Contains classes and functions related to the calculation/preciction of physicochemical molecular properties.
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CDPL_MOLPROP_API double | calcExplicitMass (const Chem::AtomContainer &cntnr) |
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CDPL_MOLPROP_API void | calcExplicitMassComposition (const Chem::AtomContainer &cntnr, MassComposition &mass_comp) |
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CDPL_MOLPROP_API void | generateExplicitMassCompositionString (const Chem::AtomContainer &cntnr, std::string &comp_str) |
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CDPL_MOLPROP_API void | generateExplicitMolecularFormula (const Chem::AtomContainer &cntnr, std::string &formula) |
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CDPL_MOLPROP_API void | generateExplicitElementHistogram (const Chem::AtomContainer &cntnr, ElementHistogram &hist, bool append=false) |
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CDPL_MOLPROP_API std::size_t | getExplicitAtomCount (const Chem::AtomContainer &cntnr) |
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CDPL_MOLPROP_API std::size_t | getExplicitAtomCount (const Chem::AtomContainer &cntnr, unsigned int type, bool strict=true) |
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CDPL_MOLPROP_API std::size_t | getExplicitChainAtomCount (const Chem::AtomContainer &cntnr) |
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CDPL_MOLPROP_API std::size_t | getRingAtomCount (const Chem::AtomContainer &cntnr) |
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CDPL_MOLPROP_API std::size_t | getAromaticAtomCount (const Chem::AtomContainer &cntnr) |
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CDPL_MOLPROP_API std::size_t | getHeavyAtomCount (const Chem::AtomContainer &cntnr) |
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CDPL_MOLPROP_API long | getNetFormalCharge (const Chem::AtomContainer &cntnr) |
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CDPL_MOLPROP_API bool | calcDipoleMoment (const Chem::AtomContainer &cntnr, const Chem::Atom3DCoordinatesFunction &coords_func, Math::Vector3D &moment) |
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CDPL_MOLPROP_API bool | calcDipoleMoment (const Chem::AtomContainer &cntnr, Math::Vector3D &moment) |
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CDPL_MOLPROP_API double | getHydrophobicity (const Chem::Atom &atom) |
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CDPL_MOLPROP_API void | setHydrophobicity (Chem::Atom &atom, double hyd) |
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CDPL_MOLPROP_API void | clearHydrophobicity (Chem::Atom &atom) |
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CDPL_MOLPROP_API bool | hasHydrophobicity (const Chem::Atom &atom) |
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CDPL_MOLPROP_API double | getPEOESigmaCharge (const Chem::Atom &atom) |
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CDPL_MOLPROP_API void | setPEOESigmaCharge (Chem::Atom &atom, double charge) |
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CDPL_MOLPROP_API void | clearPEOESigmaCharge (Chem::Atom &atom) |
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CDPL_MOLPROP_API bool | hasPEOESigmaCharge (const Chem::Atom &atom) |
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CDPL_MOLPROP_API double | getPEOESigmaElectronegativity (const Chem::Atom &atom) |
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CDPL_MOLPROP_API void | setPEOESigmaElectronegativity (Chem::Atom &atom, double e_neg) |
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CDPL_MOLPROP_API void | clearPEOESigmaElectronegativity (Chem::Atom &atom) |
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CDPL_MOLPROP_API bool | hasPEOESigmaElectronegativity (const Chem::Atom &atom) |
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CDPL_MOLPROP_API double | getMHMOPiCharge (const Chem::Atom &atom) |
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CDPL_MOLPROP_API void | setMHMOPiCharge (Chem::Atom &atom, double charge) |
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CDPL_MOLPROP_API void | clearMHMOPiCharge (Chem::Atom &atom) |
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CDPL_MOLPROP_API bool | hasMHMOPiCharge (const Chem::Atom &atom) |
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CDPL_MOLPROP_API unsigned int | getHBondDonorType (const Chem::Atom &atom) |
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CDPL_MOLPROP_API void | setHBondDonorType (Chem::Atom &atom, unsigned int type) |
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CDPL_MOLPROP_API void | clearHBondDonorType (Chem::Atom &atom) |
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CDPL_MOLPROP_API bool | hasHBondDonorType (const Chem::Atom &atom) |
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CDPL_MOLPROP_API unsigned int | getHBondAcceptorType (const Chem::Atom &atom) |
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CDPL_MOLPROP_API void | setHBondAcceptorType (Chem::Atom &atom, unsigned int type) |
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CDPL_MOLPROP_API void | clearHBondAcceptorType (Chem::Atom &atom) |
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CDPL_MOLPROP_API bool | hasHBondAcceptorType (const Chem::Atom &atom) |
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CDPL_MOLPROP_API bool | isInRing (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph) |
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CDPL_MOLPROP_API bool | isInRingOfSize (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph, std::size_t size) |
