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

Namespaces
	AtomProperty
	Provides keys for MolProp-specific Chem::Atom properties.

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

	BondProperty
	Provides keys for MolProp-specific Chem::Bond properties.

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

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

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

	MolecularGraphProperty
	Provides keys for built-in Chem::MolecularGraph properties.

Classes
class	AtomHydrophobicityCalculator
	Implementation of Greene's algorithm [CATA] for the calculation of atom hydrophobicities. 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	HBondAcceptorAtomTyper
	Perception of H-bond acceptor atom types (see namespace MolProp::HBondAcceptorAtomType) by SMARTS pattern matching. More...

class	HBondDonorAtomTyper
	Perception of H-bond donor atom types (see namespace MolProp::HBondDonorAtomType) by SMARTS pattern matching. More...

class	LogSCalculator
	LogSCalculator. More...

class	MassComposition
	Data type for the storage of mass percent compositions of chemical compounds. 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	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
CDPL_MOLPROP_API double	calcExplicitMass (const Chem::AtomContainer &cntnr)
	Calculates the total mass of the explicit atoms in cntnr. More...

CDPL_MOLPROP_API void	calcExplicitMassComposition (const Chem::AtomContainer &cntnr, MassComposition &mass_comp)
	Calculates the per-element mass composition of the explicit atoms in cntnr. More...

CDPL_MOLPROP_API void	generateExplicitMassCompositionString (const Chem::AtomContainer &cntnr, std::string &comp_str)
	Generates a string representation of the per-element mass composition of the explicit atoms in cntnr. More...

CDPL_MOLPROP_API void	generateExplicitMolecularFormula (const Chem::AtomContainer &cntnr, std::string &formula)
	Generates the molecular formula of the explicit atoms in cntnr. More...

CDPL_MOLPROP_API void	generateExplicitElementHistogram (const Chem::AtomContainer &cntnr, ElementHistogram &hist, bool append=false)
	Generates the element histogram of the explicit atoms in cntnr. More...

CDPL_MOLPROP_API std::size_t	getExplicitAtomCount (const Chem::AtomContainer &cntnr)
	Returns the total number of explicit atoms in cntnr. More...

CDPL_MOLPROP_API std::size_t	getExplicitAtomCount (const Chem::AtomContainer &cntnr, unsigned int type, bool strict=true)
	Returns the number of explicit atoms in cntnr that match the given atom type. More...

CDPL_MOLPROP_API std::size_t	getExplicitChainAtomCount (const Chem::AtomContainer &cntnr)
	Returns the number of explicit chain (non-ring) atoms in cntnr. More...

CDPL_MOLPROP_API std::size_t	getRingAtomCount (const Chem::AtomContainer &cntnr)
	Returns the number of ring atoms in cntnr. More...

CDPL_MOLPROP_API std::size_t	getAromaticAtomCount (const Chem::AtomContainer &cntnr)
	Returns the number of aromatic atoms in cntnr. More...

CDPL_MOLPROP_API std::size_t	getHeavyAtomCount (const Chem::AtomContainer &cntnr)
	Returns the number of heavy (non-hydrogen) atoms in cntnr. More...

CDPL_MOLPROP_API long	getNetFormalCharge (const Chem::AtomContainer &cntnr)
	Returns the net formal charge of cntnr (sum of per-atom formal charges). More...

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

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

CDPL_MOLPROP_API double	getHydrophobicity (const Chem::Atom &atom)
	Returns the value of the MolProp::AtomProperty::HYDROPHOBICITY property of atom. More...

CDPL_MOLPROP_API void	setHydrophobicity (Chem::Atom &atom, double hyd)
	Sets the value of the MolProp::AtomProperty::HYDROPHOBICITY property of atom to hyd. More...

CDPL_MOLPROP_API void	clearHydrophobicity (Chem::Atom &atom)
	Removes the MolProp::AtomProperty::HYDROPHOBICITY property from atom. More...

CDPL_MOLPROP_API bool	hasHydrophobicity (const Chem::Atom &atom)
	Tells whether atom carries an explicit MolProp::AtomProperty::HYDROPHOBICITY property. More...

CDPL_MOLPROP_API double	getPEOESigmaCharge (const Chem::Atom &atom)
	Returns the value of the MolProp::AtomProperty::PEOE_SIGMA_CHARGE property of atom. More...

CDPL_MOLPROP_API void	setPEOESigmaCharge (Chem::Atom &atom, double charge)
	Sets the value of the MolProp::AtomProperty::PEOE_SIGMA_CHARGE property of atom to charge. More...

CDPL_MOLPROP_API void	clearPEOESigmaCharge (Chem::Atom &atom)
	Removes the MolProp::AtomProperty::PEOE_SIGMA_CHARGE property from atom. More...

CDPL_MOLPROP_API bool	hasPEOESigmaCharge (const Chem::Atom &atom)
	Tells whether atom carries an explicit MolProp::AtomProperty::PEOE_SIGMA_CHARGE property. More...

CDPL_MOLPROP_API double	getPEOESigmaElectronegativity (const Chem::Atom &atom)
	Returns the value of the MolProp::AtomProperty::PEOE_SIGMA_ELECTRONEGATIVITY property of atom. More...

CDPL_MOLPROP_API void	setPEOESigmaElectronegativity (Chem::Atom &atom, double e_neg)
	Sets the value of the MolProp::AtomProperty::PEOE_SIGMA_ELECTRONEGATIVITY property of atom to e_neg. More...

CDPL_MOLPROP_API void	clearPEOESigmaElectronegativity (Chem::Atom &atom)
	Removes the MolProp::AtomProperty::PEOE_SIGMA_ELECTRONEGATIVITY property from atom. More...

CDPL_MOLPROP_API bool	hasPEOESigmaElectronegativity (const Chem::Atom &atom)
	Tells whether atom carries an explicit MolProp::AtomProperty::PEOE_SIGMA_ELECTRONEGATIVITY property. More...

CDPL_MOLPROP_API double	getMHMOPiCharge (const Chem::Atom &atom)
	Returns the value of the MolProp::AtomProperty::MHMO_PI_CHARGE property of atom. More...

CDPL_MOLPROP_API void	setMHMOPiCharge (Chem::Atom &atom, double charge)
	Sets the value of the MolProp::AtomProperty::MHMO_PI_CHARGE property of atom to charge. More...

CDPL_MOLPROP_API void	clearMHMOPiCharge (Chem::Atom &atom)
	Removes the MolProp::AtomProperty::MHMO_PI_CHARGE property from atom. More...

CDPL_MOLPROP_API bool	hasMHMOPiCharge (const Chem::Atom &atom)
	Tells whether atom carries an explicit MolProp::AtomProperty::MHMO_PI_CHARGE property. More...

CDPL_MOLPROP_API unsigned int	getHBondDonorType (const Chem::Atom &atom)
	Returns the value of the MolProp::AtomProperty::H_BOND_DONOR_TYPE property of atom (see namespace MolProp::HBondDonorAtomType). More...

CDPL_MOLPROP_API void	setHBondDonorType (Chem::Atom &atom, unsigned int type)
	Sets the value of the MolProp::AtomProperty::H_BOND_DONOR_TYPE property of atom to type. More...

CDPL_MOLPROP_API void	clearHBondDonorType (Chem::Atom &atom)
	Removes the MolProp::AtomProperty::H_BOND_DONOR_TYPE property from atom. More...

CDPL_MOLPROP_API bool	hasHBondDonorType (const Chem::Atom &atom)
	Tells whether atom carries an explicit MolProp::AtomProperty::H_BOND_DONOR_TYPE property. More...

CDPL_MOLPROP_API unsigned int	getHBondAcceptorType (const Chem::Atom &atom)
	Returns the value of the MolProp::AtomProperty::H_BOND_ACCEPTOR_TYPE property of atom (see namespace MolProp::HBondAcceptorAtomType). More...

CDPL_MOLPROP_API void	setHBondAcceptorType (Chem::Atom &atom, unsigned int type)
	Sets the value of the MolProp::AtomProperty::H_BOND_ACCEPTOR_TYPE property of atom to type. More...

CDPL_MOLPROP_API void	clearHBondAcceptorType (Chem::Atom &atom)
	Removes the MolProp::AtomProperty::H_BOND_ACCEPTOR_TYPE property from atom. More...

CDPL_MOLPROP_API bool	hasHBondAcceptorType (const Chem::Atom &atom)
	Tells whether atom carries an explicit MolProp::AtomProperty::H_BOND_ACCEPTOR_TYPE property. More...

CDPL_MOLPROP_API bool	isInRing (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph)
	Tells whether atom is a member of any ring in molgraph. More...

CDPL_MOLPROP_API bool	isInRingOfSize (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph, std::size_t size)
	Tells whether atom is a member of a ring of size size in molgraph. More...

CDPL_MOLPROP_API std::size_t	getNumContainingSSSRRings (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph)
	Returns the number of SSSR rings of molgraph that contain atom. More...

CDPL_MOLPROP_API double	getAtomicWeight (const Chem::Atom &atom)
	Returns the standard atomic weight of the chemical element associated with atom. More...

CDPL_MOLPROP_API std::size_t	getIUPACGroup (const Chem::Atom &atom)
	Returns the IUPAC group number of the chemical element associated with atom. More...

CDPL_MOLPROP_API std::size_t	getPeriod (const Chem::Atom &atom)
	Returns the period of the chemical element associated with atom. More...

CDPL_MOLPROP_API double	getVdWRadius (const Chem::Atom &atom)
	Returns the Van der Waals radius of the chemical element associated with atom. More...

CDPL_MOLPROP_API double	getCovalentRadius (const Chem::Atom &atom, std::size_t order)
	Returns the covalent radius of the chemical element associated with atom for the given bond order. More...

CDPL_MOLPROP_API double	getAllredRochowElectronegativity (const Chem::Atom &atom)
	Returns the Allred-Rochow electronegativity of the chemical element associated with atom. More...

CDPL_MOLPROP_API const std::string &	getElementName (const Chem::Atom &atom)
	Returns the element name of the chemical element associated with atom. More...

CDPL_MOLPROP_API std::size_t	getElementValenceElectronCount (const Chem::Atom &atom)
	Returns the number of valence electrons of the chemical element associated with atom. More...

CDPL_MOLPROP_API bool	isChemicalElement (const Chem::Atom &atom)
	Tells whether atom represents a chemical element. More...

