Chemical Terms functions by categories

The following table lists all available Chemical Terms functions by their category.

ADMET functions

Name	License	Description	Return value	Parameters	General context example(s)	Molecule context example(s)	Reaction context example(s)
hergBeta	ADMET	predicts hERG activity and returns the pActivity using ChemAxon's hERG activity model	the pActivity value	-	N/A	hergBeta() returns the predicted hERG pActivity of the input molecule	hergBeta(reactant(0)) returns the predicted hERG pActivity of the first reactant
hergActivityBeta	ADMET	predicts hERG activity (as pActivity) using ChemAxon's hERG activity model	the pActivity value	-	N/A	hergActivityBeta() returns the predicted hERG pActivity of the input molecule	hergActivityBeta(product(0)) returns the predicted hERG pActivity of the first product
hergClassBeta	ADMET	predicts hERG classification class using ChemAxon's hERG classification model	the classification class (SAFE or TOXIC)	-	N/A	hergClassBeta() returns the predicted hERG classification class of the input molecule	hergClassBeta(reactant(0)) returns the predicted hERG classification class of the first reactant

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Charge functions

Name	License	Description	Return value	Parameters	General context example(s)	Molecule context example(s)	Reaction context example(s)
atomicPolarizability atomPol pol polarizability	Structural Calculations	calculates atomic polarizability	the polarizability values	atom index or MolAtom object pH value (the calculation is run on the major microspecies at this pH value if specified)	N/A	atomicPolarizability(0) returns the polarizability of atom 0 of the input molecule atomicPolarizability(2, "7.4") returns the polarizability of atom 2 of the major microspecies at pH 7.4	atomicPolarizability(ratom(1)) returns the polarizability of reactant atom matching map 1 in the reaction equation atomicPolarizability(patom(2), "7.4") returns the polarizability of the product atom matching map 2 of the major microspecies taken at pH 7.4
averagePolarizability averagePol avgPol	Structural Calculations	calculates average molecular polarizability component considering 3D geometry	the polarizability value	pH value (the calculation is run on the major microspecies at this pH value if specified)	N/A	averagePolarizability() returns the average polarizability component of the input molecule averagePolarizability("7.4") returns the average polarizability component of the major microspecies of the input molecule at pH 7.4	averagePolarizability(reactant(1)) returns the average polarizability component of the second reactant in the reaction equation averagePolarizability(product(0), "7.4") returns the average polarizability component of the major microspecies of the first product taken at pH 7.4
axxPol	Structural Calculations	calculates the a(xx) principal component of the polarizability tensor (a(xx), a(yy), a(zz))	the a(xx) principal component of the polarizability tensor	pH value (the calculation is run on the major microspecies at this pH value if specified)	N/A	axxPol() returns the principal component a(xx) of the polarizability tensor of the input molecule	axxPol(reactant(1)) returns the principal component a(xx) of the polarizability tensor of the second reactant in the reaction equation
ayyPol	Structural Calculations	calculates the a(yy) principal component of the polarizability tensor (a(xx), a(yy), a(zz))	the a(yy) principal component of the polarizability tensor	pH value (the calculation is run on the major microspecies at this pH value if specified)	N/A	ayyPol() returns the principal component a(yy) of the polarizability tensor of the input molecule	ayyPol(reactant(1)) returns the principal component a(yy) of the polarizability tensor of the second reactant in the reaction equation
azzPol	Structural Calculations	calculates the a(zz) principal component of the polarizability tensor (a(xx), a(yy), a(zz))	the a(zz) principal component of the polarizability tensor	pH value (the calculation is run on the major microspecies at this pH value if specified)	N/A	azzPol() returns the principal component a(zz) of the polarizability tensor of the input molecule	azzPol(reactant(1)) returns the principal component a(zz) of the polarizability tensor of the second reactant in the reaction equation
charge	Structural Calculations	calculates partial charges of atoms for the "aromaticsystem" and the "aromaticring" result types calculates the sum of partial charges of the atoms in the aromatic system or the smallest aromatic ring containing the atom	the partial charge values	atom index or MolAtom object the result type ("total" (default), "pi", "sigma", "aromaticsystem", "aromaticsystemsigma", "aromaticsystempi", "aromaticring", "aromaticringsigma", "aromaticringpi") pH value (the calculation is run on the major microspecies at this pH value if specified)	N/A	charge(0) returns the partial charge of atom 0 of the input molecule charge(2, "pi", "7.4") returns the partial "pi" charge of atom 2 of the major microspecies taken at pH 7.4	charge(ratom(1), "aromaticsystem") returns the sum of partial pi charges in the aromatic system containing the reactant atom matching map 1 in the reaction equation charge(patom(2), "aromaticring", "7.4") returns the sum of partial charges in the smallest aromatic ring containing the product atom matching map 2 in the major microspecies of the input molecule taken at pH 7.4
molecularPolarizability molPol	Structural Calculations	calculates molecular polarizability	the polarizability value	pH value (the calculation is run on the major microspecies at this pH value if specified)	N/A	molecularPolarizability() returns the molecular polarizability of the input molecule molecularPolarizability("7.4") returns the molecular polarizability of the major microspecies of the input molecule taken at pH 7.4	molecularPolarizability(reactant(1)) returns the molecular polarizability of the second reactant in the reaction equation molecularPolarizability(product(0), "7.4") returns the molecular polarizability of the major microspecies of the first product taken at pH 7.4
piOrbitalElectronegativity pOEN	Structural Calculations	calculates atomic pi orbital electronegativity	the pi orbital electronegativity values	atom index or MolAtom object pH value (the calculation is run on the major microspecies at this pH value if specified)	N/A	piOrbitalElectronegativity(0) returns the pi orbital electronegativity of atom 0 of the input molecule piOrbitalElectronegativity(2, "7.4") returns the pi orbital electronegativity of atom 2 of the major microspecies of the input molecule taken at pH 7.4	pOEN(ratom(1)) returns the pi orbital electronegativity of the reactant atom matching map 1 in the reaction equation pOEN(patom(2), "7.4") returns the pi orbital electronegativity of the product atom matching map 2 of the major microspecies taken at pH 7.4
resonantCharge	Structural Calculations	calculates partial charges of atoms considering resonance effect for the "aromaticsystem" and the "aromaticring" result types calculates the sum of partial charges of the atoms in the aromatic system or the smallest aromatic ring containing the atom	the resonant charge values	atom index or MolAtom object the result type ("total" (default), "pi", "sigma", "aromaticsystem", "aromaticsystemsigma", "aromaticsystempi", "aromaticring", "aromaticringsigma", "aromaticringpi") pH value (the calculation is run on the major microspecies at this pH value if specified)	N/A	resonantCharge(0) returns the partial charge on atom 0 of the input molecule considering resonance effect resonantCharge(2, "pi", "7.4") returns the partial "pi" charge on atom 2 of the major microspecies of the input molecule taken at pH 7.4 considering resonance effect	resonantCharge(ratom(1), "aromaticsystem") returns the sum of partial pi charges in the aromatic system containing the reactant atom matching map 1 in the reaction equation considering resonance effect resonantCharge(patom(2), "aromaticring", "7.4") returns the sum of partial charges in the smallest aromatic ring containing the product atom matching map 2 of the major microspecies of the input molecule taken at pH 7.4 considering resonance effect
sigmaOrbitalElectronegativity sOEN	Structural Calculations	calculates atomic sigma orbital electronegativity	the sigma orbital electronegativity values	atom index or MolAtom object pH value (the calculation is run on the major microspecies at this pH value if specified)	N/A	sigmaOrbitalElectronegativity(0) returns the sigma orbital electronegativity of atom 0 of the input molecule sigmaOrbitalElectronegativity(2, "7.4") returns the sigma orbital electronegativity of atom 2 of the major microspecies of the input molecule taken at pH 7.4	sOEN(ratom(1)) returns the sigma orbital electronegativity of reactant atom matching map 1 in the reaction equation sOEN(patom(2), "7.4") returns the sigma orbital electronegativity of the product atom matching map 2 of the major microspecies taken at pH 7.4

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Conformation Functions

Name	License	Description	Return value	Parameters	General context example(s)	Molecule context example(s)	Reaction context example(s)
conformer	Structural Calculations	generates a conformer of the molecule	the conformer	the conformer index (0-based)	N/A	conformer(0) returns the first conformer of the input molecule	conformer(reactant(0), 1) returns the second conformer of the first reactant
conformerCount	Structural Calculations	returns the number of generated conformers	the number of generated conformers	-	N/A	conformerCount() returns the number of generated conformers of the input molecule	conformerCount(reactant(0)) returns the number of generated conformers of the first reactant
conformers	Structural Calculations	generates conformers of the molecule (maximum number of conformers to be generated can be set, default: 100)	the conformer array	-	N/A	conformers() generates conformers of the input molecule in an array	conformers(reactant(0)) generates conformers of the first reactant in an array
hasValidConformer	Structural Calculations	checks if the input molecule is in 3D space (has a valid conformer)	true if the input molecule is in 3D space	-	N/A	hasValidConformer() returns true if the input molecule is in 3D space (has a valid conformer)	hasValidConformer(reactant(0)) returns true the if the first reactant is in 3D space
lowestEnergyConformer leconformer	Structural Calculations	generates the lowest energy conformer of the molecule	the lowest energy conformer	-	N/A	lowestEnergyConformer() returns the lowest energy conformer of the input molecule	lowestEnergyConformer(reactant(0)) returns the lowest energy conformer of the first reactant
mmff94OptimizedStructure	Structural Calculations	generates the MMFF94-optimized lowest energy conformer	the MMFF94-optimized lowest energy conformer	-	N/A	mmff94OptimizedStructure() returns the MMFF94-optimized lowest energy conformer of the input molecule	mmff94OptimizedStructure(reactant(0)) returns the MMFF94-optimized lowest energy conformer of the first reactant

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Dissimilarity Functions

Name	License	Description	Return value	Parameters	General context example(s)	Molecule context example(s)	Reaction context example(s)
dissimilarity	-	calculates the dissimilarity value between two molecules (see the Notes below the table)	the dissimilarity value	descriptor:metric or descriptor (with default metric) (optional, Chemical Fingerprint with Tanimoto metric is used by default) one or two molecules (if only one is specified then the other one is taken from the context)	N/A	dissimilarity("PF", "c1ccccc1", "C1CCCCC1") returns the dissimilarity value between the benzene ring and cyclohexane computed with Pharmacophore Fingerprint and its default metric (Tanimoto) dissimilarity("c1ccccc1", "C1CCCCC1") returns the dissimilarity value between the benzene ring and cyclohexane computed with the default fingerprint and its default metric (Chemical Fingerprint with Tanimoto metric) dissimilarity("PF:Euclidean", "c1ccccc1") returns the dissimilarity value between the benzene ring and the input molecule computed with Pharmacophore Fingerprint and Euclidean metric dissimilarity("LogD", "c1ccccc1") returns the dissimilarity value between the benzene ring and the input molecule computed with the LogD descriptor and its default AbsDiff metric	dissimilarity("CF:Euclidean", "c1ccccc1", reactant(0)) returns the dissimilarity value between the benzene ring and the first reactant computed with Chemical Fingerprint and Euclidean metric dissimilarity(reactant(0), product(0)) returns the dissimilarity value between the first reactant and the first product computed with the default fingerprint and its default metric (Chemical Fingerprint with Tanimoto metric)

NOTE 1: The dissimilarity() function requires JChem.

NOTE 2: The dissimilarity values returned by the dissimilarity() function and the similarity search in JChem may differ because of the applied fingerprints. The dissimilarity() function uses the default options of the chemical fingerprints (length=1024, bonds=7, bits=2) optimized for similarity search. Database similarity search uses fingerprints specified during the generation of the given table, optimised for substructure (and related) search types.

Dissimilarity descriptors and metrics

Descriptor	Metric
Chemical Fingerprint (or CF)	Tanimoto (default), Euclidean
Pharmacophore Fingerprint (or PF)	Tanimoto (default), Euclidean
ECFP	Tanimoto (default), Euclidean
Burden Eigenvalue Descriptor (or BCUT)	Euclidean
HDon	Euclidean
HAcc	AbsDiff
Heavy	AbsDiff
LogD	AbsDiff
LogP	AbsDiff
Mass	AbsDiff
TPSA	AbsDiff

NOTE 1: BCUT is a trademark of Tripos Inc. It is used with permission.

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Elemental Analysis Functions

Name	License	Description	Return value	Parameters	General context example(s)	Molecule context example(s)	Reaction context example(s)
atomCount	-	calculates the number of atoms (all atoms or specific atoms)	the atom count	atomic number (optional) and mass number (optional) as a single string separated by "." (e.g. "6" for the number of carbon atoms, "6.12" for the number of carbon atoms with mass number 12); if omitted, all atoms are counted; if the mass number is set to 0, all non-isotope atoms are counted	N/A	atomCount() returns the number of atoms in the input molecule atomCount("6") returns the number of carbon atoms in the input molecule	atomCount(reactant(0), "7") returns the number of nitrogen atoms in the first reactant atomCount(product(1), "7.14") returns the number of nitrogen atoms with mass number 14 in the second product atomCount(product(1), "7.0") returns the number of non-isotope nitrogen atoms in the second product
composition	-	returns the composition	the composition	-	N/A	composition() returns the composition of the input molecule	N/A (reaction rules are numerical)
dotDisconnectedFormula	-	returns the dot-disconnected formula	the dot-disconnected formula	-	N/A	dotDisconnectedFormula() returns the dot-disconnected formula of the input molecule	N/A (reaction rules are numerical)
dotDisconnectedIsotopeFormula	-	returns the dot-disconnected isotope formula	the dot-disconnected isotope formula	-	N/A	dotDisconnectedIsotopeFormula() returns the dot-disconnected isotope formula of the input molecule	N/A (reaction rules are numerical)
dotDisconnectedFormulaWithGrouping	-	returns the grouped dot-disconnected formula	the grouped dot-disconnected formula	-	N/A	dotDisconnectedFormulaWithGrouping() returns the grouped dot-disconnected formula of the input molecule	N/A (reaction rules are numerical)
elementalAnalysis elemanal	-	performs elemental analysis on the molecule represented by its formula	the property calculated by the function parameter (e.g. mass)	molecular formula available function parameters: atomCount, mass, massPrecision, exactMass, exactMassPrecision, formula, isotopeFormula, dotDisconnectedFormula, dotDisconnectedIsotopeFormula, groupedDotDisconnectedFormula	N/A	elementalAnalysis('mass','C12H25O') returns the mass of molecule represented by its formula	N/A
exactMass	-	calculates the exact mass of the molecule	the exact mass	-	N/A	exactMass() returns the exact mass of the input molecule	exactMass(product(1)) returns the exact mass of the second product
formula	-	returns the formula	the formula	-	N/A	formula() returns the formula of the input molecule	N/A (reaction rules are numerical)
isotopeComposition	-	returns the isotope composition	the isotope composition	-	N/A	isotopeComposition() returns the isotope composition of the input molecule	N/A (reaction rules are numerical)
isotopeFormula	-	returns the isotope formula	the isotope formula	-	N/A	isotopeFormula() returns the isotope formula of the input molecule	N/A (reaction rules are numerical)
mass	-	calculates the molecule mass	the mass	-	N/A	mass() returns the mass of the input molecule	mass(reactant(0)) returns the mass of the first reactant
massspectrum	-	calculates the mass spectrum (the m/z:relative abundance plot)	the mass spectrum as a series of discrete values	-	N/A	massspectrum() returns the mass spectrum of the input molecule	massspectrum(reactant(0)) returns the mass spectrum of the first reactant
sortableFormula	-	returns the fixed digit sortable molecular formula	the fixed digit sortable molecular formula	the number of digits (default is 4)	N/A	sortableFormula('digits:2') returns the 2-digit sortable formula of the input molecule	N/A (reaction rules are numerical)

