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"

Go to the source code of this file.

Namespaces

namespace  ForceFields
namespace  DistGeom

Functions

double DistGeom::pickRandomDistMat (const BoundsMatrix &mmat, RDNumeric::SymmMatrix< double > &distmat, int seed=-1)
bool DistGeom::computeInitialCoords (const RDNumeric::SymmMatrix< double > &distmat, RDGeom::PointPtrVect &positions, bool randNegEig=false, unsigned int numZeroFail=2)
 Compute an initial embedded in 3D based on a distance matrix.
bool DistGeom::computeRandomCoords (RDGeom::PointPtrVect &positions, double boxSize)
 places atoms randomly in a box
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.
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Defines