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RDKit
Open-source cheminformatics and machine learning.
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11 #ifndef _RD_DISTGEOMUTILS_H_
12 #define _RD_DISTGEOMUTILS_H_
20 #include <boost/dynamic_bitset.hpp>
25 struct CrystalFFDetails;
70 unsigned int numZeroFail = 2,
int seed = -1);
75 bool randNegEig =
false,
unsigned int numZeroFail = 2);
121 double weightFourthDim = 0.1,
122 std::map<std::pair<int, int>,
double> *extraWeights = 0,
123 double basinSizeTol = 5.0, boost::dynamic_bitset<> *fixedPts =
nullptr);
172 const std::vector<std::vector<int>> &improperAtoms,
173 const std::vector<int> &atomNums);
std::vector< RDGeom::Point3D * > Point3DPtrVect
RDKIT_DISTGEOMETRY_EXPORT ForceFields::ForceField * 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.
A symmetric matrix class.
#define RDKIT_DISTGEOMETRY_EXPORT
A class to store forcefields and handle minimization.
RDKIT_DISTGEOMETRY_EXPORT ForceFields::ForceField * 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.
RDKIT_DISTGEOMETRY_EXPORT ForceFields::ForceField * 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.
boost::variate_generator< rng_type &, uniform_double > double_source_type
RDKIT_DISTGEOMETRY_EXPORT ForceFields::ForceField * 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.
RDKIT_DISTGEOMETRY_EXPORT bool computeRandomCoords(RDGeom::PointPtrVect &positions, double boxSize, int seed=-1)
places atoms randomly in a box
std::vector< ChiralSetPtr > VECT_CHIRALSET
RDKIT_DISTGEOMETRY_EXPORT double pickRandomDistMat(const BoundsMatrix &mmat, RDNumeric::SymmMatrix< double > &distmat, int seed=-1)
std::vector< RDGeom::Point * > PointPtrVect
RDKIT_DISTGEOMETRY_EXPORT bool 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.