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General Functions

Name	License	Description	Return value	Parameters	General context example(s)	Molecule context example(s)	Reaction context example(s)
abs	-	returns the absolute value of a number	the absolute value	integer or real number	abs(7) returns 7 abs(-4.9) returns 4.9	abs(charge(1)) returns the absolute value of the charge of the 2nd atom in the molecule	abs(charge(patom(0))) returns the absolute value of the charge of the product atom matching map 0
agentCount	-	counts the agents a the reaction	the number of agents in the reaction or -1 if the the input is not a reaction	-	N/A	agentCount() returns n if the input molecule is a reaction and contains n agents otherwise it returns -1	agentCount() returns n if the input molecule is a reaction and contains n agents otherwise it returns -1 agentCount(reactant(0)) and agentCount(product(1)) calls does not make sense and they will return -1
arom	-	returns if the atom has an aromatic bond	true if the atom has an aromatic bond, false otherwise	atom index or MolAtom object	N/A	arom(0) returns if the atom 0 has an aromatic bond	arom(patom(2)) returns true if the product atom matching map 2 in the reaction equation has an aromatic bond
array	-	constructs an integer array from its arguments	the integer array	integers or MolAtom objects	array(2, 5, 6, 8) creates an array from the integers 2, 5, 6, 8	array(map(2), map(5), map(6), map(8)) creates an array from the mapped atoms 2, 5, 6, 8	array(ratom(2), ratom(5), ratom(6), ratom(8)) creates an array from the mapped reactant atoms matching maps 2, 5, 6, 8
atno atomicNumber	-	returns the atomic number of an atom	the atomic number	atom index or MolAtom object	N/A	atno(0) returns the atomic number of atom 0	atno(ratom(1)) returns the atomic number of the reactant atom matching map 1
booleanToNumber	-	returns the numerical representation of a boolean value (true = 1, false = 0) or the number itself if the input is a number	the numerical representation of a boolean value	boolean expression or number	booleanToNumber(1<2) returns 1 booleanToNumber(2+2==5) returns 0 booleanToNumber(55)* returns 25	booleanToNumber(hasValenceError()) returns 0 for molecules having no valence error	booleanToNumber(ringBond(reactant(0), bond(ratom(1), ratom(2)))) returns 1 if reactant atoms matching maps 1 and 2 in the reaction equation are connected by a ring bond in the corresponding reactant, 0 otherwise
connections	-	returns the bond plus implicit H count of an atom	the bond plus implicit H count	atom index or MolAtom object	N/A	connections(2) returns the number of connections of atom 2	connections(ratom(1)) returns the number of connections of the reactant atom matching map 1 in the reaction equation
count	-	determines the number of elements in an array	the number of elements in the array	integer or real number array	count(array(3.4, 5.6, 1.2)) returns 3	count(filter("charge() > 0")) returns the number of positively charged atoms of the molecule	count(filter(reactant(1), "charge() > 0")) returns the number of atoms with positive charge in the second reactant count(filter(product(0), "match('[#8][C:1]=O', 1")) returns the number of carboxylic carbons in the first product
eval	-	evaluates a boolean expression	the evaluation result (0 or 1)	boolean expression	eval('5 > 0') returns 1	eval('charge() > 0') determines if the atoms of a molecule are positively charged	eval('charge(ratom(1)) > 0') determines if the reactant atom matching map 1 has a positive charge
field property	-	returns a molecule property (SDF field value)	the molecule property	the property key (SDF field name)	Molecule Context field('ACTIVITY') returns the value of the ACTIVITY property (SDF field) field('ACTIVITY') > 2 returns 1 if the ACTIVITY value is bigger than 2, returns 0 otherwise Reaction Context field(reactant(1), 'ACTIVITY') returns the ACTIVITY property value of the second reactant field(product(0), 'ACTIVITY') > field(reactant(0), 'ACTIVITY') returns 1 if the ACTIVITY value of the first product is bigger than that of the first reactant, returns 0 otherwise
fieldAsString propertyAsString	-	returns a molecule property (SDF field value) as string	the molecule property as string	the property key (SDF field name)	Molecule Context fieldAsString('ID') returns the value of the ID property (SDF field) Reaction Context field(reactant(0), 'ID') returns the value of the ID property field in first reactant
filter	-	filters target atoms by filtering condition	target atom indices satisfying the filtering condition	target atom indices / objects or index / atom object array (optional, all atoms taken if omitted), filtering condition (boolean expression)	Molecule Context <ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="060caeb3-8f40-46ad-a508-1aebced4275c"><ac:plain-text-body></ac:plain-text-body></ac:structured-macro> Reaction Context <ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="2639a0fc-8d39-4bd0-84aa-6a8d35a59641"><ac:plain-text-body><![CDATA[filter(reactant(0), "charge() > 0") returns the indices of atoms with positive partial charge in the first reactant filter(patom(1), patom(2), "match('[#8][C:1]=O', 1)") returns the carboxylic carbons out of product atoms matching map 1 or 2 in the reaction equation (note, that these atoms are supposed to be in the same product molecule)	]]></ac:plain-text-body></ac:structured-macro>
formalCharge totalCharge	-	calculates formal charge of molecule	the formal charge value	atom index or MolAtom object (optional)	Molecule Context formalCharge() returns the formal charge of the input molecule formalCharge(0) returns the formal charge of atom 0 Reaction Context formalCharge(reactant(0)) returns the formal charge of the first reactant formalCharge(ratom(1)) returns the formal charge of the reactant atom matching map 1
fragments	-	converts the molecule to its disconnected fragments	the disconnected fragments of the molecule	-	Molecule Context fragments() returns the disconnected fragments of the molecule Reaction Context fragments(reactant(1)) returns the disconnected fragments of the second reactant
hasAromatizationError	-	determines if there is error in the aromatization of the molecule	true if there is an error in the aromatization of the molecule, false otherwise	-	Molecule Context hasAromatizationError() returns true if there is an error in the aromatization of the molecule, false otherwise Reaction Context hasAromatizationError(reactant(0)) returns true if there is an error in the aromatization of the first reactant, false otherwise
hasIsotope	-	determines if any atom in the molecule is a specific isotope of the element	true if any atom in the molecule is a specific isotope of the element, false otherwise	-	Molecule Context hasIsotope() returns true if any atom in the molecule is a specific isotope of the element, false otherwise Reaction Context hasIsotope(reactant(1)) returns true if any atom in the second reactant is a specific isotope of the element, false otherwise
hasRadical	-	determines if any atom in the molecule has radical	true if any atom in the molecule has radical, false otherwise	-	Molecule Context hasRadical() returns true if any atom in the molecule has radical, false otherwise Reaction Context hasRadical(reactant(1)) returns true if any atom in the second reactant has radical, false otherwise
hasValenceError	-	determines if any atom in the molecule has valence error	true in case of valence error, false otherwise	-	Molecule Context hasValenceError() returns true if any atom in the molecule has valence error, false otherwise Reaction Context hasValenceError(reactant(1)) returns true if any atom in the second reactant has valence error, false otherwise
HBDA	Structural Calculations License
hCount	-	returns the hydrogen count of an atom	the hydrogen count	atom index or array of atom indeces (separated by , or or MolAtom object	Molecule Context hCount(0;2;3) returns the hydrogen count of atom 0,2,3 Reaction Context hCount(patom(3)) returns the hydrogen count on the product atom matching map 3 in the reaction equation
importMol	-	imports and returns the molecule from its string representation	the string representation of the molecule	the molecule in string representation (e.g. "c1ccccc1")	Molecule Context importMol("c1ccccc1") returns benzene molecule Reaction Context N / A (reaction rules are numerical)
in	-	determines whether an integer / atom index is contained in a given integer array	true if the array contains the specified integer, false otherwise	an integer or MolAtom object and an integer array	General (All) in(5, array(3, 5, 1)) returns true in(2, array(3, 5, 1)) returns false Molecule Context in(3, maxatom("charge()", 2)) returns true if the partial charge on atom 3 is within the first 2 largest partial charges in the input molecule in(3, minatom("pol()", 4)) returns true if the polarizability on atom 3 is within the first 4 smallest polarizability values in the input molecule Reaction Context in(ratom(3), maxatom(reactant(0), "charge()", 2)) returns true if the partial charge on reactant atom matching map 3 in the reaction equation is within the first 2 largest partial charges in the first reactant in(patom(1), minatom(product(1), "pol()", 4)) returns true if the polarizability on product atom matching map 1 in the reaction equation is within the first 4 smallest polarizability values in the second product
ionCharge	Structural Calculations License
isEmpty	-	decides whether the given molecule is empty (does not contain any atoms, bonds, or non-empty S-groups)	true if the molecule does not contain any atoms, bonds, or non-empty S-groups, false otherwise	-	Molecule Context isQuery() returns true if the given molecule does not contain any atoms, bonds, or non-empty S-groups, false otherwise Reaction Context isQuery(reactant(1)) returns true if the second reactant contains any atoms, bonds, or non-empty S-groups, false otherwise
isQuery	-	decides whether the given molecule contains any query features	true if the molecule contains any query features, false otherwise	-	Molecule Context isQuery() returns true if the given molecule contains any query features, false otherwise Reaction Context isQuery(reactant(1)) returns true if the second reactant contains any query features, false otherwise
map	-	returns the atom map number	the atom map number	atom index or MolAtom object	Molecule Context map(3) returns the atom map number of atom 3 Reaction Context map(patom(3)) returns the atom map number on the product atom matching map 3 in the reaction equation
max	-	takes maximum of its array and/or numerical parameters	the maximum value	integers, real numbers, integer arrays, real number arrays	General (All) min(2, 8, 6) returns 2 max(3.4, 5.6, 1.2) returns 5.6 Molecule Context min(charge(0), charge(2)) returns the least of the partial charge values on atoms 0 and 2 max(charge()) returns the maximal partial charge value on the input molecule Reaction Context min(charge(ratom(2)), charge(ratom(3))) returns the least of the partial charge values on reactant atoms matching maps 2 and 3 in the reaction equation max(charge(product(0))) returns the maximal partial charge value on the first product
maxAtom	-	evaluates objective function for each atom, finds largest value(s)	the atom index / indices corresponding to the largest evaluation result(s)	target atom indices / objects or index / atom object array (optional, all atoms taken if omitted), the objective function (as inner expression string), the number of largest values to be taken (optional, takes only one if omitted)	Molecule Context maxAtom(6, 7, 8, 9, "charge('7.4')", 2) selects the two largest partial charges on atoms 6, 7, 8, 9 in the major microspecies at pH 7.4 of the input molecule and returns the corresponding indices Reaction Context maxAtom(patom(1), patom(2), patom(3), "charge('7.4')", 2) selects the two largest partial charges on product atoms matching maps 1, 2, 3 in the major microspecies at pH 7.4 of the product molecule of these atoms and returns the corresponding indices (note, that these atoms are supposed to be in the same product molecule)
maxValue	-	evaluates objective function for each atom, finds largest value(s)	the largest evaluation result(s)	target atom indices / objects or index / atom object array (optional, all atoms taken if omitted), the objective function (as inner expression string), the number of largest values to be taken (optional, takes only one if omitted)	Molecule Context maxValue(6, 7, 8, 9, "charge('7.4')", 2) returns the two largest partial charges on atoms 6, 7, 8, 9 in the major microspecies at pH 7.4 of the input molecule Reaction Context maxValue(patom(1), patom(2), patom(3), "charge('7.4')", 2) returns the two largest partial charges on product atoms matching maps 1, 2, 3 in the major microspecies at pH 7.4 of the product molecule of these atoms (note, that these atoms are supposed to be in the same product molecule)
min	-	takes minimum of its array and/or numerical parameters	the minimum value	integers, real numbers, integer arrays, real number arrays	General (All) min(2, 8, 6) returns 2 max(3.4, 5.6, 1.2) returns 5.6 Molecule Context min(charge(0), charge(2)) returns the least of the partial charge values on atoms 0 and 2 max(charge()) returns the maximal partial charge value on the input molecule Reaction Context min(charge(ratom(2)), charge(ratom(3))) returns the least of the partial charge values on reactant atoms matching maps 2 and 3 in the reaction equation max(charge(product(0))) returns the maximal partial charge value on the first product
minAtom	-	evaluates objective function for each atom, finds smallest value(s)	the atom index / indices corresponding to the smallest evaluation result(s)	target atom indices / objects or index / atom object array (optional, all atoms taken if omitted), the objective function (as inner expression string), the number of smallest values to be taken (optional, takes only one if omitted)	Molecule Context minAtom("charge('7.4')") returns the atom index corresponding to minimum partial charge in the major microspecies at pH 7.4 of the input molecule Reaction Context minAtom(reactant(0), "charge('7.4')") returns the atom index corresponding to minimum partial charge in the major microspecies at pH 7.4 of the first reactant
minValue	-	evaluates objective function for each atom, finds smallest value(s)	the smallest evaluation result(s)	target atom indices / objects or index / atom object array (optional, all atoms taken if omitted), the objective function (as inner expression string), the number of smallest values to be taken (optional, takes only one if omitted)	Molecule Context minValue("charge('7.4')") returns the minimum partial charge in the major microspecies at pH 7.4 of the input molecule Reaction Context minValue(reactant(0), "charge('7.4')") returns the minimum partial charge in the major microspecies at pH 7.4 of the first reactant
molAtom	-	creates a MolAtom	the MolAtom object	atomic number	Molecule Context molAtom(6) returns a carbon atom Reaction Context molAtom(6) returns a carbon atom
molBinFormat molImage	-	returns the binary representation (image, pdf, GZIP compressed molecule file) of the molecule in specified format	the binary representation (image, pdf, GZIP compressed molecule file) of the molecule	the binary format with options (e.g. "jpeg", "png:w150,h150", "pdf", "gzip:sdf")	Molecule Context molImage("jpeg:w100,Q95,#ffff00") returns the 100x100 JPEG image of the input molecule with yellow background, 95% quality Reaction Context N / A (reaction rules are numerical)
molString molConvert molFormat	-	returns the string representation of a molecule, or an array of molecules, in specified molecule format	the string representation of the molecule(s)	the molecule format (e.g. "mol", "sdf", "mrv", "smiles") the clean dimension	Molecule Context molFormat("mrv") returns the Chemaxon Marvin Document format representation of the input molecule molFormat(tautomers(), "sdf", 2) returns the SDF format representation of the tautomers of the input molecule Reaction Context N / A (reaction rules are numerical)
pair bond	-	converts two atoms or 0-based atom indexes into an "index1-index2" 1-based atom index setter string (used for pairing atoms in shortestPath )	the generated string	two atom indexes or two MolAtom objects	General (All) pair(2, 5) returns "3-6" Reaction Context pair(ratom(1), ratom(2)) returns "index1-index2" where "index1" and "index2" are the 1-based atom indexes of the reactant atoms matching map 1 and 2 in the reaction equation bond(patom(2), patom(5) returns "index1-index2" where "index1" and "index2" are the 1-based atom indexes of the product atoms matching map 2 and 5 in the reaction equation
productCount	-	counts the products in the reaction	the number of products in the reaction, or -1 if the the input (molecule) is not a reaction	-	Molecule Context productCount() returns n if the given molecule is a reaction and contains n products. productCount() returns -1 if the given molecule is not a reaction. Reaction Context productCount() returns n if the given molecule is a reaction and contains n products. productCount(product(0)) and productCount(product(1)) calls does not make sense, and will return -1.
radicalCount	-	returns the radical count of an atom	the radical count	atom index or MolAtom object	Molecule Context radicalCount(0) returns the radical count of atom 0 Reaction Context radicalCount(patom(3)) returns the radical count on the product atom matching map 3 in the reaction equation
reactantCount	-	counts the reactants in the reaction	the number of reactants in the reaction, or -1 if the the input (molecule) is not a reaction	-	Molecule Context reactantCount() returns n if the given molecule is a reaction and contains n reactants. reactantCount() returns -1 if the given molecule is not a reaction. Reaction Context reactantCount() returns n if the given molecule is a reaction and contains n reactants. reactantCount(reactant(0)) and reactantCount(product(1)) calls does not make sense, and will return -1.
sortAsc	-	sorts an array in ascending order	the sorted array	integer array or real number array	General (All) sortAsc(array(3.4, 5.6, 1.2)) returns array(1.2, 3.4, 5.6) Molecule Context sortAsc(charge()) returns the partial charge values in ascending order Reaction Context sortAsc(charge(reactant(1))) returns the partial charge values of the second reactant in ascending order
sortDesc	-	sorts an array in descending order	the sorted array	integer array or real number array	General (All) sortDesc(array(3.4, 5.6, 1.2)) returns array(5.6, 3.4, 1.2) Molecule Context sortDesc(pka("basic")) returns the basic p K _a values in descending order Reaction Context sortDesc(pka(product(0), "basic")) returns the basic p K _a values of the first product in descending order
sum	-	computes the sum of array elements	the sum	integer array or real number array	General (All) sum(array(3.4, 5.6, 1.2)) returns 10.2 Molecule Context sum(charge()) returns the sum of charge values sum(pol()) returns the sum of atom polarizability values Reaction Context sum(charge(reactant(0))) returns the sum of charge values in the first reactant sum(pol(product(0))) returns the sum of atom polarizability values in the first product
topanal	Structural Calculations License
valence	-	returns the sum of bond orders and query H atoms of an atom	the sum of bond orders and query H atoms	atom index or MolAtom object	Molecule Context valence(0) returns the valence of atom 0 Reaction Context valence(ratom(1)) returns the valence of the reactant atom matching map 1 in the reaction equation
whereIsValenceError	-	returns the index of the first atom with valence error, or -1 if there is no valence error	the index of the first atom with valence error, or -1 if there is no valence error	-	Molecule Context whereIsValenceError() returns the index of the first atom with valence error, or -1 if there is no valence error in the molecule Reaction Context whereIsValenceError(reactant(1)) returns the index of the first atom with valence error in the second reactant, or -1 f there is no valence error in the second reactant

