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

Classes
class	AtomHydrophobicityCalculator
	Implementation of Greene's algorithm [CATA] for the calculation of atom hydrophobicities. More...

class	AtomProperty
	Provides keys for MolProp-specific Chem.Atom properties. More...

class	AtomPropertyDefault
	Provides default values for MolProp-specific Chem.Atom properties. More...

class	BondProperty
	Provides keys for MolProp-specific Chem.Bond properties. More...

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

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

class	FunctionalGroupList
	Implementation of Ertl's algorithm [FGPE] for the identification of functional groups in organic molecules. More...

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

class	HBondAcceptorAtomTyper
	Implements the perception of H-bond acceptor atom types (see namespace MolProp.HBondAcceptorAtomType). More...

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

class	HBondDonorAtomTyper
	Implements the perception of H-bond donor atom types (see namespace MolProp.HBondDonorAtomType). More...

class	LogSCalculator
	LogSCalculator. More...

class	MHMOPiChargeCalculator
	Calculator that uses a Modified Hückel Molecular Orbital (MHMO) treatment to compute pi-electron densities, pi-charges, pi-bond orders and the total pi-electron energy of a molecular graph. More...

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

class	MolecularGraphProperty
	Provides keys for built-in Chem.MolecularGraph properties. More...

class	PEOESigmaChargeCalculator
	Calculator that uses the Partial Equalization of Orbital Electronegativities (PEOE) method of Gasteiger and Marsili to compute sigma atomic charges and electronegativities of a molecular graph. More...

class	TPSACalculator
	Calculation of the topological polar surface area (TPSA) of molecular graphs based on fragment contributions. More...

class	XLogPCalculator
	Calculation of the octanol/water partition coefficient ( \( \log P \)) of molecular graphs using the atom-additive method of Wang, Gao and Lai. More...

Functions
float	getAllredRochowElectronegativity (Chem.Atom atom)
	Returns the Allred-Rochow electronegativity of the chemical element associated with the atom atom. More...

int	getAromaticAtomCount (Chem.Atom atom, Chem.MolecularGraph molgraph)
	Returns the number of aromatic neighbors of the atom atom in the molecular graph molgraph. More...

int	getAromaticAtomCount (Chem.AtomContainer cntnr)
	Returns the number of aromatic atoms in cntnr. More...

int	getAromaticBondCount (Chem.Atom atom, Chem.MolecularGraph molgraph)
	Returns the number of aromatic bonds incident to the atom atom in the molecular graph molgraph. More...

int	getAromaticBondCount (Chem.BondContainer cntnr)
	Returns the number of aromatic bonds in cntnr. More...

int	getAtomCount (Chem.Atom atom, Chem.MolecularGraph molgraph, int type, bool strict=True)
	Returns the number of neighbors of the atom atom in the molecular graph molgraph (including implicit hydrogens) whose type matches type. More...

int	getAtomCount (Chem.MolecularGraph molgraph)
	Returns the total number of atoms in the molecular graph molgraph (including implicit hydrogens). More...

int	getAtomCount (Chem.MolecularGraph molgraph, int type, bool strict=True)
	Returns the number of atoms in the molecular graph molgraph whose type property matches type. More...

float	getAtomicWeight (Chem.Atom atom)
	Returns the standard atomic weight of the chemical element associated with the atom atom. More...

int	getBondCount (Chem.Atom atom, Chem.MolecularGraph molgraph)
	Returns the total number of bonds incident to the atom atom in the molecular graph molgraph (including implicit hydrogen bonds). More...

int	getBondCount (Chem.Atom atom, Chem.MolecularGraph molgraph, int order)
	Returns the total number of bonds of the given order incident to the atom atom (including implicit hydrogen bonds). More...

int	getBondCount (Chem.Atom atom, Chem.MolecularGraph molgraph, int order, int type, bool strict=True)
	Returns the total number of bonds of the given order incident to the atom atom that bond to atoms whose type matches type. More...

int	getBondCount (Chem.MolecularGraph molgraph)
	Returns the total number of bonds in the molecular graph molgraph (including bonds to implicit hydrogens). More...

int	getBondCount (Chem.MolecularGraph molgraph, int order, bool inc_aro=True)
	Returns the number of bonds in the molecular graph molgraph with the given order, optionally including aromatic bonds. More...

int	getChainAtomCount (Chem.Atom atom, Chem.MolecularGraph molgraph)
	Returns the number of chain (non-ring) neighbors of the atom atom in the molecular graph molgraph (including implicit hydrogens). More...

int	getChainAtomCount (Chem.MolecularGraph molgraph)
	Returns the number of chain (non-ring) atoms in the molecular graph molgraph. More...

int	getChainBondCount (Chem.Atom atom, Chem.MolecularGraph molgraph)
	Returns the number of chain (non-ring) bonds incident to the atom atom in the molecular graph molgraph (including implicit hydrogen bonds). More...

int	getChainBondCount (Chem.MolecularGraph molgraph)
	Returns the number of chain (non-ring) bonds in the molecular graph molgraph. More...

int	getComponentCount (Chem.MolecularGraph molgraph)
	Returns the number of connected components in the molecular graph molgraph. More...

float	getCovalentRadius (Chem.Atom atom, int order=1)
	Returns the covalent radius of the chemical element associated with the atom atom for the given bond order. More...

str	getElementName (Chem.Atom atom)
	Returns the element name of the chemical element associated with the atom atom. More...

int	getElementValenceElectronCount (Chem.Atom atom)
	Returns the number of valence electrons of the chemical element associated with the atom atom. More...

int	getExplicitAtomCount (Chem.Atom atom, Chem.MolecularGraph molgraph, int type, bool strict=True)
	Returns the number of explicit neighbors of the atom atom in the molecular graph molgraph whose type matches type. More...

int	getExplicitAtomCount (Chem.AtomContainer cntnr)
	Returns the total number of explicit atoms in cntnr. More...

int	getExplicitAtomCount (Chem.AtomContainer cntnr, int type, bool strict=True)
	Returns the number of explicit atoms in cntnr that match the given atom type. More...

int	getExplicitBondCount (Chem.Atom atom, Chem.MolecularGraph molgraph)
	Returns the number of explicit bonds incident to the atom atom in the molecular graph molgraph. More...

int	getExplicitBondCount (Chem.Atom atom, Chem.MolecularGraph molgraph, int order)
	Returns the number of explicit bonds of the given order incident to the atom atom in the molecular graph molgraph. More...

int	getExplicitBondCount (Chem.Atom atom, Chem.MolecularGraph molgraph, int order, int type, bool strict=True)
	Returns the number of explicit bonds of the given order incident to the atom atom that bond to atoms whose type matches type. More...

int	getExplicitBondCount (Chem.BondContainer cntnr)
	Returns the total number of explicit bonds in cntnr. More...

int	getExplicitBondCount (Chem.BondContainer cntnr, int order, bool inc_aro=True)
	Returns the number of explicit bonds in cntnr that match the given bond order. More...

int	getExplicitChainAtomCount (Chem.Atom atom, Chem.MolecularGraph molgraph)
	Returns the number of explicit chain (non-ring) neighbors of the atom atom in the molecular graph molgraph. More...

int	getExplicitChainAtomCount (Chem.AtomContainer cntnr)
	Returns the number of explicit chain (non-ring) atoms in cntnr. More...

int	getExplicitChainBondCount (Chem.Atom atom, Chem.MolecularGraph molgraph)
	Returns the number of explicit chain (non-ring) bonds incident to the atom atom in the molecular graph molgraph. More...

int	getExplicitChainBondCount (Chem.BondContainer cntnr)
	Returns the number of explicit chain (non-ring) bonds in cntnr. More...

int	getExplicitHydrogenBondCount (Chem.BondContainer cntnr)
	Returns the number of explicit bonds in cntnr that involve a hydrogen atom. More...

int	getExplicitOrdinaryHydrogenCount (Chem.MolecularGraph molgraph, int flags=2147483648)
	Returns the number of explicit ordinary hydrogens in the molecular graph molgraph. More...

None	setFunctionalGroups (Chem.MolecularGraph molgraph, Chem.FragmentList fg_list)
	Sets the value of the MolProp.MolecularGraphProperty.FUNCTIONAL_GROUPS property of the molecular graph molgraph to fg_list. More...

bool	hasFunctionalGroups (Chem.MolecularGraph molgraph)
	Tells whether the MolProp.MolecularGraphProperty.FUNCTIONAL_GROUPS property of the molecular graph molgraph is set. More...

Chem.FragmentList	getFunctionalGroups (Chem.MolecularGraph molgraph)
	Returns the value of the MolProp.MolecularGraphProperty.FUNCTIONAL_GROUPS property of the molecular graph molgraph. More...

None	clearFunctionalGroups (Chem.MolecularGraph molgraph)
	Clears the value of the MolProp.MolecularGraphProperty.FUNCTIONAL_GROUPS property of the molecular graph molgraph. More...

int	getHBondAcceptorAtomCount (Chem.MolecularGraph molgraph)
	Returns the number of H-bond acceptor atoms in the molecular graph molgraph. More...

