Functions by Categories

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    Charge Functions

    Name License Description Return value Parameters Examples
    atomicPolarizability atomPol pol polarizability Structural Calculations License calculates atomic polarizability the polarizability values the atom index / MolAtom object, the major microspecies pH (takes the input molecule itself if omitted) Molecule ContextatomicPolarizability(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 taken at pH 7.4Reaction ContextatomicPolarizability(ratom(1)) returns the polarizability of reactant atom matching map 1 in the reaction equation atomicPolarizability(patom(2), "7.4") returns the polarizability of the product atom matching map 2 of the major microspecies taken at pH 7.4
    averagePolarizability averagePol avgPol Structural Calculations License calculates average molecular polarizability component considering 3D geometry the polarizability value * the major microspecies pH (takes the input molecule itself if omitted) Molecule ContextaveragePolarizability() returns the average polarizability component of the input molecule averagePolarizability("7.4") returns the average polarizability component of the major microspecies taken at pH 7.4Reaction ContextaveragePolarizability(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 first product major microspecies taken at pH 7.4
    axxPol Structural Calculations License calculates principal component of polarizability tensor (a(xx), a(yy), a(zz)) the principal component of polarizability tensor * the major microspecies pH (takes the input molecule itself if omitted) Molecule ContextaxxPol() returns the principal component a(xx) of polarizability tensor of the input molecule axxPol("7.4") returns the principal component a(xx) of polarizability tensor of the major microspecies taken at pH 7.4Reaction ContextaxxPol(reactant(1)) returns the principal component a(xx) of polarizability tensor of the second reactant in the reaction equation axxPol(product(0), "7.4") returns the principal component a(xx) of polarizability tensor of the first product major microspecies taken at pH 7.4
    ayyPol Structural Calculations License calculates principal component of polarizability tensor (a(xx), a(yy), a(zz)) the principal component of polarizability tensor * the major microspecies pH (takes the input molecule itself if omitted) Molecule ContextayyPol() returns the principal component a(yy) of polarizability tensor of the input molecule ayyPol("7.4") returns the principal component a(yy) of polarizability tensor of the major microspecies taken at pH 7.4Reaction ContextayyPol(reactant(1)) returns the principal component a(yy) of polarizability tensor of the second reactant in the reaction equation ayyPol(product(0), "7.4") returns the principal component a(yy) of polarizability tensor of the first product major microspecies taken at pH 7.4
    azzPol Structural Calculations License calculates principal component of polarizability tensor (a(xx), a(yy), a(zz)) the principal component of polarizability tensor * the major microspecies pH (takes the input molecule itself if omitted) Molecule ContextazzPol() returns the principal component a(zz) of polarizability tensor of the input molecule azzPol("7.4") returns the principal component a(zz) of polarizability tensor of the major microspecies taken at pH 7.4Reaction ContextazzPol(reactant(1)) returns the principal component a(zz) of polarizability tensor of the second reactant in the reaction equation azzPol(product(0), "7.4") returns the principal component a(zz) of polarizability tensor of the first product major microspecies taken at pH 7.4
    charge Structural Calculations License calculates partial charges on atoms for result types "aromaticsystem" / "aromaticring", calculates the sum of partial charges of the atoms in the aromatic system / smallest aromatic ring containing the atom the charge values the atom index / MolAtom object, the result type ("total" (default), "pi", "sigma", "aromaticsystem", "aromaticsystemsigma", "aromaticsystempi", "aromaticring", "aromaticringsigma", "aromaticringpi"), * the major microspecies pH (takes the input molecule itself if omitted) Molecule Contextcharge(0) returns the partial charge on atom 0 of the input molecule charge(2, "pi", "7.4") returns the partial "pi" charge on atom 2 of the major microspecies taken at pH 7.4Reaction Contextcharge(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 taken at pH 7.4
    molecularPolarizability molPol Structural Calculations License calculates molecular polarizability the polarizability value * the major microspecies pH (takes the input molecule itself if omitted) Molecule ContextmolecularPolarizability() returns the molecular polarizability of the input molecule molecularPolarizability("7.4") returns the molecular polarizability of the major microspecies taken at pH 7.4Reaction ContextmolecularPolarizability(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 first product major microspecies taken at pH 7.4
    piOrbitalElectronegativity pOEN Structural Calculations License calculates atomic pi orbital electronegativity the pi orbital electronegativity values the atom index / MolAtom object, the major microspecies pH (takes the input molecule itself if omitted) Molecule ContextpiOrbitalElectronegativity(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 taken at pH 7.4Reaction ContextpOEN(ratom(1)) returns the pi orbital electronegativity of reactant atom matching map 1 in the reaction equation pOEN(patom(2), "7.4") returns the pi orbital electronegativity of the product atom matching map 2 of the major microspecies taken at pH 7.4