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

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

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

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

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

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

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

CDPL_MOLPROP_API bool	isOrdinaryHydrogen (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph, unsigned int flags=Chem::AtomPropertyFlag::DEFAULT)
	Tells whether atom is an ordinary hydrogen. More...

CDPL_MOLPROP_API bool	isHeavy (const Chem::Atom &atom)
	Tells whether atom is a heavy (non-hydrogen) atom. More...

CDPL_MOLPROP_API bool	isUnsaturated (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph)
	Tells whether atom is unsaturated (involved in at least one multiple bond) in molgraph. More...

CDPL_MOLPROP_API bool	isHBondAcceptor (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph)
	Tells whether atom acts as an H-bond acceptor in molgraph. More...

CDPL_MOLPROP_API bool	isHBondDonor (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph)
	Tells whether atom acts as an H-bond donor in molgraph. More...

CDPL_MOLPROP_API bool	isCarbonylLike (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph, bool c_only=false, bool db_o_only=false)
	Tells whether atom is a carbonyl-like center in molgraph. More...

CDPL_MOLPROP_API bool	isAmideCenter (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph, bool c_only=false, bool db_o_only=false)
	Tells whether atom is the center of an amide group in molgraph. More...

CDPL_MOLPROP_API bool	isAmideNitrogen (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph, bool c_only=false, bool db_o_only=false)
	Tells whether atom is the nitrogen of an amide group in molgraph. More...

CDPL_MOLPROP_API bool	isInvertibleNitrogen (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph)
	Tells whether atom is an invertible (pyramidal, non-aromatic, non-amide) nitrogen in molgraph. More...

CDPL_MOLPROP_API bool	isPlanarNitrogen (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph)
	Tells whether atom is a planar nitrogen in molgraph. More...

CDPL_MOLPROP_API bool	isBridgehead (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph, bool bridged_only)
	Tells whether atom is a bridgehead atom in molgraph. More...

CDPL_MOLPROP_API bool	isSpiroCenter (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph)
	Tells whether atom is a spiro center in molgraph. More...

CDPL_MOLPROP_API std::size_t	getOrdinaryHydrogenCount (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph, unsigned int flags=Chem::AtomPropertyFlag::DEFAULT)
	Returns the number of ordinary-hydrogen neighbors of atom in molgraph (see isOrdinaryHydrogen() for the definition of "ordinary"). More...

CDPL_MOLPROP_API std::size_t	getExplicitAtomCount (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph, unsigned int type, bool strict=true)
	Returns the number of explicit neighbors of atom in molgraph whose Chem::AtomType matches type. More...

CDPL_MOLPROP_API std::size_t	getAtomCount (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph, unsigned int type, bool strict=true)
	Returns the number of neighbors of atom in molgraph (including implicit hydrogens) whose Chem::AtomType matches type. More...

CDPL_MOLPROP_API std::size_t	getExplicitChainAtomCount (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph)
	Returns the number of explicit chain (non-ring) neighbors of atom in molgraph. More...

CDPL_MOLPROP_API std::size_t	getChainAtomCount (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph)
	Returns the number of chain (non-ring) neighbors of atom in molgraph (including implicit hydrogens). More...

CDPL_MOLPROP_API std::size_t	getRingAtomCount (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph)
	Returns the number of ring-atom neighbors of atom in molgraph. More...

CDPL_MOLPROP_API std::size_t	getAromaticAtomCount (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph)
	Returns the number of aromatic neighbors of atom in molgraph. More...

CDPL_MOLPROP_API std::size_t	getHeavyAtomCount (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph)
	Returns the number of heavy atom neighbors of atom in molgraph. More...

CDPL_MOLPROP_API std::size_t	getExplicitBondCount (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph)
	Returns the number of explicit bonds incident to atom in molgraph. More...

CDPL_MOLPROP_API std::size_t	getExplicitBondCount (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph, std::size_t order)
	Returns the number of explicit bonds of the given order incident to atom in molgraph. More...

CDPL_MOLPROP_API std::size_t	getExplicitBondCount (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph, std::size_t order, unsigned int type, bool strict=true)
	Returns the number of explicit bonds of the given order incident to atom that bond to atoms whose Chem::AtomType matches type. More...

CDPL_MOLPROP_API std::size_t	getBondCount (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph)
	Returns the total number of bonds incident to atom in molgraph (including implicit-hydrogen bonds). More...

CDPL_MOLPROP_API std::size_t	getBondCount (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph, std::size_t order)
	Returns the total number of bonds of the given order incident to atom (including implicit-hydrogen bonds). More...

CDPL_MOLPROP_API std::size_t	getBondCount (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph, std::size_t order, unsigned int type, bool strict=true)
	Returns the total number of bonds of the given order incident to atom that bond to atoms whose Chem::AtomType matches type. More...

CDPL_MOLPROP_API std::size_t	getExplicitChainBondCount (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph)
	Returns the number of explicit chain (non-ring) bonds incident to atom in molgraph. More...

CDPL_MOLPROP_API std::size_t	getChainBondCount (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph)
	Returns the number of chain (non-ring) bonds incident to atom in molgraph (including implicit-hydrogen bonds). More...

CDPL_MOLPROP_API std::size_t	getRingBondCount (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph)
	Returns the number of ring bonds incident to atom in molgraph. More...

CDPL_MOLPROP_API std::size_t	getAromaticBondCount (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph)
	Returns the number of aromatic bonds incident to atom in molgraph. More...

CDPL_MOLPROP_API std::size_t	getHeavyBondCount (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph)
	Returns the number of heavy bonds incident to atom in molgraph. More...

CDPL_MOLPROP_API std::size_t	getRotatableBondCount (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph, bool h_rotors=false, bool ring_bonds=false, bool amide_bonds=false)
	Returns the number of rotatable bonds incident to atom in molgraph. More...

CDPL_MOLPROP_API std::size_t	calcExplicitValence (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph)
	Calculates the explicit valence of atom in molgraph (sum of explicit bond orders). More...

CDPL_MOLPROP_API std::size_t	calcValence (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph)
	Calculates the total valence of atom in molgraph (explicit valence plus implicit hydrogens). More...

CDPL_MOLPROP_API std::size_t	calcFreeValenceElectronCount (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph)
	Calculates the number of free (lone-pair) valence electrons of atom in molgraph. More...

CDPL_MOLPROP_API std::size_t	calcValenceElectronCount (const Chem::Atom &atom)
	Calculates the number of valence electrons of the chemical element associated with atom (corrected for the atom's formal charge). More...

CDPL_MOLPROP_API std::size_t	calcStericNumber (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph)
	Calculates the steric number of atom in molgraph (used by VSEPR theory). More...

CDPL_MOLPROP_API unsigned int	getVSEPRCoordinationGeometry (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph, std::size_t steric_num)
	Returns the VSEPR coordination geometry of atom in molgraph (see namespace MolProp::CoordinationGeometry). More...

CDPL_MOLPROP_API unsigned int	getVSEPRCoordinationGeometry (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph)
	Returns the VSEPR coordination geometry of atom in molgraph (see namespace MolProp::CoordinationGeometry). More...

CDPL_MOLPROP_API double	getHybridPolarizability (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph)
	Returns the hybridization-state-dependent atomic polarizability of atom in molgraph. More...

CDPL_MOLPROP_API double	calcEffectivePolarizability (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph, double damping=0.75)
	Calculates the effective atomic polarizability of atom in molgraph (after Kang and Jhon). More...

CDPL_MOLPROP_API double	calcTotalPartialCharge (const Chem::Atom &atom)
	Calculates the total partial charge of atom (sum of stored PEOE sigma and MHMO pi charge contributions). More...

CDPL_MOLPROP_API double	calcLonePairElectronegativity (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph)
	Calculates the lone-pair electronegativity of atom in molgraph. More...

CDPL_MOLPROP_API double	calcPiElectronegativity (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph)
	Calculates the pi electronegativity of atom in molgraph. More...

CDPL_MOLPROP_API double	calcInductiveEffect (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph, std::size_t num_bonds=10)
	Calculates the inductive effect parameter of atom in molgraph. More...

CDPL_MOLPROP_API std::size_t	getExplicitBondCount (const Chem::BondContainer &cntnr)
	Returns the total number of explicit bonds in cntnr. More...

CDPL_MOLPROP_API std::size_t	getExplicitBondCount (const Chem::BondContainer &cntnr, std::size_t order, bool inc_aro=true)
	Returns the number of explicit bonds in cntnr that match the given bond order. More...

CDPL_MOLPROP_API std::size_t	getExplicitHydrogenBondCount (const Chem::BondContainer &cntnr)
	Returns the number of explicit bonds in cntnr that involve a hydrogen atom. More...

CDPL_MOLPROP_API std::size_t	getExplicitChainBondCount (const Chem::BondContainer &cntnr)
	Returns the number of explicit chain (non-ring) bonds in cntnr. More...

CDPL_MOLPROP_API std::size_t	getRingBondCount (const Chem::BondContainer &cntnr)
	Returns the number of ring bonds in cntnr. More...

CDPL_MOLPROP_API std::size_t	getAromaticBondCount (const Chem::BondContainer &cntnr)
	Returns the number of aromatic bonds in cntnr. More...

CDPL_MOLPROP_API std::size_t	getHeavyBondCount (const Chem::BondContainer &cntnr)
	Returns the number of heavy atom bonds in cntnr. More...

CDPL_MOLPROP_API double	getMHMOPiOrder (const Chem::Bond &bond)
	Returns the value of the MolProp::BondProperty::MHMO_PI_ORDER property of bond. More...

CDPL_MOLPROP_API void	setMHMOPiOrder (Chem::Bond &bond, double order)
	Sets the value of the MolProp::BondProperty::MHMO_PI_ORDER property of bond. More...

CDPL_MOLPROP_API void	clearMHMOPiOrder (Chem::Bond &bond)
	Removes the MolProp::BondProperty::MHMO_PI_ORDER property from bond. More...

CDPL_MOLPROP_API bool	hasMHMOPiOrder (const Chem::Bond &atom)
	Tells whether bond carries an explicit MolProp::BondProperty::MHMO_PI_ORDER property. More...

CDPL_MOLPROP_API double	calcPolarizability (const Chem::Bond &bond, const Chem::MolecularGraph &molgraph, double damping=0.75)
	Calculates the bond polarizability of bond within molgraph. More...

