RDKit::MMFF::MMFFMolProperties Class Reference

#include <AtomTyper.h>

Public Member Functions
	MMFFMolProperties (ROMol &mol, const std::string &mmffVariant="MMFF94", std::uint8_t verbosity=MMFF_VERBOSITY_NONE, std::ostream &oStream=std::cout)
	~MMFFMolProperties ()=default
unsigned int	getMMFFBondType (const Bond *bond) const
unsigned int	getMMFFAngleType (const ROMol &mol, const unsigned int idx1, const unsigned int idx2, const unsigned int idx3) const
const std::pair< unsigned int, unsigned int >	getMMFFTorsionType (const ROMol &mol, const unsigned int idx1, const unsigned int idx2, const unsigned int idx3, const unsigned int idx4) const
void	computeMMFFCharges (const ROMol &mol)
const ForceFields::MMFF::MMFFTor *	getMMFFTorsionEmpiricalRuleParams (const ROMol &mol, unsigned int idx2, unsigned int idx3) const
const ForceFields::MMFF::MMFFBond *	getMMFFBondStretchEmpiricalRuleParams (const ROMol &mol, const Bond *bond) const
std::uint8_t	getMMFFAtomType (const unsigned int idx) const
double	getMMFFFormalCharge (const unsigned int idx) const
double	getMMFFPartialCharge (const unsigned int idx) const
void	setMMFFBondTerm (const bool state)
bool	getMMFFBondTerm () const
void	setMMFFAngleTerm (const bool state)
bool	getMMFFAngleTerm () const
void	setMMFFStretchBendTerm (const bool state)
bool	getMMFFStretchBendTerm () const
void	setMMFFOopTerm (const bool state)
bool	getMMFFOopTerm () const
void	setMMFFTorsionTerm (const bool state)
bool	getMMFFTorsionTerm () const
void	setMMFFVdWTerm (const bool state)
bool	getMMFFVdWTerm () const
void	setMMFFEleTerm (const bool state)
bool	getMMFFEleTerm () const
void	setMMFFVariant (const std::string &mmffVariant)
const std::string	getMMFFVariant () const
void	setMMFFDielectricConstant (const double dielConst)
double	getMMFFDielectricConstant () const
void	setMMFFDielectricModel (std::uint8_t dielModel)
std::uint8_t	getMMFFDielectricModel () const
void	setMMFFVerbosity (std::uint8_t verbosity)
std::uint8_t	getMMFFVerbosity () const
void	setMMFFOStream (std::ostream *oStream)
std::ostream &	getMMFFOStream ()
bool	isValid () const
bool	getMMFFBondStretchParams (const ROMol &mol, const unsigned int idx1, const unsigned int idx2, unsigned int &bondType, MMFFBond &mmffBondStretchParams) const
bool	getMMFFAngleBendParams (const ROMol &mol, const unsigned int idx1, const unsigned int idx2, const unsigned int idx3, unsigned int &angleType, MMFFAngle &mmffAngleBendParams) const
bool	getMMFFStretchBendParams (const ROMol &mol, const unsigned int idx1, const unsigned int idx2, const unsigned int idx3, unsigned int &stretchBendType, MMFFStbn &mmffStretchBendParams, MMFFBond mmffBondStretchParams[2], MMFFAngle &mmffAngleBendParams) const
bool	getMMFFTorsionParams (const ROMol &mol, const unsigned int idx1, const unsigned int idx2, const unsigned int idx3, const unsigned int idx4, unsigned int &torsionType, MMFFTor &mmffTorsionParams) const
bool	getMMFFOopBendParams (const ROMol &mol, const unsigned int idx1, const unsigned int idx2, const unsigned int idx3, const unsigned int idx4, MMFFOop &mmffOopBendParams) const
bool	getMMFFVdWParams (const unsigned int idx1, const unsigned int idx2, MMFFVdWRijstarEps &mmffVdWParams) const

Detailed Description

Definition at line 76 of file MMFF/AtomTyper.h.

Constructor & Destructor Documentation

MMFFMolProperties()

RDKit::MMFF::MMFFMolProperties::MMFFMolProperties	(	ROMol &	mol,
		const std::string &	mmffVariant = "MMFF94",
		std::uint8_t	verbosity = MMFF_VERBOSITY_NONE,
		std::ostream &	oStream = std::cout )

References RDKit::MMFF::MMFF_VERBOSITY_NONE.

