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Rosetta
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Pose class utilities. More...
#include <core/pose/util.hh>#include <core/pose/extra_pose_info_util.hh>#include <core/pose/PDBInfo.hh>#include <core/pose/Pose.hh>#include <core/pose/full_model_info/FullModelInfo.hh>#include <core/pose/full_model_info/FullModelParameters.hh>#include <core/pose/datacache/CacheableDataType.hh>#include <core/pose/datacache/PositionConservedResiduesStore.hh>#include <core/pose/init_id_map.hh>#include <core/pose/carbohydrates/util.hh>#include <core/chemical/ChemicalManager.hh>#include <core/chemical/ResidueType.hh>#include <core/chemical/ResidueTypeSet.hh>#include <core/chemical/VariantType.hh>#include <core/chemical/util.hh>#include <core/chemical/ResidueConnection.hh>#include <core/conformation/Conformation.hh>#include <core/conformation/Residue.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/StructFileRep.hh>#include <core/io/raw_data/DisulfideFile.hh>#include <core/io/silent/BinarySilentStruct.hh>#include <core/io/silent/SilentFileOptions.hh>#include <core/scoring/ScoreType.hh>#include <core/scoring/Energies.hh>#include <core/scoring/func/HarmonicFunc.hh>#include <core/scoring/func/CircularHarmonicFunc.hh>#include <core/scoring/constraints/AtomPairConstraint.hh>#include <core/scoring/constraints/AngleConstraint.hh>#include <core/scoring/constraints/DihedralConstraint.hh>#include <core/conformation/Residue.fwd.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/options/option.hh>#include <basic/options/keys/in.OptionKeys.gen.hh>#include <numeric/xyz.functions.hh>#include <utility/exit.hh>#include <utility/string_util.hh>#include <utility/excn/Exceptions.hh>#include <utility/vector1.hh>#include <utility/vector1.functions.hh>#include <cmath>#include <algorithm>#include <numeric>#include <ObjexxFCL/string.functions.hh>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::swap_transform (Size jump_num, kinematics::RT const &xform, Pose &pose) |
| Updates the rigid-body transform of the specified jump in <pose> More... | |
| bool | core::pose::is_position_conserved_residue (Pose const &pose, core::Size residue) |
| Returns true if <residue> is positionally conserved, false otherwise Based on the POSITION_CONSERVED_RESIDUES annotation stored in the Pose DataCache. More... | |
| bool | core::pose::create_chemical_edge (core::uint start_resnum, core::uint end_resnum, core::pose::Pose const &pose, core::kinematics::FoldTree &ft) |
| Create a chemical edge between two Residues. More... | |
| void | core::pose::set_reasonable_fold_tree (pose::Pose &pose) |
| core::chemical::ResidueTypeCOP | core::pose::virtual_type_for_pose (core::pose::Pose const &pose) |
| Return the appropritate ResidueType for the virtual residue for the "mode" (fullatom, centroid ...) the pose is in. 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... | |
| void | core::pose::remove_virtual_residues (core::pose::Pose &pose) |
| Removes all virtual residues from <pose> More... | |
| numeric::xyzVector< core::Real > | core::pose::get_center_of_mass (core::pose::Pose const &pose) |
| @detail Get center of mass of a pose. More... | |
| void | core::pose::addVirtualResAsRoot (core::pose::Pose &pose) |
| @detail Find residue closest to center-of-mass More... | |
| void | core::pose::fix_pdbinfo_damaged_by_insertion (core::pose::Pose &pose) |
| Repair pdbinfo of inserted residues that may have blank chain and zero seqpos. Assumes insertions only occur after a residue. 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) |
| 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) |
| void | core::pose::replace_pose_residue_copying_existing_coordinates (pose::Pose &pose, Size const seqpos, core::chemical::ResidueType const &new_rsd_type, utility::vector1< core::Size > const &mapping) |
| core::chemical::ResidueTypeCOP | core::pose::get_restype_for_pose (core::pose::Pose const &pose, std::string const &name) |
| Return the residue type in the correct "mode" (fullatom, centroid ...) the pose is in. More... | |
| core::chemical::ResidueTypeCOP | core::pose::get_restype_for_pose (core::pose::Pose const &pose, std::string const &name, core::chemical::TypeSetMode mode) |
| Return the residue type in the passed mode, respecting any modification that pose may make. More... | |
| core::Real | core::pose::pose_max_nbr_radius (pose::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... | |
| 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) |
| void | core::pose::initialize_disulfide_bonds (Pose &pose) |
| detect and fix disulfide bonds More... | |
| void | core::pose::initialize_disulfide_bonds (Pose &pose, io::StructFileRep const &fd) |
| detect and fix disulfide bonds More... | |
| utility::vector1< std::pair< Size, Size > > | core::pose::disulfide_pairs_from_sfr (Pose const &pose, io::StructFileRep const &fd) |
| extract disulfide pairing from SFR 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... | |
| Size | core::pose::nres_protein (pose::Pose const &pose) |
| Number of protein residues in the pose. More... | |
| core::Real | core::pose::radius_of_gyration (core::pose::Pose const &pose, numeric::xyzVector< core::Real > const ¢er_of_mass, utility::vector1< bool > const &residues) |
| Get the radius of gyration of the selected residues. More... | |
| numeric::xyzVector< Real > | core::pose::center_of_mass (core::pose::Pose const &pose, utility::vector1< bool > const &residues) |
| Get the center of the indicated residues. More... | |
| utility::vector1< bool > | core::pose::generate_vector_from_bounds (pose::Pose const &pose, int const start, int const stop) |
| 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... | |