None	setHBondAcceptorType (Chem.Atom atom, int type)
	Sets the value of the MolProp.AtomProperty.H_BOND_ACCEPTOR_TYPE property of the atom atom to type. More...

bool	hasHBondAcceptorType (Chem.Atom atom)
	Tells whether the MolProp.AtomProperty.H_BOND_ACCEPTOR_TYPE property of the atom atom is set. More...

int	getHBondAcceptorType (Chem.Atom atom)
	Returns the value of the MolProp.AtomProperty.H_BOND_ACCEPTOR_TYPE property of the atom atom. More...

None	clearHBondAcceptorType (Chem.Atom atom)
	Clears the value of the MolProp.AtomProperty.H_BOND_ACCEPTOR_TYPE property of the atom atom. More...

int	getHBondDonorAtomCount (Chem.MolecularGraph molgraph)
	Returns the number of H-bond donor atoms in the molecular graph molgraph. More...

None	setHBondDonorType (Chem.Atom atom, int type)
	Sets the value of the MolProp.AtomProperty.H_BOND_DONOR_TYPE property of the atom atom to type. More...

bool	hasHBondDonorType (Chem.Atom atom)
	Tells whether the MolProp.AtomProperty.H_BOND_DONOR_TYPE property of the atom atom is set. More...

int	getHBondDonorType (Chem.Atom atom)
	Returns the value of the MolProp.AtomProperty.H_BOND_DONOR_TYPE property of the atom atom. More...

None	clearHBondDonorType (Chem.Atom atom)
	Clears the value of the MolProp.AtomProperty.H_BOND_DONOR_TYPE property of the atom atom. More...

int	getHeavyAtomCount (Chem.Atom atom, Chem.MolecularGraph molgraph)
	Returns the number of heavy atom neighbors of the atom atom in the molecular graph molgraph. More...

int	getHeavyAtomCount (Chem.AtomContainer cntnr)
	Returns the number of heavy (non-hydrogen) atoms in cntnr. More...

int	getHeavyBondCount (Chem.Atom atom, Chem.MolecularGraph molgraph)
	Returns the number of heavy bonds incident to the atom atom in the molecular graph molgraph. More...

int	getHeavyBondCount (Chem.BondContainer cntnr)
	Returns the number of heavy atom bonds in cntnr. More...

float	getHybridPolarizability (Chem.Atom atom, Chem.MolecularGraph molgraph)
	Returns the hybridization state-dependent atomic polarizability of the atom atom in the molecular graph molgraph. More...

int	getHydrogenBondCount (Chem.MolecularGraph molgraph)
	Returns the number of bonds in the molecular graph molgraph that involve at least one hydrogen atom. More...

None	setHydrophobicity (Chem.Atom atom, float hyd)
	Sets the value of the MolProp.AtomProperty.HYDROPHOBICITY property of the atom atom to hyd. More...

bool	hasHydrophobicity (Chem.Atom atom)
	Tells whether the MolProp.AtomProperty.HYDROPHOBICITY property of the atom atom is set. More...

float	getHydrophobicity (Chem.Atom atom)
	Returns the value of the MolProp.AtomProperty.HYDROPHOBICITY property of the atom atom. More...

None	clearHydrophobicity (Chem.Atom atom)
	Clears the value of the MolProp.AtomProperty.HYDROPHOBICITY property of the atom atom. More...

int	getIUPACGroup (Chem.Atom atom)
	Returns the IUPAC group number of the chemical element associated with the atom atom. More...

int	getImplicitHydrogenCount (Chem.MolecularGraph molgraph)
	Returns the total number of implicit hydrogens in the molecular graph molgraph. More...

None	setMHMOPiCharge (Chem.Atom atom, float charge)
	Sets the value of the MolProp.AtomProperty.MHMO_PI_CHARGE property of the atom atom to charge. More...

bool	hasMHMOPiCharge (Chem.Atom atom)
	Tells whether the MolProp.AtomProperty.MHMO_PI_CHARGE property of the atom atom is set. More...

float	getMHMOPiCharge (Chem.Atom atom)
	Returns the value of the MolProp.AtomProperty.MHMO_PI_CHARGE property of the atom atom. More...

None	clearMHMOPiCharge (Chem.Atom atom)
	Clears the value of the MolProp.AtomProperty.MHMO_PI_CHARGE property of the atom atom. More...

None	setMHMOPiOrder (Chem.Bond bond, float order)
	Sets the value of the MolProp.BondProperty.MHMO_PI_ORDER property of the bond bond to order. More...

bool	hasMHMOPiOrder (Chem.Bond bond)

float	getMHMOPiOrder (Chem.Bond bond)
	Returns the value of the MolProp.BondProperty.MHMO_PI_ORDER property of the bond bond. More...

None	clearMHMOPiOrder (Chem.Bond bond)
	Clears the value of the MolProp.BondProperty.MHMO_PI_ORDER property of the bond bond. More...

int	getNetFormalCharge (Chem.AtomContainer cntnr)
	Returns the net formal charge of cntnr (sum of per-atom formal charges). More...

int	getNumContainingSSSRRings (Chem.Atom atom, Chem.MolecularGraph molgraph)
	Returns the number of SSSR rings of the molecular graph molgraph that contain the atom atom. More...

int	getNumContainingSSSRRings (Chem.Bond bond, Chem.MolecularGraph molgraph)
	Returns the number of SSSR rings of the molecular graph molgraph that contain the bond bond. More...

int	getOrdinaryHydrogenCount (Chem.Atom atom, Chem.MolecularGraph molgraph, int flags=2147483648)
	Returns the number of ordinary hydrogen neighbors of the atom atom in the molecular graph molgraph. More...

int	getOrdinaryHydrogenCount (Chem.MolecularGraph molgraph, int flags=2147483648)
	Returns the number of ordinary hydrogens in the molecular graph molgraph. More...

None	setPEOESigmaCharge (Chem.Atom atom, float charge)
	Sets the value of the MolProp.AtomProperty.PEOE_SIGMA_CHARGE property of the atom atom to charge. More...

bool	hasPEOESigmaCharge (Chem.Atom atom)
	Tells whether the MolProp.AtomProperty.PEOE_SIGMA_CHARGE property of the atom atom is set. More...

float	getPEOESigmaCharge (Chem.Atom atom)
	Returns the value of the MolProp.AtomProperty.PEOE_SIGMA_CHARGE property of the atom atom. More...

None	clearPEOESigmaCharge (Chem.Atom atom)
	Clears the value of the MolProp.AtomProperty.PEOE_SIGMA_CHARGE property of the atom atom. More...

None	setPEOESigmaElectronegativity (Chem.Atom atom, float e_neg)
	Sets the value of the MolProp.AtomProperty.PEOE_SIGMA_ELECTRONEGATIVITY property of the atom atom to e_neg. More...

bool	hasPEOESigmaElectronegativity (Chem.Atom atom)
	Tells whether the MolProp.AtomProperty.PEOE_SIGMA_ELECTRONEGATIVITY property of the atom atom is set. More...

float	getPEOESigmaElectronegativity (Chem.Atom atom)
	Returns the value of the MolProp.AtomProperty.PEOE_SIGMA_ELECTRONEGATIVITY property of the atom atom. More...

None	clearPEOESigmaElectronegativity (Chem.Atom atom)
	Clears the value of the MolProp.AtomProperty.PEOE_SIGMA_ELECTRONEGATIVITY property of the atom atom. More...

int	getPeriod (Chem.Atom atom)
	Returns the period of the chemical element associated with the atom atom. More...

int	getRingAtomCount (Chem.Atom atom, Chem.MolecularGraph molgraph)
	Returns the number of ring atom neighbors of the atom atom in the molecular graph molgraph. More...

int	getRingAtomCount (Chem.AtomContainer cntnr)
	Returns the number of ring atoms in cntnr. More...

int	getRingBondCount (Chem.Atom atom, Chem.MolecularGraph molgraph)
	Returns the number of ring bonds incident to the atom atom in the molecular graph molgraph. More...

int	getRingBondCount (Chem.BondContainer cntnr)
	Returns the number of ring bonds in cntnr. More...

int	getRotatableBondCount (Chem.Atom atom, Chem.MolecularGraph molgraph, bool h_rotors=False, bool ring_bonds=False, bool amide_bonds=False)
	Returns the number of rotatable bonds incident to the atom atom in the molecular graph molgraph. More...

int	getRotatableBondCount (Chem.MolecularGraph molgraph, bool h_rotors=False, bool ring_bonds=False, bool amide_bonds=False)
	Returns the number of rotatable bonds in the molecular graph molgraph. More...

int	getRuleOfFiveScore (Chem.MolecularGraph molgraph)
	Returns the Lipinski rule-of-five score of the molecular graph molgraph, defined as the number of satisfied criteria (0-4). More...

int	getVSEPRCoordinationGeometry (Chem.Atom atom, Chem.MolecularGraph molgraph)
	Returns the VSEPR coordination geometry of the atom atom in the molecular graph molgraph. More...

int	getVSEPRCoordinationGeometry (Chem.Atom atom, Chem.MolecularGraph molgraph, int steric_num)
	Returns the VSEPR coordination geometry of the atom atom in the molecular graph molgraph. More...

float	getVdWRadius (Chem.Atom atom)
	Returns the Van der Waals radius of the chemical element associated with the atom atom. More...