~MMFFMolProperties()

RDKit::MMFF::MMFFMolProperties::~MMFFMolProperties ( )

default

Member Function Documentation

computeMMFFCharges()

void RDKit::MMFF::MMFFMolProperties::computeMMFFCharges

(

const ROMol &

mol

)

getMMFFAngleBendParams()

bool RDKit::MMFF::MMFFMolProperties::getMMFFAngleBendParams	(	const ROMol &	mol,
		const unsigned int	idx1,
		const unsigned int	idx2,
		const unsigned int	idx3,
		unsigned int &	angleType,
		MMFFAngle &	mmffAngleBendParams ) const

getMMFFAngleTerm()

bool RDKit::MMFF::MMFFMolProperties::getMMFFAngleTerm ( ) const

inline

Definition at line 112 of file MMFF/AtomTyper.h.

getMMFFAngleType()

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

getMMFFAtomType()

std::uint8_t RDKit::MMFF::MMFFMolProperties::getMMFFAtomType ( const unsigned int idx ) const

inline

Definition at line 94 of file MMFF/AtomTyper.h.

References URANGE_CHECK.

getMMFFBondStretchEmpiricalRuleParams()

const ForceFields::MMFF::MMFFBond * RDKit::MMFF::MMFFMolProperties::getMMFFBondStretchEmpiricalRuleParams	(	const ROMol &	mol,
		const Bond *	bond ) const

getMMFFBondStretchParams()

bool RDKit::MMFF::MMFFMolProperties::getMMFFBondStretchParams	(	const ROMol &	mol,
		const unsigned int	idx1,
		const unsigned int	idx2,
		unsigned int &	bondType,
		MMFFBond &	mmffBondStretchParams ) const

getMMFFBondTerm()

bool RDKit::MMFF::MMFFMolProperties::getMMFFBondTerm ( ) const

inline

Definition at line 110 of file MMFF/AtomTyper.h.

getMMFFBondType()

unsigned int RDKit::MMFF::MMFFMolProperties::getMMFFBondType

(

const Bond *

bond

)

const

getMMFFDielectricConstant()

double RDKit::MMFF::MMFFMolProperties::getMMFFDielectricConstant ( ) const

inline

Definition at line 139 of file MMFF/AtomTyper.h.

getMMFFDielectricModel()

std::uint8_t RDKit::MMFF::MMFFMolProperties::getMMFFDielectricModel ( ) const

inline

Definition at line 143 of file MMFF/AtomTyper.h.

getMMFFEleTerm()

bool RDKit::MMFF::MMFFMolProperties::getMMFFEleTerm ( ) const

inline

Definition at line 124 of file MMFF/AtomTyper.h.

getMMFFFormalCharge()

double RDKit::MMFF::MMFFMolProperties::getMMFFFormalCharge ( const unsigned int idx ) const

inline

Definition at line 99 of file MMFF/AtomTyper.h.

References URANGE_CHECK.

getMMFFOopBendParams()

bool RDKit::MMFF::MMFFMolProperties::getMMFFOopBendParams	(	const ROMol &	mol,
		const unsigned int	idx1,
		const unsigned int	idx2,
		const unsigned int	idx3,
		const unsigned int	idx4,
		MMFFOop &	mmffOopBendParams ) const

getMMFFOopTerm()

bool RDKit::MMFF::MMFFMolProperties::getMMFFOopTerm ( ) const

inline

Definition at line 118 of file MMFF/AtomTyper.h.

getMMFFOStream()

std::ostream & RDKit::MMFF::MMFFMolProperties::getMMFFOStream ( )

inline

Definition at line 149 of file MMFF/AtomTyper.h.

getMMFFPartialCharge()

double RDKit::MMFF::MMFFMolProperties::getMMFFPartialCharge ( const unsigned int idx ) const

inline

Definition at line 104 of file MMFF/AtomTyper.h.

References URANGE_CHECK.

getMMFFStretchBendParams()

bool RDKit::MMFF::MMFFMolProperties::getMMFFStretchBendParams	(	const ROMol &	mol,
		const unsigned int	idx1,
		const unsigned int	idx2,
		const unsigned int	idx3,
		unsigned int &	stretchBendType,
		MMFFStbn &	mmffStretchBendParams,
		MMFFBond	mmffBondStretchParams[2],
		MMFFAngle &	mmffAngleBendParams ) const

getMMFFStretchBendTerm()

bool RDKit::MMFF::MMFFMolProperties::getMMFFStretchBendTerm ( ) const

inline

Definition at line 116 of file MMFF/AtomTyper.h.