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Geometry Functions

Name	License	Description	Return value	Parameters	Examples
aliphaticAtom	Structural Calculations License	checks if the specified atom is aliphatic	true for aliphatic atoms, false for non-aliphatic atoms	* the atom index / MolAtom object	Molecule Context aliphaticAtom(2) returns true if atom 2 of the input molecule is aliphatic, false otherwise Reaction Context aliphaticAtom(ratom(2)) returns true if the reactant atom matching map 2 in the reaction equation is aliphatic, false otherwise aliphaticAtom(patom(1)) returns true if the product atom matching map 1 in the reaction equation is aliphatic, false otherwise
aliphaticAtomCount	Structural Calculations License	calculates the aliphatic atom count	the aliphatic atom count	-	Molecule Context aliphaticAtomCount() returns the number of aliphatic atoms in the input molecule Reaction Context aliphaticAtomCount(reactant(0)) returns the number of aliphatic atoms in the first reactant aliphaticAtomCount(product(1)) returns the number of aliphatic atoms in the second product
aliphaticBondCount	Structural Calculations License	calculates the aliphatic bond count	the aliphatic bond count	-	Molecule Context aliphaticBondCount() returns the number of bonds in the input molecule Reaction Context aliphaticBondCount(reactant(0)) returns the number of aliphatic bonds in the first reactant aliphaticBondCount(product(1)) returns the number of aliphatic bonds in the second product
aliphaticRingCount	Structural Calculations License	calculates the aliphatic ring count	the aliphatic ring count	-	Molecule Context aliphaticRingCount() returns the number of aliphatic rings in the input molecule Reaction Context aliphaticRingCount(reactant(0)) returns the number of aliphatic rings in the first reactant aliphaticRingCount(product(1)) returns the number of aliphatic rings in the second product
aliphaticRingCountOfSize	Structural Calculations License	calculates the number of aliphatic rings of given size	the number of aliphatic rings of given size	the ring size	Molecule Context aliphaticRingCountOfSize(6) returns the number of aliphatic rings of size 6 in the input molecule Reaction Context aliphaticRingCountOfSize(reactant(0), 5) returns the number of aliphatic rings of size 5 in the first reactant aliphaticRingCountOfSize(product(1), 5) returns the number of aliphatic rings of size 5 in the second product
aliphaticRings	Structural Calculations License	identifies the aliphatic rings in the molecule	atom indexes of the aliphatic rings in the molecule (null if the molecule does not contain aliphatic rings)	-	Molecule Context aliphaticRings() returns the atom indexes of the aliphatic rings in the input molecule Reaction Context aliphaticRings(reactant(0)) returns the atom indexes of the aliphatic rings in the first reactant aliphaticRings(product(1)) returns the atom indexes of the aliphatic rings in the second product
aliphaticRingsOfSize	Structural Calculations License	identifies the aliphatic rings in the molecule having a given size (number of atoms)	atom indexes of the aliphatic rings in the molecule having the given size (null if the molecule does not contain aliphatic rings)	the ring size	Molecule Context aliphaticRings() returns the atom indexes of the aliphatic rings in the input molecule having the given size Reaction Context aliphaticRings(reactant(0)) returns the atom indexes of the aliphatic rings in the first reactant having the given size aliphaticRings(product(1)) returns the atom indexes of the aliphatic rings in the second product having the given size
angle	Structural Calculations License	calculates the angle between three atoms	the angle between three atoms	* the (1-based) atom indexes of the three atoms in a string: "index1-index2-index3" (e.g. '2-3-5')	Molecule Context angle('1-2-3') and angle(atoms(0, 1, 2)) both return the angle between atoms 1, 2 and 3 in the input molecule Reaction Context angle(reactant(0), atoms(ratom(1), ratom(2), ratom(3))) returns the angle between reactant atoms matching maps 1, 2 and 3 in the reaction equation (see note 1) angle(product(1), atoms(patom(2), patom(3), patom(4))) returns the angle between product atoms matching maps 2, 3 and 4 in the reaction equation (see note 1)
aromaticAtom	Structural Calculations License	checks if the specified atom is aromatic	true for aromatic atoms, false for non-aromatic atoms	* the atom index / MolAtom object	Molecule Context aromaticAtom(2) returns true if atom 2 of the input molecule is aromatic, false otherwise Reaction Context aromaticAtom(ratom(2)) returns true if the reactant atom matching map 2 in the reaction equation is aromatic, false otherwise aromaticAtom(patom(1)) returns true if the product atom matching map 1 in the reaction equation is aromatic, false otherwise
aromaticAtomCount	Structural Calculations License	calculates the aromatic atom count	the aromatic atom count	-	Molecule Context aromaticAtomCount() returns the number of aromatic atoms in the input molecule Reaction Context aromaticAtomCount(reactant(0)) returns the number of aromatic atoms in the first reactant aromaticAtomCount(product(1)) returns the number of aromatic atoms in the second product
aromaticBondCount	Structural Calculations License	calculates the aromatic bond count	the aromatic bond count	-	Molecule Context aromaticBondCount() returns the number of aromatic bonds in the input molecule Reaction Context aromaticBondCount(reactant(0)) returns the number of aromatic bonds in the first reactant aromaticBondCount(product(1)) returns the number of aromatic bonds in the second product
aromaticRingCount	Structural Calculations License	calculates the aromatic ring count	the aromatic ring count	-	Molecule Context aromaticRingCount() returns the number of aromatic rings in the input molecule Reaction Context aromaticRingCount(reactant(0)) returns the number of aromatic rings in the first reactant aromaticRingCount(product(1)) returns the number of aromatic rings in the second product
aromaticRingCountOfSize	Structural Calculations License	calculates the number of aromatic rings of given size	the number of aromatic rings of given size	the ring size	Molecule Context aromaticRingCountOfSize(6) returns the number of aromatic rings of size 6 in the input molecule Reaction Context aromaticRingCountOfSize(reactant(0), 5) returns the number of aromatic rings of size 5 in the first reactant aromaticRingCountOfSize(product(1), 5) returns the number of aromatic rings of size 5 in the second product
aromaticRings	Structural Calculations License	identifies the aromatic rings in the molecule	atom indexes of the aromatic rings in the molecule (null if the molecule does not contain aromatic rings)	-	Molecule Context aromaticRings() returns the atom indexes of the aromatic rings in the input molecule Reaction Context aromaticRings(reactant(0)) returns the atom indexes of the aromatic rings in the first reactant aromaticRings(product(1)) returns the atom indexes of the aromatic rings in the second product
aromaticRingsOfSize	Structural Calculations License	identifies the aromatic rings in the molecule having a given size (number of atoms)	atom indexes of the aromatic rings in the molecule having the given size (null if the molecule does not contain aromatic rings)	the ring size	Molecule Context aromaticRings() returns the atom indexes of the aromatic rings in the input molecule having the given size Reaction Context aromaticRings(reactant(0)) returns the atom indexes of the aromatic rings in the first reactant having the given size aromaticRings(product(1)) returns the atom indexes of the aromatic rings in the second product having the given size
ASAHydrophobic	Structural Calculations License	calculates the water accessible molecular surface area of all hydrophobic atoms	the molecular surface area	* the major microspecies pH (takes the input molecule itself if omitted)	Molecule Context ASAHydrophobic() returns the water accessible surface area of all atoms of the input molecule with hydrophobic partial charge ASAHydrophobic('7.4')returns the water accessible surface area of all atoms with hydrophobic partial charge of the major microspecies taken at pH 7.4 Reaction Context ASAHydrophobic(reactant(0)) returns the water accessible surface area of all atoms of the first reactant with hydrophobic partial charge ASAHydrophobic(product(0), '7.4') returns the water accessible surface area of all atoms with hydrophobic partial charge of the major microspecies of the first product taken at pH 7.4
ASANegative	Structural Calculations License	calculates the water accessible molecular surface area of all atoms with negative partial charge	the molecular surface area	* the major microspecies pH (takes the input molecule itself if omitted)	Molecule Context ASANegative() returns the water accessible surface area of all atoms of the input molecule with negative partial charge ASANegative('7.4')returns the water accessible surface area of all atoms with negative partial charge of the major microspecies taken at pH 7.4 Reaction Context ASANegative(reactant(0)) returns the water accessible surface area of all atoms of the first reactant with negative partial charge ASANegative(product(0), '7.4') returns the water accessible surface area of all atoms with negative partial charge of the major microspecies of the first product taken at pH 7.4
ASAPlus	Structural Calculations License	calculates the water accessible molecular surface area of all atoms with positive partial charge	the molecular surface area	* the major microspecies pH (takes the input molecule itself if omitted)	Molecule Context ASAPlus() returns the water accessible surface area of all atoms of the input molecule with positive partial charge ASAPlus('7.4')returns the water accessible surface area of all atoms with positive partial charge of the major microspecies taken at pH 7.4 Reaction Context ASAPlus(reactant(0)) returns the water accessible surface area of all atoms of the first reactant with positive partial charge ASAPlus(product(0), '7.4') returns the water accessible surface area of all atoms with positive partial charge of the major microspecies of the first product taken at pH 7.4
ASAPolar	Structural Calculations License	calculates the water accessible molecular surface area of all polar atoms	the molecular surface area	* the major microspecies pH (takes the input molecule itself if omitted)	Molecule Context ASAPolar() returns the water accessible surface area of all atoms of the input molecule with polar partial charge ASAPolar('7.4')returns the water accessible surface area of all atoms with polar partial charge of the major microspecies taken at pH 7.4 Reaction Context ASAPolar(reactant(0)) returns the water accessible surface area of all atoms of the first reactant with polar partial charge ASAPolar(product(0), '7.4') returns the water accessible surface area of all atoms with polar partial charge of the major microspecies of the first product taken at pH 7.4
asymmetricAtom	Structural Calculations License	checks if the specified atom is an asymmetric atom	true for asymmetric atoms, false for symmetric atoms	* the atom index / MolAtom object	Molecule Context asymmetricAtom(2) returns true if atom 2 of the input molecule is an asymmetric atom, false otherwise Reaction Context asymmetricAtom(ratom(2)) returns true if the reactant atom matching map 2 in the reaction equation is an asymmetric atom, false otherwise asymmetricAtom(patom(1)) returns true if the product atom matching map 1 in the reaction equation is an asymmetric atom, false otherwise
asymmetricAtomCount	Structural Calculations License	calculates the number of asymmetric atoms	the asymmetric atom count	-	Molecule Context asymmetricAtomCount() returns the number of asymmetric atoms in the input molecule Reaction Context asymmetricAtomCount(reactant(0)) returns the number of asymmetric atoms in the first reactant asymmetricAtomCount(product(1)) returns the number of asymmetric atoms in the second product
asymmetricAtoms	Structural Calculations License	determines the asymmetric atoms	indexes of asymmetric atoms	-	Molecule Context asymmetricAtoms() returns the indexes of asymmetric atoms in the input molecule Reaction Context asymmetricAtoms(reactant(0)) returns the indexes of asymmetric atoms in the first reactant asymmetricAtoms(product(1)) returns the indexes of asymmetric atoms in the second product
balabanIndex	Structural Calculations License	calculates the Balaban index	the Balaban index	-	Molecule Context calculates the Balaban index Reaction Context the Balaban index
bondCount	-	calculates the bond count	the bond count	-	Molecule Context bondCount() returns the number of bonds in the input molecule Reaction Context bondCount(reactant(0)) returns the number of bonds in the first reactant bondCount(product(1)) returns the number of bonds in the second product
bondType	Structural Calculations License	returns the bond type between two atoms	the bond type between two atoms, -1 if there is no bond between the two atoms	* the (1-based) atom indexes of the two atoms in a string: "index1-index2" (e.g. '2-3')	Molecule Context bondType('2-3') and bondType(bond(1, 2)) both return the bond type between atoms 1 and 2 in the input molecule Reaction Context bondType(reactant(0), bond(ratom(1), ratom(2))) returns the bond type between reactant atoms matching maps 1 and 2 in the reaction equation (see note 1) bondType(product(1), bond(patom(2), patom(3))) returns the bond type between product atoms matching maps 2 and 3 in the reaction equation (see note 1)
carboaliphaticRingCount	Structural Calculations License	calculates the number of carboaliphatic rings in the molecule (aliphatic rings containing carbon atoms only)	number of carboaliphatic rings	-	Molecule Context carboaliphaticRingCount() returns the number of carboaliphatic rings in the input molecule Reaction Context carboaliphaticRingCount(reactant(0)) returns the number of carboaliphatic rings in the first reactant carboaliphaticRingCount(product(1)) returns the number of carboaliphatic rings in the second product
carboaromaticRingCount	Structural Calculations License	calculates the number of carboaromatic rings in the molecule (aromatic rings containing carbon atoms only)	number of carboaromatic rings	-	Molecule Context carboaromaticRingCount() returns the number of carboaromatic rings in the input molecule Reaction Context carboaromaticRingCount(reactant(0)) returns the number of carboaromatic rings in the first reactant carboaromaticRingCount(product(1)) returns the number of carboaromatic rings in the second product
carboRingCount	Structural Calculations License	calculates the number of carbocyclic rings in the molecule (rings containing carbon atoms only)	number of carbocyclic rings	-	Molecule Context carboRingCount() returns the number of carbocyclic rings in the input molecule Reaction Context carboRingCount(reactant(0)) returns the number of carbocyclic rings in the first reactant carboRingCount(product(1)) returns the number of carbocyclic rings in the second product
carboRingCountOfSize	Structural Calculations License	calculates the number of carbocyclic rings of given size (rings containing carbon atoms only)	the number of carbocyclic rings of given size	the ring size	Molecule Context carboRingCountOfSize(6) returns the number of carbocyclic rings of size 6 in the input molecule Reaction Context carboRingCountOfSize(reactant(0), 5) returns the number of carbocyclic rings of size 5 in the first reactant carboRingCountOfSize(product(1), 5) returns the number of carbocyclic rings of size 5 in the second product
carboRings	Structural Calculations License	identifies the carbocyclic rings in the molecule (rings containing carbon atoms only)	atom indexes of the carbocyclic rings in the molecule (null if the molecule does not contain carbocyclic rings)	-	Molecule Context carboRings() returns the atom indexes of the carbocyclic rings in the input molecule Reaction Context carboRings(reactant(0)) returns the atom indexes of the carbocyclic rings in the first reactant carboRings(product(1)) returns the atom indexes of the carbocyclic rings in the second product
carboRingsOfSize	Structural Calculations License	identifies the carbocyclic rings in the molecule having a given size (number of atoms)	atom indexes of the carbocyclic rings in the molecule having the given size (null if the molecule does not carbocyclic carbo rings)	the ring size	Molecule Context carboRings() returns the atom indexes of the carbocyclic rings in the input molecule having the given size Reaction Context carboRings(reactant(0)) returns the atom indexes of the carbocyclic rings in the first reactant having the given size carboRings(product(1)) returns the atom indexes of the carbocyclic rings in the second product having the given size
chainAtom	Structural Calculations License	checks if the specified atom is a chain atom	true for chain atoms, false for non-chain atoms	* the atom index / MolAtom object	Molecule Context chainAtom(2) returns true if atom 2 of the input molecule is a chain atom, false otherwise Reaction Context chainAtom(ratom(2)) returns true if the reactant atom matching map 2 in the reaction equation is a chain atom, false otherwise chainAtom(patom(1)) returns true if the product atom matching map 1 in the reaction equation is a chain atom, false otherwise
chainAtomCount	Structural Calculations License	calculates the chain atom count	the chain atom count	-	Molecule Context chainAtomCount() returns the number of chain atoms in the input molecule Reaction Context chainAtomCount(reactant(0)) returns the number of chain atoms in the first reactant chainAtomCount(product(1)) returns the number of chain atoms in the second product
chainBond	Structural Calculations License	checks if two atoms are connected by a chain bond	true if the two atoms are connected by a chain bond, false otherwise	* the (1-based) atom indexes of the two atoms in a string: "index1-index2" (e.g. '2-3')	Molecule Context chainBond('2-3') and chainBond(bond(1, 2)) both return true if atoms 1 and 2 are connected by a chain bond the input molecule Reaction Context chainBond(reactant(0), bond(ratom(1), ratom(2))) returns true if reactant atoms matching maps 1 and 2 in the reaction equation are connected by a chain bond in the corresponding reactant molecule (see note 1) chainBond(product(1), bond(patom(2), patom(3))) returns true if product atoms matching maps 2 and 3 in the reaction equation are connected by a chain bond in the corresponding product molecule (see note 1)
chainBondCount	Structural Calculations License	calculates the chain bond count	the chain bond count	-	Molecule Context chainBondCount() returns the number of chain bonds in the input molecule Reaction Context chainBondCount(reactant(0)) returns the number of chain bonds in the first reactant chainBondCount(product(1)) returns the number of chain bonds in the second product
chiralCenter	Structural Calculations License	checks if the specified atom is a tetrahedral stereogenic center	true for tetrahedral stereogenic center atoms	* the atom index / MolAtom object	Molecule Context chiralCenter(2) returns true if atom 2 of the input molecule is a tetrahedral stereogenic center, false otherwise Reaction Context chiralCenter(ratom(2)) returns true if the reactant atom matching map 2 in the reaction equation is a tetrahedral stereogenic center, false otherwise chiralCenter(patom(1)) returns true if the product atom matching map 1 in the reaction equation is a tetrahedral stereogenic center, false otherwise
chiralCenterCount	Structural Calculations License	calculates the number of tetrahedral stereogenic center atoms	the tetrahedral stereogenic center count	-	Molecule Context chiralCenterCount() returns the number of tetrahedral stereogenic centers in the input molecule Reaction Context chiralCenterCount(reactant(0)) returns the number of tetrahedral stereogenic centers in the first reactant chiralCenterCount(product(1)) returns the number of tetrahedral stereogenic centers in the second product
chiralCenters	Structural Calculations License	determines the chiral center atoms	indexes of chiral center atoms	-	Molecule Context chiralCenters() returns the indexes of chiral center atoms in the input molecule Reaction Context chiralCenters(reactant(0)) returns the indexes of chiral center atoms in the first reactant chiralCenters(product(1)) returns the indexes of chiral center atoms in the second product
connected	Structural Calculations License	checks if two atoms are connected	true if the two atoms belong to the same connected component, false otherwise	* the (1-based) atom indexes of the two atoms in a string: "index1-index2" (e.g. '2-3')	Molecule Context connected('2-3') and connected(pair(1, 2)) both return true if atoms 1 and 2 are in the same connected component of the input molecule Reaction Context connected(reactant(0), pair(ratom(1), ratom(2))) returns true if reactant atoms matching maps 1 and 2 in the reaction equation are connected in the corresponding reactant molecule ( see note 1) connected(product(1), pair(patom(2), patom(3))) returns true if product atoms matching maps 2 and 3 in the reaction equation are connected in the corresponding product molecule (see note 1)
connectedGraph	Structural Calculations License	checks whether the molecule graph is connected	true if the molecule graph is connected, false otherwise	-	Molecule Context connectedGraph() returns true if the input molecule graph is connected Reaction Context connectedGraph(reactant(0)) returns true if the first reactant is connected connectedGraph(product(1)) returns true if the second product is connected
cyclomaticNumber	Structural Calculations License	calculates the cyclomatic number	the cyclomatic number	-	Molecule Context cyclomaticNumber() returns the cyclomatic number of the input molecule Reaction Context cyclomaticNumber(reactant(0)) returns the cyclomatic number of the first reactant cyclomaticNumber(product(1)) returns the cyclomatic number of the second product