None	calcAtomHydrophobicities (Chem.MolecularGraph molgraph, bool overwrite, bool from_logp=False)
	Calculates per-atom hydrophobicities for the molecular graph molgraph and stores them as atom properties. More...

int	calcCyclomaticNumber (Chem.MolecularGraph molgraph)
	Calculates the cyclomatic number of the molecular graph molgraph (number of independent cycles). More...

bool	calcDipoleMoment (Chem.AtomContainer cntnr, Math.Vector3D moment)
	Calculates the dipole moment of cntnr using the standard atom 3D-coordinates accessor. More...

bool	calcDipoleMoment (Chem.AtomContainer cntnr, Chem.Atom3DCoordinatesFunction coords_func, Math.Vector3D moment)
	Calculates the dipole moment of cntnr using the supplied atom 3D-coordinates function. More...

float	calcEffectivePolarizability (Chem.Atom atom, Chem.MolecularGraph molgraph, float damping=0.75)
	Calculates the effective atomic polarizability of the atom atom in the molecular graph molgraph . More...

float	calcExplicitMass (Chem.AtomContainer cntnr)
	Calculates the total mass of the explicit atoms in cntnr. More...

None	calcExplicitMassComposition (Chem.AtomContainer cntnr, MassComposition mass_comp)
	Calculates the per-element mass composition of the explicit atoms in cntnr. More...

int	calcExplicitValence (Chem.Atom atom, Chem.MolecularGraph molgraph)
	Calculates the explicit valence of the atom atom in the molecular graph molgraph (sum of explicit bond orders). More...

int	calcFreeValenceElectronCount (Chem.Atom atom, Chem.MolecularGraph molgraph)
	Calculates the number of valence electrons of the atom atom in the molecular graph molgraph that are not involved in bonds. More...

float	calcInductiveEffect (Chem.Atom atom, Chem.MolecularGraph molgraph, int num_bonds=10)
	Calculates the inductive effect parameter of the atom atom in the molecular graph molgraph. More...

float	calcLogS (Chem.MolecularGraph molgraph)
	Calculates the \( \log S \) (aqueous solubility) of the molecular graph molgraph using MolProp.LogSCalculator. More...

float	calcLonePairElectronegativity (Chem.Atom atom, Chem.MolecularGraph molgraph)
	Calculates the lone-pair electronegativity of the atom atom in the molecular graph molgraph. More...

None	calcMHMOProperties (Chem.MolecularGraph molgraph, bool overwrite)
	Calculates MHMO pi charges and pi bond orders for the molecular graph molgraph and stores them as atom/bond properties. More...

None	calcMassComposition (Chem.MolecularGraph molgraph, MassComposition comp)
	Calculates the per-element mass composition of the molecular graph molgraph. More...

float	calcMass (Chem.MolecularGraph molgraph)
	Calculates the total molecular mass of the molecular graph molgraph (sum of atom standard atomic weights including implicit hydrogens). More...

float	calcMeanPolarizability (Chem.MolecularGraph molgraph)
	Calculates the mean atomic polarizability of the molecular graph molgraph. More...

None	calcPEOEProperties (Chem.MolecularGraph molgraph, bool overwrite, int num_iter=20, float damping=0.48)
	Calculates PEOE sigma charges and electronegativities for the atoms of the molecular graph molgraph and stores them as atom properties. More...

float	calcPiElectronegativity (Chem.Atom atom, Chem.MolecularGraph molgraph)
	Calculates the pi electronegativity of the atom atom in the molecular graph molgraph. More...

float	calcPolarizability (Chem.Bond bond, Chem.MolecularGraph molgraph, float damping=0.75)
	Calculates the bond polarizability of the bond bond within the molecular graph molgraph. More...

int	calcStericNumber (Chem.Atom atom, Chem.MolecularGraph molgraph)
	Calculates the steric number of the atom atom in the molecular graph molgraph (used by VSEPR theory). More...

float	calcTPSA (Chem.MolecularGraph molgraph)
	Calculates the topological polar surface area (TPSA) of the molecular graph molgraph using MolProp.TPSACalculator. More...

float	calcTotalPartialCharge (Chem.Atom atom)
	Calculates the total partial charge of the atom atom. More...

int	calcValence (Chem.Atom atom, Chem.MolecularGraph molgraph)
	Calculates the total valence of the atom atom in the molecular graph molgraph (explicit valence plus implicit hydrogens). More...

int	calcValenceElectronCount (Chem.Atom atom)
	Calculates the number of valence electrons of the chemical element associated with the atom atom (corrected for the atom's formal charge). More...

float	calcXLogP (Chem.MolecularGraph molgraph)
	Calculates the \( \log P \) value of the molecular graph molgraph using MolProp.XLogPCalculator. More...

None	generateElementHistogram (Chem.MolecularGraph molgraph, ElementHistogram hist, bool append=False)
	Generates the element histogram of the molecular graph molgraph. More...

None	generateExplicitElementHistogram (Chem.AtomContainer cntnr, ElementHistogram hist, bool append=False)
	Generates the element histogram of the explicit atoms in cntnr. More...

str	generateExplicitMassCompositionString (Chem.AtomContainer cntnr)

str	generateExplicitMolecularFormula (Chem.AtomContainer cntnr)

object	generateMassCompositionString (Chem.MolecularGraph molgraph)

object	generateMolecularFormula (Chem.MolecularGraph molgraph, str sep='')

bool	isAmideBond (Chem.Bond bond, Chem.MolecularGraph molgraph, bool c_only=False, bool db_o_only=False)
	Tells whether bond is an amide bond in the molecular graph molgraph. More...

bool	isAmideCenter (Chem.Atom atom, Chem.MolecularGraph molgraph, bool c_only=False, bool db_o_only=False)
	Tells whether the atom atom is the center of an amide group in the molecular graph molgraph. More...

bool	isAmideNitrogen (Chem.Atom atom, Chem.MolecularGraph molgraph, bool c_only=False, bool db_o_only=False)
	Tells whether the atom atom is the nitrogen of an amide group in the molecular graph molgraph. More...

bool	isBridgehead (Chem.Atom atom, Chem.MolecularGraph molgraph, bool bridged_only)
	Tells whether the atom atom is a ring system bridgehead atom in the molecular graph molgraph. More...

bool	isCarbonylLike (Chem.Atom atom, Chem.MolecularGraph molgraph, bool c_only=False, bool db_o_only=False)
	Tells whether the atom atom is a carbonyl-like center in the molecular graph molgraph. More...

bool	isChemicalElement (Chem.Atom atom)
	Tells whether the atom atom represents a chemical element. More...

bool	isHBondAcceptor (Chem.Atom atom, Chem.MolecularGraph molgraph)
	Tells whether the atom atom acts as an H-bond acceptor in the molecular graph molgraph. More...

bool	isHBondDonor (Chem.Atom atom, Chem.MolecularGraph molgraph)
	Tells whether the atom atom acts as an H-bond donor in the molecular graph molgraph. More...

bool	isHalogen (Chem.Atom atom)
	Tells whether the chemical element associated with the atom atom is a halogen. More...

bool	isHeavy (Chem.Atom atom)
	Tells whether the atom atom is a heavy (non-hydrogen) atom. More...

bool	isHeteroAtomHydrogenRotor (Chem.Bond bond, Chem.MolecularGraph molgraph)
	Tells whether the bond bond is a heteroatom hydrogen-only rotor. More...

bool	isHydrogenBond (Chem.Bond bond)
	Tells whether the bond bond is a hydrogen bond (one of the bonded atoms is a hydrogen). More...

bool	isHydrogenRotor (Chem.Bond bond, Chem.MolecularGraph molgraph)
	Tells whether the bond bond is a rotatable bond whose rotation only moves hydrogen atoms. More...

bool	isInRing (Chem.Atom atom, Chem.MolecularGraph molgraph)
	Tells whether the atom atom is a member of any ring in the molecular graph molgraph. More...

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

bool	isInRingOfSize (Chem.Atom atom, Chem.MolecularGraph molgraph, int size)
	Tells whether the atom atom is a member of a ring of size size in the molecular graph molgraph. More...

bool	isInRingOfSize (Chem.Bond bond, Chem.MolecularGraph molgraph, int size)
	Tells whether the bond bond is part of a ring of the specified size in the molecular graph molgraph. More...

bool	isInvertibleNitrogen (Chem.Atom atom, Chem.MolecularGraph molgraph)
	Tells whether the atom atom is an invertible (pyramidal, non-aromatic, non-amide) nitrogen in the molecular graph molgraph. More...

bool	isMainGroupElement (Chem.Atom atom)
	Tells whether the chemical element associated with the atom atom is a main-group element. More...

bool	isMetal (Chem.Atom atom)
	Tells whether the chemical element associated with the atom atom is a metal. More...

bool	isNobleGas (Chem.Atom atom)
	Tells whether the chemical element associated with the atom atom is a noble gas. More...

bool	isNonMetal (Chem.Atom atom)
	Tells whether the chemical element associated with the atom atom is a non-metal. More...

bool	isOrdinaryHydrogen (Chem.Atom atom, Chem.MolecularGraph molgraph, int flags=2147483648)
	Tells whether the atom atom is an ordinary hydrogen. More...

bool	isPlanarNitrogen (Chem.Atom atom, Chem.MolecularGraph molgraph)
	Tells whether the atom atom is a planar nitrogen in the molecular graph molgraph. More...

bool	isRotatable (Chem.Bond bond, Chem.MolecularGraph molgraph, bool h_rotors, bool ring_bonds, bool amide_bonds)
	Tells whether the bond bond is rotatable. More...

bool	isSemiMetal (Chem.Atom atom)
	Tells whether the chemical element associated with the atom atom is a semi-metal. More...

bool	isSpiroCenter (Chem.Atom atom, Chem.MolecularGraph molgraph)
	Tells whether the atom atom is a spiro center in the molecular graph molgraph. More...

bool	isTransitionMetal (Chem.Atom atom)
	Tells whether the chemical element associated with the atom atom is a transition metal. More...

bool	isUnsaturated (Chem.Atom atom, Chem.MolecularGraph molgraph)
	Tells whether the atom atom is unsaturated (involved in at least one multiple bond) in the molecular graph molgraph. More...