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CDPL_MOLPROP_API std::size_t | getNumContainingSSSRRings (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph) |
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CDPL_MOLPROP_API double | getAtomicWeight (const Chem::Atom &atom) |
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CDPL_MOLPROP_API std::size_t | getIUPACGroup (const Chem::Atom &atom) |
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CDPL_MOLPROP_API std::size_t | getPeriod (const Chem::Atom &atom) |
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CDPL_MOLPROP_API double | getVdWRadius (const Chem::Atom &atom) |
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CDPL_MOLPROP_API double | getCovalentRadius (const Chem::Atom &atom, std::size_t order) |
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CDPL_MOLPROP_API double | getAllredRochowElectronegativity (const Chem::Atom &atom) |
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CDPL_MOLPROP_API const std::string & | getElementName (const Chem::Atom &atom) |
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CDPL_MOLPROP_API std::size_t | getElementValenceElectronCount (const Chem::Atom &atom) |
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CDPL_MOLPROP_API bool | isChemicalElement (const Chem::Atom &atom) |
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CDPL_MOLPROP_API bool | isMainGroupElement (const Chem::Atom &atom) |
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CDPL_MOLPROP_API bool | isMetal (const Chem::Atom &atom) |
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CDPL_MOLPROP_API bool | isTransitionMetal (const Chem::Atom &atom) |
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CDPL_MOLPROP_API bool | isNonMetal (const Chem::Atom &atom) |
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CDPL_MOLPROP_API bool | isSemiMetal (const Chem::Atom &atom) |
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CDPL_MOLPROP_API bool | isHalogen (const Chem::Atom &atom) |
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CDPL_MOLPROP_API bool | isNobleGas (const Chem::Atom &atom) |
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CDPL_MOLPROP_API bool | isOrdinaryHydrogen (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph, unsigned int flags=Chem::AtomPropertyFlag::DEFAULT) |
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CDPL_MOLPROP_API bool | isHeavy (const Chem::Atom &atom) |
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CDPL_MOLPROP_API bool | isUnsaturated (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph) |
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CDPL_MOLPROP_API bool | isHBondAcceptor (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph) |
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CDPL_MOLPROP_API bool | isHBondDonor (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph) |
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CDPL_MOLPROP_API bool | isCarbonylLikeAtom (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph, bool c_only=false, bool db_o_only=false) |
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CDPL_MOLPROP_API bool | isAmideCenterAtom (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph, bool c_only=false, bool db_o_only=false) |
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CDPL_MOLPROP_API bool | isAmideNitrogen (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph, bool c_only=false, bool db_o_only=false) |
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CDPL_MOLPROP_API bool | isInvertibleNitrogen (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph) |
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CDPL_MOLPROP_API bool | isPlanarNitrogen (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph) |
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CDPL_MOLPROP_API std::size_t | getOrdinaryHydrogenCount (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph, unsigned int flags=Chem::AtomPropertyFlag::DEFAULT) |
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CDPL_MOLPROP_API std::size_t | getExplicitAtomCount (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph, unsigned int type, bool strict=true) |
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CDPL_MOLPROP_API std::size_t | getAtomCount (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph, unsigned int type, bool strict=true) |
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CDPL_MOLPROP_API std::size_t | getExplicitChainAtomCount (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph) |
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CDPL_MOLPROP_API std::size_t | getChainAtomCount (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph) |
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CDPL_MOLPROP_API std::size_t | getRingAtomCount (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph) |
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CDPL_MOLPROP_API std::size_t | getAromaticAtomCount (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph) |
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CDPL_MOLPROP_API std::size_t | getHeavyAtomCount (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph) |
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CDPL_MOLPROP_API std::size_t | getExplicitBondCount (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph) |
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CDPL_MOLPROP_API std::size_t | getExplicitBondCount (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph, std::size_t order) |
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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) |
