Contains classes and functions related to the calculation/preciction of physicochemical molecular properties. More...

Classes
class	AtomHydrophobicityCalculator
	AtomHydrophobicityCalculator. More...

class	AtomProperty
	Provides keys for built-in MolProp.Atom properties. More...

class	AtomPropertyDefault
	Provides default values for built-in Chem.Atom properties. More...

class	BondProperty
	Provides keys for built-in MolProp.Bond properties. More...

class	CoordinationGeometry
	Provides constants used to specify the spatial geometry of atom arrangements around a common central atom. More...

class	ElementHistogram
	A data type for the storage of element histograms of chemical compounds. More...

class	HBondAcceptorAtomType
	Provides constants used to specify the structural class of H-bond acceptor atoms. More...

class	HBondAcceptorAtomTyper

class	HBondDonorAtomType
	Provides constants used to specify the structural class of H-bond donor atoms. More...

class	HBondDonorAtomTyper

class	LogSCalculator
	LogSCalculator. More...

class	MassComposition
	A data type for the storage of mass percent compositions of chemical compounds. More...

class	MHMOPiChargeCalculator
	MHMOPiChargeCalculator. More...

class	PEOESigmaChargeCalculator
	PEOESigmaChargeCalculator. More...

class	TPSACalculator
	TPSACalculator. More...

class	XLogPCalculator
	XLogPCalculator. More...

Functions
str	generateExplicitMolecularFormula (Chem.AtomContainer cntnr)

int	getNetFormalCharge (Chem.AtomContainer cntnr)

str	generateExplicitMassCompositionString (Chem.AtomContainer cntnr)

None	generateExplicitElementHistogram (Chem.AtomContainer cntnr, ElementHistogram hist, bool append=False)

None	calcExplicitMassComposition (Chem.AtomContainer cntnr, MassComposition mass_comp)

float	calcExplicitMass (Chem.AtomContainer cntnr)

bool	calcDipoleMoment (Chem.AtomContainer cntnr, Math.Vector3D moment)

bool	calcDipoleMoment (Chem.AtomContainer cntnr, Chem.Atom3DCoordinatesFunction coords_func, Math.Vector3D moment)

int	getAromaticAtomCount (Chem.AtomContainer cntnr)

int	getRingAtomCount (Chem.AtomContainer cntnr)

int	getExplicitChainAtomCount (Chem.AtomContainer cntnr)

int	getExplicitAtomCount (Chem.AtomContainer cntnr)

int	getExplicitAtomCount (Chem.AtomContainer cntnr, int type, bool strict=True)

int	getHeavyAtomCount (Chem.AtomContainer cntnr)

bool	isUnsaturated (Chem.Atom atom, Chem.MolecularGraph molgraph)

int	getPeriod (Chem.Atom atom)

int	calcValence (Chem.Atom atom, Chem.MolecularGraph molgraph)

int	calcExplicitValence (Chem.Atom atom, Chem.MolecularGraph molgraph)

None	clearPEOESigmaCharge (Chem.Atom atom)

bool	hasPEOESigmaCharge (Chem.Atom atom)

float	getPEOESigmaCharge (Chem.Atom atom)

None	setPEOESigmaCharge (Chem.Atom atom, float charge)

None	clearMHMOPiCharge (Chem.Atom atom)

bool	hasMHMOPiCharge (Chem.Atom atom)

float	getMHMOPiCharge (Chem.Atom atom)

None	setMHMOPiCharge (Chem.Atom atom, float charge)

float	calcTotalPartialCharge (Chem.Atom atom)

str	getElementName (Chem.Atom atom)

None	clearHBondDonorType (Chem.Atom atom)

bool	hasHBondDonorType (Chem.Atom atom)

int	getHBondDonorType (Chem.Atom atom)

None	setHBondDonorType (Chem.Atom atom, int type)

None	clearHBondAcceptorType (Chem.Atom atom)

bool	hasHBondAcceptorType (Chem.Atom atom)

int	getHBondAcceptorType (Chem.Atom atom)

None	setHBondAcceptorType (Chem.Atom atom, int type)

bool	isInRingOfSize (Chem.Atom atom, Chem.MolecularGraph molgraph, int size)

bool	isInRing (Chem.Atom atom, Chem.MolecularGraph molgraph)

bool	isSemiMetal (Chem.Atom atom)

bool	isNonMetal (Chem.Atom atom)

bool	isTransitionMetal (Chem.Atom atom)

bool	isMetal (Chem.Atom atom)

bool	isCarbonylLikeAtom (Chem.Atom atom, Chem.MolecularGraph molgraph, bool c_only=False, bool db_o_only=False)

bool	isAmideCenterAtom (Chem.Atom atom, Chem.MolecularGraph molgraph, bool c_only=False, bool db_o_only=False)

bool	isHalogen (Chem.Atom atom)

bool	isOrdinaryHydrogen (Chem.Atom atom, Chem.MolecularGraph molgraph, int flags=2147483648)

bool	isAmideNitrogen (Chem.Atom atom, Chem.MolecularGraph molgraph, bool c_only=False, bool db_o_only=False)

bool	isInvertibleNitrogen (Chem.Atom atom, Chem.MolecularGraph molgraph)

bool	isPlanarNitrogen (Chem.Atom atom, Chem.MolecularGraph molgraph)

int	getIUPACGroup (Chem.Atom atom)

int	calcStericNumber (Chem.Atom atom, Chem.MolecularGraph molgraph)

bool	isHBondDonor (Chem.Atom atom, Chem.MolecularGraph molgraph)

bool	isHBondAcceptor (Chem.Atom atom, Chem.MolecularGraph molgraph)

bool	isNobleGas (Chem.Atom atom)

int	getNumContainingSSSRRings (Chem.Atom atom, Chem.MolecularGraph molgraph)

float	getVdWRadius (Chem.Atom atom)

float	getCovalentRadius (Chem.Atom atom, int order=1)

