Chemical Terms functions by categories

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

Table of Contents

• Licensing information
• ADMET functions
• Charge functions
• Conformation functions
• Dissimilarity functions
• Dissimilarity descriptors and metrics
• Elemental Analysis functions
• General functions
• Geometry functions
• HBDA functions
• Huckel functions
• Isomers functions
• Markush functions
• Match functions
• Predefined molecules and molecule sets
• Name functions
• Partitioning functions
• Protonation functions
• Refractivity functions
• Solubility functions
• Structural Frameworks functions
• Structure Checker functions
• Notes

License information

Chemical Terms functions might require a Certara-Chemaxon Toolkit License to be used. The specific license bundles are indicated for every specific function.

The following Toolkit license bundles are available:

• Discovery Bundle (DTK)
• Descriptor Generation Toolkit (DGTK)
• Structure Preparation Toolkit (SPTK)
• Structure Enumeration Toolkit (SETK)
• Naming Toolkit (NTK)

As the Discovery Bundle covers all Chemical Terms functions, it is not individually listed for each function.

ADMET functions

Name	License	Description	Return value	Parameters	General context example(s)	Molecule context example(s)	Reaction context example(s)
bbb	DGTK	calculates the Blood Brain Barrier (BBB) Score	the BBB Score	-	N/A	bbb() returns the BBB Score of the input molecule	bbb(reactant(0)) returns the BBB Score of the first reactant
mpo	DGTK	calculates the CNS Multiparameter Optimisation (MPO) Score	the MPO score	-	N/A	mpo() returns the MPO score of the input molecule	mpo(reactant(1)) returns the MPO Score of the second reactant
herg	DGTK	predicts hERG activity and returns the pActivity value using ChemAxon's hERG activity model	the pActivity value	-	N/A	herg() returns the predicted hERG pActivity value of the input molecule	herg(reactant(0)) returns the predicted hERG pActivity value of the first reactant
hergActivity	DGTK	predicts hERG activity (as pActivity) using ChemAxon's hERG activity model	the pActivity value	-	N/A	hergActivity() returns the predicted hERG pActivity of the input molecule	hergActivity(product(0)) returns the predicted hERG pActivity of the first product
hergClass	DGTK	predicts the hERG classification class using ChemAxon's hERG classification model	the classification class (SAFE or TOXIC)	-	N/A	hergClass() returns the predicted hERG classification class of the input molecule	hergClass(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	DGTK	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	DGTK	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	DGTK	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	DGTK	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	DGTK	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	DGTK	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	DGTK	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	DGTK	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	DGTK	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	DGTK	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	DGTK	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	DGTK	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	DGTK	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	DGTK	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	DGTK	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	DGTK	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)

The dissimilarity() function requires JChem.

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), optimised 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

The fingerprints can be used with the metrics listed in the table below.

