Rosetta  2021.07
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Namespaces | Functions
util.hh File Reference

Utility functions that DO NOT require a pose. More...

#include <core/conformation/Conformation.fwd.hh>
#include <core/conformation/Residue.fwd.hh>
#include <core/conformation/carbohydrates/GlycanTreeSet.fwd.hh>
#include <core/chemical/ResidueType.fwd.hh>
#include <core/types.hh>
#include <core/id/AtomID.fwd.hh>
#include <core/id/TorsionID.fwd.hh>
#include <utility/vector1.fwd.hh>
#include <set>
#include <iosfwd>
#include <utility>

Namespaces

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

Functions

core::uint core::conformation::carbohydrates::find_seqpos_of_saccharides_parent_residue (conformation::Residue const &residue)
 Use a saccharide residue's connections to find the residue from which it follows or branches. Returns 0 if it has no parent. More...
 
core::uint core::conformation::carbohydrates::find_seqpos_of_saccharides_mainchain_child (conformation::Residue const &residue)
 Use the mainchain acceptor to find the mainchain child. Typically, this is N+1, but this is independent of the residue number. Returns 0 if it has no child. More...
 
core::uint core::conformation::carbohydrates::find_seqpos_of_saccharides_child_residue_at (conformation::Residue const &residue, core::uint linkage_position)
 Use a saccharide residue's connections to find the residue following it from a given linkage position. More...
 
core::uint core::conformation::carbohydrates::get_linkage_position_of_saccharide_residue (conformation::Residue const &rsd, conformation::Residue const &parent_rsd)
 
bool core::conformation::carbohydrates::has_exocyclic_glycosidic_linkage (conformation::Conformation const &conf, uint const seqpos)
 Get whether the glycosidic linkage between the residue and previous residue (parent residue) has an exocyclic carbon. More...
 
bool core::conformation::carbohydrates::has_exocyclic_glycosidic_linkage (conformation::Residue const &rsd, conformation::Residue const &parent_rsd)
 Get whether the glycosidic linkage between the residue and previous residue (parent residue) has an exocyclic carbon. More...
 
std::pair
< conformation::ResidueCOP,
conformation::ResidueCOP > 
core::conformation::carbohydrates::get_glycosidic_bond_residues (Conformation const &conf, uint const sequence_position)
 Return pointers to the two residues of the glycosidic bond. More...
 
utility::vector1< id::AtomID > core::conformation::carbohydrates::get_reference_atoms_for_phi (Conformation const &conf, uint const sequence_position)
 Return the AtomIDs of the four phi torsion reference atoms. More...
 
utility::vector1< id::AtomID > core::conformation::carbohydrates::get_reference_atoms_for_psi (Conformation const &conf, uint const sequence_position)
 Return the AtomIDs of the four psi torsion reference atoms. More...
 
utility::vector1< id::AtomID > core::conformation::carbohydrates::get_reference_atoms_for_1st_omega (Conformation const &conf, uint const sequence_position)
 Return the AtomIDs of the four omega torsion reference atoms. More...
 
utility::vector1< id::AtomID > core::conformation::carbohydrates::get_reference_atoms_for_2nd_omega (Conformation const &conf, uint const sequence_position)
 Return the AtomIDs of the four omega2 torsion reference atoms. More...
 
utility::vector1< id::AtomID > core::conformation::carbohydrates::get_reference_atoms (uint const named_torsion, Conformation const &conf, uint const sequence_position)
 Return the AtomIDs of the four reference atoms for the requested torsion. More...
 
core::id::TorsionID core::conformation::carbohydrates::get_non_NU_TorsionID_from_AtomIDs (Conformation const &conf, utility::vector1< core::id::AtomID > const &atoms)
 Get the main chain or branch TorsionID defined by these four AtomIDs. <atoms>: A vector1 of AtomIDs with a size of 4. More...
 
utility::vector1
< core::id::TorsionID
core::conformation::carbohydrates::get_glycosidic_TorsionIDs (core::conformation::Conformation const &conf, uint const seq_pos)
 Get a list of the TorsionIDs of all glycosidic torsions for the residue at this position. More...
 
void core::conformation::carbohydrates::align_virtual_atoms_in_carbohydrate_residue (conformation::Conformation &conf, uint const sequence_position)
 Set coordinates of virtual atoms (used as angle reference points) within a saccharide residue of the given conformation. More...
 
