfunc(), protocols::forge::remodel::RemodelMover::centroid_build(), protocols::simple_moves::CutChainMover::chain_cut(), core::pose::chain_end_res(), core::io::carbohydrates::chain_gws_string(), protocols::splice::SpliceManager::chainbreak_check(), protocols::splice::Splice::chainbreak_check(), protocols::hybridization::HybridizeProtocol::check_and_create_fragments(), protocols::denovo_design::components::StructureData::check_chains(), core::scoring::rna::RNA_TorsionPotential::check_intra_residue(), protocols::features::ProteinResidueConformationFeatures::check_num_requested_atoms(), protocols::membrane::check_orientation(), core::import_pose::cleanup(), protocols::loop_grower::LoopPartialSolutionStore::cluster_check(), protocols::splice::SampleRotamersFromPDB::combine_rot_dbs(), protocols::simple_filters::ResidueBurialFilter::compute(), protocols::simple_filters::ResidueSelectionDistanceFilter::compute(), protocols::simple_filters::SidechainRmsdFilter::compute(), protocols::simple_filters::ResidueDistanceFilter::compute(), protocols::simple_filters::AngleToVector::compute(), protocols::evolution::AASynthesisFitnessCost::compute(), protocols::simple_filters::ChainBreak::compute(), protocols::simple_filters::TerminusDistanceFilter::compute(), protocols::simple_filters::TMsSpanMembraneFilter::compute(), protocols::simple_filters::NeighborTypeFilter::compute(), protocols::protein_interface_design::filters::AverageDegreeFilter::compute(), protocols::cryst::ReportGradientsMover::compute(), protocols::simple_filters::MutationsFilter::compute(), protocols::protein_interface_design::filters::SequenceRecoveryFilter::compute(), protocols::simple_filters::MembAccesResidueLipophilicityFilter::compute(), protocols::protein_interface_design::filters::RmsdSimpleFilter::compute(), protocols::protein_interface_design::filters::SSamountFilter::compute(), protocols::protein_interface_design::filters::SpecificResiduesNearInterfaceFilter::compute(), protocols::fold_from_loops::filters::ScorePoseSegmentFromResidueSelectorFilter::compute(), protocols::protein_interface_design::filters::AtomicContactCountFilter::compute(), protocols::simple_filters::SimpleHbondsToAtomFilter::compute(), protocols::simple_filters::BuriedUnsatHbondFilter::compute(), protocols::toolbox::CalcInterNeighborGroup::compute(), protocols::protein_interface_design::filters::HbondsToAtomFilter::compute(), protocols::simple_filters::LeastNativeLike9merFilter::compute(), protocols::enzdes::LigBurialFilter::compute(), protocols::matdes::SymUnsatHbondFilter::compute(), protocols::matdes::OligomericAverageDegreeFilter::compute(), protocols::indexed_structure_store::filters::FragmentLookupFilter::compute(), core::scoring::SmoothEnvPairPotential::compute_centroid_environment(), protocols::denovo_design::components::compute_chain_beginnings(), protocols::simple_filters::SymmetricMotifFilter::compute_d2(), core::scoring::SmoothEnvPairPotential::compute_dcentroid_environment(), protocols::analysis::InterfaceAnalyzerMover::compute_interface_energy(), protocols::simple_filters::SSMotifFinder::compute_jump(), protocols::pockets::PlaidFingerprint::compute_ligand_natoms(), protocols::pockets::PlaidFingerprint::compute_ligand_natoms_with_hydrogens(), core::scoring::disulfides::DisulfideMatchingPotential::compute_matching_energy(), protocols::constraint_generator::compute_nres_in_asymmetric_unit(), 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(), protocols::ligand_docking::ComputeLigandRDF::compute_rdf(), protocols::simple_filters::ResidueIEFilter::compute_resnums(), core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric::compute_scores(), core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid::compute_total_volume_of_current_residues(), core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid::compute_volumes_of_buried_rotamers(), core::membrane::concave_shell(), core::pose::conf2pdb_chain(), core::pose::conf2pdb_chain_default_map(), protocols::rna::movers::RNAIdealizeMover::constrain_to_ideal(), protocols::denovo_design::construct_poly_ala_pose(), protocols::ligand_docking::TransformEnsemble::convert_to_full_pose(), protocols::ligand_docking::Transform::convert_to_full_pose(), protocols::helical_bundle::copy_helix_bondangles(), protocols::helical_bundle::copy_helix_bondlengths(), protocols::helical_bundle::copy_helix_dihedrals(), protocols::protein_interface_design::movers::copy_hotspot_to_pose(), protocols::helical_bundle::BundleParametrizationCalculator::copy_params_from_previous_helices_makebundlehelix_style(), protocols::simple_moves::RepeatPropagationMover::copy_phi_psi_omega(), core::pack::rotamer_set::RotamerSets::copy_residue_conenctions_and_variants(), protocols::star::copy_residues(), copy_segment(), protocols::splice::Splice::copy_stretch(), core::scoring::ScoreFunction::correct_finalize_score(), protocols::generalized_kinematic_closure::correct_polymer_dependent_atoms_in_pose_segment(), core::pose::correctly_add_2prime_connection_variants(), protocols::protein_interface_design::movers::SetAtomTree::create_atom_tree(), protocols::floppy_tail::create_extra_output(), protocols::ligand_docking::MinimizeBackbone::create_fold_tree_with_cutpoints(), protocols::ligand_docking::MinimizeBackbone::create_fold_tree_with_ligand_jumps_from_attach_pts(), protocols::membrane::create_membrane_foldtree_anchor_com(), protocols::membrane::create_membrane_foldtree_anchor_pose_tmcom(), protocols::membrane::create_membrane_foldtree_anchor_tmcom(), protocols::membrane::create_membrane_foldtree_from_anchors(), core::pack::create_packer_graph(), protocols::ligand_docking::Rotate::create_random_rotations(), protocols::denovo_design::components::RemodelLoopMoverPoseFolder::create_remodel_loop_mover(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::create_rotamers_from_chisets(), protocols::membrane::create_specific_membrane_foldtree(), protocols::simple_moves::CutChainMover::create_subpose(), core::pose::create_subpose(), core::scoring::membrane::MPSpanInsertionEnergy::create_updated_span(), protocols::cryst::crystRMS(), protocols::relax::cyclize_pose(), core::scoring::electron_density::ElectronDensity::dCCdBs(), core::pose::declare_cutpoint_chemical_bond(), protocols::seeded_abinitio::define_movemap_chains(), core::pose::carbohydrates::delete_carbohydrate_branch(), protocols::grafting::delete_overhang_residues(), protocols::grafting::delete_region(), protocols::relax::delete_virtual_residues(), protocols::simple_moves::WaterBoxMover::delete_waters(), core::scoring::constraints::ConstraintSet::deprecated_eval_atom_derivative(), core::scoring::constraints::ConstraintSet::deprecated_eval_atom_derivative_for_residue_pairs(), protocols::peptide_deriver::PeptideDeriverFilter::derive_peptide(), core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::detect_intra_residue_hydrogen_bonds_symmetric(), core::pack::hbonds::determine_atom_level_edge_info(), protocols::simple_moves::DisulfideInsertionMover::determine_cyclization_viability(), core::scoring::MultipoleElecPotential::determine_polarization_groups(), protocols::electron_density::BfactorMultifunc::dfunc(), protocols::protein_interface_design::movers::PlaceStubMover::disallowed_host_pos(), core::scoring::constraints::Constraint::dist(), protocols::abinitio::AbrelaxApplication::do_distributed_rerun(), protocols::relax::FastRelax::do_minimize(), 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::carbohydrates::dump_gws(), protocols::pockets::PlaidFingerprint::dump_oriented_pose_and_fp_to_pdb(), protocols::viewer::dump_pose_kinemage(), protocols::pockets::EggshellGrid::EggshellGrid(), core::pack::rotamers::SingleResidueRotamerLibrary::emergency_rotamer(), protocols::environment::Environment::end(), protocols::ligand_docking::InterfaceBuilder::enforce_minimum_length(), core::scoring::disulfides::FullatomDisulfideEnergy::ensure_lrenergy_container_is_up_to_date(), protocols::metal_interface::MatchGrafter::ensure_proper_his_tautomers(), protocols::environment::EnvClaimBroker::EnvClaimBroker(), protocols::rigid::MovePoseToMembraneCenterMover::estimate_membrane_center(), core::scoring::methods::BranchEnergy::eval_atom_derivative(), core::scoring::methods::ChainbreakEnergy::eval_atom_derivative(), core::scoring::membrane::FaMPEnvEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::eval_atom_derivative(), core::scoring::methods::CustomAtomPairEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensCenEnergy::eval_atom_derivative(), core::scoring::methods::MMBondAngleEnergy::eval_atom_derivative(), core::scoring::methods::RG_Energy_Fast::eval_atom_derivative(), core::scoring::electron_density::ElecDensEnergy::eval_atom_derivative(), core::scoring::methods::RamaPreProEnergy::eval_intraresidue_dof_derivative(), 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::electron_density::FastDensEnergy::eval_residue_pair_derivatives(), core::scoring::SmoothEnvPairPotential::evaluate_env_and_cbeta_deriv(), core::scoring::SmoothEnvPairPotential::evaluate_env_and_cbeta_scores(), protocols::denovo_design::components::ExtendedPoseBuilder::extend_pose(), protocols::star::Extender::extend_unaligned(), core::pose::symmetry::extract_asymmetric_unit(), core::pose::symmetry::extract_asymmetric_unit_pdb_info(), protocols::indexed_structure_store::extract_residue_entries(), protocols::forge::build::ConnectRight::extract_rt(), protocols::LoopRebuild::fast_ccd_close_loops(), protocols::loops::loop_mover::perturb::fast_ccd_close_loops(), core::pose::carbohydrates::fill_downstream_children_res_and_tips(), core::scoring::hbonds::fill_hbond_set(), core::pose::metrics::simple_calculators::InterfaceDefinitionCalculator::fill_in_chain_terminii(), protocols::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::BinarySilentStruct::fill_pose(), core::io::silent::ProteinSilentStruct_Template< T >::fill_pose(), protocols::loop_grower::LoopComparator::fill_pose(), core::pack::rotamers::SingleBasicRotamerLibrary::fill_rotamer_vector(), core::pack::rotamers::SingleLigandRotamerLibrary::fill_rotamer_vector(), core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::fill_rotamer_vector(), core::io::silent::BinarySilentStruct::fill_struct(), core::io::silent::ProteinSilentStruct_Template< T >::fill_struct(), protocols::membrane::MPLipidAccessibility::fill_up_slices(), protocols::loop_grower::LoopPartialSolutionStore::filter(), protocols::rna::denovo::coarse::CoarseRNA_LoopCloser::filter_path(), core::pack::rotamer_set::symmetry::SymmetricRotamerSets::final_visit_to_edge(), protocols::membrane::MPMutateRelaxMover::finalize_setup(), protocols::membrane::MPLipidAccessibility::finalize_setup(), protocols::relax::RangeRelaxMover::finalize_setup(), core::scoring::methods::BranchEnergy::finalize_total_energy(), core::scoring::methods::ChainbreakEnergy::finalize_total_energy(), core::scoring::methods::D2H_SA_Energy::finalize_total_energy(), core::scoring::methods::MembraneLipo::finalize_total_energy(), core::scoring::membrane::MPTMProjPenalty::finalize_total_energy(), core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy::finalize_total_energy(), protocols::ligand_docking::InterfaceBuilder::find_interface_residues(), core::select::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(), core::scoring::fiber_diffraction::find_max_r(), core::scoring::fiber_diffraction::find_min_xyz(), protocols::protein_interface_design::find_nearest_residue(), protocols::protein_interface_design::movers::find_nearest_residue_to_coord(), core::select::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::scoring::MultipoleElecPotential::find_params_and_neighbors(), core::scoring::fiber_diffraction::find_pitch(), protocols::splice::find_residues_on_chain1_inside_interface(), core::pose::symmetry::find_symmetric_basejump_anchor(), core::pack::hbonds::MCHBNetInteractionGraph::find_symmetric_hbonds(), protocols::pockets::PocketGrid::findExemplars(), protocols::splice::fix_chain_break_residue(), protocols::topology_broker::fix_internal_coords_of_siblings(), protocols::abinitio::abscript::fix_internal_coords_of_siblings(), protocols::topology_broker::fix_mainchain_connect(), protocols::abinitio::abscript::fix_mainchain_connect(), protocols::relax::fixH(), protocols::abinitio::AbrelaxApplication::fold(), protocols::splice::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::protein_interface_design::movers::DisulfideMover::form_disulfide(), protocols::denovo_design::components::Picker::fragments_for_permutation_take_X_from_pose(), protocols::kinematic_closure::ClosureProblem::frame_lower_pivot(), protocols::kinematic_closure::ClosureProblem::frame_upper_pivot(), protocols::generalized_kinematic_closure::general_set_phi(), protocols::generalized_kinematic_closure::general_set_psi(), protocols::hybridization::generate_centroid_constraints(), protocols::topology_broker::FoldandDockClaimer::generate_claims(), protocols::topology_broker::AsymFoldandDockClaimer::generate_claims(), protocols::topology_broker::FibrilModelingClaimer::generate_claims(), protocols::residue_optimization::MetapatchEnumeration::generate_derived_types(), protocols::abinitio::AbrelaxApplication::generate_extended_pose(), protocols::helical_bundle::BundleReporterFilter::generate_full_tracer_report(), protocols::motif_grafting::movers::MotifGraftMover::generate_scaffold_matches(), protocols::pose_creation::MakeJunctionsMover::generate_start_pose(), protocols::protein_interface_design::movers::MapHotspot::GenerateMap(), protocols::features::InterfaceFeatures::get_all_pose_chains(), core::pose::symmetry::get_asymmetric_pose_copy_from_symmetric_pose(), core::pose::carbohydrates::get_branching_residues(), core::pose::carbohydrates::get_carbohydrate_residues_and_tips_of_branch(), core::pose::get_chain_from_chain_id(), protocols::peptide_deriver::PeptideDeriverFilter::get_chain_indices(), core::pose::get_chain_residues(), protocols::splice::RBOutMover::get_disulf_jump(), core::pose::carbohydrates::get_downstream_residue_that_this_torsion_moves(), core::scoring::orbitals::OrbitalsScore::get_E_haro_one_way(), core::scoring::orbitals::OrbitalsScore::get_E_hpol_one_way(), core::scoring::rna::RNA_TorsionPotential::get_f1_f2(), core::scoring::rna::RNA_SuiteEnergy::get_f1_f2(), core::scoring::rna::TNA_SuiteEnergy::get_f1_f2(), protocols::antibody::AntibodyInfo::get_FoldTree_AllCDRs_LHDock(), protocols::antibody::AntibodyInfo::get_FoldTree_L_HA(), protocols::antibody::AntibodyInfo::get_FoldTree_LA_H(), protocols::antibody::AntibodyInfo::get_FoldTree_LH_A(), protocols::indexed_structure_store::FragmentLookup::get_fragment_residue_spans(), core::pose::carbohydrates::get_glycan_connecting_protein_branch_point(), core::pose::carbohydrates::get_glycan_position_from_resnum(), core::pose::carbohydrates::get_glycosidic_bond_residues(), core::pose::carbohydrates::get_glycosidic_torsion(), core::pose::get_hash_excluding_chain(), core::pose::get_hash_from_chain(), protocols::pockets::GenPharmacophore::get_ideal_hydrogenBond_atoms(), core::select::get_master_subunit_selection(), core::scoring::hbonds::get_membrane_depth_dependent_weight(), core::pose::carbohydrates::get_n_glycosidic_torsions_in_res(), protocols::hotspot_hashing::HotspotStub::get_nearest_residue(), protocols::relax::LocalRelax::get_neighbor_graph(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_new_chainIDs(), protocols::cryst::get_nres_asu(), core::pose::symmetry::get_nres_asymmetric_unit(), protocols::fold_from_loops::utils::Nub::get_nub_pieces(), protocols::hybridization::get_num_residues_nonvirt(), protocols::hybridization::get_num_residues_prot(), core::scoring::carbohydrates::get_omega_preference_for_residue_in_pose(), core::scoring::orbitals::OrbitalsScore::get_orb_orb_E(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_parametric_info(), core::pose::carbohydrates::get_reference_atoms(), core::pose::carbohydrates::get_reference_atoms_for_1st_omega(), core::pose::carbohydrates::get_reference_atoms_for_2nd_omega(), core::pose::carbohydrates::get_reference_atoms_for_phi(), core::pose::carbohydrates::get_reference_atoms_for_psi(), core::scoring::methods::NMerSVMEnergy::get_residue_energy_by_svm(), core::scoring::methods::NMerRefEnergy::get_residue_energy_by_table(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_residue_information(), protocols::hotspot_hashing::HotspotStubSet::get_residue_score_(), core::pose::carbohydrates::get_resnum_from_glycan_position(), core::pose::get_resnums_for_chain_id(), protocols::loop_grower::LoopGrower::get_resrange_hbond_energy(), core::pose::get_restype_for_pose(), protocols::loophash::get_rt_over_leap_without_foldtree_bs(), protocols::fldsgn::potentials::SetSecStructEnergies::get_secstruct(), protocols::membrane::get_secstruct(), core::pose::get_sha1_hash_excluding_chains(), core::pose::get_sha1_hash_from_chains(), core::pose::symmetry::get_symm_axis(), core::util::getMLweight_cart(), protocols::pockets::PocketGrid::getRelaxResidues(), core::pose::carbohydrates::glycosylate_pose(), core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_conect_records_for_atom(), core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_membrane_info(), protocols::metal_interface::MatchGrafter::graft(), protocols::forge::methods::grow_left_r(), protocols::forge::methods::grow_right_r(), core::pose::has_chain(), protocols::hbnet::hbnet_symm_one_body_energies(), core::scoring::SecondaryStructurePotential::hspair(), protocols::grafting::idealize_combined_pose(), protocols::loops::idealize_loop(), protocols::relax::RangeRelaxMover::idealize_pose(), core::scoring::methods::CartesianBondedEnergy::idealize_proline_nvs(), protocols::simple_moves::sidechain_moves::SidechainMoverBase::idealize_sidechains(), protocols::simple_moves::sidechain_moves::SidechainMover::idealize_sidechains(), protocols::antibody::AntibodyInfo::identify_antibody(), core::scoring::SecondaryStructurePotential::identify_ss(), protocols::pockets::NonPlaidFingerprint::include_eggshell_points_based_on_known_ligand(), protocols::denovo_design::components::StructureDataFactory::infer_from_pose(), protocols::hybridization::FragmentBiasAssigner::init(), core::scoring::membrane::FaMPEnvEnergy::init(), core::scoring::membrane::FaMPSolvEnergy::init(), protocols::forge::build::SegmentSwap::init(), protocols::forge::build::SegmentInsert::init(), protocols::floppy_tail::FloppyTailMover::init_on_new_input(), protocols::ub_e2c::ubi_e2c_modeler::initial_cter_perturbation(), protocols::hybridization::HybridizeFoldtreeDynamic::initialize(), protocols::environment::ScriptCM::initialize(), protocols::abinitio::abscript::FragmentCM::initialize(), protocols::environment::CoMTrackerCM::initialize(), protocols::rigid::UniformRigidBodyCM::initialize(), protocols::abinitio::abscript::RigidChunkCM::initialize(), protocols::chemically_conjugated_docking::UBQ_GTPaseMover::initialize(), protocols::cryst::DockLatticeMover::initialize(), protocols::hybridization::HybridizeProtocol::initialize_and_sample_loops(), core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::initialize_curstate_graph(), core::pose::initialize_disulfide_bonds(), core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::initialize_graph_for_packing(), protocols::membrane::AddMembraneMover::initialize_membrane_residue(), protocols::features::ReportToDB::initialize_pose(), core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::initialize_pose_for_rotset_creation(), core::pack::rotamer_set::symmetry::SymmetricRotamerSets::initialize_pose_for_rotsets_creation(), protocols::frags::TorsionFragment::insert(), core::fragment::rna::FullAtomRNA_Fragments::insert_fragment(), protocols::grafting::insert_pose_into_pose(), core::scoring::ScoreFunction::intersubunit_hbond_energy(), core::pose::carbohydrates::is_glycosidic_phi_torsion(), core::pose::is_ideal_position(), protocols::membrane::is_membrane_fixed(), protocols::membrane::is_membrane_moveable_by_itself(), core::pose::symmetry::is_mirror_symmetric(), core::pose::symmetry::is_symmetric(), core::pose::rna::RNA_IdealCoord::is_torsion_exists(), core::pose::rna::is_torsion_valid(), protocols::motif_grafting::movers::MotifGraftMover::join_two_poses_by_jump(), protocols::simple_filters::JumpEvaluator::JumpEvaluator(), protocols::ligand_docking::ComputeLigandRDF::ligand_protein_rdf(), 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_asymmetric_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::denovo_design::DisulfidizeMover::make_disulfide(), protocols::forge::remodel::RemodelDesignMover::make_disulfide_fast(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::make_disulfides(), protocols::struct_fragment::StructFragmentMover::make_fragment_picker(), protocols::protein_interface_design::make_hotspot_foldtree(), protocols::denovo_design::components::make_lengths_str(), protocols::loophash::LocalInserter_SimpleMin::make_local_bb_change_close_gaps(), protocols::simple_moves::MutateResidue::make_mutation(), core::pack::make_new_symmetric_PackerTask_by_intersection(), core::pack::make_new_symmetric_PackerTask_by_union(), core::fragment::make_pose_from_frags(), core::pose::make_pose_from_saccharide_sequence(), core::pose::symmetry::make_residue_mask_symmetric(), core::optimization::symmetry::SymAtomTreeMinimizer::make_semisymmetric_movemap(), protocols::forge::methods::make_star_foldtree(), 