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

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)
groupedDotDisconnectedFormula	-	returns the grouped dot-disconnected formula	the grouped dot-disconnected formula	-	N/A	groupedDotDisconnectedFormula() 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 (the 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 return -1
arom	-	decides if an 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 true if atom 0 has an aromatic bond	arom(patom(2)) returns true if 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(5*5) 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	-	returns a molecule property (SDF field value)	the molecule property	the property key (SDF field name)	N/A	field('ACTIVITY') returns the value of the ACTIVITY property (SDF field) field('ACTIVITY') > 2 returns 1 if the ACTIVITY property value is bigger than 2, 0 otherwise	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, 0 otherwise
fieldAsString propertyAsString	-	returns a molecule property (SDF field value) as string	the molecule property as string	the property key (SDF field name)	N/A	fieldAsString('ID') returns the value of the ID property (SDF field)	field(reactant(0), 'ID') returns the value of the ID property of the first reactant
filter	-	filters target atoms by a 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)	N/A	filter("charge() > 0") returns the indices of atoms with positive partial charge of the molecule	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)
formalCharge totalCharge	-	calculates the formal charge of the molecule	the formal charge value	atom index or MolAtom object (optional)	N/A	formalCharge() returns the formal charge of the input molecule formalCharge(0) returns the formal charge of atom 0	formalCharge(reactant(0)) returns the formal charge of the first reactant
fragments	-	converts the molecule into its disconnected fragments	the disconnected fragments of the molecule	-	N/A	fragments() returns the disconnected fragments of the molecule	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	-	N/A	hasAromatizationError() returns true if there is an error in the aromatization of the molecule, false otherwise	hasAromatizationError(reactant(0)) returns true if there is an error in the aromatization of the first reactant, false otherwise
hasIsotope	-	determines if any atom of 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	-	N/A	hasIsotope() returns true if any atom in the molecule is a specific isotope of the element, false otherwise	hasIsotope(reactant(1)) returns true if any atom of the second reactant is a specific isotope of the element, false otherwise
hasRadical	-	determines if any atom in the molecule has a radical	true if any atom in the molecule has a radical, false otherwise	-	N/A	hasRadical() returns true if any atom in the molecule has a radical, false otherwise	hasRadical(reactant(1)) returns true if any atom of the second reactant has a radical, false otherwise
hasValenceError	-	determines if the molecule has a valence error	true if the molecule has a valence error, false otherwise	-	N/A	hasValenceError() returns true if the molecule has a valence error, false otherwise	hasValenceError(reactant(1)) returns true if the second reactant has a valence error, false otherwise
hCount	-	returns the hydrogen count of an atom	the hydrogen count	atom index, an array of atom indices (separated by , or ;) or MolAtom object	N/A	hCount(0,2,3) returns the hydrogen count of atom 0, 2 and 3	hCount(patom(3)) returns the hydrogen count of 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 (e.g. "c1ccccc1")	the molecule imported	N/A	importMol("c1ccccc1") returns the benzene molecule	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, a MolAtom object or an integer array	in(5, array(3, 5, 1)) returns true in(2, array(3, 5, 1)) returns false	in(3, maxatom("charge()", 2)) returns true if the partial charge of atom 3 is in the first 2 largest partial charges of the input molecule in(3, minatom("pol()", 4)) returns true if the polarizability of atom 3 is in the first 4 smallest polarizability values of the input molecule	in(ratom(3), maxatom(reactant(0), "charge()", 2)) returns true if the partial charge of the reactant atom matching map 3 in the reaction equation is within the first 2 largest partial charges of the first reactant in(patom(1), minatom(product(1), "pol()", 4)) returns true if the polarizability of the product atom matching map 1 in the reaction equation is within the first 4 smallest polarizability values of the second product
isEmpty	-	decides whether a molecule is empty (does not contain any atoms, bonds, or non-empty S-groups)	true if the molecule is empty	-	N/A	isEmpty() returns true if the molecule is empty, false otherwise	isEmpty(reactant(1)) returns true if the second reactant is empty
isQuery	-	decides whether a molecule contains any query features	true if the molecule contains any query features, false otherwise	-	N/A	isQuery() returns true if the molecule contains any query features, false otherwise	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	N/A	map(3) returns the atom map number of atom 3	map(patom(3)) returns the atom map number of the product atom matching map 3 in the reaction equation
max	-	takes the maximum of numerical values and arrays	the maximum value	integers, real numbers, integer arrays, real number arrays	max(2, 8, 6) returns 8 max(3.4, 5.6, 1.2) returns 5.6	max(charge(0), charge(2)) returns the maximum of the partial charge values of atoms 0 and 2 max(charge()) returns the maximal atomic partial charge value of the input molecule	max(charge(ratom(2)), charge(ratom(3))) returns the maximum of the partial charge values of the reactant atoms matching maps 2 and 3 in the reaction equation max(charge(product(0))) returns the maximal atomic partial charge value of the first product
maxAtom	-	evaluates an objective function for atoms and 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 are considered if omitted); the function (as inner expression string); the number of largest values to be taken (optional, takes only one if omitted)	N/A	maxAtom(6, 7, 8, 9, "charge('7.4')", 2) selects the two largest partial charges of atoms 6, 7, 8, 9 in the major microspecies at pH 7.4 of the input molecule and returns the corresponding indices	maxAtom(patom(1), patom(2), patom(3), "charge('7.4')", 2) selects the two largest partial charges of 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 an objective function for atoms and finds largest value(s)	the largest evaluation value(s)	target atom indices/objects or index/atom object array (optional, all atoms taken if omitted); the function (as inner expression string); the number of largest values to be taken (optional, takes only one if omitted)	N/A	maxValue(6, 7, 8, 9, "charge('7.4')", 2) returns the two largest partial charges of atoms 6, 7, 8, 9 in the major microspecies at pH 7.4 of the input molecule	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 the maximum of numerical values and arrays	the minimum value	integers, real numbers, integer arrays, real number arrays	min(2, 8, 6) returns 2 min(3.4, 5.6, 1.2) returns 1.2	min(charge(0), charge(2)) returns the least of the partial charge values of atoms 0 and 2 min(charge()) returns the minimal partial charge value on the input molecule	min(charge(ratom(2)), charge(ratom(3))) returns the least of the partial charge values of 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 an objective function for atoms and 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 function (as inner expression string); the number of smallest values to be taken (optional, takes only one if omitted)	N/A	minAtom("charge('7.4')") returns the atom index corresponding to smallest atomic partial charge in the major microspecies at pH 7.4 of the input molecule	minAtom(reactant(0), "charge('7.4')") returns the atom index corresponding to smallest partial charge in the major microspecies at pH 7.4 of the first reactant
minValue	-	evaluates objective function for each atom and 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 function (as inner expression string); the number of smallest values to be taken (optional, takes only one if omitted)	N/A	minValue("charge('7.4')") returns the smallest atomic partial charge in the major microspecies at pH 7.4 of the input molecule	minValue(reactant(0), "charge('7.4')") returns the smallest partial charge of the major microspecies at pH 7.4 of the first reactant
molAtom	-	creates a MolAtom	the MolAtom object	atomic number	N/A	molAtom(6) returns a carbon atom	N/A
molBinFormat molImage	-	returns the binary representation (image, pdf, GZIP compressed molecule file) of the molecule in the 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")	N/A	molImage("jpeg:w100,Q95,#ffff00") returns the 100x100 JPEG image of the input molecule with yellow background with 95% quality	N/A (reaction rules are numerical)
molString molConvert molFormat	-	returns the string representation of a molecule or an array of molecules in a specified molecule format	the string representation of the molecule(s)	the molecule format (e.g. "mol", "sdf", "mrv", "smiles"); the clean dimension	N/A	molFormat("mrv") returns the Chemaxon Marvin Document format representation of the input molecule molFormat(tautomers(), "sdf", 2) returns the 2D-cleaned representation of the tautomers of the input molecule in SD format	N/A (reaction rules are numerical)
pair bond	-	converts two atoms or 0-based atom indices into an "index1-index2" 1-based atom index setter string (used for pairing atoms in shortestPath )	the generated string	the two atom indices or the two MolAtom objects	pair(2, 5) returns "3-6"	N/A	pair(ratom(1), ratom(2)) returns "index1-index2" where index1 and index2 are the 1-based atom indices 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 indices of the product atoms matching map 2 and 5 in the reaction equation
productCount	-	counts the products in a reaction	the number of products in the reaction or -1 if the input molecule is not a reaction	-	N/A	N/A	productCount() returns n if the input molecule is a reaction and contains n products productCount(product(0)) and productCount(product(1)) functions do not make sense and they return -1
radicalCount	-	returns the radical count of an atom	the radical count	atom index or MolAtom object	N/A	radicalCount(0) returns the radical count of atom 0	radicalCount(patom(3)) returns the radical count of the product atom matching map 3 in the reaction equation
reactantCount	-	counts the reactants of a reaction	the number of reactants of the reaction or -1 if the input molecule is not a reaction	-	N/A	N/A	reactantCount() returns n if the given molecule is a reaction and contains n reactants else it returns -1 if the given molecule is not a reaction reactantCount(reactant(0)) and reactantCount(product(1)) calls do not make sense and they return -1
sortAsc	-	sorts an array in ascending order	the sorted array	integer array or real number array	sortAsc(array(3.4, 5.6, 1.2)) returns array(1.2, 3.4, 5.6)	sortAsc(charge()) returns the atomic partial charge values in ascending order	sortAsc(charge(reactant(1))) returns the atomic 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	sortDesc(array(3.4, 5.6, 1.2)) returns array(5.6, 3.4, 1.2)	sortDesc(pka("basic")) returns the basic pK a values in descending order	sortDesc(pka(product(0), "basic")) returns the basic pKa values of the first product in descending order
sum	-	calculates the sum of elements in an array	the sum	integer array or real number array	sum(array(3.4, 5.6, 1.2)) returns 10.2	sum(charge()) returns the sum of the atomic partial charges	sum(charge(reactant(0))) returns the sum of the atomic partial charge values of the first reactant
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	N/A	valence(0) returns the valence of atom 0	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	-	N/A	whereIsValenceError() returns the index of the first atom with valence error or -1 if there is no valence error in the molecule	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	Molecule context example(s)	Reaction context example(s)
aliphaticAtom	DGTK	checks if an atom is aliphatic	true for aliphatic atoms, false for non-aliphatic atoms	the atom index/MolAtom object	aliphaticAtom(2) returns true if atom 2 of the input molecule is aliphatic, false otherwise	aliphaticAtom(ratom(2)) returns true if the reactant atom matching map 2 in the reaction equation is aliphatic, false otherwise
aliphaticAtomCount	DGTK	calculates the aliphatic atom count	the aliphatic atom count	-	aliphaticAtomCount() returns the number of aliphatic atoms in the input molecule	aliphaticAtomCount(reactant(0)) returns the number of aliphatic atoms in the first reactant
aliphaticBondCount	DGTK	calculates the aliphatic bond count	the aliphatic bond count	-	aliphaticBondCount() returns the number of bonds in the input molecule	aliphaticBondCount(product(1)) returns the number of aliphatic bonds in the second product
