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Classes
class	MMFFAtomProperties

class	MMFFMolProperties

Typedefs
typedef boost::shared_ptr< MMFFAtomProperties >	MMFFAtomPropertiesPtr

Enumerations
enum	{ CONSTANT = 1, DISTANCE = 2 }

enum	{ MMFF_VERBOSITY_NONE = 0, MMFF_VERBOSITY_LOW = 1, MMFF_VERBOSITY_HIGH = 2 }

Functions
unsigned int	isAngleInRingOfSize3or4 (const ROMol &mol, const unsigned int idx1, const unsigned int idx2, const unsigned int idx3)

unsigned int	isTorsionInRingOfSize4or5 (const ROMol &mol, const unsigned int idx1, const unsigned int idx2, const unsigned int idx3, const unsigned int idx4)

bool	isAtomInAromaticRingOfSize (const Atom *atom, const unsigned int ringSize)

bool	isAtomNOxide (const Atom *atom)

bool	areAtomsInSameAromaticRing (const ROMol &mol, const unsigned int idx1, const unsigned int idx2)

bool	areAtomsInSameRingOfSize (const ROMol &mol, const unsigned int ringSize, const unsigned int numAtoms,...)

unsigned int	sanitizeMMFFMol (RWMol &mol)

void	setMMFFAromaticity (RWMol &mol)

unsigned int	getMMFFStretchBendType (const unsigned int angleType, const unsigned int bondType1, const unsigned int bondType2)

unsigned int	getPeriodicTableRow (const int atomicNum)

const ForceFields::MMFF::MMFFAngle *	getMMFFAngleBendEmpiricalRuleParams (const ROMol &mol, const ForceFields::MMFF::MMFFAngle oldMMFFAngleParams, const ForceFields::MMFF::MMFFProp mmffPropParamsCentralAtom, const ForceFields::MMFF::MMFFBond mmffBondParams1, const ForceFields::MMFF::MMFFBond mmffBondParams2, unsigned int idx1, unsigned int idx2, unsigned int idx3)

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

ForceFields::ForceField *	constructForceField (ROMol &mol, MMFFMolProperties *mmffMolProperties, double nonBondedThresh=100.0, int confId=-1, bool ignoreInterfragInteractions=true)
	Builds and returns a MMFF force field for a molecule. More...

std::pair< int, double >	MMFFOptimizeMolecule (ROMol &mol, int maxIters=1000, std::string mmffVariant="MMFF94", double nonBondedThresh=10.0, int confId=-1, bool ignoreInterfragInteractions=true)
	Convenience function for optimizing a molecule using MMFF. More...

void	MMFFOptimizeMoleculeConfs (ROMol &mol, std::vector< std::pair< int, double > > &res, int numThreads=1, int maxIters=1000, std::string mmffVariant="MMFF94", double nonBondedThresh=10.0, bool ignoreInterfragInteractions=true)
	Convenience function for optimizing all of a molecule's conformations using. More...

Typedef Documentation

◆ MMFFAtomPropertiesPtr

typedef boost::shared_ptr<MMFFAtomProperties> RDKit::MMFF::MMFFAtomPropertiesPtr

Definition at line 39 of file MMFF/AtomTyper.h.

Enumeration Type Documentation

◆ anonymous enum

anonymous enum

Enumerator
CONSTANT
DISTANCE

Definition at line 40 of file MMFF/AtomTyper.h.

◆ anonymous enum

anonymous enum

Enumerator
MMFF_VERBOSITY_NONE
MMFF_VERBOSITY_LOW
MMFF_VERBOSITY_HIGH

Definition at line 41 of file MMFF/AtomTyper.h.

Function Documentation

◆ areAtomsInSameAromaticRing()

bool RDKit::MMFF::areAtomsInSameAromaticRing	(	const ROMol &	mol,
		const unsigned int	idx1,
		const unsigned int	idx2
	)

Referenced by RDKit::MMFF::MMFFMolProperties::isValid().

◆ areAtomsInSameRingOfSize()

bool RDKit::MMFF::areAtomsInSameRingOfSize	(	const ROMol &	mol,
		const unsigned int	ringSize,
		const unsigned int	numAtoms,
			...
	)

Referenced by RDKit::MMFF::MMFFMolProperties::isValid().

◆ constructForceField() [1/2]

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

Builds and returns a MMFF force field for a molecule.

Parameters

mol	the molecule to use
nonBondedThresh	the threshold to be used in adding non-bonded terms to the force field. Any non-bonded contact whose current distance is greater than `nonBondedThresh` * 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 MMFFOptimizeMolecule(), and MMFFOptimizeMoleculeConfs().

◆ constructForceField() [2/2]

ForceFields::ForceField* RDKit::MMFF::constructForceField	(	ROMol &	mol,
		MMFFMolProperties *	mmffMolProperties,
		double	nonBondedThresh = `100.0`,
		int	confId = `-1`,
		bool	ignoreInterfragInteractions = `true`
	)

Builds and returns a MMFF force field for a molecule.

Parameters

mol	the molecule to use
mmffMolProperties	pointer to a MMFFMolProperties (as obtained by a call to setupMMFFForceField())
nonBondedThresh	the threshold to be used in adding non-bonded terms to the force field. Any non-bonded contact whose current distance is greater than `nonBondedThresh` * 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.

