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. |