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util.cc File Reference

Utility function definitions for carbohydrate-containing poses. More...

#include <core/pose/carbohydrates/util.hh>
#include <core/pose/Pose.hh>
#include <core/io/carbohydrates/pose_io.hh>
#include <core/chemical/carbohydrates/CarbohydrateInfo.hh>
#include <core/chemical/carbohydrates/CarbohydrateInfoManager.hh>
#include <core/chemical/carbohydrates/database_io.hh>
#include <core/select/residue_selector/ResidueSelector.fwd.hh>
#include <core/select/residue_selector/OrResidueSelector.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/annotated_sequence.hh>
#include <core/pose/variant_util.hh>
#include <core/id/types.hh>
#include <core/id/AtomID.hh>
#include <core/id/TorsionID.hh>
#include <core/types.hh>
#include <core/chemical/AtomICoor.hh>
#include <core/chemical/AtomType.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/conformation/Conformation.hh>
#include <core/conformation/util.hh>
#include <core/conformation/carbohydrates/util.hh>
#include <core/conformation/carbohydrates/GlycanTreeSet.hh>
#include <core/conformation/carbohydrates/GlycanTree.hh>
#include <core/conformation/carbohydrates/GlycanNode.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/select/residue_selector/ResidueSelector.hh>
#include <utility/string_constants.hh>
#include <utility/vector1.hh>
#include <utility/vector1.functions.hh>
#include <utility/exit.hh>
#include <utility/string_util.hh>
#include <basic/Tracer.hh>
#include <numeric/conversions.hh>
#include <numeric/angle.functions.hh>
#include <numeric/random/random.hh>
#include <basic/basic.hh>
#include <list>
#include <utility>

Namespaces

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

Functions

static basic::Tracer TR ("core.pose.carbohydrates.util")
 
void core::pose::carbohydrates::set_glycan_iupac_chi_torsions (core::pose::Pose const &pose, core::kinematics::MoveMap &movemap, core::Size const resnum, bool action, bool cartesian)
 Turn on/off IUPAC CHI for a particular residue number. More...
 
void core::pose::carbohydrates::set_glycan_iupac_bb_torsions (core::pose::Pose const &pose, core::kinematics::MoveMap &movemap, core::Size const resnum, bool action=true, bool cartesian=false)
 Turn on/off IUPAC BBs for a particular residue number. More...
 
kinematics::MoveMapOP core::pose::carbohydrates::create_glycan_movemap_from_residue_selector (core::pose::Pose const &pose, select::residue_selector::ResidueSelectorCOP selector, bool include_iupac_chi, bool include_glycan_ring_torsions, bool include_bb_torsions, bool cartesian)
 Get a pre-configured movemap from a residue selector. Use the ReturnResidueSubsetSelector to obtain from a subset. More...
 
void core::pose::carbohydrates::glycosylate_pose (Pose &pose, uint const sequence_position, std::string const &atom_name, std::string const &iupac_sequence, bool idealize_linkages=true, bool keep_pdbinfo=true)
 Glycosylate the Pose at the given sequence position and atom using an IUPAC sequence. More...
 
void core::pose::carbohydrates::glycosylate_pose (Pose &pose, uint const sequence_position, std::string const &iupac_sequence, bool const idealize_linkages=true, bool keep_pdbinfo=true)
 Glycosylate the Pose at the given sequence position using an IUPAC sequence. More...
 
void core::pose::carbohydrates::glycosylate_pose_by_file (Pose &pose, uint const sequence_position, std::string const &atom_name, std::string const &filename, bool const idealize_linkages=true, bool keep_pdbinfo=true)
 Glycosylate the Pose at the given sequence position and atom using a .GWS or IUPAC sequence file. More...
 
void core::pose::carbohydrates::glycosylate_pose_by_file (Pose &pose, uint const sequence_position, std::string const &filename, bool const idealize_linkages=true, bool keep_pdbinfo=true)
 Glycosylate the Pose at the given sequence position using a .GWS or IUPAC sequence file. More...
 
std::pair
< conformation::ResidueCOP,
conformation::ResidueCOP > 
core::pose::carbohydrates::get_glycosidic_bond_residues (Pose const &pose, uint const sequence_position)
 Return pointers to the two residues of the glycosidic bond. More...
 
utility::vector1< id::AtomID > core::pose::carbohydrates::get_reference_atoms_for_phi (Pose const &pose, uint const sequence_position)
 Return the AtomIDs of the four phi torsion reference atoms. More...
 
utility::vector1< id::AtomID > core::pose::carbohydrates::get_reference_atoms_for_psi (Pose const &pose, uint const sequence_position)
 Return the AtomIDs of the four psi torsion reference atoms. More...
 