aliphaticRingCount	DGTK	calculates the aliphatic ring count	the aliphatic ring count	-	aliphaticRingCount() returns the number of aliphatic rings in the input molecule	aliphaticRingCount(reactant(0)) returns the number of aliphatic rings in the first reactant
aliphaticRingCountOfSize	DGTK	calculates the number of aliphatic rings of a given size	the number of aliphatic rings of the given size	the ring size	aliphaticRingCountOfSize(6) returns the number of aliphatic rings of size 6 in the input molecule	aliphaticRingCountOfSize(reactant(0), 5) returns the number of aliphatic rings of size 5 in the first reactant
aliphaticRings	DGTK	identifies the aliphatic rings in the molecule	atom indices of the aliphatic rings in the molecule (or null if the molecule does not contain aliphatic rings)	-	aliphaticRings() returns the atom indices of the aliphatic rings in the input molecule	aliphaticRings(product(1)) returns the atom indices of the aliphatic rings in the second product
aliphaticRingsOfSize	DGTK	identifies the aliphatic rings of a given size in the molecule	atom indices of the aliphatic rings in the molecule having the given size (or null if the molecule does not contain aliphatic rings)	the ring size	aliphaticRings() returns the atom indices of the aliphatic rings in the input molecule having the given size	aliphaticRings(reactant(0)) returns the atom indices of the aliphatic rings having the given size in the first reactant
angle	DGTK	calculates the angle between three atoms	the angle between three atoms	the (1-based) atom indices of the three atoms in a string "index1-index2-index3" (e.g. '2-3-5')	angle('1-2-3') and angle(atoms(0, 1, 2)) both return the angle between atoms 1, 2 and 3 of the input molecule	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	DGTK	checks if an atom is aromatic	true for aromatic atoms, false for non-aromatic atoms	the atom index/MolAtom object	aromaticAtom(2) returns true if atom 2 of the input molecule is aromatic, false otherwise	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	DGTK	calculates the aromatic atom count	the aromatic atom count	-	aromaticAtomCount() returns the number of aromatic atoms in the input molecule	aromaticAtomCount(reactant(0)) returns the number of aromatic atoms in the first reactant
aromaticBondCount	DGTK	calculates the aromatic bond count	the aromatic bond count	-	aromaticBondCount() returns the number of aromatic bonds in the input molecule	aromaticBondCount(product(1)) returns the number of aromatic bonds in the second product
aromaticRingCount	DGTK	calculates the aromatic ring count	the aromatic ring count	-	aromaticRingCount() returns the number of aromatic rings in the input molecule	aromaticRingCount(reactant(0)) returns the number of aromatic rings in the first reactant
aromaticRingCountOfSize	DGTK	calculates the number of aromatic rings of a given size	the number of aromatic rings of the given size	the ring size	aromaticRingCountOfSize(6) returns the number of aromatic rings of size 6 in the input molecule	aromaticRingCountOfSize(product(1), 5) returns the number of aromatic rings of size 5 in the second product
aromaticRings	DGTK	identifies the aromatic rings in the molecule	atom indices of the aromatic rings in the molecule (or null if the molecule does not contain aromatic rings)	-	aromaticRings() returns the atom indices of the aromatic rings in the input molecule	aromaticRings(reactant(0)) returns the atom indices of the aromatic rings in the first reactant aromaticRings(product(1)) returns the atom indices of the aromatic rings in the second product
aromaticRingsOfSize	DGTK	identifies the aromatic rings having a given size (number of atoms) in the molecule	atom indices of the aromatic rings having the given size (or null if the molecule does not contain aromatic rings)	the ring size	aromaticRingsOfSize(6) returns the atom indices of the aromatic rings of size 6 in the input molecule	aromaticRingsOfSize(reactant(0), 5) returns the atom indices of the aromatic rings of size 5 in the first reactant
ASAHydrophobic	DGTK	calculates the water accessible molecular surface area of all hydrophobic atoms in the molecule	the molecular surface area	the major microspecies pH (takes the input molecule if omitted)	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	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	DGTK	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 if omitted)	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	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	DGTK	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 if omitted)	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	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	DGTK	calculates the water accessible molecular surface area of all polar atoms	the molecular surface area	the major microspecies pH (takes the input molecule if omitted)	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	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	DGTK	checks if the specified atom is an asymmetric atom	true for asymmetric atoms, false for symmetric atoms	the atom index/MolAtom object	asymmetricAtom(2) returns true if atom 2 of the input molecule is an asymmetric atom, false otherwise	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	DGTK	calculates the number of asymmetric atoms	the asymmetric atom count	-	asymmetricAtomCount() returns the number of asymmetric atoms in the input molecule	asymmetricAtomCount(reactant(0)) returns the number of asymmetric atoms in the first reactant
asymmetricAtoms	DGTK	identifies the asymmetric atoms in the molecule	indices of asymmetric atoms	-	asymmetricAtoms() returns the indices of asymmetric atoms in the input molecule	asymmetricAtoms(product(1)) returns the indices of asymmetric atoms in the second product
balabanIndex	DGTK	calculates the Balaban index	the Balaban index	-	balabanIndex() calculates the Balaban index of the input molecule	balabanIndex(reactant(0)) calculates the Balaban index of the first reactant
bondCount	-	calculates the bond count	the bond count	-	bondCount() returns the number of bonds in the input molecule	bondCount(product(1)) returns the number of bonds in the second product
bondType	DGTK	returns the bond type between two atoms	the bond type between two atoms or -1 if there is no bond between the two atoms	the (1-based) atom indices of the two atoms in a string "index1-index2" (e.g. '2-3')	bondType('2-3') and bondType(bond(1, 2)) both return the bond type between atoms 1 and 2 of the input molecule	bondType(reactant(0), bond(ratom(1), ratom(2))) returns the bond type between reactant atoms matching maps 1 and 2 in the reaction equation bondType(product(1), bond(patom(2), patom(3))) returns the bond type between product atoms matching maps 2 and 3 in the reaction equation
carboaliphaticRingCount	DGTK	calculates the number of carboaliphatic rings (aliphatic rings containing carbon atoms only) in the molecule	the number of carboaliphatic rings	-	carboaliphaticRingCount() returns the number of carboaliphatic rings in the input molecule	carboaliphaticRingCount(reactant(0)) returns the number of carboaliphatic rings in the first reactant
carboaromaticRingCount	DGTK	calculates the number of carboaromatic rings (aromatic rings containing carbon atoms only) in the molecule	the number of carboaromatic rings	-	carboaromaticRingCount() returns the number of carboaromatic rings in the input molecule	carboaromaticRingCount(product(1)) returns the number of carboaromatic rings in the second product
carboRingCount	DGTK	calculates the number of carbocyclic rings (rings containing carbon atoms only) in the molecule	the number of carbocyclic rings	-	carboRingCount() returns the number of carbocyclic rings in the input molecule	carboRingCount(reactant(0)) returns the number of carbocyclic rings in the first reactant
carboRingCountOfSize	DGTK	calculates the number of carbocyclic rings (rings containing carbon atoms only) of a given size	the number of carbocyclic rings of the given size	the ring size	carboRingCountOfSize(6) returns the number of carbocyclic rings of size 6 in the input molecule	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	DGTK	identifies the carbocyclic rings (rings containing carbon atoms only) in the molecule	atom indices of the carbocyclic rings in the molecule (or null if the molecule does not contain carbocyclic rings)	-	carboRings() returns the atom indices of the carbocyclic rings in the input molecule	carboRings(reactant(0)) returns the atom indices of the carbocyclic rings in the first reactant
carboRingsOfSize	DGTK	identifies the carbocyclic rings in the molecule having a given size (number of atoms)	the atom indices of the carbocyclic rings in the molecule having the given size (or null if the molecule does not carbocyclic rings)	the ring size	carboRingsOfSize(6) returns the atom indices of the carbocyclic rings of size 6 in the input molecule	carboRingsOfSize(product(1), 5) returns the atom indices of the carbocyclic rings of size 5 in the second product
chainAtom	DGTK	checks if the specified atom is a chain atom	true for chain atoms, false for non-chain atoms	the atom index/MolAtom object	chainAtom(2) returns true if atom 2 of the input molecule is a chain atom, false otherwise	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	DGTK	calculates the chain atom count	the chain atom count	-	chainAtomCount() returns the number of chain atoms in the input molecule	chainAtomCount(reactant(0)) returns the number of chain atoms in the first reactant
chainBond	DGTK	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 indices of the two atoms in a string "index1-index2" (e.g. '2-3')	chainBond('2-3') and chainBond(bond(1, 2)) both return true if atoms 1 and 2 are connected by a chain bond in the input molecule	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	DGTK	calculates the chain bond count	the chain bond count	-	chainBondCount() returns the number of chain bonds in the input molecule	chainBondCount(reactant(0)) returns the number of chain bonds in the first reactant
chiralCenter	DGTK	checks if the specified atom is a tetrahedral stereogenic center	true for tetrahedral stereogenic center atoms	the atom index/MolAtom object	chiralCenter(2) returns true if atom 2 of the input molecule is a tetrahedral stereogenic center, false otherwise	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	DGTK	calculates the number of tetrahedral stereogenic center atoms	the tetrahedral stereogenic center count	-	chiralCenterCount() returns the number of tetrahedral stereogenic centers in the input molecule	chiralCenterCount(product(1)) returns the number of tetrahedral stereogenic centers in the second product
chiralCenters	DGTK	determines the chiral center atoms	indices of chiral center atoms	-	chiralCenters() returns the indices of the chiral center atoms in the input molecule	chiralCenters(reactant(0)) returns the indices of the chiral center atoms in the first reactant
connected	DGTK	checks if two atoms are connected	true if the two atoms belong to the same connected component, false otherwise	the (1-based) atom indices of the two atoms in a string "index1-index2" (e.g. '2-3')	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	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	DGTK	checks whether the molecule graph is connected	true if the molecule graph is connected, false otherwise	-	connectedGraph() returns true if the input molecule graph is connected	connectedGraph(product(1)) returns true if the second product is connected
cyclomaticNumber	DGTK	calculates the cyclomatic number	the cyclomatic number	-	cyclomaticNumber() returns the cyclomatic number of the input molecule	cyclomaticNumber(reactant(0)) returns the cyclomatic number of the first reactant
dihedral	DGTK	calculates the dihedral angle of four atoms	the dihedral angle of four atoms	the (1-based) atom indices of the four atoms in a string "index1-index2-index3-index4" (e.g. '2-3-7-4')	dihedral('1-2-3-4') and dihedral(atoms(0, 1, 2, 3)) both return the dihedral angle of atoms 1, 2, 3 and 4 in the input molecule	dihedral(reactant(0), atoms(ratom(1), ratom(2), ratom(3), ratom(4))) returns the dihedral angle 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 angle of product atoms matching maps 2, 3, 5 and 6 in the reaction equation (see note 1)
distance	DGTK	calculates the distance between two atoms	the distance between the two atoms	the (1-based) atom indices of the two atoms in a string "index1-index2" (e.g. '2-3')	distance('1-2') and distance(pair(0, 1)) both return the distance between atoms 1 and 2 in the input molecule	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	DGTK	calculates the distance degree of an atom	the distance degree	the atom index/MolAtom object	distanceDegree(2) returns the distance degree of atom 2 of the input molecule	distanceDegree(ratom(2)) returns the distance degree of the reactant atom matching map 2 in the reaction equation
