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RDKit
Open-source cheminformatics and machine learning.
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#include <RDGeneral/export.h>
#include "BoundsMatrix.h"
#include <Numerics/SymmMatrix.h>
#include <map>
#include <Geometry/point.h>
#include "ChiralSet.h"
#include <RDGeneral/utils.h>
#include <boost/dynamic_bitset.hpp>
Go to the source code of this file.
Namespaces | |
ForceFields | |
ForceFields::CrystalFF | |
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. More... | |
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. More... | |
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. More... | |
RDKIT_DISTGEOMETRY_EXPORT bool | DistGeom::computeRandomCoords (RDGeom::PointPtrVect &positions, double boxSize, int seed=-1) |
places atoms randomly in a box More... | |
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. More... | |
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=0, double basinSizeTol=5.0, boost::dynamic_bitset<> *fixedPts=nullptr) |
Setup the error function for violation of distance bounds as a forcefield. More... | |
RDKIT_DISTGEOMETRY_EXPORT ForceFields::ForceField * | DistGeom::construct3DForceField (const BoundsMatrix &mmat, RDGeom::Point3DPtrVect &positions, const ForceFields::CrystalFF::CrystalFFDetails &etkdgDetails) |
Force field with experimental torsion angle preferences and 1-2/1-3 distance. More... | |
RDKIT_DISTGEOMETRY_EXPORT ForceFields::ForceField * | DistGeom::constructPlain3DForceField (const BoundsMatrix &mmat, RDGeom::Point3DPtrVect &positions, const ForceFields::CrystalFF::CrystalFFDetails &etkdgDetails) |
Force field with experimental torsion angle preferences and 1-2/1-3 distance. More... | |
RDKIT_DISTGEOMETRY_EXPORT ForceFields::ForceField * | DistGeom::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... | |