utility::vector1< id::AtomID > core::pose::carbohydrates::get_reference_atoms_for_1st_omega (Pose const &pose, uint const sequence_position)
 Return the AtomIDs of the four omega torsion reference atoms. More...
 
utility::vector1< id::AtomID > core::pose::carbohydrates::get_reference_atoms_for_2nd_omega (Pose const &pose, uint const sequence_position)
 Return the AtomIDs of the four omega2 torsion reference atoms. More...
 
utility::vector1< id::AtomID > core::pose::carbohydrates::get_reference_atoms (uint const named_torsion, Pose const &pose, uint const sequence_position)
 Return the AtomIDs of the four reference atoms for the requested torsion. More...
 
void core::pose::carbohydrates::align_virtual_atoms_in_carbohydrate_residue (Pose &pose, uint const sequence_position)
 Set coordinates of virtual atoms (used as angle reference points) within a saccharide residue of the given pose. More...
 
core::Size core::pose::carbohydrates::which_glycosidic_torsion (Pose const &pose, id::TorsionID const &torsion_id)
 Get the torsion num that this torsionID moves. More...
 
bool core::pose::carbohydrates::is_glycosidic_phi_torsion (Pose const &pose, id::TorsionID const &torsion_id)
 Is this is the phi torsion angle of a glycosidic linkage? More...
 
bool core::pose::carbohydrates::is_glycosidic_psi_torsion (Pose const &pose, id::TorsionID const &torsion_id)
 Is this is the psi torsion angle of a glycosidic linkage? More...
 
bool core::pose::carbohydrates::is_glycosidic_omega_torsion (Pose const &pose, id::TorsionID const &torsion_id)
 Is this is a 1st omega torsion angle of a glycosidic linkage? More...
 
bool core::pose::carbohydrates::is_glycosidic_omega2_torsion (Pose const &pose, id::TorsionID const &torsion_id)
 Is this is a 2nd omega torsion angle of a glycosidic linkage? More...
 
bool core::pose::carbohydrates::is_glycosidic_omega3_torsion (Pose const &pose, id::TorsionID const &torsion_id)
 Is this is a 3rd omega torsion angle of a glycosidic linkage? More...
 
bool core::pose::carbohydrates::is_glycosidic_torsion (Pose const &pose, id::TorsionID const &torsion_id, core::id::MainchainTorsionType const &torsion_type)
 Base function to reduce code-duplication in torsion queries. More...
 
core::uint core::pose::carbohydrates::get_downstream_residue_that_this_torsion_moves (Pose const &pose, id::TorsionID const &torsion_id)
 Return the sequence position of the immediate downstream (child) residue affected by this torsion. More...
 
Size core::pose::carbohydrates::get_n_glycosidic_torsions_in_res (Pose const &pose, uint const sequence_position)
 Get the number of glycosidic torsions for this residue. Up to 4 (omega2). More...
 
core::Angle core::pose::carbohydrates::get_glycosidic_torsion (uint const named_torsion, Pose const &pose, uint const sequence_position)
 Return the requested torsion angle between a saccharide residue of the given pose and the previous residue. More...
 
void core::pose::carbohydrates::set_glycosidic_torsion (uint const named_torsion, Pose &pose, uint const sequence_position, core::Angle const setting)
 Set the requested torsion angle between a saccharide residue of the given pose and the previous residue. More...
 
void core::pose::carbohydrates::idealize_last_n_glycans_in_pose (Pose &pose, Size const n_glycans_added)
 Idealize the glycosidic torsion angles for the last n glycan residues added or built. More...
 
void core::pose::carbohydrates::set_dihedrals_from_linkage_conformer_data (Pose &pose, uint const upper_residue, core::chemical::carbohydrates::LinkageConformerData const &conformer, bool idealize=true, bool use_gaussian_sampling=false)
 Set the dihedral angles involved in a glycosidic linkage based on statistical data. More...
 
void core::pose::carbohydrates::remove_carbohydrate_branch_point_variants (Pose &pose, core::Size const seqpos)
 Remove branch points from a carbohydrate or aa residue. More...
 
void core::pose::carbohydrates::find_neighbor (Pose &pose, core::Size res_pos, core::Size atom_nr, std::pair< core::Size, core::Size > &neighbor)
 find connected atom in neighboring residue More...
 
void core::pose::carbohydrates::setup_existing_glycans (Pose &pose)
 Go through pose from non-Rosetta PDB file and infer and properly set up branching. More...
 
utility::vector1< core::Sizecore::pose::carbohydrates::get_carbohydrate_residues_of_branch (Pose const &pose, uint const starting_position)
 Get residues further down the branch from this residue. starting_position -> More...
 
utility::vector1< core::Sizecore::pose::carbohydrates::get_carbohydrate_tips_of_branch (Pose const &pose, uint const starting_position)
 Get tips (end residue of linear components of branches) further down the branch from this residue. starting_position -> More...
 