dreidingEnergy	DGTK	returns the Dreiding energy of the input molecule (conformer)	the dreiding energy	-	dreidingEnergy() returns the Dreiding energy of the input molecule (conformer)	dreidingEnergy(reactant(0)) returns the dreiding energy of the first reactant
eccentricity	DGTK	calculates the eccentricity of an atom	the eccentricity of the atom	the atom index/ MolAtom object	eccentricity(2) returns the eccentricity of atom 2 of the input molecule	eccentricity(patom(1)) returns the eccentricity of the product atom matching map 1 in the reaction equation
fragmentCount	DGTK	returns the number of fragments (disconnected parts) of a molecule	the fragment count	-	fragmentCount() returns the number of fragments in the input molecule	fragmentCount(reactant(0)) returns the number of fragments in the first reactant
fsp3	DGTK	returns the fsp3 of the molecule	the fsp3 value	-	fsp3() returns the fsp3 value of the input molecule	fsp3(reactant(0)) returns the fsp3 value of the first reactant
fusedAliphaticRingCount	DGTK	calculates the number of fused aliphatic rings (SSSR = smallest set of smallest aliphatic rings)	the fused aliphatic ring count	-	fusedAliphaticRingCount() returns the number of fused aliphatic rings in the input molecule	fusedAliphaticRingCount(reactant(0)) returns the number of fused aliphatic rings in the first reactant
fusedAliphaticRingCountOfSize	DGTK	calculates the number of fused aliphatic rings of a given size	the number of fused aliphatic rings of the given size	the ring size	fusedAliphaticRingCountOfSize(6) returns the number of fused aliphatic rings of size 6 in the input molecule	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	DGTK	identifies the fused aliphatic rings in the molecule	the atom indices of the fused aliphatic rings in the molecule (or null if the molecule does not contain fused aliphatic rings)	-	fusedAliphaticRings() returns the atom indices of the fused aliphatic rings in the input molecule	fusedAliphaticRings(reactant(0)) returns the atom indices of the fused aliphatic rings in the first reactant
fusedAliphaticRingsOfSize	DGTK	identifies the fused aliphatic rings having a given size (number of atoms) in the molecule	the atom indices of the fused aliphatic rings having the given size (or null if the molecule does not contain fused aliphatic rings)	the ring size	fusedAliphaticRings() returns the atom indices of the fused aliphatic rings having the given size in the input molecule	fusedAliphaticRings(product(1)) returns the atom indices of the fused aliphatic rings having the given size in the second product
fusedAromaticRingCount	DGTK	calculates the number of fused aromatic rings (SSSR = smallest set of smallest aromatic rings)	the fused aromatic ring count	-	fusedAromaticRingCount() returns the number of fused aromatic rings in the input molecule	fusedAromaticRingCount(reactant(0)) returns the number of fused aromatic rings in the first reactant
fusedAromaticRingCountOfSize	DGTK	calculates the number of fused aromatic rings of a given size	the number of fused aromatic rings of the given size	the ring size	fusedAromaticRingCountOfSize(6) returns the number of fused aromatic rings of size 6 in the input molecule	fusedAromaticRingCountOfSize(reactant(0), 5) returns the number of fused aromatic rings of size 5 in the first reactant
fusedAromaticRings	DGTK	identifies the fused aromatic rings in the molecule	the atom indices of the fused aromatic rings in the molecule (or null if the molecule does not contain fused aromatic rings)	-	fusedAromaticRings() returns the atom indices of the fused aromatic rings in the input molecule	fusedAromaticRings(product(1)) returns the atom indices of the fused aromatic rings in the second product
fusedAromaticRingsOfSize	DGTK	identifies the fused aromatic rings having a given size (number of atoms)	the atom indices of the fused aromatic rings having the given size in the molecule (or null if the molecule does not contain fused aromatic rings)	the ring size	fusedAromaticRings() returns the atom indices of the fused aromatic rings having the given size in the input molecule	fusedAromaticRings(reactant(0)) returns the atom indices of the fused aromatic rings having the given size in the first reactant
fusedRingCount	DGTK	calculates the number of fused rings (SSSR = smallest set of smallest rings)	the fused ring count	-	fusedRingCount() returns the number of fused rings in the input molecule	fusedRingCount(reactant(0)) returns the number of fused rings in the first reactant
hararyIndex	DGTK	calculates the Harary index	the Harary index	-	hararyIndex() calculates the Harary index of the input molecule	hararyIndex(product(1)) returns the Harary index of the second product
heteroaliphaticRingCount	DGTK	calculates the number of aliphatic heterocyclic rings (SSSR = smallest set of smallest aliphatic rings)	the aliphatic heterocyclic ring count	-	heteroaliphaticRingCount() returns the number of aliphatic heterocyclic rings in the input molecule	heteroaliphaticRingCount(reactant(0)) returns the number of aliphatic heterocyclic rings in the first reactant
heteroaliphaticRingCountOfSize	DGTK	calculates the number of aliphatic heterocyclic rings of a given size	the number of aliphatic heterocyclic rings of the given size	the ring size	heteroaliphaticRingCountOfSize(6) returns the number of aliphatic heterocyclic rings of size 6 in the input molecule	heteroaliphaticRingCountOfSize(product(1), 5) returns the number of aliphatic heterocyclic rings of size 5 in the second product
heteroaliphaticRings	DGTK	identifies the aliphatic heterocyclic rings in the molecule	atom indices of the aliphatic heterocyclic rings in the molecule (ot null if the molecule does not contain aliphatic heterocyclic rings)	-	heteroaliphaticRings() returns the atom indices of the aliphatic heterocyclic rings in the input molecule	heteroaliphaticRings(reactant(0)) returns the atom indices of the aliphatic heterocyclic rings in the first reactant
heteroaliphaticRingsOfSize	DGTK	identifies the aliphatic heterocyclic rings having a given size (number of atoms) in the molecule	atom indices of the aliphatic heterocyclic rings having the given size (or null if the molecule does not contain aliphatic heterocyclic rings)	the ring size	heteroaliphaticRingsOfSize() returns the atom indices of the aliphatic heterocyclic rings having the given size in the input molecule	heteroaliphaticRingsOfSize(product(1)) returns the atom indices of the aliphatic heterocyclic rings in the second product having the given size
heteroaromaticRingCount	DGTK	calculates the number of aromatic heterocyclic rings (SSSR = smallest set of smallest aromatic rings)	the aromatic heterocyclic ring count	-	heteroaromaticRingCount() returns the number of aromatic heterocyclic rings in the input molecule	heteroaromaticRingCount(reactant(0)) returns the number of aromatic heterocyclic rings in the first reactant
heteroaromaticRingCountOfSize	DGTK	calculates the number of aromatic heterocyclic rings of a given size	the number of aromatic heterocyclic rings of the given size	the ring size	heteroaromaticRingCountOfSize(6) returns the number of aromatic heterocyclic rings of size 6 in the input molecule	heteroaromaticRingCountOfSize(product(1), 5) returns the number of aromatic heterocyclic rings of size 5 in the second product
heteroaromaticRings	DGTK	identifies the aromatic heterocyclic rings in the molecule	atom indices of the aromatic heterocyclic rings in the molecule (or null if the molecule does not contain aromatic heterocyclic rings)	-	heteroaromaticRings() returns the atom indices of the aromatic heterocyclic rings in the input molecule	heteroaromaticRings(product(1)) returns the atom indices of the aromatic heterocyclic rings in the second product
heteroaromaticRingsOfSize	DGTK	identifies the aromatic heterocyclic rings in the molecule having a given size (number of atoms)	atom indices of the aromatic heterocyclic rings in the molecule having the given size (or null if the molecule does not contain aromatic heterocyclic rings)	the ring size	heteroaromaticRingsOfSize() returns the atom indices of the aromatic heterocyclic rings in the input molecule having the given size	heteroaromaticRingsOfSize(reactant(0)) returns the atom indices of the aromatic heterocyclic rings in the first reactant having the given size
heteroRingCount	DGTK	calculates the number of heterocyclic rings (SSSR = smallest set of smallest rings)	the heterocyclic ring count	-	heteroRingCount() returns the number of heterocyclic rings in the input molecule	heteroRingCount(reactant(0)) returns the number of heterocyclic rings in the first reactant
heteroRingCountOfSize	DGTK	calculates the number of heterocyclic rings of a given size	the number of heterocyclic rings of the given size	the ring size	heteroRingCountOfSize(6) returns the number of heterocyclic rings of size 6 in the input molecule	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	DGTK	identifies the heterocyclic rings in the molecule	atom indices of the heterocyclic rings in the molecule (or null if the molecule does not contain heterocyclic rings)	-	heteroRings() returns the atom indices of the heterocyclic rings in the input molecule	heteroRings(reactant(0)) returns the atom indices of the heterocyclic rings in the first reactant
heteroRingsOfSize	DGTK	identifies the heterocyclic rings in the molecule having a given size (number of atoms)	atom indices of the heterocyclic rings in the molecule having the given size (or null if the molecule does not contain heterocyclic rings)	the ring size	heteroRingsOfSize(6) returns the atom indices of the heterocyclic rings in the input molecule having size of 6	heteroRingsOfSize(product(1), 5) returns the atom indices of the heterocyclic rings in the second product having size of 5
hyperWienerIndex	DGTK	calculates the Hyper Wiener index	the Hyper Wiener index	-	hyperWienerIndex() calculates the Hyper Wiener index of the input molecule	hyperWienerIndex(reactant(0)) returns the Hyper Wiener index of the first reactant
largestAtomRingSize	DGTK	calculates the size of the largest ring containing a specified atom	the size of the largest ring containing the specified atom	the atom index/MolAtom object	largestAtomRingSize(1) returns the size of the largest ring containing atom 1 in the input molecule	largestAtomRingSize(patom(2)) returns the size of the largest ring containing product atom matching map 2 in the reaction equation
largestConjugatedSystem	DGTK	returns the atom list of the largest conjugated system of the molecule	the atom list of the largest conjugated system	-	largestConjugatedSystem() returns the atom list of the largest conjugated system in the input molecule	largestConjugatedSystem(product(1)) returns the atom list of the largest conjugated system in the second product
largestConjugatedSystemSize	DGTK	returns the number of pi electron pairs in the largest conjugated system of the molecule	the number of pi electron pairs in the largest conjugated system of the molecule	-	largestConjugatedSystemSize() returns the number of pi electron pairs in the largest conjugated system of the input molecule	largestConjugatedSystemSize(reactant(0)) returns the number of pi electron pairs in the largest conjugated system of the first reactant
largestConjugatedSystemMol	DGTK	returns the input molecule with its largest conjugated system coloured in green (note that this function should be used with the output option -f mrv to show the colouring in the output	the input molecule with its largest conjugated system coloured in green	-	largestConjugatedSystemMol() returns the input molecule with its largest conjugated system coloured in green	largestConjugatedSystemMol(product(1)) returns the second product with its largest conjugated system coloured in green
largestRing	DGTK	identifies the atoms of the largest ring in the molecule	the atom indices of the largest ring in the molecule (or null if the input molecule is acyclic)	-	largestRingSize() returns the atom indices of the largest ring in the input molecule	largestRingSize(product(1)) returns the atom indices of the largest ring in the second product
largestRingSize	DGTK	calculates the largest ring size in the molecule	the largest ring size	-	largestRingSize() returns the size of the largest ring in the input molecule	largestRingSize(product(1)) returns the size of the largest ring in the second product
largestRingSystem	DGTK	identifies the atoms of the largest ring system in the molecule	atom indices of the largest ring system in the molecule (or null if the molecule is acyclic)	-	largestRingSystem() returns the atom indices of the largest ring system in the input molecule	largestRingSystem(reactant(0)) returns the atom indices of the largest ring system in the first reactant
largestRingSystemSize	DGTK	calculates the size of the largest ring system (=number of rings)	the size of the largest ring system	-	largestRingSystemSize() returns the size of the largest ring system in the input molecule	largestRingSystemSize(reactant(0)) returns the size of the largest ring system in the first reactant