getMMFFTorsionEmpiricalRuleParams()

const ForceFields::MMFF::MMFFTor * RDKit::MMFF::MMFFMolProperties::getMMFFTorsionEmpiricalRuleParams	(	const ROMol &	mol,
		unsigned int	idx2,
		unsigned int	idx3 ) const

getMMFFTorsionParams()

bool RDKit::MMFF::MMFFMolProperties::getMMFFTorsionParams	(	const ROMol &	mol,
		const unsigned int	idx1,
		const unsigned int	idx2,
		const unsigned int	idx3,
		const unsigned int	idx4,
		unsigned int &	torsionType,
		MMFFTor &	mmffTorsionParams ) const

getMMFFTorsionTerm()

bool RDKit::MMFF::MMFFMolProperties::getMMFFTorsionTerm ( ) const

inline

Definition at line 120 of file MMFF/AtomTyper.h.

getMMFFTorsionType()

const std::pair< unsigned int, unsigned int > RDKit::MMFF::MMFFMolProperties::getMMFFTorsionType	(	const ROMol &	mol,
		const unsigned int	idx1,
		const unsigned int	idx2,
		const unsigned int	idx3,
		const unsigned int	idx4 ) const

getMMFFVariant()

const std::string RDKit::MMFF::MMFFMolProperties::getMMFFVariant ( ) const

inline

Definition at line 131 of file MMFF/AtomTyper.h.

getMMFFVdWParams()

bool RDKit::MMFF::MMFFMolProperties::getMMFFVdWParams	(	const unsigned int	idx1,
		const unsigned int	idx2,
		MMFFVdWRijstarEps &	mmffVdWParams ) const

getMMFFVdWTerm()

bool RDKit::MMFF::MMFFMolProperties::getMMFFVdWTerm ( ) const

inline

Definition at line 122 of file MMFF/AtomTyper.h.

getMMFFVerbosity()

std::uint8_t RDKit::MMFF::MMFFMolProperties::getMMFFVerbosity ( ) const

inline

Definition at line 147 of file MMFF/AtomTyper.h.

isValid()

bool RDKit::MMFF::MMFFMolProperties::isValid ( ) const

inline

Definition at line 150 of file MMFF/AtomTyper.h.

Referenced by RDKit::MMFF::MMFFOptimizeMolecule(), and RDKit::MMFF::MMFFOptimizeMoleculeConfs().

setMMFFAngleTerm()

void RDKit::MMFF::MMFFMolProperties::setMMFFAngleTerm ( const bool state )

inline

Definition at line 111 of file MMFF/AtomTyper.h.

setMMFFBondTerm()

void RDKit::MMFF::MMFFMolProperties::setMMFFBondTerm ( const bool state )

inline

Definition at line 109 of file MMFF/AtomTyper.h.

setMMFFDielectricConstant()

void RDKit::MMFF::MMFFMolProperties::setMMFFDielectricConstant ( const double dielConst )

inline

Definition at line 134 of file MMFF/AtomTyper.h.

References PRECONDITION.

setMMFFDielectricModel()

void RDKit::MMFF::MMFFMolProperties::setMMFFDielectricModel ( std::uint8_t dielModel )

inline

Definition at line 140 of file MMFF/AtomTyper.h.

setMMFFEleTerm()

void RDKit::MMFF::MMFFMolProperties::setMMFFEleTerm ( const bool state )

inline

Definition at line 123 of file MMFF/AtomTyper.h.

setMMFFOopTerm()

void RDKit::MMFF::MMFFMolProperties::setMMFFOopTerm ( const bool state )

inline

Definition at line 117 of file MMFF/AtomTyper.h.

setMMFFOStream()

void RDKit::MMFF::MMFFMolProperties::setMMFFOStream ( std::ostream * oStream )

inline

Definition at line 148 of file MMFF/AtomTyper.h.

setMMFFStretchBendTerm()

void RDKit::MMFF::MMFFMolProperties::setMMFFStretchBendTerm ( const bool state )

inline

Definition at line 113 of file MMFF/AtomTyper.h.

setMMFFTorsionTerm()

void RDKit::MMFF::MMFFMolProperties::setMMFFTorsionTerm ( const bool state )

inline

Definition at line 119 of file MMFF/AtomTyper.h.

setMMFFVariant()

void RDKit::MMFF::MMFFMolProperties::setMMFFVariant ( const std::string & mmffVariant )

inline

Definition at line 125 of file MMFF/AtomTyper.h.

References PRECONDITION.

setMMFFVdWTerm()

void RDKit::MMFF::MMFFMolProperties::setMMFFVdWTerm ( const bool state )

inline

Definition at line 121 of file MMFF/AtomTyper.h.

setMMFFVerbosity()

void RDKit::MMFF::MMFFMolProperties::setMMFFVerbosity ( std::uint8_t verbosity )

inline

Definition at line 144 of file MMFF/AtomTyper.h.

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The documentation for this class was generated from the following file:

• MMFF/AtomTyper.h