    resonantCharge Structural Calculations License calculates partial charges on atoms considering resonance effect for result types "aromaticsystem" / "aromaticring", calculates the sum of partial charges of the atoms in the aromatic system / smallest aromatic ring containing the atom the charge values the atom index / MolAtom object, the result type ("total" (default), "pi", "sigma", "aromaticsystem", "aromaticsystemsigma", "aromaticsystempi", "aromaticring", "aromaticringsigma", "aromaticringpi"), * the major microspecies pH (takes the input molecule itself if omitted) Molecule ContextresonantCharge(0) returns the partial charge on atom 0 of the input molecule considering resonance effectresonantCharge(2, "pi", "7.4") returns the partial "pi" charge on atom 2 of the major microspecies taken at pH 7.4 considering resonance effectReaction ContextresonantCharge(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 effectresonantCharge(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 taken at pH 7.4 considering resonance effect
    sigmaOrbitalElectronegativity sOEN Structural Calculations License calculates atomic sigma orbital electronegativity the sigma orbital electronegativity values the atom index / MolAtom object, the major microspecies pH (takes the input molecule itself if omitted) Molecule ContextsigmaOrbitalElectronegativity(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 taken at pH 7.4Reaction ContextsOEN(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 Examples
    conformer Structural Calculations License calculates a conformer of the molecule the conformer * the conformer index (0-based) Molecule Context (All)conformer(0) returns the first conformer of the input moleculeReaction Context (All)conformer(reactant(0), 1) returns the second conformer of the first reactant
    conformerCount Structural Calculations License returns the number of calculated conformers the number of calculated conformers - Molecule Context (All)conformerCount() returns the number of calculated conformers of the input moleculeReaction Context (All)conformerCount(reactant(0)) returns the number of calculated conformers of the first reactant
    conformers Structural Calculations License calculates conformers of the molecule (maximum number of conformers to be calculated can be set, default: 100) the conformer array - Molecule Context (All)conformers() returns conformers of the input molecule in an arrayReaction Context (All)conformers(reactant(0)) returns conformers of the first reactant in an array
    hasValidConformer Structural Calculations License returns true if the input molecule exist in 3D space (has a valid conformer) true if the input molecule exist in 3D space - Molecule Context (All)hasValidConformer() returns true if the input molecule exists in 3D space (has a valid conformer)Reaction Context (All)hasValidConformer(reactant(0)) returns true the if the first reactant exists in 3D space hasValidConformer(product(1)) returns true the if the second product exist in 3D space
    lowestEnergyConformer leconformer Structural Calculations License calculates the lowest energy conformer of the molecule the lowest energy conformer - Molecule Context (All)lowestEnergyConformer() returns the lowest energy conformer of the input moleculeReaction Context (All)lowestEnergyConformer(reactant(0)) returns the lowest energy conformer of the first reactant lowestEnergyConformer(product(1)) returns the lowest energy conformer of the second product
    mmff94OptimizedStructure Structural Calculations License calculates the MMFF94 optimized lowest energy conformer the MMFF94 optimized lowest energy conformer - Molecule Context (All)mmff94OptimizedStructure() returns the MMFF94 optimized lowest energy conformer of the input moleculeReaction Context (All)mmff94OptimizedStructure(reactant(0)) returns the MMFF94 optimized lowest energy conformer of the first reactant mmff94OptimizedStructure(product(1)) returns the MMFF94 optimized lowest energy conformer of the second product

    Conformation Functions

    Name License Description Return value Parameters Examples
    conformer Structural Calculations License calculates a conformer of the molecule the conformer * the conformer index (0-based) Molecule Context conformer(0) returns the first conformer of the input molecule Reaction Context conformer(reactant(0), 1) returns the second conformer of the first reactant
    conformerCount Structural Calculations License returns the number of calculated conformers the number of calculated conformers - Molecule Context conformerCount() returns the number of calculated conformers of the input molecule Reaction Context conformerCount(reactant(0)) returns the number of calculated conformers of the first reactant
    conformers Structural Calculations License calculates conformers of the molecule (maximum number of conformers to be calculated can be set, default: 100) the conformer array - Molecule Context conformers() returns conformers of the input molecule in an array Reaction Context conformers(reactant(0)) returns conformers of the first reactant in an array
    hasValidConformer Structural Calculations License returns true if the input molecule exist in 3D space (has a valid conformer) true if the input molecule exist in 3D space - Molecule Context hasValidConformer() returns true if the input molecule exists in 3D space (has a valid conformer) Reaction Context hasValidConformer(reactant(0)) returns true the if the first reactant exists in 3D space hasValidConformer(product(1)) returns true the if the second product exist in 3D space
    lowestEnergyConformer leconformer Structural Calculations License calculates the lowest energy conformer of the molecule the lowest energy conformer - Molecule Context lowestEnergyConformer() returns the lowest energy conformer of the input molecule Reaction Context lowestEnergyConformer(reactant(0)) returns the lowest energy conformer of the first reactant lowestEnergyConformer(product(1)) returns the lowest energy conformer of the second product
    mmff94OptimizedStructure Structural Calculations License calculates the MMFF94 optimized lowest energy conformer the MMFF94 optimized lowest energy conformer - Molecule Context mmff94OptimizedStructure() returns the MMFF94 optimized lowest energy conformer of the input molecule Reaction Context mmff94OptimizedStructure(reactant(0)) returns the MMFF94 optimized lowest energy conformer of the first reactant mmff94OptimizedStructure(product(1)) returns the MMFF94 optimized lowest energy conformer of the second product

