RDKit::UFF::Tools Namespace Reference

Classes
class	DefaultTorsionBondSmarts

Enumerations
enum	{ RELATION_1_2 = 0 , RELATION_1_3 = 1 , RELATION_1_4 = 2 , RELATION_1_X = 3 }

Functions
RDKIT_FORCEFIELDHELPERS_EXPORT void	addAtomChargeFlags (const Atom *atom, std::string &atomKey, bool tolerateChargeMismatch=true)
RDKIT_FORCEFIELDHELPERS_EXPORT std::string	getAtomLabel (const Atom *atom)
RDKIT_FORCEFIELDHELPERS_EXPORT unsigned int	twoBitCellPos (unsigned int nAtoms, int i, int j)
RDKIT_FORCEFIELDHELPERS_EXPORT void	setTwoBitCell (boost::shared_array< std::uint8_t > &res, unsigned int pos, std::uint8_t value)
RDKIT_FORCEFIELDHELPERS_EXPORT std::uint8_t	getTwoBitCell (boost::shared_array< std::uint8_t > &res, unsigned int pos)
RDKIT_FORCEFIELDHELPERS_EXPORT boost::shared_array< std::uint8_t >	buildNeighborMatrix (const ROMol &mol)
RDKIT_FORCEFIELDHELPERS_EXPORT void	addBonds (const ROMol &mol, const AtomicParamVect &params, ForceFields::ForceField *field)
RDKIT_FORCEFIELDHELPERS_EXPORT void	addAngles (const ROMol &mol, const AtomicParamVect &params, ForceFields::ForceField *field)
RDKIT_FORCEFIELDHELPERS_EXPORT void	addNonbonded (const ROMol &mol, int confId, const AtomicParamVect &params, ForceFields::ForceField *field, boost::shared_array< std::uint8_t > neighborMatrix, double vdwThresh=100.0, bool ignoreInterfragInteractions=true)
RDKIT_FORCEFIELDHELPERS_EXPORT void	addTorsions (const ROMol &mol, const AtomicParamVect &params, ForceFields::ForceField *field, const std::string &torsionBondSmarts=DefaultTorsionBondSmarts::string())
RDKIT_FORCEFIELDHELPERS_EXPORT void	addInversions (const ROMol &mol, const AtomicParamVect &params, ForceFields::ForceField *field)

Enumeration Type Documentation

anonymous enum

anonymous enum

Enumerator
RELATION_1_2
RELATION_1_3
RELATION_1_4
RELATION_1_X

Definition at line 96 of file UFF/Builder.h.

Function Documentation

addAngles()

RDKIT_FORCEFIELDHELPERS_EXPORT void RDKit::UFF::Tools::addAngles	(	const ROMol &	mol,
		const AtomicParamVect &	params,
		ForceFields::ForceField *	field
	)

addAtomChargeFlags()

RDKIT_FORCEFIELDHELPERS_EXPORT void RDKit::UFF::Tools::addAtomChargeFlags	(	const Atom *	atom,
		std::string &	atomKey,
		bool	tolerateChargeMismatch = true
	)

addBonds()

RDKIT_FORCEFIELDHELPERS_EXPORT void RDKit::UFF::Tools::addBonds	(	const ROMol &	mol,
		const AtomicParamVect &	params,
		ForceFields::ForceField *	field
	)

addInversions()

RDKIT_FORCEFIELDHELPERS_EXPORT void RDKit::UFF::Tools::addInversions	(	const ROMol &	mol,
		const AtomicParamVect &	params,
		ForceFields::ForceField *	field
	)

addNonbonded()

RDKIT_FORCEFIELDHELPERS_EXPORT void RDKit::UFF::Tools::addNonbonded	(	const ROMol &	mol,
		int	confId,
		const AtomicParamVect &	params,
		ForceFields::ForceField *	field,
		boost::shared_array< std::uint8_t >	neighborMatrix,
		double	vdwThresh = 100.0,
		bool	ignoreInterfragInteractions = true
	)

addTorsions()

RDKIT_FORCEFIELDHELPERS_EXPORT void RDKit::UFF::Tools::addTorsions	(	const ROMol &	mol,
		const AtomicParamVect &	params,
		ForceFields::ForceField *	field,
		const std::string &	torsionBondSmarts = DefaultTorsionBondSmarts::string()
	)

buildNeighborMatrix()

RDKIT_FORCEFIELDHELPERS_EXPORT boost::shared_array< std::uint8_t > RDKit::UFF::Tools::buildNeighborMatrix

(

const ROMol &

mol

)

getAtomLabel()

RDKIT_FORCEFIELDHELPERS_EXPORT std::string RDKit::UFF::Tools::getAtomLabel

(

const Atom *

atom

)

getTwoBitCell()

RDKIT_FORCEFIELDHELPERS_EXPORT std::uint8_t RDKit::UFF::Tools::getTwoBitCell	(	boost::shared_array< std::uint8_t > &	res,
		unsigned int	pos
	)

setTwoBitCell()

RDKIT_FORCEFIELDHELPERS_EXPORT void RDKit::UFF::Tools::setTwoBitCell	(	boost::shared_array< std::uint8_t > &	res,
		unsigned int	pos,
		std::uint8_t	value
	)

twoBitCellPos()

RDKIT_FORCEFIELDHELPERS_EXPORT unsigned int RDKit::UFF::Tools::twoBitCellPos	(	unsigned int	nAtoms,
		int	i,
		int	j
	)