◆ getMMFFAngleBendEmpiricalRuleParams()

const ForceFields::MMFF::MMFFAngle* RDKit::MMFF::getMMFFAngleBendEmpiricalRuleParams	(	const ROMol &	mol,
		const ForceFields::MMFF::MMFFAngle *	oldMMFFAngleParams,
		const ForceFields::MMFF::MMFFProp *	mmffPropParamsCentralAtom,
		const ForceFields::MMFF::MMFFBond *	mmffBondParams1,
		const ForceFields::MMFF::MMFFBond *	mmffBondParams2,
		unsigned int	idx1,
		unsigned int	idx2,
		unsigned int	idx3
	)

Referenced by RDKit::MMFF::MMFFMolProperties::isValid().

◆ getMMFFStretchBendType()

unsigned int RDKit::MMFF::getMMFFStretchBendType	(	const unsigned int	angleType,
		const unsigned int	bondType1,
		const unsigned int	bondType2
	)

Referenced by RDKit::MMFF::MMFFMolProperties::isValid().

◆ getPeriodicTableRow()

unsigned int RDKit::MMFF::getPeriodicTableRow ( const int atomicNum )

Referenced by RDKit::MMFF::MMFFMolProperties::isValid().

◆ isAngleInRingOfSize3or4()

unsigned int RDKit::MMFF::isAngleInRingOfSize3or4	(	const ROMol &	mol,
		const unsigned int	idx1,
		const unsigned int	idx2,
		const unsigned int	idx3
	)

Referenced by RDKit::MMFF::MMFFMolProperties::isValid().

◆ isAtomInAromaticRingOfSize()

bool RDKit::MMFF::isAtomInAromaticRingOfSize	(	const Atom *	atom,
		const unsigned int	ringSize
	)

Referenced by RDKit::MMFF::MMFFMolProperties::isValid().

◆ isAtomNOxide()

bool RDKit::MMFF::isAtomNOxide ( const Atom * atom )

Referenced by RDKit::MMFF::MMFFMolProperties::isValid().

◆ isTorsionInRingOfSize4or5()

unsigned int RDKit::MMFF::isTorsionInRingOfSize4or5	(	const ROMol &	mol,
		const unsigned int	idx1,
		const unsigned int	idx2,
		const unsigned int	idx3,
		const unsigned int	idx4
	)

Referenced by RDKit::MMFF::MMFFMolProperties::isValid().

◆ MMFFOptimizeMolecule()

std::pair<int, double> RDKit::MMFF::MMFFOptimizeMolecule	(	ROMol &	mol,
		int	maxIters = `1000`,
		std::string	mmffVariant = `"MMFF94"`,
		double	nonBondedThresh = `10.0`,
		int	confId = `-1`,
		bool	ignoreInterfragInteractions = `true`
	)

Convenience function for optimizing a molecule using MMFF.

Definition at line 43 of file MMFF.h.

References RDKit::ROMol::beginConformers(), ForceFields::ForceField::calcEnergy(), constructForceField(), RDKit::ROMol::endConformers(), RDKit::ROMol::getNumAtoms(), ForceFields::ForceField::initialize(), RDKit::MMFF::MMFFMolProperties::isValid(), ForceFields::ForceField::minimize(), and ForceFields::ForceField::positions().

◆ MMFFOptimizeMoleculeConfs()

void RDKit::MMFF::MMFFOptimizeMoleculeConfs	(	ROMol &	mol,
		std::vector< std::pair< int, double > > &	res,
		int	numThreads = `1`,
		int	maxIters = `1000`,
		std::string	mmffVariant = `"MMFF94"`,
		double	nonBondedThresh = `10.0`,
		bool	ignoreInterfragInteractions = `true`
	)

Convenience function for optimizing all of a molecule's conformations using.

Definition at line 104 of file MMFF.h.

References RDKit::ROMol::beginConformers(), ForceFields::ForceField::calcEnergy(), constructForceField(), RDKit::ROMol::endConformers(), RDKit::ROMol::getNumAtoms(), RDKit::ROMol::getNumConformers(), RDKit::getNumThreadsToUse(), ForceFields::ForceField::initialize(), RDKit::MMFF::MMFFMolProperties::isValid(), ForceFields::ForceField::minimize(), and ForceFields::ForceField::positions().

◆ sanitizeMMFFMol()

unsigned int RDKit::MMFF::sanitizeMMFFMol ( RWMol & mol )

Referenced by RDKit::MMFF::MMFFMolProperties::isValid().

◆ setMMFFAromaticity()

void RDKit::MMFF::setMMFFAromaticity ( RWMol & mol )

Referenced by RDKit::MMFF::MMFFMolProperties::isValid().

Namespaces

Classes

Typedefs

Enumerations

Functions

Typedef Documentation

◆ MMFFAtomPropertiesPtr

Enumeration Type Documentation

◆ anonymous enum

◆ anonymous enum

Function Documentation

◆ areAtomsInSameAromaticRing()

◆ areAtomsInSameRingOfSize()

◆ constructForceField() [1/2]

◆ constructForceField() [2/2]

◆ getMMFFAngleBendEmpiricalRuleParams()

◆ getMMFFStretchBendType()

◆ getPeriodicTableRow()

◆ isAngleInRingOfSize3or4()

◆ isAtomInAromaticRingOfSize()

◆ isAtomNOxide()

◆ isTorsionInRingOfSize4or5()

◆ MMFFOptimizeMolecule()

◆ MMFFOptimizeMoleculeConfs()

◆ sanitizeMMFFMol()

◆ setMMFFAromaticity()