Chem.FragmentList	perceiveFunctionalGroups (Chem.MolecularGraph molgraph)
	Perceives the functional groups of the molecular graph molgraph using MolProp.FunctionalGroupList. More...

Chem.FragmentList	perceiveFunctionalGroups (Chem.MolecularGraph molgraph, bool overwrite)
	Perceives the functional groups of the molecular graph molgraph and stores them as a property. More...

None	perceiveHBondAcceptorAtomTypes (Chem.MolecularGraph molgraph, bool overwrite)
	Perceives the H-bond acceptor types of the atoms in the molecular graph molgraph and stores them as atom properties. More...

None	perceiveHBondDonorAtomTypes (Chem.MolecularGraph molgraph, bool overwrite)
	Perceives the H-bond donor types of the atoms in the molecular graph molgraph and stores them as atom properties. More...

Detailed Description

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

Function Documentation

◆ getAllredRochowElectronegativity()

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

Returns the Allred-Rochow electronegativity of the chemical element associated with the atom atom.

Parameters

atom The atom.

Returns: The Allred-Rochow electronegativity.

◆ getAromaticAtomCount() [1/2]

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

Returns the number of aromatic neighbors of the atom atom in the molecular graph molgraph.

Parameters

atom	The atom.
molgraph	The molecular graph.

Returns: The aromatic neighbor count.

◆ getAromaticAtomCount() [2/2]

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

Returns the number of aromatic atoms in cntnr.

Parameters

cntnr The atom container.

Returns: The number of aromatic atoms.

◆ getAromaticBondCount() [1/2]

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

Returns the number of aromatic bonds incident to the atom atom in the molecular graph molgraph.

Parameters

atom	The atom.
molgraph	The molecular graph.

Returns: The aromatic bond count.

◆ getAromaticBondCount() [2/2]

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

Returns the number of aromatic bonds in cntnr.

Parameters

cntnr The bond container.

Returns: The number of aromatic bonds.

◆ getAtomCount() [1/3]

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

Returns the number of neighbors of the atom atom in the molecular graph molgraph (including implicit hydrogens) whose type matches type.

Parameters

atom	The atom.
molgraph	The molecular graph.
type	The atom type to count (see namespace Chem.AtomType).
strict	If `True`, the atom type must match type exactly. Otherwise, generic types match via Chem.atomTypesMatch().

Returns: The matching neighbor count.

◆ getAtomCount() [2/3]

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

Returns the total number of atoms in the molecular graph molgraph (including implicit hydrogens).

Parameters

molgraph The molecular graph.

Returns: The total atom count.

◆ getAtomCount() [3/3]

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

Returns the number of atoms in the molecular graph molgraph whose type property matches type.

Parameters

molgraph	The molecular graph.
type	The atom type to count (see namespace Chem.AtomType).
strict	If `True`, the atom type must match type exactly. Otherwise, generic types match via Chem.atomTypesMatch().

Returns: The number of matching atoms (including implicit hydrogens when type matches Chem.AtomType.H).

Since: 1.1

◆ getAtomicWeight()

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

Returns the standard atomic weight of the chemical element associated with the atom atom.

Parameters

atom The atom.

Returns: The standard atomic weight.

◆ getBondCount() [1/5]

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

Returns the total number of bonds incident to the atom atom in the molecular graph molgraph (including implicit hydrogen bonds).

Parameters

atom	The atom.
molgraph	The molecular graph.

Returns: The total bond count.

◆ getBondCount() [2/5]

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

Returns the total number of bonds of the given order incident to the atom atom (including implicit hydrogen bonds).

Parameters

atom	The atom.
molgraph	The molecular graph.
order	The bond order to count.

Returns: The number of matching bonds.

◆ getBondCount() [3/5]

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

Returns the total number of bonds of the given order incident to the atom atom that bond to atoms whose type matches type.

Parameters

atom	The atom.
molgraph	The molecular graph.
order	The bond order to count.
type	The atom type of the bonded partner (see namespace Chem.AtomType).
strict	If `True`, the atom type must match type exactly. Otherwise, generic types match via Chem.atomTypesMatch().

Returns: The number of matching bonds.

◆ getBondCount() [4/5]

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

Returns the total number of bonds in the molecular graph molgraph (including bonds to implicit hydrogens).

Parameters

molgraph The molecular graph.

Returns: The total bond count.

◆ getBondCount() [5/5]

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

Returns the number of bonds in the molecular graph molgraph with the given order, optionally including aromatic bonds.

Parameters

molgraph	The molecular graph.
order	The bond order to count.
inc_aro	If `True`, aromatic bonds are counted in addition to bonds of the given order.

Returns: The number of matching bonds.

◆ getChainAtomCount() [1/2]

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

Returns the number of chain (non-ring) neighbors of the atom atom in the molecular graph molgraph (including implicit hydrogens).

Parameters

atom	The atom.
molgraph	The molecular graph.

Returns: The chain atom neighbor count.

◆ getChainAtomCount() [2/2]

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

Returns the number of chain (non-ring) atoms in the molecular graph molgraph.

Parameters

molgraph The molecular graph.

Returns: The chain-atom count.

◆ getChainBondCount() [1/2]

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

Returns the number of chain (non-ring) bonds incident to the atom atom in the molecular graph molgraph (including implicit hydrogen bonds).

Parameters

atom	The atom.
molgraph	The molecular graph.

Returns: The chain bond count.

◆ getChainBondCount() [2/2]

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

Returns the number of chain (non-ring) bonds in the molecular graph molgraph.

Parameters

molgraph The molecular graph.

Returns: The chain-bond count.

◆ getComponentCount()

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

Returns the number of connected components in the molecular graph molgraph.

Parameters

molgraph The molecular graph.

Returns: The component count.

◆ getCovalentRadius()

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

Returns the covalent radius of the chemical element associated with the atom atom for the given bond order.

Parameters

atom	The atom.
order	The bond order.

Returns: The covalent radius.

◆ getElementName()

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

Returns the element name of the chemical element associated with the atom atom.

Parameters

atom The atom.

Returns: A reference to the element name.

◆ getElementValenceElectronCount()

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

Returns the number of valence electrons of the chemical element associated with the atom atom.

Parameters

atom The atom.

Returns: The number of valence electrons.

◆ getExplicitAtomCount() [1/3]

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

Returns the number of explicit neighbors of the atom atom in the molecular graph molgraph whose type matches type.

Parameters

atom	The atom.
molgraph	The molecular graph.
type	The atom type to count (see namespace Chem.AtomType).
strict	If `True`, the atom type must match type exactly. Otherwise, generic types match via Chem.atomTypesMatch().

Returns: The matching explicit atom neighbor count.

◆ getExplicitAtomCount() [2/3]

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

Returns the total number of explicit atoms in cntnr.

Parameters

cntnr The atom container.

Returns: The number of explicit atoms.

◆ getExplicitAtomCount() [3/3]

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

Returns the number of explicit atoms in cntnr that match the given atom type.

Parameters

cntnr	The atom container.
type	The atom type to match (see namespace Chem.AtomType).
strict	If `True`, atoms must match the type strictly. Otherwise, generic-type matching applies.

Returns: The number of matching explicit atoms.

◆ getExplicitBondCount() [1/5]

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

Returns the number of explicit bonds incident to the atom atom in the molecular graph molgraph.

Parameters

atom	The atom.
molgraph	The molecular graph.

Returns: The explicit bond count.

◆ getExplicitBondCount() [2/5]

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

Returns the number of explicit bonds of the given order incident to the atom atom in the molecular graph molgraph.

Parameters

atom	The atom.
molgraph	The molecular graph.
order	The bond order to count.

Returns: The number of matching explicit bonds.

◆ getExplicitBondCount() [3/5]

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

Returns the number of explicit bonds of the given order incident to the atom atom that bond to atoms whose type matches type.

Parameters

atom	The atom.
molgraph	The molecular graph.
order	The bond order to count.
type	The atom type of the bonded partner (see namespace Chem.AtomType).
strict	If `True`, the atom type must match type exactly. Otherwise, generic types match via Chem.atomTypesMatch().

Returns: The number of matching explicit bonds.

◆ getExplicitBondCount() [4/5]

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

Returns the total number of explicit bonds in cntnr.

Parameters

cntnr The bond container.

Returns: The number of explicit bonds.