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(), core::pack::make_symmetric_task(), protocols::fold_from_loops::NubInitioMover::make_unfolded_pose(), protocols::pockets::ElectrostaticpotentialGrid::mark_protein_espGrid_points(), protocols::rotamer_recovery::RRComparerAutomorphicRMSD::measure_rotamer_recovery(), protocols::membrane::mem_all_atom_rmsd_no_super(), protocols::membrane::mem_all_atom_rmsd_with_super(), protocols::membrane::mem_bb_rmsd_no_super(), protocols::membrane::mem_bb_rmsd_with_super(), protocols::membrane::membrane_axis(), protocols::membrane::membrane_normal_to_length_15(), core::scoring::constraints::MembraneSpanConstraint::MembraneSpanConstraint(), core::scoring::constraints::MembraneSpanTermZConstraint::MembraneSpanTermZConstraint(), protocols::stepwise::modeler::merge_in_other_pose(), protocols::splice::min_seg(), protocols::peptide_deriver::PeptideDeriverFilter::minimize(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::minimize_all(), protocols::simple_moves::CyclizationMover::minimize_rebuild(), protocols::make_rot_lib::MakeRotLibMover::minimize_rotamer(), protocols::protein_interface_design::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::loop_grower::LoopGrower::modifiedscore(), 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_initial_cter_perturbation(), protocols::pockets::PocketGrid::move_pose_to_standard_orie(), protocols::denovo_design::DisulfidizeMover::mutate_disulfides_to_ala(), core::pose::rna::mutate_position(), protocols::splice::nearest_to_entry_stop_on_pose(), protocols::hbnet::HBNetStapleInterface::network_meets_final_criteria(), protocols::denovo_design::movers::new_jump_and_cutpoint(), core::scoring::MembranePotential::non_helix_in_membrane_penalty(), protocols::cryst::ReportGradientsMover::normalization(), protocols::loop_grower::LoopGrower::nton3_hbond_score(), protocols::electron_density::BfactorMultifunc::operator()(), core::scoring::DockingScoreFunction::operator()(), core::pose::operator<<(), protocols::membrane::OptimizeMembranePositionMover::optimize_membrane_center(), protocols::membrane::OptimizeMembranePositionMover::optimize_membrane_normal(), 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(), core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::orient_rotamer_to_symmetric_partner(), protocols::protein_interface_design::movers::MapHotspot::output_pose(), protocols::frag_picker::FragmentCandidate::output_silent(), protocols::chemically_conjugated_docking::pack_extra_bodies(), protocols::branch_angle::BranchAngleOptimizer::param1(), protocols::branch_angle::BranchAngleOptimizer::param2(), protocols::seeded_abinitio::DefineMovableLoops::parse_my_tag(), protocols::protein_interface_design::movers::TopologyBrokerMover::parse_my_tag(), protocols::seeded_abinitio::CloseFold::parse_my_tag(), protocols::protein_interface_design::movers::PlaceOnLoop::parse_my_tag(), protocols::simple_moves::SwitchChainOrderMover::parse_my_tag(), protocols::calc_taskop_movers::DesignRepackMover::parse_my_tag(), protocols::simple_ddg::ddG::parse_my_tag(), protocols::simple_filters::BuriedUnsatHbondFilter::parse_my_tag(), protocols::ligand_docking::Rotate::parse_my_tag(), protocols::contact_map::ContactMap::parse_region_string(), protocols::rna::movers::RNA_LoopCloser::passes_fast_scan(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::perform_bump_check(), protocols::hybridization::BackboneTorsionPerturbation::perturb(), protocols::hybridization::BackboneTorsionSampler::perturb(), protocols::anchored_design::AnchoredDesignMover::perturb_anchor(), protocols::cryst::DockLatticeMover::perturb_chis(), protocols::rna::movers::RNAIdealizeMover::perturb_pose(), protocols::comparative_modeling::pick_loops_chainbreak(), protocols::splice::SpliceOut::place_cut_site_in_segment(), protocols::flexpep_docking::FlexPepDockingProtocol::place_peptide_on_binding_site(), 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(), protocols::matdes::MatDesGreedyOptMutationMover::pose_coords_are_same(), core::import_pose::atom_tree_diffs::pose_from_atom_tree_diff(), core::import_pose::pose_from_file(), protocols::jd2::ScreeningJobInputter::pose_from_job(), protocols::denovo_design::components::pose_matches_description(), protocols::membrane::pose_tilt_angle_and_center_distance(), core::pack::rotamer_set::symmetry::SymmetricRotamerSets::precompute_two_body_energies(), protocols::hotspot_hashing::HotspotStubSet::prepare_hashing_packer_task_(), protocols::peptide_deriver::PeptideDeriverFilter::prepare_pose(), core::pose::rna::prepare_scratch_residue(), protocols::ligand_docking::HighResEnsemble::prepare_single_ligand_pose(), protocols::ligand_docking::ProtLigEnsemble::prepare_single_ligand_pose(), core::pack::rotamer_set::symmetry::SymmetricRotamerSets::prepare_symm_otf_interaction_graph(), protocols::stepwise::modeler::rna::print_torsion_info(), core::pose::rna::print_torsion_info(), protocols::rna::movers::RNAThreadAndMinimizeMover::process_insertions(), protocols::match::MatcherMover::process_pose(), protocols::ligand_docking::ComputeLigandRDF::protein_protein_rdf(), core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::provide_pymol_commands_to_show_groups(), protocols::denovo_design::components::prune_unpaired_residues(), core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid::prune_voxels_for_fixed_residues(), protocols::loop_grower::LoopPartialSolutionStore::push(), protocols::peptide_deriver::PeptideDeriverFilter::push_chain_residue_indices(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::rama_energy(), protocols::cryst::DockLatticeMover::randomize_chis(), protocols::anchored_design::AnchoredDesignMover::randomize_input_sequence(), core::io::serialization::read_binary(), protocols::sic_dock::read_biounit(), core::io::raw_data::DisulfideFile::read_in_and_set_disulfides(), real_to_virtual(), protocols::cyclic_peptide::PeptideStubMover::rebuild_atoms(), core::util::rebuild_disulfide(), core::util::rebuild_fa_disulfides(), protocols::comparative_modeling::rebuild_loops_until_closed(), protocols::denovo_design::rebuild_missing_atoms(), core::pose::metrics::simple_calculators::InterfaceNeighborDefinitionCalculator::recompute(), protocols::pose_metric_calculators::NeighborsByDistanceCalculator::recompute(), protocols::pose_metric_calculators::NeighborhoodByDistanceCalculator::recompute(), protocols::pose_metric_calculators::ResidueDecompositionByChainCalculator::recompute(), protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::recompute(), protocols::splice::AlignEndsMover::reference_positions(), protocols::loop_grower::LoopGrower::refine_cycle(), core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose(), protocols::protein_interface_design::movers::PlacementMinimizationMover::refresh_bbstub_constraints(), protocols::cryst::DockLatticeMover::regenerate_lattice(), protocols::environment::Environment::remove_chainbreak_variants(), protocols::jumping::remove_cut(), protocols::splice::SpliceOut::remove_hairpin(), protocols::splice::Splice::remove_hairpin(), core::pose::remove_ligand_canonical_residues(), protocols::toolbox::pose_manipulation::remove_non_protein_residues(), protocols::environment::Environment::remove_nonpermenant_features(), core::pose::remove_nonprotein_residues(), protocols::hybridization::remove_residues(), core::pose::remove_variant_type_from_pose_residue(), core::pose::remove_variant_type_from_residue(), core::pose::remove_virtual_residues(), core::pose::renumber_pdbinfo_based_on_conf_chains(), protocols::denovo_design::components::reorder_chains(), protocols::analysis::InterfaceAnalyzerMover::reorder_foldtree_find_jump(), protocols::fold_from_loops::NubInitioMover::repack_minimize_disulfides(), 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::toolbox::match_enzdes_util::replace_residue_keeping_all_atom_positions(), protocols::simple_ddg::AlaScan::report(), protocols::features::AtomInResidueAtomInResiduePairFeatures::report_atom_pairs(), protocols::features::AtomAtomPairFeatures::report_atom_pairs(), protocols::features::ScreeningFeatures::report_features(), protocols::features::ProteinResidueConformationFeatures::report_features(), protocols::features::ResidueConformationFeatures::report_features(), protocols::features::TaskOperationFeatures::report_features(), protocols::features::LoopAnchorFeatures::report_features(), protocols::features::HBondFeatures::report_features(), protocols::features::PoseConformationFeatures::report_features_implementation(), protocols::features::PairFeatures::report_residue_pairs(), core::scoring::membrane::MPResidueLipophilicityEnergy::report_ressolv(), protocols::simple_ddg::AlaScan::report_symmetry(), core::scoring::symmetry::SymmetricEnergies::require_context_graph_(), protocols::simple_filters::res_res_min_distance(), protocols::simple_filters::res_rmsd(), protocols::protein_interface_design::filters::res_rmsd(), core::scoring::electron_density::ElectronDensity::rescale_fastscoring_temp_bins(), protocols::loop_grower::LoopGrower::rescoresolutionset(), protocols::hybridization::HybridizeFoldtreeDynamic::reset(), protocols::backbone_moves::local_backbone_mover::Residue::Residue(), core::scoring::methods::EnvEnergy::residue_energy(), core::scoring::membrane::MPCbetaEnergy::residue_energy(), core::scoring::methods::carbohydrates::SugarBackboneEnergy::residue_energy(), core::scoring::membrane::MPTerminiPenalty::residue_energy(), core::scoring::methods::NMerPSSMEnergy::residue_energy(), core::scoring::membrane::MPNonHelixPenalty::residue_energy(), core::scoring::membrane::MPHelicalityEnergy::residue_energy(), core::scoring::membrane::MPEnvEnergy::residue_energy(), protocols::simple_filters::NonSequentialNeighborsFilter::residue_neighbors(), core::scoring::methods::CenPairEnergy::residue_pair_energy(), core::scoring::methods::MembraneCenPairEnergy::residue_pair_energy(), core::scoring::membrane::MPPairEnergy::residue_pair_energy(), core::scoring::electron_density::FastDensEnergy::residue_pair_energy(), core::scoring::methods::RamaPreProEnergy::residue_pair_energy(), core::scoring::methods::MMBondAngleEnergy::residue_pair_energy(), core::scoring::electron_density::ElecDensEnergy::residue_pair_energy(), core::scoring::hbonds::HBondEnergy::residue_pair_energy(), core::scoring::hbonds::HBondEnergy::residue_pair_energy_ext(), residue_type_set_for_pose(), core::pose::ResidueIndexDescriptionChainEnd::resolve_index(), protocols::ub_e2c::ubi_e2c_modeler::restore_cter(), protocols::forge::methods::restore_residues(), protocols::grafting::return_region(), protocols::denovo_design::components::reverse_chains(), protocols::pockets::PlaidFingerprint::rmsd(), protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::ROT2res(), core::pose::symmetry::rotate_anchor_to_x_axis(), protocols::ligand_docking::Rotate::rotate_ligand(), protocols::membrane::rsd_closest_to_chain_com(), protocols::jumping::MembraneJump::rt_templates(), core::optimization::symmetry::SymAtomTreeMinimizer::run(), protocols::hybridization::DomainAssembly::run(), core::io::external::PsiPredInterface::run_psipred(), core::io::external::PsiPredInterface::run_psipred_prob(), protocols::environment::ClientMover::sandboxed_copy(), protocols::pmut_scan::AlterSpecDisruptionDriver::score(), core::scoring::constraints::Constraint::score(), protocols::ligand_docking::Transform::score_constraints(), core::scoring::MembranePotential::score_normal_center(), core::pose::symmetry::scorefxn_is_symmetric(), protocols::relax::RepeatProteinRelax::seal_jumps(), core::pose::symmetry::sealed_symmetric_fold_tree(), core::select::residue_selector::ChainSelector::select_chain_by_index(), protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::semiexpl_water_hbgeom_score(), protocols::moves::PyMOLMover::send_membrane_planes(), protocols::protein_interface_design::movers::SetAtomTree::set_ab_fold_tree(), 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::splice::RBOutMover::set_fold_tree_nodes(), protocols::splice::SpliceOutAntibody::set_fold_tree_nodes(), protocols::splice::SpliceInTail::set_fold_tree_nodes(), protocols::splice::RBInMover::set_fold_tree_nodes(), protocols::splice::SpliceOutTail::set_fold_tree_nodes(), protocols::splice::SpliceInAntibody::set_fold_tree_nodes(), protocols::splice::SpliceIn::set_fold_tree_nodes(), protocols::splice::SpliceOut::set_fold_tree_nodes(), core::pose::carbohydrates::set_glycan_iupac_bb_torsions(), core::pose::carbohydrates::set_glycosidic_torsion(), protocols::loops::set_loop_cutpoint_in_pose_fold_tree(), protocols::generalized_kinematic_closure::set_loop_pose(), protocols::seeded_abinitio::SeedSetupMover::set_packerTasks_target_and_seeds(), protocols::flexpep_docking::FlexPepDockingProtocol::set_receptor_constraints(), core::scoring::ScoreFunction::set_symmetric_cenlist(), protocols::scoring::Interface::set_symmetric_pack(), core::scoring::ScoreFunction::set_symmetric_residue_neighbors_hbonds(), protocols::hbnet::HBNet::set_symmetry(), 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::symmetry::SymmetrySlider::setup(), core::scoring::NeighborList::setup(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_chainbreak_variants(), protocols::qsar::scoring_grid::ChargeGrid::setup_charge_atoms(), protocols::simple_moves::CyclizationMover::setup_connections(), protocols::star::setup_constraints(), protocols::medal::setup_coordinate_constraints(), core::scoring::constraints::SiteConstraint::setup_csts(), core::scoring::constraints::FabConstraint::setup_csts(), core::scoring::fiber_diffraction::setup_cylindrical_coords(), protocols::rbsegment_relax::setup_disconnected(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::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::hybridization::FoldTreeHybridize::setup_foldtree(), protocols::docking::setup_foldtree(), protocols::membrane::setup_foldtree_from_anchors(), protocols::membrane::setup_foldtree_pose_com(), core::scoring::methods::SmoothEnvEnergy::setup_for_derivatives(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::setup_for_derivatives(), core::scoring::electron_density::ElecDensCenEnergy::setup_for_derivatives(), core::scoring::electron_density::ElecDensEnergy::setup_for_derivatives(), core::scoring::methods::EnvSmoothEnergy::setup_for_derivatives(), core::scoring::electron_density::FastDensEnergy::setup_for_derivatives(), core::scoring::methods::RG_Energy_Fast::setup_for_derivatives(), core::scoring::constraints::ConstraintSet::setup_for_derivatives(), protocols::analysis::InterfaceAnalyzerMover::setup_for_dock_chains(), core::scoring::hbonds::HBondEnergy::setup_for_packing(), core::scoring::methods::Abego::setup_for_scoring(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::setup_for_scoring(), core::scoring::electron_density::FastDensEnergy::setup_for_scoring(), core::scoring::electron_density::ElecDensEnergy::setup_for_scoring(), core::scoring::electron_density::ElecDensCenEnergy::setup_for_scoring(), core::scoring::hbonds::HBondEnergy::setup_for_scoring(), core::scoring::constraints::ConstraintSet::setup_for_scoring(), protocols::antibody::AntibodyInfo::setup_FrameWorkInfo(), protocols::idealize::IdealizeMover::setup_idealize_constraints(), protocols::simple_moves::SmallMover::setup_list(), protocols::simple_moves::ShearMover::setup_list(), protocols::simple_moves::ShearMover::setup_list_for_saccharide_residue(), protocols::simple_moves::CyclizationMover::setup_minimizer(), protocols::carbohydrates::RingPlaneFlipMover::setup_movable_torsion_pairs(), protocols::rna::denovo::movers::RNA_Minimizer::setup_movemap(), core::pose::toolbox::AtomLevelDomainMap::setup_movemap(), protocols::ncbb::setup_pert_foldtree(), protocols::rbsegment_relax::setup_pose_rbsegs_keep_loops(), protocols::relax::membrane::MPFastRelaxMover::setup_relax_foldtree(), protocols::relax::RepeatProteinRelax::setup_repeat_pose(), protocols::relax::RepeatProteinRelax::setup_repeat_pose_jumping(), core::scoring::SecondaryStructurePotential::sheets_from_dimers(), protocols::loop_grower::LoopGrower::sheetscore(), protocols::relax::membrane::MPFastRelaxMover::show_protocol(), core::scoring::constraints::DihedralConstraint::show_violations(), core::scoring::constraints::AngleConstraint::show_violations(), core::scoring::constraints::AtomPairConstraint::show_violations(), core::scoring::hbonds::HBondEnergy::sidechain_sidechain_energy(), protocols::loop_grower::LoopGrower::single_grow(), protocols::stepwise::modeler::slice(), protocols::stepwise::modeler::slice_out_pose(), protocols::symmetry::SymmetrySlider::slide(), protocols::symmetry::SymmetrySlider::slide_away(), protocols::rna::denovo::coarse::MultipleDomainMover::slide_back_to_origin(), protocols::simple_filters::SpanTopologyMatchPoseFilter::span_file_topology(), protocols::fldsgn::CircularPermutation::split_chains(), core::scoring::SecondaryStructurePotential::sspair(), protocols::protein_interface_design::star_fold_tree(), protocols::environment::Environment::start(), core::fragment::BBTorsionAndAnglesSRFD::steal(), core::fragment::DownJumpSRFD::steal(), core::scoring::constraints::LocalCoordinateConstraint::steal_def(), core::scoring::constraints::CoordinateConstraint::steal_def(), protocols::protein_interface_design::movers::PlaceStubMover::StubMinimize(), protocols::dna::substitute_residue(), protocols::simple_moves::AddChainMover::swap_chain(), protocols::seeded_abinitio::SwapSegment::swap_chain(), core::pose::swap_transform(), core::util::switch_to_centroid_rot_set(), protocols::topology_broker::TopologyBroker::switch_to_fullatom(), core::util::switch_to_residue_type_set(), core::scoring::ScoreFunction::sym_eval_long_range_twobody_energies(), core::scoring::ScoreFunction::sym_eval_onebody_energies(), core::scoring::ScoreFunction::sym_eval_twobody_neighbor_energies(), core::scoring::sym_rmsd_with_super_subset(), core::scoring::ScoreFunction::sym_setup_for_derivatives(), core::scoring::ScoreFunction::sym_setup_for_minimizing(), protocols::denovo_design::symmetric_fold_tree(), protocols::scoring::Interface::symmetric_protein_calculate(), core::pack::symmetric_repackable_residues(), protocols::denovo_design::symmetric_residue_subset(), core::pack::symmetric_rotamer_trials(), protocols::denovo_design::symmetric_secstruct(), protocols::simple_task_operations::RestrictToInterface::symmetric_task(), core::scoring::ScoreFunction::symmetrical_allow_hbonds(), core::pose::symmetry::symmetrize_fold_tree(), protocols::membrane::symmetry::symmetrize_spans(), protocols::electron_density::symmetrizeBfactors(), core::pose::symmetry::symmetry_info(), core::optimization::symmetry::SymMinimizerMap::SymMinimizerMap(), protocols::splice::Splice::tail_fold_tree(), protocols::nonlocal::StarTreeBuilder::tear_down(), protocols::star::StarAbinitio::tear_down_kinematics(), core::scoring::MembranePotential::termini_penalty(), protocols::calc_taskop_filters::RelativePoseFilter::thread_seq(), protocols::legacy_sewing::Assembly::to_multichain_pose(), protocols::legacy_sewing::Assembly::to_pose(), protocols::fold_from_loops::utils::Nub::transfer_unfolded_conformation(), protocols::protein_interface_design::PatchdockReader::transform_pose(), protocols::loop_grower::transform_res_to_subunit(), protocols::loop_grower::transform_to_closest_symmunit(), protocols::simple_moves::RepeatPropagationMover::trim_back_repeat_to_repair_scar(), protocols::legacy_sewing::Model::trim_db_pose(), protocols::pose_creation::MakeJunctionsMover::trim_pose(), protocols::features::ModelFeatures::trim_pose(), protocols::rna::denovo::coarse::MultipleDomainMover::try_to_slide_into_contact(), protocols::features::InterfaceDdGMover::unbind(), protocols::protein_interface_design::filters::BindingStrainFilter::unbind(), protocols::simple_ddg::ddG::unbind(), protocols::hybridization::HybridizeFoldtreeDynamic::update(), core::pose::update_cutpoint_virtual_atoms_if_connected(), core::pose::full_model_info::update_disulfides_from_full_model_info(), protocols::simple_moves::oop::OopMover::update_hydrogens_(), protocols::simple_moves::triazolamer::TriazolamerMover::update_hydrogens_(), core::scoring::symmetry::SymmetricEnergies::update_neighbor_links(), protocols::cyclic_peptide::crosslinker::TMA_Helper::update_tma_amide_bond_dependent_atoms_asymmetric(), protocols::cyclic_peptide::crosslinker::TMA_Helper::update_tma_amide_bond_dependent_atoms_symmetric(), protocols::loop_grower::LoopGrower::update_to_stored(), protocols::environment::CoMTrackerCM::update_tracking_residue(), protocols::surface_docking::SurfaceDockingProtocol::valid_surface_pose(), protocols::simple_moves::ConstrainToIdealMover::vary_bond_geometry(), protocols::symmetry::SymmetrySlider::very_far_away(), virtual_to_real(), protocols::fldsgn::CircularPermutation::which_chain(), core::scoring::constraints::LocalCoordinateConstraint::xyz_target(), protocols::environment::claims::JumpClaim::yield_elements(), protocols::environment::claims::VirtResClaim::yield_elements(), protocols::environment::claims::XYZClaim::yield_elements(), and protocols::environment::claims::TorsionClaim::yield_elements().