float	calcInductiveEffect (Chem.Atom atom, Chem.MolecularGraph molgraph, int num_bonds=10)

float	getAtomicWeight (Chem.Atom atom)

bool	isChemicalElement (Chem.Atom atom)

bool	isMainGroupElement (Chem.Atom atom)

int	getAromaticBondCount (Chem.Atom atom, Chem.MolecularGraph molgraph)

int	getRotatableBondCount (Chem.Atom atom, Chem.MolecularGraph molgraph, bool h_rotors=False, bool ring_bonds=False, bool amide_bonds=False)

int	getRingBondCount (Chem.Atom atom, Chem.MolecularGraph molgraph)

int	getChainBondCount (Chem.Atom atom, Chem.MolecularGraph molgraph)

int	getExplicitChainBondCount (Chem.Atom atom, Chem.MolecularGraph molgraph)

int	getBondCount (Chem.Atom atom, Chem.MolecularGraph molgraph)

int	getBondCount (Chem.Atom atom, Chem.MolecularGraph molgraph, int order)

int	getBondCount (Chem.Atom atom, Chem.MolecularGraph molgraph, int order, int type, bool strict=True)

int	getExplicitBondCount (Chem.Atom atom, Chem.MolecularGraph molgraph)

int	getExplicitBondCount (Chem.Atom atom, Chem.MolecularGraph molgraph, int order)

int	getExplicitBondCount (Chem.Atom atom, Chem.MolecularGraph molgraph, int order, int type, bool strict=True)

int	getHeavyBondCount (Chem.Atom atom, Chem.MolecularGraph molgraph)

int	getAromaticAtomCount (Chem.Atom atom, Chem.MolecularGraph molgraph)

int	getRingAtomCount (Chem.Atom atom, Chem.MolecularGraph molgraph)

int	getChainAtomCount (Chem.Atom atom, Chem.MolecularGraph molgraph)

int	getExplicitChainAtomCount (Chem.Atom atom, Chem.MolecularGraph molgraph)

int	getAtomCount (Chem.Atom atom, Chem.MolecularGraph molgraph, int type, bool strict=True)

int	getExplicitAtomCount (Chem.Atom atom, Chem.MolecularGraph molgraph, int type, bool strict=True)

int	getHeavyAtomCount (Chem.Atom atom, Chem.MolecularGraph molgraph)

int	getOrdinaryHydrogenCount (Chem.Atom atom, Chem.MolecularGraph molgraph, int flags=2147483648)

int	calcValenceElectronCount (Chem.Atom atom)

int	calcFreeValenceElectronCount (Chem.Atom atom, Chem.MolecularGraph molgraph)

int	getElementValenceElectronCount (Chem.Atom atom)

int	getVSEPRCoordinationGeometry (Chem.Atom atom, Chem.MolecularGraph molgraph)

int	getVSEPRCoordinationGeometry (Chem.Atom atom, Chem.MolecularGraph molgraph, int steric_num)

None	clearHydrophobicity (Chem.Atom atom)

bool	hasHydrophobicity (Chem.Atom atom)

float	getHydrophobicity (Chem.Atom atom)

None	setHydrophobicity (Chem.Atom atom, float hyd)

float	getHybridPolarizability (Chem.Atom atom, Chem.MolecularGraph molgraph)

float	calcEffectivePolarizability (Chem.Atom atom, Chem.MolecularGraph molgraph, float damping=0.75)

None	clearPEOESigmaElectronegativity (Chem.Atom atom)

bool	hasPEOESigmaElectronegativity (Chem.Atom atom)

float	getPEOESigmaElectronegativity (Chem.Atom atom)

None	setPEOESigmaElectronegativity (Chem.Atom atom, float e_neg)

float	calcPiElectronegativity (Chem.Atom atom, Chem.MolecularGraph molgraph)

float	calcLonePairElectronegativity (Chem.Atom atom, Chem.MolecularGraph molgraph)

float	getAllredRochowElectronegativity (Chem.Atom atom)

bool	isHeavy (Chem.Atom atom)

int	getAromaticBondCount (Chem.BondContainer cntnr)

int	getRingBondCount (Chem.BondContainer cntnr)

int	getExplicitHydrogenBondCount (Chem.BondContainer cntnr)

int	getExplicitChainBondCount (Chem.BondContainer cntnr)

int	getExplicitBondCount (Chem.BondContainer cntnr)

int	getExplicitBondCount (Chem.BondContainer cntnr, int order, bool inc_aro=True)

int	getHeavyBondCount (Chem.BondContainer cntnr)

bool	isAmideBond (Chem.Bond bond, Chem.MolecularGraph molgraph, bool c_only=False, bool db_o_only=False)

bool	isHydrogenBond (Chem.Bond bond)

bool	isRotatable (Chem.Bond bond, Chem.MolecularGraph molgraph, bool h_rotors, bool ring_bonds, bool amide_bonds)

bool	isInRingOfSize (Chem.Bond bond, Chem.MolecularGraph molgraph, int size)

bool	isInRing (Chem.Bond bond, Chem.MolecularGraph molgraph)

None	clearMHMOPiOrder (Chem.Bond bond)

bool	hasMHMOPiOrder (Chem.Bond bond)

float	getMHMOPiOrder (Chem.Bond bond)

None	setMHMOPiOrder (Chem.Bond bond, float order)

bool	isHeteroAtomHydrogenRotor (Chem.Bond bond, Chem.MolecularGraph molgraph)

bool	isHydrogenRotor (Chem.Bond bond, Chem.MolecularGraph molgraph)

int	getNumContainingSSSRRings (Chem.Bond bond, Chem.MolecularGraph molgraph)

float	calcPolarizability (Chem.Bond bond, Chem.MolecularGraph molgraph, float damping=0.75)

float	calcTPSA (Chem.MolecularGraph molgraph)

float	calcXLogP (Chem.MolecularGraph molgraph)

float	calcLogS (Chem.MolecularGraph molgraph)

object	generateMolecularFormula (Chem.MolecularGraph molgraph)

int	getRuleOfFiveScore (Chem.MolecularGraph molgraph)

object	generateMassCompositionString (Chem.MolecularGraph molgraph)