CDPL_MOLPROP_API bool	isInRing (const Chem::Bond &Bond, const Chem::MolecularGraph &molgraph)
	Tells whether Bond is part of any ring of molgraph. More...

CDPL_MOLPROP_API bool	isInRingOfSize (const Chem::Bond &bond, const Chem::MolecularGraph &molgraph, std::size_t size)
	Tells whether bond is part of a ring of the specified size in molgraph. More...

CDPL_MOLPROP_API std::size_t	getNumContainingSSSRRings (const Chem::Bond &bond, const Chem::MolecularGraph &molgraph)
	Returns the number of SSSR rings of molgraph that contain bond. More...

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

CDPL_MOLPROP_API bool	isHeteroAtomHydrogenRotor (const Chem::Bond &bond, const Chem::MolecularGraph &molgraph)
	Tells whether bond is a hydrogen-only rotor where the rotating end is a heteroatom-bound hydrogen. More...

CDPL_MOLPROP_API bool	isRotatable (const Chem::Bond &bond, const Chem::MolecularGraph &molgraph, bool h_rotors=false, bool ring_bonds=false, bool amide_bonds=false)
	Tells whether bond is rotatable. More...

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

CDPL_MOLPROP_API bool	isAmideBond (const Chem::Bond &bond, const Chem::MolecularGraph &molgraph, bool c_only=false, bool db_o_only=false)
	Tells whether bond is an amide bond in molgraph. More...

CDPL_MOLPROP_API double	calcMass (const Chem::MolecularGraph &molgraph)
	Calculates the total molecular mass of molgraph (sum of atom standard atomic weights including implicit hydrogens). More...

CDPL_MOLPROP_API void	calcMassComposition (const Chem::MolecularGraph &molgraph, MassComposition &comp)
	Calculates the per-element mass composition of molgraph. More...

CDPL_MOLPROP_API void	generateMassCompositionString (const Chem::MolecularGraph &molgraph, std::string &comp)
	Generates a string representation of the per-element mass composition of molgraph. More...

CDPL_MOLPROP_API void	generateMolecularFormula (const Chem::MolecularGraph &molgraph, std::string &formula, const std::string &sep=std::string())
	Generates the molecular formula of the molecular graph molgraph. More...

CDPL_MOLPROP_API void	generateElementHistogram (const Chem::MolecularGraph &molgraph, ElementHistogram &hist, bool append=false)
	Generates the element histogram of molgraph. More...

CDPL_MOLPROP_API std::size_t	calcCyclomaticNumber (const Chem::MolecularGraph &molgraph)
	Calculates the cyclomatic number of molgraph (number of independent cycles). More...

CDPL_MOLPROP_API std::size_t	getAtomCount (const Chem::MolecularGraph &molgraph)
	Returns the total number of atoms in molgraph (including implicit hydrogens). More...

CDPL_MOLPROP_API std::size_t	getAtomCount (const Chem::MolecularGraph &molgraph, unsigned int type, bool strict=true)
	Returns the number of atoms in molgraph whose Chem::AtomType matches type. More...

CDPL_MOLPROP_API std::size_t	getImplicitHydrogenCount (const Chem::MolecularGraph &molgraph)
	Returns the total number of implicit hydrogens in molgraph. More...

CDPL_MOLPROP_API std::size_t	getOrdinaryHydrogenCount (const Chem::MolecularGraph &molgraph, unsigned int flags=Chem::AtomPropertyFlag::DEFAULT)
	Returns the number of ordinary hydrogens in molgraph (see MolProp::isOrdinaryHydrogen() for the definition of "ordinary"). More...

CDPL_MOLPROP_API std::size_t	getExplicitOrdinaryHydrogenCount (const Chem::MolecularGraph &molgraph, unsigned int flags=Chem::AtomPropertyFlag::DEFAULT)
	Returns the number of explicit ordinary hydrogens in molgraph (see MolProp::isOrdinaryHydrogen() for the definition of "ordinary"). More...

CDPL_MOLPROP_API std::size_t	getChainAtomCount (const Chem::MolecularGraph &molgraph)
	Returns the number of chain (non-ring) atoms in molgraph. More...

CDPL_MOLPROP_API std::size_t	getHBondAcceptorAtomCount (const Chem::MolecularGraph &molgraph)
	Returns the number of H-bond acceptor atoms in molgraph. More...

CDPL_MOLPROP_API std::size_t	getHBondDonorAtomCount (const Chem::MolecularGraph &molgraph)
	Returns the number of H-bond donor atoms in molgraph. More...

CDPL_MOLPROP_API std::size_t	getBondCount (const Chem::MolecularGraph &molgraph)
	Returns the total number of bonds in molgraph (including bonds to implicit hydrogens). More...

CDPL_MOLPROP_API std::size_t	getBondCount (const Chem::MolecularGraph &molgraph, std::size_t order, bool inc_aro=true)
	Returns the number of bonds in molgraph with the given order, optionally including aromatic bonds. More...

CDPL_MOLPROP_API std::size_t	getHydrogenBondCount (const Chem::MolecularGraph &molgraph)
	Returns the number of bonds in molgraph that involve at least one hydrogen atom. More...

CDPL_MOLPROP_API std::size_t	getChainBondCount (const Chem::MolecularGraph &molgraph)
	Returns the number of chain (non-ring) bonds in molgraph. More...

CDPL_MOLPROP_API std::size_t	getRotatableBondCount (const Chem::MolecularGraph &molgraph, bool h_rotors=false, bool ring_bonds=false, bool amide_bonds=false)
	Returns the number of rotatable bonds in molgraph. More...

CDPL_MOLPROP_API std::size_t	getComponentCount (const Chem::MolecularGraph &molgraph)
	Returns the number of connected components in molgraph. More...

CDPL_MOLPROP_API double	calcXLogP (const Chem::MolecularGraph &molgraph)
	Calculates the XLogP value of molgraph using MolProp::XLogPCalculator. More...

CDPL_MOLPROP_API double	calcLogS (const Chem::MolecularGraph &molgraph)
	Calculates the \( \log S \) (aqueous solubility) of molgraph using MolProp::LogSCalculator. More...

CDPL_MOLPROP_API double	calcTPSA (const Chem::MolecularGraph &molgraph)
	Calculates the topological polar surface area (TPSA) of molgraph using MolProp::TPSACalculator. More...

CDPL_MOLPROP_API std::size_t	getRuleOfFiveScore (const Chem::MolecularGraph &molgraph)
	Returns the Lipinski rule-of-five score of molgraph, defined as the number of satisfied criteria (0-4). More...

CDPL_MOLPROP_API double	calcMeanPolarizability (const Chem::MolecularGraph &molgraph)
	Calculates the mean atomic polarizability of molgraph. More...

CDPL_MOLPROP_API void	calcPEOEProperties (Chem::MolecularGraph &molgraph, bool overwrite, std::size_t num_iter=20, double damping=0.48)
	Calculates PEOE sigma charges and electronegativities for the atoms of molgraph and stores them as atom properties. More...

CDPL_MOLPROP_API void	calcMHMOProperties (Chem::MolecularGraph &molgraph, bool overwrite)
	Calculates MHMO pi charges and pi-bond orders for molgraph and stores them as atom/bond properties. More...

CDPL_MOLPROP_API void	calcAtomHydrophobicities (Chem::MolecularGraph &molgraph, bool overwrite, bool from_logp=false)
	Calculates per-atom hydrophobicities for molgraph and stores them as atom properties. More...

CDPL_MOLPROP_API void	perceiveHBondDonorAtomTypes (Chem::MolecularGraph &molgraph, bool overwrite)
	Perceives the H-bond donor types of the atoms in molgraph and stores them as atom properties. More...

CDPL_MOLPROP_API void	perceiveHBondAcceptorAtomTypes (Chem::MolecularGraph &molgraph, bool overwrite)
	Perceives the H-bond acceptor types of the atoms in molgraph and stores them as atom properties. More...

CDPL_MOLPROP_API const Chem::FragmentList::SharedPointer &	getFunctionalGroups (const Chem::MolecularGraph &molgraph)
	Returns the value of the MolProp::MolecularGraphProperty::FUNCTIONAL_GROUPS property of molgraph. More...

CDPL_MOLPROP_API void	setFunctionalGroups (Chem::MolecularGraph &molgraph, const Chem::FragmentList::SharedPointer &fg_list)
	Sets the value of the MolProp::MolecularGraphProperty::FUNCTIONAL_GROUPS property of molgraph. More...

CDPL_MOLPROP_API void	clearFunctionalGroups (Chem::MolecularGraph &molgraph)
	Removes the MolProp::MolecularGraphProperty::FUNCTIONAL_GROUPS property from molgraph. More...

CDPL_MOLPROP_API bool	hasFunctionalGroups (const Chem::MolecularGraph &molgraph)
	Tells whether molgraph carries an explicit MolProp::MolecularGraphProperty::FUNCTIONAL_GROUPS property. More...

CDPL_MOLPROP_API Chem::FragmentList::SharedPointer	perceiveFunctionalGroups (const Chem::MolecularGraph &molgraph)
	Perceives the functional groups of molgraph using MolProp::FunctionalGroupList. More...

CDPL_MOLPROP_API Chem::FragmentList::SharedPointer	perceiveFunctionalGroups (Chem::MolecularGraph &molgraph, bool overwrite)
	Perceives the functional groups of molgraph and stores them as a property. More...

Detailed Description

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

Function Documentation

◆ calcExplicitMass()

CDPL_MOLPROP_API double CDPL::MolProp::calcExplicitMass ( const Chem::AtomContainer & cntnr )

Calculates the total mass of the explicit atoms in cntnr.

Parameters

cntnr The atom container.

Returns: The total explicit mass.

◆ calcExplicitMassComposition()

CDPL_MOLPROP_API void CDPL::MolProp::calcExplicitMassComposition	(	const 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.

◆ generateExplicitMassCompositionString()

CDPL_MOLPROP_API void CDPL::MolProp::generateExplicitMassCompositionString	(	const Chem::AtomContainer &	cntnr,
		std::string &	comp_str
	)

Generates a string representation of the per-element mass composition of the explicit atoms in cntnr.

Parameters

cntnr	The atom container.
comp_str	The output mass composition string.

◆ generateExplicitMolecularFormula()

CDPL_MOLPROP_API void CDPL::MolProp::generateExplicitMolecularFormula	(	const Chem::AtomContainer &	cntnr,
		std::string &	formula
	)

Generates the molecular formula of the explicit atoms in cntnr.

