Rosetta 3.4
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src/core/pose/util.hh File Reference

Pose utilities. More...

#include <map>
#include <set>
#include <numeric/xyzVector.hh>
#include <utility/vector1.fwd.hh>
#include <core/types.hh>
#include <core/conformation/Residue.hh>
#include <core/chemical/ResidueType.fwd.hh>
#include <core/chemical/VariantType.fwd.hh>
#include <core/id/AtomID.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/kinematics/FoldTree.fwd.hh>
#include <core/kinematics/Jump.fwd.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 <core/pose/MiniPose.fwd.hh>
#include <utility/vector1.hh>
#include <core/id/AtomID_Map.fwd.hh>
#include <core/kinematics/Jump.hh>
#include <core/pose/Pose.fwd.hh>

Namespaces

namespace  core
 

A class for defining atom parameters, known as atom_types.


namespace  core::pose

Typedefs

typedef std::set< intcore::pose::Jumps

Functions

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.
void core::pose::remove_virtual_residues (core::pose::Pose *pose)
 Removes all virtual residues from <pose>
void core::pose::swap_transform (int jump_num, const kinematics::RT &xform, Pose *pose)
 Updates the rigid-body transform of the specified jump in <pose>
bool core::pose::is_position_conserved_residue (const Pose &pose, core::Size residue)
 Returns true if <residue> is positionally conserved, false otherwise.
void core::pose::create_subpose (Pose const &src, utility::vector1< Size > const &positions, kinematics::FoldTree const &f, Pose &pose)
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.
utility::vector1< char > core::pose::read_psipred_ss2_file (pose::Pose const &pose)
bool core::pose::getPoseExtraScores (core::pose::Pose &pose, std::string name, core::Real &value)
 getters/setters for things in the Pose DataCache
void core::pose::setPoseExtraScores (core::pose::Pose &pose, std::string name, core::Real value)
void core::pose::clearPoseExtraScore (core::pose::Pose &pose, std::string const &name)
void core::pose::clearPoseExtraScores (core::pose::Pose &pose)
void core::pose::addVirtualResAsRoot (core::pose::Pose &pose)
 Find residue closest to center-of-mass
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.
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.
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.
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.
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.
void core::pose::add_score_line_string (core::pose::Pose &pose, std::string const &key, std::string const &val)
 Sets a PDB-style REMARK entry in the Pose.
bool core::pose::get_score_line_string (core::pose::Pose const &pose, std::string const &key, std::string &val)
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.
std::map< int, char > core::pose::conf2pdb_chain (core::pose::Pose const &pose)
 get Conformation chain -> PDBInfo chain mapping
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
bool core::pose::is_ideal_pose (core::pose::Pose const &pose)
 checks if the pose geometry is ideal
bool core::pose::is_ideal_position (core::Size seqpos, core::pose::Pose const &pose)
 checks if the pose geometry is ideal in position seqpos
void core::pose::remove_nonprotein_residues (core::pose::Pose &pose)
 this function removes all residues from the pose which are not protein residues. This removal includes, but is not limited to, metals, DNA, RNA, and ligands. It will NOT remove ligands which are canonical residues (for example, if a protein binds an alanine monomer, the monomer will be untouched).
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.
bool core::pose::compare_atom_coordinates (core::pose::Pose const &lhs, core::pose::Pose const &rhs, core::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.
void core::pose::copy_dofs (pose::Pose &pose, MiniPose const &scratch_pose, core::pose::ResMap const &res_map)
 A very useful function that copies degrees of freedom from one pose to another. res_map defines how to map residue numbers from the large pose to the smaller "scratch" pose.
void core::pose::copy_dofs_match_atom_names (pose::Pose &pose, MiniPose const &chunk_pose, core::pose::ResMap const &res_map)
void core::pose::copy_dofs (pose::Pose &pose, Pose const &scratch_pose, core::pose::ResMap const &res_map)
void core::pose::copy_dofs_match_atom_names (pose::Pose &pose, Pose const &scratch_pose, core::pose::ResMap const &res_map, bool const backbone_only, bool const ignore_virtual)
void core::pose::copy_dofs (pose::Pose &pose, Pose const &scratch_pose, std::map< id::AtomID, id::AtomID > const &atom_id_map)
void core::pose::copy_dofs (pose::Pose &pose, MiniPose const &scratch_pose, std::map< id::AtomID, id::AtomID > const &atom_id_map)