maximalProjectionArea	DGTK	returns the maximal projection area	the maximal projection area	-	maximalProjectionArea() returns the maximal projection area of the input molecule	maximalProjectionArea((reactant(0)) returns the maximal projection area of the first reactant
maximalProjectionRadius	DGTK	returns the maximal projection radius	the maximal projection radius	-	maximalProjectionRadius() returns the maximal projection radius of the input molecule	maximalProjectionRadius((reactant(0)) returns the maximal projection radius of the first reactant
maximalProjectionSize	DGTK	returns the maximal distance in the molecule perpendicular to its maximal projection area	the maximal distance in the molecule (the actual conformer) perpendicular to its maximal projection area	-	maximalProjectionSize() returns the maximal distance in the input molecule perpendicular to its maximal projection area	maximalProjectionSize((reactant(0)) returns the maximal distance of the first reactant perpendicular to its maximal projection area
minimalProjectionArea	DGTK	returns the minimal projection area	the minimal projection area	-	minimalProjectionArea() returns the minimal projection area of the input molecule	minimalProjectionArea((reactant(0)) returns the minimal projection area of the first reactant
minimalProjectionRadius	DGTK	returns the minimal projection radius	the minimal projection radius	-	minimalProjectionRadius() returns the minimal projection radius of the input molecule	minimalProjectionRadius(product(1)) returns the minimal projection radius of the second product
minimalProjectionSize	DGTK	returns the maximal distance in the molecule perpendicular to its minimal projection area	the maximal distance of the molecule (the actual conformer) perpendicular to its minimal projection area	-	minimalProjectionSize() returns the maximal distance in the input molecule perpendicular to its the minimal projection area	minimalProjectionSize(product(1)) returns the maximal distance of the second product perpendicular to its minimal projection area
mmff94Energy	DGTK	returns the MMFF94 energy of the input molecule (conformer)	the MMFF94 energy	-	mmff94Energy() returns the MMFF94 energy of the input molecule (conformer)	mmff94Energy(reactant(0)) returns the MMFF94 energy of the first reactant
plattIndex	DGTK	calculates the Platt index	the Platt index	-	plattIndex() returns the Platt index of the input molecule	plattIndex(product(1)) returns the Platt index of the second product
randicIndex	DGTK	calculates the Randic index	the Randic index	-	randicIndex() calculates the Randic index of the input molecule	randicIndex(reactant(0)) returns the Randic index of the first reactant
ringAtom	DGTK	checks if a specified atom is a ring atom	true for ring atoms, false for non-ring atoms	the atom index/MolAtom object	ringAtom(2) returns true if atom 2 of the input molecule is a ring atom, false otherwise	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	DGTK	calculates the ring atom count	the ring atom count	-	ringAtomCount() returns the number of ring atoms in the input molecule	ringAtomCount(reactant(0)) returns the number of ring atoms in the first reactant
ringBond	DGTK	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 indices of the two atoms in a string "index1-index2" (e.g. '2-3')	ringBond('2-3') and ringBond(bond(1, 2)) both return true if atoms 1 and 2 are connected by a ring bond in the input molecule	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 first 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 second product molecule (see note 1)
ringBondCount	DGTK	calculates the ring bond count	the ring bond count	-	ringBondCount() returns the number of ring bonds in the input molecule	ringBondCount(reactant(0)) returns the number of ring bonds in the first reactant
ringCount	DGTK	calculates the ring count	the ring count	-	ringCount() returns the number of rings in the input molecule	ringCount(reactant(0)) returns the number of rings in the first reactant
ringCountOfAtom	DGTK	calculates the number of rings passing through an atom	the number of rings passing through the atom	the atom index/MolAtom object	ringCountOfAtom(2) returns the number of rings passsing through atom 2 of the input molecule	ringCountOfAtom(ratom(2)) returns the number of rings passing through the reactant atom matching map 2 in the reaction equation ringCountOfAtom(patom(1)) returns the number of rings passing through the product atom matching map 1 in the reaction equation
ringCountOfSize	DGTK	calculates the number of rings of a given size	the number of rings of the given size	the ring size	ringCountOfSize(6) returns the number of rings of size 6 in the input molecule	ringCountOfSize(reactant(0), 5) returns the number of rings of size 5 in the first reactant ringCountOfSize(product(1), 6) returns the number of rings of size 6 in the second product
rings	DGTK	identifies the rings in the molecule	atom indices of the rings in the molecule (or null if the molecule is acyclic)	-	rings() returns the atom indices of the rings in the input molecule	rings(product(1)) returns the atom indices of the rings in the second product
ringsOfSize	DGTK	identifies the rings in the molecule having a given size (number of atoms)	atom indices of the rings having the given size in the molecule	the ring size	ringsOfSize(6) returns the atom indices of the rings of size 6 in the input molecule	ringsOfSize(reactant(0), 5) returns the atom indices of the rings of size 5 in the first reactant
ringSystemCount	DGTK	calculates the number of ring systems	the number of ring systems	-	ringSystemCount() returns the number of ring systems in the input molecule	ringSystemCount(reactant(0)) returns the number of ring systems in the first reactant
ringSystemCountOfSize	DGTK	calculates the number of ring systems of a given size	the number of ring systems of the given size	the ring system size	ringSystemCountOfSize(10) returns the number of 10-membered ring systems in the input molecule	ringSystemCountOfSize(product(1), 12) returns the number of 12-membered ring systems in the second product
ringSystems	DGTK	identifies the ring systems in the molecule (fused and spiro rings belong to one ring system)	atom indices of the ring systems in the molecule (or null if the molecule is acyclic)	-	ringSystems() returns the atom indices of the ring systems in the input molecule	ringSystems(reactant(0)) returns the atom indices of the ring systems in the first reactant
ringSystemsOfSize	DGTK	identifies the ring systems in the molecule having a given size (number of atoms, fused and spiro rings belong to one ring system)	atom indices of the ring systems in the molecule having the given size (or null if the molecule is acyclic or contains different ringSystems only)	the ring size	ringSystemsOfSize(10) returns the atom indices of the 10-membered ring systems in the input molecule	ringSystemsOfSize(reactant(0), 8) returns the atom indices of the 8-membered ring systems in the first reactant
rotatableBond	DGTK	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 indices of the two atoms in a string "index1-index2" (e.g. '2-3')	rotatableBond('2-3') and rotatableBond(bond(1, 2)) both return true if atoms 1 and 2 are connected by a rotatable bond in the input molecule	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 first 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 second product molecule (see note 1)
rotatableBondCount	DGTK	calculates the rotatable bond count	the rotatable bond count	-	rotatableBondCount() returns the number of rotatable bonds in the input molecule	rotatableBondCount(reactant(0)) returns the number of rotatable bonds in the first reactant
shortestPath	DGTK	calculates the length of the shortest path between two atoms	the length of the shortest path between two atoms (returns Integer.MAX_VALUE if the two atoms are disconnected)	the (1-based) atom indices of the two atoms in a string "index1-index2" (e.g. '2-3')	shortestPath('2-3') and shortestPath(pair(1, 2)) both return the shortest path length between atoms 1 and 2 in the input molecule	shortestPath(reactant(0), pair(ratom(1), ratom(2))) returns the length of the shortest path in the first reactant 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 in the second product between product atoms matching maps 2 and 3 in the reaction equation (see note 1)
smallestAtomRingSize	DGTK	calculates the size of the smallest ring containing a specified atom	the size of the smallest ring containing the specified atom	the atom index/MolAtom object	smallestAtomRingSize(0) returns the size of the smallest ring containing atom 0 in the input molecule	smallestAtomRingSize(ratom(1)) returns the size of the smallest ring containing reactant atom matching map 1 in the reaction equation
smallestRing	DGTK	identifies the atoms of the smallest ring (number of atoms) in the molecule	atom indices of the smallest ring in the molecule (null when the molecule is acyclic)	-	smallestRing() returns the atom indices of the smallest ring in the input molecule	smallestRing(product(1)) returns the atom indices of the smallest ring in the second product
smallestRingSize	DGTK	calculates the smallest ring size	the smallest ring size	-	smallestRingSize() returns the size of the smallest ring in the input molecule	smallestRingSize(reactant(0)) returns the size of the smallest ring in the first reactant
smallestRingSystem	DGTK	identifies the atoms of the smallest ring system (number of rings) in the molecule	atom indices of the smallest ring system in the molecule (null when the molecule is acyclic)	-	smallestRingSystem() returns the atom indices of the smallest ring system in the input molecule	smallestRingSystem(product(1)) returns the atom indices of the smallest ring system in the second product
smallestRingSystemSize	DGTK	calculates the size of the smallest ring system (number of rings)	the size of the smallest ring system	-	smallestRingSystemSize() returns the size of the smallest ring system in the input molecule	smallestRingSystemSize(reactant(0)) returns the size of the smallest ring system in the first reactant
stereoDoubleBondCount	DGTK	calculates the number of stereo double bonds	the stereo double bond count	-	stereoDoubleBondCount() returns the number of stereo double bonds in the input molecule	stereoDoubleBondCount(product(1)) returns the number of stereo double bonds in the second product
stericEffectIndex	DGTK	calculates the steric effect index of an atom	the steric effect index of the atom	the atom index/MolAtom object	stericEffectIndex(1) returns the steric effect index of atom 1	stericEffectIndex(ratom(1)) returns the steric effect index of reactant atom matching map 1 in the reaction equation
stericHindrance	DGTK	calculates the steric hindrance of an atom	the steric hindrance of the atom	the atom index/MolAtom object	stericHindrance(2) returns the steric hindrance of atom 2 in the input molecule	stericHindrance(patom(2)) returns the steric hindrance of the product atom matching map 2 in the reaction equation
szegedIndex	DGTK	calculates the Szeged index	the Szeged index	-	szegedIndex() calculates the Szeged index of the input molecule	szegedIndex(reactant(0)) returns the Szeged index of the first reactant
topologicalPolarSurfaceArea PSA	-	calculates the (2D) topological polar surface area	the polar surface area	the major microspecies pH (takes the input molecule if omitted)	topologicalPolarSurfaceArea() returns the polar surface area of the input molecule topologicalPolarSurfaceArea('7.4') returns the polar surface area of the major microspecies at pH 7.4 of the input molecule	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 at pH 7.4
vanDerWaalsSurfaceArea	DGTK	calculates the van der Waals surface area	the van der Waals surface area	the major microspecies pH (takes the input molecule if omitted)	vanDerWaalsSurfaceArea() returns the van der Waals surface area of the input molecule vanDerWaalsSurfaceArea('7.4') returns the van der Waals surface area of the major microspecies of the input molecule at pH 7.4	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 at pH 7.4
waterAccessibleSurfaceArea ASA solventAccessibleSurfaceArea	DGTK	calculates the solvent accessible/water accessible molecular surface area	the water accesible molecular surface area	the major microspecies pH (takes the input molecule if omitted)	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 of the input molecule at pH 7.4	waterAccessibleSurfaceArea(reactant(0)) returns the solvent accessible/water accessible surface area of the first reactant solventAccessibleSurfaceArea(product(0), '7.4') returns the solvent accessible/water accessible surface area of the major microspecies of the first product at pH 7.4
wienerIndex	DGTK	calculates the Wiener index	the Wiener index	-	wienerIndex() returns the Wiener index of the input molecule	wienerIndex(reactant(0)) returns the Wiener index of the first reactant
wienerPolarity	DGTK	calculates the Wiener polarity	the Wiener polarity	-	wienerPolarity() returns the Wiener polarity of the input molecule	wienerPolarity(product(1)) returns the Wiener polarity of the second product