Parameters

cntnr	The atom container.
formula	The output molecular formula string.

◆ generateExplicitElementHistogram()

CDPL_MOLPROP_API void CDPL::MolProp::generateExplicitElementHistogram	(	const 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.

◆ getExplicitAtomCount() [1/3]

CDPL_MOLPROP_API std::size_t CDPL::MolProp::getExplicitAtomCount ( const Chem::AtomContainer & cntnr )

Returns the total number of explicit atoms in cntnr.

Parameters

cntnr The atom container.

Returns: The number of explicit atoms.

◆ getExplicitAtomCount() [2/3]

CDPL_MOLPROP_API std::size_t CDPL::MolProp::getExplicitAtomCount	(	const Chem::AtomContainer &	cntnr,
		unsigned 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.

◆ getExplicitChainAtomCount() [1/2]

CDPL_MOLPROP_API std::size_t CDPL::MolProp::getExplicitChainAtomCount ( const 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.

◆ getRingAtomCount() [1/2]

CDPL_MOLPROP_API std::size_t CDPL::MolProp::getRingAtomCount ( const Chem::AtomContainer & cntnr )

Returns the number of ring atoms in cntnr.

Parameters

cntnr The atom container.

Returns: The number of ring atoms.

◆ getAromaticAtomCount() [1/2]

CDPL_MOLPROP_API std::size_t CDPL::MolProp::getAromaticAtomCount ( const Chem::AtomContainer & cntnr )

Returns the number of aromatic atoms in cntnr.

Parameters

cntnr The atom container.

Returns: The number of aromatic atoms.

◆ getHeavyAtomCount() [1/2]

CDPL_MOLPROP_API std::size_t CDPL::MolProp::getHeavyAtomCount ( const Chem::AtomContainer & cntnr )

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

Parameters

cntnr The atom container.

Returns: The number of heavy atoms.

◆ getNetFormalCharge()

CDPL_MOLPROP_API long CDPL::MolProp::getNetFormalCharge ( const 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.

◆ calcDipoleMoment() [1/2]

CDPL_MOLPROP_API bool CDPL::MolProp::calcDipoleMoment	(	const Chem::AtomContainer &	cntnr,
		const 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.

◆ calcDipoleMoment() [2/2]

CDPL_MOLPROP_API bool CDPL::MolProp::calcDipoleMoment	(	const 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.

◆ getHydrophobicity()

CDPL_MOLPROP_API double CDPL::MolProp::getHydrophobicity ( const Chem::Atom & atom )

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

Parameters

atom The atom.

Returns: The hydrophobicity value.

◆ setHydrophobicity()

CDPL_MOLPROP_API void CDPL::MolProp::setHydrophobicity	(	Chem::Atom &	atom,
		double	hyd
	)

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

Parameters

atom	The atom.
hyd	The new hydrophobicity value.

◆ clearHydrophobicity()

CDPL_MOLPROP_API void CDPL::MolProp::clearHydrophobicity ( Chem::Atom & atom )

Removes the MolProp::AtomProperty::HYDROPHOBICITY property from atom.

Parameters

atom The atom.

◆ hasHydrophobicity()

CDPL_MOLPROP_API bool CDPL::MolProp::hasHydrophobicity ( const Chem::Atom & atom )

Tells whether atom carries an explicit MolProp::AtomProperty::HYDROPHOBICITY property.

Parameters

atom The atom.

Returns: true if the hydrophobicity property is set, and false otherwise.

◆ getPEOESigmaCharge()

CDPL_MOLPROP_API double CDPL::MolProp::getPEOESigmaCharge ( const Chem::Atom & atom )

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

Parameters

atom The atom.

Returns: The PEOE sigma charge value.

◆ setPEOESigmaCharge()

CDPL_MOLPROP_API void CDPL::MolProp::setPEOESigmaCharge	(	Chem::Atom &	atom,
		double	charge
	)

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

Parameters

atom	The atom.
charge	The new PEOE sigma charge value.

◆ clearPEOESigmaCharge()

CDPL_MOLPROP_API void CDPL::MolProp::clearPEOESigmaCharge ( Chem::Atom & atom )

Removes the MolProp::AtomProperty::PEOE_SIGMA_CHARGE property from atom.

Parameters

atom The atom.

◆ hasPEOESigmaCharge()

CDPL_MOLPROP_API bool CDPL::MolProp::hasPEOESigmaCharge ( const Chem::Atom & atom )

Tells whether atom carries an explicit MolProp::AtomProperty::PEOE_SIGMA_CHARGE property.

Parameters

atom The atom.

Returns: true if the PEOE sigma charge property is set, and false otherwise.

◆ getPEOESigmaElectronegativity()

CDPL_MOLPROP_API double CDPL::MolProp::getPEOESigmaElectronegativity ( const Chem::Atom & atom )

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

Parameters

atom The atom.

Returns: The PEOE sigma electronegativity value.

◆ setPEOESigmaElectronegativity()

CDPL_MOLPROP_API void CDPL::MolProp::setPEOESigmaElectronegativity	(	Chem::Atom &	atom,
		double	e_neg
	)

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

Parameters

atom	The atom.
e_neg	The new PEOE sigma electronegativity value.

◆ clearPEOESigmaElectronegativity()

CDPL_MOLPROP_API void CDPL::MolProp::clearPEOESigmaElectronegativity ( Chem::Atom & atom )

Removes the MolProp::AtomProperty::PEOE_SIGMA_ELECTRONEGATIVITY property from atom.

Parameters

atom The atom.

◆ hasPEOESigmaElectronegativity()

CDPL_MOLPROP_API bool CDPL::MolProp::hasPEOESigmaElectronegativity ( const Chem::Atom & atom )

Tells whether atom carries an explicit MolProp::AtomProperty::PEOE_SIGMA_ELECTRONEGATIVITY property.

Parameters

atom The atom.

Returns: true if the PEOE sigma electronegativity property is set, and false otherwise.

◆ getMHMOPiCharge()

CDPL_MOLPROP_API double CDPL::MolProp::getMHMOPiCharge ( const Chem::Atom & atom )

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

Parameters

atom The atom.

Returns: The MHMO pi charge value.

◆ setMHMOPiCharge()

CDPL_MOLPROP_API void CDPL::MolProp::setMHMOPiCharge	(	Chem::Atom &	atom,
		double	charge
	)

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

Parameters

atom	The atom.
charge	The new MHMO pi charge value.

◆ clearMHMOPiCharge()

CDPL_MOLPROP_API void CDPL::MolProp::clearMHMOPiCharge ( Chem::Atom & atom )

Removes the MolProp::AtomProperty::MHMO_PI_CHARGE property from atom.

Parameters

atom The atom.

◆ hasMHMOPiCharge()

CDPL_MOLPROP_API bool CDPL::MolProp::hasMHMOPiCharge ( const Chem::Atom & atom )

Tells whether atom carries an explicit MolProp::AtomProperty::MHMO_PI_CHARGE property.

Parameters

atom The atom.

Returns: true if the MHMO pi charge property is set, and false otherwise.

◆ getHBondDonorType()

CDPL_MOLPROP_API unsigned int CDPL::MolProp::getHBondDonorType ( const Chem::Atom & atom )

Returns the value of the MolProp::AtomProperty::H_BOND_DONOR_TYPE property of atom (see namespace MolProp::HBondDonorAtomType).

Parameters

atom The atom.

Returns: The H-bond donor type identifier.

◆ setHBondDonorType()

CDPL_MOLPROP_API void CDPL::MolProp::setHBondDonorType	(	Chem::Atom &	atom,
		unsigned int	type
	)

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

Parameters

atom	The atom.
type	The new MolProp::HBondDonorAtomType identifier.

◆ clearHBondDonorType()

CDPL_MOLPROP_API void CDPL::MolProp::clearHBondDonorType ( Chem::Atom & atom )

Removes the MolProp::AtomProperty::H_BOND_DONOR_TYPE property from atom.

Parameters

atom The atom.

◆ hasHBondDonorType()

CDPL_MOLPROP_API bool CDPL::MolProp::hasHBondDonorType ( const Chem::Atom & atom )

Tells whether atom carries an explicit MolProp::AtomProperty::H_BOND_DONOR_TYPE property.

Parameters

atom The atom.

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

◆ getHBondAcceptorType()

CDPL_MOLPROP_API unsigned int CDPL::MolProp::getHBondAcceptorType ( const Chem::Atom & atom )

Returns the value of the MolProp::AtomProperty::H_BOND_ACCEPTOR_TYPE property of atom (see namespace MolProp::HBondAcceptorAtomType).

Parameters

atom The atom.

Returns: The H-bond acceptor type identifier.

◆ setHBondAcceptorType()

CDPL_MOLPROP_API void CDPL::MolProp::setHBondAcceptorType	(	Chem::Atom &	atom,
		unsigned int	type
	)

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

Parameters

atom	The atom.
type	The new MolProp::HBondAcceptorAtomType identifier.

◆ clearHBondAcceptorType()

CDPL_MOLPROP_API void CDPL::MolProp::clearHBondAcceptorType ( Chem::Atom & atom )

Removes the MolProp::AtomProperty::H_BOND_ACCEPTOR_TYPE property from atom.

Parameters

atom The atom.

◆ hasHBondAcceptorType()

CDPL_MOLPROP_API bool CDPL::MolProp::hasHBondAcceptorType ( const Chem::Atom & atom )

Tells whether atom carries an explicit MolProp::AtomProperty::H_BOND_ACCEPTOR_TYPE property.

Parameters

atom The atom.

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

◆ isInRing() [1/2]

CDPL_MOLPROP_API bool CDPL::MolProp::isInRing	(	const Chem::Atom &	atom,
		const Chem::MolecularGraph &	molgraph
	)

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

Parameters

atom	The atom.
molgraph	The molecular graph.

Returns: true if atom is in a ring, and false otherwise.

◆ isInRingOfSize() [1/2]

CDPL_MOLPROP_API bool CDPL::MolProp::isInRingOfSize	(	const Chem::Atom &	atom,
		const Chem::MolecularGraph &	molgraph,
		std::size_t	size
	)

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

Parameters

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

Returns: true if atom is in a ring of size size, and false otherwise.