bool core::conformation::carbohydrates::is_glycosidic_phi_torsion (Conformation const &conf, id::TorsionID const &torsion_id)
 Is this is the phi torsion angle of a glycosidic linkage? More...
 
bool core::conformation::carbohydrates::is_glycosidic_psi_torsion (Conformation const &conf, id::TorsionID const &torsion_id)
 Is this is the psi torsion angle of a glycosidic linkage? More...
 
bool core::conformation::carbohydrates::is_glycosidic_omega_torsion (Conformation const &conf, id::TorsionID const &torsion_id)
 Is this is an omega torsion angle of a glycosidic linkage? More...
 
core::uint core::conformation::carbohydrates::get_downstream_residue_that_this_torsion_moves (Conformation const &conf, id::TorsionID const &torsion_id)
 Return the sequence position of the immediate downstream (child) residue affected by this torsion. More...
 
Size core::conformation::carbohydrates::get_n_glycosidic_torsions_in_res (Conformation const &conf, uint const sequence_position)
 Get the number of glycosidic torsions for this residue. Up to 4 (omega2). More...
 
core::Angle core::conformation::carbohydrates::get_glycosidic_torsion (uint const named_torsion, Conformation const &conf, uint const sequence_position)
 Return the requested torsion angle between a saccharide residue of the given pose and the previous residue. More...
 
void core::conformation::carbohydrates::set_glycosidic_torsion (uint const named_torsion, Conformation &conf, 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::conformation::carbohydrates::get_branching_residues (conformation::Conformation const &conf, Size parent_residue, utility::vector1< Size > const &children_residues, utility::vector1< Size > &list_of_residues, utility::vector1< Size > &tips, std::set< Size > const &ancestors)
 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::conformation::carbohydrates::fill_downstream_children_res_and_tips (conformation::Conformation const &conf, 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...
 
core::Size core::conformation::carbohydrates::get_glycan_tree_size (conformation::Conformation const &conf, core::Size const first_glycan_resnum)
 Get the size of the glycan tree given the first carbohydrate residue in the tree. On-the-fly calculation. More...
 
core::Size core::conformation::carbohydrates::get_largest_glycan_tree_size (conformation::Conformation const &conf)
 Get the largest glycan tree size int he pose. More...
 
core::Size core::conformation::carbohydrates::get_distance_to_start (conformation::Conformation const &conf, core::Size const position)
 Get the residue distance from the position to the root/end of the glycan. On-the-fly calculation. More...
 
utility::vector1< boolcore::conformation::carbohydrates::get_glycan_start_points (conformation::Conformation const &conf)
 Get which residues denote starting a glycan. These are the first residue of the glycan tree, and the tree can be branching from protein or not. More...
 
utility::vector1< core::Sizecore::conformation::carbohydrates::get_carbohydrate_residues_of_branch (conformation::Conformation const &conf, uint const starting_position)
 Get residues further down the branch from this residue. starting_position -> More...
 
utility::vector1< core::Sizecore::conformation::carbohydrates::get_carbohydrate_tips_of_branch (conformation::Conformation const &conf, 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::conformation::carbohydrates::get_carbohydrate_residues_and_tips_of_branch (conformation::Conformation const &conf, uint const starting_position, bool include_starting_position=false)
 Get residues further down the branch from this residue. starting_position -> Returns pair of all_upstream_residues, tips. Tips are the ends of linear glycan branches. More...
 
core::Size core::conformation::carbohydrates::get_glycan_connecting_protein_branch_point (conformation::Conformation const &conf, core::Size const protein_branch_point_resnum)
 Get the carbohydrate residue connecting the protein branch point. More...
 
core::Size core::conformation::carbohydrates::get_resnum_from_glycan_position (conformation::Conformation const &conf, core::Size const glycan_one, core::Size const glycan_position)
 Get the particular resnum from a glycan position, given 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::conformation::carbohydrates::get_glycan_position_from_resnum (conformation::Conformation const &conf, core::Size const first_glycan_resnum, core::Size const resnum)
 Get the particular resnum from a glycan position, given 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...
 

Detailed Description

Utility functions that DO NOT require a pose.

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