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HBDA Functions

Name	License	Description	Return value	Parameters	Molecule context example(s)	Reaction context example(s)
acceptor acc	DGTK	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 if omitted)	acceptor(2) returns the hydrogen bond acceptor multiplicity on atom 2 of the input molecule	acceptor(ratom(2)) returns the hydrogen bond acceptor multiplicity on the reactant atom matching map 2 in the reaction equation
acceptorCount	DGTK	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 if omitted)	acceptorCount('7.4') returns the number of hydrogen bond acceptor atoms in the major microspecies of the input molecule at pH 7.4	acceptorCount(reactant(0)) returns the number of hydrogen bond acceptor atoms in the first reactant
acceptorSiteCount accSiteCount	DGTK	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 if omitted)	acceptorSiteCount() returns the hydrogen bond acceptor multiplicity of the input molecule	acceptorSiteCount(reactant(0), '7.4') returns the hydrogen bond acceptor multiplicity of the major microspecies of the first reactant at pH 7.4
donor don	DGTK	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 if omitted)	donor(1, "7.4") returns the hydrogen bond donor multiplicity on atom 1 of the major microspecies at pH 7.4	donor(patom(3), '7.4') returns the hydrogen bond donor multiplicity of the product atom matching map 3 in the reaction equation, taking the major microspecies of the corresponding product at pH 7.4
donorCount	DGTK	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 if omitted)	donorCount("7.4") returns the number of hydrogen bond donor atoms in the major microspecies of the input molecule at pH 7.4	donorCount(product(1), "7.4") returns the number of hydrogen bond donor atoms in the major microspecies of the first product at pH 7.4
donorSiteCount donSiteCount	DGTK	calculates the molecular hydrogen bond donor multiplicity (the sum of atomic multiplicities)	the molecular hydrogen bond donor multiplicity	the major microspecies pH (takes the input molecule if omitted)	donorSiteCount("7.4") returns the hydrogen bond donor multiplicity of the major microspecies at pH 7.4	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	Molecule context example(s)	Reaction context example(s)
chargeDensity totalChargeDensity	DGTK	calculates the charge density of atoms	the charge density of the atom or NaN for non-existing values	the atom index/MolAtom object the major microspecies pH (takes the input molecule if omitted)	chargeDensity(2) returns the charge density of atom 2 of the input molecule or NaN for non-existing value	chargeDensity(ratom(1)) returns the charge density of the reactant atom matching map 1 in the reaction equation
electronDensity piChargeDensity	DGTK	calculates the electron density of an atom	the electron density of the atom or NaN for non-existing values	the atom index/MolAtom object the major microspecies pH (takes the input molecule if omitted)	electronDensity(2) returns the electron density of atom 2 of the input molecule or NaN for non-existing values	electronDensity(ratom(1)) returns the electron density of the reactant atom matching map 1 in the reaction equation
electrophilicity energyNu nucleophilicLocalizationEnergy	DGTK	calculates the electrophilicity of an atom	the electrophilicity of the atom or NaN for non-aromatic atoms	the atom index/MolAtom object the major microspecies pH (takes the input molecule if omitted)	electrophilicity(2) returns the electrophilicity of atom 2 of the input molecule or NaN if atom 2 is non-aromatic	electrophilicity(ratom(1)) returns the electrophilicity of the reactant atom matching map 1 in the reaction equation
electrophilicityOrder aromaticElectrophilicityOrder orderEA	DGTK	calculates the electrophilicity (E+) order of an atom	the E+ order of the atom	the atom index/MolAtom object the major microspecies pH (takes the input molecule if omitted)	electrophilicityOrder(2) returns the E+ order 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 most electrophilic atom etc.	electrophilicityOrder(ratom(1)) returns the E+ order of the reactant atom matching map 1 in the reaction equation
hmoChargeDensity	DGTK	calculates the HMO charge density of an atom	the charge density of the atom or NaN for non-existing values	the atom index/MolAtom object the major microspecies pH (takes the input molecule if omitted)	hmoChargeDensity(2) returns the charge density of atom 2 of the input molecule or NaN for non-existing values	hmoChargeDensity(ratom(1)) returns the charge density of the reactant atom matching map 1 in the reaction equation
hmoElectronDensity	DGTK	calculates the HMO electron density of an atom	the electron density of the atom or NaN for non-existing values	the atom index/MolAtom object the major microspecies pH (takes the input molecule if omitted)	hmoElectronDensity(2) returns the electron density of atom 2 of the input molecule or NaN for non-existing values	hmoElectronDensity(ratom(1)) returns the electron density of the reactant atom matching map 1 in the reaction equation
hmoElectrophilicityOrder hmoOrderE	DGTK	calculates HMO electrophilic (HMO E+) order of an atom	the HMO E+ order index of the atom (0, 1, 2, ...)	the atom index/MolAtom object the major microspecies pH (takes the input molecule if omitted)	hmoElectrophilicityOrder(2) returns the HMO 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 most electrophilic atom etc.	hmoElectrophilicityOrder(ratom(1)) returns the HMO E+ order index of the reactant atom matching map 1 in the reaction equation
hmoElectrophilicLocalizationEnergy	DGTK	calculates the HMO localization energy (L+) of an atom	the localization energy (L+) of the atom or NaN for non-aromatic atoms	the atom index/MolAtom object the major microspecies pH (takes the input molecule if omitted)	hmoElectrophilicLocalizationEnergy(2) returns the L+ energy of atom 2 of the input molecule or NaN if atom 2 is non-aromatic	hmoElectrophilicLocalizationEnergy(ratom(1)) returns the L+ localization energy of the reactant atom matching map 1 in the reaction equation
hmoNucleophilicityOrder hmoOrderNu	DGTK	calculates the HMO nucleophilic (HMO Nu-) order index of the atom (0, 1, 2, ...)	the HMO Nu- order index of the atom (0, 1, 2, ...)	the atom index/MolAtom object the major microspecies pH (takes the input molecule if omitted)	hmoNucleophilicityOrder(2, '7.4') returns the Nu- order index of atom 2 of the major microspecies of the input molecule at pH 7.4, e.g. returns 0 if atom 2 is the most nucleophilic atom, 1 if atom 2 is the second strongest nucleophilic atom etc.	hmoNucleophilicityOrder(ratom(1)) returns the Nu+ order index of the reactant atom matching map 1 in the reaction equation
hmoNucleophilicLocalizationEnergy	DGTK	calculates the HMO nucleophilic (HMO L-) localization energy of an atom	the HMO L- energy of the atom or NaN for non-aromatic atoms	the atom index/MolAtom object the major microspecies pH (takes the input molecule if omitted)	hmoNucleophilicLocalizationEnergy(2) returns the nucleophilic localization energy of atom 2 of the input molecule or NaN if atom 2 is non-aromatic	hmoNucleophilicLocalizationEnergy(ratom(1)) returns the HMO L- energy of the reactant atom matching map 1 in the reaction equation
hmoPiEnergy	DGTK	calculates the HMO pi energy of the molecule	the HMO pi energy of the molecule	the atom index/MolAtom object the major microspecies pH (takes the input molecule if omitted)	hmoPiEnergy('7.4') returns the pi energy of the major microspecies of the input molecule at pH 7.4	hmoPiEnergy(product(1)) returns the pi energy of the second product
nucleophilicity electrophilicLocalizationEnergy energyE	DGTK	calculates nucleophilicity of an atom	the nucleophilicity of the atom or NaN for non-aromatic atoms	the atom index/MolAtom object the major microspecies pH (takes the input molecule if omitted)	nucleophilicity(2) returns the nucleophilicity of atom 2 of the input molecule or NaN if atom 2 is non-aromatic	nucleophilicity(ratom(1)) returns the nucleophilicity of the reactant atom matching map 1 in the reaction equation
nucleophilicityOrder aromaticNucleophilicityOrder orderNu	DGTK	calculates the nucleophilic (Nu-) order index of an atom (0, 1, 2, ...)	the Nu- order index of the atom (0,1,2, ...)	the atom index/MolAtom object the major microspecies pH (takes the input molecule if omitted)	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 most nucleophilic atom etc.	nucleophilicityOrder(ratom(1)) returns the Nu- order index of the reactant atom matching map 1 in the reaction equation
piEnergy	DGTK	calculates the pi energy of a molecule	the pi energy of the molecule	the major microspecies pH (takes the input molecule if omitted)	piEnergy() returns the pi energy of the input molecule	piEnergy(product(1)) returns the pi energy of the second product

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Isomers Functions

Name	License	Description	Return value	Parameters	Molecule context example(s)	Reaction context example(s)
allTautomer	DGTK, SPTK	returns a tautomer from all tautomers	the tautomer	the tautomer index (0-based)	allTautomer(0) returns the first tautomer of the input molecule	allTautomer(reactant(0), 1) returns the second tautomer of the first reactant
allTautomers	DGTK, SPTK	returns all tautomers in an array	the tautomer array	the normalization option normal (the default is false)	allTautomers('normal:true') returns all normalised tautomers of the input molecule in an array	allTautomers(reactant(0)) returns all tautomers of the first reactant in an array
canonicalResonant	-	generates the canonical resonant structure	the canonical resonant structure	-	canonicalResonant() returns the canonical resonant structure of the input molecule	canonicalResonant(reactant(0)) returns the canonical resonant structure of the first reactant
canonicalTautomer	DGTK, SPTK	generates the canonical tautomer structure	the canonical tautomer	the normalization option normal (the default is false and the canonical tautomer is generated )	canonicalTautomer('normal:true') returns the normal canonical tautomer of the input molecule	canonicalTautomer(reactant(0)) returns the canonical tautomer structure of the first reactant
dominantTautomer tautomer	DGTK, SPTK	returns a dominant tautomeric form	the dominant tautomer	the dominant tautomer index (0-based) the pH value (set if the pH effect should be considered)	dominantTautomer(0) returns the first dominant tautomer of the input molecule with no pH effect considered dominantTautomer(1, "2.0") returns the second dominant tautomer of the input molecule at pH 2.0	dominantTautomer(reactant(0), 1, '7.4') returns the second dominant tautomer of the first reactant at pH 7.4
dominantTautomerCount	DGTK, SPTK	calculates the number of dominant tautomers	the number of dominant tautomers	the pH value as string (set if the pH effect should be considered)	dominantTautomerCount("7.4") returns the number of dominant tautomers of the input molecule at pH 7.4	dominantTautomerCount(reactant(0)) returns the number of dominant tautomers of the first reactant without the pH effect considered
dominantTautomers tautomers	DGTK, SPTK	generates all dominant tautomers ordered by distribution %	the dominant tautomers in an array	the pH value as a string (set if the pH effect should be considered)	dominantTautomers() returns all dominant tautomers of the input molecule in an array dominantTautomers("2.0") returns all dominant tautomers of the input molecule at pH 2.0 in an array	dominantTautomers(product(1), "7.4") returns all dominant tautomers of the second product at pH 7.4 in an array
doubleBondStereoisomer	DGTK, SPTK	generates a double bond stereoisomer of the molecule	the double bond stereoisomer	the double bond stereoisomer index (0-based)	doubleBondStereoisomer(0) returns the first double bond stereoisomer of the input molecule	doubleBondStereoisomer(reactant(0), 1) returns the second double bond stereoisomer of the first reactant
doubleBondStereoisomerCount	DGTK, SPTK	returns the number of generated double bond stereoisomers	the number of generated double bond stereoisomers	-	doubleBondStereoisomerCount() returns the number of generated double bond stereoisomers of the input molecule	doubleBondStereoisomerCount(reactant(0)) returns the number of calculated double bond stereoisomers of the first reactant
doubleBondStereoisomers	DGTK, SPTK	generates double bond stereoisomers of the molecule	the double bond stereoisomer array	the maximum number of stereoisomers to be generated (the default is all)	doubleBondStereoisomers(100) returns at most 100 double bond stereoisomers of the input molecule in an array	doubleBondStereoisomers(reactant(0)) returns all double bond stereoisomers of the first reactant in an array
genericTautomer	DGTK, SPTK	generates the generic tautomer structure	the generic tautomer structure	-	genericTautomer() returns the generic tautomer structure of the input molecule	genericTautomer(reactant(0)) returns the generic tautomer structure of the first reactant
majorTautomer	DGTK, SPTK	generates the major tautomer structure	the major tautomer structure	the pH value as a string (set if the pH effect should be considered)	majorTautomer('7.4') returns the major tautomer structure of the input molecule at pH 7.4	majorTautomer(reactant(0)) returns the major tautomer structure of the first reactant with the pH effect not considered
resonant	-	generates a resonant structure of the molecule	the resonant structure	the resonant index (0-based)	resonant(0) returns the first resonant structure of the input molecule	resonant(reactant(0), 1) returns the second resonant structure of the first reactant
resonantCount	-	calculates the number of resonant structures of the input molecule	the number of resonant structures	-	resonantCount() returns the number of resonant structures of the input molecule	resonantCount(reactant(0)) returns the number of resonant structures of the first reactant
resonants	-	generates all resonant structures of the input molecule	the array of resonant structures	-	resonants() returns all resonant structures of the input molecule in an array	resonants(reactant(0)) returns all resonant structures of the first reactant in an array
stereoAnalysis	-	recognises stereo descriptors in a molecule	the list of stereo descriptors	the stereo descriptor type listed here	stereoAnalysis() returns all stereo descriptors of the input molecule stereoAnalysis('tetrahedralStereoCenters') returns the array of tetrahedral stereocenters of the input molecule	stereoAnalysis(reactant(1)) returns the stereo descriptors of the second reactant stereoAnalysis(reactant(1), 'axialStereoCenters') returns the axial stereocenters of the second reactant
stereoisomer	DGTK, SPTK	generates a stereoisomer of the molecule	the stereoisomer	the stereoisomer index (0-based)	stereoisomer(0) returns the first stereoisomer of the input molecule	stereoisomer(reactant(0), 1) returns the second stereoisomer of the first reactant
stereoisomerCount	DGTK, SPTK	returns the number of generated stereoisomers	the number of generated stereoisomers	-	stereoisomerCount() returns the number of generated stereoisomers of the input molecule	stereoisomerCount(reactant(0)) returns the number of generated stereoisomers of the first reactant
stereoisomers	DGTK, SPTK	generates stereoisomers for a molecule	the array of stereoisomers generated	the maximum number of stereoisomers to be generated (the default is all)	stereoisomers(10) returns maximum 10 stereoisomers of the input molecule in an array	stereoisomers(reactant(0)) returns all stereoisomers of the first reactant in an array
tautomerCount	DGTK, SPTK	calculates the number of tautomers for a molecule	the number of tautomers	-	tautomerCount() returns the number of tautomers of the input molecule	tautomerCount(product(1)) returns the number of tautomers of the second product
tetrahedralStereoisomer	DGTK, SPTK	generates a tetrahedral stereoisomer of a molecule	the tetrahedral stereoisomer	the stereoisomer index (0-based)	tetrahedralStereoisomer(0) returns the first tetrahedral stereoisomer of the input molecule	tetrahedralStereoisomer(reactant(0), 1) returns the second tetrahedral stereoisomer of the first reactant
tetrahedralStereoisomerCount	DGTK, SPTK	returns the number of generated tetrahedral stereoisomers	the number of generated tetrahedral stereoisomers	-	tetrahedralStereoisomerCount() returns the number of generated tetrahedral stereoisomers of the input molecule	tetrahedralStereoisomerCount(reactant(0)) returns the number of generated tetrahedral stereoisomers of the first reactant
tetrahedralStereoisomers	DGTK, SPTK	generates tetrahedral stereoisomers for a molecule	the tetrahedral stereoisomers in an array	the maximum number of tetrahedral stereoisomers to be generated (the default is all)	tetrahedralStereoisomers() returns all tetrahedral stereoisomers of the input molecule in an array	tetrahedralStereoisomers(reactant(0), 15) returns maximum 15 tetrahedral stereoisomers of the first reactant in an array