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

Returns the pose Conformation (non-const access)

References conformation_.

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

Returns the pose Conformation pointer (const access)

References conformation_.

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

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

Returns the pose Conformation pointer (nonconst access)

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

References conformation_.

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

Read access to the const data cache.

References constant_cache_.

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

References constraint_set_.

Referenced by protocols::forge::remodel::RemodelLoopMover::abinitio_stage(), protocols::rna::movers::RNAThreadAndMinimizeMover::accomodate_length_change(), protocols::topology_broker::TopologyBroker::add_chainbreak_variants(), protocols::metal_interface::AddZincSiteConstraints::add_constraints(), 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::stepwise::modeler::align::StepWisePoseAligner::add_coordinate_constraints_from_map(), core::scoring::constraints::add_fa_constraints_from_cmdline_to_pose(), protocols::stepwise::modeler::rna::add_fade_chain_break_constraint_across_gap(), protocols::rna::movers::ErraserMinimizerMover::add_fixed_res_constraints(), protocols::stepwise::modeler::rna::add_harmonic_chain_break_constraint(), core::pose::ncbb::add_oop_constraint(), protocols::toolbox::match_enzdes_util::EnzConstraintIO::add_pregenerated_constraints_to_pose(), protocols::splice::SpliceManager::add_sequence_constraints(), protocols::splice::Splice::add_sequence_constraints(), protocols::loops::add_single_cutpoint_variant(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::add_terminal_res_repulsion(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::add_terminal_res_repulsion(), protocols::loop_grower::LoopGrower::add_user_csts(), protocols::forge::remodel::RemodelGlobalFrame::align_segment(), protocols::anchored_design::AnchorMoversData::anchor_noise_constraints_setup(), protocols::simple_moves::PSSM2BfactorMover::apply(), protocols::relax::MiniRelax::apply(), protocols::seeded_abinitio::CAcstGenerator::apply(), protocols::domain_assembly::AddAssemblyConstraints::apply(), protocols::medal::MedalExchangeMover::apply(), protocols::fold_from_loops::movers::ReleaseConstraintFromResidueMover::apply(), protocols::abinitio::ResolutionSwitcher::apply(), protocols::constraint_movers::ConstraintSetMover::apply(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::apply(), protocols::fold_from_loops::movers::NubInitioLoopClosureMover::apply(), protocols::anchored_design::AnchoredDesignMover::apply(), protocols::dna::RestrictDesignToProteinDNAInterface::apply(), protocols::protein_interface_design::movers::SetupHotspotConstraintsMover::apply(), protocols::rna::denovo::movers::RNA_Minimizer::apply(), protocols::hbnet::ConstrainHBondNetwork::apply(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::apply(), protocols::abinitio::AbrelaxMover::apply(), protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMover::apply(), protocols::forge::constraints::RemoveRemodelCsts::apply(), protocols::fold_from_loops::selectors::ConstraintResidueSelector::apply(), protocols::rna::denovo::RNA_FragmentMonteCarlo::apply(), protocols::abinitio::abscript::AbscriptStageMover::apply(), protocols::rna::denovo::movers::RNA_Relaxer::apply(), protocols::rna::denovo::movers::RNP_HighResMover::apply(), protocols::antibody::constraints::ParatopeSiteConstraintMover::apply(), protocols::rna::movers::RNAIdealizeMover::apply(), protocols::enzdes::EnzRepackMinimize::apply(), protocols::hybridization::CartesianSampler::apply(), protocols::simple_filters::TruncatedScoreEvaluator::apply(), protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover::apply(), protocols::rna::movers::ErraserMinimizerMover::apply(), protocols::task_operations::SeqprofConsensusOperation::apply(), protocols::abinitio::KinematicAbinitio::apply(), protocols::membrane::MPQuickRelaxMover::apply(), protocols::ddg::ddGMover::apply(), protocols::abinitio::FoldConstraints::apply(), protocols::protein_interface_design::movers::PlaceStubMover::apply(), protocols::idealize::IdealizeMover::apply(), protocols::abinitio::ConstraintFragmentSampler::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::relax::FastRelax::apply(), protocols::abinitio::ClassicAbinitio::apply(), protocols::abinitio::ShowViolation::apply(), protocols::abinitio::ComputeTotalDistCst::apply(), protocols::forge::remodel::RemodelLoopMover::apply(), protocols::hbnet::HBNet::apply(), protocols::stepwise::legacy::modeler::rna::apply_chi_cst(), protocols::relax::FastRelax::batch_apply(), core::pack::rotamer_set::build_lib_dna_rotamers(), protocols::LoopRebuild::build_loop_with_ccd_closure(), protocols::abinitio::abscript::AbscriptMover::calculate_iterations(), protocols::antibody::constraints::cdr_has_res_constraints(), protocols::fldsgn::BluePrintBDR::centroid_build(), protocols::stepwise::modeler::check_scorefxn_has_constraint_terms_if_pose_has_constraints(), protocols::abinitio::FragmentSampler::checkpointed_cycle_block(), protocols::abinitio::AbrelaxApplication::close_loops(), protocols::constraint_filters::ShowConstraintsFilter::compute(), protocols::fold_from_loops::filters::ConstraintFulfilmentFilter::compute(), 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_cart_relax(), 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::stepwise::modeler::StepWiseMinimizer::do_minimize(), 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(), protocols::relax::RangeRelaxMover::finalize_setup(), core::scoring::constraints::ConstraintsEnergy::finalize_total_energy(), protocols::enzdes::EnzdesConstraintReporter::find_constraints_to_ligand(), protocols::abinitio::AbrelaxApplication::fold(), protocols::protein_interface_design::get_bbcsts(), protocols::constraint_movers::CstInfoMover::get_constraints_from_pose(), core::scoring::netcharge_energy::NetChargeEnergy::get_helpers_from_pose(), core::scoring::aa_composition_energy::AACompositionEnergy::get_helpers_from_pose(), core::scoring::mhc_epitope_energy::MHCEpitopeEnergy::get_helpers_from_pose(), protocols::constraint_filters::ConstraintScoreCutoffFilter::get_score(), protocols::relax::RangeRelaxMover::idealize_pose(), protocols::motifs::MotifSearch::incorporate_motifs(), protocols::motifs::LigandMotifSearch::incorporate_motifs(), protocols::simple_moves::RepeatPropagationMover::initial_constrained_residues(), protocols::rna::denovo::RNA_DeNovoProtocol::initialize_constraints(), protocols::stepwise::modeler::StepWiseModeler::initialize_constraints(), protocols::stepwise::modeler::StepWiseModeler::initialize_working_parameters_and_root(), protocols::loophash::MPI_LoopHashRefine::load_structures_from_cmdline_into_library(), protocols::mpi_refinement::MPI_Refinement::load_structures_from_cmdline_into_library(), protocols::rna::denovo::movers::RNA_Relaxer::lores_monte_carlo(), protocols::fold_from_loops::NubInitioMover::manage_constraints(), core::scoring::constraints::map_constraints_from_original_pose(), protocols::abinitio::FoldConstraints::min_trial(), protocols::peptide_deriver::PeptideDeriverFilter::minimize(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::minimize_all(), protocols::stepwise::modeler::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(), protocols::hbnet::HBNet::output_networks(), protocols::abinitio::abscript::ConstraintPreparer::prepare(), 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(), core::scoring::constraints::print_atom_pair_constraints(), core::import_pose::RNA_HelixAssembler::put_constraints_on_base_step(), protocols::stepwise::modeler::StepWiseModeler::reinitialize(), protocols::abinitio::AbrelaxApplication::relax(), protocols::ddg::ddGMover::relax_wildtype_structure(), core::scoring::constraints::remove_constraints_of_type(), 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::remove_nonbb_constraints(), protocols::simple_moves::RepeatPropagationMover::repeat_ligand_constraints(), protocols::forge::remodel::RemodelLoopMover::repeat_propagation(), protocols::constraint_filters::SavePoseConstraintToFileFilter::report(), protocols::simple_filters::PoseInfoFilter::report(), protocols::splice::report_coordinate_constraints(), protocols::md::CartesianMD::report_MD(), protocols::hybridization::HybridizeFoldtreeDynamic::reset(), core::scoring::constraints::ConstraintsEnergy::residue_pair_energy(), protocols::canonical_sampling::SilentTrajectoryRecorder::restart_simulation(), protocols::forge::remodel::RemodelGlobalFrame::restore_original_cst(), protocols::symmetry::SymShakeStructureMover::run_mc(), protocols::simple_moves::ShakeStructureMover::run_mc(), protocols::fold_from_loops::NubInitioMover::sanity_check(), protocols::rbsegment_relax::set_constraints(), protocols::abinitio::FoldConstraints::set_max_seq_sep(), protocols::abinitio::ConstraintFragmentSampler::set_max_seq_sep(), protocols::forge::remodel::RemodelGlobalFrame::set_native_cst_set(), protocols::rbsegment_relax::set_rb_constraints(), protocols::flexpep_docking::FlexPepDockingProtocol::set_receptor_constraints(), protocols::relax::RelaxProtocolBase::set_up_constraints(), protocols::enzdes::EnzdesBaseProtocol::setup_bbmin_ft_and_csts(), protocols::hybridization::setup_centroid_constraints(), protocols::forge::remodel::RemodelGlobalFrame::setup_CM_helical_constraint(), protocols::ligand_docking::ResidueTorsionRestraints::setup_constraints(), protocols::simple_moves::DisulfideInsertionMover::setup_constraints(), protocols::hybridization::setup_constraints(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::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::forge::remodel::RemodelGlobalFrame::setup_helical_constraint(), protocols::forge::remodel::RemodelLoopMover::small_move_stage(), protocols::protein_interface_design::movers::PlaceStubMover::StubMinimize(), protocols::motifs::IRCollection::successful_loop_closure(), protocols::topology_broker::TopologyBroker::switch_to_fullatom(), protocols::fold_from_loops::utils::Nub::transfer_unfolded_conformation(), core::pose::full_model_info::update_constraint_set_from_full_model_info(), protocols::abinitio::abscript::AbscriptStageMover::update_max_seq_sep(), protocols::rna::denovo::RNA_FragmentMonteCarlo::update_pose_constraints(), protocols::star::update_sequence_separation(), protocols::simple_moves::ConstrainToIdealMover::vary_bond_geometry(), and protocols::hbnet::HBNet::write_network_pdb().

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

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

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

void core::pose::Pose::copy_segment ( Size const  size,
Pose const &  src,
Size const  begin,
Size const  src_begin 
)
core::Size core::pose::Pose::corresponding_residue_in_current ( core::Size const  ref_residue_index,
std::string const &  ref_pose_name 
) const

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

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

References reference_pose_set_cop().

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

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

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

References data_cache_.

