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301
Custom Excel Chemical Functions
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.
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Custom Excel Chemical Functions
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.
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Custom Excel Chemical Functions
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.
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Custom Excel Chemical Functions
Specify the input molecule, the function name and atom numbers on
the Function Arguments form.
Click OK to check.
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Custom Excel Chemical Functions
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
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306
Custom Excel Chemical Functions
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
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Custom Excel Chemical Functions
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"
308
Custom Excel Chemical Functions
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
309
Custom Excel Chemical Functions
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
14.2.1.3
Dissimilarity
Computes dissimilarity  values between  two molecules.
JCDissimilarityCFEuclidean
Returns  dissimilarities calculated  with  Euclidean distances based on a
chemical fingerprint. You can find detailed information about this
fingerprint here: 
http://www.chemaxon.com/jchem/doc/user/fingerprint.html
JCDissimilarityCFTanimoto
Returns  dissimilarities calculated  with  Tanimoto distances based  on  a
310
Custom Excel Chemical Functions
chemical fingerprint.
JCDissimilarityPFEuclidean
Returns  dissimilarities calculated  with  Euclidean distances based on a
pharmacophore fingerprint. You can find detailed information about
this fingerprint here:
http://www.chemaxon.com/jchem/doc/user/PFp2D.html
JCDissimilarityPFTanimoto
Returns  dissimilarities calculated  with  Tanimoto distances based  on  a
pharmacophore fingerprint.
JCDissimilarityBCUTEuclidean
Returns dissimilarites based on Euclidean distances and BCUT values.
You can find related information about dissimilarity functions here.
JCHitColorStructure
Substructure search can be performed with this function, returns
colored  hit  molecules.
JCHitColorSimilarityStructure
Similarity search can be performed with this function, returns colored
hit  molecules.
You can find more detailed information about functions related to hit
coloring here.
JCSubstructureMatch
Returns TRUE if the query (substructure) is present in the target
molecule, and FALSE if it doesn't.
JCSubstructureMatchCount
Returns the number of query molecules (substructures) in the target
molecule.
You can find more detailed information about "match" function in the 
Chemical Terms Reference Tables.
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