◆ getNumContainingSSSRRings() [1/2]

CDPL_MOLPROP_API std::size_t CDPL::MolProp::getNumContainingSSSRRings	(	const Chem::Atom &	atom,
		const Chem::MolecularGraph &	molgraph
	)

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

Parameters

atom	The atom.
molgraph	The molecular graph.

Returns: The number of containing SSSR rings.

◆ getAtomicWeight()

CDPL_MOLPROP_API double CDPL::MolProp::getAtomicWeight ( const Chem::Atom & atom )

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

Parameters

atom The atom.

Returns: The standard atomic weight.

◆ getIUPACGroup()

CDPL_MOLPROP_API std::size_t CDPL::MolProp::getIUPACGroup ( const Chem::Atom & atom )

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

Parameters

atom The atom.

Returns: The IUPAC group number.

◆ getPeriod()

CDPL_MOLPROP_API std::size_t CDPL::MolProp::getPeriod ( const Chem::Atom & atom )

Returns the period of the chemical element associated with atom.

Parameters

atom The atom.

Returns: The element period.

◆ getVdWRadius()

CDPL_MOLPROP_API double CDPL::MolProp::getVdWRadius ( const Chem::Atom & atom )

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

Parameters

atom The atom.

Returns: The Van der Waals radius.

◆ getCovalentRadius()

CDPL_MOLPROP_API double CDPL::MolProp::getCovalentRadius	(	const Chem::Atom &	atom,
		std::size_t	order
	)

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

Parameters

atom	The atom.
order	The bond order.

Returns: The covalent radius.

◆ getAllredRochowElectronegativity()

CDPL_MOLPROP_API double CDPL::MolProp::getAllredRochowElectronegativity ( const Chem::Atom & atom )

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

Parameters

atom The atom.

Returns: The Allred-Rochow electronegativity.

◆ getElementName()

CDPL_MOLPROP_API const std::string& CDPL::MolProp::getElementName ( const Chem::Atom & atom )

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

Parameters

atom The atom.

Returns: A const reference to the element name.

◆ getElementValenceElectronCount()

CDPL_MOLPROP_API std::size_t CDPL::MolProp::getElementValenceElectronCount ( const Chem::Atom & atom )

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

Parameters

atom The atom.

Returns: The number of valence electrons.

◆ isChemicalElement()

CDPL_MOLPROP_API bool CDPL::MolProp::isChemicalElement ( const Chem::Atom & atom )

Tells whether atom represents a chemical element.

Parameters

atom The atom.

Returns: true if atom represents a chemical element, and false otherwise.

◆ isMainGroupElement()

CDPL_MOLPROP_API bool CDPL::MolProp::isMainGroupElement ( const Chem::Atom & atom )

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

Parameters

atom The atom.

Returns: true if the element is a main-group element, and false otherwise.

◆ isMetal()

CDPL_MOLPROP_API bool CDPL::MolProp::isMetal ( const Chem::Atom & atom )

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

Parameters

atom The atom.

Returns: true if the element is a metal, and false otherwise.

◆ isTransitionMetal()

CDPL_MOLPROP_API bool CDPL::MolProp::isTransitionMetal ( const Chem::Atom & atom )

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

Parameters

atom The atom.

Returns: true if the element is a transition metal, and false otherwise.

◆ isNonMetal()

CDPL_MOLPROP_API bool CDPL::MolProp::isNonMetal ( const Chem::Atom & atom )

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

Parameters

atom The atom.

Returns: true if the element is a non-metal, and false otherwise.

◆ isSemiMetal()

CDPL_MOLPROP_API bool CDPL::MolProp::isSemiMetal ( const Chem::Atom & atom )

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

Parameters

atom The atom.

Returns: true if the element is a semi-metal, and false otherwise.

◆ isHalogen()

CDPL_MOLPROP_API bool CDPL::MolProp::isHalogen ( const Chem::Atom & atom )

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

Parameters

atom The atom.

Returns: true if the element is a halogen, and false otherwise.

◆ isNobleGas()

CDPL_MOLPROP_API bool CDPL::MolProp::isNobleGas ( const Chem::Atom & atom )

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

Parameters

atom The atom.

Returns: true if the element is a noble gas, and false otherwise.

◆ isOrdinaryHydrogen()

CDPL_MOLPROP_API bool CDPL::MolProp::isOrdinaryHydrogen	(	const Chem::Atom &	atom,
		const Chem::MolecularGraph &	molgraph,
		unsigned int	flags = `Chem::AtomPropertyFlag::DEFAULT`
	)

Tells whether 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.

Parameters

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

Returns: true if atom is an ordinary hydrogen, and false otherwise.

◆ isHeavy()

CDPL_MOLPROP_API bool CDPL::MolProp::isHeavy ( const Chem::Atom & atom )

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

Parameters

atom The atom.

Returns: true if atom is a heavy atom, and false otherwise.

◆ isUnsaturated()

CDPL_MOLPROP_API bool CDPL::MolProp::isUnsaturated	(	const Chem::Atom &	atom,
		const Chem::MolecularGraph &	molgraph
	)

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

Parameters

atom	The atom.
molgraph	The molecular graph.

Returns: true if atom is unsaturated, and false otherwise.

◆ isHBondAcceptor()

CDPL_MOLPROP_API bool CDPL::MolProp::isHBondAcceptor	(	const Chem::Atom &	atom,
		const Chem::MolecularGraph &	molgraph
	)

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

Parameters

atom	The atom.
molgraph	The molecular graph.

Returns: true if atom is an H-bond acceptor, and false otherwise.

◆ isHBondDonor()

CDPL_MOLPROP_API bool CDPL::MolProp::isHBondDonor	(	const Chem::Atom &	atom,
		const Chem::MolecularGraph &	molgraph
	)

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

Parameters

atom	The atom.
molgraph	The molecular graph.

Returns: true if atom is an H-bond donor, and false otherwise.

◆ isCarbonylLike()

CDPL_MOLPROP_API bool CDPL::MolProp::isCarbonylLike	(	const Chem::Atom &	atom,
		const Chem::MolecularGraph &	molgraph,
		bool	c_only = `false`,
		bool	db_o_only = `false`
	)

Tells whether atom is a carbonyl-like center in 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 atom is a carbonyl-like center, and false otherwise.

Since: 1.2

◆ isAmideCenter()

CDPL_MOLPROP_API bool CDPL::MolProp::isAmideCenter	(	const Chem::Atom &	atom,
		const Chem::MolecularGraph &	molgraph,
		bool	c_only = `false`,
		bool	db_o_only = `false`
	)

Tells whether atom is the center of an amide group in 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 atom is an amide center, and false otherwise.

Since: 1.2

◆ isAmideNitrogen()

CDPL_MOLPROP_API bool CDPL::MolProp::isAmideNitrogen	(	const Chem::Atom &	atom,
		const Chem::MolecularGraph &	molgraph,
		bool	c_only = `false`,
		bool	db_o_only = `false`
	)

Tells whether atom is the nitrogen of an amide group in 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 atom is an amide nitrogen, and false otherwise.

◆ isInvertibleNitrogen()

CDPL_MOLPROP_API bool CDPL::MolProp::isInvertibleNitrogen	(	const Chem::Atom &	atom,
		const Chem::MolecularGraph &	molgraph
	)

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

Parameters

atom	The atom.
molgraph	The molecular graph.

Returns: true if atom is an invertible nitrogen, and false otherwise.

◆ isPlanarNitrogen()

CDPL_MOLPROP_API bool CDPL::MolProp::isPlanarNitrogen	(	const Chem::Atom &	atom,
		const Chem::MolecularGraph &	molgraph
	)

Tells whether atom is a planar nitrogen in molgraph.

Parameters

atom	The atom.
molgraph	The molecular graph.

Returns: true if atom is a planar nitrogen, and false otherwise.

◆ isBridgehead()

CDPL_MOLPROP_API bool CDPL::MolProp::isBridgehead	(	const Chem::Atom &	atom,
		const Chem::MolecularGraph &	molgraph,
		bool	bridged_only
	)

Tells whether atom is a bridgehead atom in 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 atom is a bridgehead, and false otherwise.

Since: 1.2

◆ isSpiroCenter()

CDPL_MOLPROP_API bool CDPL::MolProp::isSpiroCenter	(	const Chem::Atom &	atom,
		const Chem::MolecularGraph &	molgraph
	)

Tells whether atom is a spiro center in molgraph.

Parameters

atom	The atom.
molgraph	The molecular graph.

Returns: true if atom is a spiro center, and false otherwise.

Since: 1.2

◆ getOrdinaryHydrogenCount() [1/2]

CDPL_MOLPROP_API std::size_t CDPL::MolProp::getOrdinaryHydrogenCount	(	const Chem::Atom &	atom,
		const Chem::MolecularGraph &	molgraph,
		unsigned int	flags = `Chem::AtomPropertyFlag::DEFAULT`
	)

Returns the number of ordinary-hydrogen neighbors of atom in molgraph (see isOrdinaryHydrogen() for the definition of "ordinary").

Parameters

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

Returns: The ordinary-hydrogen neighbor count.

◆ getExplicitAtomCount() [3/3]

CDPL_MOLPROP_API std::size_t CDPL::MolProp::getExplicitAtomCount	(	const Chem::Atom &	atom,
		const Chem::MolecularGraph &	molgraph,
		unsigned int	type,
		bool	strict = `true`
	)

Returns the number of explicit neighbors of atom in molgraph whose Chem::AtomType matches type.

Parameters

atom	The atom.
molgraph	The molecular graph.
type	The Chem::AtomType to count.
strict	If `true`, the atom type must match type exactly; otherwise generic types match via Chem::atomTypesMatch().

Returns: The matching explicit-atom neighbor count.

◆ getAtomCount() [1/3]

CDPL_MOLPROP_API std::size_t CDPL::MolProp::getAtomCount	(	const Chem::Atom &	atom,
		const Chem::MolecularGraph &	molgraph,
		unsigned int	type,
		bool	strict = `true`
	)

Returns the number of neighbors of atom in molgraph (including implicit hydrogens) whose Chem::AtomType matches type.

Parameters

atom	The atom.
molgraph	The molecular graph.
type	The Chem::AtomType to count.
strict	If `true`, the atom type must match type exactly; otherwise generic types match via Chem::atomTypesMatch().

Returns: The matching neighbor count.