Referenced by core::io::raw_data::ScoreMap::add_arbitrary_score_data_from_pose(), core::io::raw_data::ScoreMap::add_arbitrary_string_data_from_pose(), protocols::antibody::clusters::add_cluster_comments_to_pose(), core::pose::add_comment(), core::pose::add_score_line_string(), protocols::simple_moves::AddCavitiesMover::add_suckers(), core::scoring::MultipoleElecPotential::align_multipole_axes(), protocols::hydrate::append_single_far_away_water(), protocols::task_operations::StoreTaskMover::apply(), protocols::task_operations::StoreCombinedStoredTasksMover::apply(), protocols::rbsegment_relax::IdealizeHelicesMover::apply(), protocols::ub_e2c::ubi_e2c_modeler::apply(), protocols::residue_selectors::StoredResidueSubsetSelector::apply(), protocols::symmetry::SymmetricRMSMover::apply(), protocols::task_operations::RetrieveStoredTaskOperation::apply(), protocols::task_operations::StoreCompoundTaskMover::apply(), protocols::simple_ddg::ddG::apply(), protocols::enzdes::SecondaryMatchProtocol::apply(), protocols::rbsegment_relax::OptimizeThreadingMover::apply(), protocols::simple_moves::MembraneTopology::apply(), protocols::abinitio::AbrelaxMover::apply(), protocols::pb_potential::SetupPoissonBoltzmannPotential::apply(), protocols::antibody_legacy::AntibodyModeler::apply(), protocols::hybridization::CartesianSampler::apply(), protocols::docking::ConformerSwitchMover::apply(), protocols::hybridization::CartesianHybridize::apply(), protocols::docking::DockSetupMover::apply(), protocols::simple_moves::ScoreMover::apply(), protocols::cryst::UpdateCrystInfo::apply(), protocols::antibody::constraints::CDRDihedralConstraintMover::apply(), protocols::relax::ClassicRelax::apply(), protocols::antibody::design::MutateFrameworkForCluster::apply(), protocols::symmetry::SetupNCSMover::apply(), protocols::cryst::CrystRMS::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::symmetric_docking::SymDockProtocol::apply(), protocols::hybridization::CartesianSampler::apply_frame(), core::scoring::VdWTinkerPotential::assign_all_amoeba_types(), core::scoring::MultipoleElecPotential::assign_all_amoeba_types(), core::pack::rotamer_set::RotamerSet_::build_dependent_rotamers(), core::pack::rotamer_set::build_dependent_water_rotamers(), core::pack::rotamer_set::build_independent_water_rotamers(), core::scoring::MultipoleElecPotential::calculate_and_store_all_derivs(), core::scoring::methods::ProQ_Energy::calculate_feature_vector(), core::scoring::methods::ProQ_Energy::calculate_feature_vector_proq2(), core::scoring::MultipoleElecPotential::calculate_fixed_fields_for_polarization(), core::scoring::MultipoleElecPotential::calculate_induced_fields_for_polarization(), core::scoring::CenRotEnvPairPotential::cenlist_from_pose(), core::scoring::EnvPairPotential::cenlist_from_pose(), core::scoring::SmoothEnvPairPotential::cenlist_from_pose(), protocols::ub_e2c::ubi_e2c_modeler::centroid_mode_perturbation(), protocols::abinitio::FragmentSampler::check_loops(), protocols::denovo_design::components::StructureDataFactory::clear_cached_data(), core::scoring::MultipoleElecPotential::clear_induced_fields(), core::scoring::rna::clear_rna_scoring_info(), core::pose::rna::secstruct_legacy::clear_rna_secstruct_legacy_info(), protocols::simple_moves::AddCavitiesMover::clear_suckers(), core::pose::clearPoseExtraScore(), core::pose::clearPoseExtraScores(), protocols::pose_length_moves::NearNativeLoopCloser::close_loop(), protocols::environment::EnvClaimBroker::collect_claims(), core::pose::full_model_info::const_full_model_info(), protocols::scoring::const_vdw_cached_rep_screen_info_from_pose(), protocols::enzdes::PoseFoundResiduesCombination::construct_and_dump_outpose(), core::scoring::ScoreFunction::correct_arrays_for_symmetry(), core::scoring::CenRotEnvPairPotential::dcenlist_from_pose(), core::scoring::SmoothEnvPairPotential::dcenlist_from_pose(), core::pose::delete_comment(), core::scoring::MultipoleElecPotential::determine_polarization_groups(), protocols::jd2::SilentFileJobOutputter::dump_pose(), protocols::environment::Environment::end(), core::io::silent::SilentStruct::energies_from_pose(), core::io::silent::SilentStruct::energies_into_pose(), protocols::hydrate::enforce_all_waters(), protocols::environment::EnvClaimBroker::EnvClaimBroker(), core::scoring::packing::SurfEnergy::eval_atom_derivative(), core::scoring::packing::SurfVolEnergy::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::elec::FA_GrpElecEnergy::eval_intrares_derivatives(), core::scoring::methods::FACTSEnergy::eval_intrares_energy(), core::scoring::methods::GenBornEnergy::eval_intrares_energy(), core::scoring::elec::FA_GrpElecEnergy::eval_intrares_energy(), core::scoring::methods::VdWTinkerEnergy::eval_intrares_energy(), core::scoring::methods::MultipoleElecEnergy::eval_intrares_energy(), core::scoring::elec::FA_GrpElecEnergy::eval_residue_pair_derivatives(), core::scoring::VdWTinkerPotential::eval_residue_pair_derivatives(), 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::elec::FA_GrpElecEnergy::evaluate_rotamer_background_energies(), core::scoring::methods::FACTSEnergy::evaluate_rotamer_background_energy_maps(), core::scoring::methods::GenBornEnergy::evaluate_rotamer_background_energy_maps(), core::scoring::elec::FA_GrpElecEnergy::evaluate_rotamer_pair_energies(), protocols::jd2::archive::EvaluatedArchive::evaluate_silent_struct(), core::pose::extract_tag_from_pose(), core::io::silent::SilentStruct::extract_writeable_cacheable_data(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::FARFAR_setup_using_user_input_VDW_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::pack::rotamer_set::RotamerSet_::filter_water_rotamers(), protocols::docking::DockingLowRes::finalize_setup(), core::scoring::methods::MembraneLipo::finalize_total_energy(), protocols::scoring::methods::EnsembleEnergy::finalize_total_energy(), protocols::scoring::VDW_GridEnergy::finalize_total_energy(), core::scoring::MultipoleElecPotential::find_params_and_neighbors(), protocols::features::FeaturesReporter::find_tag(), core::io::silent::SilentStruct::finish_pose(), protocols::abinitio::AbrelaxApplication::fold(), core::select::residue_selector::CachedResidueSubset::from_pose_datacache(), core::pose::full_model_info::full_model_info_defined(), protocols::rosetta_scripts::AdditionalOutputWrapper::generate_pose(), protocols::rosetta_scripts::MultipleOutputWrapper::generate_pose(), core::scoring::GenBornPotential::get_all_born_radii(), core::pose::get_all_comments(), core::pose::get_all_score_line_strings(), core::scoring::membrane::MembraneData::get_cenlist_from_pose(), protocols::antibody::clusters::get_cluster_from_cache_or_ab_info(), core::scoring::MultipoleElecPotential::get_effective_radii(), core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty::get_energies_cache(), protocols::topology_broker::TMHTopologySamplerClaimer::get_membrane_topology(), protocols::antibody::design::get_native_sequence(), protocols::jobdist::get_output_tag(), protocols::enzdes::enzutil::get_pdb_code_from_pose_tag(), core::scoring::MultipoleElecPotential::get_polarization_from_fields(), protocols::hydrate::get_ready_for_sew_packing(), core::pose::rna::secstruct_legacy::get_rna_secstruct_legacy(), core::pose::rna::secstruct_legacy::get_rna_secstruct_legacy_from_const_pose(), core::scoring::FACTSPotential::get_rotamers_born_radii(), core::scoring::GenBornPotential::get_rotamers_born_radii(), core::scoring::MultipoleElecPotential::get_rotamers_effective_radii(), protocols::jobdist::get_score_map(), core::simple_metrics::get_sm_data(), protocols::denovo_design::components::get_writeable_cacheable_map(), core::pose::getPoseExtraFloatScores(), core::pose::getPoseExtraScore(), core::pose::getPoseExtraStringScores(), core::scoring::SecondaryStructurePotential::hairpin_killing_score(), protocols::denovo_design::components::StructureDataFactory::has_cached_data(), protocols::antibody::design::has_native_sequence(), core::pose::rna::secstruct_legacy::has_rna_secstruct_legacy(), core::simple_metrics::has_sm_data(), protocols::constraint_generator::ConstraintsManager::has_stored_constraints(), core::pose::hasPoseExtraScore(), core::pose::hasPoseExtraScore_str(), protocols::hydrate::hydrate_cavities(), protocols::hydrate::hydrate_hyfile(), core::scoring::MultipoleElecPotential::induce_polarizable_dipoles(), 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(), protocols::antibody::AntibodyDatabaseManager::load_cdr_design_data_for_cdrs(), protocols::antibody::AntibodyDatabaseManager::load_cdr_poses(), protocols::antibody::AntibodyDatabaseManager::load_cdr_sequences(), protocols::symmetry::SetupForSymmetryMover::make_symmetric_pose(), 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_LocalEnergy::mindata_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_centroid_mode_perturbation(), protocols::ub_e2c::ubi_e2c_modeler::monoub_first_perturbation(), protocols::ub_e2c::ubi_e2c_modeler::monoub_initial_perturbation(), core::scoring::CenRotEnvPairPotential::nonconst_cenlist_from_pose(), core::scoring::EnvPairPotential::nonconst_cenlist_from_pose(), core::scoring::SmoothEnvPairPotential::nonconst_cenlist_from_pose(), core::scoring::CenRotEnvPairPotential::nonconst_dcenlist_from_pose(), core::scoring::SmoothEnvPairPotential::nonconst_dcenlist_from_pose(), core::pose::full_model_info::nonconst_full_model_info(), 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_LocalEnergy::nonconst_mindata_from_pose(), core::scoring::methods::RG_Energy_Fast::nonconst_mindata_from_pose(), core::scoring::rna::nonconst_rna_scoring_info_from_pose(), protocols::scoring::nonconst_vdw_cached_rep_screen_info_from_pose(), protocols::ub_e2c::ubi_e2c_modeler::optimize_cov_bond(), core::scoring::methods::ProQ_Energy::output_local_prediction(), protocols::frag_picker::FragmentCandidate::output_silent(), protocols::scoring::methods::pcsTs2::PCS_Energy_Ts2::PCS_data_from_pose(), protocols::scoring::methods::pcsTs3::PCS_Energy_Ts3::PCS_data_from_pose(), protocols::scoring::methods::pcsTs4::PCS_Energy_Ts4::PCS_data_from_pose(), protocols::scoring::methods::pcsTs1::PCS_Energy_Ts1::PCS_data_from_pose(), protocols::scoring::methods::pcs::PCS_Energy::PCS_data_from_pose(), protocols::scoring::methods::pcs2::PcsEnergy::PCS_multi_data_from_pose(), protocols::hydrate::place_de_novo_wat_at_anchor(), protocols::moves::StructureRestrictor::pose_name(), protocols::topology_broker::MembraneTopologyClaimer::pre_process(), protocols::abinitio::AbrelaxApplication::process_decoy(), protocols::rbsegment_relax::OptimizeThreadingMover::rebuild_unaligned(), protocols::docking::DockingEnsemble::recover_and_pack_conformer_sidechains(), core::scoring::MultipoleElecPotential::relax_induced_dipoles(), protocols::hydrate::remove_all_anchors_and_ENF(), protocols::constraint_generator::ConstraintsManager::remove_constraints(), protocols::hydrate::remove_high_energy_water_molecules(), 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(), core::scoring::elec::FA_GrpElecEnergy::residue_pair_energy(), core::scoring::elec::FA_GrpElecEnergy::residue_pair_energy_ext(), protocols::canonical_sampling::SilentTrajectoryRecorder::restart_simulation(), core::scoring::dna::retrieve_base_partner_from_pose(), core::scoring::methods::retrieve_base_partner_from_pose_inline(), protocols::denovo_design::components::StructureDataFactory::retrieve_cached_data(), protocols::denovo_design::components::StructureDataFactory::retrieve_cached_data_ptr(), core::scoring::fiber_diffraction::retrieve_centroid_scatter_from_pose(), core::scoring::retrieve_const_ss_info_from_pose(), protocols::constraint_generator::ConstraintsManager::retrieve_constraints_map(), core::scoring::retrieve_CSA_from_pose(), core::scoring::retrieve_DC_from_pose(), core::scoring::fiber_diffraction::retrieve_fa_scatter_from_pose(), core::scoring::methods::retrieve_mp_residue_info(), core::scoring::methods::retrieve_nonconst_mp_residue_info(), core::scoring::retrieve_nonconst_ss_info_from_pose(), core::scoring::methods::retrieve_nonconst_vdw_residue_info(), core::scoring::retrieve_RDC_from_pose(), core::scoring::retrieve_RDC_ROHL_from_pose(), protocols::scoring::retrieve_RDC_segments_from_pose(), core::scoring::methods::retrieve_vdw_residue_info(), core::scoring::rna::rna_scoring_info_from_pose(), protocols::environment::safe_set_conf(), core::scoring::dna::set_base_partner(), protocols::hybridization::InsertChunkMover::set_bb_xyz_aligned(), protocols::antibody::clusters::CDRClusterSet::set_cacheable_cluster_data_to_pose(), protocols::denovo_design::components::StructureDataFactory::set_cached_data(), protocols::hydrate::set_dew_waters_not_to_be_included(), core::pose::full_model_info::set_full_model_info(), protocols::antibody::design::set_native_cdr_sequence(), core::pose::rna::secstruct_legacy::set_rna_secstruct_legacy(), core::scoring::ScoreFunction::set_symmetric_cenlist(), core::io::silent::SilentStruct::set_tag_from_pose(), protocols::antibody::design::NativeAntibodySeq::set_to_pose(), protocols::scoring::set_vdw_cached_rep_screen_info(), protocols::hydrate::set_water_info_and_add_de_novo_water(), core::pose::setPoseExtraScore(), protocols::antibody::AntibodyInfo::setup_CDR_cluster(), core::scoring::fiber_diffraction::setup_centroid_scatter(), protocols::jumping::MembraneJump::setup_fold_tree(), core::scoring::FACTSPotential::setup_for_derivatives(), core::scoring::packing::SurfEnergy::setup_for_derivatives(), core::scoring::packing::SurfVolEnergy::setup_for_derivatives(), core::scoring::packing::HolesEnergy::setup_for_derivatives(), core::scoring::packing::HolesEnergyRes::setup_for_derivatives(), core::scoring::methods::MultipoleElecEnergy::setup_for_minimizing_for_residue(), core::scoring::methods::VdWTinkerEnergy::setup_for_minimizing_for_residue(), core::scoring::FACTSPotential::setup_for_packing(), core::scoring::GenBornPotential::setup_for_packing(), core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty::setup_for_packing_with_rotsets(), core::scoring::FACTSPotential::setup_for_scoring(), core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty::setup_for_scoring(), core::scoring::methods::PoissonBoltzmannEnergy::setup_for_scoring(), core::scoring::elec::FA_GrpElecEnergy::setup_for_scoring(), core::scoring::electron_density_atomwise::ElecDensAtomwiseEnergy::setup_for_scoring(), core::scoring::VdWTinkerPotential::setup_for_scoring(), core::scoring::MultipoleElecPotential::setup_for_scoring(), core::scoring::fiber_diffraction::setup_form_factors(), protocols::relax::setup_membrane_topology(), protocols::abinitio::AbrelaxApplication::setup_membrane_topology(), protocols::antibody::design::AntibodyDesignMover::setup_native_sequence(), protocols::stepwise::modeler::slice_out_pose(), core::scoring::SecondaryStructurePotential::sspair(), protocols::environment::Environment::start(), core::scoring::store_CSA_in_pose(), core::scoring::store_DC_in_pose(), protocols::constraint_generator::ConstraintsManager::store_empty_constraints_map(), core::scoring::MultipoleElecPotential::store_induced_dipoles(), core::scoring::store_RDC_in_pose(), core::scoring::store_RDC_ROHL_in_pose(), protocols::scoring::store_RDC_segments_in_pose(), protocols::stepwise::modeler::switch_focus_to_other_pose(), core::pose::tag_from_pose(), core::pose::tag_into_pose(), core::pose::full_model_info::update_res_list_in_full_model_info_and_pdb_info(), core::scoring::FACTSPotential::update_residue_for_packing(), core::scoring::VdWTinkerPotential::update_residue_for_packing(), core::scoring::GenBornPotential::update_residue_for_packing(), core::scoring::MultipoleElecPotential::update_residue_for_packing(), and protocols::scoring::vdw_cached_rep_screen_info_is_setup().

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

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

References data_cache_.

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

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

If there is no ReferencePose object, do nothing.

References reference_pose_set_.

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

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

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

Delete a residue from the Conformation the slow way – triggers a rebuild of the atomtree Fires a LengthEvent::RESIDUE_DELETE signal.

Note
Could be upstream and/or downstream of a jump or chemical edge, or the root of the tree
Not well-tested. Expect funny behavior in new or different situations (email pbrad.nosp@m.ley@.nosp@m.fhcrc.nosp@m..org)

LOGIC: uses fold_tree.delete_seqpos to handle shifting the topology around if necessary, then calls setup_atom_tree

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

Referenced by protocols::protein_interface_design::movers::LoopLengthChange::apply(), protocols::antibody::snugdock::SnugDockProtocol::apply(), core::pose::carbohydrates::delete_leaf(), and protocols::rna::movers::RNAThreadAndMinimizeMover::process_deletions().

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

Returns the delta torsion angle of residue <seqpos>

Note
assumes the residue is an nucleic acid

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

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

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

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

detach ConformationEvent observer function

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

References conformation_obs_hub_.

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

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

detach DestructionEvent observer function

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

References destruction_obs_hub_.

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

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

detach EnergyEvent observer function

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

References energy_obs_hub_.

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

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

detach GeneralEvent observer function

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

References general_obs_hub_.

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

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

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

References conformation_, constraint_set_, and on_conf_xyz_change().