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CDPL_MOLPROP_API std::size_t | getBondCount (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph) |
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CDPL_MOLPROP_API std::size_t | getBondCount (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph, std::size_t order) |
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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) |
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CDPL_MOLPROP_API std::size_t | getExplicitChainBondCount (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph) |
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CDPL_MOLPROP_API std::size_t | getChainBondCount (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph) |
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CDPL_MOLPROP_API std::size_t | getRingBondCount (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph) |
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CDPL_MOLPROP_API std::size_t | getAromaticBondCount (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph) |
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CDPL_MOLPROP_API std::size_t | getHeavyBondCount (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph) |
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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) |
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CDPL_MOLPROP_API std::size_t | calcExplicitValence (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph) |
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CDPL_MOLPROP_API std::size_t | calcValence (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph) |
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CDPL_MOLPROP_API std::size_t | calcFreeValenceElectronCount (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph) |
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CDPL_MOLPROP_API std::size_t | calcValenceElectronCount (const Chem::Atom &atom) |
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CDPL_MOLPROP_API std::size_t | calcStericNumber (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph) |
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CDPL_MOLPROP_API unsigned int | getVSEPRCoordinationGeometry (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph, std::size_t steric_num) |
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CDPL_MOLPROP_API unsigned int | getVSEPRCoordinationGeometry (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph) |
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CDPL_MOLPROP_API double | getHybridPolarizability (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph) |
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CDPL_MOLPROP_API double | calcEffectivePolarizability (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph, double damping=0.75) |
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CDPL_MOLPROP_API double | calcTotalPartialCharge (const Chem::Atom &atom) |
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CDPL_MOLPROP_API double | calcLonePairElectronegativity (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph) |
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CDPL_MOLPROP_API double | calcPiElectronegativity (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph) |
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CDPL_MOLPROP_API double | calcInductiveEffect (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph, std::size_t num_bonds=10) |
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CDPL_MOLPROP_API std::size_t | getExplicitBondCount (const Chem::BondContainer &cntnr) |
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CDPL_MOLPROP_API std::size_t | getExplicitBondCount (const Chem::BondContainer &cntnr, std::size_t order, bool inc_aro=true) |
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CDPL_MOLPROP_API std::size_t | getExplicitHydrogenBondCount (const Chem::BondContainer &cntnr) |
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CDPL_MOLPROP_API std::size_t | getExplicitChainBondCount (const Chem::BondContainer &cntnr) |
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CDPL_MOLPROP_API std::size_t | getRingBondCount (const Chem::BondContainer &cntnr) |
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CDPL_MOLPROP_API std::size_t | getAromaticBondCount (const Chem::BondContainer &cntnr) |
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CDPL_MOLPROP_API std::size_t | getHeavyBondCount (const Chem::BondContainer &cntnr) |
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CDPL_MOLPROP_API double | getMHMOPiOrder (const Chem::Bond &bond) |
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CDPL_MOLPROP_API void | setMHMOPiOrder (Chem::Bond &bond, double order) |
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CDPL_MOLPROP_API void | clearMHMOPiOrder (Chem::Bond &bond) |
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CDPL_MOLPROP_API bool | hasMHMOPiOrder (const Chem::Bond &atom) |
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CDPL_MOLPROP_API double | calcPolarizability (const Chem::Bond &bond, const Chem::MolecularGraph &molgraph, double damping=0.75) |
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CDPL_MOLPROP_API bool | isInRing (const Chem::Bond &Bond, const Chem::MolecularGraph &molgraph) |
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CDPL_MOLPROP_API bool | isInRingOfSize (const Chem::Bond &bond, const Chem::MolecularGraph &molgraph, std::size_t size) |
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CDPL_MOLPROP_API std::size_t | getNumContainingSSSRRings (const Chem::Bond &bond, const Chem::MolecularGraph &molgraph) |
