Namespaces
namespace	Tools

Typedefs
typedef std::vector< const ForceFields::UFF::AtomicParams * >	AtomicParamVect

Functions
RDKIT_FORCEFIELDHELPERS_EXPORT std::pair< AtomicParamVect, bool >	getAtomTypes (const ROMol &mol, const std::string &paramData="")

RDKIT_FORCEFIELDHELPERS_EXPORT bool	getUFFBondStretchParams (const ROMol &mol, unsigned int idx1, unsigned int idx2, ForceFields::UFF::UFFBond &uffBondStretchParams)

RDKIT_FORCEFIELDHELPERS_EXPORT bool	getUFFAngleBendParams (const ROMol &mol, unsigned int idx1, unsigned int idx2, unsigned int idx3, ForceFields::UFF::UFFAngle &uffAngleBendParams)

RDKIT_FORCEFIELDHELPERS_EXPORT bool	getUFFTorsionParams (const ROMol &mol, unsigned int idx1, unsigned int idx2, unsigned int idx3, unsigned int idx4, ForceFields::UFF::UFFTor &uffTorsionParams)

RDKIT_FORCEFIELDHELPERS_EXPORT bool	getUFFInversionParams (const ROMol &mol, unsigned int idx1, unsigned int idx2, unsigned int idx3, unsigned int idx4, ForceFields::UFF::UFFInv &uffInversionParams)

RDKIT_FORCEFIELDHELPERS_EXPORT bool	getUFFVdWParams (const ROMol &mol, unsigned int idx1, unsigned int idx2, ForceFields::UFF::UFFVdW &uffVdWParams)

RDKIT_FORCEFIELDHELPERS_EXPORT ForceFields::ForceField *	constructForceField (ROMol &mol, double vdwThresh=100.0, int confId=-1, bool ignoreInterfragInteractions=true)
	Builds and returns a UFF force field for a molecule.

RDKIT_FORCEFIELDHELPERS_EXPORT ForceFields::ForceField *	constructForceField (ROMol &mol, const AtomicParamVect &params, double vdwThresh=100.0, int confId=-1, bool ignoreInterfragInteractions=true)
	Builds and returns a UFF force field for a molecule.

std::pair< int, double >	UFFOptimizeMolecule (ROMol &mol, int maxIters=1000, double vdwThresh=10.0, int confId=-1, bool ignoreInterfragInteractions=true)
	Convenience function for optimizing a molecule using UFF.

void	UFFOptimizeMoleculeConfs (ROMol &mol, std::vector< std::pair< int, double > > &res, int numThreads=1, int maxIters=1000, double vdwThresh=10.0, bool ignoreInterfragInteractions=true)

Typedef Documentation

◆ AtomicParamVect

typedef std::vector< const ForceFields::UFF::AtomicParams * > RDKit::UFF::AtomicParamVect

Definition at line 28 of file UFF/AtomTyper.h.

Function Documentation

◆ constructForceField() [1/2]

RDKIT_FORCEFIELDHELPERS_EXPORT ForceFields::ForceField * RDKit::UFF::constructForceField	(	ROMol &	mol,
		const AtomicParamVect &	params,
		double	vdwThresh = `100.0`,
		int	confId = `-1`,
		bool	ignoreInterfragInteractions = `true`
	)

Builds and returns a UFF force field for a molecule.

Parameters

mol	the molecule to use
params	a vector with pointers to the ForceFields::UFF::AtomicParams structures to be used
vdwThresh	the threshold to be used in adding van der Waals terms to the force field. Any non-bonded contact whose current distance is greater than `vdwThresh` * the minimum value for that contact will not be included.
confId	the optional conformer id, if this isn't provided, the molecule's default confId will be used.
ignoreInterfragInteractions	if true, nonbonded terms will not be added between fragments

Returns: the new force field. The client is responsible for free'ing this.

◆ constructForceField() [2/2]

RDKIT_FORCEFIELDHELPERS_EXPORT ForceFields::ForceField * RDKit::UFF::constructForceField	(	ROMol &	mol,
		double	vdwThresh = `100.0`,
		int	confId = `-1`,
		bool	ignoreInterfragInteractions = `true`
	)

Builds and returns a UFF force field for a molecule.

Parameters

mol	the molecule to use
vdwThresh	the threshold to be used in adding van der Waals terms to the force field. Any non-bonded contact whose current distance is greater than `vdwThresh` * the minimum value for that contact will not be included.
confId	the optional conformer id, if this isn't provided, the molecule's default confId will be used.
ignoreInterfragInteractions	if true, nonbonded terms will not be added between fragments

Returns: the new force field. The client is responsible for free'ing this.

Referenced by UFFOptimizeMolecule(), and UFFOptimizeMoleculeConfs().

◆ getAtomTypes()

RDKIT_FORCEFIELDHELPERS_EXPORT std::pair< AtomicParamVect, bool > RDKit::UFF::getAtomTypes	(	const ROMol &	mol,
		const std::string &	paramData = `""`
	)

◆ getUFFAngleBendParams()

RDKIT_FORCEFIELDHELPERS_EXPORT bool RDKit::UFF::getUFFAngleBendParams	(	const ROMol &	mol,
		unsigned int	idx1,
		unsigned int	idx2,
		unsigned int	idx3,
		ForceFields::UFF::UFFAngle &	uffAngleBendParams
	)

◆ getUFFBondStretchParams()

RDKIT_FORCEFIELDHELPERS_EXPORT bool RDKit::UFF::getUFFBondStretchParams	(	const ROMol &	mol,
		unsigned int	idx1,
		unsigned int	idx2,
		ForceFields::UFF::UFFBond &	uffBondStretchParams
	)

◆ getUFFInversionParams()

RDKIT_FORCEFIELDHELPERS_EXPORT bool RDKit::UFF::getUFFInversionParams	(	const ROMol &	mol,
		unsigned int	idx1,
		unsigned int	idx2,
		unsigned int	idx3,
		unsigned int	idx4,
		ForceFields::UFF::UFFInv &	uffInversionParams
	)

◆ getUFFTorsionParams()

RDKIT_FORCEFIELDHELPERS_EXPORT bool RDKit::UFF::getUFFTorsionParams	(	const ROMol &	mol,
		unsigned int	idx1,
		unsigned int	idx2,
		unsigned int	idx3,
		unsigned int	idx4,
		ForceFields::UFF::UFFTor &	uffTorsionParams
	)

◆ getUFFVdWParams()

RDKIT_FORCEFIELDHELPERS_EXPORT bool RDKit::UFF::getUFFVdWParams	(	const ROMol &	mol,
		unsigned int	idx1,
		unsigned int	idx2,
		ForceFields::UFF::UFFVdW &	uffVdWParams
	)

◆ UFFOptimizeMolecule()

std::pair< int, double > RDKit::UFF::UFFOptimizeMolecule	(	ROMol &	mol,
		int	maxIters = `1000`,
		double	vdwThresh = `10.0`,
		int	confId = `-1`,
		bool	ignoreInterfragInteractions = `true`
	)

inline

Convenience function for optimizing a molecule using UFF.

Definition at line 40 of file UFF.h.

References constructForceField(), RDKit::ForceFieldsHelper::OptimizeMolecule(), and RDKit::rdvalue_is().

◆ UFFOptimizeMoleculeConfs()

void RDKit::UFF::UFFOptimizeMoleculeConfs	(	ROMol &	mol,
		std::vector< std::pair< int, double > > &	res,
		int	numThreads = `1`,
		int	maxIters = `1000`,
		double	vdwThresh = `10.0`,
		bool	ignoreInterfragInteractions = `true`
	)