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

Real core::pose::Pose::dof ( DOF_ID const &  id) const
void core::pose::Pose::dump_cif ( std::string const &  file_name) const

Export pose data to the mmCIF file <file_name>

example(s): pose.dump_cif('new_01.cif') See also: Pose pose_from_cif dump_file

References core::io::mmcif::dump_cif().

void core::pose::Pose::dump_file ( std::string const &  file_name) const

Export pose data to a file, <file_name>, determining which type of file format to write based on the file extension.

example(s): pose.dump_file('new_01.pdb') pose.dump_file('new_01.cif') See also: Pose dump_cif dump_file

Dumps an mmcif formatted file if the extension on the input file_name_string is .cif

References core::io::mmcif::dump_cif(), and core::io::pdb::dump_pdb().

bool core::pose::Pose::dump_pdb ( std::string const &  file_name) const

Export pose data to the PDB file <file_name>

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

save pose data to file with supplied file_name

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

Referenced by protocols::monte_carlo::GenericMonteCarloMover::accept(), protocols::topology_broker::ConstraintClaimer::add_constraints(), protocols::loop_grower::LoopGrower::addnativesolution(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::align_VDW_rep_screen_pose(), protocols::comparative_modeling::AlignmentClustering::AlignmentClustering(), protocols::denovo_design::components::append_new_residues(), protocols::denovo_design::components::append_residues_from_template_segment(), protocols::cutoutdomain::CutOutDomain::apply(), protocols::medal::MedalExchangeMover::apply(), protocols::simple_moves::DumpPdb::apply(), protocols::simple_moves::PDBReloadMover::apply(), protocols::magnesium::MgMonteCarlo::apply(), protocols::simple_filters::ExternalEvaluator::apply(), protocols::enzdes::SecondaryMatchProtocol::apply(), protocols::antibody::GraftCDRLoopsProtocol::apply(), protocols::backrub::BackrubProtocol::apply(), protocols::indel::IndelOptimizationMover::apply(), protocols::loops::loop_mover::IndependentLoopMover::apply(), protocols::splice::SpliceIn::apply(), protocols::splice::SpliceInTail::apply(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::apply(), protocols::splice::SpliceOut::apply(), protocols::rna::denovo::RNA_DeNovoProtocol::apply(), protocols::hybridization::CartesianSampler::apply(), protocols::recces::scratch::ThermalSamplingMover::apply(), protocols::loop_grower::FragmentExtension::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::hybridization::BackboneTorsionPerturbation::apply(), protocols::hybridization::BackboneTorsionSampler::apply(), protocols::simple_moves::sidechain_moves::SidechainMCMover::apply(), protocols::splice::Splice::apply(), protocols::flxbb::InterlockAroma::apply(), protocols::docking::membrane::QuickRelaxPartnersSeparately::apply(), protocols::docking::membrane::MPFindInterfaceMover::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::membrane::MPQuickRelaxMover::apply(), protocols::ddg::ddGMover::apply(), protocols::monte_carlo::GenericMonteCarloMover::apply(), protocols::relax::FastRelax::apply(), protocols::topology_broker::TopologyBroker::apply(), protocols::fldsgn::BluePrintBDR::apply(), protocols::cryst::TagPoseWithRefinementStatsMover::apply(), protocols::moves::PyMOLMover::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::loop_grower::LoopGrower::apply(), protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::apply_solutions(), protocols::rna::denovo::coarse::CoarseRNA_LoopCloser::apply_solutions(), protocols::splice::SpliceIn::assign_from_res_to_res(), core::import_pose::RNA_HelixAssembler::build_helix(), protocols::splice::SpliceOutTail::build_ideal_segment(), protocols::splice::SpliceInTail::build_ideal_segment(), protocols::splice::SpliceIn::build_ideal_segment(), protocols::splice::SpliceOut::build_ideal_segment(), protocols::docking::DockingEnsemble::calculate_highres_ref_energy(), core::scoring::packstat::cavity_distance_constraint(), protocols::splice::SpliceOut::ccd_mover(), protocols::splice::SpliceManager::chainbreak_check(), protocols::splice::Splice::chainbreak_check(), protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::check_screen(), protocols::rna::denovo::coarse::MultipleDomainMover::close_all_loops(), protocols::abinitio::AbrelaxApplication::close_loops(), protocols::loop_grower::LoopPartialSolutionStore::cluster_check(), 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::TaskAwareSASAFilter::compute(), core::scoring::ResidualDipolarCoupling::compute_dipscore(), protocols::enzdes::PoseFoundResiduesCombination::construct_and_dump_outpose(), protocols::splice::Splice::copy_stretch(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::correctly_copy_HO2prime_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::forge::remodel::RemodelMover::design_refine(), protocols::rna::denovo::movers::RNA_DeNovoMasterMover::do_random_moves(), protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::do_test_move(), core::optimization::AtomTreeMultifunc::dump(), core::optimization::CartesianMultifunc::dump(), protocols::normalmode::NormalModeMultifunc::dump(), core::optimization::symmetry::SymAtomTreeMultifunc::dump(), protocols::simple_moves::PeriodicBoxMover::dump_ASU(), core::pose::dump_comment_pdb(), protocols::sic_dock::dump_loophash_linkers(), core::scoring::motif::MotifHits::dump_motifs_pdb(), protocols::helix_capper::HelixNCapperMover::dump_pdb_to_file(), protocols::vip::VIP_Mover::dump_pdb_to_file(), core::import_pose::dump_stems(), protocols::recces::RECCES_Mover::dump_stuff(), protocols::environment::EnvClaimBroker::EnvClaimBroker(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_energy(), protocols::rna::denovo::export_packer_results(), protocols::loop_grower::LoopPartialSolutionStore::filter(), protocols::recces::RECCES_Mover::final_dump_stuff(), protocols::splice::SpliceIn::find_dbase_entry(), protocols::splice::SpliceInTail::find_dbase_entry(), protocols::splice::Splice::find_dbase_entry(), protocols::splice::RotLibOut::find_matching_res(), core::scoring::cryst::PhenixInterface::fitBfactors(), protocols::abinitio::AbrelaxApplication::fold(), protocols::legacy_sewing::LegacyEnumerateAssemblyMover::generate_assembly(), protocols::splice::Splice::generate_sequence_profile(), protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::get_all_solutions(), protocols::rna::denovo::coarse::CoarseRNA_LoopCloser::get_all_solutions(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::get_matching_res_in_VDW_rep_screen_pose(), protocols::vip::VIP_Mover::get_neighbors(), protocols::stepwise::modeler::align::StepWisePoseAligner::get_rmsd_no_superimpose(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::go(), protocols::motifs::IRCollection::incorporate_motifs(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::initialize_pose_from_streams(), core::import_pose::libraries::RNA_ChunkLibrary::initialize_random_chunks(), core::scoring::cryst::PhenixInterface::initialize_target_evaluator(), protocols::stepwise::modeler::protein::loop_close::kic_close_loops_in_samples(), protocols::sparta::PDB::loadPDB(), protocols::toolbox::match_enzdes_util::EnzConstraintParameters::make_constraint_covalent(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::make_extended_pose(), protocols::splice::SpliceOut::min_mover(), protocols::splice::min_seg(), protocols::splice::SpliceIn::minimize_segment(), protocols::splice::SpliceOut::minimize_segment(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::model_loop(), protocols::recces::RECCES_Mover::more_dump_stuff(), protocols::topology_broker::TMHTopologySamplerClaimer::move_spans(), protocols::relax::LocalRelax::optimization_loop(), protocols::abinitio::MembraneAbinitio::output_debug_structure(), protocols::abinitio::ClassicAbinitio::output_debug_structure(), protocols::protein_interface_design::movers::MapHotspot::output_pose(), protocols::legacy_sewing::LegacyAssemblyMover::output_stats(), protocols::loop_grower::LoopPartialSolutionStore::parametercheck_filter(), protocols::hybridization::BackboneTorsionPerturbation::perturb(), protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::prepare_from_prior_sampled_sugar_jobs_for_chain_break(), protocols::denovo_design::components::prepend_new_residues(), protocols::cluster::ClusterBase::print_cluster_PDBs(), protocols::loop_grower::LoopPartialSolutionStore::push(), protocols::rna::denovo::coarse::MultipleDomainMover::randomize_orientations(), protocols::splice::Splice::rb_adjust_template(), protocols::sic_dock::read_biounit(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::read_input_pose_and_copy_dofs(), protocols::loop_grower::LoopGrower::refine_cycle(), protocols::ddg::ddGMover::relax_wildtype_structure(), protocols::legacy_sewing::Assembly::reorder(), protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::resample_full_model(), protocols::loop_grower::LoopGrower::rescoresolutionset(), protocols::rna::movers::RNA_LoopCloser::rna_ccd_close(), protocols::splice::SpliceIn::rtmin(), protocols::recces::RECCES_Mover::run_sampler(), protocols::toolbox::sample_around::sample_all_rotations_at_jump(), protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger::sample_omega_recursively(), protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure::select_final_loop(), protocols::denovo_design::components::Segment::set_template_pose(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::setup_native_pose(), protocols::rna::denovo::movers::RNA_DeNovoMasterMover::setup_rnp_fold_tree(), protocols::loop_grower::LoopGrower::single_grow(), protocols::splice::SpliceOutTail::superimpose_source_on_pose(), protocols::splice::SpliceOut::superimpose_source_on_pose(), protocols::splice::Splice::superimpose_source_on_pose(), protocols::splice::SpliceOut::tail_mover(), protocols::rna::denovo::coarse::MultipleDomainMover::try_to_slide_into_contact(), protocols::dna::write_checkpoint(), protocols::canonical_sampling::PDBTrajectoryRecorder::write_model(), protocols::hbnet::HBNet::write_network_pdb(), and protocols::flxbb::LayerDesignOperation::write_pymol_script().