◆ getExplicitBondCount() [5/5]

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

Returns the number of explicit bonds in cntnr that match the given bond order.

Parameters

cntnr	The bond container.
order	The bond order to match.
inc_aro	If `True`, aromatic bonds are included in the count for any order.

Returns: The number of matching explicit bonds.

◆ getExplicitChainAtomCount() [1/2]

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

Returns the number of explicit chain (non-ring) neighbors of the atom atom in the molecular graph molgraph.

Parameters

atom	The atom.
molgraph	The molecular graph.

Returns: The explicit chain atom neighbor count.

◆ getExplicitChainAtomCount() [2/2]

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

Returns the number of explicit chain (non-ring) atoms in cntnr.

Parameters

cntnr The atom container.

Returns: The number of chain atoms.

◆ getExplicitChainBondCount() [1/2]

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

Returns the number of explicit chain (non-ring) bonds incident to the atom atom in the molecular graph molgraph.

Parameters

atom	The atom.
molgraph	The molecular graph.

Returns: The explicit chain bond count.

◆ getExplicitChainBondCount() [2/2]

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

Returns the number of explicit chain (non-ring) bonds in cntnr.

Parameters

cntnr The bond container.

Returns: The number of explicit chain bonds.

◆ getExplicitHydrogenBondCount()

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

Returns the number of explicit bonds in cntnr that involve a hydrogen atom.

Parameters

cntnr The bond container.

Returns: The number of explicit hydrogen-involving bonds.

◆ getExplicitOrdinaryHydrogenCount()

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

Returns the number of explicit ordinary hydrogens in the molecular graph molgraph.

Parameters

molgraph	The molecular graph.
flags	Bitmask of Chem.AtomPropertyFlag values that qualify "ordinary"; an empty bitmask makes any hydrogen ordinary.

Returns: The explicit ordinary hydrogen count.

See also: MolProp.isOrdinaryHydrogen() for the definition of "ordinary".

◆ setFunctionalGroups()

None CDPL.MolProp.setFunctionalGroups	(	Chem.MolecularGraph	molgraph,
		Chem.FragmentList	fg_list
	)

Sets the value of the MolProp.MolecularGraphProperty.FUNCTIONAL_GROUPS property of the molecular graph molgraph to fg_list.

Parameters

molgraph	The molecular graph for which to set the property value.
fg_list	The new functional group list.

Since: 1.3

◆ hasFunctionalGroups()

bool CDPL.MolProp.hasFunctionalGroups ( Chem.MolecularGraph molgraph )

Tells whether the MolProp.MolecularGraphProperty.FUNCTIONAL_GROUPS property of the molecular graph molgraph is set.

Parameters

molgraph The molecular graph for which to query the property value.

Returns: True if the property is set, and False otherwise.

Since: 1.3

◆ getFunctionalGroups()

Chem.FragmentList CDPL.MolProp.getFunctionalGroups ( Chem.MolecularGraph molgraph )

Returns the value of the MolProp.MolecularGraphProperty.FUNCTIONAL_GROUPS property of the molecular graph molgraph.

Parameters

molgraph The molecular graph for which to return the property value.

Returns: A shared reference to the functional group list.

Since: 1.3

◆ clearFunctionalGroups()

None CDPL.MolProp.clearFunctionalGroups ( Chem.MolecularGraph molgraph )

Clears the value of the MolProp.MolecularGraphProperty.FUNCTIONAL_GROUPS property of the molecular graph molgraph.

Parameters

molgraph The molecular graph for which to clear the property value.

Since: 1.3

◆ getHBondAcceptorAtomCount()

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

Returns the number of H-bond acceptor atoms in the molecular graph molgraph.

Parameters

molgraph The molecular graph.

Returns: The H-bond acceptor count.

◆ setHBondAcceptorType()

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

Sets the value of the MolProp.AtomProperty.H_BOND_ACCEPTOR_TYPE property of the atom atom to type.

Parameters

atom	The atom for which to set the property value.
type	The new H-bond acceptor type identifier (see namespace MolProp.HBondAcceptorAtomType).

◆ hasHBondAcceptorType()

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

Tells whether the MolProp.AtomProperty.H_BOND_ACCEPTOR_TYPE property of the atom atom is set.

Parameters

atom	The atom for which to query the property value.

Returns: True if the H-bond acceptor type property is set, and False otherwise.

◆ getHBondAcceptorType()

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

Returns the value of the MolProp.AtomProperty.H_BOND_ACCEPTOR_TYPE property of the atom atom.

Parameters

atom	The atom for which to return the property value.

Returns: The H-bond acceptor type identifier (see namespace MolProp.HBondAcceptorAtomType).

◆ clearHBondAcceptorType()

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

Clears the value of the MolProp.AtomProperty.H_BOND_ACCEPTOR_TYPE property of the atom atom.

Parameters

atom	The atom for which to clear the property value.

◆ getHBondDonorAtomCount()

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

Returns the number of H-bond donor atoms in the molecular graph molgraph.

Parameters

molgraph The molecular graph.

Returns: The H-bond donor count.

◆ setHBondDonorType()

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

Sets the value of the MolProp.AtomProperty.H_BOND_DONOR_TYPE property of the atom atom to type.

Parameters

atom	The atom for which to set the property value.
type	The new H-bond donor type identifier (see namespace MolProp.HBondDonorAtomType).

◆ hasHBondDonorType()

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

Tells whether the MolProp.AtomProperty.H_BOND_DONOR_TYPE property of the atom atom is set.

Parameters

atom	The atom for which to query the property value.

Returns: True if the H-bond donor type property is set, and False otherwise.

◆ getHBondDonorType()

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

Returns the value of the MolProp.AtomProperty.H_BOND_DONOR_TYPE property of the atom atom.

Parameters

atom	The atom for which to return the property value.

Returns: The H-bond donor type identifier (see namespace MolProp.HBondDonorAtomType).

◆ clearHBondDonorType()

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

Clears the value of the MolProp.AtomProperty.H_BOND_DONOR_TYPE property of the atom atom.

Parameters

atom	The atom for which to clear the property value.

◆ getHeavyAtomCount() [1/2]

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

Returns the number of heavy atom neighbors of the atom atom in the molecular graph molgraph.

Parameters

atom	The atom.
molgraph	The molecular graph.

Returns: The heavy atom neighbor count.

◆ getHeavyAtomCount() [2/2]

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

Returns the number of heavy (non-hydrogen) atoms in cntnr.

Parameters

cntnr The atom container.

Returns: The number of heavy atoms.

◆ getHeavyBondCount() [1/2]

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

Returns the number of heavy bonds incident to the atom atom in the molecular graph molgraph.

Parameters

atom	The atom.
molgraph	The molecular graph.

Returns: The heavy bond count.

◆ getHeavyBondCount() [2/2]

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

Returns the number of heavy atom bonds in cntnr.

Parameters

cntnr The bond container.

Returns: The number of heavy bonds.

◆ getHybridPolarizability()

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

Returns the hybridization state-dependent atomic polarizability of the atom atom in the molecular graph molgraph.

Parameters

atom	The atom.
molgraph	The molecular graph.

Returns: The hybrid polarizability.

◆ getHydrogenBondCount()

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

Returns the number of bonds in the molecular graph molgraph that involve at least one hydrogen atom.

Parameters

molgraph The molecular graph.

Returns: The hydrogen-bond count.

◆ setHydrophobicity()

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

Sets the value of the MolProp.AtomProperty.HYDROPHOBICITY property of the atom atom to hyd.

Parameters

atom	The atom for which to set the property value.
hyd	The new hydrophobicity value.

◆ hasHydrophobicity()

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

Tells whether the MolProp.AtomProperty.HYDROPHOBICITY property of the atom atom is set.

Parameters

atom	The atom for which to query the property value.

Returns: True if the hydrophobicity property is set, and False otherwise.

◆ getHydrophobicity()

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

Returns the value of the MolProp.AtomProperty.HYDROPHOBICITY property of the atom atom.

Parameters

atom	The atom for which to return the property value.

Returns: The hydrophobicity value.

◆ clearHydrophobicity()

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

Clears the value of the MolProp.AtomProperty.HYDROPHOBICITY property of the atom atom.

Parameters

atom	The atom for which to clear the property value.

◆ getIUPACGroup()

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

Returns the IUPAC group number of the chemical element associated with the atom atom.

Parameters

atom The atom.

Returns: The IUPAC group number.

◆ getImplicitHydrogenCount()

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

Returns the total number of implicit hydrogens in the molecular graph molgraph.

Parameters

molgraph The molecular graph.

Returns: The implicit hydrogen count.

◆ setMHMOPiCharge()

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

Sets the value of the MolProp.AtomProperty.MHMO_PI_CHARGE property of the atom atom to charge.

Parameters

atom	The atom for which to set the property value.
charge	The new MHMO pi charge value.

◆ hasMHMOPiCharge()

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

Tells whether the MolProp.AtomProperty.MHMO_PI_CHARGE property of the atom atom is set.

Parameters

atom	The atom for which to query the property value.

Returns: True if the MHMO pi charge property is set, and False otherwise.

◆ getMHMOPiCharge()

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

Returns the value of the MolProp.AtomProperty.MHMO_PI_CHARGE property of the atom atom.

Parameters

atom	The atom for which to return the property value.