void core::pose::copy_dofs (pose::Pose &pose, MiniPose const &scratch_pose, std::map< id::AtomID, id::AtomID > const &atom_id_map, std::map< id::AtomID, Size > const &atom_id_domain_map)
bool core::pose::get_scratch_atom_id (id::AtomID &other_scratch_atom_id, std::map< core::id::AtomID, core::id::AtomID > const &atom_id_map, core::kinematics::tree::Atom const *other_atom)
void core::pose::setup_atom_id_map (std::map< core::id::AtomID, core::id::AtomID > &atom_id_map, ResMap const &res_map, core::pose::Pose const &pose)
void core::pose::setup_atom_id_map_match_atom_names (std::map< core::id::AtomID, core::id::AtomID > &atom_id_map, ResMap const &res_map, core::pose::Pose const &pose, MiniPose const &chunk_pose)
void core::pose::setup_atom_id_map_match_atom_names (std::map< core::id::AtomID, core::id::AtomID > &atom_id_map, ResMap const &res_map, core::pose::Pose const &pose, core::pose::Pose const &reference_pose, bool const backbone_only, bool const ignore_virtual)
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 &pose, core::scoring::ScoreType const &sc_type)
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
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
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
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
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)
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)
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
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)
std::set< core::Sizecore::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::Sizecore::pose::get_chain_ids_from_chain (std::string const &chain, core::pose::Pose const &pose)
utility::vector1< core::Sizecore::pose::get_chain_ids_from_chain (char const &chain, core::pose::Pose const &pose)
char core::pose::get_chain_from_chain_id (core::Size const &chain_id, 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)
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)
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)
template<typename T >
void core::pose::initialize_dof_id_map (id::DOF_ID_Map< T > &dof_map, Pose const &pose)
 Initialize a DOF_ID_Map for a given Pose using the DOF_ID_Map's current default fill values.
template<typename T >
void core::pose::initialize_dof_id_map (id::DOF_ID_Map< T > &dof_map, Pose const &pose, T const &value)
 Initialize a DOF_ID_Map for a given Pose using a specified fill value.
core::Real core::pose::pose_max_nbr_radius (Pose const &pose)
 returns a Distance
template<typename T >
void core::pose::initialize_atomid_map (id::AtomID_Map< T > &atom_map, pose::Pose const &pose)
 Initialize an AtomID_Map for a given Pose using the AtomID_Map's current default fill values.
template<typename T >
void core::pose::initialize_atomid_map (id::AtomID_Map< T > &atom_map, pose::Pose const &pose, T const &value)
 Initialize an AtomID_Map for a given Pose using a specified fill value.
template<typename T >
void core::pose::initialize_atomid_map (id::AtomID_Map< T > &atom_map, conformation::Conformation const &conformation)
 Initialize an AtomID_Map for a given Conformation using the AtomID_Map's current default fill values.
template<typename T >
void core::pose::initialize_atomid_map (id::AtomID_Map< T > &atom_map, conformation::Conformation const &conformation, T const &value)
 Initialize an AtomID_Map for a given Conformation using a specified fill value.
template<typename T >
void core::pose::initialize_atomid_map_heavy_only (id::AtomID_Map< T > &atom_map, pose::Pose const &pose)
 Initialize an AtomID_Map for a given Pose using the AtomID_Map's current default fill values.
template<typename T >
void core::pose::initialize_atomid_map_heavy_only (id::AtomID_Map< T > &atom_map, pose::Pose const &pose, T const &value)
 Initialize an AtomID_Map for a given Pose using a specified fill value.
template<typename T >
void core::pose::initialize_atomid_map_heavy_only (id::AtomID_Map< T > &atom_map, conformation::Conformation const &conformation)
 Initialize an AtomID_Map for a given Conformation using the AtomID_Map's current default fill values.
template<typename T >
void core::pose::initialize_atomid_map_heavy_only (id::AtomID_Map< T > &atom_map, conformation::Conformation const &conformation, T const &value)
 Initialize an AtomID_Map for a given Conformation using a specified fill value.
void core::pose::initialize_disulfide_bonds (Pose &pose)
 detect and fix disulfide bonds

Detailed Description

Pose utilities.

Author:
Phil Bradley
Modified by Sergey Lyskov
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