util.cc File Reference

Pose class utilities. More...

#include <core/pose/util.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/Pose.hh>
#include <core/pose/MiniPose.hh>
#include <core/pose/datacache/CacheableDataType.hh>
#include <core/pose/datacache/PositionConservedResiduesStore.hh>
#include <core/pose/util.tmpl.hh>
#include <core/pose/rna/util.hh>
#include <core/pose/full_model_info/FullModelInfo.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/ResidueType.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/VariantType.hh>
#include <core/chemical/carbohydrates/CarbohydrateInfo.hh>
#include <core/chemical/Patch.hh>
#include <core/chemical/PatchOperation.hh>
#include <core/conformation/Conformation.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/conformation/util.hh>
#include <core/id/DOF_ID_Map.hh>
#include <core/id/Exceptions.hh>
#include <core/id/NamedStubID.hh>
#include <core/id/NamedAtomID.hh>
#include <core/id/TorsionID.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/io/raw_data/DisulfideFile.hh>
#include <core/io/silent/BinarySilentStruct.hh>
#include <core/scoring/ScoreType.hh>
#include <core/scoring/Energies.hh>
#include <core/conformation/Residue.hh>
#include <core/id/SequenceMapping.hh>
#include <core/sequence/Sequence.hh>
#include <core/sequence/util.hh>
#include <basic/Tracer.hh>
#include <basic/datacache/BasicDataCache.hh>
#include <basic/datacache/CacheableString.hh>
#include <basic/datacache/CacheableStringFloatMap.hh>
#include <basic/datacache/CacheableStringMap.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <numeric/constants.hh>
#include <numeric/xyz.functions.hh>
#include <numeric/xyzVector.string.hh>
#include <utility/io/izstream.hh>
#include <utility/exit.hh>
#include <utility/string_util.hh>
#include <utility/excn/Exceptions.hh>
#include <utility/vector1.hh>
#include <cmath>
#include <iostream>
#include <ObjexxFCL/string.functions.hh>
#include <boost/functional/hash.hpp>
#include <boost/foreach.hpp>