Returns: The MHMO pi charge value.

◆ clearMHMOPiCharge()

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

Clears the value of the MolProp.AtomProperty.MHMO_PI_CHARGE property of the atom atom.

Parameters

atom	The atom for which to clear the property value.

◆ setMHMOPiOrder()

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

Sets the value of the MolProp.BondProperty.MHMO_PI_ORDER property of the bond bond to order.

Parameters

bond	The bond for which to set the property value.
order	The MHMO pi-bond order.

◆ hasMHMOPiOrder()

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

Parameters

bond

Returns

◆ getMHMOPiOrder()

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

Returns the value of the MolProp.BondProperty.MHMO_PI_ORDER property of the bond bond.

Parameters

bond	The bond for which to return the property value.

Returns: The MHMO pi-bond order.

◆ clearMHMOPiOrder()

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

Clears the value of the MolProp.BondProperty.MHMO_PI_ORDER property of the bond bond.

Parameters

bond	The bond for which to clear the property value.

◆ getNetFormalCharge()

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

Returns the net formal charge of cntnr (sum of per-atom formal charges).

Parameters

cntnr The atom container.

Returns: The net formal charge.

◆ getNumContainingSSSRRings() [1/2]

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

Returns the number of SSSR rings of the molecular graph molgraph that contain the atom atom.

Parameters

atom	The atom.
molgraph	The molecular graph.

Returns: The number of SSSR rings containing the atom atom.

◆ getNumContainingSSSRRings() [2/2]

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

Returns the number of SSSR rings of the molecular graph molgraph that contain the bond bond.

Parameters

bond	The bond.
molgraph	The molecular graph containing the bond.

Returns: The number of SSSR rings containing the bond.

◆ getOrdinaryHydrogenCount() [1/2]

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

Returns the number of ordinary hydrogen neighbors of the atom atom in the molecular graph molgraph.

Parameters

atom	The atom.
molgraph	The molecular graph.
flags	Bitmask of Chem.AtomPropertyFlag values that qualify "ordinary".

Returns: The ordinary hydrogen neighbor count.

See also: MolProp.isOrdinaryHydrogen() for the definition of "ordinary".

◆ getOrdinaryHydrogenCount() [2/2]

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

Returns the number of ordinary hydrogens in the molecular graph molgraph.

Parameters

molgraph	The molecular graph.
flags	Bitmask of Chem.AtomPropertyFlag values that qualify "ordinary"; an empty bitmask makes any hydrogen ordinary.

Returns: The ordinary hydrogen count.

See also: MolProp.isOrdinaryHydrogen() for the definition of "ordinary".

◆ setPEOESigmaCharge()

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

Sets the value of the MolProp.AtomProperty.PEOE_SIGMA_CHARGE property of the atom atom to charge.

Parameters

atom	The atom for which to set the property value.
charge	The new PEOE sigma charge value.

◆ hasPEOESigmaCharge()

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

Tells whether the MolProp.AtomProperty.PEOE_SIGMA_CHARGE property of the atom atom is set.

Parameters

atom	The atom for which to query the property value.

Returns: True if the PEOE sigma charge property is set, and False otherwise.

◆ getPEOESigmaCharge()

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

Returns the value of the MolProp.AtomProperty.PEOE_SIGMA_CHARGE property of the atom atom.

Parameters

atom	The atom for which to return the property value.

Returns: The PEOE sigma charge value.

◆ clearPEOESigmaCharge()

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

Clears the value of the MolProp.AtomProperty.PEOE_SIGMA_CHARGE property of the atom atom.

Parameters

atom	The atom for which to clear the property value.

◆ setPEOESigmaElectronegativity()

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

Sets the value of the MolProp.AtomProperty.PEOE_SIGMA_ELECTRONEGATIVITY property of the atom atom to e_neg.

Parameters

atom	The atom for which to set the property value.
e_neg	The new PEOE sigma electronegativity value.

◆ hasPEOESigmaElectronegativity()

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

Tells whether the MolProp.AtomProperty.PEOE_SIGMA_ELECTRONEGATIVITY property of the atom atom is set.

Parameters

atom	The atom for which to query the property value.

Returns: True if the PEOE sigma electronegativity property is set, and False otherwise.

◆ getPEOESigmaElectronegativity()

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

Returns the value of the MolProp.AtomProperty.PEOE_SIGMA_ELECTRONEGATIVITY property of the atom atom.

Parameters

atom	The atom for which to return the property value.

Returns: The PEOE sigma electronegativity value.

◆ clearPEOESigmaElectronegativity()

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

Clears the value of the MolProp.AtomProperty.PEOE_SIGMA_ELECTRONEGATIVITY property of the atom atom.

Parameters

atom	The atom for which to clear the property value.

◆ getPeriod()

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

Returns the period of the chemical element associated with the atom atom.

Parameters

atom The atom.

Returns: The element period.

◆ getRingAtomCount() [1/2]

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

Returns the number of ring atom neighbors of the atom atom in the molecular graph molgraph.

Parameters

atom	The atom.
molgraph	The molecular graph.

Returns: The ring atom neighbor count.

◆ getRingAtomCount() [2/2]

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

Returns the number of ring atoms in cntnr.

Parameters

cntnr The atom container.

Returns: The number of ring atoms.

◆ getRingBondCount() [1/2]

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

Returns the number of ring bonds incident to the atom atom in the molecular graph molgraph.

Parameters

atom	The atom.
molgraph	The molecular graph.

Returns: The ring bond count.

◆ getRingBondCount() [2/2]

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

Returns the number of ring bonds in cntnr.

Parameters

cntnr The bond container.

Returns: The number of ring bonds.

◆ 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`
	)

Returns the number of rotatable bonds incident to the atom atom in the molecular graph molgraph.

Parameters

atom	The atom.
molgraph	The molecular graph.
h_rotors	If `True`, hydrogen-only rotors are counted as rotatable.
ring_bonds	If `True`, ring bonds are also considered.
amide_bonds	If `True`, amide bonds are also considered.

Returns: The rotatable bond count.

◆ getRotatableBondCount() [2/2]

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

Returns the number of rotatable bonds in the molecular graph molgraph.

Parameters

molgraph	The molecular graph.
h_rotors	If `True`, hydrogen-only rotors are counted.
ring_bonds	If `True`, ring bonds are also considered.
amide_bonds	If `True`, amide bonds are also considered.

Returns: The rotatable-bond count.

◆ getRuleOfFiveScore()

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

Returns the Lipinski rule-of-five score of the molecular graph molgraph, defined as the number of satisfied criteria (0-4).

The four criteria evaluated are:

the number of H-bond donor atoms is ≤ 5,
the number of H-bond acceptor atoms is ≤ 10,
the XLogP value is ≤ 5.0,
the molecular mass is ≤ 500.0.

A score of 4 indicates full compliance with the Lipinski rule of five.

Parameters

molgraph The molecular graph.

Returns: The rule-of-five score (0-4).

◆ getVSEPRCoordinationGeometry() [1/2]

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

Returns the VSEPR coordination geometry of the atom atom in the molecular graph molgraph.

Parameters

atom	The atom.
molgraph	The molecular graph.

Returns: The coordination geometry identifier (see namespace MolProp.CoordinationGeometry).

◆ getVSEPRCoordinationGeometry() [2/2]

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

Returns the VSEPR coordination geometry of the atom atom in the molecular graph molgraph.

Parameters

atom	The atom.
molgraph	The molecular graph.
steric_num	The pre-computed steric number of the atom atom (avoids re-computation).

Returns: The coordination geometry identifier (see namespace MolProp.CoordinationGeometry).

◆ getVdWRadius()

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

Returns the Van der Waals radius of the chemical element associated with the atom atom.

Parameters

atom The atom.

Returns: The Van der Waals radius.

◆ calcAtomHydrophobicities()

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

Calculates per-atom hydrophobicities for the molecular graph molgraph and stores them as atom properties.

Parameters

molgraph	The molecular graph (modified in place).
overwrite	If `True`, existing atom hydrophobicity properties are overwritten.
from_logp	If `True`, the hydrophobicities are derived from the XLogP atom contributions [XLOGP] instead of the Greene algorithm [CATA].

◆ calcCyclomaticNumber()

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

Calculates the cyclomatic number of the molecular graph molgraph (number of independent cycles).

Parameters

molgraph The molecular graph.

Returns: The cyclomatic number.

◆ calcDipoleMoment() [1/2]

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

Calculates the dipole moment of cntnr using the standard atom 3D-coordinates accessor.

Parameters

cntnr	The atom container.
moment	The output dipole-moment vector.

Returns: True if the dipole moment could be calculated, and False otherwise.

◆ calcDipoleMoment() [2/2]

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

Calculates the dipole moment of cntnr using the supplied atom 3D-coordinates function.

Parameters

cntnr	The atom container.
coords_func	The function used to retrieve atom 3D-coordinates.
moment	The output dipole-moment vector.

Returns: True if the dipole moment could be calculated, and False otherwise.

◆ calcEffectivePolarizability()

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

Calculates the effective atomic polarizability of the atom atom in the molecular graph molgraph .

Parameters

atom	The atom.
molgraph	The molecular graph.
damping	The damping factor applied to remote atom contributions.

Returns: The effective polarizability.

