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

Namespaces
	AtomProperty
	Provides keys for built-in Chem::Atom properties.

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

	BondProperty
	Provides keys for built-in 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
	Implements the perception of H-bond acceptor atom types (see namespace MolProp::HBondAcceptorAtomType). More...

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

class	LogSCalculator
	Calculation of the aqueous solubility ( \( \log S \)) of molecular graphs using the atom-contribution method of Hou, Xia, Zhang and Xu [LOGS]. 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 π-electron densities, π-charges, π-bond orders and the total π-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 σ 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 XLogP method of Wang, Gao and Lai [XLOGP]. 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 the atom atom. More...

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

CDPL_MOLPROP_API void	clearHydrophobicity (Chem::Atom &atom)
	Clears the value of the MolProp::AtomProperty::HYDROPHOBICITY property of the atom atom. More...

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

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

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

CDPL_MOLPROP_API void	clearPEOESigmaCharge (Chem::Atom &atom)
	Clears the value of the MolProp::AtomProperty::PEOE_SIGMA_CHARGE property of the atom atom. More...

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

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

CDPL_MOLPROP_API void	clearPEOESigmaElectronegativity (Chem::Atom &atom)
	Clears the value of the MolProp::AtomProperty::PEOE_SIGMA_ELECTRONEGATIVITY property of the atom atom. More...

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

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

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

CDPL_MOLPROP_API void	clearMHMOPiCharge (Chem::Atom &atom)
	Clears the value of the MolProp::AtomProperty::MHMO_PI_CHARGE property of the atom atom. More...

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

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

CDPL_MOLPROP_API void	clearHBondDonorType (Chem::Atom &atom)
	Clears the value of the MolProp::AtomProperty::H_BOND_DONOR_TYPE property of the atom atom. More...

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

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

CDPL_MOLPROP_API void	clearHBondAcceptorType (Chem::Atom &atom)
	Clears the value of the MolProp::AtomProperty::H_BOND_ACCEPTOR_TYPE property of the atom atom. More...

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

CDPL_MOLPROP_API bool	isNobleGas (const Chem::Atom &atom)
	Tells whether the chemical element associated with the atom 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 the atom atom is an ordinary hydrogen. More...

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

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

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

CDPL_MOLPROP_API bool	isHBondDonor (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph)
	Tells whether the atom atom acts as an H-bond donor in the molecular graph 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 the atom atom is a carbonyl-like center in the molecular graph 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 the atom atom is the center of an amide group in the molecular graph 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 the atom atom is the nitrogen of an amide group in the molecular graph molgraph. More...

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

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

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

CDPL_MOLPROP_API bool	isSpiroCenter (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph)
	Tells whether the atom atom is a spiro center in the molecular graph 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 the atom atom in the molecular graph molgraph. 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 the atom atom in the molecular graph molgraph whose type 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 the atom atom in the molecular graph molgraph (including implicit hydrogens) whose type 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 the atom atom in the molecular graph 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 the atom atom in the molecular graph 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 the atom atom in the molecular graph molgraph. More...

CDPL_MOLPROP_API std::size_t	getAromaticAtomCount (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph)
	Returns the number of aromatic neighbors of the atom atom in the molecular graph 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 the atom atom in the molecular graph 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 the atom atom in the molecular graph 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 the atom atom in the molecular graph 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 the atom atom that bond to atoms whose type 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 the atom atom in the molecular graph 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 the atom 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 the atom atom that bond to atoms whose type 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 the atom atom in the molecular graph 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 the atom atom in the molecular graph 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 the atom atom in the molecular graph 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 the atom atom in the molecular graph 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 the atom atom in the molecular graph 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 the atom atom in the molecular graph molgraph. More...

CDPL_MOLPROP_API std::size_t	calcExplicitValence (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph)
	Calculates the explicit valence of the atom atom in the molecular graph 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 the atom atom in the molecular graph 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 valence electrons of the atom atom in the molecular graph molgraph that are not involved in bonds. More...