dihedral	Structural Calculations License	calculates the dihedral of four atoms	the dihedral of four atoms	* the (1-based) atom indexes of the four atoms in a string: "index1-index2-index3-index4" (e.g. '2-3-7-4')	Molecule Context dihedral('1-2-3-4') and dihedral(atoms(0, 1, 2, 3)) both return the dihedral of atoms 1, 2, 3 and 4 in the input molecule Reaction Context dihedral(reactant(0), atoms(ratom(1), ratom(2), ratom(3), ratom(4))) returns the dihedral of reactant atoms matching maps 1, 2, 3 and 4 in the reaction equation (see note 1) dihedral(product(1), atoms(patom(2), patom(3), patom(5), patom(6))) returns the dihedral of product atoms matching maps 2, 3, 5 and 6 in the reaction equation (see note 1)
distance	Structural Calculations License	calculates the distance between two atoms	the distance between two atoms	* the (1-based) atom indexes of the two atoms in a string: "index1-index2" (e.g. '2-3')	Molecule Context distance('1-2') and distance(pair(0, 1)) both return the distance between atoms 1 and 2 in the input molecule Reaction Context distance(reactant(0), pair(ratom(1), ratom(2))) returns the distance between reactant atoms matching maps 1 and 2 in the reaction equation (see note 1) distance(product(1), pair(patom(2), patom(3))) returns the distance between product atoms matching maps 2 and 3 in the reaction equation (see note 1)
distanceDegree	Structural Calculations License	calculates the distance degree of an atom	the distance degree	* the atom index / MolAtom object	Molecule Context distanceDegree(2) returns the distance degree of atom 2 of the input molecule Reaction Context distanceDegree(ratom(2)) returns the distance degree of the reactant atom matching map 2 in the reaction equation distanceDegree(patom(1)) returns the distance degree of the product atom matching map 1 in the reaction equation
dreidingEnergy	Structural Calculations License	returns the Dreiding energy of the input molecule (conformer)	the dreiding energy	-	Molecule Context dreidingEnergy() returns the dreiding energy of the input molecule (conformer) Reaction Context dreidingEnergy(reactant(0)) returns the dreiding energy of the first reactant dreidingEnergy(product(1)) returns the dreiding energy of the second product
eccentricity	Structural Calculations License	calculates the eccentricity of an atom	the eccentricity of an atom	* the atom index / MolAtom object	Molecule Context eccentricity(2) returns the eccentricity of atom 2 of the input molecule Reaction Context eccentricity(ratom(2)) returns the eccentricity of the reactant atom matching map 2 in the reaction equation eccentricity(patom(1)) returns the distance degree of the product atom matching map 1 in the reaction equation
fragmentCount	Structural Calculations License	returns the number of fragments (disconnected parts)	the fragment count	-	Molecule Context fragmentCount() returns the number of fragments in the input molecule Reaction Context fragmentCount(reactant(0)) returns the number of fragments in the first reactant fragmentCount(product(1)) returns the number of fragments in the second product
fsp3	Structural Calculations License	returns the fsp3 of the molecule	the fsp3 value	-	Molecule Context fsp3() returns the fsp3 value of the input molecule Reaction Context fsp3(reactant(0)) returns the fsp3 value of the first reactant fsp3(product(1)) returns the fsp3 value of the second product
fusedAliphaticRingCount	Structural Calculations License	calculates the number of fused aliphatic rings (SSSR smallest set of smallest aliphatic rings)	the fused aliphatic ring count	-	Molecule Context fusedAliphaticRingCount() returns the number of fused aliphatic rings in the input molecule Reaction Context fusedAliphaticRingCount(reactant(0)) returns the number of fused aliphatic rings in the first reactant fusedAliphaticRingCount(product(1)) returns the number of fused aliphatic rings in the second product
fusedAliphaticRingCountOfSize	Structural Calculations License	calculates the number of fused aliphatic rings of given size	the number of fused aliphatic rings of given size	the ring size	Molecule Context fusedAliphaticRingCountOfSize(6) returns the number of fused aliphatic rings of size 6 in the input molecule Reaction Context fusedAliphaticRingCountOfSize(reactant(0), 5) returns the number of fused aliphatic rings of size 5 in the first reactant fusedAliphaticRingCountOfSize(product(1), 5) returns the number of fused aliphatic rings of size 5 in the second product
fusedAliphaticRings	Structural Calculations License	identifies the fused aliphatic rings in the molecule	atom indexes of the fused aliphatic rings in the molecule (null if the molecule does not contain fused aliphatic rings)	-	Molecule Context fusedAliphaticRings() returns the atom indexes of the fused aliphatic rings in the input molecule Reaction Context fusedAliphaticRings(reactant(0)) returns the atom indexes of the fused aliphatic rings in the first reactant fusedAliphaticRings(product(1)) returns the atom indexes of the fused aliphatic rings in the second product
fusedAliphaticRingsOfSize	Structural Calculations License	identifies the fused aliphatic rings in the molecule having a given size (number of atoms)	atom indexes of the fused aliphatic rings in the molecule having the given size (null if the molecule does not contain fused aliphatic rings)	the ring size	Molecule Context fusedAliphaticRings() returns the atom indexes of the fused aliphatic rings in the input molecule having the given size Reaction Context fusedAliphaticRings(reactant(0)) returns the atom indexes of the fused aliphatic rings in the first reactant having the given size fusedAliphaticRings(product(1)) returns the atom indexes of the fused aliphatic rings in the second product having the given size
fusedAromaticRingCount	Structural Calculations License	calculates the number of fused aromatic rings (SSSR smallest set of smallest aromatic rings)	the fused aromatic ring count	-	Molecule Context fusedAromaticRingCount() returns the number of fused aromatic rings in the input molecule Reaction Context fusedAromaticRingCount(reactant(0)) returns the number of fused aromatic rings in the first reactant fusedAromaticRingCount(product(1)) returns the number of fused aromatic rings in the second product
fusedAromaticRingCountOfSize	Structural Calculations License	calculates the number of fused aromatic rings of given size	the number of fused aromatic rings of given size	the ring size	Molecule Context fusedAromaticRingCountOfSize(6) returns the number of fused aromatic rings of size 6 in the input molecule Reaction Context fusedAromaticRingCountOfSize(reactant(0), 5) returns the number of fused aromatic rings of size 5 in the first reactant fusedAromaticRingCountOfSize(product(1), 5) returns the number of fused aromatic rings of size 5 in the second product
fusedAromaticRings	Structural Calculations License	identifies the fused aromatic rings in the molecule	atom indexes of the fused aromatic rings in the molecule (null if the molecule does not contain fused aromatic rings)	-	Molecule Context fusedAromaticRings() returns the atom indexes of the fused aromatic rings in the input molecule Reaction Context fusedAromaticRings(reactant(0)) returns the atom indexes of the fused aromatic rings in the first reactant fusedAromaticRings(product(1)) returns the atom indexes of the fused aromatic rings in the second product
fusedAromaticRingsOfSize	Structural Calculations License	identifies the fused aromatic rings in the molecule having a given size (number of atoms)	atom indexes of the fused aromatic rings in the molecule having the given size (null if the molecule does not contain fused aromatic rings)	the ring size	Molecule Context fusedAromaticRings() returns the atom indexes of the fused aromatic rings in the input molecule having the given size Reaction Context fusedAromaticRings(reactant(0)) returns the atom indexes of the fused aromatic rings in the first reactant having the given size fusedAromaticRings(product(1)) returns the atom indexes of the fused aromatic rings in the second product having the given size
fusedRingCount	Structural Calculations License	calculates the number of fused rings (SSSR smallest set of smallest rings)	the fused ring count	-	Molecule Context fusedRingCount() returns the number of fused rings in the input molecule Reaction Context fusedRingCount(reactant(0)) returns the number of fused rings in the first reactant fusedRingCount(product(1)) returns the number of fused rings in the second product
hararyIndex	Structural Calculations License	calculates the Harary index	the Harary index	-	Molecule Context calculates the Harary index Reaction Context the Harary index
heteroaliphaticRingCount	Structural Calculations License	calculates the number of aliphatic heterocyclic rings (SSSR smallest set of smallest aliphatic rings)	the aliphatic heterocyclic ring count	-	Molecule Context heteroaliphaticRingCount() returns the number of aliphatic heterocyclic rings in the input molecule Reaction Context heteroaliphaticRingCount(reactant(0)) returns the number of aliphatic heterocyclic rings in the first reactant heteroaliphaticRingCount(product(1)) returns the number of aliphatic heterocyclic rings in the second product
heteroaliphaticRingCountOfSize	Structural Calculations License	calculates the number of aliphatic heterocyclic rings of given size	the number of aliphatic heterocyclic rings of given size	the ring size	Molecule Context heteroaliphaticRingCountOfSize(6) returns the number of aliphatic heterocyclic rings of size 6 in the input molecule Reaction Context heteroaliphaticRingCountOfSize(reactant(0), 5) returns the number of aliphatic heterocyclic rings of size 5 in the first reactant heteroaliphaticRingCountOfSize(product(1), 5) returns the number of aliphatic heterocyclic rings of size 5 in the second product
heteroaliphaticRings	Structural Calculations License	identifies the aliphatic heterocyclic rings in the molecule	atom indexes of the aliphatic heterocyclic rings in the molecule (null if the molecule does not contain aliphatic heterocyclic rings)	-	Molecule Context heteroaliphaticRings() returns the atom indexes of the aliphatic heterocyclic rings in the input molecule Reaction Context heteroaliphaticRings(reactant(0)) returns the atom indexes of the aliphatic heterocyclic rings in the first reactant heteroaliphaticRings(product(1)) returns the atom indexes of the aliphatic heterocyclic rings in the second product
heteroaliphaticRingsOfSize	Structural Calculations License	identifies the aliphatic heterocyclic rings in the molecule having a given size (number of atoms)	atom indexes of the aliphatic heterocyclic rings in the molecule having the given size (null if the molecule does not contain aliphatic heterocyclic rings)	the ring size	Molecule Context heteroaliphaticRings() returns the atom indexes of the aliphatic heterocyclic rings in the input molecule having the given size Reaction Context heteroaliphaticRings(reactant(0)) returns the atom indexes of the aliphatic heterocyclic rings in the first reactant having the given size heteroaliphaticRings(product(1)) returns the atom indexes of the aliphatic heterocyclic rings in the second product having the given size
heteroaromaticRingCount	Structural Calculations License	calculates the number of aromatic heterocyclic rings (SSSR smallest set of smallest aromatic rings)	the aromatic heterocyclic ring count	-	Molecule Context heteroaromaticRingCount() returns the number of aromatic heterocyclic rings in the input molecule Reaction Context heteroaromaticRingCount(reactant(0)) returns the number of aromatic heterocyclic rings in the first reactant heteroaromaticRingCount(product(1)) returns the number of aromatic heterocyclic rings in the second product
heteroaromaticRingCountOfSize	Structural Calculations License	calculates the number of aromatic heterocyclic rings of given size	the number of aromatic heterocyclic rings of given size	the ring size	Molecule Context heteroaromaticRingCountOfSize(6) returns the number of aromatic heterocyclic rings of size 6 in the input molecule Reaction Context heteroaromaticRingCountOfSize(reactant(0), 5) returns the number of aromatic heterocyclic rings of size 5 in the first reactant heteroaromaticRingCountOfSize(product(1), 5) returns the number of aromatic heterocyclic rings of size 5 in the second product
heteroaromaticRings	Structural Calculations License	identifies the aromatic heterocyclic rings in the molecule	atom indexes of the aromatic heterocyclic rings in the molecule (null if the molecule does not contain aromatic heterocyclic rings)	-	Molecule Context heteroaromaticRings() returns the atom indexes of the aromatic heterocyclic rings in the input molecule Reaction Context heteroaromaticRings(reactant(0)) returns the atom indexes of the aromatic heterocyclic rings in the first reactant heteroaromaticRings(product(1)) returns the atom indexes of the aromatic heterocyclic rings in the second product
heteroaromaticRingsOfSize	Structural Calculations License	identifies the aromatic heterocyclic rings in the molecule having a given size (number of atoms)	atom indexes of the aromatic heterocyclic rings in the molecule having the given size (null if the molecule does not contain aromatic heterocyclic rings)	the ring size	Molecule Context heteroaromaticRings() returns the atom indexes of the aromatic heterocyclic rings in the input molecule having the given size Reaction Context heteroaromaticRings(reactant(0)) returns the atom indexes of the aromatic heterocyclic rings in the first reactant having the given size heteroaromaticRings(product(1)) returns the atom indexes of the aromatic heterocyclic rings in the second product having the given size
heteroRingCount	Structural Calculations License	calculates the number of heterocyclic rings (SSSR smallest set of smallest rings)	the heterocyclic ring count	-	Molecule Context heteroRingCount() returns the number of heterocyclic rings in the input molecule Reaction Context heteroRingCount(reactant(0)) returns the number of heterocyclic rings in the first reactant heteroRingCount(product(1)) returns the number of heterocyclic rings in the second product
heteroRingCountOfSize	Structural Calculations License	calculates the number of heterocyclic rings of given size	the number of heterocyclic rings of given size	the ring size	Molecule Context heteroRingCountOfSize(6) returns the number of heterocyclic rings of size 6 in the input molecule Reaction Context heteroRingCountOfSize(reactant(0), 5) returns the number of heterocyclic rings of size 5 in the first reactant heteroRingCountOfSize(product(1), 5) returns the number of heterocyclic rings of size 5 in the second product
heteroRings	Structural Calculations License	identifies the heterocyclic rings in the molecule	atom indexes of the heterocyclic rings in the molecule (null if the molecule does not contain heterocyclic rings)	-	Molecule Context heteroRings() returns the atom indexes of the heterocyclic rings in the input molecule Reaction Context heteroRings(reactant(0)) returns the atom indexes of the heterocyclic rings in the first reactant heteroRings(product(1)) returns the atom indexes of the heterocyclic rings in the second product
heteroRingsOfSize	Structural Calculations License	identifies the heterocyclic rings in the molecule having a given size (number of atoms)	atom indexes of the heterocyclic rings in the molecule having the given size (null if the molecule does not contain heterocyclic rings)	the ring size	Molecule Context heteroRings() returns the atom indexes of the heterocyclic rings in the input molecule having the given size Reaction Context heteroRings(reactant(0)) returns the atom indexes of the heterocyclic rings in the first reactant having the given size heteroRings(product(1)) returns the atom indexes of the heterocyclic rings in the second product having the given size
hyperWienerIndex	Structural Calculations License	calculates the Hyper Wiener index	the Hyper Wiener index	-	Molecule Context calculates the Hyper Wiener index Reaction Context the Hyper Wiener index
largestAtomRingSize	Structural Calculations License	calculates the size of the largest ring containing the specified atom	the size of the largest ring containing the specified atom	* the atom index / MolAtom object	Molecule Context largestAtomRingSize(1) returns the size of the largest ring containing atom 1 in the input molecule Reaction Context largestAtomRingSize(patom(2)) returns the size of the largest ring containing product atom matching map 2 in the reaction equation
largestConjugatedSystem	Structural Calculations License	returns the atom list of the largest conjugated system in the molecule	-		Molecule Context largestConjugatedSystem() returns the atom list of the largest conjugated system in the input molecule Reaction Context largestConjugatedSystem(product(1)) returns the atom list of the largest conjugated system in the 2nd product
largestConjugatedSystemSize	Structural Calculations License	returns the number of pi electron pairs in the largest conjugated system	-		Molecule Context largestConjugatedSystemSize() returns the number of pi electron pairs in the largest conjugated system Reaction Context largestConjugatedSystemSize(product(1)) returns the number of pi electron pairs in the largest conjugated system of the 2nd product
largestConjugatedSystemMol	Structural Calculations License	returns the input molecule with the largest conjugated system coloured in green	This function should be used with the output option -f mrv to export colour in the output		Molecule Context largestConjugatedSystemMol() returns the input molecule with the largest conjugated system coloured in green Reaction Context largestConjugatedSystemMol(product(1)) returns the 2nd product with the largest conjugated system coloured in green
largestRing	Structural Calculations License	identifies the atoms of the largest ring (number of atoms) in the molecule.	atom indexes of the largest ring in the molecule (null when acyclic)	-	Molecule Context largestRingSize() returns the atom indexes of the largest ring in the input molecule Reaction Context largestRingSize(product(1)) returns the atom indexes of the largest ring in the second product
largestRingSize	Structural Calculations License	calculates the largest ring size	the largest ring size	-	Molecule Context largestRingSize() returns the size of the largest ring in the input molecule Reaction Context largestRingSize(product(1)) returns the size of the largest ring in the second product
largestRingSystem	Structural Calculations License	identifies the atoms of the largest ring system (number of rings) in the molecule.	atom indexes of the largest ring system in the molecule (null when acyclic)	-	Molecule Context largestRingSize() returns the atom indexes of the largest ring system in the input molecule Reaction Context largestRingSize(product(1)) returns the atom indexes of the largest ring system in the second product
largestRingSystemSize	Structural Calculations License	calculates the size of the largest ring system (number of rings)	the size of the largest ring system	-	Molecule Context largestRingSystemSize() returns the size of the largest ring system in the input molecule Reaction Context largestRingSystemSize(reactant(0)) returns the size of the largest ring system in the first reactant largestringsystemsize(product(1)) returns the size of the largest ring system in the second product
maximalProjectionArea	Structural Calculations License	returns the maximal projection area	the maximal projection area	-	Molecule Context maximalProjectionArea() returns the maximal projection area Reaction Context maximalProjectionArea((reactant(0)) returns the maximal projection area of the first reactant maximalProjectionArea(product(1)) returns the maximal projection area of the second product
maximalProjectionRadius	Structural Calculations License	returns the maximal projection radius	the maximal projection radius	-	Molecule Context maximalProjectionRadius() returns the maximal projection radius Reaction Context maximalProjectionRadius((reactant(0)) returns the maximal projection radius of the first reactant maximalProjectionRadius(product(1)) returns the maximal projection radius of the second product
maximalProjectionSize	Structural Calculations License	returns the maximal distance in the molecule perpendicular to the maximal projection area	the maximal distance in the molecule (the actual conformer) perpendicular to its maximal projection area	-	Molecule Context maximalProjectionSize() returns the maximal distance in the molecule perpendicular to the maximal projection area Reaction Context maximalProjectionSize((reactant(0)) returns the maximal distance of the first reactant perpendicular to the maximal projection area maximalProjectionSize(product(1)) returns the maximal distance of the second product perpendicular to the maximal projection area
minimalProjectionArea	Structural Calculations License	returns the minimal projection area	the minimal projection area	-	Molecule Context minimalProjectionArea() returns the minimal projection area Reaction Context minimalProjectionArea((reactant(0)) returns the minimal projection area of the first reactant minimalProjectionArea(product(1)) returns the minimal projection area of the second product
minimalProjectionRadius	Structural Calculations License	returns the minimal projection radius	the minimal projection radius	-	Molecule Context minimalProjectionRadius() returns the minimal projection radius Reaction Context minimalProjectionRadius((reactant(0)) returns the minimal projection radius of the first reactant minimalProjectionRadius(product(1)) returns the minimal projection radius of the second product
minimalProjectionSize	Structural Calculations License	returns the maximal distance in the molecule perpendicular to the minimal projection area	the maximal distance of the molecule (the actual conformer) perpendicular to its minimal projection area	-	Molecule Context minimalProjectionSize() returns the maximal distance in the molecule perpendicular to the minimal projection area Reaction Context minimalProjectionSize((reactant(0)) returns the maximal distance of the first reactant perpendicular to the minimal projection area minimalProjectionSize(product(1)) returns the maximal distance of the second product perpendicular to the minimal projection area

