residue_support.hh File Reference

support functions for class residue; functions that should not be included as part of the class. More...

#include <core/chemical/ResidueType.fwd.hh>
#include <core/chemical/MutableResidueType.fwd.hh>
#include <core/chemical/ResidueConnection.fwd.hh>
#include <core/chemical/AtomICoor.fwd.hh>
#include <core/chemical/ResidueGraphTypes.hh>
#include <ObjexxFCL/FArray2D.hh>

Classes
class	core::chemical::VDDistanceMatrix
	Utility class for VD-indexed matrix. More...

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

Functions
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_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...

Detailed Description

support functions for class residue; functions that should not be included as part of the class.

Author

Phil Bradley

Rocco Moretti (rmore.nosp@m.ttia.nosp@m.se@gm.nosp@m.ail..nosp@m.com)

Steven Combs