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/kinematics/FoldTree.hh>
#include <core/conformation/Residue.hh>
#include <basic/Tracer.hh>
#include <numeric/xyzVector.string.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 <algorithm>

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::Size >	core::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::Size >	core::pose::chain_end_res (Pose const &pose)
	compute last residue numbers of all chains More...
utility::vector1< bool >	core::pose::compute_unique_chains (Pose &pose)
	Compute uniq chains in a complex @detail 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::Size >	core::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::Size >	core::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::Size >	core::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::Size >	core::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::Size >	core::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::Size >	core::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::Size >	core::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::Size >	core::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::Size >	core::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_pos (PointPosition const &pos)
	Utility function for get_hash_from_chain() - get hash for an isolated position. 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...