| core::Vector | core::pose::all_atom_center (core::pose::Pose const &pose, utility::vector1< core::Size > const &residues) |
| Get the center of the indicated residues. More... | |
| int | core::pose::residue_center_of_mass (pose::Pose const &pose, utility::vector1< bool > residues) |
| 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, utility::vector1< bool > const &residues, Vector center) |
| 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) |
| std::map< std::string, core::Size > | core::pose::get_pdb2pose_numbering_as_stdmap (core::pose::Pose const &pose) |
| Create std::map from PDBPoseMap in pose (JKLeman) More... | |
| void | core::pose::declare_cutpoint_chemical_bond (core::pose::Pose &pose, Size const cutpoint_res, Size const next_res_in) |
| Create a chemical bond from lower to upper residue across CUTPOINT_LOWER/CUTPOINT_UPPER. More... | |
| void | core::pose::update_cutpoint_virtual_atoms_if_connected (core::pose::Pose &pose, core::Size const cutpoint_res, bool recurse) |
| Given a pose and a position that may or may not be CUTPOINT_UPPER or CUTPOINT_LOWER, determine whether this position has either of these variant types, and if it does, determine whether it's connected to anything. If it is, update the C-OVL1-OVL2 bond lengths and bond angle (for CUTPOINT_LOWER) or OVU1-N bond length (for CUTPOINT_UPPER) to match any potentially non-ideal geometry in the residue to which it's bonded. More... | |
| void | core::pose::get_constraints_from_link_records (core::pose::Pose &pose, io::StructFileRep const &sfr) |
| utility::vector1< Size > | core::pose::pdb_to_pose (pose::Pose const &pose, utility::vector1< int > const &pdb_res) |
| Convert PDB numbering to pose numbering. Must exist somewhere else, but I couldn't find it. – rhiju. More... | |
| utility::vector1< Size > | core::pose::pdb_to_pose (pose::Pose const &pose, std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &pdb_res) |
| Convert PDB numbering to pose numbering. Must exist somewhere else, but I couldn't find it. – rhiju. More... | |
| Size | core::pose::pdb_to_pose (pose::Pose const &pose, int const res_num, char const chain) |
| Convert PDB numbering to pose numbering. Must exist somewhere else, but I couldn't find it. – rhiju. More... | |
| utility::vector1< Size > | core::pose::pose_to_pdb (pose::Pose const &pose, utility::vector1< Size > const &pose_res) |
| Convert pose numbering to pdb numbering. Must exist somewhere else, but I couldn't find it. – rhiju. More... | |
| chemical::rings::AxEqDesignation | core::pose::is_atom_axial_or_equatorial_to_ring (Pose const &pose, uint seqpos, uint query_atom, utility::vector1< uint > const &ring_atoms) |
| Is the query atom in this pose residue axial or equatorial to the given ring or neither? More... | |
| chemical::rings::AxEqDesignation | core::pose::is_atom_axial_or_equatorial_to_ring (Pose const &pose, id::AtomID const &query_atom, utility::vector1< id::AtomID > const &ring_atoms) |
| void | core::pose::set_bb_torsion (uint torsion_id, Pose &pose, core::Size sequence_position, core::Angle new_angle) |
| core::Angle | core::pose::get_bb_torsion (uint torsion_id, Pose const &pose, core::Size sequence_position) |
| Get a particular backbone torsion, phi, psi, omega (see core::types) Works with carbohydrates. Think about moving this to pose itself. More... | |
| void | core::pose::set_bfactors_from_atom_id_map (Pose &pose, id::AtomID_Map< Real > const &bfactors) |
| Set bfactors in a pose PDBInfo. More... | |
| bool | core::pose::just_modeling_RNA (std::string const &sequence) |
| bool | core::pose::stepwise_addable_pose_residue (Size const n, pose::Pose const &pose) |
| bool | core::pose::stepwise_addable_residue (Size const n, std::map< Size, std::string > const &non_standard_residue_map) |
| bool | core::pose::effective_lower_terminus_based_on_working_res (Size const i, utility::vector1< Size > const &working_res, utility::vector1< Size > const &res_list, utility::vector1< Size > const &cutpoint_open_in_full_model) |
| bool | core::pose::effective_upper_terminus_based_on_working_res (Size const i, utility::vector1< Size > const &working_res, utility::vector1< Size > const &res_list, utility::vector1< Size > const &cutpoint_open_in_full_model, Size const nres_full) |
| bool | core::pose::definite_terminal_root (utility::vector1< Size > const &cutpoint_open_in_full_model, utility::vector1< Size > const &working_res, utility::vector1< Size > const &res_list, Size const nres, Size const i) |
| bool | core::pose::definite_terminal_root (pose::Pose const &pose, Size const i) |
| Size | core::pose::get_definite_terminal_root (pose::Pose const &pose, utility::vector1< Size > const &partition_res, utility::vector1< Size > const &res_list, utility::vector1< Size > const &fixed_domain_map, utility::vector1< Size > const &cutpoint_open_in_full_model, utility::vector1< Size > const &working_res, bool const disallow_cutpoint_closed_upper) |
| Size | core::pose::get_definite_terminal_root (pose::Pose const &pose, utility::vector1< Size > const &partition_res, bool const disallow_cutpoint_closed_upper) |
| utility::vector1< Size > | core::pose::reorder_root_partition_res (utility::vector1< Size > const &root_partition_res, utility::vector1< Size > const &res_list, utility::vector1< Size > const &fixed_domain_map) |
| void | core::pose::reroot (pose::Pose &pose, utility::vector1< Size > const &root_partition_res, utility::vector1< Size > const &res_list, utility::vector1< Size > const &preferred_root_res, utility::vector1< Size > const &fixed_domain_map, utility::vector1< Size > const &cutpoint_open_in_full_model, utility::vector1< Size > const &working_res) |
Pose class utilities.
1.9.1