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

for writing a specified subset of residues in pdb format

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

void core::pose::Pose::dump_scored_pdb ( std::string const &  file_name,
scoring::ScoreFunction const &  scorefxn 
)
bool core::pose::Pose::empty ( ) const
iterator core::pose::Pose::end ( )
noexcept
const_iterator core::pose::Pose::end ( ) const
noexcept
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 core::scoring::methods::FreeDOF_Energy::accumulate_stack_energy(), protocols::enzdes::SecondaryMatchProtocol::add_enz_cst_interaction_to_pose(), protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_pose(), protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_wholepose(), 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::evolution::AlignmentAAFinder::apply(), protocols::task_operations::SelectByDeltaScoreOperation::apply(), protocols::evolution::AlignmentGapInserter::apply(), core::select::residue_selector::ScoreTermValueBasedSelector::apply(), protocols::cluster::GatherPosesMover::apply(), protocols::flexpack::FlexPacker::apply(), protocols::protein_interface_design::movers::DockWithHotspotMover::apply(), protocols::matdes::BuildingBlockInterfaceOperation::apply(), protocols::simple_moves::MSDMover::apply(), protocols::normalmode::NormalModeMinimizer::apply(), protocols::simple_moves::DisulfideInsertionMover::apply(), protocols::simple_moves::ReturnSidechainMover::apply(), protocols::moves::JumpOutMover::apply(), protocols::analysis::LoopAnalyzerMover::apply(), protocols::ncbb::SecStructMinimizeMover::apply(), protocols::recces::scratch::ThermalMinimizer::apply(), protocols::simple_filters::EvaluatedTrialMover::apply(), protocols::simple_moves::ScoreMover::apply(), protocols::antibody::RefineOneCDRLoop::apply(), protocols::surface_docking::SurfaceDockingProtocol::apply(), protocols::flxbb::InterlockAroma::apply(), protocols::helical_bundle::BundleGridSampler::apply(), protocols::symmetry::SymDockingSlideIntoContact::apply(), protocols::docking::membrane::MPFindInterfaceMover::apply(), protocols::moves::MCShowMover::apply(), core::select::residue_selector::NeighborhoodResidueSelector::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::membrane::MPQuickRelaxMover::apply(), protocols::relax::RangeRelaxMover::apply(), protocols::ddg::ddGMover::apply(), protocols::dna_dock::DNAClashCheckFilter::apply(), protocols::fldsgn::filters::HelixKinkFilter::apply(), protocols::dna_dock::PropagateClashCheckFilter::apply(), protocols::symmetry::FaSymDockingSlideTogether::apply(), protocols::legacy_sewing::LegacyAssemblyConstraintsMover::apply(), protocols::monte_carlo::GenericMonteCarloMover::apply(), protocols::moves::TrialMover::apply(), protocols::docking::DockingProtocol::apply(), protocols::docking::DockingSlideIntoContact::apply(), protocols::docking::FaDockingSlideIntoContact::apply(), protocols::abinitio::ComputeTotalDistCst::apply(), protocols::docking::SlideIntoContact::apply(), protocols::forge::remodel::RemodelLoopMover::apply(), protocols::loop_grower::LoopGrower::apply(), core::scoring::ScoreFunction::asym_eval_long_range_twobody_energies(), core::scoring::ScoreFunction::asym_eval_onebody_energies(), core::scoring::ScoreFunction::asym_eval_twobody_neighbor_energies(), core::scoring::ScoreFunction::asym_setup_for_derivatives(), core::scoring::ScoreFunction::asym_setup_for_minimizing(), core::scoring::methods::ProQ_Energy::atom_feature(), 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::canonical_sampling::BiasedMonteCarlo::boltzmann(), core::pack::rotamer_set::RotamerSet_::build_rotamers_for_concrete(), protocols::hybridization::FragmentBiasAssigner::cal_perrsd_score(), protocols::flexpep_docking::FlexPepDockingPoseMetrics::calc_pep_scores(), protocols::analysis::InterfaceAnalyzerMover::calc_per_residue_and_regional_data(), core::scoring::electron_density::calc_per_rsd_score(), protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetric::calculate(), core::simple_metrics::composite_metrics::CompositeEnergyMetric::calculate(), core::simple_metrics::per_residue_metrics::PerResidueEnergyMetric::calculate(), protocols::scoring::Interface::calculate(), core::scoring::MultipoleElecPotential::calculate_and_store_all_derivs(), core::scoring::electron_density::calculate_density_nbr(), core::scoring::methods::LK_hack::calculate_derivatives_for_atoms_and_pseudo_base_atoms(), protocols::peptide_deriver::PeptideDeriverFilter::calculate_per_residue_interface_score(), core::scoring::electron_density::calculate_rama(), protocols::ncbb::calculate_statistics(), protocols::hydrate::calculate_water_overcoordinated_hb_correction(), core::optimization::cartesian_collect_atompairE_deriv(), protocols::antibody::cdr_energy(), 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(), core::scoring::membrane::MPHelicalityEnergy::centroid_neighbors(), core::scoring::membrane::MPResidueLipophilicityEnergy::centroid_neighbors(), protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker::chain_break_screening_general(), protocols::fldsgn::topology::check_internal_hbonds(), protocols::fldsgn::topology::check_kink_helix(), protocols::stepwise::modeler::check_scores_from_parts(), protocols::stepwise::modeler::protein::checker::ProteinAtrRepChecker::check_screen(), protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::check_screen(), protocols::enzdes::PackRotamersMoverPartGreedy::choose_n_best(), core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::clean_up_residuearrayannealableenergy_after_packing(), core::scoring::rna::RNA_PairwiseLowResolutionEnergy::clean_up_rna_two_body_energy_tables(), core::pack::interaction_graph::InteractionGraphFactory::clear_cached_residuearrayannealableenergy_information(), 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::TaskAwareScoreTypeFilter::compute(), protocols::simple_filters::ResidueSetChainEnergyFilter::compute(), protocols::simple_filters::InterfaceHbondsFilter::compute(), protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter::compute(), protocols::fldsgn::filters::CoreDunbrackFilter::compute(), protocols::fldsgn::filters::InterlockingAromaFilter::compute(), protocols::enzdes::RepackWithoutLigandFilter::compute(), protocols::minimization_packing::GreenPacker::compute_absent_energies(), protocols::sasa_scores::compute_avge_scores(), core::scoring::CenRotEnvPairPotential::compute_centroid_environment(), core::scoring::SmoothEnvPairPotential::compute_centroid_environment(), core::scoring::EnvPairPotential::compute_centroid_environment(), core::scoring::CenRotEnvPairPotential::compute_dcentroid_environment(), core::scoring::SmoothEnvPairPotential::compute_dcentroid_environment(), protocols::features::StructureScoresFeatures::compute_energies(), protocols::simple_pose_metric_calculators::NumberHBondsCalculator::compute_Hbonds_for_residue(), protocols::enzdes::EnzdesScorefileFilter::compute_metrics_for_residue_subset(), core::pack::rotamer_set::RotamerSet_::compute_one_and_two_body_energies(), 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::pack::interaction_graph::SurfacePotential::compute_pose_surface_energy(), core::pack::interaction_graph::SurfacePotential::compute_residue_surface_energy(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_sho_acceptor_atom_energy(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_sho_donor_atom_energy(), protocols::enzdes::LigInterfaceEnergyFilter::constraint_energy(), core::scoring::ScoreFunction::correct_finalize_score(), core::pack::hbonds::create_init_and_create_edges_for_atom_level_hbond_graph(), core::scoring::methods::create_long_range_energy_container(), 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::CentroidDisulfideEnergy::defines_residue_pair_energy(), core::scoring::disulfides::DisulfideMatchingEnergy::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_cart_relax(), protocols::forge::remodel::RemodelMover::design_refine_seq_relax(), protocols::enzdes::EnzdesBaseProtocol::design_targets_score(), protocols::toolbox::match_enzdes_util::EnzConstraintParameters::determine_best_constraint(), protocols::simple_pose_metric_calculators::NumberHBondsCalculator::determine_res_to_recompute(), protocols::electron_density::BfactorMultifunc::dfunc(), protocols::stepwise::modeler::StepWiseMinimizer::do_full_minimizing(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::do_initial_import_and_scoring(), protocols::stepwise::monte_carlo::StepWiseMonteCarlo::do_main_loop(), protocols::symmetric_docking::SymDockProtocol::docking_highres_filter(), core::optimization::AtomTreeMultifunc::dump(), core::optimization::CartesianMultifunc::dump(), protocols::normalmode::NormalModeMultifunc::dump(), core::optimization::symmetry::SymAtomTreeMultifunc::dump(), dump_scored_pdb(), protocols::jobdist::PlainPdbJobDistributor::dump_scores(), protocols::antibody::AntibodyModelerProtocol::echo_metrics_to_output(), 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::hackaro::HackAroEnergy::eval_atom_derivative(), core::scoring::methods::MembraneEnvSmoothEnergy::eval_atom_derivative(), core::scoring::membrane::FaMPSolvEnergy::eval_atom_derivative(), core::scoring::methods::EnvSmoothEnergy::eval_atom_derivative(), core::scoring::membrane::FaMPEnvSmoothEnergy::eval_atom_derivative(), core::scoring::rna::RNA_VDW_Energy::eval_atom_derivative(), core::scoring::methods::HybridVDW_Energy::eval_atom_derivative(), core::scoring::rna::data::RNA_DataBackboneEnergy::eval_atom_derivative(), core::scoring::rna::StackElecEnergy::eval_atom_derivative(), core::scoring::methods::WaterAdductHBondEnergy::eval_atom_derivative(), core::scoring::hbonds::NPDHBondEnergy::eval_atom_derivative(), core::scoring::methods::MMLJEnergyInter::eval_atom_derivative(), core::scoring::vdwaals::VDW_Energy::eval_atom_derivative(), core::scoring::elec::FA_ElecEnergyAroAll::eval_atom_derivative(), core::scoring::elec::FA_ElecEnergyAroAro::eval_atom_derivative(), core::scoring::methods::LK_PolarNonPolarEnergy::eval_atom_derivative(), core::scoring::rna::RNA_FullAtomStackingEnergy::eval_atom_derivative(), core::scoring::elec::RNA_FA_ElecEnergy::eval_atom_derivative(), core::scoring::elec::FA_ElecEnergy::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::GeometricSolEnergyEvaluator::eval_atom_energy(), core::scoring::ScoreFunction::eval_dof_derivative(), core::scoring::methods::MMLJEnergyIntra::eval_intrares_derivatives(), core::scoring::hbonds::HBondEnergy::eval_intrares_derivatives(), core::scoring::elec::FA_GrpElecEnergy::eval_intrares_derivatives(), core::scoring::elec::FA_ElecEnergy::eval_intrares_derivatives(), core::scoring::etable::BaseEtableEnergy< Derived >::eval_intrares_derivatives(), core::scoring::elec::FA_GrpElecEnergy::eval_intrares_energy(), core::scoring::hbonds::HBondEnergy::eval_intrares_energy(), core::scoring::etable::TableLookupEtableEnergy::eval_intrares_energy(), core::scoring::etable::AnalyticEtableEnergy::eval_intrares_energy(), core::scoring::methods::MMLJEnergyIntra::eval_intrares_energy_ext(), core::scoring::etable::BaseEtableEnergy< Derived >::eval_intrares_energy_ext(), protocols::moves::MonteCarlo::eval_lowest_score_pose(), core::scoring::ScoreFunction::eval_npd_atom_derivative(), core::scoring::Ramachandran::eval_rama_score_all(), core::scoring::Ramachandran2B::eval_rama_score_all(), core::scoring::rna::StackElecEnergy::eval_residue_pair_derivatives(), core::scoring::methods::PairEnergy::eval_residue_pair_derivatives(), core::scoring::methods::LK_PolarNonPolarEnergy::eval_residue_pair_derivatives(), core::scoring::elec::FA_GrpElecEnergy::eval_residue_pair_derivatives(), core::scoring::elec::RNA_FA_ElecEnergy::eval_residue_pair_derivatives(), core::scoring::hbonds::HBondEnergy::eval_residue_pair_derivatives(), core::scoring::elec::FA_ElecEnergy::eval_residue_pair_derivatives(), core::scoring::etable::BaseEtableEnergy< Derived >::eval_residue_pair_derivatives(), core::scoring::VdWTinkerPotential::eval_residue_pair_derivatives(), protocols::multistate_design::SingleStateFitnessFunction::evaluate(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_env_and_cbeta_deriv(), protocols::abinitio::FoldConstraints::evaluate_constraint_energy(), protocols::abinitio::ConstraintFragmentSampler::evaluate_constraint_energy(), core::scoring::SmoothEnvPairPotential::evaluate_env_and_cbeta_deriv(), core::scoring::methods::MMLJEnergyInter::evaluate_rotamer_background_energies(), core::scoring::hbonds::HBondEnergy::evaluate_rotamer_background_energies(), core::scoring::elec::FA_ElecEnergy::evaluate_rotamer_background_energies(), core::scoring::etable::BaseEtableEnergy< Derived >::evaluate_rotamer_background_energies(), core::scoring::lkball::LK_BallEnergy::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::canonical_sampling::WTEBiasEnergy::extract_collective_var(), protocols::pockets::GenPharmacophore::extract_Hbond_atoms_from_protein_rna_complex(), protocols::enzdes::EnzdesFlexibleRegion::extract_lig_designability_score(), protocols::stepwise::modeler::packer::figure_out_working_interface_res(), protocols::simple_ddg::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(), core::scoring::hbonds::fill_intra_res_hbond_set(), protocols::simple_ddg::ddG::fill_per_residue_energy_vector(), core::io::silent::BinarySilentStruct::fill_pose(), core::select::fill_tenA_neighbor_residues(), protocols::cyclic_peptide::crosslinker::CrosslinkerMoverHelper::filter_by_constraints_energy(), protocols::cyclic_peptide::CrosslinkerMover::filter_by_total_score(), core::pack::interaction_graph::HPatchEnergy::finalize_total_energy(), core::pack::interaction_graph::SurfaceEnergy::finalize_total_energy(), core::scoring::elec::RNA_FA_ElecEnergy::finalize_total_energy(), core::scoring::hbonds::NPDHBondEnergy::finalize_total_energy(), core::scoring::rna::StackElecEnergy::finalize_total_energy(), core::scoring::elec::FA_ElecEnergy::finalize_total_energy(), core::scoring::hbonds::HBondEnergy::finalize_total_energy(), core::scoring::etable::BaseEtableEnergy< Derived >::finalize_total_energy(), core::pack::hbonds::find_satisfying_interactions_with_background(), protocols::denovo_design::movers::BuildDeNovoBackboneMover::fold_attempt(), protocols::loop_grower::LoopGrower::full_atom_beam(), protocols::ub_e2c::ubi_e2c_modeler::fullatom_filter(), protocols::enzdes::EnzdesFlexBBProtocol::generate_alc_ensemble_for_region(), protocols::residue_optimization::MetapatchEnumeration::generate_derived_types(), protocols::enzdes::EnzdesFlexibleRegion::get_10A_neighbors(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_acceptor(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_donor(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::get_atom_lk_energy(), core::pose::symmetry::get_buildingblock_and_neighbor_subs(), protocols::motif_grafting::movers::MotifGraftMover::get_clash_score_from_pose(), protocols::features::get_current_model_score(), protocols::moves::get_energies(), protocols::vip::VIP_Report::get_GOE_relaxed_report(), protocols::vip::VIP_Report::get_GOE_repack_report(), protocols::hbnet::get_hbond_atom_pairs(), protocols::optimize_weights::IterativeOptEDriver::get_nat_aa_opte_data(), protocols::helix_capper::HelixNCapperMover::get_Ncap_scores(), protocols::ligand_docking::LigandBaseProtocol::get_non_bb_clashing_rotamers(), protocols::nonlocal::get_per_residue_score(), protocols::relax::get_per_residue_scores(), protocols::trajectory::DbTrajectoryReader::get_pose(), protocols::stepwise::monte_carlo::rna::RNA_O2PrimeMover::get_random_o2prime_residue_near_moving_residue(), protocols::hydrate::get_ready_for_sew_packing(), protocols::enzdes::EnzdesFlexibleRegion::get_region_mm_bend_score(), protocols::enzdes::EnzdesFlexibleRegion::get_region_total_score(), protocols::score_filters::ScoreCutoffFilter::get_score(), protocols::ligand_docking::InterfaceScoreCalculator::get_scores(), core::scoring::ScoreFunction::get_sub_score(), core::scoring::ScoreFunction::get_sub_score_exclude_res(), protocols::enzdes::EnzdesFlexBBProtocol::get_tenA_neighbor_residues(), core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_pose_energies_table(), protocols::enzdes::PackRotamersMoverPartGreedy::greedy_around(), core::util::ChainbreakUtil::has_chainbreak(), core::scoring::SecondaryStructurePotential::hspair(), protocols::neighbor::in_nrg_graph(), protocols::motifs::MotifSearch::incorporate_motifs(), protocols::motifs::LigandMotifSearch::incorporate_motifs(), core::pack::interaction_graph::SimpleInteractionGraph::initialize(), core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy::initialize_graphs(), 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::calc_taskop_filters::RotamerBoltzmannWeight::interface_interaction_energy(), core::scoring::ScoreFunction::intersubunit_hbond_energy(), protocols::moves::PyMOLMover::label_energy(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::let_neighboring_chis_minimize(), protocols::ligand_docking::ComputeLigandRDF::ligand_protein_rdf(), 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::matchRes(), core::pack::min_pack_optimize(), protocols::make_rot_lib::min_rotamers(), core::scoring::rna::StackElecEnergy::minimize_in_whole_structure_context(), core::scoring::etable::BaseEtableEnergy< Derived >::minimize_in_whole_structure_context(), core::scoring::elec::RNA_FA_ElecEnergy::minimize_in_whole_structure_context(), core::scoring::elec::FA_GrpElecEnergy::minimize_in_whole_structure_context(), core::scoring::elec::FA_ElecEnergy::minimize_in_whole_structure_context(), protocols::enzdes::EnzdesFlexibleRegion::minimize_region(), protocols::make_rot_lib::MakeRotLibMover::minimize_rotamer(), 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(), protocols::simple_moves::SmallMover::move_with_scorefxn(), protocols::simple_moves::ShearMover::move_with_scorefxn(), protocols::cryst::ReportGradientsMover::normalization(), core::scoring::disulfides::FullatomDisulfideEnergy::old_eval_atom_derivative(), protocols::electron_density::BfactorMultifunc::operator()(), core::optimization::SingleResidueMultifunc::operator()(), core::scoring::DockingScoreFunction::operator()(), core::scoring::MinScoreScoreFunction::operator()(), core::scoring::ScoreFunction::operator()(), core::pose::rna::output_ligands(), core::pose::rna::output_other_contacts(), protocols::score_filters::ScoreCutoffFilter::output_residue_pair_energies(), protocols::frag_picker::FragmentCandidate::output_silent(), protocols::surface_docking::FullatomRelaxMover::output_solution_state(), protocols::legacy_sewing::LegacyAssemblyMover::output_stats(), protocols::rpc::pose_energies_to_json(), core::scoring::elec::FA_GrpElecEnergy::precalc_context(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::precalculate_bb_bb_energy_for_design(), 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::relax::RangeRelaxMover::print_score(), protocols::scoring::Interface::protein_calculate(), protocols::ligand_docking::ComputeLigandRDF::protein_protein_rdf(), protocols::hbnet::HBNet::rec_trav_native(), protocols::mean_field::EnergiesByTaskCalculator::recompute(), core::pose::metrics::simple_calculators::InterfaceDeltaEnergeticsCalculator::recompute(), protocols::pose_metric_calculators::NonlocalContactsCalculator::recompute(), protocols::vardist_solaccess::VarSolDistSasaCalculator::recompute(), protocols::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator::recompute(), protocols::loop_modeling::utilities::TrajectoryLogger::record_endpoint(), protocols::vip::VIP_Mover::relax_favorable_poses(), protocols::ddg::ddGMover::relax_wildtype_structure(), protocols::hydrate::remove_high_energy_water_molecules(), protocols::toolbox::pose_manipulation::remove_non_protein_residues(), protocols::score_filters::ScoreCutoffFilter::report(), protocols::features::AtomInResidueAtomInResiduePairFeatures::report_atom_pairs(), protocols::features::AtomAtomPairFeatures::report_atom_pairs(), protocols::features::ProteinBackboneAtomAtomPairFeatures::report_features(), protocols::features::ResidueBurialFeatures::report_features(), protocols::features::TaskOperationFeatures::report_features(), protocols::features::ModelFeatures::report_features(), protocols::features::HBondFeatures::report_features(), protocols::features::PairFeatures::report_residue_pairs(), protocols::constraint_filters::ConstraintScoreFilter::report_sm(), protocols::simple_moves::PeriodicBoxMover::report_thermodynamics(), core::scoring::methods::ProQ_Energy::res_feature(), core::scoring::methods::BurialEnergy::residue_energy(), core::scoring::nv::NVscore::residue_energy(), core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::residue_energy(), core::scoring::methods::MembraneEnvSmoothEnergy::residue_energy(), core::scoring::methods::EnvSmoothEnergy::residue_energy(), core::scoring::membrane::FaMPEnvSmoothEnergy::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::rna::StackElecEnergy::residue_pair_energy(), core::scoring::methods::PairEnergy::residue_pair_energy(), core::scoring::elec::RNA_FA_ElecEnergy::residue_pair_energy(), core::scoring::hbonds::HBondEnergy::residue_pair_energy(), core::scoring::elec::FA_GrpElecEnergy::residue_pair_energy(), core::scoring::disulfides::FullatomDisulfideEnergy::residue_pair_energy(), core::scoring::elec::FA_ElecEnergy::residue_pair_energy(), core::scoring::etable::BaseEtableEnergy< Derived >::residue_pair_energy(), core::scoring::elec::RNA_FA_ElecEnergy::residue_pair_energy_ext(), core::scoring::hbonds::HBondEnergy::residue_pair_energy_ext(), core::scoring::rna::StackElecEnergy::residue_pair_energy_ext(), core::scoring::elec::FA_GrpElecEnergy::residue_pair_energy_ext(), core::scoring::elec::FA_ElecEnergy::residue_pair_energy_ext(), core::scoring::etable::BaseEtableEnergy< Derived >::residue_pair_energy_ext(), protocols::forge::methods::restore_residues(), protocols::rna::denovo::movers::RNA_DeNovoMasterMover::rnp_docking_trial(), core::pack::RTMin::rtmin(), core::optimization::symmetry::SymAtomTreeMinimizer::run(), core::optimization::AtomTreeMinimizer::run(), core::optimization::CartesianMinimizer::run(), protocols::mpi_refinement::WorkUnit_PartialAbinitio::run(), protocols::fldsgn::potentials::sspot::HSPairPotential::score(), protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential::score(), protocols::fldsgn::potentials::sspot::SSPairPotential::score(), core::scoring::ScoreFunction::score_by_scoretype(), protocols::abinitio::abscript::score_cst(), protocols::moves::MonteCarlo::score_function(), protocols::optimize_weights::IterativeOptEDriver::score_ligand_interface(), core::io::raw_data::ScoreMap::score_map_from_scored_pose(), protocols::hbnet::HBNet::score_network_on_pose(), protocols::analysis::InterfaceAnalyzerMover::score_separated_chains(), protocols::rna::denovo::movers::RNA_DeNovoMasterMover::search_rigid_body_orientation(), protocols::hbnet::HBNet::select_best_networks(), protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::semiexpl_water_hbgeom_score(), protocols::moves::PyMOLMover::send_energy(), protocols::moves::PyMOLMover::send_hbonds(), protocols::vip::set_local_movemap(), protocols::moves::MonteCarlo::set_lowest_score_pose(), core::pack::interaction_graph::NPDHBSimpleInteractionGraph::set_pose_no_initialize(), protocols::loop_grower::LoopComparator::set_scores(), core::scoring::ScoreFunction::set_symmetric_residue_neighbors_hbonds(), core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::set_up_residuearrayannealableenergy_for_packing(), core::io::sequence_comparation::DesignContrast::setNeighbors(), protocols::minimization_packing::EnergyCutRotamerTrialsMover::setup_energycut_task(), protocols::minimization_packing::EnergyCutRotamerTrialsMinMover::setup_energycut_task(), core::scoring::methods::WaterAdductHBondEnergy::setup_for_derivatives(), core::scoring::FACTSPotential::setup_for_derivatives(), core::scoring::methods::MembraneEnvSmoothEnergy::setup_for_derivatives(), core::scoring::methods::EnvSmoothEnergy::setup_for_derivatives(), core::scoring::membrane::FaMPEnvSmoothEnergy::setup_for_derivatives(), core::scoring::methods::MultipoleElecEnergy::setup_for_derivatives(), core::scoring::methods::VdWTinkerEnergy::setup_for_derivatives(), core::scoring::methods::SASAEnergy::setup_for_derivatives(), core::scoring::etable::BaseEtableEnergy< Derived >::setup_for_derivatives(), core::scoring::methods::MMLJEnergyInter::setup_for_minimizing(), core::scoring::rna::RNA_FullAtomStackingEnergy::setup_for_minimizing(), core::scoring::elec::RNA_FA_ElecEnergy::setup_for_minimizing(), core::scoring::methods::LK_PolarNonPolarEnergy::setup_for_minimizing(), core::scoring::elec::FA_GrpElecEnergy::setup_for_minimizing(), core::scoring::etable::BaseEtableEnergy< Derived >::setup_for_minimizing(), core::scoring::elec::FA_ElecEnergy::setup_for_minimizing(), core::scoring::rna::StackElecEnergy::setup_for_minimizing(), core::scoring::ScoreFunction::setup_for_minimizing_for_node(), core::scoring::methods::MMLJEnergyIntra::setup_for_minimizing_for_residue(), core::scoring::hbonds::HBondEnergy::setup_for_minimizing_for_residue(), core::scoring::etable::BaseEtableEnergy< Derived >::setup_for_minimizing_for_residue(), core::scoring::elec::RNA_FA_ElecEnergy::setup_for_minimizing_for_residue_pair(), core::scoring::rna::StackElecEnergy::setup_for_minimizing_for_residue_pair(), core::scoring::elec::FA_GrpElecEnergy::setup_for_minimizing_for_residue_pair(), core::scoring::etable::BaseEtableEnergy< Derived >::setup_for_minimizing_for_residue_pair(), core::scoring::elec::FA_ElecEnergy::setup_for_minimizing_for_residue_pair(), core::scoring::geometric_solvation::ContextDependentGeometricSolEnergy::setup_for_packing(), core::scoring::methods::MMLJEnergyInter::setup_for_packing(), core::scoring::hbonds::HBondEnergy::setup_for_packing(), core::scoring::lkball::LK_BallEnergy::setup_for_packing(), core::scoring::elec::FA_ElecEnergy::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::rna::RNA_SuiteEnergy::setup_for_scoring(), core::scoring::rna::TNA_SuiteEnergy::setup_for_scoring(), core::scoring::disulfides::DisulfideMatchingEnergy::setup_for_scoring(), core::scoring::disulfides::CentroidDisulfideEnergy::setup_for_scoring(), core::scoring::methods::P_AA_ss_Energy::setup_for_scoring(), core::scoring::rna::RNA_StubCoordinateEnergy::setup_for_scoring(), core::scoring::rna::RNA_FullAtomStackingEnergy::setup_for_scoring(), core::scoring::FACTSPotential::setup_for_scoring(), core::scoring::rna::StackElecEnergy::setup_for_scoring(), core::scoring::methods::GenericBondedEnergy::setup_for_scoring(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::setup_for_scoring(), core::scoring::electron_density::FastDensEnergy::setup_for_scoring(), core::scoring::electron_density::ElecDensCenEnergy::setup_for_scoring(), core::scoring::electron_density::ElecDensEnergy::setup_for_scoring(), core::scoring::methods::dfire::DFIRE_Energy::setup_for_scoring(), core::scoring::geometric_solvation::ContextDependentGeometricSolEnergy::setup_for_scoring(), core::scoring::methods::LK_PolarNonPolarEnergy::setup_for_scoring(), core::scoring::hbonds::NPDHBondEnergy::setup_for_scoring(), core::scoring::elec::RNA_FA_ElecEnergy::setup_for_scoring(), core::scoring::methods::VdWTinkerEnergy::setup_for_scoring(), core::scoring::methods::MultipoleElecEnergy::setup_for_scoring(), core::scoring::methods::SASAEnergy::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::elec::FA_GrpElecEnergy::setup_for_scoring(), core::scoring::etable::BaseEtableEnergy< Derived >::setup_for_scoring(), core::scoring::elec::FA_ElecEnergy::setup_for_scoring(), core::scoring::electron_density_atomwise::ElecDensAtomwiseEnergy::setup_for_scoring(), core::scoring::methods::CartesianBondedEnergy::setup_for_scoring(), core::scoring::ScoreFunction::setup_for_scoring(), core::scoring::MultipoleElecPotential::setup_for_scoring(), protocols::ncbb::SecStructMinimizeMultiFunc::setup_minimization_graph(), protocols::rna::denovo::movers::RNA_DeNovoMasterMover::setup_rnp_fold_tree(), core::scoring::ScoreFunction::show(), core::scoring::ScoreFunction::show_line(), protocols::hydrate::show_water_hb_network(), 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::symmetry::SymmetrySlider::slide_score(), protocols::flexpep_docking::FlexPepDockingProtocol::SlideIntoContact(), 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(), core::scoring::ScoreFunction::sym_eval_long_range_twobody_energies(), core::scoring::ScoreFunction::sym_eval_onebody_energies(), core::scoring::ScoreFunction::sym_eval_twobody_neighbor_energies(), core::scoring::ScoreFunction::sym_setup_for_derivatives(), core::scoring::ScoreFunction::sym_setup_for_minimizing(), protocols::scoring::Interface::symmetric_protein_calculate(), core::scoring::ScoreFunction::symmetrical_allow_hbonds(), protocols::symmetry::SymmetrySlider::SymmetrySlider(), core::optimization::symmetry::SymMinimizerMap::SymMinimizerMap(), protocols::canonical_sampling::TemperatureController::temperature_move(), core::pose::total_energy_from_pose(), protocols::hbnet::HBNet::traverse_native(), protocols::vip::VIP_Mover::try_point_mutants(), protocols::canonical_sampling::MetricRecorder::update_after_boltzmann(), protocols::rna::setup::RNA_CSA_JobDistributor::update_bank(), core::scoring::FACTSPoseInfo::update_enumeration_shell(), core::scoring::methods::MMLJEnergyInter::update_residue_for_packing(), core::scoring::hbonds::HBondEnergy::update_residue_for_packing(), core::scoring::lkball::LK_BallEnergy::update_residue_for_packing(), core::scoring::etable::BaseEtableEnergy< Derived >::update_residue_for_packing(), core::scoring::elec::FA_ElecEnergy::update_residue_for_packing(), core::scoring::rna::RNA_LowResolutionPotential::update_rna_base_base_interactions(), protocols::hydrate::water_specific_hbond_energy(), protocols::features::ProteinSilentReport::write_full_report(), protocols::canonical_sampling::PDBTrajectoryRecorder::write_model(), protocols::features::strand_assembly::write_p_aa_pp_of_AAs_to_a_file(), and protocols::features::strand_assembly::write_rama_of_AAs_to_a_file().