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    Dissimilarity Functions

    Name License Description Return value Parameters Examples
    dissimilarity - computes the dissimilarity value between two molecules Note 1: Dissimilarity function requires JChem. Note 2: The dissimilarity values returned by dissimilarity function and similarity search in JChem database may differ because of the applied fingerprints. Dissimilarity function uses the default options of the chemical fingerprints (length=1024, bonds=7, bits=2) optimized for similarity search. Database similarity search uses fingerprints specified during the generation of the given table, optimized for substructure (and related) search types. the dissimilarity value descriptor:metricor descriptor (with default metric) (optional, chemical fingerprint with Tanimoto metric is taken by default), one or two molecules (if only one is specified then the other one is taken from the context) Molecule Context 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 default fingerprint and its default metric (chemical fingerprint with Tanimoto) 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 Reaction Context 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 default fingerprint and its default metric (chemical fingerprint with Tanimoto)

    Dissimilarity descriptors and metrics

    Descriptor Metric
    ChemicalFingerprint (or CF) Tanimoto (default) Euclidean
    PharmacophoreFingerprint (or PF) Tanimoto (default) Euclidean
    ECFP Tanimoto (default) Euclidean
    Burden eigenvalue descriptor (or BCUT) (BCUT is a trademark of Tripos, Inc., used with permission) Euclidean
    HDon Euclidean
    HAcc AbsDiff
    Heavy AbsDiff
    LogD AbsDiff
    LogP AbsDiff
    Mass AbsDiff
    TPSA AbsDiff

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    Elemental Analysis Functions

    Name License Description Return value Parameters Examples
    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 then all non-isotope atoms are counted Molecule Context atomCount() returns the number of atoms in the input molecule atomCount("6") returns the number of carbon atoms in the input molecule Reaction Context 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 - Molecule Context composition() returns the composition of the input molecule Reaction Context N / A (reaction rules are numerical)
    dotDisconnectedFormula - returns the dot-disconnected formula the dot-disconnected formula - Molecule Context dotDisconnectedFormula() returns the dot-disconnected formula of the input molecule Reaction Context N / A (reaction rules are numerical)
    dotDisconnectedIsotopeFormula - returns the dot-disconnected isotope formula the dot-disconnected isotope formula - Molecule Context dotDisconnectedIsotopeFormula() returns the dot-disconnected isotope formula of the input molecule Reaction Context N / A (reaction rules are numerical)
    dotDisconnectedFormulaWithGrouping - returns the grouped dot-disconnected formula the grouped dot-disconnected formula - Molecule Context dotDisconnectedFormulaWithGrouping() returns the grouped dot-disconnected formula of the input molecule Reaction Context N / A (reaction rules are numerical)
    elementalAnalysis - performs elemental analysis on molecule represented by formula the value calculated by the invoked function (e.g., mass) molecular formula available functions: atomCount mass massPrecision exactMass exactMassPrecision formula isotopeFormula dotDisconnectedFormula dotDisconnectedIsotopeFormula groupedDotDisconnectedFormula Molecule Context elementalAnalysis('mass','C12H25O') returns the mass of molecule represented by formula Reaction Context N / A
    exactMass - calculates the exact mass of the molecule the exact mass - Molecule Context exactMass() returns the exact mass of the input molecule Reaction Context exactMass(product(1)) returns the exact mass of the second product
    formula - returns the formula the formula - Molecule Context formula() returns the formula of the input molecule Reaction Context N / A (reaction rules are numerical)
    isotopeComposition - returns the isotope composition the isotope composition - Molecule Context isotopeComposition() returns the isotope composition of the input molecule Reaction Context N / A (reaction rules are numerical)
    isotopeFormula - returns the isotope formula the isotope formula - Molecule Context isotopeFormula() returns the isotope formula of the input molecule Reaction Context N / A (reaction rules are numerical)
    mass - calculates the molecule mass the mass - Molecule Context mass() returns the mass of the input molecule Reaction Context 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 - Molecule Context massspectrum() returns the mass spectrum of the input molecule Reaction Context massspectrum(reactant(0)) returns the mass spectrum of the first reactant
    sortableFormula - returns the fixed digit sortable formula fixed digit sortable molecular formula - Molecule Context sortableFormula() returns the sortable formula of the input molecule; sortableFormula('digits:4') returns the 4 digit sortable formula of the input molecule Reaction Context N / A (reaction rules are numerical)

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    General Functions

    Name License Description Return value Parameters Examples
    abs - returns the absolute value of a number the absolute value integer or real number General (All) abs(7)returns 7 abs(-4.9)returns 4.9 Molecule Context abs(7)returns 7abs(-4.9)returns 4.9 Reaction Context abs(7)returns 7abs(-4.9)returns 4.9
    agentCount - counts the agents in the reaction the number of agents in the reaction, or -1 if the the input (molecule) is not a reaction - Molecule Context agentCount() returns n if the given molecule is a reaction and contains n agents. agentCount() returns -1 if the given molecule is not a reaction. Reaction Context agentCount() returns n if the given molecule is a reaction and contains n agents. agentCount(reactant(0)) and agentCount(product(1)) calls does not make sense, and will return -1.
