Namespaces
namespace	DefaultParameters

namespace	Tools

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

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

RDKIT_FORCEFIELDHELPERS_EXPORT bool	isRingAromatic (const ROMol &mol, const INT_VECT &ringIndxVect)

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

RDKIT_FORCEFIELDHELPERS_EXPORT bool	isAtomNOxide (const Atom *atom)

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

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

RDKIT_FORCEFIELDHELPERS_EXPORT unsigned int	sanitizeMMFFMol (RWMol &mol)

RDKIT_FORCEFIELDHELPERS_EXPORT void	setMMFFAromaticity (RWMol &mol)

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

RDKIT_FORCEFIELDHELPERS_EXPORT unsigned int	getPeriodicTableRow (const int atomicNum)

RDKIT_FORCEFIELDHELPERS_EXPORT 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)

RDKIT_FORCEFIELDHELPERS_EXPORT 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.

RDKIT_FORCEFIELDHELPERS_EXPORT 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.

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.

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)

Typedef Documentation

◆ MMFFAtomPropertiesPtr

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

Definition at line 67 of file MMFF/AtomTyper.h.

Enumeration Type Documentation

◆ anonymous enum

anonymous enum

Enumerator
CONSTANT
DISTANCE

Definition at line 68 of file MMFF/AtomTyper.h.

◆ anonymous enum

anonymous enum

Enumerator
MMFF_VERBOSITY_NONE
MMFF_VERBOSITY_LOW
MMFF_VERBOSITY_HIGH

Definition at line 69 of file MMFF/AtomTyper.h.

Function Documentation

◆ areAtomsInSameAromaticRing()

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

◆ areAtomsInSameRingOfSize()

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

◆ constructForceField() [1/2]

RDKIT_FORCEFIELDHELPERS_EXPORT 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]

RDKIT_FORCEFIELDHELPERS_EXPORT 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 object
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()

RDKIT_FORCEFIELDHELPERS_EXPORT 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 )

◆ getMMFFStretchBendType()

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

◆ getPeriodicTableRow()

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

◆ isAngleInRingOfSize3or4()

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

◆ isAtomInAromaticRingOfSize()

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

◆ isAtomNOxide()

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

◆ isRingAromatic()

RDKIT_FORCEFIELDHELPERS_EXPORT bool RDKit::MMFF::isRingAromatic	(	const ROMol &	mol,
		const INT_VECT &	ringIndxVect )

◆ isTorsionInRingOfSize4or5()

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

◆ 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 )

inline

Convenience function for optimizing a molecule using MMFF.

Definition at line 45 of file MMFF.h.

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

◆ 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 )

inline

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

Definition at line 82 of file MMFF.h.

References constructForceField(), RDKit::ROMol::getNumConformers(), RDKit::ForceFieldsHelper::OptimizeMoleculeConfs(), and RDKit::rdvalue_is().

◆ sanitizeMMFFMol()

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

◆ setMMFFAromaticity()

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

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()

◆ isRingAromatic()

◆ isTorsionInRingOfSize4or5()

◆ MMFFOptimizeMolecule()

◆ MMFFOptimizeMoleculeConfs()

◆ sanitizeMMFFMol()

◆ setMMFFAromaticity()