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CDPL_MOLPROP_API bool | isHydrogenRotor (const Chem::Bond &bond, const Chem::MolecularGraph &molgraph) |
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CDPL_MOLPROP_API bool | isHeteroAtomHydrogenRotor (const Chem::Bond &bond, const Chem::MolecularGraph &molgraph) |
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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) |
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CDPL_MOLPROP_API bool | isHydrogenBond (const Chem::Bond &bond) |
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CDPL_MOLPROP_API bool | isAmideBond (const Chem::Bond &bond, const Chem::MolecularGraph &molgraph, bool c_only=false, bool db_o_only=false) |
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CDPL_MOLPROP_API double | calcMass (const Chem::MolecularGraph &molgraph) |
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CDPL_MOLPROP_API void | calcMassComposition (const Chem::MolecularGraph &molgraph, MassComposition &comp) |
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CDPL_MOLPROP_API void | generateMassCompositionString (const Chem::MolecularGraph &molgraph, std::string &comp) |
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CDPL_MOLPROP_API void | generateMolecularFormula (const Chem::MolecularGraph &molgraph, std::string &formula) |
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CDPL_MOLPROP_API void | generateElementHistogram (const Chem::MolecularGraph &molgraph, ElementHistogram &hist, bool append=false) |
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CDPL_MOLPROP_API std::size_t | calcCyclomaticNumber (const Chem::MolecularGraph &molgraph) |
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CDPL_MOLPROP_API std::size_t | getAtomCount (const Chem::MolecularGraph &molgraph) |
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CDPL_MOLPROP_API std::size_t | getAtomCount (const Chem::MolecularGraph &molgraph, unsigned int type, bool strict=true) |
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CDPL_MOLPROP_API std::size_t | getImplicitHydrogenCount (const Chem::MolecularGraph &molgraph) |
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CDPL_MOLPROP_API std::size_t | getOrdinaryHydrogenCount (const Chem::MolecularGraph &molgraph, unsigned int flags=Chem::AtomPropertyFlag::DEFAULT) |
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CDPL_MOLPROP_API std::size_t | getExplicitOrdinaryHydrogenCount (const Chem::MolecularGraph &molgraph, unsigned int flags=Chem::AtomPropertyFlag::DEFAULT) |
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CDPL_MOLPROP_API std::size_t | getChainAtomCount (const Chem::MolecularGraph &molgraph) |
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CDPL_MOLPROP_API std::size_t | getHBondAcceptorAtomCount (const Chem::MolecularGraph &molgraph) |
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CDPL_MOLPROP_API std::size_t | getHBondDonorAtomCount (const Chem::MolecularGraph &molgraph) |
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CDPL_MOLPROP_API std::size_t | getBondCount (const Chem::MolecularGraph &molgraph) |
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CDPL_MOLPROP_API std::size_t | getBondCount (const Chem::MolecularGraph &molgraph, std::size_t order, bool inc_aro=true) |
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CDPL_MOLPROP_API std::size_t | getHydrogenBondCount (const Chem::MolecularGraph &molgraph) |
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CDPL_MOLPROP_API std::size_t | getChainBondCount (const Chem::MolecularGraph &molgraph) |
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CDPL_MOLPROP_API std::size_t | getRotatableBondCount (const Chem::MolecularGraph &molgraph, bool h_rotors=false, bool ring_bonds=false, bool amide_bonds=false) |
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CDPL_MOLPROP_API std::size_t | getComponentCount (const Chem::MolecularGraph &molgraph) |
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CDPL_MOLPROP_API double | calcXLogP (const Chem::MolecularGraph &molgraph) |
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CDPL_MOLPROP_API double | calcLogS (const Chem::MolecularGraph &molgraph) |
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CDPL_MOLPROP_API double | calcTPSA (const Chem::MolecularGraph &molgraph) |
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CDPL_MOLPROP_API std::size_t | getRuleOfFiveScore (const Chem::MolecularGraph &molgraph) |
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CDPL_MOLPROP_API double | calcMeanPolarizability (const Chem::MolecularGraph &molgraph) |
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CDPL_MOLPROP_API void | calcPEOEProperties (Chem::MolecularGraph &molgraph, bool overwrite, std::size_t num_iter=20, double damping=0.48) |
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CDPL_MOLPROP_API void | calcMHMOProperties (Chem::MolecularGraph &molgraph, bool overwrite) |
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CDPL_MOLPROP_API void | calcAtomHydrophobicities (Chem::MolecularGraph &molgraph, bool overwrite, bool from_logp=false) |
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CDPL_MOLPROP_API void | perceiveHBondDonorAtomTypes (Chem::MolecularGraph &molgraph, bool overwrite) |
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CDPL_MOLPROP_API void | perceiveHBondAcceptorAtomTypes (Chem::MolecularGraph &molgraph, bool overwrite) |
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Contains classes and functions related to the calculation/preciction of physicochemical molecular properties.