None	generateElementHistogram (Chem.MolecularGraph molgraph, ElementHistogram hist, bool append=False)

None	calcMassComposition (Chem.MolecularGraph molgraph, MassComposition comp)

int	calcCyclomaticNumber (Chem.MolecularGraph molgraph)

None	calcAtomHydrophobicities (Chem.MolecularGraph molgraph, bool overwrite, bool from_logp=False)

None	calcPEOEProperties (Chem.MolecularGraph molgraph, bool overwrite, int num_iter=20, float damping=0.48)

None	calcMHMOProperties (Chem.MolecularGraph molgraph, bool overwrite)

None	perceiveHBondDonorAtomTypes (Chem.MolecularGraph molgraph, bool overwrite)

None	perceiveHBondAcceptorAtomTypes (Chem.MolecularGraph molgraph, bool overwrite)

float	calcMass (Chem.MolecularGraph molgraph)

int	getRotatableBondCount (Chem.MolecularGraph molgraph, bool h_rotors=False, bool ring_bonds=False, bool amide_bonds=False)

int	getHydrogenBondCount (Chem.MolecularGraph molgraph)

int	getChainBondCount (Chem.MolecularGraph molgraph)

int	getBondCount (Chem.MolecularGraph molgraph)

int	getBondCount (Chem.MolecularGraph molgraph, int order, bool inc_aro=True)

int	getChainAtomCount (Chem.MolecularGraph molgraph)

int	getHBondDonorAtomCount (Chem.MolecularGraph molgraph)

int	getHBondAcceptorAtomCount (Chem.MolecularGraph molgraph)

int	getAtomCount (Chem.MolecularGraph molgraph)

int	getAtomCount (Chem.MolecularGraph molgraph, int type, bool strict=True)

int	getImplicitHydrogenCount (Chem.MolecularGraph molgraph)

int	getOrdinaryHydrogenCount (Chem.MolecularGraph molgraph, int flags=2147483648)

int	getExplicitOrdinaryHydrogenCount (Chem.MolecularGraph molgraph, int flags=2147483648)

int	getComponentCount (Chem.MolecularGraph molgraph)

float	calcMeanPolarizability (Chem.MolecularGraph molgraph)

Detailed Description

Contains classes and functions related to the calculation/preciction of physicochemical molecular properties.

Function Documentation

◆ generateExplicitMolecularFormula()

str CDPL.MolProp.generateExplicitMolecularFormula ( Chem.AtomContainer cntnr )

Parameters

cntnr

Returns

◆ getNetFormalCharge()

int CDPL.MolProp.getNetFormalCharge ( Chem.AtomContainer cntnr )

Parameters

cntnr

Returns

◆ generateExplicitMassCompositionString()

str CDPL.MolProp.generateExplicitMassCompositionString ( Chem.AtomContainer cntnr )

Parameters

cntnr

Returns

◆ generateExplicitElementHistogram()

None CDPL.MolProp.generateExplicitElementHistogram	(	Chem.AtomContainer	cntnr,
		ElementHistogram	hist,
		bool	append = `False`
	)

Parameters

cntnr
hist
append

◆ calcExplicitMassComposition()

None CDPL.MolProp.calcExplicitMassComposition	(	Chem.AtomContainer	cntnr,
		MassComposition	mass_comp
	)

Parameters

cntnr
mass_comp

◆ calcExplicitMass()

float CDPL.MolProp.calcExplicitMass ( Chem.AtomContainer cntnr )

Parameters

cntnr

Returns

◆ calcDipoleMoment() [1/2]

bool CDPL.MolProp.calcDipoleMoment	(	Chem.AtomContainer	cntnr,
		Math.Vector3D	moment
	)

Parameters

cntnr
moment

Returns

◆ calcDipoleMoment() [2/2]

bool CDPL.MolProp.calcDipoleMoment	(	Chem.AtomContainer	cntnr,
		Chem.Atom3DCoordinatesFunction	coords_func,
		Math.Vector3D	moment
	)

Parameters

cntnr
coords_func
moment

Returns

◆ getAromaticAtomCount() [1/2]

int CDPL.MolProp.getAromaticAtomCount ( Chem.AtomContainer cntnr )

Parameters

cntnr

Returns

◆ getRingAtomCount() [1/2]

int CDPL.MolProp.getRingAtomCount ( Chem.AtomContainer cntnr )

Parameters

cntnr

Returns

◆ getExplicitChainAtomCount() [1/2]

int CDPL.MolProp.getExplicitChainAtomCount ( Chem.AtomContainer cntnr )

Parameters

cntnr

Returns

◆ getExplicitAtomCount() [1/3]

int CDPL.MolProp.getExplicitAtomCount ( Chem.AtomContainer cntnr )

Parameters

cntnr

Returns

◆ getExplicitAtomCount() [2/3]

int CDPL.MolProp.getExplicitAtomCount	(	Chem.AtomContainer	cntnr,
		int	type,
		bool	strict = `True`
	)

Parameters

cntnr
type
strict

Returns

◆ getHeavyAtomCount() [1/2]

int CDPL.MolProp.getHeavyAtomCount ( Chem.AtomContainer cntnr )

Parameters

cntnr

Returns

◆ isUnsaturated()

bool CDPL.MolProp.isUnsaturated	(	Chem.Atom	atom,
		Chem.MolecularGraph	molgraph
	)

Parameters

atom
molgraph

Returns

◆ getPeriod()

int CDPL.MolProp.getPeriod ( Chem.Atom atom )

Parameters

atom

Returns

◆ calcValence()

int CDPL.MolProp.calcValence	(	Chem.Atom	atom,
		Chem.MolecularGraph	molgraph
	)

Parameters

atom
molgraph

Returns

◆ calcExplicitValence()

int CDPL.MolProp.calcExplicitValence	(	Chem.Atom	atom,
		Chem.MolecularGraph	molgraph
	)