CDPL_MOLPROP_API std::size_t	calcValenceElectronCount (const 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...

CDPL_MOLPROP_API std::size_t	calcStericNumber (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph)
	Calculates the steric number of the atom atom in the molecular graph 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 the atom atom in the molecular graph molgraph. More...

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

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

CDPL_MOLPROP_API double	calcTotalPartialCharge (const Chem::Atom &atom)
	Calculates the total partial charge of the atom atom. More...

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

CDPL_MOLPROP_API double	calcPiElectronegativity (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph)
	Calculates the π-electronegativity of the atom atom in the molecular graph 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 the atom atom in the molecular graph 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 the bond bond. More...

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

CDPL_MOLPROP_API void	clearMHMOPiOrder (Chem::Bond &bond)
	Clears the value of the MolProp::BondProperty::MHMO_PI_ORDER property of the bond bond. More...

CDPL_MOLPROP_API bool	hasMHMOPiOrder (const Chem::Bond &atom)
	Tells whether the MolProp::BondProperty::MHMO_PI_ORDER property of the bond bond is set. More...

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

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

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

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

CDPL_MOLPROP_API bool	isHydrogenRotor (const Chem::Bond &bond, const Chem::MolecularGraph &molgraph)
	Tells whether the bond 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 the bond bond is a heteroatom hydrogen-only rotor. 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 the bond bond is rotatable. More...

CDPL_MOLPROP_API bool	isHydrogenBond (const Chem::Bond &bond)
	Tells whether the bond 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 the molecular graph molgraph. More...

CDPL_MOLPROP_API double	calcMass (const Chem::MolecularGraph &molgraph)
	Calculates the total molecular mass of the molecular graph 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 the molecular graph 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 the molecular graph 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 the molecular graph molgraph. More...

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

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

CDPL_MOLPROP_API std::size_t	getAtomCount (const Chem::MolecularGraph &molgraph)
	Returns the total number of atoms in the molecular graph 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 the molecular graph molgraph whose type property matches type. More...

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

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

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

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

CDPL_MOLPROP_API std::size_t	getBondCount (const Chem::MolecularGraph &molgraph)
	Returns the total number of bonds in the molecular graph 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 the molecular graph 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 the molecular graph 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 the molecular graph 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 the molecular graph molgraph. More...

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

CDPL_MOLPROP_API double	calcXLogP (const Chem::MolecularGraph &molgraph)
	Calculates the \( \log P \) value of the molecular graph molgraph using MolProp::XLogPCalculator. More...

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

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

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

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

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

CDPL_MOLPROP_API void	calcMHMOProperties (Chem::MolecularGraph &molgraph, bool overwrite)
	Calculates MHMO π-charges and π-bond orders for the molecular graph 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 the molecular graph 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 the molecular graph 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 the molecular graph 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 the molecular graph 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 the molecular graph molgraph to fg_list. More...

CDPL_MOLPROP_API void	clearFunctionalGroups (Chem::MolecularGraph &molgraph)
	Clears the value of the MolProp::MolecularGraphProperty::FUNCTIONAL_GROUPS property of the molecular graph molgraph. More...

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

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

CDPL_MOLPROP_API Chem::FragmentList::SharedPointer	perceiveFunctionalGroups (Chem::MolecularGraph &molgraph, bool overwrite)
	Perceives the functional groups of the molecular graph 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 the atom atom.

Parameters

atom	The atom for which to return the property value.

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 the atom atom to hyd.

Parameters

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

◆ clearHydrophobicity()

CDPL_MOLPROP_API void 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.

◆ hasHydrophobicity()

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

◆ getPEOESigmaCharge()

CDPL_MOLPROP_API double CDPL::MolProp::getPEOESigmaCharge ( const 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 σ-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 the atom atom to charge.

Parameters

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

◆ clearPEOESigmaCharge()

CDPL_MOLPROP_API void 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.

◆ hasPEOESigmaCharge()

CDPL_MOLPROP_API bool CDPL::MolProp::hasPEOESigmaCharge ( const 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 σ-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 the atom atom.