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

Functions
void	core::pose::append_pose_to_pose (core::pose::Pose &pose1, core::pose::Pose const &pose2, bool new_chain=true)
	Append residues of pose2 to pose1. More...
void	core::pose::append_subpose_to_pose (core::pose::Pose &pose1, core::pose::Pose const &pose2, core::Size start_res, core::Size end_res, bool new_chain=true)
	Append specified residues of pose2 to pose1. More...
void	core::pose::jumps_from_pose (const core::pose::Pose &pose, Jumps *jumps)
	Retrieves jump information from <pose>, storing the result in <jumps>. Jumps are keyed by their jump id. More...
void	core::pose::remove_virtual_residues (core::pose::Pose *pose)
	Removes all virtual residues from <pose> More...
void	core::pose::swap_transform (Size jump_num, const kinematics::RT &xform, Pose *pose)
	Updates the rigid-body transform of the specified jump in <pose> More...
bool	core::pose::is_position_conserved_residue (const Pose &pose, core::Size residue)
	Returns true if <residue> is positionally conserved, false otherwise. More...
void	core::pose::create_subpose (Pose const &src, utility::vector1< Size > const &positions, kinematics::FoldTree const &f, Pose &pose)
	Create a subpose of the src pose. PDBInfo is set as NULL. More...
void	core::pose::pdbslice (pose::Pose &new_pose, pose::Pose const &pose, utility::vector1< Size > const &slice_res)
	Create a subpose of the src pose – figures out a reasonable fold tree. More...
void	core::pose::pdbslice (pose::Pose &pose, utility::vector1< Size > const &slice_res)
	Create a subpose of the src pose – figures out a reasonable fold tree. More...
void	core::pose::partition_pose_by_jump (pose::Pose const &src, int const jump_number, pose::Pose &partner1, pose::Pose &partner2)
void	core::pose::set_ss_from_phipsi (pose::Pose &pose)
	Analyzes <pose> residue phi/psi sets and guesses the secondary structure, ideally dssp should be used for that. More...
void	core::pose::addVirtualResAsRoot (const numeric::xyzVector< core::Real > &xyz, core::pose::Pose &pose)
	Adds a virtual residue to the end of the pose at the specified location. Roots the structure on this residue. More...
numeric::xyzVector< core::Real >	core::pose::get_center_of_mass (core::pose::Pose const &pose)
	Get center of mass of a pose. More...
void	core::pose::addVirtualResAsRoot (core::pose::Pose &pose)
	Adds a VRT res to the end of the pose at the center of mass. Reroots the structure on this res. More...
void	core::pose::read_comment_pdb (std::string const &file_name, core::pose::Pose &pose)
	Reads the comments from the pdb file and adds it into comments. More...
void	core::pose::dump_comment_pdb (std::string const &file_name, core::pose::Pose const &pose)
	dumps pose+ comments to pdb file More...
bool	core::pose::getPoseExtraScore (core::pose::Pose const &pose, std::string const name, core::Real &value)
	getters/setters for things in the Pose DataCache More...
bool	core::pose::getPoseExtraScore (core::pose::Pose const &pose, std::string const name, std::string &value)
void	core::pose::setPoseExtraScore (core::pose::Pose &pose, std::string name, core::Real value)
void	core::pose::setPoseExtraScore (core::pose::Pose &pose, std::string const name, std::string value)
void	core::pose::add_comment (core::pose::Pose &pose, std::string const &key, std::string const &val)
	Adds a key-value pair to the STRING_MAP in the Pose DataCache. If there is no STRING_MAP in the DataCache, one is created. More...
void	core::pose::add_score_line_string (core::pose::Pose &pose, std::string const &key, std::string const &val)
	Dumps a pdb with comments at end of file. More...
void	core::pose::clearPoseExtraScores (core::pose::Pose &pose)
void	core::pose::clearPoseExtraScore (core::pose::Pose &pose, std::string const &name)
bool	core::pose::get_comment (core::pose::Pose const &pose, std::string const &key, std::string &val)
	Attempts to access the entry in the STRING_MAP associated with the given key. If an entry for the key exists, the value associated with the key is put into val, and this function returns true. Otherwise, this function returns false and val left unmodified. More...
bool	core::pose::get_score_line_string (core::pose::Pose const &pose, std::string const &key, std::string &val)
void	core::pose::delete_comment (core::pose::Pose &pose, std::string const &key)
	Deletes the entry in the STRING_MAP associated with the given key. More...
std::map< std::string, std::string >	core::pose::get_all_score_line_strings (core::pose::Pose const &pose)
	Gets a map< string, string > representing score_line_strings about the Pose in the form of key-value pairs. More...
std::map< std::string, std::string >	core::pose::get_all_comments (core::pose::Pose const &pose)
	Gets a map< string, string > representing comments about the Pose in the form of key-value pairs. More...
