RDKit
Open-source cheminformatics and machine learning.
DistGeomUtils.h File Reference
#include "BoundsMatrix.h"
#include <Numerics/SymmMatrix.h>
#include <map>
#include <Geometry/point.h>
#include "ChiralSet.h"
#include <RDGeneral/utils.h>

Go to the source code of this file.

Namespaces

 ForceFields
 
 DistGeom
 

Functions

double DistGeom::pickRandomDistMat (const BoundsMatrix &mmat, RDNumeric::SymmMatrix< double > &distmat, int seed=-1)
 
double DistGeom::pickRandomDistMat (const BoundsMatrix &mmat, RDNumeric::SymmMatrix< double > &distmat, RDKit::double_source_type &rng)
 
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. More...
 
bool DistGeom::computeInitialCoords (const RDNumeric::SymmMatrix< double > &distmat, RDGeom::PointPtrVect &positions, RDKit::double_source_type &rng, bool randNegEig=false, unsigned int numZeroFail=2)
 
bool DistGeom::computeRandomCoords (RDGeom::PointPtrVect &positions, double boxSize, int seed=-1)
 places atoms randomly in a box More...
 
bool DistGeom::computeRandomCoords (RDGeom::PointPtrVect &positions, double boxSize, RDKit::double_source_type &rng)
 
ForceFields::ForceFieldDistGeom::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=0, double basinSizeTol=5.0)
 Setup the error function for violation of distance bounds as a forcefield. More...
 
ForceFields::ForceFieldDistGeom::construct3DForceField (const BoundsMatrix &mmat, RDGeom::Point3DPtrVect &positions, const std::vector< std::pair< int, int > > &bonds, const std::vector< std::vector< int > > &angles, const std::vector< std::vector< int > > &expTorsionAtoms, const std::vector< std::pair< std::vector< int >, std::vector< double > > > &expTorsionAngles, const std::vector< std::vector< int > > &improperAtoms, const std::vector< int > &atomNums)
 Force field with experimental torsion angle preferences and 1-2/1-3 distance. More...
 
ForceFields::ForceFieldDistGeom::constructPlain3DForceField (const BoundsMatrix &mmat, RDGeom::Point3DPtrVect &positions, const std::vector< std::pair< int, int > > &bonds, const std::vector< std::vector< int > > &angles, const std::vector< std::vector< int > > &expTorsionAtoms, const std::vector< std::pair< std::vector< int >, std::vector< double > > > &expTorsionAngles, const std::vector< int > &atomNums)
 Force field with experimental torsion angle preferences and 1-2/1-3 distance. More...
 
ForceFields::ForceFieldDistGeom::construct3DImproperForceField (const BoundsMatrix &mmat, RDGeom::Point3DPtrVect &positions, const std::vector< std::vector< int > > &improperAtoms, const std::vector< int > &atomNums)
 Force field with only improper terms. More...