DistGeomUtils.h File Reference

#include <RDGeneral/export.h>
#include "BoundsMatrix.h"
#include <Numerics/SymmMatrix.h>
#include <map>
#include <Geometry/point.h>
#include <GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.h>
#include "ChiralSet.h"
#include <RDGeneral/utils.h>
#include <boost/dynamic_bitset.hpp>

Go to the source code of this file.

Namespaces
namespace	ForceFields
namespace	DistGeom

Functions
RDKIT_DISTGEOMETRY_EXPORT double	DistGeom::pickRandomDistMat (const BoundsMatrix &mmat, RDNumeric::SymmMatrix< double > &distmat, int seed=-1)
RDKIT_DISTGEOMETRY_EXPORT double	DistGeom::pickRandomDistMat (const BoundsMatrix &mmat, RDNumeric::SymmMatrix< double > &distmat, RDKit::double_source_type &rng)
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
RDKIT_DISTGEOMETRY_EXPORT bool	DistGeom::computeInitialCoords (const RDNumeric::SymmMatrix< double > &distmat, RDGeom::PointPtrVect &positions, bool randNegEig=false, unsigned int numZeroFail=2, int seed=-1)
	Compute an initial embedded in 3D based on a distance matrix.
RDKIT_DISTGEOMETRY_EXPORT bool	DistGeom::computeInitialCoords (const RDNumeric::SymmMatrix< double > &distmat, RDGeom::PointPtrVect &positions, RDKit::double_source_type &rng, bool randNegEig=false, unsigned int numZeroFail=2)
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
RDKIT_DISTGEOMETRY_EXPORT bool	DistGeom::computeRandomCoords (RDGeom::PointPtrVect &positions, double boxSize, int seed=-1)
	places atoms randomly in a box
RDKIT_DISTGEOMETRY_EXPORT bool	DistGeom::computeRandomCoords (RDGeom::PointPtrVect &positions, double boxSize, RDKit::double_source_type &rng)
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
RDKIT_DISTGEOMETRY_EXPORT ForceFields::ForceField *	DistGeom::constructForceField (const BoundsMatrix &mmat, RDGeom::PointPtrVect &positions, const VECT_CHIRALSET &csets, double weightChiral=1.0, double weightFourthDim=0.1, std::map< std::pair< int, int >, double > *extraWeights=nullptr, double basinSizeTol=5.0, boost::dynamic_bitset<> *fixedPts=nullptr)
	Setup the error function for violation of distance bounds as a forcefield.
RDKIT_DISTGEOMETRY_EXPORT ForceFields::ForceField *	DistGeom::construct3DForceField (const BoundsMatrix &mmat, RDGeom::Point3DPtrVect &positions, const ForceFields::CrystalFF::CrystalFFDetails &etkdgDetails)
RDKIT_DISTGEOMETRY_EXPORT ForceFields::ForceField *	DistGeom::construct3DForceField (const BoundsMatrix &mmat, RDGeom::Point3DPtrVect &positions, const ForceFields::CrystalFF::CrystalFFDetails &etkdgDetails, const std::map< std::pair< unsigned int, unsigned int >, double > &CPCI)
RDKIT_DISTGEOMETRY_EXPORT ForceFields::ForceField *	DistGeom::constructPlain3DForceField (const BoundsMatrix &mmat, RDGeom::Point3DPtrVect &positions, const ForceFields::CrystalFF::CrystalFFDetails &etkdgDetails)
RDKIT_DISTGEOMETRY_EXPORT ForceFields::ForceField *	DistGeom::construct3DImproperForceField (const BoundsMatrix &mmat, RDGeom::Point3DPtrVect &positions, const std::vector< std::vector< int > > &improperAtoms, const std::vector< std::vector< int > > &angles, const std::vector< int > &atomNums)
	Force field with improper terms and SP linearity contributions.
ForceFields::ForceField *	DistGeom::construct3DImproperForceField (const BoundsMatrix &mmat, RDGeom::Point3DPtrVect &positions, const ForceFields::CrystalFF::CrystalFFDetails &etkdgDetails)
	Force field with improper terms and SP linearity contributions.