Parameters

atom
molgraph

Returns

◆ clearPEOESigmaCharge()

None CDPL.MolProp.clearPEOESigmaCharge ( Chem.Atom atom )

Parameters

atom

◆ hasPEOESigmaCharge()

bool CDPL.MolProp.hasPEOESigmaCharge ( Chem.Atom atom )

Parameters

atom

Returns

◆ getPEOESigmaCharge()

float CDPL.MolProp.getPEOESigmaCharge ( Chem.Atom atom )

Parameters

atom

Returns

◆ setPEOESigmaCharge()

None CDPL.MolProp.setPEOESigmaCharge	(	Chem.Atom	atom,
		float	charge
	)

Parameters

atom
charge

◆ clearMHMOPiCharge()

None CDPL.MolProp.clearMHMOPiCharge ( Chem.Atom atom )

Parameters

atom

◆ hasMHMOPiCharge()

bool CDPL.MolProp.hasMHMOPiCharge ( Chem.Atom atom )

Parameters

atom

Returns

◆ getMHMOPiCharge()

float CDPL.MolProp.getMHMOPiCharge ( Chem.Atom atom )

Parameters

atom

Returns

◆ setMHMOPiCharge()

None CDPL.MolProp.setMHMOPiCharge	(	Chem.Atom	atom,
		float	charge
	)

Parameters

atom
charge

◆ calcTotalPartialCharge()

float CDPL.MolProp.calcTotalPartialCharge ( Chem.Atom atom )

Parameters

atom

Returns

◆ getElementName()

str CDPL.MolProp.getElementName ( Chem.Atom atom )

Parameters

atom

Returns

◆ clearHBondDonorType()

None CDPL.MolProp.clearHBondDonorType ( Chem.Atom atom )

Parameters

atom

◆ hasHBondDonorType()

bool CDPL.MolProp.hasHBondDonorType ( Chem.Atom atom )

Parameters

atom

Returns

◆ getHBondDonorType()

int CDPL.MolProp.getHBondDonorType ( Chem.Atom atom )

Parameters

atom

Returns

◆ setHBondDonorType()

None CDPL.MolProp.setHBondDonorType	(	Chem.Atom	atom,
		int	type
	)

Parameters

atom
type

◆ clearHBondAcceptorType()

None CDPL.MolProp.clearHBondAcceptorType ( Chem.Atom atom )

Parameters

atom

◆ hasHBondAcceptorType()

bool CDPL.MolProp.hasHBondAcceptorType ( Chem.Atom atom )

Parameters

atom

Returns

◆ getHBondAcceptorType()

int CDPL.MolProp.getHBondAcceptorType ( Chem.Atom atom )

Parameters

atom

Returns

◆ setHBondAcceptorType()

None CDPL.MolProp.setHBondAcceptorType	(	Chem.Atom	atom,
		int	type
	)

Parameters

atom
type

◆ isInRingOfSize() [1/2]

bool CDPL.MolProp.isInRingOfSize	(	Chem.Atom	atom,
		Chem.MolecularGraph	molgraph,
		int	size
	)

Parameters

atom
molgraph
size

Returns

◆ isInRing() [1/2]

bool CDPL.MolProp.isInRing	(	Chem.Atom	atom,
		Chem.MolecularGraph	molgraph
	)

Parameters

atom
molgraph

Returns

◆ isSemiMetal()

bool CDPL.MolProp.isSemiMetal ( Chem.Atom atom )

Parameters

atom

Returns

◆ isNonMetal()

bool CDPL.MolProp.isNonMetal ( Chem.Atom atom )

Parameters

atom

Returns

◆ isTransitionMetal()

bool CDPL.MolProp.isTransitionMetal ( Chem.Atom atom )

Parameters

atom

Returns

◆ isMetal()

bool CDPL.MolProp.isMetal ( Chem.Atom atom )

Parameters

atom

Returns

◆ isCarbonylLikeAtom()

bool CDPL.MolProp.isCarbonylLikeAtom	(	Chem.Atom	atom,
		Chem.MolecularGraph	molgraph,
		bool	c_only = `False`,
		bool	db_o_only = `False`
	)

Parameters

atom
molgraph
c_only
db_o_only

Returns

◆ isAmideCenterAtom()

bool CDPL.MolProp.isAmideCenterAtom	(	Chem.Atom	atom,
		Chem.MolecularGraph	molgraph,
		bool	c_only = `False`,
		bool	db_o_only = `False`
	)

Parameters

atom
molgraph
c_only
db_o_only

Returns

◆ isHalogen()

bool CDPL.MolProp.isHalogen ( Chem.Atom atom )

Parameters

atom

Returns

◆ isOrdinaryHydrogen()

bool CDPL.MolProp.isOrdinaryHydrogen	(	Chem.Atom	atom,
		Chem.MolecularGraph	molgraph,
		int	flags = `2147483648`
	)

Parameters

atom
molgraph
flags

Returns

◆ isAmideNitrogen()

bool CDPL.MolProp.isAmideNitrogen	(	Chem.Atom	atom,
		Chem.MolecularGraph	molgraph,
		bool	c_only = `False`,
		bool	db_o_only = `False`
	)

Parameters

atom
molgraph
c_only
db_o_only

Returns

◆ isInvertibleNitrogen()

bool CDPL.MolProp.isInvertibleNitrogen	(	Chem.Atom	atom,
		Chem.MolecularGraph	molgraph
	)

Parameters

atom
molgraph

Returns

◆ isPlanarNitrogen()

bool CDPL.MolProp.isPlanarNitrogen	(	Chem.Atom	atom,
		Chem.MolecularGraph	molgraph
	)

Parameters

atom
molgraph

Returns

◆ getIUPACGroup()

int CDPL.MolProp.getIUPACGroup ( Chem.Atom atom )

Parameters

atom

Returns

◆ calcStericNumber()

int CDPL.MolProp.calcStericNumber	(	Chem.Atom	atom,
		Chem.MolecularGraph	molgraph
	)