    arom - returns if the atom has an aromatic bond true if the atom has an aromatic bond, false otherwise atom index or MolAtom object Molecule Context arom(0) returns if the atom 0 has an aromatic bond Reaction Context arom(patom(2)) returns true if the product atom matching map 2 in the reaction equation has an aromatic bond
    array - constructs an integer array from its arguments the integer array integers or MolAtom objects General (All) array(2, 5, 6, 8) Molecule Context array(2, 5, 6, 8) Reaction Context array(ratom(2), ratom(5), ratom(6), ratom(8)) array(patom(2), patom(5), patom(6), patom(8))
    atno atomicNumber - returns the atomic number the atomic number atom index or MolAtom object Molecule Context atno(0) returns the atomic number of atom 0 Reaction Context atno(ratom(1)) returns the atomic number of the reactant atom matching map 1
    atomProp -
    atoms -
    booleanToNumber - returns the number representation of a boolean value (true = 1, false = 0), or the number itself, if the input is a number the number representation of a boolean value boolean or number General (All) booleanToNumber(1<2)returns 1 booleanToNumber(2+2==5)returns 0 booleanToNumber(5*5)returns 25 Molecule Context booleanToNumber(hasValenceError())returns 0 for molecules having no valence error Reaction Context 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 Molecule Context connections(2) returns the number of connections of atom 2 Reaction Context 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 array elements integer array or real number array General (All) count(array(3.4, 5.6, 1.2)) returns 3 Molecule Context </ac:plain-text-body></ac:structured-macro> Reaction Context <![CDATA[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 ]]></ac:plain-text-body></ac:structured-macro>
    elemanal -
    eval -
    field property - returns a molecule property (SDF field value) the molecule property the property key (SDF field name) Molecule Context field('ACTIVITY') returns the value of the ACTIVITY property (SDF field) field('ACTIVITY') > 2 returns 1 if the ACTIVITY value is bigger than 2, returns 0 otherwise Reaction Context field(reactant(1), 'ACTIVITY') returns the ACTIVITY property value of the second reactant field(product(0), 'ACTIVITY') > field(reactant(0), 'ACTIVITY') returns 1 if the ACTIVITY value of the first product is bigger than that of the first reactant, returns 0 otherwise
    fieldAsString propertyAsString - returns a molecule property (SDF field value) as string the molecule property as string the property key (SDF field name) Molecule Context fieldAsString('ID') returns the value of the ID property (SDF field) Reaction Context field(reactant(0), 'ID') returns the value of the ID property field in first reactant
    filter - filters target atoms by filtering condition target atom indices satisfying the filtering condition target atom indices / objects or index / atom object array (optional, all atoms taken if omitted), filtering condition (boolean expression) Molecule Context </ac:plain-text-body></ac:structured-macro> Reaction Context <![CDATA[filter(reactant(0), "charge() > 0") returns the indices of atoms with positive partial charge in the first reactant filter(patom(1), patom(2), "match('[#8][C:1]=O', 1)") returns the carboxylic carbons out of product atoms matching map 1 or 2 in the reaction equation (note, that these atoms are supposed to be in the same product molecule) ]]></ac:plain-text-body></ac:structured-macro>
    formalCharge totalCharge - calculates formal charge of molecule the formal charge value atom index or MolAtom object (optional) Molecule Context formalCharge() returns the formal charge of the input molecule formalCharge(0) returns the formal charge of atom 0 Reaction Context formalCharge(reactant(0)) returns the formal charge of the first reactant formalCharge(ratom(1)) returns the formal charge of the reactant atom matching map 1
    fragments - converts the molecule to its disconnected fragments the disconnected fragments of the molecule - Molecule Context fragments() returns the disconnected fragments of the molecule Reaction Context fragments(reactant(1)) returns the disconnected fragments of the second reactant
    hasAromatizationError - determines if there is error in the aromatization of the molecule true if there is an error in the aromatization of the molecule, false otherwise - Molecule Context hasAromatizationError() returns true if there is an error in the aromatization of the molecule, false otherwise Reaction Context hasAromatizationError(reactant(0)) returns true if there is an error in the aromatization of the first reactant, false otherwise
    hasIsotope - determines if any atom in the molecule is a specific isotope of the element true if any atom in the molecule is a specific isotope of the element, false otherwise - Molecule Context hasIsotope() returns true if any atom in the molecule is a specific isotope of the element, false otherwise Reaction Context hasIsotope(reactant(1)) returns true if any atom in the second reactant is a specific isotope of the element, false otherwise
    hasRadical - determines if any atom in the molecule has radical true if any atom in the molecule has radical, false otherwise - Molecule Context hasRadical() returns true if any atom in the molecule has radical, false otherwise Reaction Context hasRadical(reactant(1)) returns true if any atom in the second reactant has radical, false otherwise
    hasValenceError - determines if any atom in the molecule has valence error true in case of valence error, false otherwise - Molecule Context hasValenceError() returns true if any atom in the molecule has valence error, false otherwise Reaction Context hasValenceError(reactant(1)) returns true if any atom in the second reactant has valence error, false otherwise
    HBDA Structural Calculations License
    hCount - returns the hydrogen count of an atom the hydrogen count atom index or array of atom indeces (separated by , or images/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/wink.svg or MolAtom object Molecule Context hCount(0;2;3) returns the hydrogen count of atom 0,2,3 Reaction Context hCount(patom(3)) returns the hydrogen count on the product atom matching map 3 in the reaction equation
    importMol - imports and returns the molecule from its string representation the string representation of the molecule the molecule in string representation (e.g. "c1ccccc1") Molecule Context importMol("c1ccccc1") returns benzene molecule Reaction Context N / A (reaction rules are numerical)
    in - determines whether an integer / atom index is contained in a given integer array true if the array contains the specified integer, false otherwise an integer or MolAtom object and an integer array General (All) in(5, array(3, 5, 1)) returns true in(2, array(3, 5, 1)) returns false Molecule Context in(3, maxatom("charge()", 2)) returns true if the partial charge on atom 3 is within the first 2 largest partial charges in the input molecule in(3, minatom("pol()", 4)) returns true if the polarizability on atom 3 is within the first 4 smallest polarizability values in the input molecule Reaction Context in(ratom(3), maxatom(reactant(0), "charge()", 2)) returns true if the partial charge on reactant atom matching map 3 in the reaction equation is within the first 2 largest partial charges in the first reactant in(patom(1), minatom(product(1), "pol()", 4)) returns true if the polarizability on product atom matching map 1 in the reaction equation is within the first 4 smallest polarizability values in the second product
    ionCharge Structural Calculations License