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(), size(), and torsion().

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::rna::movers::RNAThreadAndMinimizeMover::accomodate_length_change(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::add_aa_virt_rsd_as_root(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::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::splice::Splice::add_coordinate_constraints(), protocols::splice::SpliceManager::add_coordinate_constraints(), core::scoring::constraints::add_coordinate_constraints(), protocols::stepwise::modeler::align::StepWisePoseAligner::add_coordinate_constraints_from_map(), protocols::relax::add_coordinate_constraints_to_pose(), protocols::loops::add_coordinate_constraints_to_pose(), protocols::forge::methods::add_cutpoint_variants(), protocols::protein_interface_design::movers::SetAtomTree::add_cutpoint_variants(), protocols::loops::add_cutpoint_variants(), protocols::chemically_conjugated_docking::add_extra_bodies(), protocols::membrane::symmetry::SymmetricAddMembraneMover::add_membrane_virtual(), protocols::membrane::AddMembraneMover::add_membrane_virtual(), protocols::cryst::MakeLatticeMover::add_monomers_to_lattice(), protocols::cryst::MakeLayerMover::add_monomers_to_layer(), core::import_pose::RNA_JumpMover::add_new_RNA_jump(), protocols::abinitio::MembraneAbinitio::add_spanning_region(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::add_terminal_res_repulsion(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::add_terminal_res_repulsion(), protocols::denovo_design::components::add_to_pose(), protocols::rna::movers::ErraserMinimizerMover::add_virtual_res(), protocols::toolbox::sample_around::add_virtual_res(), core::import_pose::add_virtual_sugar_res(), core::pose::addVirtualResAsRoot(), protocols::topology_broker::MembraneTopologyClaimer::addVirtualResAsRootMembrane(), protocols::splice::SpliceInAntibody::adjust_template_jump(), protocols::stepwise::modeler::align::align_pose_and_add_rmsd_constraints(), protocols::denovo_design::movers::AlignResiduesMover::align_residues(), protocols::antibody_legacy::Antibody::all_cdr_fold_tree(), protocols::antibody_legacy::AntibodyModeler::all_cdr_VL_VH_fold_tree(), protocols::chemically_conjugated_docking::UBQ_GTPaseMover::analyze_and_filter(), protocols::antibody_legacy::CDRH3Modeler::antibody_modeling_insert_ter(), core::import_pose::RNA_HelixAssembler::append_Aform_residue(), protocols::ligand_docking::LigandDockProtocol::append_ligand_docking_scores(), protocols::fold_from_loops::utils::append_pose_to_pose_keep_fold_tree(), protocols::stepwise::monte_carlo::mover::AddMover::append_residue(), protocols::pose_metric_calculators::append_rsd_by_jump_near_atom(), protocols::RBSegmentRelaxImpl::apply(), protocols::simple_moves::ResetFoldTree::apply(), protocols::loops::FoldTreeFromLoops::apply(), protocols::simple_moves::VirtualRootMover::apply(), protocols::protein_interface_design::movers::AddChainBreak::apply(), protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspots::apply(), protocols::seeded_abinitio::CoordinateCst::apply(), protocols::seeded_abinitio::DefineMovableLoops::apply(), protocols::simple_moves::LoadPDBMover::apply(), protocols::protein_interface_design::movers::LoopLengthChange::apply(), protocols::protein_interface_design::movers::DockAndRetrieveSidechains::apply(), protocols::cyclic_peptide::PeptideStubMover::apply(), protocols::seeded_abinitio::CAcstGenerator::apply(), protocols::seeded_abinitio::GrowPeptides::apply(), protocols::simple_moves::ChainSplitMover::apply(), protocols::simple_moves::SwitchChainOrderMover::apply(), protocols::star::StarAbinitio::apply(), protocols::medal::MedalExchangeMover::apply(), protocols::protein_interface_design::movers::SetAtomTree::apply(), protocols::rbsegment_relax::MakeStarTopologyMover::apply(), protocols::rigid::RigidBodyMotionMover::apply(), protocols::antibody::CloseOneCDRLoop::apply(), protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover::apply(), protocols::protein_interface_design::movers::SpinMover::apply(), protocols::simple_moves::PeptideStapleMover::apply(), protocols::seeded_abinitio::CloseFold::apply(), protocols::seeded_abinitio::SeedFoldTree::apply(), protocols::stepwise::modeler::precomputed::PrecomputedLibraryMover::apply(), protocols::enzdes::BackboneSampler::apply(), protocols::loops::loop_closure::ccd::ShortLoopClosure::apply(), protocols::medal::MedalMover::apply(), protocols::dna::SeparateDnaFromNonDna::apply(), protocols::fold_from_loops::movers::DisplayPoseLabelsMover::apply(), protocols::topology_broker::RigidBodyRandomTMHMover::apply(), protocols::antibody::GraftedStemOptimizer::apply(), protocols::metal_interface::ZincHeterodimerMover::apply(), protocols::nonlocal::SheetTranslate::apply(), protocols::rigid::RotateJumpAxisMover::apply(), protocols::dna::DesignProteinBackboneAroundDNA::apply(), protocols::domain_assembly::AssembleLinkerMover::apply(), protocols::magnesium::MgMonteCarlo::apply(), protocols::nonlocal::HelixRotate::apply(), protocols::fold_from_loops::movers::NubInitioLoopClosureMover::apply(), protocols::ligand_docking::FinalMinimizer::apply(), protocols::antibody::H3CterInsert::apply(), protocols::constraint_generator::CoordinateConstraintGenerator::apply(), protocols::rna::denovo::movers::RNA_HelixMover::apply(), protocols::simple_moves::MissingDensityToJumpMover::apply(), protocols::protein_interface_design::movers::BackrubDDMover::apply(), protocols::backrub::BackrubProtocol::apply(), protocols::simple_ddg::ddG::apply(), protocols::ligand_docking::MinimizeBackbone::apply(), protocols::antibody::AntibodyModelerProtocol::apply(), protocols::rbsegment_relax::OptimizeThreadingMover::apply(), core::select::jump_selector::InterchainJumpSelector::apply(), protocols::indel::IndelOptimizationMover::apply(), protocols::protein_interface_design::movers::DesignMinimizeHbonds::apply(), protocols::abinitio::AbrelaxMover::apply(), protocols::splice::SpliceIn::apply(), protocols::loops::loop_mover::IndependentLoopMover::apply(), protocols::denovo_design::movers::SealFoldTreeMover::apply(), protocols::splice::SpliceInTail::apply(), protocols::splice::SpliceOut::apply(), core::select::jump_selector::JumpIndexSelector::apply(), protocols::rna::denovo::coarse::CoarseRNA_LoopCloser::apply(), protocols::antibody::H3PerturbCCD::apply(), protocols::rbsegment_relax::RBSegmentRelax::apply(), protocols::simple_moves::SetTorsion::apply(), protocols::splice::TailSegmentMover::apply(), protocols::fold_from_loops::selectors::CutpointResidueSelector::apply(), core::select::residue_selector::JumpDownstreamSelector::apply(), core::select::residue_selector::JumpUpstreamSelector::apply(), protocols::rna::movers::RNAIdealizeMover::apply(), protocols::floppy_tail::FloppyTailMover::apply(), protocols::moves::ChangeFoldTreeMover::apply(), protocols::flexpep_docking::FlexPepDockingProtocol::apply(), protocols::enzdes::EnzRepackMinimize::apply(), protocols::nonlocal::BiasedFragmentMover::apply(), protocols::protein_interface_design::movers::LoopMoverFromCommandLine::apply(), protocols::denovo_design::components::RemodelLoopMoverPoseFolder::apply(), protocols::abinitio::abscript::AbscriptLoopCloserCM::apply(), protocols::chemically_conjugated_docking::UBQ_GTPaseMover::apply(), protocols::hybridization::CartesianHybridize::apply(), protocols::protein_interface_design::movers::LoopRemodel::apply(), protocols::rna::movers::ErraserMinimizerMover::apply(), protocols::denovo_design::movers::FoldTreeFromFoldGraphMover::apply(), protocols::protein_interface_design::movers::TryRotamers::apply(), protocols::hybridization::DomainAssembly::apply(), protocols::ligand_docking::LigandDockProtocol::apply(), protocols::simple_task_operations::DockingNoRepack1::apply(), protocols::membrane::SetMembranePositionMover::apply(), protocols::abinitio::KinematicTaskControl::apply(), protocols::membrane::RandomPositionRotationMover::apply(), protocols::cryst::UpdateCrystInfo::apply(), protocols::splice::Splice::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::apply(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::apply(), protocols::denovo_design::movers::RotateSegmentMover::apply(), protocols::docking::DockMCMProtocol::apply(), protocols::membrane::OptimizeProteinEmbeddingMover::apply(), protocols::membrane::MPMutateRelaxMover::apply(), protocols::abinitio::KinematicAbinitio::apply(), protocols::membrane::MembranePositionFromTopologyMover::apply(), protocols::backrub::BackrubMover::apply(), protocols::docking::membrane::QuickRelaxPartnersSeparately::apply(), protocols::nonlocal::SingleFragmentMover::apply(), protocols::docking::membrane::MPFindInterfaceMover::apply(), protocols::backrub::BackrubSidechainMover::apply(), protocols::relax::membrane::MPRangeRelaxMover::apply(), protocols::simple_moves::ChangeAndResetFoldTreeMover::apply(), protocols::docking::InterfaceSidechainMinMover::apply(), protocols::enzdes::DetectProteinLigandInterface::apply(), protocols::membrane::OptimizeMembranePositionMover::apply(), protocols::docking::TemperedDocking::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::simple_task_operations::DockingNoRepack2::apply(), protocols::membrane::AddMPLigandMover::apply(), protocols::membrane::MPQuickRelaxMover::apply(), protocols::relax::RangeRelaxMover::apply(), protocols::abinitio::FoldConstraints::apply(), protocols::protein_interface_design::movers::PlaceStubMover::apply(), protocols::idealize::IdealizeMover::apply(), protocols::docking::membrane::MPDockingSetupMover::apply(), protocols::fold_from_loops::movers::SplitAndMixPoseMover::apply(), protocols::abinitio::ConstraintFragmentSampler::apply(), protocols::membrane::FlipMover::apply(), protocols::rna::movers::RNAThreadAndMinimizeMover::apply(), protocols::membrane::TiltMover::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::membrane::SpinAroundPartnerMover::apply(), protocols::membrane::TransformIntoMembraneMover::apply(), protocols::loop_modeling::LoopMover::apply(), protocols::membrane::TranslationMover::apply(), protocols::docking::membrane::MPDockingMover::apply(), protocols::membrane::AddMembraneMover::apply(), protocols::membrane::RandomPositionTranslationMover::apply(), protocols::fldsgn::CircularPermutation::apply(), protocols::cryst::MakeLayerMover::apply(), protocols::relax::FastRelax::apply(), protocols::simple_task_operations::RestrictToInterface::apply(), protocols::topology_broker::TopologyBroker::apply(), protocols::docking::DockingProtocol::apply(), core::fragment::DownJumpSRFD::apply(), protocols::abinitio::JumpingFoldConstraintsWrapper::apply(), protocols::antibody_legacy::LoopRlxMover::apply(), protocols::membrane::RotationMover::apply(), protocols::LoopRefine::apply(), protocols::cryst::MakeLatticeMover::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::membrane::TranslationRotationMover::apply(), protocols::forge::remodel::RemodelLoopMover::apply(), protocols::forge::components::VarLengthBuild::apply(), protocols::loop_grower::LoopGrower::apply(), protocols::rna::denovo::coarse::CoarseRNA_LoopCloser::apply_after_jump_change(), protocols::backbone_moves::local_backbone_mover::GapCloser::apply_closure(), protocols::fold_from_loops::movers::NubInitioLoopClosureMover::apply_closure_trust(), protocols::hybridization::CartesianSampler::apply_fragcsts(), protocols::simple_moves::WobbleMover::apply_fragment(), protocols::simple_filters::EnergyPerResidueFilter::apply_helper(), protocols::loops::apply_sequence_mapping(), protocols::antibody::design::AntibodyDesignMover::apply_to_cdr(), protocols::loophash::BackboneSegment::apply_to_pose(), core::pose::rna::apply_virtual_rna_residue_variant_type(), core::optimization::symmetry::atom_tree_get_atompairE_deriv(), protocols::fold_from_loops::utils::attach_n_and_c_unfolded_poses_to_pose(), protocols::abinitio::abscript::AbscriptLoopCloserCM::attempt_idealize(), protocols::idealize::basic_idealize(), protocols::forge::remodel::RemodelLoopMover::boost_closure_stage(), protocols::ligand_docking::MoveMapBuilder::build(), protocols::metal_interface::MatchGrafter::build_combined_pose_with_zinc_overlay(), protocols::topology_broker::MembraneTopologyClaimer::build_fold_tree(), protocols::topology_broker::TMHTopologySamplerClaimer::build_fold_tree(), protocols::cryst::MakeLatticeMover::build_lattice_of_virtuals(), protocols::cryst::MakeLayerMover::build_layer_of_virtuals(), core::import_pose::build_pose_as_is2(), protocols::LoopRebuild::build_random_loops(), core::scoring::sc::MolecularSurfaceCalculator::Calc(), protocols::docking::calc_CA_Irmsd(), protocols::docking::calc_Fnat(), protocols::docking::calc_Fnonnat(), protocols::docking::calc_Irmsd(), protocols::docking::calc_Irmsd_legacy(), protocols::docking::calc_Lrmsd(), protocols::docking::calc_P1rmsd(), protocols::docking::calc_P2rmsd(), protocols::scoring::Interface::calculate(), protocols::analysis::LoopAnalyzerMover::calculate_all_chainbreaks(), protocols::abinitio::abscript::AbscriptMover::calculate_iterations(), protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::calculate_jump(), protocols::splice::SpliceOut::ccd_mover(), protocols::geometry::centroids_by_jump(), protocols::geometry::centroids_by_jump_int(), protocols::hybridization::FragmentBiasAssigner::chainbreak(), protocols::topology_broker::TopologyBroker::check_chainbreak_variants(), core::import_pose::libraries::ChunkSet::check_fold_tree_OK(), core::import_pose::libraries::RNA_ChunkLibrary::check_fold_tree_OK(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::check_for_intramolecular_submotif_jump(), core::scoring::loop_graph::LoopGraph::check_for_unexpected_cutpoints(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::check_from_scratch(), protocols::stepwise::modeler::check_jump_to_next_residue_in_chain(), protocols::stepwise::modeler::check_jump_to_previous_residue_in_chain(), protocols::abinitio::FragmentSampler::check_loops(), core::scoring::rna::check_rna_loop(), protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::check_screen(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::check_superimpose_res(), protocols::jumping::close_chainbreaks(), protocols::antibody_legacy::CloseOneMover::close_one_loop_stem_helper(), protocols::abinitio::AbrelaxMover::close_with_idealization(), protocols::matdes::InterfacePackingFilter::compute(), protocols::protein_interface_design::filters::AtomicContactCountFilter::compute(), protocols::matdes::OligomericAverageDegreeFilter::compute(), core::scoring::ResidualDipolarCoupling::compute_dipscore(), core::scoring::ResidualDipolarCoupling::compute_dipscore_nls(), protocols::hybridization::FragmentBiasAssigner::compute_frag_bias(), protocols::simple_filters::InterfaceHbondsFilter::compute_hbonds(), 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::denovo_design::construct_poly_ala_pose(), protocols::loop_grower::LoopGrower::coordinate_filter(), protocols::protein_interface_design::movers::copy_hotspot_to_pose(), protocols::topology_broker::copy_internal_coords(), protocols::splice::Splice::copy_stretch(), protocols::rna::denovo::RNA_FragmentMonteCarlo::copy_structure_keep_fold_tree(), protocols::metal_interface::ZincHeterodimerMover::copy_to_centroid(), core::pose::correctly_add_cutpoint_variants(), 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_cutpoints(), 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::hybridization::create_fragment_set_no_ssbias(), protocols::membrane::create_membrane_docking_foldtree_from_partners(), protocols::membrane::create_membrane_foldtree_from_anchors(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::create_pose_from_input_poses(), protocols::rna::denovo::create_rna_vall_torsions(), protocols::membrane::create_specific_membrane_foldtree(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::create_starting_pose(), core::pose::create_subpose(), protocols::enzdes::EnzdesBaseProtocol::cst_minimize(), core::import_pose::define_chains(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::define_moving_res(), protocols::peptide_deriver::PeptideDeriverFilter::derive_peptide(), protocols::forge::components::BDR::design_refine(), protocols::forge::remodel::RemodelMover::design_refine(), protocols::forge::remodel::RemodelMover::design_refine_cart_relax(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::determine_loop(), protocols::enzdes::DiversifyStoredRBConfs::diversify_all_confs(), protocols::stepwise::modeler::align::StepWisePoseAligner::do_checks(), protocols::medal::MedalMover::do_loop_closure(), protocols::simple_ddg::ddG::do_minimize(), protocols::cyclic_peptide::SymmetricCycpepAlign::do_trim_to_single_repeat(), protocols::antibody::design::GeneralAntibodyModeler::dock_high_res(), protocols::antibody::design::GeneralAntibodyModeler::dock_low_res(), protocols::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::fold_from_loops::NubInitioMover::dump_centroid(), 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_ddg::ddG::duplicate_waters_across_jump(), protocols::environment::Environment::end(), protocols::simple_moves::ClassicFragmentMover::end_bias_check(), protocols::stepwise::monte_carlo::mover::ensure_appropriate_foldtree_for_move(), 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_residue_pair_derivatives(), protocols::LoopRebuild::extend_barcode_regions_if_chain_break(), protocols::antibody::design::GeneralAntibodyModeler::extend_CDR(), 