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chains_util.hh File Reference

Pose utilities. More...

#include <core/pose/Pose.fwd.hh>
#include <core/pose/util.tmpl.hh>
#include <core/pose/MiniPose.fwd.hh>
#include <core/types.hh>
#include <core/conformation/Residue.fwd.hh>
#include <core/chemical/ResidueType.fwd.hh>
#include <core/chemical/VariantType.hh>
#include <core/chemical/rings/AxEqDesignation.hh>
#include <core/id/AtomID.fwd.hh>
#include <core/id/AtomID_Map.fwd.hh>
#include <core/id/DOF_ID_Mask.fwd.hh>
#include <core/id/NamedAtomID.fwd.hh>
#include <core/id/NamedStubID.fwd.hh>
#include <core/id/TorsionID.fwd.hh>
#include <core/id/SequenceMapping.fwd.hh>
#include <core/io/StructFileRep.fwd.hh>
#include <core/kinematics/FoldTree.fwd.hh>
#include <core/kinematics/Jump.hh>
#include <core/kinematics/MoveMap.fwd.hh>
#include <core/kinematics/RT.fwd.hh>
#include <core/kinematics/tree/Atom.fwd.hh>
#include <core/scoring/ScoreType.hh>
#include <numeric/xyzVector.hh>
#include <utility/vector1.hh>
#include <map>
#include <set>

Namespaces

 core
 A class for reading in the atom type properties.
 
 core::pose
 

Typedefs

typedef std::set< int > core::pose::Jumps
 

Functions

void core::pose::jumps_from_pose (core::pose::Pose const &pose, Jumps &jumps)
 Retrieves jump information from <pose>, storing the result in <jumps>. Jumps are keyed by their jump id. More...
 
std::map< core::Size, char > core::pose::conf2pdb_chain (core::pose::Pose const &pose)
 get Conformation chain number -> PDBInfo chain mapping More...
 
utility::vector1< core::Sizecore::pose::get_chains (core::pose::Pose const &pose)
 Get all the chain numbers from conformation. More...
 
core::Size core::pose::chain_end_res (Pose const &pose, core::Size const chain)
 compute last residue number of a chain More...
 
utility::vector1< core::Sizecore::pose::chain_end_res (Pose const &pose)
 compute last residue numbers of all chains More...
 
utility::vector1< boolcore::pose::compute_unique_chains (Pose &pose)
 Compute uniq chains in a complex Returns a vector of pose length with true/false of uniq chain. More...
 
bool core::pose::renumber_pdbinfo_based_on_conf_chains (core::pose::Pose &pose, bool fix_chains, bool const start_from_existing_numbering, bool const keep_insertion_codes, bool const rotate_chain_ids)
 renumber PDBInfo based on Conformation chains; each chain starts from 1 More...
 
bool core::pose::has_chain (std::string const &chain, core::pose::Pose const &pose)
 Does the pose have a residue with the given chain letter. More...
 
bool core::pose::has_chain (char const &chain, core::pose::Pose const &pose)
 Does the pose have a residue with the given chain letter. More...
 
bool core::pose::has_chain (core::Size chain_id, core::pose::Pose const &pose)
 Does the pose have a residue with the given chain number. More...
 
utility::vector1< core::Sizecore::pose::get_chain_ids_from_chains (utility::vector1< std::string > const &chains, core::pose::Pose const &pose)
 Get all chain numbers for the residues with the given chain letters. More...
 
utility::vector1< core::Sizecore::pose::get_chain_ids_from_chains (utility::vector1< char > const &chains, core::pose::Pose const &pose)
 Get all chain numbers for the residues with the given chain letters. More...
 
utility::vector1< core::Sizecore::pose::get_chain_ids_from_chain (std::string const &chain, core::pose::Pose const &pose)
 Get all chain numbers for the residues with the given chain letter. More...
 
utility::vector1< core::Sizecore::pose::get_chain_ids_from_chain (char const &chain, core::pose::Pose const &pose)
 Get all chain numbers for the residues with the given chain letter. More...
 
core::Size core::pose::get_chain_id_from_chain (std::string const &chain, core::pose::Pose const &pose)
 Attempt to get the chain number which correspond to the given chain letter. More...
 
core::Size core::pose::get_chain_id_from_chain (char const &chain, core::pose::Pose const &pose)
 Attempt to get the chain number which correspond to the given chain letter. More...
 