◆ getExplicitChainAtomCount() [2/2]

CDPL_MOLPROP_API std::size_t CDPL::MolProp::getExplicitChainAtomCount	(	const Chem::Atom &	atom,
		const Chem::MolecularGraph &	molgraph
	)

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

Parameters

atom	The atom.
molgraph	The molecular graph.

Returns: The explicit chain-atom neighbor count.

◆ getChainAtomCount() [1/2]

CDPL_MOLPROP_API std::size_t CDPL::MolProp::getChainAtomCount	(	const Chem::Atom &	atom,
		const Chem::MolecularGraph &	molgraph
	)

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

Parameters

atom	The atom.
molgraph	The molecular graph.

Returns: The chain-atom neighbor count.

◆ getRingAtomCount() [2/2]

CDPL_MOLPROP_API std::size_t CDPL::MolProp::getRingAtomCount	(	const Chem::Atom &	atom,
		const Chem::MolecularGraph &	molgraph
	)

Returns the number of ring-atom neighbors of atom in molgraph.

Parameters

atom	The atom.
molgraph	The molecular graph.

Returns: The ring-atom neighbor count.

◆ getAromaticAtomCount() [2/2]

CDPL_MOLPROP_API std::size_t CDPL::MolProp::getAromaticAtomCount	(	const Chem::Atom &	atom,
		const Chem::MolecularGraph &	molgraph
	)

Returns the number of aromatic neighbors of atom in molgraph.

Parameters

atom	The atom.
molgraph	The molecular graph.

Returns: The aromatic neighbor count.

◆ getHeavyAtomCount() [2/2]

CDPL_MOLPROP_API std::size_t CDPL::MolProp::getHeavyAtomCount	(	const Chem::Atom &	atom,
		const Chem::MolecularGraph &	molgraph
	)

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

Parameters

atom	The atom.
molgraph	The molecular graph.

Returns: The heavy atom neighbor count.

◆ getExplicitBondCount() [1/5]

CDPL_MOLPROP_API std::size_t CDPL::MolProp::getExplicitBondCount	(	const Chem::Atom &	atom,
		const Chem::MolecularGraph &	molgraph
	)

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

Parameters

atom	The atom.
molgraph	The molecular graph.

Returns: The explicit-bond count.

◆ getExplicitBondCount() [2/5]

CDPL_MOLPROP_API std::size_t CDPL::MolProp::getExplicitBondCount	(	const Chem::Atom &	atom,
		const Chem::MolecularGraph &	molgraph,
		std::size_t	order
	)

Returns the number of explicit bonds of the given order incident to atom in 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]

CDPL_MOLPROP_API std::size_t CDPL::MolProp::getExplicitBondCount	(	const Chem::Atom &	atom,
		const Chem::MolecularGraph &	molgraph,
		std::size_t	order,
		unsigned int	type,
		bool	strict = `true`
	)

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

Parameters

atom	The atom.
molgraph	The molecular graph.
order	The bond order to count.
type	The Chem::AtomType of the bonded partner.
strict	If `true`, the atom type must match type exactly; otherwise generic types match via Chem::atomTypesMatch().

Returns: The number of matching explicit bonds.

◆ getBondCount() [1/5]

CDPL_MOLPROP_API std::size_t CDPL::MolProp::getBondCount	(	const Chem::Atom &	atom,
		const Chem::MolecularGraph &	molgraph
	)

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

Parameters

atom	The atom.
molgraph	The molecular graph.

Returns: The total bond count.

◆ getBondCount() [2/5]

CDPL_MOLPROP_API std::size_t CDPL::MolProp::getBondCount	(	const Chem::Atom &	atom,
		const Chem::MolecularGraph &	molgraph,
		std::size_t	order
	)

Returns the total number of bonds of the given order incident to 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]

CDPL_MOLPROP_API std::size_t CDPL::MolProp::getBondCount	(	const Chem::Atom &	atom,
		const Chem::MolecularGraph &	molgraph,
		std::size_t	order,
		unsigned int	type,
		bool	strict = `true`
	)

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

Parameters

atom	The atom.
molgraph	The molecular graph.
order	The bond order to count.
type	The Chem::AtomType of the bonded partner.
strict	If `true`, the atom type must match type exactly; otherwise generic types match via Chem::atomTypesMatch().

Returns: The number of matching bonds.

◆ getExplicitChainBondCount() [1/2]

CDPL_MOLPROP_API std::size_t CDPL::MolProp::getExplicitChainBondCount	(	const Chem::Atom &	atom,
		const Chem::MolecularGraph &	molgraph
	)

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

Parameters

atom	The atom.
molgraph	The molecular graph.

Returns: The explicit chain-bond count.

◆ getChainBondCount() [1/2]

CDPL_MOLPROP_API std::size_t CDPL::MolProp::getChainBondCount	(	const Chem::Atom &	atom,
		const Chem::MolecularGraph &	molgraph
	)

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

Parameters

atom	The atom.
molgraph	The molecular graph.

Returns: The chain-bond count.

◆ getRingBondCount() [1/2]

CDPL_MOLPROP_API std::size_t CDPL::MolProp::getRingBondCount	(	const Chem::Atom &	atom,
		const Chem::MolecularGraph &	molgraph
	)

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

Parameters

atom	The atom.
molgraph	The molecular graph.

Returns: The ring-bond count.

◆ getAromaticBondCount() [1/2]

CDPL_MOLPROP_API std::size_t CDPL::MolProp::getAromaticBondCount	(	const Chem::Atom &	atom,
		const Chem::MolecularGraph &	molgraph
	)

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

Parameters

atom	The atom.
molgraph	The molecular graph.

Returns: The aromatic-bond count.

◆ getHeavyBondCount() [1/2]

CDPL_MOLPROP_API std::size_t CDPL::MolProp::getHeavyBondCount	(	const Chem::Atom &	atom,
		const Chem::MolecularGraph &	molgraph
	)

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

Parameters

atom	The atom.
molgraph	The molecular graph.

Returns: The heavy bond count.

◆ getRotatableBondCount() [1/2]

CDPL_MOLPROP_API std::size_t CDPL::MolProp::getRotatableBondCount	(	const Chem::Atom &	atom,
		const Chem::MolecularGraph &	molgraph,
		bool	h_rotors = `false`,
		bool	ring_bonds = `false`,
		bool	amide_bonds = `false`
	)

Returns the number of rotatable bonds incident to atom in 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.

◆ calcExplicitValence()

CDPL_MOLPROP_API std::size_t CDPL::MolProp::calcExplicitValence	(	const Chem::Atom &	atom,
		const Chem::MolecularGraph &	molgraph
	)

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

Parameters

atom	The atom.
molgraph	The molecular graph.

Returns: The explicit valence.

◆ calcValence()

CDPL_MOLPROP_API std::size_t CDPL::MolProp::calcValence	(	const Chem::Atom &	atom,
		const Chem::MolecularGraph &	molgraph
	)

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

Parameters

atom	The atom.
molgraph	The molecular graph.

Returns: The total valence.

◆ calcFreeValenceElectronCount()

CDPL_MOLPROP_API std::size_t CDPL::MolProp::calcFreeValenceElectronCount	(	const Chem::Atom &	atom,
		const Chem::MolecularGraph &	molgraph
	)

Calculates the number of free (lone-pair) valence electrons of atom in molgraph.

Parameters

atom	The atom.
molgraph	The molecular graph.

Returns: The number of free valence electrons.

◆ calcValenceElectronCount()

CDPL_MOLPROP_API std::size_t CDPL::MolProp::calcValenceElectronCount ( const Chem::Atom & atom )

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

Parameters

atom The atom.

Returns: The valence-electron count.

◆ calcStericNumber()

CDPL_MOLPROP_API std::size_t CDPL::MolProp::calcStericNumber	(	const Chem::Atom &	atom,
		const Chem::MolecularGraph &	molgraph
	)

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

Parameters

atom	The atom.
molgraph	The molecular graph.

Returns: The steric number.

◆ getVSEPRCoordinationGeometry() [1/2]

CDPL_MOLPROP_API unsigned int CDPL::MolProp::getVSEPRCoordinationGeometry	(	const Chem::Atom &	atom,
		const Chem::MolecularGraph &	molgraph,
		std::size_t	steric_num
	)

Returns the VSEPR coordination geometry of atom in molgraph (see namespace MolProp::CoordinationGeometry).

Parameters

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

Returns: The MolProp::CoordinationGeometry identifier.

◆ getVSEPRCoordinationGeometry() [2/2]

CDPL_MOLPROP_API unsigned int CDPL::MolProp::getVSEPRCoordinationGeometry	(	const Chem::Atom &	atom,
		const Chem::MolecularGraph &	molgraph
	)

Returns the VSEPR coordination geometry of atom in molgraph (see namespace MolProp::CoordinationGeometry).

Parameters

atom	The atom.
molgraph	The molecular graph.

Returns: The MolProp::CoordinationGeometry identifier.

◆ getHybridPolarizability()

CDPL_MOLPROP_API double CDPL::MolProp::getHybridPolarizability	(	const Chem::Atom &	atom,
		const Chem::MolecularGraph &	molgraph
	)

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

Parameters

atom	The atom.
molgraph	The molecular graph.

Returns: The hybrid polarizability.

◆ calcEffectivePolarizability()

CDPL_MOLPROP_API double CDPL::MolProp::calcEffectivePolarizability	(	const Chem::Atom &	atom,
		const Chem::MolecularGraph &	molgraph,
		double	damping = `0.75`
	)

Calculates the effective atomic polarizability of atom in molgraph (after Kang and Jhon).

Parameters

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

Returns: The effective polarizability.

◆ calcTotalPartialCharge()

CDPL_MOLPROP_API double CDPL::MolProp::calcTotalPartialCharge ( const Chem::Atom & atom )

Calculates the total partial charge of atom (sum of stored PEOE sigma and MHMO pi charge contributions).

Parameters

atom The atom.

Returns: The total partial charge.

◆ calcLonePairElectronegativity()

CDPL_MOLPROP_API double CDPL::MolProp::calcLonePairElectronegativity	(	const Chem::Atom &	atom,
		const Chem::MolecularGraph &	molgraph
	)

Calculates the lone-pair electronegativity of atom in molgraph.

Parameters

atom	The atom.
molgraph	The molecular graph.

Returns: The lone-pair electronegativity.

◆ calcPiElectronegativity()

CDPL_MOLPROP_API double CDPL::MolProp::calcPiElectronegativity	(	const Chem::Atom &	atom,
		const Chem::MolecularGraph &	molgraph
	)

Calculates the pi electronegativity of atom in molgraph.