std::pair< utility::vector1
< core::Size >
, utility::vector1< core::Size > > 
core::pose::carbohydrates::get_carbohydrate_residues_and_tips_of_branch (Pose const &pose, uint const starting_position)
 Get residues further down the branch from this residue. starting_position -> May require a better name. Returns pair of all_upstream_residues, tips. Tips are the ends of linear glycan branches. More...
 
core::Size core::pose::carbohydrates::get_glycan_connecting_protein_branch_point (Pose const &pose, core::Size const protein_branch_point_resnum)
 Get the carbohydrate residue connecting the protein branch point. More...
 
core::Size core::pose::carbohydrates::get_resnum_from_glycan_position (Pose const &pose, core::Size const glycan_one, core::Size const glycan_position)
 Get the particular resnum from a glycan position, givin the protein branch point. The glycan_position is numbered 1 -> length of glycan. This is useful for easily identifying a particular glycan position. More...
 
core::Size core::pose::carbohydrates::get_glycan_position_from_resnum (Pose const &pose, core::Size const first_glycan_resnum, core::Size const resnum)
 Get the particular resnum from a glycan position, givin the protein branch point. The glycan_position is numbered 1 -> length of glycan. This is useful for easily identifying a particular glycan position. Returns 0 if that glycan_position is not part of the glycan we are interested in or not in pose. More...
 
select::residue_selector::ResidueSubset core::pose::carbohydrates::get_resnums_from_glycan_positions (Pose const &pose, core::Size const first_glycan_resnum, utility::vector1< core::Size > const &glycan_positions)
 Get all resnums from specific glycan positions given the particular glycan. Positions correspond to a number 1 -> that corresponds to each residue. Use glycan_info app for more. More...
 
select::residue_selector::ResidueSubset core::pose::carbohydrates::get_resnums_from_glycan_positions (Pose const &pose, utility::vector1< core::Size > const &glycan_positions)
 Get all resnums for all glycans in the pose. Positions correspond to a number 1 -> that corresponds to each residue. Use glycan_info app for more. Glycan positions do not need to exist for all glcyans. More...
 
utility::vector1< boolcore::pose::carbohydrates::get_mainchain_children (Pose const &pose, core::Size starting_resnum, bool include_starting_resnum)
 
void core::pose::carbohydrates::delete_carbohydrate_branch (Pose &pose, uint const delete_to)
 Delete the glycan from this residue onward toward the end of the branch. Like chopping off a tree trunk at position resnum (not including resnum). Also known as defoliating. If resnum is the protein branch point, will change variant. More...
 
void core::pose::carbohydrates::get_branching_residues (Pose const &pose, Size parent_residue, utility::vector1< Size > &children_residues, utility::vector1< Size > &list_of_residues, utility::vector1< Size > &tips)
 Recursive function to get branches of a set of residues, etc. list_of_residues and tips are arrays are non-const references and modified by this function. More...
 
void core::pose::carbohydrates::fill_downstream_children_res_and_tips (Pose const &pose, Size res, Size parent_residue, utility::vector1< Size > &children_residues, utility::vector1< Size > &list_of_residues, utility::vector1< Size > &tips)
 Find all children residues, list of residues, and any found tips from a given residue not including parent. More...
 
utility::vector1< core::Sizecore::pose::carbohydrates::get_resnums_in_leaf (Pose const &pose, Size tip_residue, Size stop_at_residue)
 Get all residue numbers in order from the tip to (and not including) stop_at_residue or a branch point. All residue numbers are the tip or a linear polymer of glycans. Useful for glycan stripping. More...
 
utility::vector1< core::Sizecore::pose::carbohydrates::get_resnums_in_leaf_on_the_fly (Pose const &pose, Size tip_residue, Size stop_at_residue)
 Get all residue numbers in order from the tip to (and not including) stop_at_residue or a branch point. All residue numbers are the tip or a linear polymer of glycans. Useful for glycan stripping. More...
 
void core::pose::carbohydrates::delete_leaf (Pose &pose, utility::vector1< Size > leaf, std::string ref_pose_name)
 Delete a leaf of glycan residues. Use the ReferencePose to associate residue numbers. More...
 
void core::pose::carbohydrates::tautomerize_anomer (Pose &pose, core::uint const seqpos)
 Switch one saccharide sugar with its anomer. More...
 

Detailed Description

Utility function definitions for carbohydrate-containing poses.

Author
Labonte JWLab.nosp@m.onte.nosp@m.@jhu..nosp@m.edu
Jared Adolf-Bryfogle jadol.nosp@m.fbr@.nosp@m.gmail.nosp@m..com

Function Documentation

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