Chemical Terms

Back to index pageThere are functions that are not listed in the JChemExcel.Functions list but they are available by choosing the JCChemicalTerms function.

Function Arguments

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

- Molecule: 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 1 molecule, it can be specified with this index, which one of them should be displayed.

Note: 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 JCAtomNumberImage function.)

Examples

Example 1: You want to calculate the number of tautomers and display the structure of each tautomer. The number of tautomers can be calculated with JCTautomerCount, the structure of tautomers can be calculated with JCChemicalTerms function allTautomers expression.

1. Select JCTautomerCount and calculate the number of tautomers for each molecule.

2. To calculate the structures of each tautomer select JCChemicalTerms function:

and specify all arguments. If you want to calculate the structure of the first tautomer specify "1" as the value of ResultIndex, if you specify "smiles" in ResultFormat field, the structure of the first tautomer will be displayed in SMILES.

The structure of the first tautomer for each molecule are calculated and displayed in column C. You can calculate the structure of the second tautomer by specifying 2 in ResultIndex field.

If the molecule has more than 1 tautomer the structure of the second tautomer is displayed in column D. If the molecule has only one tautomer, an error message appears.

You can calculate all tautomer structures (in this example, 11) and display the results in many other formats like: mrv, smiles, cxsmiles, iupac name, inchi, smarts, cxsmarts. The usage of these can be found here:

http://www.chemaxon.com/marvin/help/chemicalterms/EvaluatorFunctions.html

By using the From Text button in the ribbon, these formats can easily be converted to structure.

Example 2: You want to calculate the electron density value of atom 2 of the input molecule.

Select the JCChemicalTerms JChem Excel function.

Specify the input molecule, the function name and the atom number on the Function Arguments form.

Click OK to calculate the required value.

Example 3: You want to calculate the van der Waals surface area of the input molecule.

Select the JCChemicalTerms JChem Excel function.

Specify the input molecule and the function name on the Function Arguments form.

Click OK to calculate the required value.

Example 4: You want to check if the input molecule contains any query features.

Select the JCChemicalTerms JChem Excel function.

Specify the input molecule and the function name on the Function Arguments form.

Click OK to check.

Example 5: You want to check if atoms 1 and 2 are connected by a ring bond in the input molecule.

Select the JCChemicalTerms JChem Excel function.

Specify the input molecule, the function name and atom numbers on the Function Arguments form.

Click OK to check.

Detailed information about the Chemical Terms can be found via this link:

http://www.chemaxon.com/marvin/help/chemicalterms/EvaluatorFunctions.html

The following functions are available only by choosing the JCChemicalTerms function:

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 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 an asymmetric atom

atomicNumber - returns the atomic number

averagePolarizability - calculates 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 given size

chainBond - checks if two atoms are connected by a chain bond

charge - calculates partial charges on atoms for result types "aromaticsystem" / "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 given size

fusedAromaticRingCountOfSize - calculates the number of fused aromatic rings of given size

hasAromatizationError - determines if there is error in the aromatization of the molecule

hasIsotope - determines if any atom in the molecule is a specific isotope of the element

hasRadical - determines if any atom in the molecule has 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 given size

heteroaromaticRingCountOfSize - calculates the number of aromatic heterocyclic rings of given size

heteroRingCountOfSize - calculates the number of heterocyclic rings of given size

hmoChargeDensity - calculates the HMO charge density of atoms

hmoElectronDensity - calculates the HMO electron density of atoms

hmoElectrophilicityOrder - calculates 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 specified pH using method "KLOP"

logDPHYS - calculates logD at specified pH using method "PHYS"

logDVG - calculates logD at specified pH using method "VG"

logDWeighted - calculates logD at specified pH using 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 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 string, no enumeration is done

mmff94Energy - returns the MMFF94 energy of the input molecule

nucleophilicity - calculates 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" / "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

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