 |
Rosetta
2021.07
|
All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
|
Rosetta
2021.07
|
Utility functions that DO NOT require a pose. More...
#include <core/conformation/carbohydrates/util.hh>#include <core/chemical/carbohydrates/CarbohydrateInfo.hh>#include <core/chemical/carbohydrates/CarbohydrateInfoManager.hh>#include <core/chemical/carbohydrates/database_io.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/conformation/carbohydrates/GlycanTreeSet.hh>#include <core/conformation/Residue.hh>#include <core/conformation/ResidueFactory.hh>#include <core/conformation/Conformation.hh>#include <core/conformation/util.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 <numeric/conversions.hh>#include <numeric/angle.functions.hh>#include <numeric/random/random.hh>#include <basic/options/keys/OptionKeys.hh>#include <basic/options/option.hh>#include <basic/options/keys/in.OptionKeys.gen.hh>#include <basic/basic.hh>#include <list>#include <utility>#include <basic/Tracer.hh>Namespaces | |
| core | |
| A class for reading in the atom type properties. | |
| core::conformation | |
| core::conformation::carbohydrates | |
Functions | |
| static basic::Tracer | TR ("core.conformation.carbohydrates.util") |
| 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< bool > | core::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::Size > | core::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::Size > | core::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... | |
Utility functions that DO NOT require a pose.
|
static |
1.8.7