utility::vector1< char >	core::pose::read_psipred_ss2_file (pose::Pose const &pose)
void	core::pose::conf2pdb_chain_default_map (core::pose::Pose const &pose, std::map< int, char > &chainmap)
std::map< int, char >	core::pose::conf2pdb_chain (core::pose::Pose const &pose)
	get Conformation chain -> PDBInfo chain mapping 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::is_ideal_pose (core::pose::Pose const &pose)
	checks if the pose geometry is ideal More...
bool	core::pose::is_ideal_position (core::Size seqpos, core::pose::Pose const &pose)
	checks if the pose geometry is ideal in position seqpos More...
void	core::pose::remove_nonprotein_residues (core::pose::Pose &pose)
	this function removes all residues from the pose which are not protein residues. More...
void	core::pose::remove_ligand_canonical_residues (core::pose::Pose &pose)
	this function removes all residues with both UPPER and LOWER terminus types. This is intended for removing ligands that are canonical residues. More...
bool	core::pose::compare_atom_coordinates (Pose const &lhs, Pose const &rhs, Size const n_dec_places=3)
	this function compares pose atom coordinates for equality; it is not the == operator because it does not compare all pose data. More...
bool	core::pose::compare_binary_protein_silent_struct (Pose const &lhs, Pose const &rhs)
	this function compares poses for equality up to the information stored in the binary protein silent struct format. More...
id::NamedAtomID	core::pose::atom_id_to_named_atom_id (core::id::AtomID const &atom_id, Pose const &pose)
id::AtomID	core::pose::named_atom_id_to_atom_id (core::id::NamedAtomID const &named_atom_id, Pose const &pose, bool raise_exception)
id::NamedStubID	core::pose::stub_id_to_named_stub_id (id::StubID const &stub_id, core::pose::Pose const &pose)
id::StubID	core::pose::named_stub_id_to_stub_id (id::NamedStubID const &named_stub_id, core::pose::Pose const &pose)
std::string	core::pose::tag_from_pose (core::pose::Pose const &pose)
void	core::pose::tag_into_pose (core::pose::Pose &pose, std::string const &tag)
core::Real	core::pose::energy_from_pose (core::pose::Pose const &pose, core::scoring::ScoreType const &sc_type)
core::Real	core::pose::energy_from_pose (core::pose::Pose const &pose, std::string const &sc_type)
core::Real	core::pose::total_energy_from_pose (core::pose::Pose const &pose)
bool	core::pose::sort_pose_by_score (core::pose::PoseOP const &pose1, core::pose::PoseOP const &pose2)
void	core::pose::transfer_phi_psi (const core::pose::Pose &srcpose, core::pose::Pose &tgtpose, core::Size ir, core::Size jr)
void	core::pose::transfer_phi_psi (const core::pose::Pose &srcpose, core::pose::Pose &tgtpose)
void	core::pose::transfer_jumps (const core::pose::Pose &srcpose, core::pose::Pose &tgtpose)
void	core::pose::replace_pose_residue_copying_existing_coordinates (pose::Pose &pose, Size const seqpos, core::chemical::ResidueType const &new_rsd_type)
core::conformation::ResidueOP	core::pose::remove_variant_type_from_residue (core::conformation::Residue const &old_rsd, core::chemical::VariantType const &variant_type, pose::Pose const &pose)
	removes variant from an existing residue More...
conformation::ResidueOP	core::pose::add_variant_type_to_residue (conformation::Residue const &old_rsd, chemical::VariantType const &variant_type, pose::Pose const &pose)
	construct a variant of an existing residue More...
void	core::pose::add_variant_type_to_pose_residue (pose::Pose &pose, chemical::VariantType const &variant_type, Size const seqpos)
	construct a variant of an existing pose residue More...
void	core::pose::remove_variant_type_from_pose_residue (pose::Pose &pose, chemical::VariantType const &variant_type, Size const seqpos)
	construct a non-variant of an existing pose residue More...
void	core::pose::add_lower_terminus_type_to_pose_residue (pose::Pose &pose, Size const seqpos)
void	core::pose::add_upper_terminus_type_to_pose_residue (pose::Pose &pose, Size const seqpos)
void	core::pose::remove_lower_terminus_type_from_pose_residue (pose::Pose &pose, Size const seqpos)
void	core::pose::remove_upper_terminus_type_from_pose_residue (pose::Pose &pose, Size const seqpos)
core::Real	core::pose::pose_max_nbr_radius (Pose const &pose)
	returns a Distance More...
void	core::pose::setup_dof_to_torsion_map (pose::Pose const &pose, id::DOF_ID_Map< id::TorsionID > &dof_map)
	set up a map to look up TORSION_ID by DOF_ID (Map[DOF_ID] = TORISION_ID) More...
void	core::pose::setup_dof_mask_from_move_map (core::kinematics::MoveMap const &mm, pose::Pose const &pose, id::DOF_ID_Mask &dof_mask)
	convert from allow-bb/allow-chi MoveMap to simple DOF_ID boolean mask needed by the minimizer More...
bool	core::pose::has_chain (std::string const &chain, core::pose::Pose const &pose)
bool	core::pose::has_chain (char const &chain, core::pose::Pose const &pose)
bool	core::pose::has_chain (core::Size chain_id, core::pose::Pose const &pose)