char core::pose::get_chain_from_chain_id (core::Size const &chain_id, core::pose::Pose const &pose)
 Get the chain letter for the first residue in a given chain number. More...
 
std::set< core::Sizecore::pose::get_jump_ids_from_chain_ids (std::set< core::Size > const &chain_ids, core::pose::Pose const &pose)
 Attempt to get jump IDs which correspond to the given chain number. More...
 
core::Size core::pose::get_jump_id_from_chain_id (core::Size const &chain_id, core::pose::Pose const &pose)
 Attempt to get the jump number which correspond to the given chain number. More...
 
utility::vector1< core::Sizecore::pose::get_jump_ids_from_chain (char const &chain, core::pose::Pose const &pose)
 Get all the jump numbers for the given chain letter. More...
 
utility::vector1< core::Sizecore::pose::get_jump_ids_from_chain (std::string const &chain, core::pose::Pose const &pose)
 Get all the jump numbers for the given chain letter. More...
 
core::Size core::pose::get_jump_id_from_chain (std::string const &chain, core::pose::Pose const &pose)
 Get the jump number for the given chain letter. More...
 
core::Size core::pose::get_jump_id_from_chain (char const &chain, core::pose::Pose const &pose)
 Get the jump number for the given chain letter. More...
 
core::Size core::pose::get_chain_id_from_jump_id (core::Size const &jump_id, core::pose::Pose const &pose)
 Get the chain ID of the residue directly built by the given jump. More...
 
char core::pose::get_chain_from_jump_id (core::Size const &jump_id, core::pose::Pose const &pose)
 Get the chain letter of the chain built by the given jump. More...
 
utility::vector1< core::Sizecore::pose::get_resnums_for_chain (core::pose::Pose const &pose, char chain)
 Get a vector of all residues numbers which are represented by this chain letter. More...
 
utility::vector1< core::Sizecore::pose::get_resnums_for_chain_id (core::pose::Pose const &pose, core::Size chain_id)
 Get a vector of all residues numbers which are represented by this chain number. More...
 
core::conformation::ResidueCOPs core::pose::get_chain_residues (core::pose::Pose const &pose, core::Size chain_id)
 Get all residues which correspond to the given chain number. More...
 
core::conformation::ResidueCOPs core::pose::get_residues_from_chains (core::pose::Pose const &pose, utility::vector1< core::Size > const &chain_ids)
 Get all residues which correspond to the given chain numbers. More...
 
bool core::pose::res_in_chain (core::pose::Pose const &pose, core::Size resnum, std::string const &chain)
 Does this residue number have this chain letter? More...
 
core::Size core::pose::get_hash_from_chain (char const &chain, core::pose::Pose const &pose, std::string const &extra_label="")
 Get a value representing the position of all the atoms for residues with the given chain letter. More...
 
core::Size core::pose::get_hash_excluding_chain (char const &chain, core::pose::Pose const &pose, std::string const &extra_label="")
 Get a value representing the position of all the atoms for residues which don't have the given chain letter. More...
 
std::string core::pose::get_sha1_hash_from_chain (char const &chain, core::pose::Pose const &pose, std::string const &extra_label="")
 Get a value representing the position of all the atoms for residues with the given chain letter. More...
 
std::string core::pose::get_sha1_hash_from_chains (utility::vector1< std::string > const &chains, core::pose::Pose const &pose, std::string const &extra_label="")
 Get a value representing the position of all the atoms for residues with the given chain letters. More...
 
std::string core::pose::get_sha1_hash_excluding_chain (char const &chain, core::pose::Pose const &pose, std::string const &extra_label="")
 Get a value representing the position of all the atoms for residues which don't have the given chain letter. More...
 
std::string core::pose::get_sha1_hash_excluding_chains (utility::vector1< std::string > const &chains, core::pose::Pose const &pose, std::string const &extra_label="")
 Get a value representing the position of all the atoms for residues which don't have the given chain letter. More...
 
std::string core::pose::get_sha1_hash_excluding_chain (std::string const &chain, core::pose::Pose const &pose, std::string const &extra_label="")
 Get a value representing the position of all the atoms for residues which don't have the given chain letter. More...
 

Detailed Description

Pose utilities.

Author
Phil Bradley
Modified by Sergey Lyskov, Vikram K. Mulligan, Jared Adolf-Bryfogle