Rosetta  2020.46
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residue_support.cc File Reference
#include <core/chemical/residue_support.hh>
#include <core/chemical/MutableResidueType.hh>
#include <core/chemical/ResidueType.hh>
#include <core/chemical/ResidueGraphTypes.hh>
#include <core/chemical/ChemicalManager.hh>
#include <utility/graph/Graph.hh>
#include <core/chemical/AtomType.hh>
#include <core/chemical/Atom.hh>
#include <core/chemical/AtomProperties.hh>
#include <core/chemical/Bond.hh>
#include <core/chemical/Elements.hh>
#include <core/chemical/ResidueConnection.hh>
#include <core/chemical/MutableResidueConnection.hh>
#include <utility/graph/RingDetection.hh>
#include <core/chemical/gasteiger/GasteigerAtomTypeData.hh>
#include <basic/Tracer.hh>
#include <utility/exit.hh>
#include <boost/unordered_map.hpp>
#include <utility/vector1.hh>
#include <utility/string_util.hh>
#include <utility/graph/BFS_prune.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <ObjexxFCL/string.functions.hh>
#include <boost/graph/breadth_first_search.hpp>
#include <algorithm>

Classes

class  core::chemical::RigidDistanceVisitor
 Utility visitor for find_nbr_dist Will only traverse those atoms in the "rigid" portion of graph around the starting atom. "Rigid" includes direct neighbors and atoms connected by non-rotatable bonds e.g. all rings, all double/triple bonds, methyl groups, single atoms, etc. More...
 

Namespaces

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

Functions

static basic::Tracer core::chemical::TR ("core.chemical.residue_support")
 
ObjexxFCL::FArray2D_int core::chemical::get_residue_path_distances (ResidueType const &res)
 relies on class Graph to find all pairs shortest path information More...
 
utility::vector1< VD > core::chemical::mainchain_path (MutableResidueType const &res)
 Figure out the shortest path between the upper and lower connect atoms (inclusive) Will return an empty vector if one does not exist. More...
 
utility::vector1< VD > core::chemical::shortest_path (MutableResidueType const &res, VD start, VD end)
 Figure out the shortest path between two atoms (inclusive) Will return an empty vector if one does not exist. More...
 
void core::chemical::annotate_backbone (MutableResidueType &restype)
 Annotate "backbone" atoms. For the purpose of this function, backbone atoms are any atoms which are connected to another backbone atom by a non-rotatable, non-cut bond. Atoms connected to the upper and/or lower connect points are always backbone. Important - if Chis/cuts aren't properly annotated, all atoms will be backbone. More...
 
void core::chemical::real_to_virtual (MutableResidueType &restype)
 Virtualize convert the MutableResidueType to a virtual type NOTE: This function does not rename the residue type. More...
 
LightWeightResidueGraph core::chemical::convert_residuetype_to_light_graph (MutableResidueType const &res)
 
void core::chemical::rename_atoms (MutableResidueType &res, bool preserve)
 Rename atoms in the residue type such that their names are unique. If preserve is true, only rename those which have no names or who have name conflicts. (Both of the conflicting atoms will be renamed.) More...
 
void core::chemical::calculate_rigid_matrix (MutableResidueType const &res, VDDistanceMatrix &distances)
 Calculate the rigid matrix - assume that distances has been initialized to some really large value, and is square. More...
 
core::Real core::chemical::find_nbr_dist (MutableResidueType const &res, VD &nbr_atom)
 Find the neighbor distance to the given neighbor atom. If nbr_atom is null_vertex, give the smallest neighbor distance, and set nbr_atom to the atom for that distance. More...
 
void core::chemical::rosetta_recharge_fullatom (MutableResidueType &res)
 Apply molfile_to_params style partial charges to the ResidueType. More...
 
MutableResidueTypeOP core::chemical::make_centroid (ResidueType const &res)
 Make a centroid version of the fullatom ResidueType passed in. More...
 
MutableResidueTypeOP core::chemical::make_centroid (MutableResidueType const &res)
 
bool core::chemical::residue_type_bases_identical (ResidueTypeBase const &r1, ResidueTypeBase const &r2)
 
bool core::chemical::residue_types_identical (ResidueType const &res1, ResidueType const &res2)
 Are two ResidueTypes equivalent? This is here rather than as an operator on ResidueType because it's not the sort of thing one should be doing normally. This looks for exact equivalence, including atom order. More...
 
bool core::chemical::compare_residue_connection (ResidueConnection const &rc1, ResidueConnection const &rc2, bool fuzzy=false)
 Are the two ResidueConnection objects equivalent Here instead of in operator== because of the fuzzy-real issue. More...
 
bool core::chemical::compare_atom_icoor (AtomICoor const &aic1, AtomICoor const &aic2, bool fuzzy=false)
 Are the two ResidueConnection objects equivalent Here instead of in operator== because of the fuzzy-real issue. More...