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RDKit
Open-source cheminformatics and machine learning.
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Namespaces | |
namespace | detail |
Functions | |
std::pair< int, double > | OptimizeMolecule (ForceFields::ForceField &ff, int maxIters=1000) |
void | OptimizeMoleculeConfs (ROMol &mol, ForceFields::ForceField &ff, std::vector< std::pair< int, double > > &res, int numThreads=1, int maxIters=1000) |
void RDKIT_FORCEFIELD_EXPORT | normalizeAngleDeg (double &angleDeg) |
void RDKIT_FORCEFIELD_EXPORT | computeDihedral (const RDGeom::PointPtrVect &pos, unsigned int idx1, unsigned int idx2, unsigned int idx3, unsigned int idx4, double *dihedral=nullptr, double *cosPhi=nullptr, RDGeom::Point3D r[4]=nullptr, RDGeom::Point3D t[2]=nullptr, double d[2]=nullptr) |
void RDKIT_FORCEFIELD_EXPORT | computeDihedral (const double *pos, unsigned int idx1, unsigned int idx2, unsigned int idx3, unsigned int idx4, double *dihedral=nullptr, double *cosPhi=nullptr, RDGeom::Point3D r[4]=nullptr, RDGeom::Point3D t[2]=nullptr, double d[2]=nullptr) |
void RDKIT_FORCEFIELD_EXPORT | computeDihedral (const RDGeom::Point3D *p1, const RDGeom::Point3D *p2, const RDGeom::Point3D *p3, const RDGeom::Point3D *p4, double *dihedral=nullptr, double *cosPhi=nullptr, RDGeom::Point3D r[4]=nullptr, RDGeom::Point3D t[2]=nullptr, double d[2]=nullptr) |
void RDKIT_FORCEFIELD_EXPORT RDKit::ForceFieldsHelper::computeDihedral | ( | const double * | pos, |
unsigned int | idx1, | ||
unsigned int | idx2, | ||
unsigned int | idx3, | ||
unsigned int | idx4, | ||
double * | dihedral = nullptr , |
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double * | cosPhi = nullptr , |
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RDGeom::Point3D | r[4] = nullptr , |
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RDGeom::Point3D | t[2] = nullptr , |
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double | d[2] = nullptr |
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void RDKIT_FORCEFIELD_EXPORT RDKit::ForceFieldsHelper::computeDihedral | ( | const RDGeom::Point3D * | p1, |
const RDGeom::Point3D * | p2, | ||
const RDGeom::Point3D * | p3, | ||
const RDGeom::Point3D * | p4, | ||
double * | dihedral = nullptr , |
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double * | cosPhi = nullptr , |
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RDGeom::Point3D | r[4] = nullptr , |
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RDGeom::Point3D | t[2] = nullptr , |
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double | d[2] = nullptr |
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void RDKIT_FORCEFIELD_EXPORT RDKit::ForceFieldsHelper::computeDihedral | ( | const RDGeom::PointPtrVect & | pos, |
unsigned int | idx1, | ||
unsigned int | idx2, | ||
unsigned int | idx3, | ||
unsigned int | idx4, | ||
double * | dihedral = nullptr , |
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double * | cosPhi = nullptr , |
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RDGeom::Point3D | r[4] = nullptr , |
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RDGeom::Point3D | t[2] = nullptr , |
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double | d[2] = nullptr |
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void RDKIT_FORCEFIELD_EXPORT RDKit::ForceFieldsHelper::normalizeAngleDeg | ( | double & | angleDeg | ) |
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inline |
Convenience function for optimizing a molecule using a pre-generated force-field
Definition at line 93 of file FFConvenience.h.
References ForceFields::ForceField::calcEnergy(), ForceFields::ForceField::initialize(), and ForceFields::ForceField::minimize().
Referenced by RDKit::MMFF::MMFFOptimizeMolecule(), and RDKit::UFF::UFFOptimizeMolecule().
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inline |
Convenience function for optimizing all of a molecule's conformations using a pre-generated force-field
Definition at line 114 of file FFConvenience.h.
References RDKit::ROMol::getNumConformers(), RDKit::getNumThreadsToUse(), and RDKit::ForceFieldsHelper::detail::OptimizeMoleculeConfsST().
Referenced by RDKit::MMFF::MMFFOptimizeMoleculeConfs(), and RDKit::UFF::UFFOptimizeMoleculeConfs().