std::set< core::Size >	core::pose::get_jump_ids_from_chain_ids (std::set< core::Size > const chain_ids, core::pose::Pose const &pose)
core::Size	core::pose::get_jump_id_from_chain_id (core::Size const &chain_id, const core::pose::Pose &pose)
core::Size	core::pose::get_chain_id_from_chain (std::string const &chain, core::pose::Pose const &pose)
core::Size	core::pose::get_chain_id_from_chain (char const &chain, core::pose::Pose const &pose)
utility::vector1< core::Size >	core::pose::get_chain_ids_from_chain (std::string const &chain, core::pose::Pose const &pose)
utility::vector1< core::Size >	core::pose::get_chain_ids_from_chain (char const &chain, core::pose::Pose const &pose)
core::Size	core::pose::get_jump_id_from_chain (std::string const &chain, core::pose::Pose const &pose)
core::Size	core::pose::get_jump_id_from_chain (char const &chain, core::pose::Pose const &pose)
utility::vector1< core::Size >	core::pose::get_jump_ids_from_chain (char const &chain, core::pose::Pose const &pose)
utility::vector1< core::Size >	core::pose::get_jump_ids_from_chain (std::string const &chain, core::pose::Pose const &pose)
core::Size	core::pose::get_chain_id_from_jump_id (core::Size const &jump_id, core::pose::Pose const &pose)
char	core::pose::get_chain_from_jump_id (core::Size const &jump_id, core::pose::Pose const &pose)
core::conformation::ResidueCOPs	core::pose::get_chain_residues (core::pose::Pose const &pose, core::Size const chain_id)
char	core::pose::get_chain_from_chain_id (core::Size const &chain_id, core::pose::Pose const &pose)
core::Size	core::pose::num_heavy_atoms (core::Size begin, core::Size const end, core::pose::Pose const &pose)
core::Size	core::pose::num_atoms (core::Size begin, core::Size const end, core::pose::Pose const &pose)
core::Size	core::pose::num_hbond_acceptors (core::Size begin, core::Size const end, core::pose::Pose const &pose)
core::Size	core::pose::num_hbond_donors (core::Size begin, core::Size const end, core::pose::Pose const &pose)
core::Size	core::pose::num_chi_angles (core::Size begin, core::Size const end, core::pose::Pose const &pose)
core::Real	core::pose::mass (core::Size begin, core::Size const end, core::pose::Pose const &pose)
core::Size	core::pose::get_hash_from_chain (char const &chain, core::pose::Pose const &pose)
core::Size	core::pose::get_hash_excluding_chain (char const &chain, core::pose::Pose const &pose)
std::string	core::pose::get_sha1_hash_excluding_chain (char const &chain, core::pose::Pose const &pose)
void	core::pose::initialize_disulfide_bonds (Pose &pose)
	detect and fix disulfide bonds More...
std::string	core::pose::extract_tag_from_pose (core::pose::Pose &pose)
	Returns a string giving the pose's tag if there is such a thing or "UnknownTag" otherwise. More...
core::id::SequenceMapping	core::pose::sequence_map_from_pdbinfo (Pose const &first, Pose const &second)
	Create a sequence map of first pose onto the second, matching the PDBInfo If the PDBInfo of either Pose is missing or invalid, do a simple sequence alignment matching. More...
core::Size	core::pose::canonical_residue_count (core::pose::Pose const &pose)
	count the number of canonical residues in the pose More...
core::Size	core::pose::noncanonical_residue_count (core::pose::Pose const &pose)
	count the number of non-canonical residues in the pose More...
core::Size	core::pose::canonical_atom_count (core::pose::Pose const &pose)
	count the number of canonical amino acid atoms in the pose More...
core::Size	core::pose::noncanonical_atom_count (core::pose::Pose const &pose)
	count the number of non-canonical amino acids in thepose More...
core::Size	core::pose::noncanonical_chi_count (core::pose::Pose const &pose)
	count the number of non-canonical chi angles in the pose More...
numeric::xyzVector< core::Real >	core::pose::center_of_mass (pose::Pose const &pose, int const start, int const stop)
	calculates the center of mass of a pose More...
int	core::pose::residue_center_of_mass (pose::Pose const &pose, int const start, int const stop)
	calculates the center of mass of a pose More...
int	core::pose::return_nearest_residue (pose::Pose const &pose, int const begin, int const end, Vector center)
	finds the residue nearest some position passed in (normally a center of mass) More...
id::AtomID_Map< id::AtomID >	core::pose::convert_from_std_map (std::map< id::AtomID, id::AtomID > const &atom_map, core::pose::Pose const &pose)
void	core::pose::correctly_add_cutpoint_variants (core::pose::Pose &pose)
	Add cutpoint variants to all residues annotated as cutpoints in the pose. More...
void	core::pose::correctly_add_cutpoint_variants (core::pose::Pose &pose, Size const cutpoint_res, bool const check_fold_tree)

Variables
static basic::Tracer	core::pose::TR ("core.pose.util")

Detailed Description

Pose class utilities.

Author

Phil Bradley

Modified by Sergey Lyskov, Rhiju Das, Steven Lewis, Vikram K. Mulligan