Parameters

atom	The atom for which to return the property value.

Returns: The PEOE σ-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 the atom atom to e_neg.

Parameters

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

◆ clearPEOESigmaElectronegativity()

CDPL_MOLPROP_API void 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.

◆ hasPEOESigmaElectronegativity()

CDPL_MOLPROP_API bool CDPL::MolProp::hasPEOESigmaElectronegativity ( const 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 σ-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 the atom atom.

Parameters

atom	The atom for which to return the property value.

Returns: The MHMO π-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 the atom atom to charge.

Parameters

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

◆ clearMHMOPiCharge()

CDPL_MOLPROP_API void 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.

◆ hasMHMOPiCharge()

CDPL_MOLPROP_API bool CDPL::MolProp::hasMHMOPiCharge ( const 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 π-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 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).

◆ 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 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).

◆ clearHBondDonorType()

CDPL_MOLPROP_API void 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.

◆ hasHBondDonorType()

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

◆ 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 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).

◆ 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 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).

◆ clearHBondAcceptorType()

CDPL_MOLPROP_API void 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.

◆ hasHBondAcceptorType()

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

◆ isInRing() [1/2]

CDPL_MOLPROP_API bool CDPL::MolProp::isInRing	(	const Chem::Atom &	atom,
		const 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.

◆ isInRingOfSize() [1/2]

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

◆ 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 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.

◆ getAtomicWeight()

CDPL_MOLPROP_API double CDPL::MolProp::getAtomicWeight ( const 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.

◆ 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 the atom 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 the atom 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 the atom 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 the atom 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 the atom 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 the atom 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 the atom 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 the atom atom represents a chemical element.

Parameters

atom The atom.

Returns: true if the atom 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 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()

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

◆ isTransitionMetal()

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

◆ isNonMetal()

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

◆ isSemiMetal()

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

◆ isHalogen()

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

◆ isNobleGas()

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

◆ isOrdinaryHydrogen()

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

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.

◆ isHeavy()

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

◆ isUnsaturated()

CDPL_MOLPROP_API bool CDPL::MolProp::isUnsaturated	(	const Chem::Atom &	atom,
		const 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.

◆ isHBondAcceptor()

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

CDPL_MOLPROP_API bool CDPL::MolProp::isHBondDonor	(	const Chem::Atom &	atom,
		const 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.

◆ 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 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

◆ 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 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()

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 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.

◆ isInvertibleNitrogen()

CDPL_MOLPROP_API bool CDPL::MolProp::isInvertibleNitrogen	(	const Chem::Atom &	atom,
		const 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.

◆ isPlanarNitrogen()

CDPL_MOLPROP_API bool CDPL::MolProp::isPlanarNitrogen	(	const Chem::Atom &	atom,
		const 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.

◆ isBridgehead()

CDPL_MOLPROP_API bool CDPL::MolProp::isBridgehead	(	const Chem::Atom &	atom,
		const 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

◆ isSpiroCenter()

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

◆ 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 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".

◆ 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 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.

◆ 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 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.

◆ 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 the atom atom in the molecular graph 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 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.

◆ 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 the atom atom in the molecular graph 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 the atom atom in the molecular graph 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 the atom atom in the molecular graph 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 the atom atom in the molecular graph 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 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]

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 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.

◆ 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 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]

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 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]

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 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.

◆ 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 the atom atom in the molecular graph 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 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.

◆ 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 the atom atom in the molecular graph 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 the atom atom in the molecular graph 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 the atom atom in the molecular graph 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 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.

◆ calcExplicitValence()

CDPL_MOLPROP_API std::size_t CDPL::MolProp::calcExplicitValence	(	const Chem::Atom &	atom,
		const 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.

◆ calcValence()

CDPL_MOLPROP_API std::size_t CDPL::MolProp::calcValence	(	const Chem::Atom &	atom,
		const 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.

