ValenceHandler.cc File Reference

A bunch of functions to determine where to place atoms based on hybridization of atoms and number of bonds It should be noted that a vector of coordinates are returned. This is because it creates the angles for all hydrogens that can be placed. If you are combining a fragment, you really only need the first index of coords. More...

#include <core/chemical/modifications/ValenceHandler.hh>
#include <numeric/constants.hh>
#include <core/chemical/MutableResidueType.hh>
#include <core/chemical/ResidueGraphTypes.hh>
#include <numeric/xyzVector.hh>
#include <core/chemical/gasteiger/GasteigerAtomTypeData.hh>
#include <basic/Tracer.hh>

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

Functions
static basic::Tracer	core::chemical::modifications::TR ("core.chemical.modifications.ValenceHandler")
utility::vector1< numeric::xyzVector< core::Real > >	core::chemical::modifications::determine_coordinates (core::chemical::MutableResidueType const &res, core::chemical::VD const &atom)
numeric::xyzVector< core::Real >	core::chemical::modifications::linear_coordinates (numeric::xyzVector< core::Real > const &vector_a, numeric::xyzVector< core::Real > const &vector_b, core::Real const distance_xa)
	calculates point X in B->A->X where A, B and X are on the same line More...
numeric::xyzVector< core::Real >	core::chemical::modifications::angle_coordinates (const numeric::xyzVector< core::Real > &VECTOR_A, const numeric::xyzVector< core::Real > &VECTOR_B, const numeric::xyzVector< core::Real > &VECTOR_C, const core::Real DISTANCE_XA, const core::Real ANGLE_XAB, const core::Real ANGLE_XAC, const bool SIDE, const numeric::xyzVector< core::Real > &VECTOR_SIDE)
	calculates coordinates using angle information (point X in B,C->A->X) More...
numeric::xyzVector< core::Real >	core::chemical::modifications::triganol_coordinates (const numeric::xyzVector< core::Real > &VECTOR_A, const numeric::xyzVector< core::Real > &VECTOR_B, const numeric::xyzVector< core::Real > &VECTOR_C, const double DISTANCE_XA)
	calculates the unit vector starting from one linal::Vector3D to another More...
numeric::xyzVector< core::Real >	core::chemical::modifications::tetrahedral_coordinates (const numeric::xyzVector< core::Real > &VECTOR_A, const numeric::xyzVector< core::Real > &VECTOR_B, const numeric::xyzVector< core::Real > &VECTOR_C, const numeric::xyzVector< core::Real > &VECTOR_D, const double DISTANCE_XA)
	calculates point X in B,C,D->A->X More...
double	core::chemical::modifications::projection_angle (const numeric::xyzVector< core::Real > &VECTOR_A, const numeric::xyzVector< core::Real > &VECTOR_B)
	calculates projection angle between two linal::Vector3D More...
double	core::chemical::modifications::projection_angle_cosin (const numeric::xyzVector< core::Real > &VECTOR_A, const numeric::xyzVector< core::Real > &VECTOR_B)
double	core::chemical::modifications::dihedral_coordinates (const numeric::xyzVector< core::Real > &VECTOR_A, const numeric::xyzVector< core::Real > &VECTOR_B, const numeric::xyzVector< core::Real > &VECTOR_C, const numeric::xyzVector< core::Real > &VECTOR_D)
	dihedral angle between four points (A->B -x-> C->D) More...

Detailed Description

A bunch of functions to determine where to place atoms based on hybridization of atoms and number of bonds It should be noted that a vector of coordinates are returned. This is because it creates the angles for all hydrogens that can be placed. If you are combining a fragment, you really only need the first index of coords.

Author

Rosetta conversion: Steven Combs / Sandeep Kothiwale