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Markush Functions

Name	License	Description	Return value	Parameters	Molecule context example(s)	Reaction context example(s)
isMarkush	-	decides whether a molecule contains any Markush features	true if the molecule contains any Markush features, false otherwise	-	isMarkush() returns true if the given molecule contains any Markush features, false otherwise	isMarkush(reactant(1)) returns true if the second reactant contains any Markush features, false otherwise
markushEnumerationCount enumerationCount	SETK	calculates the number of Markush enumerations	the number of Markush enumerations	the (1-based) atom indices of the query atoms to be enumerated (the default is all)	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	markushEnumerationCount(reactant(0)) returns the number of all 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 (note that the atoms() function converts 0-based indices to a '-' separated, 1-based atom index string)
markushEnumeration markushEnumerations enumeration enumerations	SETK	enumerates Markush structures sequentially	the enumerated structures	the number of structures to be enumerated (default is all) the (1-based) atom indices of the query atoms to be enumerated (default is all)	markushEnumerations() returns all Markush enumerated structures of the input molecule markushEnumerations(5, '2,3') returns five Markush enumerated structures of the input molecule, enumerating atoms 2, 3	markushEnumerations(reactant(0), 10) returns ten Markush enumerated structures of the first reactant markushEnumerations(product(1), 5, '2,3') returns five Markush enumerated structures of the second product, enumerating atoms 2, 3
markushEnumerationsDisplay	SETK	generates Markush enumerated structures sequentially with scaffold alignment and scaffold/R-group colouring and enumeration ID	the enumerated structures with alignment, colouring data and enumeration ID	the number of structures to be returned (default is all)	the (1-based) atom indices of the query atoms to be enumerated (default is all)	markushEnumerationsDisplay() returns all Markush enumerated structures of the input molecule with scaffold alignment and colouring data markushEnumerationsDisplay(10, '2,3') returns ten Markush enumerated structures of the input molecule, enumerating atoms 2, 3 (1-based) with scaffold alignment and colouring data
markushLibraryMagnitude	SETK	calculates the Markush library magnitude with no enumeration	the Markush library magnitude	the (1-based) atom indices of the query atoms to be enumerated (default is all)	markushLibraryMagnitude() returns the Markush library magnitude for the input molecule markushLibraryMagnitude('4,5') returns the Markush library magnitude for the input molecule with only atoms 4, 5 (1-based) being enumerated	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 with only atoms 4, 5 (1-based) being enumerated (note that the atoms() function converts 0-based indices to a '-' separated 1-based atom index string)
markushLibrarySize	SETK	calculates the Markush library size with no enumeration	the Markush library size	the (1-based) atom indices of the query atoms to be enumerated (default is all)	markushLibrarySize() returns the Markush library size for the input molecule markushLibrarySize('4,5') returns the Markush library size for the input molecule with only atoms 4, 5 (1-based) being enumerated	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 with only atoms 4, 5 (1-based) being enumerated (note that the atoms() function converts 0-based indices to a '-' separated 1-based atom index string)
markushLibrarySizeAsString	SETK	calculates the Markush library size and returns it as a string with no enumeration done	the Markush library size	the (1-based) atom indices of the query atoms to be enumerated (default is all)	markushLibrarySize() returns the Markush library size as string for the input molecule markushLibrarySize('4,5') returns the Markush library size as a string for the input molecule with only atoms 4, 5 (1-based) being enumerated	markushLibrarySize(reactant(0)) returns the Markush library size as a string for the first reactant markushLibrarySize(product(1), atoms(3,4)) returns the Markush library size as a string for the second product with only atoms 4, 5 (1-based) being enumerated (note that the atoms() function converts 0-based indices to a '-' separated 1-based atom index string)
randomMarkushEnumeration randomMarkushEnumerations randomEnumeration randomEnumerations	SETK	enumerates Markush structures randomly	the enumerated structures	the number of structures to be enumerated (default is 1) the (1-based) atom indices of the query atoms to be enumerated (default is all)	randomMarkushEnumeration() returns a randomly enumerated Markush structure of the input molecule randomMarkushEnumerations(4, '2,3') returns 4 randomly enumerated structures of the input molecule, enumerating only atoms 2, 3 (1-based)	randomMarkushEnumerations(reactant(0), 100) returns 100 randomly enumerated Markush structures of the first reactant randomMarkushEnumerations(product(1), 20, '3,4,5') returns 20 randomly enumerated Markush structures of the second product, enumerating atoms 3, 4, 5 (1-based)
randomMarkushEnumerationsDisplay	SETK	generates Markush enumerated structures randomly with scaffold alignment and scaffold/R-group colouring and enumeration ID	the enumerated structures with alignment, colouring data and enumeration ID	the number of structures to be returned (default is 1) the (1-based) atom indices of the query atoms to be enumerated (default is all)	randomMarkushEnumerationsDisplay() returns a randomly enumerated Markush structure of the input molecule with scaffold alignment and scaffold/R-group colouring randomMarkushEnumerationsDisplay(4, '2,3') returns 4 randomly enumerated structures of the input molecule, enumerating only atoms 2, 3 (1-based) with scaffold alignment and colouring data	randomMarkushEnumerationsDisplay(reactant(0), 100) returns 100 randomly enumerated Markush structures of the first reactant with scaffold alignment and colouring data randomMarkushEnumerationsDisplay(product(1), '3,4,5') returns a randomly enumerated structure of the second product, enumerating atoms 3, 4, 5 (1-based) with scaffold alignment and colouring data

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Match Functions

Name	License	Description	Return value	Parameters	Molecule context example(s)	Reaction context example(s)
disjointMatchCount	Structure Search	performs substructure search and 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) Note: The function returns the maximal number of pairwise disjoint query structures found in the target molecule. If the target atom index and optional query atom maps are specified, the return value can only be 0 or 1, therefore the result is similar to the result of the match() function.	disjointMatchCount("[#8]C=O") counts the maximal number of pairwise disjoint carboxylic groups in the input molecule	disjointMatchCount(reactant(0), "[#8]C=O") counts the maximal number of pairwise disjoint carboxylic groups in the first reactant
match	Structure Search	performs substructure search and optionally checks for atom matching	true if a matching substructure found, false otherwise	target atom index/MolAtom object (optional) query Molecule object/SMARTS string query atom map(s) (optional) Note: 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.	match("[#8]C=O") performs substructure search without atom matching requirement, the target is the input molecule and the query is the carboxylic group given in the string parameter	match(reactant(0), "[#8]C=O") performs substructure search without atom matching requirement, the target is the first reactant and the query is the carboxylic group given in the string parameter match(patom(2), "[#8]C=O") performs substructure search and checks if product atom matching map 2 of the reaction equation matches any atom of the carboxylic group query match(ratom(1), "[#8:1]C=[O:2]", 1, 2) performs substructure search and checks if reactant atom matching map 1 of the reaction equation is a carboxylic oxygen
matchCount	Structure Search	performs substructure search, optionally checks for atom matching and counts search hits	the number of search hits	target atom index/MolAtom object (optional) query Molecule object/SMARTS string query atom map(s) (optional) Note: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.	matchCount("[#8]C=O") counts search hits without atom matching requirement, the target is the input molecule and the query is the carboxylic group given in the string parameter	matchCount(reactant(0), "[#8]C=O") counts search hits without atom matching requirement, the target is the first reactant and 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 of 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 of the reaction equation being a carboxylic oxygen
matchFirst	Structure Search	performs substructure search and optionally checks for atom matching	the (1-based) index of the first matching substructure	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) Note: 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.	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. Note: The 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. It 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 the amide group of the query structure. It returns the index of the query if a match is found, 0 otherwise. matchFirst(6, {"[#8:1]C=[O:2]","[#6][OX2:1]CX3[#6]"}, 1, 2) performs substructure search, checks if target atom 6 of the input molecule is a carboxylic oxygen or an oxigen of an ester group. It returns the index of the query if a match is found, 0 otherwise.	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. The 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. It returns 0 if none of the listed groups is found in the first reactant. matchFirst(patom(2), {"[#8][C]=O","[NX3][CX3]=[OX1]"}) performs substructure search and checks if product atom matching map 2 of the reaction equation matches any atom of the carboxylic or amide group query. It returns the index of the matching query or 0 if no match is found. matchFirst(ratom(1), {"[#8:1]C=[O:2]","[#6][OX2:1]CX3[#6]"}, 1, 2) performs substructure search, checks if reactant atom matching map 1 of the reaction equation is a carboxylic oxygen or an oxygen of an ester group. It returns the index of the query if a match is found, 0 otherwise.

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.