mmff94Energy	Structural Calculations License	returns the MMFF94 energy of the input molecule (conformer)	the MMFF94 energy	-	Molecule Context mmff94Energy() returns the MMFF94 energy of the input molecule (conformer) Reaction Context mmff94Energy(reactant(0)) returns the MMFF94 energy of the first reactant mmff94Energy(product(1)) returns the MMFF94 energy of the second product
plattIndex	Structural Calculations License	calculates the Platt index	the Platt index	-	Molecule Context calculates the Platt index Reaction Context the Platt index
randicIndex	Structural Calculations License	calculates the Randic index	the Randic index	-	Molecule Context calculates the Randic index Reaction Context the Randic index
ringAtom	Structural Calculations License	checks if the specified atom is a ring atom	true for ring atoms, false for non-ring atoms	* the atom index / MolAtom object	Molecule Context ringAtom(2) returns true if atom 2 of the input molecule is a ring atom, false otherwise Reaction Context ringAtom(ratom(2)) returns true if the reactant atom matching map 2 in the reaction equation is a ring atom, false otherwise ringAtom(patom(1)) returns true if the product atom matching map 1 in the reaction equation is a ring atom, false otherwise
ringAtomCount	Structural Calculations License	calculates the ring atom count	the ring atom count	-	Molecule Context ringAtomCount() returns the number of ring atoms in the input molecule Reaction Context ringAtomCount(reactant(0)) returns the number of ring atoms in the first reactant ringAtomCount(product(1)) returns the number of ring atoms in the second product
ringBond	Structural Calculations License	checks if two atoms are connected by a ring bond	true if the two atoms are connected by a ring bond, false otherwise	* the (1-based) atom indexes of the two atoms in a string: "index1-index2" (e.g. '2-3')	Molecule Context ringBond('2-3') and ringBond(bond(1, 2)) both return true if atoms 1 and 2 are connected by a ring bond the input molecule Reaction Context ringBond(reactant(0), bond(ratom(1), ratom(2))) returns true if reactant atoms matching maps 1 and 2 in the reaction equation are connected by a ring bond in the corresponding reactant molecule (see note 1) ringBond(product(1), bond(patom(2), patom(3))) returns true if product atoms matching maps 2 and 3 in the reaction equation are connected by a ring bond in the corresponding product molecule (see note 1)
ringBondCount	Structural Calculations License	calculates the ring bond count	the ring bond count	-	Molecule Context ringBondCount() returns the number of ring bonds in the input molecule Reaction Context ringBondCount(reactant(0)) returns the number of ring bonds in the first reactant ringBondCount(product(1)) returns the number of ring bonds in the second product
ringCount	Structural Calculations License	calculates the ring count	the ring count	-	Molecule Context ringCount() returns the number of rings in the input molecule Reaction Context ringCount(reactant(0)) returns the number of rings in the first reactant ringCount(product(1)) returns the number of rings in the second product
ringCountOfAtom	Structural Calculations License	calculates the number of rings passing through an atom	the number of rings passing through an atom	* the atom index / MolAtom object	Molecule Context ringCountOfAtom(2) returns the number of rings passsing through atom 2 of the input molecule Reaction Context ringCountOfAtom(ratom(2)) returns the number of rings passsing through the reactant atom matching map 2 in the reaction equation ringCountOfAtom(patom(1)) returns the number of rings passsing through the product atom matching map 1 in the reaction equation
ringCountOfSize	Structural Calculations License	calculates the number of rings of given size	the number of rings of given size	the ring size	Molecule Context ringCountOfSize(6) returns the number of rings of size 6 in the input molecule Reaction Context ringCountOfSize(reactant(0), 5) returns the number of rings of size 5 in the first reactant ringCountOfSize(product(1), 5) returns the number of rings of size 5 in the second product
rings	Structural Calculations License	identifies the rings in the molecule	atom indexes of the rings in the molecule (null if the molecule is acyclic)	-	Molecule Context rings() returns the atom indexes of the rings in the input molecule Reaction Context rings(reactant(0)) returns the atom indexes of the rings in the first reactant rings(product(1)) returns the atom indexes of the rings in the second product
ringsOfSize	Structural Calculations License	identifies the rings in the molecule having a given size (number of atoms)	atom indexes of the rings in the molecule having the given size (null if the molecule is acyclic or contains different rings only)	the ring size	Molecule Context rings() returns the atom indexes of the rings in the input molecule having the given size Reaction Context rings(reactant(0)) returns the atom indexes of the rings in the first reactant having the given size rings(product(1)) returns the atom indexes of the rings in the second product having the given size
ringSystemCount	Structural Calculations License	calculates the number of rings systems	the number of rings systems	-	Molecule Context ringSystemCount() returns the number of ring systems in the input molecule Reaction Context ringSystemCount(reactant(0)) returns the number of ring systems in the first reactant ringsystemCount(product(1)) returns the number of ring systems in the second product
ringSystemCountOfSize	Structural Calculations License	calculates the number of rings systems of given size	the number of rings systems of given size	the ring system size	Molecule Context ringSystemCountOfSize(4) returns the number of four-membered ring systems in the input molecule Reaction Context ringSystemCountOfSize(reactant(0),3) returns the number of three-membered ring systems in the first reactant ringsystemCountOfSize(product(1),3) returns the number of three-membered ring systems in the second product
ringSystems	Structural Calculations License	identifies the ring systems in the molecule (fused and spiro rings belong to one ring system)	atom indexes of the ring systems in the molecule (null if the molecule is acyclic)	-	Molecule Context ringSystems() returns the atom indexes of the ring systems in the input molecule Reaction Context ringSystems(reactant(0)) returns the atom indexes of the ring systems in the first reactant ringSystems(product(1)) returns the atom indexes of the ring systems in the second product
ringSystemsOfSize	Structural Calculations License	identifies the ring systems in the molecule having a given size (number of atoms, fused and spiro rings belong to one ring system)	atom indexes of the ring systems in the molecule having the given size (null if the molecule is acyclic or contains different ringSystems only)	the ring size	Molecule Context ringSystems() returns the atom indexes of the ring systems in the input molecule having the given size Reaction Context ringSystems(reactant(0)) returns the atom indexes of the ring systems in the first reactant having the given size ringSystems(product(1)) returns the atom indexes of the ring systems in the second product having the given size
rotatableBond	Structural Calculations License	checks if two atoms are connected by a rotatable bond	true if the two atoms are connected by a rotatable bond, false otherwise	* the (1-based) atom indexes of the two atoms in a string: "index1-index2" (e.g. '2-3')	Molecule Context rotatableBond('2-3') and rotatableBond(bond(1, 2)) both return true if atoms 1 and 2 are connected by a rotatable bond the input molecule Reaction Context rotatableBond(reactant(0), bond(ratom(1), ratom(2))) returns true if reactant atoms matching maps 1 and 2 in the reaction equation are connected by a rotatable bond in the corresponding reactant molecule (see note 1) rotatableBond(product(1), bond(patom(2), patom(3))) returns true if product atoms matching maps 2 and 3 in the reaction equation are connected by a rotatable bond in the corresponding product molecule (see note 1)
rotatableBondCount	Structural Calculations License	calculates the rotatable bond count	the rotatable bond count	-	Molecule Context rotatableBondCount() returns the number of rotatable bonds in the input molecule Reaction Context rotatableBondCount(reactant(0)) returns the number of rotatable bonds in the first reactant rotatableBondCount(product(1)) returns the number of rotatable bonds in the second product
shortestPath	Structural Calculations License	calculates the length of the shortest path between two atoms	the length of the shortest path between two atoms, Integer.MAX_VALUE if disconnected	* the (1-based) atom indexes of the two atoms in a string: "index1-index2" (e.g. '2-3')	Molecule Context shortestPath('2-3') and shortestPath(pair(1, 2)) both return the shortest path length between atoms 1 and 2 in the input molecule Reaction Context shortestPath(reactant(0), pair(ratom(1), ratom(2))) returns the length of the shortest path between reactant atoms matching maps 1 and 2 in the reaction equation (see note 1) shortestPath(product(1), pair(patom(2), patom(3))) returns the length of the shortest path between product atoms matching maps 2 and 3 in the reaction equation (see note 1)
smallestAtomRingSize	Structural Calculations License	calculates the size of the smallest ring containing the specified atom	the size of the smallest ring containing the specified atom	* the atom index / MolAtom object	Molecule Context smallestAtomRingSize(0) returns the size of the smallest ring containing atom 0 in the input molecule Reaction Context smallestAtomRingSize(ratom(1)) returns the size of the smallest ring containing reactant atom matching map 1 in the reaction equation
smallestRing	Structural Calculations License	identifies the atoms of the smallest ring (number of atoms) in the molecule.	atom indexes of the smallest ring in the molecule (null when acyclic)	-	Molecule Context smallestRingSize() returns the atom indexes of the smallest ring in the input molecule Reaction Context smallestRingSize(product(1)) returns the atom indexes of the smallest ring in the second product
smallestRingSize	Structural Calculations License	calculates the smallest ring size	the smallest ring size	-	Molecule Context smallestRingSize() returns the size of the smallest ring in the input molecule Reaction Context smallestRingSize(reactant(0)) returns the size of the smallest ring in the first reactant
smallestRingSystem	Structural Calculations License	identifies the atoms of the smallest ring system (number of rings) in the molecule.	atom indexes of the smallest ring system in the molecule (null when acyclic)	-	Molecule Context smallestRingSize() returns the atom indexes of the smallest ring system in the input molecule Reaction Context smallestRingSize(product(1)) returns the atom indexes of the smallest ring system in the second product
smallestRingSystemSize	Structural Calculations License	calculates the size of the smallest ring system (number of rings)	the size of the smallest ring system	-	Molecule Context smallestRingSystemSize() returns the size of the smallest ring system in the input molecule Reaction Context smallestRingSystemSize(reactant(0)) returns the size of the smallest ring system in the first reactant smallestringsystemsize(product(1)) returns the size of the smallest ring system in the second product
stereoDoubleBondCount	Structural Calculations License	calculates the number of stereo double bonds	the stereo double bond count	-	Molecule Context stereoDoubleBondCount() returns the number of stereo double bonds in the input molecule Reaction Context stereoDoubleBondCount(reactant(0)) returns the number of stereo double bonds in the first reactant stereoDoubleBondCount(product(1)) returns the number of stereo double bonds in the second product
stericEffectIndex	Structural Calculations License	calculates the steric effect index of an atom	the steric effect index of an atom	* the atom index / MolAtom object	Molecule Context calculates the steric effect index of an atom Reaction Context the steric effect index of an atom
stericHindrance	Structural Calculations License	calculates the steric hindrance of an atom	the steric hindrance of an atom	* the atom index / MolAtom object	Molecule Context stericHindrance(2) returns the steric hindrance of atom 2 of the input molecule Reaction Context stericHindrance(ratom(2)) returns the steric hindrance of the reactant atom matching map 2 in the reaction equation stericHindrance(patom(1)) returns the steric hindrance of the product atom matching map 1 in the reaction equation
szegedIndex	Structural Calculations License	calculates the Szeged index	the Szeged index	-	Molecule Context calculates the Szeged index Reaction Context the Szeged index
topologicalPolarSurfaceArea PSA	-	calculates the topological polar surface area (2D)	the polar surface area (2D)	* the major microspecies pH (takes the input molecule itself if omitted)	Molecule Context topologicalPolarSurfaceArea() returns the polar surface area of the input molecule topologicalPolarSurfaceArea('7.4') returns the polar surface area of the major microspecies taken at pH 7.4 Reaction Context topologicalPolarSurfaceArea(reactant(0)) returns the polar surface area of the first reactant topologicalPolarSurfaceArea(product(0), '7.4') returns the polar surface area of the major microspecies of the first product taken at pH 7.4
vanDerWaalsSurfaceArea	Structural Calculations License	calculates the van der Waals surface area	the molecular surface area	* the major microspecies pH (takes the input molecule itself if omitted)	Molecule Context vanDerWaalsSurfaceArea() returns the van der Waals surface area of the input molecule vanDerWaalsSurfaceArea('7.4') returns the van der Waals accessible surface area of the major microspecies taken at pH 7.4 Reaction Context vanDerWaalsSurfaceArea(reactant(0)) returns the van der Waals surface area of the first reactant vanDerWaalsSurfaceArea(product(0), '7.4') returns the van der Waals surface area of the major microspecies of the first product taken at pH 7.4
waterAccessibleSurfaceArea ASA solventAccessibleSurfaceArea	Structural Calculations License	calculates the solvent accessible / water accessible molecular surface area	the molecular surface area	* the major microspecies pH (takes the input molecule itself if omitted)	Molecule Context waterAccessibleSurfaceArea() returns the solvent accessible / water accessible surface area of the input molecule solventAccessibleSurfaceArea('7.4')returns the solvent accessible / water accessible surface area of the major microspecies taken at pH 7.4 Reaction Context waterAccessibleSurfaceArea(reactant(0)) returns the solvent accessible / water accessible surface area of the first reactantsolventAccessibleSurfaceArea(product(0), '7.4') returns the solvent accessible / water accessible surface area of the major microspecies of the first product taken at pH 7.4
wienerIndex	Structural Calculations License	calculates the Wiener index	the Wiener index	-	Molecule Context wienerIndex() returns the Wiener index of the input molecule Reaction Context wienerIndex(reactant(0)) returns the Wiener index of the first reactant wienerIndex(product(1)) returns the Wiener index of the second product
wienerPolarity	Structural Calculations License	calculates the Wiener polarity	the Wiener polarity	-	Molecule Context wienerPolarity() returns the Wiener polarity of the input molecule Reaction Context wienerPolarity(reactant(0)) returns the Wiener polarity of the first reactant wienerPolarity(product(1)) returns the Wiener polarity of the second product

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HBDA Functions

Name	License	Description	Return value	Parameters	Examples
acceptor acc	Structural Calculations License	calculates atomic hydrogen bond acceptor multiplicity	the atomic hydrogen bond acceptor multiplicity	the atom index / MolAtom object the major microspecies pH (takes the input molecule itself if omitted)	Molecule Context acceptor(2) returns the hydrogen bond acceptor multiplicity on atom 2 of the input molecule Reaction Context acceptor(ratom(2)) returns the hydrogen bond acceptor multiplicity on the reactant atom matching map 2 in the reaction equation
acceptorCount	Structural Calculations License	calculates molecular hydrogen bond acceptor count (the number of acceptor atoms)	the molecular hydrogen bond acceptor count	* the major microspecies pH (takes the input molecule itself if omitted)	Molecule Context acceptorCount() returns the number of hydrogen bond acceptor atoms in the input molecule Reaction Context acceptorCount(reactant(0)) returns the number of hydrogen bond acceptor atoms in the first reactant
acceptorSiteCount accSiteCount	Structural Calculations License	calculates molecular hydrogen bond acceptor multiplicity (the sum of atomic multiplicities)	the molecular hydrogen bond acceptor multiplicity	* the major microspecies pH (takes the input molecule itself if omitted)	Molecule Context acceptorSiteCount() returns the hydrogen bond acceptor multiplicity of the input molecule Reaction Context acceptorSiteCount(reactant(0)) returns the hydrogen bond acceptor multiplicity of the first reactant
donor don	Structural Calculations License	calculates atomic hydrogen bond donor multiplicity	the atomic hydrogen bond donor multiplicity	the atom index / MolAtom object the major microspecies pH (takes the input molecule itself if omitted)	Molecule Context donor(1, "7.4") returns the hydrogen bond donor multiplicity on atom 1 of the major microspecies at pH 7.4 Reaction Context returns the hydrogen bond donor multiplicity on the product atom matching map 3 in the reaction equation, taking the major microspecies of the corresponding product at pH 7.4
donorCount	Structural Calculations License	calculates molecular hydrogen bond donor count (the number of donor atoms)	the molecular hydrogen bond donor count	* the major microspecies pH (takes the input molecule itself if omitted)	Molecule Context donorCount("7.4") returns the number of hydrogen bond donor atoms in the major microspecies at pH 7.4 Reaction Context donorCount(product(1), "7.4") returns the number of hydrogen bond donor atoms in the major microspecies of the first product taken at pH 7.4
donorSiteCount donSiteCount	Structural Calculations License	calculates molecular hydrogen bond acceptor / donor multiplicity (the sum of atomic multiplicities)	the molecular hydrogen bond acceptor / donor multiplicity	* the major microspecies pH (takes the input molecule itself if omitted)	Molecule Context donorSiteCount("7.4") returns the hydrogen bond donor multiplicity of the major microspecies at pH 7.4 Reaction Context donorSiteCount(product(1), "7.4") returns the hydrogen bond donor multiplicity of the major microspecies of the first product taken at pH 7.4