    isEmpty - decides whether the given molecule is empty (does not contain any atoms, bonds, or non-empty S-groups) true if the molecule does not contain any atoms, bonds, or non-empty S-groups, false otherwise - Molecule Context isQuery() returns true if the given molecule does not contain any atoms, bonds, or non-empty S-groups, false otherwise Reaction Context isQuery(reactant(1)) returns true if the second reactant contains any atoms, bonds, or non-empty S-groups, false otherwise
    isQuery - decides whether the given molecule contains any query features true if the molecule contains any query features, false otherwise - Molecule Context isQuery() returns true if the given molecule contains any query features, false otherwise Reaction Context isQuery(reactant(1)) returns true if the second reactant contains any query features, false otherwise
    map - returns the atom map number the atom map number atom index or MolAtom object Molecule Context map(3) returns the atom map number of atom 3 Reaction Context map(patom(3)) returns the atom map number on the product atom matching map 3 in the reaction equation
    max - takes maximum of its array and/or numerical parameters the maximum value integers, real numbers, integer arrays, real number arrays General (All) min(2, 8, 6) returns 2 max(3.4, 5.6, 1.2) returns 5.6 Molecule Context min(charge(0), charge(2)) returns the least of the partial charge values on atoms 0 and 2 max(charge()) returns the maximal partial charge value on the input molecule Reaction Context min(charge(ratom(2)), charge(ratom(3))) returns the least of the partial charge values on reactant atoms matching maps 2 and 3 in the reaction equation max(charge(product(0))) returns the maximal partial charge value on the first product
    maxAtom - evaluates objective function for each atom, finds largest value(s) the atom index / indices corresponding to the largest evaluation result(s) target atom indices / objects or index / atom object array (optional, all atoms taken if omitted), the objective function (as inner expression string), the number of largest values to be taken (optional, takes only one if omitted) Molecule Context maxAtom(6, 7, 8, 9, "charge('7.4')", 2) selects the two largest partial charges on atoms 6, 7, 8, 9 in the major microspecies at pH 7.4 of the input molecule and returns the corresponding indices Reaction Context maxAtom(patom(1), patom(2), patom(3), "charge('7.4')", 2) selects the two largest partial charges on product atoms matching maps 1, 2, 3 in the major microspecies at pH 7.4 of the product molecule of these atoms and returns the corresponding indices (note, that these atoms are supposed to be in the same product molecule)
    maxValue - evaluates objective function for each atom, finds largest value(s) the largest evaluation result(s) target atom indices / objects or index / atom object array (optional, all atoms taken if omitted), the objective function (as inner expression string), the number of largest values to be taken (optional, takes only one if omitted) Molecule Context maxValue(6, 7, 8, 9, "charge('7.4')", 2) returns the two largest partial charges on atoms 6, 7, 8, 9 in the major microspecies at pH 7.4 of the input molecule Reaction Context maxValue(patom(1), patom(2), patom(3), "charge('7.4')", 2) returns the two largest partial charges on product atoms matching maps 1, 2, 3 in the major microspecies at pH 7.4 of the product molecule of these atoms (note, that these atoms are supposed to be in the same product molecule)
    min - takes minimum of its array and/or numerical parameters the minimum value integers, real numbers, integer arrays, real number arrays General (All) min(2, 8, 6) returns 2 max(3.4, 5.6, 1.2) returns 5.6 Molecule Context min(charge(0), charge(2)) returns the least of the partial charge values on atoms 0 and 2 max(charge()) returns the maximal partial charge value on the input molecule Reaction Context min(charge(ratom(2)), charge(ratom(3))) returns the least of the partial charge values on reactant atoms matching maps 2 and 3 in the reaction equation max(charge(product(0))) returns the maximal partial charge value on the first product
    minAtom - evaluates objective function for each atom, finds smallest value(s) the atom index / indices corresponding to the smallest evaluation result(s) target atom indices / objects or index / atom object array (optional, all atoms taken if omitted), the objective function (as inner expression string), the number of smallest values to be taken (optional, takes only one if omitted) Molecule Context minAtom("charge('7.4')") returns the atom index corresponding to minimum partial charge in the major microspecies at pH 7.4 of the input molecule Reaction Context minAtom(reactant(0), "charge('7.4')") returns the atom index corresponding to minimum partial charge in the major microspecies at pH 7.4 of the first reactant
    minValue - evaluates objective function for each atom, finds smallest value(s) the smallest evaluation result(s) target atom indices / objects or index / atom object array (optional, all atoms taken if omitted), the objective function (as inner expression string), the number of smallest values to be taken (optional, takes only one if omitted) Molecule Context minValue("charge('7.4')") returns the minimum partial charge in the major microspecies at pH 7.4 of the input molecule Reaction Context minValue(reactant(0), "charge('7.4')") returns the minimum partial charge in the major microspecies at pH 7.4 of the first reactant
    molAtom - creates a MolAtom the MolAtom object atomic number Molecule Context molAtom(6) returns a carbon atom Reaction Context molAtom(6) returns a carbon atom
    molBinFormat molImage - returns the binary representation (image, pdf, GZIP compressed molecule file) of the molecule in specified format the binary representation (image, pdf, GZIP compressed molecule file) of the molecule the binary format with options (e.g. "jpeg", "png:w150,h150", "pdf", "gzip:sdf") Molecule Context molImage("jpeg:w100,Q95,#ffff00") returns the 100x100 JPEG image of the input molecule with yellow background, 95% quality Reaction Context N / A (reaction rules are numerical)
    molString molConvert molFormat - returns the string representation of a molecule, or an array of molecules, in specified molecule format the string representation of the molecule(s) the molecule format (e.g. "mol", "sdf", "mrv", "smiles") the clean dimension Molecule Context molFormat("mrv") returns the ChemAxon Marvin Document format representation of the input molecule molFormat(tautomers(), "sdf", 2) returns the SDF format representation of the tautomers of the input molecule Reaction Context N / A (reaction rules are numerical)
    pair bond - converts two atoms or 0-based atom indexes into an "index1-index2" 1-based atom index setter string (used for pairing atoms in shortestPath ) the generated string two atom indexes or two MolAtom objects General (All) pair(2, 5) returns "3-6" Reaction Context pair(ratom(1), ratom(2)) returns "index1-index2" where "index1" and "index2" are the 1-based atom indexes of the reactant atoms matching map 1 and 2 in the reaction equation bond(patom(2), patom(5) returns "index1-index2" where "index1" and "index2" are the 1-based atom indexes of the product atoms matching map 2 and 5 in the reaction equation
    productCount - counts the products in the reaction the number of products in the reaction, or -1 if the the input (molecule) is not a reaction - Molecule Context productCount() returns n if the given molecule is a reaction and contains n products. productCount() returns -1 if the given molecule is not a reaction. Reaction Context productCount() returns n if the given molecule is a reaction and contains n products. productCount(product(0)) and productCount(product(1)) calls does not make sense, and will return -1.
