RDKit::ForceFieldsHelper Namespace Reference

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)
std::unique_ptr< ForceFields::ForceField >	createEmptyForceFieldForMol (ROMol &mol, int confId=-1)
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)

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

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

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

createEmptyForceFieldForMol()

std::unique_ptr< ForceFields::ForceField > RDKit::ForceFieldsHelper::createEmptyForceFieldForMol ( ROMol &  mol, int  confId = -1  )

inline

Convenience Function for generating an empty force Field with just the molecules' atoms position.

Definition at line 137 of file FFConvenience.h.

References RDKit::ROMol::getConformer(), and RDKit::rdvalue_is().

normalizeAngleDeg()

void RDKIT_FORCEFIELD_EXPORT RDKit::ForceFieldsHelper::normalizeAngleDeg

(

double &

angleDeg

)

OptimizeMolecule()

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

inline

Convenience function for optimizing a molecule using a pre-generated force-field

Definition at line 94 of file FFConvenience.h.

References RDKit::rdvalue_is().

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  )

inline

Convenience function for optimizing all of a molecule's conformations using a pre-generated force-field

Definition at line 115 of file FFConvenience.h.

References RDKit::ROMol::getNumConformers(), RDKit::getNumThreadsToUse(), RDKit::ForceFieldsHelper::detail::OptimizeMoleculeConfsST(), and RDKit::rdvalue_is().

Referenced by RDKit::MMFF::MMFFOptimizeMoleculeConfs(), and RDKit::UFF::UFFOptimizeMoleculeConfs().