Parameters

atom
molgraph

Returns

◆ isHBondDonor()

bool CDPL.MolProp.isHBondDonor	(	Chem.Atom	atom,
		Chem.MolecularGraph	molgraph
	)

Parameters

atom
molgraph

Returns

◆ isHBondAcceptor()

bool CDPL.MolProp.isHBondAcceptor	(	Chem.Atom	atom,
		Chem.MolecularGraph	molgraph
	)

Parameters

atom
molgraph

Returns

◆ isNobleGas()

bool CDPL.MolProp.isNobleGas ( Chem.Atom atom )

Parameters

atom

Returns

◆ getNumContainingSSSRRings() [1/2]

int CDPL.MolProp.getNumContainingSSSRRings	(	Chem.Atom	atom,
		Chem.MolecularGraph	molgraph
	)

Parameters

atom
molgraph

Returns

◆ getVdWRadius()

float CDPL.MolProp.getVdWRadius ( Chem.Atom atom )

Parameters

atom

Returns

◆ getCovalentRadius()

float CDPL.MolProp.getCovalentRadius	(	Chem.Atom	atom,
		int	order = `1`
	)

Parameters

atom
order

Returns

◆ calcInductiveEffect()

float CDPL.MolProp.calcInductiveEffect	(	Chem.Atom	atom,
		Chem.MolecularGraph	molgraph,
		int	num_bonds = `10`
	)

Parameters

atom
molgraph
num_bonds

Returns

◆ getAtomicWeight()

float CDPL.MolProp.getAtomicWeight ( Chem.Atom atom )

Parameters

atom

Returns

◆ isChemicalElement()

bool CDPL.MolProp.isChemicalElement ( Chem.Atom atom )

Parameters

atom

Returns

◆ isMainGroupElement()

bool CDPL.MolProp.isMainGroupElement ( Chem.Atom atom )

Parameters

atom

Returns

◆ getAromaticBondCount() [1/2]

int CDPL.MolProp.getAromaticBondCount	(	Chem.Atom	atom,
		Chem.MolecularGraph	molgraph
	)

Parameters

atom
molgraph

Returns

◆ getRotatableBondCount() [1/2]

int CDPL.MolProp.getRotatableBondCount	(	Chem.Atom	atom,
		Chem.MolecularGraph	molgraph,
		bool	h_rotors = `False`,
		bool	ring_bonds = `False`,
		bool	amide_bonds = `False`
	)

Parameters

atom
molgraph
h_rotors
ring_bonds
amide_bonds

Returns

◆ getRingBondCount() [1/2]

int CDPL.MolProp.getRingBondCount	(	Chem.Atom	atom,
		Chem.MolecularGraph	molgraph
	)

Parameters

atom
molgraph

Returns

◆ getChainBondCount() [1/2]

int CDPL.MolProp.getChainBondCount	(	Chem.Atom	atom,
		Chem.MolecularGraph	molgraph
	)

Parameters

atom
molgraph

Returns

◆ getExplicitChainBondCount() [1/2]

int CDPL.MolProp.getExplicitChainBondCount	(	Chem.Atom	atom,
		Chem.MolecularGraph	molgraph
	)

Parameters

atom
molgraph

Returns

◆ getBondCount() [1/5]

int CDPL.MolProp.getBondCount	(	Chem.Atom	atom,
		Chem.MolecularGraph	molgraph
	)

Parameters

atom
molgraph

Returns

◆ getBondCount() [2/5]

int CDPL.MolProp.getBondCount	(	Chem.Atom	atom,
		Chem.MolecularGraph	molgraph,
		int	order
	)

Parameters

atom
molgraph
order

Returns

◆ getBondCount() [3/5]

int CDPL.MolProp.getBondCount	(	Chem.Atom	atom,
		Chem.MolecularGraph	molgraph,
		int	order,
		int	type,
		bool	strict = `True`
	)

Parameters

atom
molgraph
order
type
strict

Returns

◆ getExplicitBondCount() [1/5]

int CDPL.MolProp.getExplicitBondCount	(	Chem.Atom	atom,
		Chem.MolecularGraph	molgraph
	)

Parameters

atom
molgraph

Returns

◆ getExplicitBondCount() [2/5]

int CDPL.MolProp.getExplicitBondCount	(	Chem.Atom	atom,
		Chem.MolecularGraph	molgraph,
		int	order
	)

Parameters

atom
molgraph
order

Returns

◆ getExplicitBondCount() [3/5]

int CDPL.MolProp.getExplicitBondCount	(	Chem.Atom	atom,
		Chem.MolecularGraph	molgraph,
		int	order,
		int	type,
		bool	strict = `True`
	)

Parameters

atom
molgraph
order
type
strict

Returns

◆ getHeavyBondCount() [1/2]

int CDPL.MolProp.getHeavyBondCount	(	Chem.Atom	atom,
		Chem.MolecularGraph	molgraph
	)

Parameters

atom
molgraph

Returns

◆ getAromaticAtomCount() [2/2]

int CDPL.MolProp.getAromaticAtomCount	(	Chem.Atom	atom,
		Chem.MolecularGraph	molgraph
	)

Parameters

atom
molgraph

Returns

◆ getRingAtomCount() [2/2]

int CDPL.MolProp.getRingAtomCount	(	Chem.Atom	atom,
		Chem.MolecularGraph	molgraph
	)

Parameters

atom
molgraph

Returns

◆ getChainAtomCount() [1/2]

int CDPL.MolProp.getChainAtomCount	(	Chem.Atom	atom,
		Chem.MolecularGraph	molgraph
	)

Parameters

atom
molgraph

Returns

◆ getExplicitChainAtomCount() [2/2]

int CDPL.MolProp.getExplicitChainAtomCount	(	Chem.Atom	atom,
		Chem.MolecularGraph	molgraph
	)