    radicalCount - returns the radical count of an atom the radical count atom index or MolAtom object Molecule Context radicalCount(0) returns the radical count of atom 0 Reaction Context radicalCount(patom(3)) returns the radical count on the product atom matching map 3 in the reaction equation
    reactantCount - counts the reactants in the reaction the number of reactants in the reaction, or -1 if the the input (molecule) is not a reaction - Molecule Context reactantCount() returns n if the given molecule is a reaction and contains n reactants. reactantCount() returns -1 if the given molecule is not a reaction. Reaction Context reactantCount() returns n if the given molecule is a reaction and contains n reactants. reactantCount(reactant(0)) and reactantCount(product(1)) calls does not make sense, and will return -1.
    sortAsc - sorts an array in ascending order the sorted array integer array or real number array General (All) sortAsc(array(3.4, 5.6, 1.2)) returns array(1.2, 3.4, 5.6) Molecule Context sortAsc(charge()) returns the partial charge values in ascending order Reaction Context sortAsc(charge(reactant(1))) returns the partial charge values of the second reactant in ascending order
    sortDesc - sorts an array in descending order the sorted array integer array or real number array General (All) sortDesc(array(3.4, 5.6, 1.2)) returns array(5.6, 3.4, 1.2) Molecule Context sortDesc(pka("basic")) returns the basic p K a values in descending order Reaction Context sortDesc(pka(product(0), "basic")) returns the basic p K a values of the first product in descending order
    sum - computes the sum of array elements the sum integer array or real number array General (All) sum(array(3.4, 5.6, 1.2)) returns 10.2 Molecule Context sum(charge()) returns the sum of charge values sum(pol()) returns the sum of atom polarizability values Reaction Context sum(charge(reactant(0))) returns the sum of charge values in the first reactant sum(pol(product(0))) returns the sum of atom polarizability values in the first product
    topanal Structural Calculations License
    valence - returns the sum of bond orders and query H atoms of an atom the sum of bond orders and query H atoms atom index or MolAtom object Molecule Context valence(0) returns the valence of atom 0 Reaction Context valence(ratom(1)) returns the valence of the reactant atom matching map 1 in the reaction equation
    whereIsValenceError - returns the index of the first atom with valence error, or -1 if there is no valence error the index of the first atom with valence error, or -1 if there is no valence error - Molecule Context whereIsValenceError() returns the index of the first atom with valence error, or -1 if there is no valence error in the molecule Reaction Context whereIsValenceError(reactant(1)) returns the index of the first atom with valence error in the second reactant, or -1 f there is no valence error in the second reactant

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    Geometry Functions

    Name License Description Return value Parameters Examples
    aliphaticAtom Structural Calculations License checks if the specified atom is aliphatic true for aliphatic atoms, false for non-aliphatic atoms * the atom index / MolAtom object Molecule Context aliphaticAtom(2) returns true if atom 2 of the input molecule is aliphatic, false otherwise Reaction Context aliphaticAtom(ratom(2)) returns true if the reactant atom matching map 2 in the reaction equation is aliphatic, false otherwise aliphaticAtom(patom(1)) returns true if the product atom matching map 1 in the reaction equation is aliphatic, false otherwise
    aliphaticAtomCount Structural Calculations License calculates the aliphatic atom count the aliphatic atom count - Molecule Context aliphaticAtomCount() returns the number of aliphatic atoms in the input molecule Reaction Context aliphaticAtomCount(reactant(0)) returns the number of aliphatic atoms in the first reactant aliphaticAtomCount(product(1)) returns the number of aliphatic atoms in the second product
    aliphaticBondCount Structural Calculations License calculates the aliphatic bond count the aliphatic bond count - Molecule Context aliphaticBondCount() returns the number of bonds in the input molecule Reaction Context aliphaticBondCount(reactant(0)) returns the number of aliphatic bonds in the first reactant aliphaticBondCount(product(1)) returns the number of aliphatic bonds in the second product
    aliphaticRingCount Structural Calculations License calculates the aliphatic ring count the aliphatic ring count - Molecule Context aliphaticRingCount() returns the number of aliphatic rings in the input molecule Reaction Context aliphaticRingCount(reactant(0)) returns the number of aliphatic rings in the first reactant aliphaticRingCount(product(1)) returns the number of aliphatic rings in the second product
    aliphaticRingCountOfSize Structural Calculations License calculates the number of aliphatic rings of given size the number of aliphatic rings of given size the ring size Molecule Context aliphaticRingCountOfSize(6) returns the number of aliphatic rings of size 6 in the input molecule Reaction Context aliphaticRingCountOfSize(reactant(0), 5) returns the number of aliphatic rings of size 5 in the first reactant aliphaticRingCountOfSize(product(1), 5) returns the number of aliphatic rings of size 5 in the second product
    aliphaticRings Structural Calculations License identifies the aliphatic rings in the molecule atom indexes of the aliphatic rings in the molecule (null if the molecule does not contain aliphatic rings) - Molecule Context aliphaticRings() returns the atom indexes of the aliphatic rings in the input molecule Reaction Context aliphaticRings(reactant(0)) returns the atom indexes of the aliphatic rings in the first reactant aliphaticRings(product(1)) returns the atom indexes of the aliphatic rings in the second product