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Huckel Functions

Name	License	Description	Return value	Parameters	Examples
chargeDensity totalChargeDensity	Structural Calculations License	calculates the charge density of atoms	the charge density of the atom, NaN for non-existing values	he atom index / MolAtom object the major microspecies pH (takes the input molecule itself if omitted)	Molecule Context chargeDensity(2) returns the charge density of atom 2 of the input molecule, NaN for non-existing value Reaction Context chargeDensity(ratom(1)) returns the charge density of the reactant atom matching map 1 in the reaction equation
electronDensity piChargeDensity	Structural Calculations License	calculates the electron density of atoms	the electron density of the atom, NaN for non-existing values	he atom index / MolAtom object the major microspecies pH (takes the input molecule itself if omitted)	Molecule Context electronDensity(2) returns the electron density of atom 2 of the input molecule, NaN for non-existing value Reaction Context electronDensity(ratom(1)) returns the electron density of the reactant atom matching map 1 in the reaction equation
electrophilicity energyNu nucleophilicLocalizationEnergy	Structural Calculations License	calculates electrophilicity of atoms	the electrophilicity of the atom, NaN for non-aromatic atoms	the atom index / MolAtom object the major microspecies pH (takes the input molecule itself if omitted)	Molecule Context electrophilicity(2) returns the electrophilicity of atom 2 of the input molecule, NaN if atom 2 is non-aromatic Reaction Context electrophilicity(ratom(1)) returns the electrophilicity of the reactant atom matching map 1 in the reaction equation
electrophilicityOrder aromaticElectrophilicityOrder orderE	Structural Calculations License	calculates E order of atoms	the E order index of the atom (0, 1, 2, ...),	the atom index / MolAtom object the major microspecies pH (takes the input molecule itself if omitted)	Molecule Context electrophilicityOrder(2) returns the E order index of atom 2 of the input molecule, e.g. returns 0 if atom 2 is the most electrophilic atom, 1 if atom 2 is the second strongest electrophilic atom, etc., Reaction Context electrophilicityOrder(ratom(1)) returns the E order index of the reactant atom matching map 1 in the reaction equation
hmoChargeDensity	Structural Calculations License	calculates the HMO charge density of atoms	the charge density of the atom, NaN for non-existing values	he atom index / MolAtom object the major microspecies pH (takes the input molecule itself if omitted)	Molecule Context hmoChargeDensity(2) returns the charge density of atom 2 of the input molecule, NaN for non-existing value Reaction Context hmoChargeDensity(ratom(1)) returns the charge density of the reactant atom matching map 1 in the reaction equation
hmoElectronDensity	Structural Calculations License	calculates the HMO electron density of atoms	the electron density of the atom, NaN for non-existing values	he atom index / MolAtom object the major microspecies pH (takes the input molecule itself if omitted)	Molecule Context hmoElectronDensity(2) returns the electron density of atom 2 of the input molecule, NaN for non-existing value Reaction Context hmoElectronDensity(ratom(1)) returns the electron density of the reactant atom matching map 1 in the reaction equation
hmoElectrophilicityOrder hmoOrderE	Structural Calculations License	calculates HMO E order of atoms	the E order index of the atom (0, 1, 2, ...),	the atom index / MolAtom object the major microspecies pH (takes the input molecule itself if omitted)	Molecule Context hmoElectrophilicityOrder(2) returns the E order index of atom 2 of the input molecule, e.g. returns 0 if atom 2 is the most electrophilic atom, 1 if atom 2 is the second strongest electrophilic atom, etc., Reaction Context hmoElectrophilicityOrder(ratom(1)) returns the E order index of the reactant atom matching map 1 in the reaction equation
hmoElectrophilicLocalizationEnergy	Structural Calculations License	calculates HMO localization energy L of atoms	the localization energy L of the atom, NaN for non-aromatic atoms	the atom index / MolAtom object the major microspecies pH (takes the input molecule itself if omitted)	Molecule Context hmoElectrophilicLocalizationEnergy(2) returns the electrophilic L localization energy of atom 2 of the input molecule, NaN if atom 2 is non-aromatic Reaction Context hmoElectrophilicLocalizationEnergy(ratom(1)) returns the electrophilic L localization energy of the reactant atom matching map 1 in the reaction equation
hmoNucleophilicityOrder hmoOrderNu	Structural Calculations License	calculates HMO Nu order of atoms	the Nu order index of the atom (0, 1, 2, ...),	the atom index / MolAtom object the major microspecies pH (takes the input molecule itself if omitted)	Molecule Context hmoNucleophilicityOrder(2) returns the Nu order index of atom 2 of the input molecule, e.g. returns 0 if atom 2 is the most nucleophilic atom, 1 if atom 2 is the second strongest nucleophilic atom, etc., Reaction Context hmoNucleophilicityOrder(ratom(1)) returns the Nu order index of the reactant atom matching map 1 in the reaction equation
hmoNucleophilicLocalizationEnergy	Structural Calculations License	calculates HMO localization energy L of atoms	the localization energy L of the atom, NaN for non-aromatic atoms	the atom index / MolAtom object the major microspecies pH (takes the input molecule itself if omitted)	Molecule Context hmoNucleophilicLocalizationEnergy(2) returns the nucleophilic L localization energy of atom 2 of the input molecule, NaN if atom 2 is non-aromatic Reaction Context hmoNucleophilicLocalizationEnergy(ratom(1)) returns the nucleophilic L localization energy of the reactant atom matching map 1 in the reaction equation
hmoPiEnergy	Structural Calculations License	calculates the HMO pi energy of the molecule	the pi energy of the molecule	* the major microspecies pH (takes the input molecule itself if omitted)	Molecule Context hmoPiEnergy() returns the pi energy of the input molecule Reaction Context hmoPiEnergy(product(1)) returns the pi energy of the second product
nucleophilicity electrophilicLocalizationEnergy energyE	Structural Calculations License	calculates nucleophilicity of atoms	the nucleophilicity of the atom, NaN for non-aromatic atoms	the atom index / MolAtom object the major microspecies pH (takes the input molecule itself if omitted)	Molecule Context nucleophilicity(2) returns the nucleophilicity of atom 2 of the input molecule, NaN if atom 2 is non-aromatic Reaction Context nucleophilicity(ratom(1)) returns the nucleophilicity of the reactant atom matching map 1 in the reaction equation
nucleophilicityOrder aromaticNucleophilicityOrder orderNu	Structural Calculations License	calculates Nu order of atoms	the Nu order index of the atom (0, 1, 2, ...),	the atom index / MolAtom object the major microspecies pH (takes the input molecule itself if omitted)	Molecule Context nucleophilicityOrder(2) returns the Nu order index of atom 2 of the input molecule, e.g. returns 0 if atom 2 is the most nucleophilic atom, 1 if atom 2 is the second strongest nucleophilic atom, etc., Reaction Context nucleophilicityOrder(ratom(1)) returns the Nu order index of the reactant atom matching map 1 in the reaction equation
piEnergy	Structural Calculations License	calculates the pi energy of the molecule. Deprecated.	the pi energy of the molecule	* the major microspecies pH (takes the input molecule itself if omitted)	Molecule Context piEnergy() returns the pi energy of the input molecule Reaction Context piEnergy(product(1)) returns the pi energy of the second product

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Isomers Functions

Name	License	Description	Return value	Parameters	Examples
allTautomer	Isomers License	returns a tautomeric form from all tautomers	the tautomer	* the tautomer index (0-based)	Molecule Context allTautomer(0) returns the first tautomer of the input molecule Reaction Context allTautomer(reactant(0), 1) returns the second tautomer of the first reactant
allTautomers	Isomers License	returns all tautomer forms in an array	the tautomer array	the normalization option (default is false)	Molecule Context allTautomers('normal:true') returns all normal tautomers of the input molecule in an array Reaction Context allTautomers(reactant(0)) returns all tautomers of the first reactant in an array
canonicalResonant	-	constructs the canonical resonant structure	the canonical resonant structure	-	Molecule Context canonicalResonant() returns the canonical resonant structure of the input molecule Reaction Context canonicalResonant(reactant(0)) returns the canonical resonant structure of the first reactant
canonicalTautomer	Isomers License	generates the canonical tautomer structure	the canonical tautomer	option that switches on the normalization (defaults is false)	Molecule Context canonicalTautomer('normal:true') returns the normal canonical tautomer structure of the input molecule Reaction Context canonicalTautomer(reactant(0)) returns the canonical tautomer structure of the first reactant/td>
dominantTautomer tautomer	Isomers License	returns the i-th dominant tautomeric form	the i-th dominant tautomer	the dominant tautomer index (0-based) the pH value as string (set if pH effect should be considered)	Molecule Context dominantTautomer(0) returns the first dominant tautomer of the input molecule dominantTautomer(1, "2.0") returns the second dominant tautomer of the input molecule, considering pH effect at pH 2.0 Reaction Context dominantTautomer(reactant(0), 1) returns the second dominant tautomer of the first reactant dominantTautomer(product(1), 0, "7.4") returns the first dominant tautomer of the second product, considering pH effect at pH 7.4
dominantTautomerCount	Isomers License	calculates the number of dominant tautomers	the number of dominant tautomers	* the pH value as string (set if pH effect should be considered)	Molecule Context dominantTautomerCount() returns the number of dominant tautomers of the input molecule dominantTautomerCount("7.4") returns the number of dominant tautomers of the input molecule, considering pH effect at pH 7.4 Reaction Context dominantTautomerCount(reactant(0)) returns the number of dominant tautomers of the first reactant dominantTautomerCount(product(1), "2.5") returns the number of dominant tautomers of the second product, considering pH effect at pH 2.5
dominantTautomers tautomers	Isomers License	constructs all dominant tautomeric forms (ordered by distribution)	the dominant tautomer array	* the pH value as string (set if pH effect should be considered)	Molecule Context dominantTautomers() returns all dominant tautomers of the input molecule in an array dominantTautomers("2.0") returns all dominant tautomers of the input molecule in an array, considering pH effect at pH 2.0 Reaction Context dominantTautomers(reactant(0)) returns all dominant tautomers of the first reactant in an array dominantTautomers(product(1), "7.4") returns all dominant tautomers of the second product in an array, considering pH effect at pH 7.4
doubleBondStereoisomer	Isomers License	generates a double bond stereoisomer of the molecule	the double bond stereoisomer	* the double bond stereoisomer index (0-based)	Molecule Context doubleBondStereoisomer(0) returns the first double bond stereoisomer of the input molecule Reaction Context doubleBondStereoisomer(reactant(0), 1) returns the second double bond stereoisomer of the first reactant
doubleBondStereoisomerCount	Isomers License	returns the number of generated double bond stereoisomers	the number of generated double bond stereoisomers	-	Molecule Context doubleBondStereoisomerCount() returns the number of generated double bond stereoisomers of the input molecule Reaction Context doubleBondStereoisomerCount(reactant(0)) returns the number of calculated double bond stereoisomers of the first reactant
doubleBondStereoisomers	Isomers License	generates double bond stereoisomers of the molecule (maximum number of double bond stereoisomers to be generated can be set, default: all)	the double bond stereoisomer array	-	Molecule Context doubleBondStereoisomers() returns double bond stereoisomers of the input molecule in an array Reaction Context doubleBondStereoisomers(reactant(0)) returns double bond stereoisomers of the first reactant in an array
genericTautomer	Isomers License	constructs the generic tautomer structure	the generic tautomer structure	-	Molecule Context genericTautomer() returns the generic tautomer structure of the input molecule Reaction Context genericTautomer(reactant(0)) returns the generic tautomer structure of the first reactant/td>
majorTautomer	Isomers License	constructs the major tautomer structure	the major tautomer structure	* the pH value as string (set if pH effect should be considered)	Molecule Context majorTautomer() returns the major tautomer structure of the input molecule Reaction Context majorTautomer(reactant(0)) returns the major tautomer structure of the first reactant/td>
mostStableTautomer	Isomers License	deprecated, use majorTautomer instead. constructs the most stable tautomer structure	the most stable tautomer structure	-	Molecule Context mostStableTautomer() returns the most stable tautomer structure of the input molecule Reaction Context mostStableTautomer(reactant(0)) returns the most stable tautomer structure of the first reactant/td>
resonant	-	constructs a resonant structure	the resonant structure	-	Molecule Context resonant(0) returns the first resonant structure of the input molecule Reaction Context resonant(reactant(0), 1) returns the second resonant structure of the first reactant
resonantCount	-	calculates the number of resonant structures	the number of resonant structures	-	Molecule Context resonantCount() returns the number of resonant structures of the input molecule Reaction Context resonantCount(reactant(0)) returns the number of resonant structures of the first reactant
resonants	-	constructs all resonant structures	the resonant structure array	-	Molecule Context resonants() returns all resonants of the input molecule in an array Reaction Context resonants(reactant(0)) returns all resonants of the first reactant in an array
stereoAnalysis	-	calculates stereo descriptors of molecule	list of stereo descriptors	- the type of stereo descriptor: see the API function names	Molecule Context stereoAnalysis() returns the stereo descriptors of the input molecule as a string stereoAnalysis('tetrahedralStereoCenters') returns the array of tetrahedral stereo descriptors of the input molecule Reaction Context stereoAnalysis(reactant(1)) returns the stereo descriptors of the second reactant stereoAnalysis(reactant(1), 'tetrahedral') returns the tetrahedral stereo descriptors of the second reactant
stereoisomer	Isomers License	generates a stereoisomer of the molecule	the stereoisomer	* the stereoisomer index (0-based)	Molecule Context stereoisomer(0) returns the first stereoisomer of the input molecule Reaction Context stereoisomer(reactant(0), 1) returns the second stereoisomer of the first reactant
stereoisomerCount	Isomers License	returns the number of generated stereoisomers	the number of generated stereoisomers	-	Molecule Context stereoisomerCount() returns the number of generated stereoisomers of the input molecule Reaction Context stereoisomerCount(reactant(0)) returns the number of calculated stereoisomers of the first reactant
stereoisomers	Isomers License	generates stereoisomers of the molecule (maximum number of stereoisomers to be generated can be set, default: all)	the stereoisomer array	-	Molecule Context stereoisomers() returns stereoisomers of the input molecule in an array Reaction Context stereoisomers(reactant(0)) returns stereoisomers of the first reactant in an array
tautomerCount	Isomers License	calculates the number of tautomers	the number of tautomers	-	Molecule Context tautomerCount() returns the number of tautomers of the input molecule Reaction Context tautomerCount(reactant(0)) returns the number of tautomers of the first reactant
tetrahedralStereoisomer	Isomers License	generates a tetrahedral stereoisomer of the molecule	the tetrahedral stereoisomer	-	Molecule Context tetrahedralStereoisomer(0) returns the first tetrahedral stereoisomer of the input molecule Reaction Context tetrahedralStereoisomer(reactant(0), 1) returns the second tetrahedral stereoisomer of the first reactant
tetrahedralStereoisomerCount	Isomers License	returns the number of generated tetrahedral stereoisomers	the number of generated tetrahedral stereoisomers	-	Molecule Context tetrahedralStereoisomerCount() returns the number of generated tetrahedral stereoisomers of the input molecule Reaction Context tetrahedralStereoisomerCount(reactant(0)) returns the number of calculated tetrahedral stereoisomers of the first reactant
tetrahedralStereoisomers	Isomers License	generates tetrahedral stereoisomers of the molecule (maximum number of tetrahedral stereoisomers to be generated can be set, default: all)	the tetrahedral stereoisomer array	-	Molecule Context tetrahedralStereoisomers() returns tetrahedral stereoisomers of the input molecule in an array Reaction Context tetrahedralStereoisomers(reactant(0)) returns tetrahedral stereoisomers of the first reactant in an array