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::rna::denovo::coarse::CoarseRNA_LoopCloser::figure_out_dof_ids_and_offsets(), protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger::figure_out_loop(), protocols::stepwise::modeler::figure_out_moving_chain_break_res(), protocols::stepwise::modeler::figure_out_moving_chain_breaks(), protocols::toolbox::rigid_body::figure_out_moving_partition_res(), protocols::stepwise::modeler::figure_out_moving_partition_res_for_jump(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::figure_out_partition_definition(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::figure_out_Prepend_Internal(), protocols::stepwise::modeler::protein::figure_out_protein_modeling_info(), core::pose::rna::figure_out_reasonable_rna_fold_tree(), protocols::stepwise::modeler::working_parameters::figure_out_rebuild_bulge_mode(), protocols::toolbox::rigid_body::figure_out_reference_res_for_jump(), protocols::stepwise::modeler::figure_out_reference_res_for_suite(), protocols::stepwise::modeler::figure_out_root_and_moving_partition_res(), protocols::rna::denovo::coarse::CoarseRNA_LoopCloser::figure_out_which_cutpoints_were_affected(), protocols::hotspot_hashing::HotspotStubSet::fill(), core::pose::rna::fill_in_default_jump_atoms(), core::io::silent::ScoreJumpFileSilentStruct::fill_pose(), core::io::silent::RigidBodySilentStruct::fill_pose(), core::io::silent::BinarySilentStruct::fill_pose(), core::io::silent::RNA_SilentStruct::fill_pose(), core::io::silent::ProteinSilentStruct_Template< T >::fill_pose(), protocols::loop_grower::LoopComparator::fill_pose(), core::io::silent::ScoreJumpFileSilentStruct::fill_struct(), core::io::silent::RigidBodySilentStruct::fill_struct(), core::io::silent::BinarySilentStruct::fill_struct(), core::io::silent::ProteinSilentStruct_Template< T >::fill_struct(), core::io::silent::RNA_SilentStruct::fill_struct(), protocols::residue_optimization::MetapatchEnumeration::final_sampling(), protocols::antibody::RefineBetaBarrel::finalize_setup(), protocols::docking::DockingEnsemblePrepackProtocol::finalize_setup(), protocols::antibody::CDRsMinPackMin::finalize_setup(), protocols::docking::membrane::QuickRelaxPartnersSeparately::finalize_setup(), protocols::antibody::H3RefineCCD::finalize_setup(), protocols::docking::TemperedDocking::finalize_setup(), protocols::relax::RangeRelaxMover::finalize_setup(), protocols::antibody::AntibodyModelerProtocol::finalize_setup(), protocols::docking::DockingProtocol::finalize_setup(), core::scoring::methods::ChainbreakEnergy::finalize_total_energy(), core::scoring::methods::CenPairMotifDegreeEnergy::finalize_total_energy(), core::scoring::methods::CenPairMotifEnergy::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::magnesium::find_bound_waters_that_are_daughters_in_fold_tree(), protocols::forge::methods::find_cutpoint(), protocols::stepwise::modeler::find_downstream_connection_res(), protocols::ligand_docking::LigandBaseProtocol::find_interface_backbone(), protocols::ligand_docking::LigandBaseProtocol::find_interface_rsds(), core::select::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::magnesium::MgHydrater::fix_fold_tree_in_excised_pose_for_mg_bound_waters(), protocols::stepwise::modeler::fix_protein_jump_atom(), protocols::stepwise::modeler::fix_up_jump_atoms(), protocols::magnesium::fix_water_jump(), protocols::abinitio::AbrelaxApplication::fold(), protocols::splice::SpliceManager::fold_tree(), protocols::splice::Splice::fold_tree(), protocols::forge::methods::fold_tree_from_loops(), protocols::loops::fold_tree_from_loops(), protocols::simple_moves::CutChainMover::foldTree(), protocols::stepwise::modeler::freeze_waters(), protocols::loop_grower::LoopGrower::GDThatonative(), protocols::topology_broker::MembraneTopologyClaimer::generate_claims(), protocols::topology_broker::AsymFoldandDockClaimer::generate_claims(), protocols::relax::AtomCoordinateCstMover::generate_constraints(), protocols::enzdes::EnzdesFlexBBProtocol::generate_ensemble_for_region(), protocols::loop_grower::SheetSampler::generate_jump_frags(), protocols::stepwise::modeler::rna::get_anchor_res(), core::import_pose::get_anchor_rsd(), protocols::stepwise::sampler::protein::ProteinBetaAntiParallelStepWiseSampler::get_antiparallel_beta_jumps(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_attachments(), protocols::magnesium::get_bound_water_res(), protocols::stepwise::modeler::align::StepWisePoseAligner::get_calc_rms_atom_id_map(), core::pose::get_chain_from_jump_id(), core::pose::get_chain_id_from_jump_id(), core::import_pose::RNA_HelixAssembler::get_cutpoint(), protocols::rna::denovo::get_default_allowed_bulge_res(), core::pose::get_definite_terminal_root(), protocols::splice::RBOutMover::get_disulf_jump(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_docking_split_move_elements(), protocols::stepwise::modeler::get_domain_boundary_res(), protocols::stepwise::modeler::get_domain_boundary_suites(), protocols::stepwise::modeler::get_endpoints_from_pose(), protocols::topology_broker::MembraneTopologyClaimer::get_fold_tree(), protocols::topology_broker::TMHTopologySamplerClaimer::get_fold_tree(), protocols::fldsgn::potentials::sspot::get_foldtree_seqsep(), core::scoring::SecondaryStructurePotential::get_foldtree_seqsep(), core::pose::symmetry::get_full_intracomponent_and_neighbor_subs(), protocols::docking::EllipsoidalRandomizationMover::get_interface_residues(), core::pose::symmetry::get_intracomponent_and_neighbor_subs(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_intramolecular_add_move_elements(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_intramolecular_split_move_elements(), core::pose::get_jump_ids_from_chain(), core::pose::get_jump_ids_from_chain_ids(), protocols::cyclic_peptide::CrosslinkerMover::get_jump_index_for_crosslinker(), protocols::cyclic_peptide::CrosslinkerMover::get_jump_indices_for_symmetric_crosslinker(), protocols::stepwise::modeler::get_jump_partners_from_pose(), protocols::ligand_docking::get_ligand_grid_scores(), protocols::ligand_docking::LigandBaseProtocol::get_ligand_id(), protocols::hybridization::InsertChunkMover::get_local_sequence_mapping(), protocols::stepwise::monte_carlo::submotif::SubMotifLibrary::get_matches_for_one_submotif_sequence_set(), protocols::magnesium::MgMinimizer::get_mg_hoh_minimize_move_map(), protocols::stepwise::modeler::get_partition_definition(), protocols::stepwise::modeler::get_partition_definition_by_jump(), protocols::stepwise::modeler::rna::get_partition_definition_floating_base(), protocols::stepwise::modeler::rna::sugar::get_possible_reference_res_list_from_pose_without_fold_tree(), protocols::recces::sampler::get_recces_turner_sampler_from_secstruct(), protocols::recces::sampler::get_recces_turner_sampler_legacy(), protocols::stepwise::monte_carlo::mover::ResampleMover::get_remodel_res(), core::import_pose::RNA_HelixAssembler::get_rid_of_capping_base_pairs(), core::pose::rna::get_rigid_body_jumps(), protocols::stepwise::modeler::align::StepWisePoseAligner::get_rmsd_res_and_superimpose_res_in_pose(), protocols::stepwise::modeler::align::StepWisePoseAligner::get_root_triad_atom_id_map(), protocols::loophash::get_rt_over_leap(), protocols::loophash::get_rt_over_leap_fast(), core::scoring::methods::SSElementMotifContactEnergy::get_SSelements_in_contact(), protocols::simple_filters::SSElementMotifContactFilter::get_SSelements_in_contact(), protocols::stepwise::monte_carlo::submotif::SubMotifLibrary::get_submotif_sequence_set(), core::pose::symmetry::get_symdof_subunits(), protocols::hybridization::CartesianSampler::get_transform(), protocols::stepwise::modeler::get_unique_connection_res(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::get_working_pose(), core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_foldtree(), protocols::seeded_abinitio::GrowPeptides::grow_from_vertices(), protocols::loops::Loops::grow_loop(), protocols::loops::Loops::grow_loop_away_from_sheets(), protocols::rbsegment_relax::guess_rbsegs_from_pose(), protocols::stepwise::modeler::precomputed::PrecomputedLibraryMover::has_precomputed_move(), protocols::seeded_abinitio::SegmentHybridizer::hybridize(), protocols::loop_modeling::LoopBuilder::idealize_loop(), protocols::forge::remodel::RemodelLoopMover::independent_stage(), protocols::topology_broker::FragmentJumpClaimer::init_jumps(), protocols::floppy_tail::FloppyTailMover::init_on_new_input(), protocols::residue_optimization::MetapatchEnumeration::initial_sampling(), protocols::abinitio::abscript::RigidChunkCM::initialize(), protocols::cryst::DockLatticeMover::initialize(), protocols::hybridization::HybridizeProtocol::initialize_and_sample_loops(), protocols::topology_broker::TopologyBroker::initialize_cuts(), protocols::topology_broker::BasicJumpClaimer::initialize_dofs(), protocols::topology_broker::AsymFoldandDockClaimer::initialize_dofs(), protocols::topology_broker::FragmentClaimer::initialize_dofs(), protocols::topology_broker::TopologyBroker::initialize_dofs(), protocols::stepwise::modeler::rna::o2prime::O2PrimePacker::initialize_o2prime_green_packer(), protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::initialize_phosphate_move_list(), protocols::recces::sampler::initialize_sampler(), protocols::backrub::BackrubMover::initialize_simulation(), protocols::backrub::BackrubSidechainMover::initialize_simulation(), protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::Initialize_terminal_res(), protocols::recces::sampler::initialize_thermal_sampler(), core::scoring::motif::Xfrag::insert(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::insert_base_pair_jumps(), protocols::grafting::insert_pose_into_pose(), core::import_pose::libraries::ChunkSet::insert_protein_chunk_into_pose(), protocols::forge::remodel::RemodelLoopMover::insert_random_smallestmer_per_loop(), protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::instantiate_sugars_at_cutpoint_closed(), core::pose::symmetry::intracomponent_contact(), core::pose::rna::is_cutpoint_open(), core::scoring::methods::is_lower_cutpoint(), core::pose::rna::is_torsion_valid(), core::scoring::methods::is_upper_cutpoint(), protocols::motif_grafting::movers::MotifGraftMover::join_two_poses_by_jump(), protocols::simple_filters::JumpEvaluator::JumpEvaluator(), protocols::forge::methods::jumps_and_cuts_from_pose(), protocols::forge::methods::linear_chainbreak(), protocols::denovo_design::linear_chainbreak(), protocols::features::PoseConformationFeatures::load_fold_tree(), protocols::stepwise::modeler::rna::sugar::look_for_jumps(), protocols::stepwise::modeler::rna::sugar::look_for_jumps_to_next(), protocols::stepwise::modeler::rna::sugar::look_for_jumps_to_previous(), protocols::stepwise::modeler::rna::sugar::look_for_non_jump_reference_to_next(), protocols::stepwise::modeler::rna::sugar::look_for_non_jump_reference_to_previous(), protocols::antibody::RefineOneCDRLoopCentroid::loop_centroid_relax(), protocols::antibody_legacy::CDRH3Modeler::loop_centroid_relax(), protocols::antibody_legacy::CDRH3Modeler::loop_fa_relax(), protocols::forge::remodel::RemodelLoopMover::loophash_stage(), core::optimization::symmetry::SymAtomTreeMinimizer::make_asymmetric_movemap(), core::import_pose::make_coarse_pose(), protocols::stepwise::modeler::make_cut_at_moving_suite(), protocols::fold_from_loops::movers::NubInitioLoopClosureMover::make_cutpoints_coherent_to_foldtree(), protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover::make_disjointed_foldtree(), protocols::fold_from_loops::movers::NubInitioLoopClosureMover::make_final_tree(), protocols::ligand_docking::LigandBaseProtocol::make_movemap(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::make_pose(), core::fragment::make_pose_from_frags(), protocols::analysis::InterfaceAnalyzerMover::make_separated_pose(), protocols::forge::methods::make_star_foldtree(), protocols::fibril::make_symmetric_fibril(), core::pose::symmetry::make_symmetric_movemap(), core::scoring::electron_density::ElectronDensity::matchRes(), protocols::recces::sampler::rna::MC_RNA_OneJump::MC_RNA_OneJump(), protocols::stepwise::modeler::merge_two_poses(), protocols::splice::SpliceOut::min_mover(), protocols::splice::min_seg(), protocols::forge::remodel::RemodelLigandHandler::minimize(), protocols::antibody::design::GeneralAntibodyModeler::minimize_cdrs(), protocols::antibody::design::GeneralAntibodyModeler::minimize_interface(), protocols::pose_creation::MergePDBatOverlapMover::minimize_overlap(), protocols::enzdes::EnzdesFlexibleRegion::minimize_region(), protocols::splice::SpliceIn::minimize_segment(), protocols::splice::SpliceOut::minimize_segment(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::minimize_sugar(), protocols::protein_interface_design::movers::PlaceOnLoop::minimize_toward_stub(), protocols::protein_interface_design::movers::MapHotspot::MinimizeHotspots(), protocols::protein_interface_design::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::stepwise::sampler::rna::modeler_sugar_at_five_prime(), protocols::stepwise::sampler::rna::modeler_sugar_at_three_prime(), protocols::forge::build::BuildManager::modify(), protocols::denovo_design::components::modify_ft_for_residue_insertion(), 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::topology_broker::TMHTopologySamplerClaimer::move_spans(), protocols::rna::movers::ErraserMinimizerMover::movemap_setup(), protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::moves_for_pose(), protocols::kinematic_closure::ClosureProblem::mutate_residues(), protocols::denovo_design::movers::new_jump_and_cutpoint(), protocols::abinitio::DoubleLayerKinematicAbinitio::new_kinematics(), protocols::abinitio::LoopJumpFoldCst::new_kinematics(), protocols::denovo_design::components::num_strands(), core::pose::operator<<(), protocols::stepwise::legacy::modeler::rna::output_fold_tree_info(), protocols::topology_broker::TMHTopologySamplerClaimer::output_membrane_vector(), protocols::stepwise::modeler::output_movemap(), protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo::output_silent_file(), core::pose::rna::output_stems(), protocols::forge::methods::overlap_chainbreak(), protocols::rbsegment_relax::MakeStarTopologyMover::parse_my_tag(), protocols::enzdes::PredesignPerturbMover::parse_my_tag(), core::pose::partition_pose_by_jump(), core::pose::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(), core::scoring::electron_density::FastDensEnergy::pose_is_setup_for_density_scoring(), protocols::simple_moves::CopyDofMover::pose_string(), protocols::fold_from_loops::NubInitioMover::post_process(), protocols::topology_broker::TMHTopologySamplerClaimer::pre_process(), protocols::abinitio::abscript::ConstraintPreparer::prepare(), protocols::constraint_generator::CoordinateConstraintGenerator::prepare_constraint_target_pose(), protocols::stepwise::monte_carlo::mover::TransientCutpointHandler::prepare_fold_tree_for_erraser(), protocols::constraints_additional::ConstraintEvaluator::prepare_pose(), protocols::abinitio::KinematicControl::prepare_pose_for_sampling(), core::import_pose::RNA_HelixAssembler::prepend_Aform_residue(), protocols::stepwise::monte_carlo::mover::AddMover::prepend_residue(), protocols::abinitio::AbrelaxApplication::process_decoy(), protocols::denovo_design::DisulfidizeMover::process_pose(), core::import_pose::put_in_cutpoint(), protocols::forge::methods::quadratic_chainbreak(), protocols::seeded_abinitio::CloseFold::quick_closure(), core::import_pose::RNA_JumpMover::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::backrub::read_fold_tree_from_file(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::read_input_pose_and_copy_dofs(), protocols::protein_interface_design::PatchdockReader::read_poses(), protocols::rbsegment_relax::OptimizeThreadingMover::rebuild_unaligned(), protocols::loop_grower::LoopGrower::refine_cycle(), protocols::protein_interface_design::movers::PlacementMinimizationMover::refresh_bbstub_constraints(), protocols::cryst::DockLatticeMover::regenerate_lattice(), protocols::antibody_legacy::AntibodyModeler::relax_cdrs(), protocols::antibody::design::GeneralAntibodyModeler::relax_cdrs(), protocols::antibody::design::GeneralAntibodyModeler::relax_interface(), protocols::stepwise::legacy::modeler::rna::remove_chain_break_jump_point(), protocols::toolbox::pose_manipulation::remove_chainbreaks_according_to_jumps(), protocols::jumping::remove_cut(), core::import_pose::remove_cutpoint_closed(), core::util::remove_cutpoint_variants(), protocols::forge::methods::remove_cutpoint_variants(), protocols::loops::remove_cutpoint_variants(), core::import_pose::remove_cutpoints_closed(), protocols::environment::Environment::remove_nonpermenant_features(), 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::membrane::reorder_membrane_foldtree(), protocols::antibody::design::GeneralAntibodyModeler::repack_antibody_interface(), protocols::antibody::design::GeneralAntibodyModeler::repack_antigen_ab_interface(), protocols::antibody::design::GeneralAntibodyModeler::repack_antigen_interface(), protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue(), protocols::forge::remodel::RemodelLoopMover::repeat_propagation(), protocols::simple_filters::PoseInfoFilter::report(), protocols::features::ProteinBondGeometryFeatures::report_interres_angles(), protocols::features::ProteinBondGeometryFeatures::report_interres_lengths(), protocols::fold_from_loops::utils::report_unfolded(), core::pose::reroot(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::reroot_fold_tree(), protocols::rna::denovo::RNA_FragmentMonteCarlo::reroot_pose_before_align_and_return_moving_res(), protocols::hybridization::HybridizeFoldtreeDynamic::reset(), protocols::rbsegment_relax::restore_pose_from_rbsegs(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::reverse_add_move(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::reverse_add_submotif_move(),