See also: [KJPM]

◆ calcExplicitMass()

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

Calculates the total mass of the explicit atoms in cntnr.

Parameters

cntnr The atom container.

Returns: The total explicit mass.

◆ calcExplicitMassComposition()

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

Calculates the per-element mass composition of the explicit atoms in cntnr.

Parameters

cntnr	The atom container.
mass_comp	The output mass composition.

◆ calcExplicitValence()

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

Calculates the explicit valence of the atom atom in the molecular graph molgraph (sum of explicit bond orders).

Parameters

atom	The atom.
molgraph	The molecular graph.

Returns: The explicit valence.

◆ calcFreeValenceElectronCount()

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

Calculates the number of valence electrons of the atom atom in the molecular graph molgraph that are not involved in bonds.

Parameters

atom	The atom.
molgraph	The molecular graph.

Returns: The number of free valence electrons.

◆ calcInductiveEffect()

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

Calculates the inductive effect parameter of the atom atom in the molecular graph molgraph.

Parameters

atom	The atom.
molgraph	The molecular graph.
num_bonds	The maximum number of bonds over which to accumulate the inductive contributions.

Returns: The inductive effect value.

◆ calcLogS()

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

Calculates the \( \log S \) (aqueous solubility) of the molecular graph molgraph using MolProp.LogSCalculator.

Parameters

molgraph The molecular graph.

Returns: The \( \log S \) value.

See also: [LOGS]

◆ calcLonePairElectronegativity()

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

Calculates the lone-pair electronegativity of the atom atom in the molecular graph molgraph.

Parameters

atom	The atom.
molgraph	The molecular graph.

Returns: The lone-pair electronegativity.

◆ calcMHMOProperties()

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

Calculates MHMO pi charges and pi bond orders for the molecular graph molgraph and stores them as atom/bond properties.

Parameters

molgraph	The molecular graph (modified in place).
overwrite	If `True`, existing atom/bond properties are overwritten.

◆ calcMassComposition()

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

Calculates the per-element mass composition of the molecular graph molgraph.

Parameters

molgraph	The molecular graph.
comp	The output mass composition.

◆ calcMass()

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

Calculates the total molecular mass of the molecular graph molgraph (sum of atom standard atomic weights including implicit hydrogens).

Parameters

molgraph The molecular graph.

Returns: The molecular mass.

◆ calcMeanPolarizability()

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

Calculates the mean atomic polarizability of the molecular graph molgraph.

Parameters

molgraph The molecular graph.

Returns: The mean atomic polarizability.

◆ calcPEOEProperties()

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

Calculates PEOE sigma charges and electronegativities for the atoms of the molecular graph molgraph and stores them as atom properties.

Parameters

molgraph	The molecular graph (modified in place).
overwrite	If `True`, existing atom properties are overwritten.
num_iter	The number of charge-shifting iterations.
damping	The per-iteration damping factor.

◆ calcPiElectronegativity()

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

Calculates the pi electronegativity of the atom atom in the molecular graph molgraph.

Parameters

atom	The atom.
molgraph	The molecular graph.

Returns: The pi electronegativity.

◆ calcPolarizability()

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

Calculates the bond polarizability of the bond bond within the molecular graph molgraph.

Parameters

bond	The bond.
molgraph	The molecular graph containing the bond bond.
damping	The damping factor applied to remote atom contributions.

Returns: The calculated bond polarizability.

◆ calcStericNumber()

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

Calculates the steric number of the atom atom in the molecular graph molgraph (used by VSEPR theory).

Parameters

atom	The atom.
molgraph	The molecular graph.

Returns: The steric number.

◆ calcTPSA()

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

Calculates the topological polar surface area (TPSA) of the molecular graph molgraph using MolProp.TPSACalculator.

Parameters

molgraph The molecular graph.

Returns: The TPSA value.

See also: [TPSA]

◆ calcTotalPartialCharge()

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

Calculates the total partial charge of the atom atom.

The total partial charge is calculated as the sum of stored PEOE sigma and MHMO pi charge contributions.

Parameters

atom The atom.

Returns: The total partial charge.

◆ calcValence()

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

Calculates the total valence of the atom atom in the molecular graph molgraph (explicit valence plus implicit hydrogens).

Parameters

atom	The atom.
molgraph	The molecular graph.

Returns: The total valence.

◆ calcValenceElectronCount()

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

Calculates the number of valence electrons of the chemical element associated with the atom atom (corrected for the atom's formal charge).

Parameters

atom The atom.

Returns: The valence electron count.

◆ calcXLogP()

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

Calculates the \( \log P \) value of the molecular graph molgraph using MolProp.XLogPCalculator.

Parameters

molgraph The molecular graph.

Returns: The \( \log P \) value.

See also: [XLOGP]

◆ generateElementHistogram()

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

Generates the element histogram of the molecular graph molgraph.

Parameters

molgraph	The molecular graph.
hist	The output element histogram.
append	If `True`, hist is appended to instead of cleared first.

◆ generateExplicitElementHistogram()

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

Generates the element histogram of the explicit atoms in cntnr.

Parameters

cntnr	The atom container.
hist	The output element histogram.
append	If `True`, hist is appended to instead of cleared first.

◆ generateExplicitMassCompositionString()

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

Parameters

cntnr

Returns

◆ generateExplicitMolecularFormula()

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

Parameters

cntnr

Returns

◆ generateMassCompositionString()

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

Parameters

molgraph

Returns

◆ generateMolecularFormula()

object CDPL.MolProp.generateMolecularFormula	(	Chem.MolecularGraph	molgraph,
		str	sep = `''`
	)

Parameters

molgraph
sep

Returns

◆ isAmideBond()

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

Tells whether bond is an amide bond in the molecular graph molgraph.

Parameters

bond	The bond.
molgraph	The molecular graph containing the bond.
c_only	If `True`, only C(=X)N bonds are recognized (more restrictive).
db_o_only	If `True`, the C=X must be a double bond to oxygen only.

Returns: True if the bond is an amide bond under the given criteria, and False otherwise.

◆ isAmideCenter()

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

Tells whether the atom atom is the center of an amide group in the molecular graph molgraph.

Parameters

atom	The atom.
molgraph	The molecular graph.
c_only	If `True`, only carbon amides are recognized.
db_o_only	If `True`, a double bond to oxygen must be present. Otherwise, a double bond to sulfur is also allowed.

Returns: True if the atom atom is an amide center, and False otherwise.

Since: 1.2

◆ isAmideNitrogen()

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

Tells whether the atom atom is the nitrogen of an amide group in the molecular graph molgraph.

Parameters

atom	The atom.
molgraph	The molecular graph.
c_only	If `True`, only carbon amides are recognized.
db_o_only	If `True`, the center atom must be double bonded to oxygen. Otherwise, a double bond to sulfur is also allowed.

Returns: True if the atom atom is an amide nitrogen, and False otherwise.

◆ isBridgehead()

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

Tells whether the atom atom is a ring system bridgehead atom in the molecular graph molgraph.

Parameters

atom	The atom.
molgraph	The molecular graph.
bridged_only	If `True`, only bridgeheads of bridged (non-fused) ring systems are recognized.

Returns: True if the atom atom is a bridgehead, and False otherwise.

Since: 1.2

◆ isCarbonylLike()

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

Tells whether the atom atom is a carbonyl-like center in the molecular graph molgraph.

Parameters

atom	The atom.
molgraph	The molecular graph.
c_only	If `True`, only carbon centers are recognized.
db_o_only	If `True`, a double bond to oxygen must be present. Otherwise, a double bond to sulfur is also allowed.

Returns: True if the atom atom is a carbonyl-like center, and False otherwise.

Since: 1.2

◆ isChemicalElement()

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

Tells whether the atom atom represents a chemical element.

Parameters

atom The atom.

Returns: True if the atom atom represents a chemical element, and False otherwise.

◆ isHBondAcceptor()

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

Tells whether the atom atom acts as an H-bond acceptor in the molecular graph molgraph.

Parameters

atom	The atom.
molgraph	The molecular graph.

Returns: True if the atom atom is an H-bond acceptor, and False otherwise.

◆ isHBondDonor()

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

Tells whether the atom atom acts as an H-bond donor in the molecular graph molgraph.

Parameters

atom	The atom.
molgraph	The molecular graph.

Returns: True if the atom atom is an H-bond donor, and False otherwise.

◆ isHalogen()

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

Tells whether the chemical element associated with the atom atom is a halogen.

Parameters

atom The atom.

Returns: True if the element is a halogen, and False otherwise.

◆ isHeavy()

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

Tells whether the atom atom is a heavy (non-hydrogen) atom.

Parameters

atom The atom.

Returns: True if the atom atom is a heavy atom, and False otherwise.

◆ isHeteroAtomHydrogenRotor()

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

Tells whether the bond bond is a heteroatom hydrogen-only rotor.

Parameters

bond	The bond.
molgraph	The molecular graph containing the bond.

Returns: True if the bond is a heteroatom hydrogen-only rotor, and False otherwise.

◆ isHydrogenBond()

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

Tells whether the bond bond is a hydrogen bond (one of the bonded atoms is a hydrogen).

Parameters

bond The bond.

Returns: True if the bond involves a hydrogen, and False otherwise.