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

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Name Functions

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

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Partitioning Functions

Name	License	Description	Return value	Parameters	Molecule context example(s)	Reaction context example(s)
HLB number	DGTK	calculates the HLB number	the HLB number	the HLB method (can be chemaxon, davies, griffin and required; the default is chemaxon)	hlb() returns the HLB number of the input molecule calculated by the ChemAxon method hlb('davies') returns the HLB number of the input molecule calculated by the Davies method	hlb(reactant(1), 'griffin') returns the HLB number of the second reactant calculated by the Griffin method
logD	DGTK	calculates logD at a specified pH value using the ChemAxon method	the logD value	the pH value	logD('7.4') returns the logD value of the input molecule at pH 7.4	logD(reactant(1), '7.4') returns the logD of the second reactant at pH 7.4
logDKLOP	DGTK	calculates logD at a specified pH value using the Klopman method	the logD value	the pH value	logDKLOP('7.4') returns the logD at pH 7.4 of the input molecule	logDKLOP(reactant(1), '7.4') returns the logD of the second reactant at pH 7.4
logDPHYS	DGTK	calculates logD at a specified pH value using the PhysProp method	the logD value	the pH value	logDPHYS('7.4') returns the logD at pH 7.4 of the input molecule	logDPHYS(reactant(1), '7.4') returns the logD at pH 7.4 of the second reactant
logDUser	DGTK	calculates logD at specified a pH value using the user defined method	the logD value	the pH value	logDUser('7.4') returns the logD value at pH 7.4 of the input molecule	logDUser(reactant(1), '7.4') returns the logD at pH 7.4 of the second reactant
logDVG	DGTK	calculates logD at a specified pH value using the VG method	the logD value	the pH value	logDVG('7.4') returns the logD at pH 7.4 of the input molecule	logDVG(reactant(1), '7.4') returns the logD at pH 7.4 of the second reactant
logDWeighted	DGTK	calculates logD at a specified pH value using the weighted method	the logD value	the pH value	logDWeighted('7.4') returns the logD at pH 7.4 of the input molecule	logDWeighted(reactant(1), '7.4') returns the logD at pH 7.4 of the second reactant
logP	DGTK	calculates the logP	the logP value	the value type: logPMicro: the logP of the input molecule logPNonionic: the logP of the non-ionic form of the input molecule logDpI: the logD predicted at the iso-electric point (pI) of the input molecule logPTrue: the most typical logP from the above values (default type)	logP() returns the most typical logP of the input molecule	logP(reactant(1), 'logDpI') returns the logD value of the second reactant at its pI logP(product(1), 'logPNonionic') returns the non-ionic logP of the second product
logPincrement logPi	DGTK	calculates atomic logP increments	the atomic logP increment	the atom index/ MolAtom object	logPincrement(2) returns the logP increment on atom 2 of the input molecule	logPi(ratom(1)) returns the logP increment of the reactant atom matching map 1 in the reaction equation
logPKLOP	DGTK	calculates logP using the Klopman method	the logP value	the value type: logPMicro: the logP of the input molecule logPNonionic: the logP of the non-ionic form of the input molecule logDpI: the logD predicted at the iso-electric point (pI) of the input molecule logPTrue: the most typical logP from the above values (default type)	logPKLOP() returns the most typical logP value of the input molecule logPKLOP('logPMicro') returns the logP of the input molecule itself	logPKLOP(reactant(1), 'logDpI') returns the logD of the second reactant at its pI logPKLOP(product(1), 'logPNonionic') returns the non-ionic logP of the second product
logPPHYS	DGTK	calculates logP using the PhysProp method	the logP value	the value type: logPMicro: the logP of the input molecule logPNonionic: the logP of the non-ionic form of the input molecule logDpI: the logD predicted at the iso-electric point (pI) of the input molecule logPTrue: the most typical logP from the above values (default type)	logPPHYS('logPNonionic') returns the non-ionic logP of the input molecule logPPHYS('logPMicro') returns the logP of the input molecule itself	logPPHYS(reactant(1), 'logDpI') returns the logD at the pI of the second reactant logPPHYS(product(1), 'logPNonionic') returns logP of the nonionic species of the second product
logPUser	DGTK	calculates logP using the user defined method	the logP value	the value type: logPMicro: the logP of the input molecule logPNonionic: the logP of the non-ionic form of the input molecule logDpI: the logD predicted at the iso-electric point (pI) of the input molecule logPTrue: the most typical logP from the above values (default type)	logPUser() returns the most typical logP of the input molecule	logPUser(reactant(1), 'logDpI') returns the logD at the pI of the second reactant logPUser(product(1), 'logPNonionic') returns the logP of the nonionic species of the second product
logPVG	DGTK	calculates the logP using the VG method	the logP value	the value type: logPMicro: the logP of the input molecule logPNonionic: the logP of the non-ionic form of the input molecule logDpI: the logD predicted at the iso-electric point (pI) of the input molecule logPTrue: the most typical logP from the above values (default type)	logPVG() returns the most typical logP value of the input molecule logPVG('logPMicro') returns the logP of the input molecule itself	logPVG(reactant(1), 'logDpI') returns the logD at the pI of the second reactant logPVG(product(1), 'logPNonionic') returns the logP of the nonionic species of the second product
logPWeighted	DGTK	calculates the logP using the weighted method	the logP value	the value type: logPMicro: the logP of the input molecule logPNonionic: the logP of the non-ionic form of the input molecule logDpI: the logD predicted at the iso-electric point (pI) of the input molecule logPTrue: the most typical logP from the above values (default type)	logPWeighted() returns the most typical logP value of the input molecule logPWeighted('logPMicro') returns the logP of the input molecule itself	logPWeighted(reactant(1), 'logDpI') returns the logD at the pI of the second reactant logPWeighted(product(1), 'logPNonionic') returns the logP of the nonionic species of the second product

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Protonation Functions

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

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Refractivity Functions

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

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Solubility Functions

Name	License	Description	Return value	Parameters	Molecule context example(s)	Reaction context example(s)
logS	DGTK	Calculates intrinsic or pH-dependent solubility (logS)	the logS value	the pH value (for pH-dependent logS) the solubility unit: logS, mol/l, mg/ml or category (default is logS)	logS('mol/l') returns the intrinsic solubility of the input molecule in mol/l unit logS('7.4', 'category') returns the solubility category of the input molecule at pH 7.4	logS(product(1), '7.4', 'mg/ml') returns the solubility of the second product at pH 7.4 in mg/ml unit

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Structural Frameworks Functions

Name	License	Description	Return value	Parameters	Molecule context example(s)	Reaction context example(s)
bmf	DGTK	generates the Bemis-Murcko Framework (BMF) of the input molecule	the BMF	-	bmf() returns the BMF of the input molecule	bmf(reactant(0)) returns the BMF of the first reactant
bemisMurckoFrameworkLoose bmfl	DGTK	generates the Bemis-Murcko Loose Framework (BMLF, which is generated from the BMF by removing side chains, keeping exocyclic non-single bonded atoms, while not changing the remaining atom and bond types) of the input molecule	the BMLF	-	bmfl() returns the BMFL of the input molecule	bmfl(reactant(0)) returns the BMLF of the first reactant
bemisMurckoFrameworkLoosePruned bmflp	DGTK	generates the Bemis-Murcko Loose Pruned Framework (BMFLP, which is generated from the BMF by removing side chains. Atom and bond types are generalised by replacing all atoms with carbon atoms and setting all bond types to single. Exocyclic non-single bonded atoms are kept as single bonded carbons.)	The BMFLP	-	bmflp() returns the BMFLP of the input molecule	bmflp(reactant(0)) returns the BMFLP of the first reactant

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Structure Checker Functions

Name	License	Description	Return value	Parameters	Molecule context example(s)	Reaction context example(s)
check	-	checks a structure for errors according to a configuration and returns an error report	the error report	the structure checker/fixer configuration as an action string or an XML string	check("aromaticity..valence") checks aromaticity and valence errors in the input molecule and returns an error report check('" "') checks aromaticity and valence errors in the input molecule and returns an error report	check(reactant(0), "aromaticity..valence") checks aromaticity and valence errors in the first reactant and returns the error report
checkErrorCount	-	checks a structure for errors according to a configuration and returns the total error count	the total error count	the structure checker/fixer configuration as an action string or an XML string	checkErrorCount("aromaticity..valence") checks aromaticity and valence errors in the input molecule and returns the total error count checkErrorCount('""') checks aromaticity and valence errors in the input molecule and returns the total error count	checkErrorCount(reactant(0), "aromaticity..valence") checks aromaticity and valence errors in the first reactant and returns the total error count
fix	-	checks a structure for errors according to a configuration and fixes them	the fixed structure	the structure checker/fixer configuration as an action string or an XML string	Both fix("chiralflag..isotope->converttoelementalform") and fix('""') search for chiral flags and isotopes and then removes them or converts them to elemental form	fix(product(1), "chiralflag..isotope->converttoelementalform") searches for chiral flags and isotopes in the second product and then removes them or converts them to elemental form
isValid	-	checks if a structure is valid (has no errors) according to a configuration	true if the structure is valid, false otherwise	the structure checker/fixer configuration as an action string or an XML string	Both isValid("aromaticity..valence") and isValid('" "') check for aromaticity and valence errors and then returns if the structure is valid	isValid(reactant(0), "aromaticity..valence") checks for aromaticity and valence errors in the first reactant and then returns if it is valid

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Notes

1. If atoms referred by their atom indices are used as parameters in a Chemical Terms function in a reaction context (including cases when a Chemical Terms function is used to convert reactant or product atom maps to atom indices), then a (reactant or product) molecule must be specified and must contain all the referred atoms (e.g. in the shortestPath(reactant(0), pair(ratom(1), ratom(2))) function ratom(1) and ratom(2) must be atoms of the first reactant).

2. Although function names are case-sensitive, lowercase names are always accepted, e.g. aromaticAtomCount() is equivalent to aromaticatomcount(), but AromaticAtomCount() and AROMATICATOMCOUNT() names are not recognised by the parser.

3. match, matchCount, disjointMatchCount and the dissimilarity functions are not available in Marvin. They can be used only if the JChem software package is installed.

4. Structure-based calculations are performed using the Calculator Plugins (those calculations are also referred as "plugin calculations"). Since Marvin 5.2 all those functions can have an additional string argument that specifies plugin parameters, specified using the format "key1:value1 key2:value2 key3:value3...". Some examples are: charge(8, "type:pi pH:3.5") computes the pi charge of atom 8 of the major microspecies at pH=3.5 of the input molecule; markushEnumerations("code:true max:4","1,2") enumerates maximum 4 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, e.g. charge(8, "type:pi pH:3.5") cannot be specified as charge(8, "type:pi", "3.5"), while charge("pi", 8, "3.5") is accepted (because of backward compatibility).