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Markush Functions

Name	License	Description	Return value	Parameters	Examples
isMarkush	-	decides whether the given molecule contains any Markush features	true if the molecule contains any Markush features, false otherwise	-	Molecule Context isMarkush() returns true if the given molecule contains any Markush features, false otherwise Reaction Context isMarkush(reactant(1)) returns true if the second reactant contains any Markush features, false otherwise
markushEnumerationCount enumerationCount	Markush Enumeration Plugin	calculates the number of Markush enumerations	the number of Markush enumerations	* the (1-based) atom indexes of the query atoms to be enumerated (default: all)	Molecule Context markushEnumerationCount() returns the number of Markush enumerated structures of the input molecule markushEnumerationCount('4,5') returns the number of Markush enumerated structures of the input molecule, enumerating only atoms 4, 5 (1-based) Reaction Context markushEnumerationCount(reactant(0)) returns the number of Markush enumerated structures of the first reactant markushEnumerationCount(product(1), atoms(3,4)) returns the number of Markush enumerated structures of the second product, enumerating only atoms 4, 5 (1-based) (the atoms() function converts 0-based indexes to a '-'-separated 1-based atom index string)
markushEnumerations enumeration enumerations markushEnumeration	Markush Enumeration Plugin	constructs Markush enumerated structures sequentially	the enumerated structures	the number of structures to be returned (default: all) the (1-based) atom indexes of the query atoms to be enumerated (default: all)	Molecule Context markushEnumerations() returns all Markush enumerated structures of the input molecule markushEnumerations(1, '2,3') returns one Markush enumerated structure of the input molecule, enumerating atoms 2, 3 (1-based) Reaction Context markushEnumerations(reactant(0), 1) returns one Markush enumerated structure of the first reactant markushEnumerations(product(1), 2, '2,3') returns two Markush enumerated structures of the second product, enumerating atoms 2, 3 (1-based)
markushEnumerationsDisplay	Markush Enumeration Plugin	constructs Markush enumerated structures sequentially with scaffold alignment and scaffold/R-group coloring and enumeration ID	the enumerated structures with alignment and coloring data and enumeration ID	the number of structures to be returned (default: all) the (1-based) atom indexes of the query atoms to be enumerated (default: all)	Molecule Context markushEnumerationsDisplay() returns all Markush enumerated structures of the input molecule, with scaffold alignment and coloring data markushEnumerationsDisplay(1, '2,3') returns one Markush enumerated structure of the input molecule, enumerating atoms 2, 3 (1-based), with scaffold alignment and coloring data Reaction Context markushEnumerationsDisplay(reactant(0), 1) returns one Markush enumerated structure of the first reactant, with scaffold alignment and coloring data with scaffold alignment and coloring data markushEnumerationsDisplay(product(1), 2, '2,3') returns two Markush enumerated structures of the second product, enumerating atoms 2, 3 (1-based), with scaffold alignment and coloring data
markushLibraryMagnitude	Markush Enumeration Plugin	calculates the Markush library magnitude, no enumeration is done	the Markush library magnitude	* the (1-based) atom indexes of the query atoms to be enumerated (default: all)	Molecule Context markushLibraryMagnitude() returns the Markush library magnitude for the input molecule markushLibraryMagnitude('4,5') returns the Markush library magnitude for the input molecule, presuming only atoms 4, 5 (1-based) are enumerated Reaction Context markushLibraryMagnitude(reactant(0)) returns the Markush library magnitude for the first reactant markushLibraryMagnitude(product(1), atoms(3,4)) returns the Markush library magnitude for the second product, presuming only atoms 4, 5 (1-based) are enumerated (the atoms() function converts 0-based indexes to a '-'-separated 1-based atom index string)
markushLibrarySize	Markush Enumeration Plugin	calculates the Markush library size, no enumeration is done	the Markush library size	* the (1-based) atom indexes of the query atoms to be enumerated (default: all)	Molecule Context markushLibrarySize() returns the Markush library size for the input molecule markushLibrarySize('4,5') returns the Markush library size for the input molecule, presuming only atoms 4, 5 (1-based) are enumerated Reaction Context markushLibrarySize(reactant(0)) returns the Markush library size for the first reactant markushLibrarySize(product(1), atoms(3,4)) returns the Markush library size for the second product, presuming only atoms 4, 5 (1-based) are enumerated (the atoms() function converts 0-based indexes to a '-'-separated 1-based atom index string)
markushLibrarySizeAsString	Markush Enumeration Plugin	calculates the Markush library size and returns it as string, no enumeration is done	the Markush library size	* the (1-based) atom indexes of the query atoms to be enumerated (default: all)	Molecule Context markushLibrarySize() returns the Markush library size as string for the input molecule markushLibrarySize('4,5') returns the Markush library size as string for the input molecule, presuming only atoms 4, 5 (1-based) are enumerated Reaction Context markushLibrarySize(reactant(0)) returns the Markush library size as string for the first reactant markushLibrarySize(product(1), atoms(3,4)) returns the Markush library size as string for the second product, presuming only atoms 4, 5 (1-based) are enumerated (the atoms() function converts 0-based indexes to a '-'-separated 1-based atom index string)
randomMarkushEnumerations randomEnumeration randomEnumerations randomMarkushEnumeration	Markush Enumeration Plugin	constructs Markush enumerated structures randomly	the enumerated structures	the number of structures to be returned (default: 1) the (1-based) atom indexes of the query atoms to be enumerated (default: all)	Molecule Context randomMarkushEnumerations() returns a randomly constructed enumerated structure of the input molecule randomMarkushEnumerations(4, '2,3') returns 4 randomly constructed enumerated structures of the input molecule, enumerating only atoms 2, 3 (1-based) Reaction Context randomMarkushEnumerations(reactant(0), 100) returns 100 randomly constructed enumerated structures of the first reactant randomMarkushEnumerations(product(1), '3,4,5') returns a randomly constructed enumerated structure of the second product, enumerating atoms 3, 4, 5 (1-based)
randomMarkushEnumerationsDisplay	Markush Enumeration Plugin	constructs Markush enumerated structures randomly with scaffold alignment and scaffold/R-group coloring and enumeration ID	the enumerated structures with alignment and coloring data and enumeration ID	the number of structures to be returned (default: 1) the (1-based) atom indexes of the query atoms to be enumerated (default: all)	Molecule Context randomMarkushEnumerationsDisplay() returns a randomly constructed enumerated structure of the input molecule, with scaffold alignment and scaffold/R-group coloring datarandomMarkushEnumerationsDisplay(4, '2,3') returns 4 randomly constructed enumerated structures of the input molecule, enumerating only atoms 2, 3 (1-based), with scaffold alignment and coloring data Reaction Context randomMarkushEnumerationsDisplay(reactant(0), 100) returns 100 randomly constructed enumerated structures of the first reactant, with scaffold alignment and coloring data randomMarkushEnumerationsDisplay(product(1), '3,4,5') returns a randomly constructed enumerated structure of the second product, enumerating atoms 3, 4, 5 (1-based), with scaffold alignment and coloring data

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Match Functions

Name	License	Description	Return value	Parameters	Examples
disjointMatchCount	Structure Search	performs substructure search, returns the maximal number of pairwise disjoint search hits	the maximal number of pairwise disjoint search hits	target atom index / MolAtom object (optional) query Molecule object / SMARTS string * query atom map(s) (optional) The function returns the maximal number of pairwise disjoint query structures found in the target molecule. Warning: if the target atom index and optionally query atom maps are specified then the return value can only be 0 or 1, therefore the result is similar to the result of the match function.	Molecule Context <ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="32063639-03ca-4f1c-9f87-82aa66315fac"><ac:plain-text-body></ac:plain-text-body></ac:structured-macro> Reaction Context <ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="c7696101-9696-47e1-89e4-bd6f6914fb9b"><ac:plain-text-body><![CDATA[disjointMatchCount(reactant(0), "[#8]C=O") counts the maximal number of pairwise disjoint carboxylic groups in the first reactant	]]></ac:plain-text-body></ac:structured-macro>
match	Structure Search	performs substructure search and optionally checks for atom matching	true if matching substructure found, false otherwise	target atom index / MolAtom object (optional) query Molecule object / SMARTS string * query atom map(s) (optional) The function returns true if the query structure is found in the target molecule, the hit is required to include the target atom if specified, furthermore if query atom map(s) are specified then these mapped atoms should match the target atom.	Molecule Context <ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="e12cb441-0b95-4bd7-b3b7-825793aa9439"><ac:plain-text-body></ac:plain-text-body></ac:structured-macro> Reaction Context <ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="f39f6396-975c-4b7b-ae76-24f463898f0f"><ac:plain-text-body><![CDATA[match(reactant(0), "[#8]C=O") performs substructure search without atom matching requirement, the target is the first reactant, the query is the carboxylic group given in the string parameter match(patom(2), "[#8]C=O") performs substructure search, checks if product atom matching map 2 in the reaction equation matches any atom of the carboxylic group query match(ratom(1), "[#8:1]C=[O:2]", 1, 2) performs substructure search, checks if reactant atom matching map 1 in the reaction equation is a carboxylic oxygen	]]></ac:plain-text-body></ac:structured-macro>
matchCount	Structure Search	performs substructure search and optionally checks for atom matching, counts search hits	the number of search hits	target atom index / MolAtom object (optional) query Molecule object / SMARTS string * query atom map(s) (optional) The function returns the number of query structures found in the target molecule, the hit is required to include the target atom if specified, furthermore if query atom map(s) are specified then these mapped atoms should match the target atom.	Molecule Context <ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="8a943b00-ca03-44ba-8942-d5b1a2c43197"><ac:plain-text-body></ac:plain-text-body></ac:structured-macro> Reaction Context <ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="c77d67a8-f859-48a3-a482-c99ca63b1d49"><ac:plain-text-body><![CDATA[matchCount(reactant(0), "[#8]C=O") counts search hits without atom matching requirement, the target is the first reactant, the query is the carboxylic group given in the string parameter matchCount(patom(2), "[#8]C=O") counts search hits, checks if product atom matching map 2 in the reaction equation matches any atom of the carboxylic group query matchCount(ratom(1), "[#8:1]C=[O:2]", 1, 2) counts search hits with reactant atom matching map 1 in the reaction equation being a carboxylic oxygen	]]></ac:plain-text-body></ac:structured-macro>
matchFirst	Structure Search	performs substructure search and optionally checks for atom matching	index of the first matching substructure (1-based indexing)	target atom index / MolAtom object (optional) query Molecule objects / SMARTS strings in collection (e.g. {amine,amide,"[#8][C:1]=O"}) * query atom map(s) (optional)The function returns the index of the first matching query structure found in the target molecule, the hit is required to include the target atom if specified, furthermore if query atom map(s) are specified then these mapped atoms should match the target atom.	Molecule Context `matchFirst({amine,amide,alcohol})` performs substructure search without atom matching requirement, the target is the input molecule, the queries are the amine, amide, and alcohol groups given in the string parameter. Function returns `1` if there is an amine group in the input molecule, `2` if there is no amine, but there is an amide group in the input molecule, and returns `3` if there is no amine or amide group, but there is an alcohol group in the input molecule. Returns `0` if none of the listed groups is found in input molecule. `matchFirst(6, {"[#8][C:1]=O","[NX3:2][CX3:1]=[OX1:3]"}, 1)` performs substructure search, checks if target atom `6` matches the carbon (atom with map `1`) of the carboxylic or amide group in query. Returns the index of the query if match found, `0` otherwise. `matchFirst(6, {"[#8:1]C=[O:2]","[#6][OX2:1][CX3](o-2)[#6]"}, 1, 2)` performs substructure search, checks if target atom `6` of the input molecule is a carboxylic oxygen or an oxigen in an ester group. Returns the index of the query if match found, `0` otherwise. Reaction Context `matchFirst(reactant(0), {amine,amide,alcohol})` performs substructure search without atom matching requirement, the target is the first reactant, the queries are the amine, amide, and alcohol groups given in the string parameter. Function returns `1` if there is an amine group in the first reactant, `2` if there is no amine group, but there is an amide group in the first reactant, and returns `3` if there is no amine or amide group, but there is an alcohol group in the first reactant. Returns `0` if none of the listed groups is found in first reactant. `matchFirst(patom(2), {"[#8][C]=O","[NX3][CX3]=[OX1]"})` performs substructure search, checks if product atom matching map `2` in the reaction equation matches any atom of the carboxylic or amide group query. Returns the index of mathing query, or `0` if no match found. `matchFirst(ratom(1), {"[#8:1]C=[O:2]","[#6][OX2:1][CX3](o-2)[#6]"}, 1, 2)` performs substructure search, checks if reactant atom matching map `1` in the reaction equation is a carboxylic oxygen or an oxigen in an ester group. Returns the index of the query if match found, `0` otherwise.	]]></ac:plain-text-body></ac:structured-macro>

Predefined Molecules and Molecule Sets

It is sometimes easier to refer molecules by names rather than explicit SMARTS strings or molecule file paths. For example, you may want to write nitro or carboxyl as query in a match function. Frequently used queries are pre-defined in the built-in functional groups file (chemaxon/marvin/templates/functionalgroups.cxsmi within MarvinBeans-templates.jar).

You can also define your favourite query SMARTS in marvin/config/marvin/templates/functionalgroups.cxsmi file and in $HOME\chemaxon\marvin emplates\functionalgroups.cxsmi (Windows) or $HOME/.chemaxon/marvin/templates/functionalgroups.cxsmi (UNIX / Linux) file where marvin is the Marvin istallation directory, $HOME is your user home directory.

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Name Functions

Name	License	Description	Return value	Parameters	Examples
name	Structure To Name License	returns the name(s) of the molecule specified by the export option	the name(s) of the molecule	either empty (IUPAC export option) or the specified name export option	Molecule Context name() returns the preferred IUPAC name of the input molecule name('CAS#') returns CAS Registry Number(s) of the input molecule Reaction Context N / A (reaction rules are numerical)
traditionalName	Structure To Name License	returns the traditional name of the molecule	the traditional name of the molecule	-	Molecule Context traditionalName() returns the traditional name of the input molecule Reaction Context N / A (reaction rules are numerical)

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Other functions

Name	License	Description	Return value	Parameters	Molecule context example(s)	Reaction context example(s)
mpo	Protonation, Partitioning, Structural Calculations	calculates the CNS Multiparameter Optimisation (MPO) Score	the MPO score	-	mpo() returns the MPO score of the input molecule	mpo(product(1)) returns the MPO score of the second product

Partitioning Functions

Name	License	Description	Return value	Parameters	Examples
HLB number	Partitioning License	calculates the HLB number	the HLB number	* the calculation method or empty	Molecule Context hlb() returns the HLB number of the input molecule using the default calculation method hlb('davies') returns the HLB number of the input molecule using the Davies calculation method Reaction Context hlb(reactant(1), 'griffin') returns the HLB number of the second reactant using the Griffin method
logD	Partitioning License	calculates log D at specified pH	the log D value	* the pH value	Molecule Context logD('7.4') returns the log D at pH 7.4 of the input molecule Reaction Context logD(reactant(1), '7.4') returns the log D at pH 7.4 of the second reactant
logDKLOP	Partitioning License	calculates log D at specified pH using method "KLOP"	the log D value	* the pH value	Molecule Context logDKLOP('7.4') returns the log D at pH 7.4 of the input molecule Reaction Context logDKLOP(reactant(1), '7.4') returns the log D at pH 7.4 of the second reactant
logDPHYS	Partitioning License	calculates log D at specified pH using method "PHYS"	the log D value	* the pH value	Molecule Context logDPHYS('7.4') returns the log D at pH 7.4 of the input molecule Reaction Context logDPHYS(reactant(1), '7.4') returns the log D at pH 7.4 of the second reactant
logDUser	Partitioning License	calculates log D at specified pH using the user defined method	the log D value	* the pH value	Molecule Context logDUser('7.4') returns the log D at pH 7.4 of the input molecule Reaction Context logDUser(reactant(1), '7.4') returns the log D at pH 7.4 of the second reactant
logDVG	Partitioning License	calculates log D at specified pH using method "VG"	the log D value	* the pH value	Molecule Context logDVG('7.4') returns the log D at pH 7.4 of the input molecule Reaction Context logDVG(reactant(1), '7.4') returns the log D at pH 7.4 of the second reactant
logDWeighted	Partitioning License	calculates log D at specified pH using weighted method	the log D value	* the pH value	Molecule Context logDWeighted('7.4') returns the log D at pH 7.4 of the input molecule Reaction Context logDWeighted(reactant(1), '7.4') returns the log D at pH 7.4 of the second reactant
logP	Partitioning License	calculates log P	the log P value	the result type: "logPMicro": the log P of the input molecule itself "logPNonionic": the log P of the nonionic species "logDpI": log D at p I * "logPTrue": the most typical from the above (default)	Molecule Context logP() returns the most typical log P of the input molecule log P , the log P of the nonionic species and log D at pI logP('logPMicro') returns the log P of the input molecule itself Reaction Context logP(reactant(1), 'logDpI') returns the log D at p I of the second reactant logP(product(1), 'logPNonionic') returns log P of the nonionic species of the second product
logPincrement logPi	Partitioning License	calculates the atomic log P increment	the atomic log P increment	* the atom index / MolAtom object	Molecule Context logPincrement(2) returns the log P increment on atom 2 of the input molecule Reaction Context logPincrement(ratom(1)) returns the log P increment on the reactant atom matching map 1 in the reaction equation
logPKLOP	Partitioning License	calculates log P using method "KLOP"	the log P value	the result type: "logPMicro": the log P of the input molecule itself "logPNonionic": the log P of the nonionic species "logDpI": log D at p I * "logPTrue": the most typical from the above (default)	Molecule Context logPKLOP() returns the most typical log P out of the input molecule log P , the log P of the nonionic species and log D at p I logPKLOP('logPMicro') returns the log P of the input molecule itself Reaction Context logPKLOP(reactant(1), 'logDpI') returns the log D at p I of the second reactant logPKLOP(product(1), 'logPNonionic') returns log P of the nonionic species of the second product
logPPHYS	Partitioning License	calculates log P using method "PHYS"	the log P value	the result type: "logPMicro": the log P of the input molecule itself "logPNonionic": the log P of the nonionic species "logDpI": log D at p I * "logPTrue": the most typical from the above (default)	Molecule Context logPPHYS() returns the most typical log P out of the input molecule log P , the log P of the nonionic species and log D at p I logPPHYS('logPMicro') returns the log P of the input molecule itself Reaction Context logPPHYS(reactant(1), 'logDpI') returns the log D at p I of the second reactant logPPHYS(product(1), 'logPNonionic') returns log P of the nonionic species of the second product
logPUser	Partitioning License	calculates log P using the user defined method	the log P value	the result type: "logPMicro": the log P of the input molecule itself "logPNonionic": the log P of the nonionic species "logDpI": log D at p I * "logPTrue": the most typical from the above (default)	Molecule Context logPUser() returns the most typical log P out of the input molecule log P , the log P of the nonionic species and log D at p I logPUser('logPMicro') returns the log P of the input molecule itself Reaction Context logPUser(reactant(1), 'logDpI') returns the log D at p I of the second reactant logPUser(product(1), 'logPNonionic') returns log P of the nonionic species of the second product
logPVG	Partitioning License	calculates log P using method "VG"	the log P value	the result type: "logPMicro": the log P of the input molecule itself "logPNonionic": the log P of the nonionic species "logDpI": log D at p I * "logPTrue": the most typical from the above (default)	Molecule Context logPVG() returns the most typical log P out of the input molecule log P , the log P of the nonionic species and log D at p I logPVG('logPMicro') returns the log P of the input molecule itself Reaction Context logPVG(reactant(1), 'logDpI') returns the log D at p I of the second reactant logPVG(product(1), 'logPNonionic') returns log P of the nonionic species of the second product
logPWeighted	Partitioning License	calculates log P using weighted method	the log P value	the result type: "logPMicro": the log P of the input molecule itself "logPNonionic": the log P of the nonionic species "logDpI": log D at p I * "logPTrue": the most typical from the above (default)	Molecule Context logPWeighted() returns the most typical log P out of the input molecule log P , the log P of the nonionic species and log D at p I logPWeighted('logPMicro') returns the log P of the input molecule itself Reaction Context logPWeighted(reactant(1), 'logDpI') returns the log D at p I of the second reactant logPWeighted(product(1), 'logPNonionic') returns log P of the nonionic species of the second product

