Chemical Terms in JChem for Excel

    Some functions are not listed under JChemExcel.Functions but are available by choosing the JCChemicalTerms function.

    Function Arguments

    The following arguments have to be determined in case of each function:

    • Molecule: The molecule string or JChem for Excel structure on which the calculation will be performed.

    • Expression: The function name you want to use.

    The following arguments can be used only with a few functions:

    • ResultIndex: If the calculation algorithm results in more than one molecule, it can be specified with this index, which one of them should be displayed. If the value of this index exceeds this range, the following error message appears: Index out of the molecule list range!

    • ResultFormat: Here can be specified in which format should be the results displayed. If this field remains empty, the results will be returned in CXSMILES by default.

    • Atom Number(s): Depending on the applied expression, atom numbers can be visualized with the JCAtomNumberImage function.

    For more information regarding the Chemical Terms, see Chemical Terms Evaluator.

    The functions below are available only if the JCChemicalTerms function is chosen.

    Function Description
    acidicpKaUseCorrection Calculates acidic pKa values using the correction library.
    aliphaticAtom Checks if the specified atom is aliphatic.
    arom Returns if the atom has an aromatic bond.
    ASAHydrophobic Calculates the water accessible molecular surface area of all hydrophobic atoms.
    ASANegative Calculates the water accessible molecular surface area of all atoms with a negative partial charge.
    ASAPlus Calculates the water accessible molecular surface area of all atoms with positive partial charge.
    ASAPolar Calculates the water accessible molecular surface area of all polar atoms.
    asymmetricAtoms Checks if the specified atom is asymmetric.
    atomicNumber Returns the atomic number.
    averagePolarizability Calculates the average molecular polarizability component considering 3D geometry.
    axxPol Calculates principal component of polarizability tensor (a(xx), a(yy), a(zz)).
    ayyPol Calculates principal component of polarizability tensor (a(xx), a(yy), a(zz)).
    azzPol Calculates principal component of polarizability tensor (a(xx), a(yy), a(zz)).
    basicpKaUseCorrection Calculates basic pKa values using the correction library.
    carboaliphaticRingCount Calculates the number of carboaliphatic rings in the molecule.
    carboRingCountOfSize Calculates the number of carbocyclic rings of a given size.
    chainBond Checks if two atoms are connected by a chain bond.
    charge Calculates partial charges on atoms for result types aromaticsystem and aromaticring, calculates the sum of partial charges of the atoms in the aromatic system / smallest aromatic ring containing the atom.
    chargeDensity Calculates the charge density of atoms.
    chiralCenters Determines the chiral center atoms.
    connections Returns the bond plus implicit H count of an atom.
    count Determines the number of elements in an array.
    electronDensity Calculates the electron density of atoms.
    electrophilicity Calculates electrophilicity of atoms.
    electrophilicityOrder Calculates E(+) order of atoms.
    formula Returns the formula.
    fusedAliphaticRingCountOfSize Calculates the number of fused aliphatic rings of a given size.
    fusedAromaticRingCountOfSize Calculates the number of fused aromatic rings of a given size.
    hasAromatizationError Determines if there is an error in the aromatization of the molecule.
    hasIsotope Determines if any of the atoms in the molecule are a specific isotope of the element.
    hasRadical Determines if any of the atoms in the molecule have radical.
    hCount Returns the hydrogen count of an atom.
    heteroaliphaticRingCount Calculates the number of aliphatic heterocyclic rings.
    heteroaliphaticRingCountOfSize Calculates the number of aliphatic heterocyclic rings of a given size.
    heteroaromaticRingCountOfSize Calculates the number of aromatic heterocyclic rings of a given size.
    heteroRingCountOfSize Calculates the number of heterocyclic rings of a given size.
    hmoChargeDensity Calculates the HMO charge density of atoms.
    hmoElectronDensity Calculates the HMO electron density of atoms.
    hmoElectrophilicityOrder Calculates the HMO E(+) order of atoms.
    hmoElectrophilicLocalizationEnergy Calculates HMO localization energy L(+) of atoms.
    hmoNucleophilicityOrder Calculates HMO Nu(-) order of atoms.
    hmoNucleophilicLocalizationEnergy Calculates HMO localization energy L(-) of atoms.
    hmoPiEnergy Calculates the HMO pi energy of the molecule.
    isMarkush Decides whether the given molecule contains any Markush features.
    isQuery Decides whether the given molecule contains any query features.
    largestRing Identifies the atoms of the largest ring (number of atoms) in the molecule.
    largestRingSystem Identifies the atoms of the largest ring system (number of rings) in the molecule.
    logDKLOP Calculates logD at a specified pH using method KLOP.
    logDPHYS Calculates logD at a specified pH using method PHYS.
    logDVG Calculates logD at a specified pH using method VG.
    logDWeighted Calculates logD at a specified pH using a weighted method.
    logPincrement Calculates the atomic logP increment.
    logPKLOP Calculates logP using method KLOP.
    logPPHYS Calculates logP using method PHYS.
    logPVG Calculates logP using method VG.
    logPWeighted Calculates logP using a weighted method.
    map Returns the atom map number.
    markushLibraryMagnitude Calculates the Markush library magnitude, no enumeration is done.
    markushLibrarySize Calculates the Markush library size, no enumeration is done.
    markushLibrarySizeAsString Calculates the Markush library size and returns it as a string, no enumeration is done.
    mmff94Energy Returns the MMFF94 energy of the input molecule.
    nucleophilicity Calculates the nucleophilicity of atoms.
    nucleophilicityOrder Calculates Nu(-) order of atoms.
    pair Converts two atoms or 0-based atom indexes into an index1-index2 1-based atom index setter string.
    piOrbitalElectronegativity Calculates atomic pi orbital electronegativity.
    pKa Calculates pKa values.
    pKaUseCorrection Calculates pKa values using the correction library.
    radicalCount Returns the radical count of an atom.
    resonantCharge Calculates partial charges on atoms considering resonance effect for result types aromaticsystem and aromaticring, calculates the sum of partial charges of the atoms in the aromatic system / smallest aromatic ring containing the atom.
    ringBond Checks if two atoms are connected by a ring bond.
    rotatableBond Checks if two atoms are connected by a rotatable bond.
    smallestRing Identifies the atoms of the smallest ring (number of atoms) in the molecule.
    smallestRingSystem Identifies the atoms of the smallest ring system (number of rings) in the molecule.
    stereoDoubleBondCount Calculates the number of stereo double bonds.
    stereoisomer Generates a stereoisomer of the molecule.
    tetrahedralStereoisomer Generates a tetrahedral stereoisomer of the molecule.
    topologicalPolarSurfaceArea Calculates the topological polar surface area (2D).
    vanDerWaalsSurfaceArea Calculates the van der Waals surface area.
    waterAccessibleSurfaceArea Calculates the water accessible molecular surface area.
    solventAccessibleSurfaceArea Calculates the solvent-accessible molecular surface area.
    whereIsValenceError Returns the index of the first atom with valence error, or -1 if there is no valence error.
    wienerPolarity Calculates the Wiener polarity.