Parameters

atom
molgraph

Returns

◆ getAtomCount() [1/3]

int CDPL.MolProp.getAtomCount	(	Chem.Atom	atom,
		Chem.MolecularGraph	molgraph,
		int	type,
		bool	strict = `True`
	)

Parameters

atom
molgraph
type
strict

Returns

◆ getExplicitAtomCount() [3/3]

int CDPL.MolProp.getExplicitAtomCount	(	Chem.Atom	atom,
		Chem.MolecularGraph	molgraph,
		int	type,
		bool	strict = `True`
	)

Parameters

atom
molgraph
type
strict

Returns

◆ getHeavyAtomCount() [2/2]

int CDPL.MolProp.getHeavyAtomCount	(	Chem.Atom	atom,
		Chem.MolecularGraph	molgraph
	)

Parameters

atom
molgraph

Returns

◆ getOrdinaryHydrogenCount() [1/2]

int CDPL.MolProp.getOrdinaryHydrogenCount	(	Chem.Atom	atom,
		Chem.MolecularGraph	molgraph,
		int	flags = `2147483648`
	)

Parameters

atom
molgraph
flags

Returns

◆ calcValenceElectronCount()

int CDPL.MolProp.calcValenceElectronCount ( Chem.Atom atom )

Parameters

atom

Returns

◆ calcFreeValenceElectronCount()

int CDPL.MolProp.calcFreeValenceElectronCount	(	Chem.Atom	atom,
		Chem.MolecularGraph	molgraph
	)

Parameters

atom
molgraph

Returns

◆ getElementValenceElectronCount()

int CDPL.MolProp.getElementValenceElectronCount ( Chem.Atom atom )

Parameters

atom

Returns

◆ getVSEPRCoordinationGeometry() [1/2]

int CDPL.MolProp.getVSEPRCoordinationGeometry	(	Chem.Atom	atom,
		Chem.MolecularGraph	molgraph
	)

Parameters

atom
molgraph

Returns

◆ getVSEPRCoordinationGeometry() [2/2]

int CDPL.MolProp.getVSEPRCoordinationGeometry	(	Chem.Atom	atom,
		Chem.MolecularGraph	molgraph,
		int	steric_num
	)

Parameters

atom
molgraph
steric_num

Returns

◆ clearHydrophobicity()

None CDPL.MolProp.clearHydrophobicity ( Chem.Atom atom )

Parameters

atom

◆ hasHydrophobicity()

bool CDPL.MolProp.hasHydrophobicity ( Chem.Atom atom )

Parameters

atom

Returns

◆ getHydrophobicity()

float CDPL.MolProp.getHydrophobicity ( Chem.Atom atom )

Parameters

atom

Returns

◆ setHydrophobicity()

None CDPL.MolProp.setHydrophobicity	(	Chem.Atom	atom,
		float	hyd
	)

Parameters

atom
hyd

◆ getHybridPolarizability()

float CDPL.MolProp.getHybridPolarizability	(	Chem.Atom	atom,
		Chem.MolecularGraph	molgraph
	)

Parameters

atom
molgraph

Returns

◆ calcEffectivePolarizability()

float CDPL.MolProp.calcEffectivePolarizability	(	Chem.Atom	atom,
		Chem.MolecularGraph	molgraph,
		float	damping = `0.75`
	)

Parameters

atom
molgraph
damping

Returns

◆ clearPEOESigmaElectronegativity()

None CDPL.MolProp.clearPEOESigmaElectronegativity ( Chem.Atom atom )

Parameters

atom

◆ hasPEOESigmaElectronegativity()

bool CDPL.MolProp.hasPEOESigmaElectronegativity ( Chem.Atom atom )

Parameters

atom

Returns

◆ getPEOESigmaElectronegativity()

float CDPL.MolProp.getPEOESigmaElectronegativity ( Chem.Atom atom )

Parameters

atom

Returns

◆ setPEOESigmaElectronegativity()

None CDPL.MolProp.setPEOESigmaElectronegativity	(	Chem.Atom	atom,
		float	e_neg
	)

Parameters

atom
e_neg

◆ calcPiElectronegativity()

float CDPL.MolProp.calcPiElectronegativity	(	Chem.Atom	atom,
		Chem.MolecularGraph	molgraph
	)

Parameters

atom
molgraph

Returns

◆ calcLonePairElectronegativity()

float CDPL.MolProp.calcLonePairElectronegativity	(	Chem.Atom	atom,
		Chem.MolecularGraph	molgraph
	)

Parameters

atom
molgraph

Returns

◆ getAllredRochowElectronegativity()

float CDPL.MolProp.getAllredRochowElectronegativity ( Chem.Atom atom )

Parameters

atom

Returns

◆ isHeavy()

bool CDPL.MolProp.isHeavy ( Chem.Atom atom )

Parameters

atom

Returns

◆ getAromaticBondCount() [2/2]

int CDPL.MolProp.getAromaticBondCount ( Chem.BondContainer cntnr )

Parameters

cntnr

Returns

◆ getRingBondCount() [2/2]

int CDPL.MolProp.getRingBondCount ( Chem.BondContainer cntnr )

Parameters

cntnr

Returns

◆ getExplicitHydrogenBondCount()

int CDPL.MolProp.getExplicitHydrogenBondCount ( Chem.BondContainer cntnr )

Parameters

cntnr

Returns

◆ getExplicitChainBondCount() [2/2]

int CDPL.MolProp.getExplicitChainBondCount ( Chem.BondContainer cntnr )

Parameters

cntnr

Returns

◆ getExplicitBondCount() [4/5]

int CDPL.MolProp.getExplicitBondCount ( Chem.BondContainer cntnr )

Parameters

cntnr

Returns

◆ getExplicitBondCount() [5/5]

int CDPL.MolProp.getExplicitBondCount	(	Chem.BondContainer	cntnr,
		int	order,
		bool	inc_aro = `True`
	)

Parameters

cntnr
order
inc_aro

Returns

◆ getHeavyBondCount() [2/2]

int CDPL.MolProp.getHeavyBondCount ( Chem.BondContainer cntnr )