    aliphaticRingsOfSize Structural Calculations License identifies the aliphatic rings in the molecule having a given size (number of atoms) atom indexes of the aliphatic rings in the molecule having the given size (null if the molecule does not contain aliphatic rings) the ring size Molecule Context aliphaticRings() returns the atom indexes of the aliphatic rings in the input molecule having the given size Reaction Context aliphaticRings(reactant(0)) returns the atom indexes of the aliphatic rings in the first reactant having the given size aliphaticRings(product(1)) returns the atom indexes of the aliphatic rings in the second product having the given size
    angle Structural Calculations License calculates the angle between three atoms the angle between three atoms * the (1-based) atom indexes of the three atoms in a string: "index1-index2-index3" (e.g. '2-3-5') Molecule Context angle('1-2-3') and angle(atoms(0, 1, 2)) both return the angle between atoms 1, 2 and 3 in the input molecule Reaction Context angle(reactant(0), atoms(ratom(1), ratom(2), ratom(3))) returns the angle between reactant atoms matching maps 1, 2 and 3 in the reaction equation (see note 1) angle(product(1), atoms(patom(2), patom(3), patom(4))) returns the angle between product atoms matching maps 2, 3 and 4 in the reaction equation (see note 1)
    aromaticAtom Structural Calculations License checks if the specified atom is aromatic true for aromatic atoms, false for non-aromatic atoms * the atom index / MolAtom object Molecule Context aromaticAtom(2) returns true if atom 2 of the input molecule is aromatic, false otherwise Reaction Context aromaticAtom(ratom(2)) returns true if the reactant atom matching map 2 in the reaction equation is aromatic, false otherwise aromaticAtom(patom(1)) returns true if the product atom matching map 1 in the reaction equation is aromatic, false otherwise
    aromaticAtomCount Structural Calculations License calculates the aromatic atom count the aromatic atom count - Molecule Context aromaticAtomCount() returns the number of aromatic atoms in the input molecule Reaction Context aromaticAtomCount(reactant(0)) returns the number of aromatic atoms in the first reactant aromaticAtomCount(product(1)) returns the number of aromatic atoms in the second product
    aromaticBondCount Structural Calculations License calculates the aromatic bond count the aromatic bond count - Molecule Context aromaticBondCount() returns the number of aromatic bonds in the input molecule Reaction Context aromaticBondCount(reactant(0)) returns the number of aromatic bonds in the first reactant aromaticBondCount(product(1)) returns the number of aromatic bonds in the second product
    aromaticRingCount Structural Calculations License calculates the aromatic ring count the aromatic ring count - Molecule Context aromaticRingCount() returns the number of aromatic rings in the input molecule Reaction Context aromaticRingCount(reactant(0)) returns the number of aromatic rings in the first reactant aromaticRingCount(product(1)) returns the number of aromatic rings in the second product
    aromaticRingCountOfSize Structural Calculations License calculates the number of aromatic rings of given size the number of aromatic rings of given size the ring size Molecule Context aromaticRingCountOfSize(6) returns the number of aromatic rings of size 6 in the input molecule Reaction Context aromaticRingCountOfSize(reactant(0), 5) returns the number of aromatic rings of size 5 in the first reactant aromaticRingCountOfSize(product(1), 5) returns the number of aromatic rings of size 5 in the second product
    aromaticRings Structural Calculations License identifies the aromatic rings in the molecule atom indexes of the aromatic rings in the molecule (null if the molecule does not contain aromatic rings) - Molecule Context aromaticRings() returns the atom indexes of the aromatic rings in the input molecule Reaction Context aromaticRings(reactant(0)) returns the atom indexes of the aromatic rings in the first reactant aromaticRings(product(1)) returns the atom indexes of the aromatic rings in the second product
    aromaticRingsOfSize Structural Calculations License identifies the aromatic rings in the molecule having a given size (number of atoms) atom indexes of the aromatic rings in the molecule having the given size (null if the molecule does not contain aromatic rings) the ring size Molecule Context aromaticRings() returns the atom indexes of the aromatic rings in the input molecule having the given size Reaction Context aromaticRings(reactant(0)) returns the atom indexes of the aromatic rings in the first reactant having the given size aromaticRings(product(1)) returns the atom indexes of the aromatic rings in the second product having the given size
    ASAHydrophobic Structural Calculations License calculates the water accessible molecular surface area of all hydrophobic atoms the molecular surface area * the major microspecies pH (takes the input molecule itself if omitted) Molecule Context ASAHydrophobic() returns the water accessible surface area of all atoms of the input molecule with hydrophobic partial charge ASAHydrophobic('7.4')returns the water accessible surface area of all atoms with hydrophobic partial charge of the major microspecies taken at pH 7.4 Reaction Context ASAHydrophobic(reactant(0)) returns the water accessible surface area of all atoms of the first reactant with hydrophobic partial charge ASAHydrophobic(product(0), '7.4') returns the water accessible surface area of all atoms with hydrophobic partial charge of the major microspecies of the first product taken at pH 7.4