◆ calcFreeValenceElectronCount()

CDPL_MOLPROP_API std::size_t CDPL::MolProp::calcFreeValenceElectronCount	(	const Chem::Atom &	atom,
		const 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.

◆ 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 the atom 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 the atom atom in the molecular graph 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 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).

◆ 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 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).

◆ getHybridPolarizability()

CDPL_MOLPROP_API double CDPL::MolProp::getHybridPolarizability	(	const Chem::Atom &	atom,
		const 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.

◆ 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 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]

◆ calcTotalPartialCharge()

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

Calculates the total partial charge of the atom atom.

The total partial charge is calculated as the sum of stored PEOE σ- and MHMO π-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 the atom atom in the molecular graph 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 π-electronegativity of the atom atom in the molecular graph molgraph.

Parameters

atom	The atom.
molgraph	The molecular graph.

Returns: The π-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 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.

◆ 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 the bond bond.

Parameters

bond	The bond for which to return the property value.

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 the bond bond to order.

Parameters

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

◆ clearMHMOPiOrder()

CDPL_MOLPROP_API void 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.

◆ hasMHMOPiOrder()

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

Tells whether the MolProp::BondProperty::MHMO_PI_ORDER property of the bond bond is set.

Parameters

atom	The bond for which to query the property value.

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 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.

◆ isInRing() [2/2]

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

Tells whether the bond bond is part of any ring of the molecular graph 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 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.

◆ 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 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.

◆ isHydrogenRotor()

CDPL_MOLPROP_API bool CDPL::MolProp::isHydrogenRotor	(	const Chem::Bond &	bond,
		const 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.

◆ isHeteroAtomHydrogenRotor()

CDPL_MOLPROP_API bool CDPL::MolProp::isHeteroAtomHydrogenRotor	(	const Chem::Bond &	bond,
		const 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.

◆ 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 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.

◆ isHydrogenBond()

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

◆ 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 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.

◆ calcMass()

CDPL_MOLPROP_API double CDPL::MolProp::calcMass ( const 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.

◆ calcMassComposition()

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

◆ 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 the molecular graph 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 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 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.

◆ calcCyclomaticNumber()

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

◆ getAtomCount() [2/3]

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

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 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

◆ getImplicitHydrogenCount()

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

◆ 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 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".

◆ 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 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".

◆ 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 the molecular graph 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 the molecular graph 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 the molecular graph 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 the molecular graph 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 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.

◆ getHydrogenBondCount()

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

◆ 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 the molecular graph 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 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.

◆ getComponentCount()

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

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

Parameters

molgraph The molecular graph.

Returns: The component count.

◆ calcXLogP()

CDPL_MOLPROP_API double CDPL::MolProp::calcXLogP ( const 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]

◆ calcLogS()

CDPL_MOLPROP_API double CDPL::MolProp::calcLogS ( const 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]

◆ calcTPSA()

CDPL_MOLPROP_API double CDPL::MolProp::calcTPSA ( const 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]

◆ getRuleOfFiveScore()

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

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

◆ calcMeanPolarizability()

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

Calculates the mean atomic polarizability of the molecular graph 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 σ-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.

◆ calcMHMOProperties()

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

Calculates MHMO π-charges and π-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.

◆ calcAtomHydrophobicities()

CDPL_MOLPROP_API void 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].

◆ perceiveHBondDonorAtomTypes()

CDPL_MOLPROP_API void 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.

◆ perceiveHBondAcceptorAtomTypes()

CDPL_MOLPROP_API void 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.

◆ 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 the molecular graph molgraph.

Parameters

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

Returns: A const shared pointer to the functional group 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 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

◆ clearFunctionalGroups()

CDPL_MOLPROP_API void 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

◆ hasFunctionalGroups()

CDPL_MOLPROP_API bool CDPL::MolProp::hasFunctionalGroups ( const 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

◆ perceiveFunctionalGroups() [1/2]

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

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

Parameters

molgraph The molecular graph.

Returns: A shared pointer to the perceived functional group 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 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 pointer to the perceived functional group 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]