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Protonation Functions

Name	License	Description	Return value	Parameters	Examples
acidicpKa apKa	Protonation License	calculates acidic p K _a values	the acidic p K _a values	the atom index / MolAtom object, the strength index as string (e.g. '1' for the strongest, '2' for the second strongest p K _a), Note, that the strength index is specified between quotation marks.	Molecule Context acidicpKa(0) returns the acidic p K _a of atom 0 of the input molecule acidicpKa("2") returns the second strongest acidic p K _a value Reaction Context acidicpKa(ratom(1)) returns the acidic p K _a of reactant atom matching map 1 in the reaction equation acidicpKa(product(0), "1") returns the strongest basic p K _a value in the first product
acidicpKaLargeModel	Protonation License	calculates acidic p K _a values using large model (this model is optimized for a large number of ionizable atoms)	the acidic p K _a values	the atom index / MolAtom object, the strength index as string (e.g. '1' for the strongest, '2' for the second strongest p K _a), Note, that the strength index is specified between quotation marks.	Molecule Context acidicpKaLargeModel(0) returns the acidic p K _a of atom 0 of the input molecule acidicpKaLargeModel("2") returns the second strongest acidic p K _a value Reaction Context acidicpKaLargeModel(ratom(1)) returns the acidic p K _a of reactant atom matching map 1 in the reaction equation acidicpKaLargeModel(product(0), "1") returns the strongest basic p K _a value in the first product
acidicpKaUseCorrection	Protonation License	calculates acidic p K _a values using the correction library	the acidic p K _a values	the atom index / MolAtom object, the strength index as string (e.g. '1' for the strongest, '2' for the second strongest p K _a), Note, that the strength index is specified between quotation marks.	Molecule Context acidicpKaUseCorrection(0) returns the acidic p K _a of atom 0 of the input molecule "acidicpKaUseCorrection"("2") returns the second strongest acidic p K _a value Reaction Context "acidicpKaUseCorrection"(ratom(1)) returns the acidic p K _a of reactant atom matching map 1 in the reaction equation "acidicpKaUseCorrection"(product(0), "1") returns the strongest basic p K _a value in the first product
averageMicrospeciesCharge	Protonation License	calculates the average microspecies charge (weighted sum of charges of all the microspecies of the molecule) at the given pH	the average charge	* the major microspecies pH	Molecule Context averageMicrospeciesCharge() returns the average charge of the microspecies of the input molecule Reaction Context averageMicrospeciesCharge(reactant(1)) returns the average charge of the microspecies of the second reactant
basicpKa bpKa	Protonation License	calculates basic p K _a values	the basic p K _a values	the atom index / MolAtom object, the strength index as string (e.g. '1' for the strongest, '2' for the second strongest p K _a), Note, that the strength index is specified between quotation marks.	Molecule Context basicpKa(0) returns the basic p K _a of atom 0 of the input molecule basicpKa("2") returns the second strongest basic p K _a value Reaction Context basicpKa(ratom(1)) returns the basic p K _a of reactant atom matching map 1 in the reaction equation basicpKa(product(0), "1") returns the strongest basic p K _a value in the first product
basicpKaLargeModel	Protonation License	calculates basic p K _a values using large model (this model is optimized for a large number of ionizable atoms)	the basic p K _a values	the atom index / MolAtom object, the strength index as string (e.g. '1' for the strongest, '2' for the second strongest p K _a), Note, that the strength index is specified between quotation marks.	Molecule Context basicpKaLargeModel(0) returns the basic p K _a of atom 0 of the input molecule basicpKaLargeModel("2") returns the second strongest basic p K _a value Reaction Context basicpKaLargeModel(ratom(1)) returns the basic p K _a of reactant atom matching map 1 in the reaction equation basicpKaLargeModel(product(0), "1") returns the strongest basic p K _a value in the first product
basicpKaUseCorrection	Protonation License	calculates basic p K _a values using the correction library	the basic p K _a values	the atom index / MolAtom object, the strength index as string (e.g. '1' for the strongest, '2' for the second strongest p K _a), Note, that the strength index is specified between quotation marks.	Molecule Context basicpKaUseCorrection(0) returns the basic p K _a of atom 0 of the input molecule basicpKaUseCorrection("2") returns the second strongest basic p K _a value Reaction Context basicpKaUseCorrection(ratom(1)) returns the basic p K _a of reactant atom matching map 1 in the reaction equation basicpKaUseCorrection(product(0), "1") returns the strongest basic p K _a value in the first product
isoelectricPoint pI	Protonation License	calculates isoelectric point	the isoelectric point	-	Molecule Context isoelectricPoint() returns the isoelectric point of the input molecule Reaction Context isoelectricPoint(reactant(1)) returns the isoelectric point of the second reactant
majorMicrospecies majorMs	Protonation License	calculates major microspecies at specified pH	the major microspecies	* the pH value as string	Molecule Context majorMicrospecies("7.4") returns the major microspecies of the input molecule at pH 7.4 Reaction Context majorMicrospecies(reactant(0), "7.4") returns the major microspecies of the first reactant at pH 7.4 majorMicrospecies(product(1), "7.4") returns the major microspecies of the second product at pH 7.4
microspecies ms	Protonation License	calculates microspecies at specified pH	the microspecies	the pH value as string the microspecies index by descending order of microspecies distributions	Molecule Context microspecies("7.4", 1) returns the microspecies of the input molecule with second largest distribution at pH 7.4 Reaction Context microspecies(reactant(0), "7.4", 2) returns the microspecies of the first reactant with third largest distribution at pH 7.4 microspecies(product(1), "7.4", 1) returns the microspecies of the second product with second largest distribution at pH 7.4
microspeciesCount msCount	Protonation License	calculates the number of microspecies at specified pH	the number of microspecies	-	Molecule Context microspeciesCount() returns the number of microspecies of the input molecule Reaction Context microspeciesCount(reactant(0)) returns the number of microspecies of the first reactant microspeciesCount(product(1)) returns the number of microspecies of the second product
microspeciesDistribution msDistr	Protonation License	calculates microspecies distribution at specified pH	the microspecies distribution	the pH value as string the microspecies index by descending order of microspecies distributions	Molecule Context microspeciesDistribution("5.4", 0) returns the largest microspecies distribution of the input molecule at pH 5.4 Reaction Context microspeciesDistribution(reactant(0), "5.4", 2) returns the third largest microspecies distribution of the first reactant at pH 5.4 microspeciesDistribution(product(1), "3.2", 1) returns the second largest microspecies distribution of the second product at pH 3.2
pKa	Protonation License	calculates p K _a values	the p K _a values	the atom index / MolAtom object, the strength index as string (e.g., '1' for the strongest, '2' for the second strongest p K _a), the result type ("acidic", "basic", or "pka" for both (default)) Note, that the strength index is specified between quotation marks. In case of strength index the result type can be specified as "acidic" or "basic". In case of "pka"result type the returned p K _a values are acidic or basic (mixed!), depending on the acidic or basic character of the given atom. Acidic p K _a is returned for an atom, if acidicpKa() ≤ 14.8-basicpKa() , otherwise basic p K _a is returned. Specifying "acidic" or "basic" result type is required to get the acidic or basic p K* _a values only (also acidicpKa or basicpKa functions can be used alternatively).	Molecule Context pKa(0) returns the p K _a of atom 0 of the input molecule pKa("acidic", "2") returns the second strongest acidic p K _a value Reaction Context pKa(ratom(1)) returns the p K _a of reactant atom matching map 1 in the reaction equation pKa(product(0), "basic", "1") returns the strongest basic p K _a value in the first product
pKaUseCorrection	Protonation License	calculates p K _a values using the correction library	the p K _a values	the atom index / MolAtom object, the strength index as string (e.g. '1' for the strongest, '2' for the second strongest p K _a), the result type ("acidic", "basic", or "pka" for both (default)) Note, that the strength index is specified between quotation marks. In case of strength index the result type can be specified as "acidic" or "basic". In case of "pka"result type the returned p K _a values are acidic or basic (mixed!), depending on the acidic or basic character of the given atom. Acidic p K _a is returned for an atom, if acidicpKa() ≤ 14.8-basicpKa() , otherwise basic p K _a is returned. Specifying "acidic" or "basic" result type is required to get the acidic or basic p K* _a values only (also acidicpKaUseCorrection() or basicpKaUseCorrection() functions can be used alternatively).	Molecule Context pKaUseCorrection(0) returns the p K _a of atom 0 of the input molecule pKaUseCorrection("acidic", "2") returns the second strongest acidic p K _a value Reaction Context pKaUseCorrection(ratom(1)) returns the p K _a of reactant atom matching map 1 in the reaction equation pKaUseCorrection(product(0), "basic", "1") returns the strongest basic p K _a value in the first product

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Refractivity Functions

Name	License	Description	Return value	Parameters	Examples
refractivity refrac	Structural Calculations License	calculates molar refractivity	the refractivity value	-	Molecule Context refractivity() returns the molar refractivity of the input molecule Reaction Context refractivity(reactant(1)) returns the molar refractivity of the second reactant
refractivityIncrements refraci	Structural Calculations License	calculates atomic refractivity increments	the atomic refractivity increment	* the atom index / MolAtom object	Molecule Context refractivityIncrements(2) returns the refractivity increment on atom 2 of the input molecule Reaction Context refractivityIncrements(ratom(1)) returns the refractivity increment on the reactant atom matching map 1 in the reaction equation

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Solubility Functions

Name	License	Description	Return value	Parameters	Examples
logS	Solubility License	Calculates intrinsic solubility or solubility at a specified pH	the log S value	the pH value the solubility unit: logS, mol/l, mg/ml, category	Molecule Context logS() returns the intrinsic solubility of the input molecule in logS unit (default) logS('7.4', 'category') returns the qualitative log S at pH 7.4 of the input molecule logS('7.4', 'mol/l') returns the log S at pH 7.4 of the input molecule in mol/l unit

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StructuralFrameworks Functions

Name	License	Description	Return value	Parameters	Examples
bmf	Structural Calculations License	Returns the Bemis-Murcko framework of the input structure	BMF of the input structure	-	Molecule Context bmf() returns the Bemis-Murcko framework of the input molecule Reaction Context bmf(reactant(0)) returns the Bemis-Murcko framework of the first reactant
bmfl bemisMurckoFrameworkLoose	Structural Calculations License	Returns the Bemis-Murcko loose framework of the input structure. Calculated by removing side chains. Exocyclic non single bonded atoms are kept. Remaining atom and bond types are not changed.	Loose BMF of the input structure	-	Molecule Context bmfl() returns the loose Bemis-Murcko framework of the input molecule Reaction Context bmfl(reactant(0)) returns the loose Bemis-Murcko framework of the first reactant
bmflp bemisMurckoFrameworkLoosePruned	Structural Calculations License	Returns the Bemis-Murcko loose framework of the input structure. Calculated by removing side cains. Atom and bond types are generalized by replacing all atoms with carbons and setting all bond types to single. Exocyclic non single bonded atoms are kept as single bonded carbons.	Generalized loose BMF of the input structure	-	Molecule Context bmflp() returns the generalized loose Bemis-Murcko framework of the input molecule Reaction Context bmflp(reactant(0)) returns the generalized loose Bemis-Murcko framework of the first reactant

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Structure Checker Functions

Name	License	Description	Return value	Parameters	Examples
check	-	checks the structure for errors, according to the configuration	the error report	Structure checker/fixer configuration as action string or XML string	Molecule Context (All) check("aromaticity..valence"), or check('"<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"no\"?><checkers><AromaticityErrorChecker fixMode=\"fix\" fixerClassName=\"chemaxon.fixers.RearomatizeFixer\" type=\"general\"/><ValenceErrorChecker allowTraditionalNitrogen=\"false\" fixMode=\"fix\" fixerClassName=\"chemaxon.fixers.ValenceFixer\"/> "') checks for aromaticity and valence errors, and returns the error report Reaction Context check(reactant(0), "aromaticity..valence") checks for aromaticity and valence errors in first reactant, and returns the error report
checkErrorCount	-	checks the structure for errors, according to the configuration	the total error count	Structure checker/fixer configuration as XML or action string	Molecule Context checkErrorCount('"<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"no\"?><checkers><AromaticityErrorChecker fixMode=\"fix\" fixerClassName=\"chemaxon.fixers.RearomatizeFixer\" type=\"general\"/><ValenceErrorChecker allowTraditionalNitrogen=\"false\" fixMode=\"fix\" fixerClassName=\"chemaxon.fixers.ValenceFixer\"/> "') or checkErrorCount("aromaticity..valence") checks for aromaticity and valence errors, and returns the total error count Reaction Context check(reactant(0), "aromaticity..valence") checks for aromaticity and valence errors in first reactant, and returns the error report
fix	-	checks the structure for errors, according to the configuration, and then fixes the errors	the fixed molecule	Structure checker/fixer configuration as action string or XML string	Molecule Context (All) fix("chiralflag..isotope->converttoelementalform"), or fix('"<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"no\"?><checkers><ChiralFlagChecker fixMode=\"fix\" fixerClassName=\"chemaxon.fixers.RemoveChiralFlagFixer\"/><IsotopeChecker fixMode=\"fix\" fixerClassName=\"chemaxon.fixers.ConvertToElementalFormFixer\"/>"') searches for ciral flags and isotopes, and removes them or converts them to elemental form Reaction Context fix(product(1), "chiralflag..isotope->converttoelementalform") searches for ciral flags and isotopes in second product, and removes them or converts them to elemental form
isValid	-	checks the structure for errors, according to the configuration	true, if the structure is valid (has no errors), false otherwise	Structure checker/fixer configuration as action string or XML string	Molecule Context (All) isValid("aromaticity..valence"), or isValid('"<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"no\"?><checkers><AromaticityErrorChecker fixMode=\"fix\" fixerClassName=\"chemaxon.fixers.RearomatizeFixer\" type=\"general\"/><ValenceErrorChecker allowTraditionalNitrogen=\"false\" fixMode=\"fix\" fixerClassName=\"chemaxon.fixers.ValenceFixer\"/> "') checks for aromaticity and valence errors, and returns if the structure is valid Reaction Context isValid(reactant(0), "aromaticity..valence") checks for aromaticity and valence errors in first reactant, and returns if it is valid

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Notes

If in reaction context in the parameter list of a Chemical Terms function atoms are referred by atom index - including cases when a Chemical Terms function is used to convert reactant or product atom maps to atom indexes - then the molecule (reactant / product) parameter always have to be specified (e.g. shortestPath(reactant(0), pair(ratom(1), ratom(2)))) and must contain all the atoms referred by atom indexes.
Although the function/calculation names are case-sensitive, the lowercase versions are always accepted. For example, aromaticAtomCount() is equivalent to aromaticatomcount(), but AromaticAtomCount() and AROMATICATOMCOUNT() are not recognized by the parser.
match, matchCount, disjointMatchCount and dissimilarity functions are not available in Marvin, they can be used only if JChem software package is installed.
Structure based calculations are performed using Calculator Plugins (these calculations are also referred as "plugin calculations").Since Marvin 5.2, all of these functions can have an additional string argument that specifies plugin parameters in "key1:value1 key2:value2 key3:value3 ..." fashion. For example: charge(8, "type:pi pH:3.5") will compute the pi charge of atom 8 in the major microspecies at pH=3.5 of the input molecule, markushEnumerations("code:true max:4","1,2") will generate maximum 4 enumerated structures with enumeration ID, enumerating only atoms 1 and 2 of the input Markush structure. Note, that this feature cannot be combined with the former possibility of specifying the pH in a string argument, for example: charge(8, "type:pi pH:3.5") cannot be written in the form charge(8, "type:pi", "3.5"), while charge("pi", 8, "3.5") is accepted (backward compatibility).