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Namespaces | Functions
chains_util.cc File Reference
#include <core/pose/chains_util.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/Pose.hh>
#include <core/conformation/Conformation.hh>
#include <core/conformation/util.hh>
#include <core/id/DOF_ID_Map.hh>
#include <core/id/Exceptions.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/conformation/Residue.hh>
#include <basic/Tracer.hh>
#include <numeric/xyzVector.string.hh>
#include <utility/io/izstream.hh>
#include <utility/exit.hh>
#include <utility/string_constants.hh>
#include <utility/string_util.hh>
#include <utility/excn/Exceptions.hh>
#include <utility/vector1.hh>
#include <utility/vector1.functions.hh>
#include <cmath>
#include <iostream>
#include <algorithm>
#include <numeric>

Namespaces

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

Functions

static basic::Tracer core::pose::TR ("core.pose.util")
 
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...
 
void core::pose::conf2pdb_chain_default_map (core::pose::Pose const &pose, std::map< core::Size, char > &chainmap)
 
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_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...
 
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...