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.