Parameters

atom	The atom.
molgraph	The molecular graph.

Returns: The pi electronegativity.

◆ calcInductiveEffect()

CDPL_MOLPROP_API double CDPL::MolProp::calcInductiveEffect	(	const Chem::Atom &	atom,
		const Chem::MolecularGraph &	molgraph,
		std::size_t	num_bonds = `10`
	)

Calculates the inductive effect parameter of atom in 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.

◆ getExplicitBondCount() [4/5]

CDPL_MOLPROP_API std::size_t CDPL::MolProp::getExplicitBondCount ( const 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]

CDPL_MOLPROP_API std::size_t CDPL::MolProp::getExplicitBondCount	(	const Chem::BondContainer &	cntnr,
		std::size_t	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.

◆ getExplicitHydrogenBondCount()

CDPL_MOLPROP_API std::size_t CDPL::MolProp::getExplicitHydrogenBondCount ( const 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.

◆ getExplicitChainBondCount() [2/2]

CDPL_MOLPROP_API std::size_t CDPL::MolProp::getExplicitChainBondCount ( const 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.

◆ getRingBondCount() [2/2]

CDPL_MOLPROP_API std::size_t CDPL::MolProp::getRingBondCount ( const Chem::BondContainer & cntnr )

Returns the number of ring bonds in cntnr.

Parameters

cntnr The bond container.

Returns: The number of ring bonds.

◆ getAromaticBondCount() [2/2]

CDPL_MOLPROP_API std::size_t CDPL::MolProp::getAromaticBondCount ( const Chem::BondContainer & cntnr )

Returns the number of aromatic bonds in cntnr.

Parameters

cntnr The bond container.

Returns: The number of aromatic bonds.

◆ getHeavyBondCount() [2/2]

CDPL_MOLPROP_API std::size_t CDPL::MolProp::getHeavyBondCount ( const Chem::BondContainer & cntnr )

Returns the number of heavy atom bonds in cntnr.

Parameters

cntnr The bond container.

Returns: The number of heavy bonds.

◆ getMHMOPiOrder()

CDPL_MOLPROP_API double CDPL::MolProp::getMHMOPiOrder ( const Chem::Bond & bond )

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

Parameters

bond The bond.

Returns: The MHMO pi-bond order.

◆ setMHMOPiOrder()

CDPL_MOLPROP_API void CDPL::MolProp::setMHMOPiOrder	(	Chem::Bond &	bond,
		double	order
	)

Sets the value of the MolProp::BondProperty::MHMO_PI_ORDER property of bond.

Parameters

bond	The bond.
order	The MHMO pi-bond order.

◆ clearMHMOPiOrder()

CDPL_MOLPROP_API void CDPL::MolProp::clearMHMOPiOrder ( Chem::Bond & bond )

Removes the MolProp::BondProperty::MHMO_PI_ORDER property from bond.

Parameters

bond The bond.

◆ hasMHMOPiOrder()

CDPL_MOLPROP_API bool CDPL::MolProp::hasMHMOPiOrder ( const Chem::Bond & atom )

Tells whether bond carries an explicit MolProp::BondProperty::MHMO_PI_ORDER property.

Parameters

atom The bond.

Returns: true if the property is set, and false otherwise.

◆ calcPolarizability()

CDPL_MOLPROP_API double CDPL::MolProp::calcPolarizability	(	const Chem::Bond &	bond,
		const Chem::MolecularGraph &	molgraph,
		double	damping = `0.75`
	)

Calculates the bond polarizability of bond within molgraph.

Parameters

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

Returns: The calculated bond polarizability.

◆ isInRing() [2/2]

CDPL_MOLPROP_API bool CDPL::MolProp::isInRing	(	const Chem::Bond &	Bond,
		const Chem::MolecularGraph &	molgraph
	)

Tells whether Bond is part of any ring of molgraph.

Parameters

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

Returns: true if the bond is part of a ring, and false otherwise.

◆ isInRingOfSize() [2/2]

CDPL_MOLPROP_API bool CDPL::MolProp::isInRingOfSize	(	const Chem::Bond &	bond,
		const Chem::MolecularGraph &	molgraph,
		std::size_t	size
	)

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

◆ getNumContainingSSSRRings() [2/2]

CDPL_MOLPROP_API std::size_t CDPL::MolProp::getNumContainingSSSRRings	(	const Chem::Bond &	bond,
		const Chem::MolecularGraph &	molgraph
	)

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

Parameters

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

Returns: The number of SSSR rings containing the bond.

◆ isHydrogenRotor()

CDPL_MOLPROP_API bool CDPL::MolProp::isHydrogenRotor	(	const Chem::Bond &	bond,
		const Chem::MolecularGraph &	molgraph
	)

Tells whether 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.

◆ isHeteroAtomHydrogenRotor()

CDPL_MOLPROP_API bool CDPL::MolProp::isHeteroAtomHydrogenRotor	(	const Chem::Bond &	bond,
		const Chem::MolecularGraph &	molgraph
	)

Tells whether bond is a hydrogen-only rotor where the rotating end is a heteroatom-bound hydrogen.

Parameters

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

Returns: true if the bond is a heteroatom-hydrogen rotor, and false otherwise.

◆ isRotatable()

CDPL_MOLPROP_API bool CDPL::MolProp::isRotatable	(	const Chem::Bond &	bond,
		const Chem::MolecularGraph &	molgraph,
		bool	h_rotors = `false`,
		bool	ring_bonds = `false`,
		bool	amide_bonds = `false`
	)

Tells whether 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.

◆ isHydrogenBond()

CDPL_MOLPROP_API bool CDPL::MolProp::isHydrogenBond ( const Chem::Bond & bond )

Tells whether 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.

◆ isAmideBond()

CDPL_MOLPROP_API bool CDPL::MolProp::isAmideBond	(	const Chem::Bond &	bond,
		const Chem::MolecularGraph &	molgraph,
		bool	c_only = `false`,
		bool	db_o_only = `false`
	)

Tells whether bond is an amide bond in molgraph.

Parameters

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

Returns: true if the bond is an amide bond under the given criteria, and false otherwise.

◆ calcMass()

CDPL_MOLPROP_API double CDPL::MolProp::calcMass ( const Chem::MolecularGraph & molgraph )

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

Parameters

molgraph The molecular graph.

Returns: The molecular mass.

◆ calcMassComposition()

CDPL_MOLPROP_API void CDPL::MolProp::calcMassComposition	(	const Chem::MolecularGraph &	molgraph,
		MassComposition &	comp
	)

Calculates the per-element mass composition of molgraph.

Parameters

molgraph	The molecular graph.
comp	The output mass composition.

◆ generateMassCompositionString()

CDPL_MOLPROP_API void CDPL::MolProp::generateMassCompositionString	(	const Chem::MolecularGraph &	molgraph,
		std::string &	comp
	)

Generates a string representation of the per-element mass composition of molgraph.

Parameters

molgraph	The molecular graph.
comp	The output mass composition string.

◆ generateMolecularFormula()

CDPL_MOLPROP_API void CDPL::MolProp::generateMolecularFormula	(	const Chem::MolecularGraph &	molgraph,
		std::string &	formula,
		const std::string &	sep = `std::string()`
	)

Generates the molecular formula of the molecular graph molgraph.

Parameters

molgraph	The molecular graph.
formula	A reference to the output string.
sep	A string separating the output for each element (since 1.2).

◆ generateElementHistogram()

CDPL_MOLPROP_API void CDPL::MolProp::generateElementHistogram	(	const Chem::MolecularGraph &	molgraph,
		ElementHistogram &	hist,
		bool	append = `false`
	)

Generates the element histogram of molgraph.

Parameters

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

◆ calcCyclomaticNumber()

CDPL_MOLPROP_API std::size_t CDPL::MolProp::calcCyclomaticNumber ( const Chem::MolecularGraph & molgraph )

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

Parameters

molgraph The molecular graph.

Returns: The cyclomatic number.

◆ getAtomCount() [2/3]

CDPL_MOLPROP_API std::size_t CDPL::MolProp::getAtomCount ( const Chem::MolecularGraph & molgraph )

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

Parameters

molgraph The molecular graph.

Returns: The total atom count.

◆ getAtomCount() [3/3]

CDPL_MOLPROP_API std::size_t CDPL::MolProp::getAtomCount	(	const Chem::MolecularGraph &	molgraph,
		unsigned int	type,
		bool	strict = `true`
	)

Returns the number of atoms in molgraph whose Chem::AtomType matches type.

Parameters

molgraph	The molecular graph.
type	The Chem::AtomType to count.
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

◆ getImplicitHydrogenCount()

CDPL_MOLPROP_API std::size_t CDPL::MolProp::getImplicitHydrogenCount ( const Chem::MolecularGraph & molgraph )

Returns the total number of implicit hydrogens in molgraph.

Parameters

molgraph The molecular graph.

Returns: The implicit-hydrogen count.

◆ getOrdinaryHydrogenCount() [2/2]

CDPL_MOLPROP_API std::size_t CDPL::MolProp::getOrdinaryHydrogenCount	(	const Chem::MolecularGraph &	molgraph,
		unsigned int	flags = `Chem::AtomPropertyFlag::DEFAULT`
	)

Returns the number of ordinary hydrogens in molgraph (see MolProp::isOrdinaryHydrogen() for the definition of "ordinary").

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.

◆ getExplicitOrdinaryHydrogenCount()

CDPL_MOLPROP_API std::size_t CDPL::MolProp::getExplicitOrdinaryHydrogenCount	(	const Chem::MolecularGraph &	molgraph,
		unsigned int	flags = `Chem::AtomPropertyFlag::DEFAULT`
	)

Returns the number of explicit ordinary hydrogens in molgraph (see MolProp::isOrdinaryHydrogen() for the definition of "ordinary").

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.

◆ getChainAtomCount() [2/2]

CDPL_MOLPROP_API std::size_t CDPL::MolProp::getChainAtomCount ( const Chem::MolecularGraph & molgraph )

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

Parameters

molgraph The molecular graph.

Returns: The chain-atom count.

◆ getHBondAcceptorAtomCount()

CDPL_MOLPROP_API std::size_t CDPL::MolProp::getHBondAcceptorAtomCount ( const Chem::MolecularGraph & molgraph )

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

Parameters

molgraph The molecular graph.

Returns: The H-bond acceptor count.

