RDKit
Open-source cheminformatics and machine learning.
RDKit::ForceFieldsHelper Namespace Reference

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)
 

Function Documentation

◆ computeDihedral() [1/3]

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,
double *  cosPhi = NULL,
RDGeom::Point3D  r[4] = NULL,
RDGeom::Point3D  t[2] = NULL,
double  d[2] = NULL 
)

◆ computeDihedral() [2/3]

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,
double *  cosPhi = NULL,
RDGeom::Point3D  r[4] = NULL,
RDGeom::Point3D  t[2] = NULL,
double  d[2] = NULL 
)

◆ computeDihedral() [3/3]

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,
double *  cosPhi = NULL,
RDGeom::Point3D  r[4] = NULL,
RDGeom::Point3D  t[2] = NULL,
double  d[2] = NULL 
)

◆ normalizeAngleDeg()

void RDKIT_FORCEFIELD_EXPORT RDKit::ForceFieldsHelper::normalizeAngleDeg ( double &  angleDeg)

◆ OptimizeMolecule()

std::pair<int, double> RDKit::ForceFieldsHelper::OptimizeMolecule ( ForceFields::ForceField ff,
int  maxIters = 1000 
)

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().

◆ OptimizeMoleculeConfs()

void RDKit::ForceFieldsHelper::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.

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().