Parameters

cntnr

Returns

◆ isAmideBond()

bool CDPL.MolProp.isAmideBond	(	Chem.Bond	bond,
		Chem.MolecularGraph	molgraph,
		bool	c_only = `False`,
		bool	db_o_only = `False`
	)

Parameters

bond
molgraph
c_only
db_o_only

Returns

◆ isHydrogenBond()

bool CDPL.MolProp.isHydrogenBond ( Chem.Bond bond )

Parameters

bond

Returns

◆ isRotatable()

bool CDPL.MolProp.isRotatable	(	Chem.Bond	bond,
		Chem.MolecularGraph	molgraph,
		bool	h_rotors,
		bool	ring_bonds,
		bool	amide_bonds
	)

Parameters

bond
molgraph
h_rotors
ring_bonds
amide_bonds

Returns

◆ isInRingOfSize() [2/2]

bool CDPL.MolProp.isInRingOfSize	(	Chem.Bond	bond,
		Chem.MolecularGraph	molgraph,
		int	size
	)

Parameters

bond
molgraph
size

Returns

◆ isInRing() [2/2]

bool CDPL.MolProp.isInRing	(	Chem.Bond	bond,
		Chem.MolecularGraph	molgraph
	)

Parameters

bond
molgraph

Returns

◆ clearMHMOPiOrder()

None CDPL.MolProp.clearMHMOPiOrder ( Chem.Bond bond )

Parameters

bond

◆ hasMHMOPiOrder()

bool CDPL.MolProp.hasMHMOPiOrder ( Chem.Bond bond )

Parameters

bond

Returns

◆ getMHMOPiOrder()

float CDPL.MolProp.getMHMOPiOrder ( Chem.Bond bond )

Parameters

bond

Returns

◆ setMHMOPiOrder()

None CDPL.MolProp.setMHMOPiOrder	(	Chem.Bond	bond,
		float	order
	)

Parameters

bond
order

◆ isHeteroAtomHydrogenRotor()

bool CDPL.MolProp.isHeteroAtomHydrogenRotor	(	Chem.Bond	bond,
		Chem.MolecularGraph	molgraph
	)

Parameters

bond
molgraph

Returns

◆ isHydrogenRotor()

bool CDPL.MolProp.isHydrogenRotor	(	Chem.Bond	bond,
		Chem.MolecularGraph	molgraph
	)

Parameters

bond
molgraph

Returns

◆ getNumContainingSSSRRings() [2/2]

int CDPL.MolProp.getNumContainingSSSRRings	(	Chem.Bond	bond,
		Chem.MolecularGraph	molgraph
	)

Parameters

bond
molgraph

Returns

◆ calcPolarizability()

float CDPL.MolProp.calcPolarizability	(	Chem.Bond	bond,
		Chem.MolecularGraph	molgraph,
		float	damping = `0.75`
	)

Parameters

bond
molgraph
damping

Returns

◆ calcTPSA()

float CDPL.MolProp.calcTPSA ( Chem.MolecularGraph molgraph )

Parameters

molgraph

Returns

◆ calcXLogP()

float CDPL.MolProp.calcXLogP ( Chem.MolecularGraph molgraph )

Parameters

molgraph

Returns

◆ calcLogS()

float CDPL.MolProp.calcLogS ( Chem.MolecularGraph molgraph )

Parameters

molgraph

Returns

◆ generateMolecularFormula()

object CDPL.MolProp.generateMolecularFormula ( Chem.MolecularGraph molgraph )

Parameters

molgraph

Returns

◆ getRuleOfFiveScore()

int CDPL.MolProp.getRuleOfFiveScore ( Chem.MolecularGraph molgraph )

Parameters

molgraph

Returns

◆ generateMassCompositionString()

object CDPL.MolProp.generateMassCompositionString ( Chem.MolecularGraph molgraph )

Parameters

molgraph

Returns

◆ generateElementHistogram()

None CDPL.MolProp.generateElementHistogram	(	Chem.MolecularGraph	molgraph,
		ElementHistogram	hist,
		bool	append = `False`
	)

Parameters

molgraph
hist
append

◆ calcMassComposition()

None CDPL.MolProp.calcMassComposition	(	Chem.MolecularGraph	molgraph,
		MassComposition	comp
	)

Parameters

molgraph
comp

◆ calcCyclomaticNumber()

int CDPL.MolProp.calcCyclomaticNumber ( Chem.MolecularGraph molgraph )

Parameters

molgraph

Returns

◆ calcAtomHydrophobicities()

None CDPL.MolProp.calcAtomHydrophobicities	(	Chem.MolecularGraph	molgraph,
		bool	overwrite,
		bool	from_logp = `False`
	)

Parameters

molgraph
overwrite
from_logp

◆ calcPEOEProperties()

None CDPL.MolProp.calcPEOEProperties	(	Chem.MolecularGraph	molgraph,
		bool	overwrite,
		int	num_iter = `20`,
		float	damping = `0.48`
	)

Parameters

molgraph
overwrite
num_iter
damping

◆ calcMHMOProperties()

None CDPL.MolProp.calcMHMOProperties	(	Chem.MolecularGraph	molgraph,
		bool	overwrite
	)

Parameters

molgraph
overwrite

◆ perceiveHBondDonorAtomTypes()

None CDPL.MolProp.perceiveHBondDonorAtomTypes	(	Chem.MolecularGraph	molgraph,
		bool	overwrite
	)

Parameters

molgraph
overwrite

◆ perceiveHBondAcceptorAtomTypes()

None CDPL.MolProp.perceiveHBondAcceptorAtomTypes	(	Chem.MolecularGraph	molgraph,
		bool	overwrite
	)

Parameters

molgraph
overwrite

◆ calcMass()

float CDPL.MolProp.calcMass ( Chem.MolecularGraph molgraph )