◆ isHydrogenRotor()

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

Tells whether the bond bond is a rotatable bond whose rotation only moves hydrogen atoms.

Parameters

bond	The bond.
molgraph	The molecular graph containing the bond.

Returns: True if the bond is a hydrogen-only rotor, and False otherwise.

◆ isInRing() [1/2]

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

Tells whether the atom atom is a member of any ring in the molecular graph molgraph.

Parameters

atom	The atom.
molgraph	The molecular graph.

Returns: True if the atom atom is in a ring, and False otherwise.

◆ isInRing() [2/2]

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

Parameters

bond
molgraph

Returns

◆ isInRingOfSize() [1/2]

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

Tells whether the atom atom is a member of a ring of size size in the molecular graph molgraph.

Parameters

atom	The atom.
molgraph	The molecular graph.
size	The ring size to test for.

Returns: True if the atom atom is in a ring of size size, and False otherwise.

◆ isInRingOfSize() [2/2]

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

Tells whether the bond bond is part of a ring of the specified size in the molecular graph molgraph.

Parameters

bond	The bond.
molgraph	The molecular graph containing the bond.
size	The ring size to test for.

Returns: True if the bond is part of a ring of size size, and False otherwise.

◆ isInvertibleNitrogen()

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

Tells whether the atom atom is an invertible (pyramidal, non-aromatic, non-amide) nitrogen in the molecular graph molgraph.

Parameters

atom	The atom.
molgraph	The molecular graph.

Returns: True if the atom atom is an invertible nitrogen, and False otherwise.

◆ isMainGroupElement()

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

Tells whether the chemical element associated with the atom atom is a main-group element.

Parameters

atom The atom.

Returns: True if the element is a main-group element, and False otherwise.

◆ isMetal()

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

Tells whether the chemical element associated with the atom atom is a metal.

Parameters

atom The atom.

Returns: True if the element is a metal, and False otherwise.

◆ isNobleGas()

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

Tells whether the chemical element associated with the atom atom is a noble gas.

Parameters

atom The atom.

Returns: True if the element is a noble gas, and False otherwise.

◆ isNonMetal()

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

Tells whether the chemical element associated with the atom atom is a non-metal.

Parameters

atom The atom.

Returns: True if the element is a non-metal, and False otherwise.

◆ isOrdinaryHydrogen()

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

Tells whether the atom atom is an ordinary hydrogen.

An "ordinary" hydrogen is a hydrogen atom that has the default values for every atom property named by the flags bitmask (e.g. with the Chem.AtomPropertyFlag.ISOTOPE flag set, only unspecified-isotope hydrogens count as ordinary; with Chem.AtomPropertyFlag.FORMAL_CHARGE set, only neutral hydrogens count as ordinary; etc.). All other hydrogens are deemed special. An empty bitmask makes any hydrogen ordinary.

Parameters

atom	The atom.
molgraph	The molecular graph.
flags	Bitmask of Chem.AtomPropertyFlag values that qualify "ordinary".

Returns: True if the atom atom is an ordinary hydrogen, and False otherwise.

◆ isPlanarNitrogen()

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

Tells whether the atom atom is a planar nitrogen in the molecular graph molgraph.

Parameters

atom	The atom.
molgraph	The molecular graph.

Returns: True if the atom atom is a planar nitrogen, and False otherwise.

◆ isRotatable()

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

Tells whether the bond bond is rotatable.

Parameters

bond	The bond.
molgraph	The molecular graph containing the bond.
h_rotors	If `True`, hydrogen-only rotors are counted as rotatable.
ring_bonds	If `True`, ring bonds are also considered.
amide_bonds	If `True`, amide bonds are also considered.

Returns: True if the bond is rotatable, and False otherwise.

◆ isSemiMetal()

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

Tells whether the chemical element associated with the atom atom is a semi-metal.

Parameters

atom The atom.

Returns: True if the element is a semi-metal, and False otherwise.

◆ isSpiroCenter()

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

Tells whether the atom atom is a spiro center in the molecular graph molgraph.

Parameters

atom	The atom.
molgraph	The molecular graph.

Returns: True if the atom atom is a spiro center, and False otherwise.

Since: 1.2

◆ isTransitionMetal()

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

Tells whether the chemical element associated with the atom atom is a transition metal.

Parameters

atom The atom.

Returns: True if the element is a transition metal, and False otherwise.

◆ isUnsaturated()

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

Tells whether the atom atom is unsaturated (involved in at least one multiple bond) in the molecular graph molgraph.

Parameters

atom	The atom.
molgraph	The molecular graph.

Returns: True if the atom atom is unsaturated, and False otherwise.

◆ perceiveFunctionalGroups() [1/2]

Chem.FragmentList CDPL.MolProp.perceiveFunctionalGroups ( Chem.MolecularGraph molgraph )

Perceives the functional groups of the molecular graph molgraph using MolProp.FunctionalGroupList.

Parameters

molgraph The molecular graph.

Returns: A shared reference to the perceived functional group list.

Since: 1.3

◆ perceiveFunctionalGroups() [2/2]

Chem.FragmentList CDPL.MolProp.perceiveFunctionalGroups	(	Chem.MolecularGraph	molgraph,
		bool	overwrite
	)

Perceives the functional groups of the molecular graph molgraph and stores them as a property.

Parameters

molgraph	The molecular graph (modified in place).
overwrite	If `True`, an existing MolProp.MolecularGraphProperty.FUNCTIONAL_GROUPS property is overwritten.

Returns: A shared reference to the perceived functional group list.

Since: 1.3

◆ perceiveHBondAcceptorAtomTypes()

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

Perceives the H-bond acceptor types of the atoms in the molecular graph molgraph and stores them as atom properties.

Parameters

molgraph	The molecular graph (modified in place).
overwrite	If `True`, existing atom H-bond acceptor type properties are overwritten.

◆ perceiveHBondDonorAtomTypes()

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

Perceives the H-bond donor types of the atoms in the molecular graph molgraph and stores them as atom properties.

Parameters

molgraph	The molecular graph (modified in place).
overwrite	If `True`, existing atom H-bond donor type properties are overwritten.

Classes

Functions

Detailed Description

Function Documentation

◆ getAllredRochowElectronegativity()

◆ getAromaticAtomCount() [1/2]

◆ getAromaticAtomCount() [2/2]

◆ getAromaticBondCount() [1/2]

◆ getAromaticBondCount() [2/2]

◆ getAtomCount() [1/3]

◆ getAtomCount() [2/3]

◆ getAtomCount() [3/3]

◆ getAtomicWeight()

◆ getBondCount() [1/5]

◆ getBondCount() [2/5]

◆ getBondCount() [3/5]

◆ getBondCount() [4/5]

◆ getBondCount() [5/5]

◆ getChainAtomCount() [1/2]

◆ getChainAtomCount() [2/2]

◆ getChainBondCount() [1/2]

◆ getChainBondCount() [2/2]

◆ getComponentCount()

◆ getCovalentRadius()

◆ getElementName()

◆ getElementValenceElectronCount()

◆ getExplicitAtomCount() [1/3]

◆ getExplicitAtomCount() [2/3]

◆ getExplicitAtomCount() [3/3]

◆ getExplicitBondCount() [1/5]

◆ getExplicitBondCount() [2/5]

◆ getExplicitBondCount() [3/5]

◆ getExplicitBondCount() [4/5]

◆ getExplicitBondCount() [5/5]

◆ getExplicitChainAtomCount() [1/2]

◆ getExplicitChainAtomCount() [2/2]

◆ getExplicitChainBondCount() [1/2]

◆ getExplicitChainBondCount() [2/2]

◆ getExplicitHydrogenBondCount()

◆ getExplicitOrdinaryHydrogenCount()

◆ setFunctionalGroups()

◆ hasFunctionalGroups()

◆ getFunctionalGroups()

◆ clearFunctionalGroups()

◆ getHBondAcceptorAtomCount()

◆ setHBondAcceptorType()

◆ hasHBondAcceptorType()

◆ getHBondAcceptorType()

◆ clearHBondAcceptorType()

◆ getHBondDonorAtomCount()

◆ setHBondDonorType()

◆ hasHBondDonorType()

◆ getHBondDonorType()

◆ clearHBondDonorType()

◆ getHeavyAtomCount() [1/2]

◆ getHeavyAtomCount() [2/2]

◆ getHeavyBondCount() [1/2]

◆ getHeavyBondCount() [2/2]

◆ getHybridPolarizability()

◆ getHydrogenBondCount()

◆ setHydrophobicity()

◆ hasHydrophobicity()

◆ getHydrophobicity()

◆ clearHydrophobicity()

◆ getIUPACGroup()

◆ getImplicitHydrogenCount()

◆ setMHMOPiCharge()

◆ hasMHMOPiCharge()

◆ getMHMOPiCharge()

◆ clearMHMOPiCharge()

◆ setMHMOPiOrder()

◆ hasMHMOPiOrder()

◆ getMHMOPiOrder()

◆ clearMHMOPiOrder()

◆ getNetFormalCharge()

◆ getNumContainingSSSRRings() [1/2]

◆ getNumContainingSSSRRings() [2/2]

◆ getOrdinaryHydrogenCount() [1/2]

◆ getOrdinaryHydrogenCount() [2/2]

◆ setPEOESigmaCharge()