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RDKit
Open-source cheminformatics and machine learning.
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Namespaces | |
detail | |
Functions | |
std::pair< int, double > | OptimizeMolecule (ForceFields::ForceField &ff, int maxIters=1000) |
Convenience function for optimizing a molecule using a pre-generated force-field. More... | |
void | OptimizeMoleculeConfs (ROMol &mol, ForceFields::ForceField &ff, std::vector< std::pair< int, double >> &res, int numThreads=1, int maxIters=1000) |
Convenience function for optimizing all of a molecule's conformations using. More... | |
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=NULL, double *cosPhi=NULL, RDGeom::Point3D r[4]=NULL, RDGeom::Point3D t[2]=NULL, double d[2]=NULL) |
void RDKIT_FORCEFIELD_EXPORT | computeDihedral (const double *pos, unsigned int idx1, unsigned int idx2, unsigned int idx3, unsigned int idx4, double *dihedral=NULL, double *cosPhi=NULL, RDGeom::Point3D r[4]=NULL, RDGeom::Point3D t[2]=NULL, double d[2]=NULL) |
void RDKIT_FORCEFIELD_EXPORT | computeDihedral (const RDGeom::Point3D *p1, const RDGeom::Point3D *p2, const RDGeom::Point3D *p3, const RDGeom::Point3D *p4, double *dihedral=NULL, double *cosPhi=NULL, RDGeom::Point3D r[4]=NULL, RDGeom::Point3D t[2]=NULL, double d[2]=NULL) |
void RDKIT_FORCEFIELD_EXPORT RDKit::ForceFieldsHelper::computeDihedral | ( | const double * | pos, |
unsigned int | idx1, | ||
unsigned int | idx2, | ||
unsigned int | idx3, | ||
unsigned int | idx4, | ||
double * | dihedral = NULL , |
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double * | cosPhi = NULL , |
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RDGeom::Point3D | r[4] = NULL , |
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RDGeom::Point3D | t[2] = NULL , |
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double | d[2] = NULL |
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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 = NULL , |
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double * | cosPhi = NULL , |
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RDGeom::Point3D | r[4] = NULL , |
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RDGeom::Point3D | t[2] = NULL , |
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double | d[2] = NULL |
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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 = NULL , |
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double * | cosPhi = NULL , |
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RDGeom::Point3D | r[4] = NULL , |
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RDGeom::Point3D | t[2] = NULL , |
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double | d[2] = NULL |
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void RDKIT_FORCEFIELD_EXPORT RDKit::ForceFieldsHelper::normalizeAngleDeg | ( | double & | angleDeg | ) |
std::pair<int, double> RDKit::ForceFieldsHelper::OptimizeMolecule | ( | ForceFields::ForceField & | ff, |
int | maxIters = 1000 |
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Convenience function for optimizing a molecule using a pre-generated force-field.
Definition at line 86 of file FFConvenience.h.
References ForceFields::ForceField::calcEnergy(), ForceFields::ForceField::initialize(), and ForceFields::ForceField::minimize().
Referenced by RDKit::MMFF::MMFFOptimizeMolecule(), and RDKit::UFF::UFFOptimizeMolecule().
void RDKit::ForceFieldsHelper::OptimizeMoleculeConfs | ( | ROMol & | mol, |
ForceFields::ForceField & | ff, | ||
std::vector< std::pair< int, double >> & | res, | ||
int | numThreads = 1 , |
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int | maxIters = 1000 |
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Convenience function for optimizing all of a molecule's conformations using.
Definition at line 106 of file FFConvenience.h.
References RDKit::ROMol::getNumConformers(), RDKit::getNumThreadsToUse(), and RDKit::ForceFieldsHelper::detail::OptimizeMoleculeConfsST().
Referenced by RDKit::MMFF::MMFFOptimizeMoleculeConfs(), and RDKit::UFF::UFFOptimizeMoleculeConfs().