◆ getHBondDonorAtomCount()

CDPL_MOLPROP_API std::size_t CDPL::MolProp::getHBondDonorAtomCount ( const Chem::MolecularGraph & molgraph )

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

Parameters

molgraph The molecular graph.

Returns: The H-bond donor count.

◆ getBondCount() [4/5]

CDPL_MOLPROP_API std::size_t CDPL::MolProp::getBondCount ( const Chem::MolecularGraph & molgraph )

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

Parameters

molgraph The molecular graph.

Returns: The total bond count.

◆ getBondCount() [5/5]

CDPL_MOLPROP_API std::size_t CDPL::MolProp::getBondCount	(	const Chem::MolecularGraph &	molgraph,
		std::size_t	order,
		bool	inc_aro = `true`
	)

Returns the number of bonds in 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.

◆ getHydrogenBondCount()

CDPL_MOLPROP_API std::size_t CDPL::MolProp::getHydrogenBondCount ( const Chem::MolecularGraph & molgraph )

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

Parameters

molgraph The molecular graph.

Returns: The hydrogen-bond count.

◆ getChainBondCount() [2/2]

CDPL_MOLPROP_API std::size_t CDPL::MolProp::getChainBondCount ( const Chem::MolecularGraph & molgraph )

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

Parameters

molgraph The molecular graph.

Returns: The chain-bond count.

◆ getRotatableBondCount() [2/2]

CDPL_MOLPROP_API std::size_t CDPL::MolProp::getRotatableBondCount	(	const Chem::MolecularGraph &	molgraph,
		bool	h_rotors = `false`,
		bool	ring_bonds = `false`,
		bool	amide_bonds = `false`
	)

Returns the number of rotatable bonds in 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.

◆ getComponentCount()

CDPL_MOLPROP_API std::size_t CDPL::MolProp::getComponentCount ( const Chem::MolecularGraph & molgraph )

Returns the number of connected components in molgraph.

Parameters

molgraph The molecular graph.

Returns: The component count.

◆ calcXLogP()

CDPL_MOLPROP_API double CDPL::MolProp::calcXLogP ( const Chem::MolecularGraph & molgraph )

Calculates the XLogP value of molgraph using MolProp::XLogPCalculator.

Parameters

molgraph The molecular graph.

Returns: The XLogP value.

See also: [XLOGP]

◆ calcLogS()

CDPL_MOLPROP_API double CDPL::MolProp::calcLogS ( const Chem::MolecularGraph & molgraph )

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

Parameters

molgraph The molecular graph.

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

See also: [LOGS]

◆ calcTPSA()

CDPL_MOLPROP_API double CDPL::MolProp::calcTPSA ( const Chem::MolecularGraph & molgraph )

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

Parameters

molgraph The molecular graph.

Returns: The TPSA value.

See also: [TPSA]

◆ getRuleOfFiveScore()

CDPL_MOLPROP_API std::size_t CDPL::MolProp::getRuleOfFiveScore ( const Chem::MolecularGraph & molgraph )

Returns the Lipinski rule-of-five score of 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).

◆ calcMeanPolarizability()

CDPL_MOLPROP_API double CDPL::MolProp::calcMeanPolarizability ( const Chem::MolecularGraph & molgraph )

Calculates the mean atomic polarizability of molgraph.

Parameters

molgraph The molecular graph.

Returns: The mean atomic polarizability.

◆ calcPEOEProperties()

CDPL_MOLPROP_API void CDPL::MolProp::calcPEOEProperties	(	Chem::MolecularGraph &	molgraph,
		bool	overwrite,
		std::size_t	num_iter = `20`,
		double	damping = `0.48`
	)

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

Parameters

molgraph	The molecular graph (modified in place).
overwrite	If `true`, existing atom properties are overwritten; otherwise only atoms without the property are populated.
num_iter	The number of charge-shifting iterations.
damping	The per-iteration damping factor.

◆ calcMHMOProperties()

CDPL_MOLPROP_API void CDPL::MolProp::calcMHMOProperties	(	Chem::MolecularGraph &	molgraph,
		bool	overwrite
	)

Calculates MHMO pi charges and pi-bond orders for 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.

◆ calcAtomHydrophobicities()

CDPL_MOLPROP_API void CDPL::MolProp::calcAtomHydrophobicities	(	Chem::MolecularGraph &	molgraph,
		bool	overwrite,
		bool	from_logp = `false`
	)

Calculates per-atom hydrophobicities for 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 instead of the Greene algorithm.

◆ perceiveHBondDonorAtomTypes()

CDPL_MOLPROP_API void CDPL::MolProp::perceiveHBondDonorAtomTypes	(	Chem::MolecularGraph &	molgraph,
		bool	overwrite
	)

Perceives the H-bond donor types of the atoms in 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.

◆ perceiveHBondAcceptorAtomTypes()

CDPL_MOLPROP_API void CDPL::MolProp::perceiveHBondAcceptorAtomTypes	(	Chem::MolecularGraph &	molgraph,
		bool	overwrite
	)

Perceives the H-bond acceptor types of the atoms in 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.

◆ getFunctionalGroups()

CDPL_MOLPROP_API const Chem::FragmentList::SharedPointer& CDPL::MolProp::getFunctionalGroups ( const Chem::MolecularGraph & molgraph )

Returns the value of the MolProp::MolecularGraphProperty::FUNCTIONAL_GROUPS property of molgraph.

Parameters

molgraph The molecular graph.

Returns: A const reference to the functional-groups fragment list.

Since: 1.3

◆ setFunctionalGroups()

CDPL_MOLPROP_API void CDPL::MolProp::setFunctionalGroups	(	Chem::MolecularGraph &	molgraph,
		const Chem::FragmentList::SharedPointer &	fg_list
	)

Sets the value of the MolProp::MolecularGraphProperty::FUNCTIONAL_GROUPS property of molgraph.

Parameters

molgraph	The molecular graph.
fg_list	The new functional-groups fragment list.

Since: 1.3

◆ clearFunctionalGroups()

CDPL_MOLPROP_API void CDPL::MolProp::clearFunctionalGroups ( Chem::MolecularGraph & molgraph )

Removes the MolProp::MolecularGraphProperty::FUNCTIONAL_GROUPS property from molgraph.

Parameters

molgraph The molecular graph.

Since: 1.3

◆ hasFunctionalGroups()

CDPL_MOLPROP_API bool CDPL::MolProp::hasFunctionalGroups ( const Chem::MolecularGraph & molgraph )

Tells whether molgraph carries an explicit MolProp::MolecularGraphProperty::FUNCTIONAL_GROUPS property.

Parameters

molgraph The molecular graph.

Returns: true if the FUNCTIONAL_GROUPS property is set, and false otherwise.

Since: 1.3

◆ perceiveFunctionalGroups() [1/2]

CDPL_MOLPROP_API Chem::FragmentList::SharedPointer CDPL::MolProp::perceiveFunctionalGroups ( const Chem::MolecularGraph & molgraph )

Perceives the functional groups of molgraph using MolProp::FunctionalGroupList.

Parameters

molgraph The molecular graph.

Returns: A shared pointer to the perceived functional-groups fragment list.

Since: 1.3

◆ perceiveFunctionalGroups() [2/2]

CDPL_MOLPROP_API Chem::FragmentList::SharedPointer CDPL::MolProp::perceiveFunctionalGroups	(	Chem::MolecularGraph &	molgraph,
		bool	overwrite
	)

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

Parameters

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

Returns: A shared pointer to the perceived functional-groups fragment list.

Since: 1.3

Namespaces

Classes

Functions

Detailed Description

Function Documentation

◆ calcExplicitMass()

◆ calcExplicitMassComposition()

◆ generateExplicitMassCompositionString()

◆ generateExplicitMolecularFormula()

◆ generateExplicitElementHistogram()

◆ getExplicitAtomCount() [1/3]

◆ getExplicitAtomCount() [2/3]

◆ getExplicitChainAtomCount() [1/2]

◆ getRingAtomCount() [1/2]

◆ getAromaticAtomCount() [1/2]

◆ getHeavyAtomCount() [1/2]

◆ getNetFormalCharge()

◆ calcDipoleMoment() [1/2]

◆ calcDipoleMoment() [2/2]

◆ getHydrophobicity()

◆ setHydrophobicity()

◆ clearHydrophobicity()

◆ hasHydrophobicity()

◆ getPEOESigmaCharge()

◆ setPEOESigmaCharge()

◆ clearPEOESigmaCharge()

◆ hasPEOESigmaCharge()

◆ getPEOESigmaElectronegativity()

◆ setPEOESigmaElectronegativity()

◆ clearPEOESigmaElectronegativity()

◆ hasPEOESigmaElectronegativity()

◆ getMHMOPiCharge()

◆ setMHMOPiCharge()

◆ clearMHMOPiCharge()

◆ hasMHMOPiCharge()

◆ getHBondDonorType()

◆ setHBondDonorType()

◆ clearHBondDonorType()

◆ hasHBondDonorType()

◆ getHBondAcceptorType()

◆ setHBondAcceptorType()

◆ clearHBondAcceptorType()

◆ hasHBondAcceptorType()

◆ isInRing() [1/2]

◆ isInRingOfSize() [1/2]

◆ getNumContainingSSSRRings() [1/2]

◆ getAtomicWeight()

◆ getIUPACGroup()

◆ getPeriod()

◆ getVdWRadius()

◆ getCovalentRadius()

◆ getAllredRochowElectronegativity()

◆ getElementName()

◆ getElementValenceElectronCount()

◆ isChemicalElement()

◆ isMainGroupElement()

◆ isMetal()

◆ isTransitionMetal()

◆ isNonMetal()

◆ isSemiMetal()

◆ isHalogen()

◆ isNobleGas()

◆ isOrdinaryHydrogen()

◆ isHeavy()

◆ isUnsaturated()

◆ isHBondAcceptor()

◆ isHBondDonor()

◆ isCarbonylLike()

◆ isAmideCenter()

◆ isAmideNitrogen()

◆ isInvertibleNitrogen()

◆ isPlanarNitrogen()

◆ isBridgehead()

◆ isSpiroCenter()

◆ getOrdinaryHydrogenCount() [1/2]

◆ getExplicitAtomCount() [3/3]

◆ getAtomCount() [1/3]

◆ getExplicitChainAtomCount() [2/2]

◆ getChainAtomCount() [1/2]

◆ getRingAtomCount() [2/2]