Parameters

molgraph

Returns

◆ getRotatableBondCount() [2/2]

int CDPL.MolProp.getRotatableBondCount	(	Chem.MolecularGraph	molgraph,
		bool	h_rotors = `False`,
		bool	ring_bonds = `False`,
		bool	amide_bonds = `False`
	)

Parameters

molgraph
h_rotors
ring_bonds
amide_bonds

Returns

◆ getHydrogenBondCount()

int CDPL.MolProp.getHydrogenBondCount ( Chem.MolecularGraph molgraph )

Parameters

molgraph

Returns

◆ getChainBondCount() [2/2]

int CDPL.MolProp.getChainBondCount ( Chem.MolecularGraph molgraph )

Parameters

molgraph

Returns

◆ getBondCount() [4/5]

int CDPL.MolProp.getBondCount ( Chem.MolecularGraph molgraph )

Parameters

molgraph

Returns

◆ getBondCount() [5/5]

int CDPL.MolProp.getBondCount	(	Chem.MolecularGraph	molgraph,
		int	order,
		bool	inc_aro = `True`
	)

Parameters

molgraph
order
inc_aro

Returns

◆ getChainAtomCount() [2/2]

int CDPL.MolProp.getChainAtomCount ( Chem.MolecularGraph molgraph )

Parameters

molgraph

Returns

◆ getHBondDonorAtomCount()

int CDPL.MolProp.getHBondDonorAtomCount ( Chem.MolecularGraph molgraph )

Parameters

molgraph

Returns

◆ getHBondAcceptorAtomCount()

int CDPL.MolProp.getHBondAcceptorAtomCount ( Chem.MolecularGraph molgraph )

Parameters

molgraph

Returns

◆ getAtomCount() [2/3]

int CDPL.MolProp.getAtomCount ( Chem.MolecularGraph molgraph )

Parameters

molgraph

Returns

◆ getAtomCount() [3/3]

int CDPL.MolProp.getAtomCount	(	Chem.MolecularGraph	molgraph,
		int	type,
		bool	strict = `True`
	)

Parameters

molgraph
type
strict

Returns

◆ getImplicitHydrogenCount()

int CDPL.MolProp.getImplicitHydrogenCount ( Chem.MolecularGraph molgraph )

Parameters

molgraph

Returns

◆ getOrdinaryHydrogenCount() [2/2]

int CDPL.MolProp.getOrdinaryHydrogenCount	(	Chem.MolecularGraph	molgraph,
		int	flags = `2147483648`
	)

Parameters

molgraph
flags

Returns

◆ getExplicitOrdinaryHydrogenCount()

int CDPL.MolProp.getExplicitOrdinaryHydrogenCount	(	Chem.MolecularGraph	molgraph,
		int	flags = `2147483648`
	)

Parameters

molgraph
flags

Returns

◆ getComponentCount()

int CDPL.MolProp.getComponentCount ( Chem.MolecularGraph molgraph )

Parameters

molgraph

Returns

◆ calcMeanPolarizability()

float CDPL.MolProp.calcMeanPolarizability ( Chem.MolecularGraph molgraph )

Parameters

molgraph

Returns

Classes

Functions

Detailed Description

Function Documentation

◆ generateExplicitMolecularFormula()

◆ getNetFormalCharge()

◆ generateExplicitMassCompositionString()

◆ generateExplicitElementHistogram()

◆ calcExplicitMassComposition()

◆ calcExplicitMass()

◆ calcDipoleMoment() [1/2]

◆ calcDipoleMoment() [2/2]

◆ getAromaticAtomCount() [1/2]

◆ getRingAtomCount() [1/2]

◆ getExplicitChainAtomCount() [1/2]

◆ getExplicitAtomCount() [1/3]

◆ getExplicitAtomCount() [2/3]

◆ getHeavyAtomCount() [1/2]

◆ isUnsaturated()

◆ getPeriod()

◆ calcValence()

◆ calcExplicitValence()

◆ clearPEOESigmaCharge()

◆ hasPEOESigmaCharge()

◆ getPEOESigmaCharge()

◆ setPEOESigmaCharge()

◆ clearMHMOPiCharge()

◆ hasMHMOPiCharge()

◆ getMHMOPiCharge()

◆ setMHMOPiCharge()

◆ calcTotalPartialCharge()

◆ getElementName()

◆ clearHBondDonorType()

◆ hasHBondDonorType()

◆ getHBondDonorType()

◆ setHBondDonorType()

◆ clearHBondAcceptorType()

◆ hasHBondAcceptorType()

◆ getHBondAcceptorType()

◆ setHBondAcceptorType()

◆ isInRingOfSize() [1/2]

◆ isInRing() [1/2]

◆ isSemiMetal()

◆ isNonMetal()

◆ isTransitionMetal()

◆ isMetal()

◆ isCarbonylLikeAtom()

◆ isAmideCenterAtom()

◆ isHalogen()

◆ isOrdinaryHydrogen()

◆ isAmideNitrogen()

◆ isInvertibleNitrogen()

◆ isPlanarNitrogen()

◆ getIUPACGroup()

◆ calcStericNumber()

◆ isHBondDonor()

◆ isHBondAcceptor()

◆ isNobleGas()

◆ getNumContainingSSSRRings() [1/2]

◆ getVdWRadius()

◆ getCovalentRadius()

◆ calcInductiveEffect()

◆ getAtomicWeight()

◆ isChemicalElement()

◆ isMainGroupElement()

◆ getAromaticBondCount() [1/2]

◆ getRotatableBondCount() [1/2]

◆ getRingBondCount() [1/2]

◆ getChainBondCount() [1/2]

◆ getExplicitChainBondCount() [1/2]

◆ getBondCount() [1/5]

◆ getBondCount() [2/5]

◆ getBondCount() [3/5]

◆ getExplicitBondCount() [1/5]

◆ getExplicitBondCount() [2/5]

◆ getExplicitBondCount() [3/5]

◆ getHeavyBondCount() [1/2]

◆ getAromaticAtomCount() [2/2]

◆ getRingAtomCount() [2/2]

◆ getChainAtomCount() [1/2]