    ASANegative Structural Calculations License calculates the water accessible molecular surface area of all atoms with negative partial charge the molecular surface area * the major microspecies pH (takes the input molecule itself if omitted) Molecule Context ASANegative() returns the water accessible surface area of all atoms of the input molecule with negative partial charge ASANegative('7.4')returns the water accessible surface area of all atoms with negative partial charge of the major microspecies taken at pH 7.4 Reaction Context ASANegative(reactant(0)) returns the water accessible surface area of all atoms of the first reactant with negative partial charge ASANegative(product(0), '7.4') returns the water accessible surface area of all atoms with negative partial charge of the major microspecies of the first product taken at pH 7.4
    ASAPlus Structural Calculations License calculates the water accessible molecular surface area of all atoms with positive partial charge the molecular surface area * the major microspecies pH (takes the input molecule itself if omitted) Molecule Context ASAPlus() returns the water accessible surface area of all atoms of the input molecule with positive partial charge ASAPlus('7.4')returns the water accessible surface area of all atoms with positive partial charge of the major microspecies taken at pH 7.4 Reaction Context ASAPlus(reactant(0)) returns the water accessible surface area of all atoms of the first reactant with positive partial charge ASAPlus(product(0), '7.4') returns the water accessible surface area of all atoms with positive partial charge of the major microspecies of the first product taken at pH 7.4
    ASAPolar Structural Calculations License calculates the water accessible molecular surface area of all polar atoms the molecular surface area * the major microspecies pH (takes the input molecule itself if omitted) Molecule Context ASAPolar() returns the water accessible surface area of all atoms of the input molecule with polar partial charge ASAPolar('7.4')returns the water accessible surface area of all atoms with polar partial charge of the major microspecies taken at pH 7.4 Reaction Context ASAPolar(reactant(0)) returns the water accessible surface area of all atoms of the first reactant with polar partial charge ASAPolar(product(0), '7.4') returns the water accessible surface area of all atoms with polar partial charge of the major microspecies of the first product taken at pH 7.4
    asymmetricAtom Structural Calculations License checks if the specified atom is an asymmetric atom true for asymmetric atoms, false for symmetric atoms * the atom index / MolAtom object Molecule Context asymmetricAtom(2) returns true if atom 2 of the input molecule is an asymmetric atom, false otherwise Reaction Context asymmetricAtom(ratom(2)) returns true if the reactant atom matching map 2 in the reaction equation is an asymmetric atom, false otherwise asymmetricAtom(patom(1)) returns true if the product atom matching map 1 in the reaction equation is an asymmetric atom, false otherwise
    asymmetricAtomCount Structural Calculations License calculates the number of asymmetric atoms the asymmetric atom count - Molecule Context asymmetricAtomCount() returns the number of asymmetric atoms in the input molecule Reaction Context asymmetricAtomCount(reactant(0)) returns the number of asymmetric atoms in the first reactant asymmetricAtomCount(product(1)) returns the number of asymmetric atoms in the second product
    asymmetricAtoms Structural Calculations License determines the asymmetric atoms indexes of asymmetric atoms - Molecule Context asymmetricAtoms() returns the indexes of asymmetric atoms in the input molecule Reaction Context asymmetricAtoms(reactant(0)) returns the indexes of asymmetric atoms in the first reactant asymmetricAtoms(product(1)) returns the indexes of asymmetric atoms in the second product
    balabanIndex Structural Calculations License calculates the Balaban index the Balaban index - Molecule Context calculates the Balaban index Reaction Context the Balaban index
    bondCount - calculates the bond count the bond count - Molecule Context bondCount() returns the number of bonds in the input molecule Reaction Context bondCount(reactant(0)) returns the number of bonds in the first reactant bondCount(product(1)) returns the number of bonds in the second product
    bondType Structural Calculations License returns the bond type between two atoms the bond type between two atoms, -1 if there is no bond between the two atoms * the (1-based) atom indexes of the two atoms in a string: "index1-index2" (e.g. '2-3') Molecule Context bondType('2-3') and bondType(bond(1, 2)) both return the bond type between atoms 1 and 2 in the input molecule Reaction Context bondType(reactant(0), bond(ratom(1), ratom(2))) returns the bond type between reactant atoms matching maps 1 and 2 in the reaction equation (see note 1) bondType(product(1), bond(patom(2), patom(3))) returns the bond type between product atoms matching maps 2 and 3 in the reaction equation (see note 1)
    carboaliphaticRingCount Structural Calculations License calculates the number of carboaliphatic rings in the molecule (aliphatic rings containing carbon atoms only) number of carboaliphatic rings - Molecule Context carboaliphaticRingCount() returns the number of carboaliphatic rings in the input molecule Reaction Context carboaliphaticRingCount(reactant(0)) returns the number of carboaliphatic rings in the first reactant carboaliphaticRingCount(product(1)) returns the number of carboaliphatic rings in the second product
    carboaromaticRingCount Structural Calculations License calculates the number of carboaromatic rings in the molecule (aromatic rings containing carbon atoms only) number of carboaromatic rings - Molecule Context carboaromaticRingCount() returns the number of carboaromatic rings in the input molecule Reaction Context carboaromaticRingCount(reactant(0)) returns the number of carboaromatic rings in the first reactant carboaromaticRingCount(product(1)) returns the number of carboaromatic rings in the second product
    carboRingCount Structural Calculations License calculates the number of carbocyclic rings in the molecule (rings containing carbon atoms only) number of carbocyclic rings - Molecule Context carboRingCount() returns the number of carbocyclic rings in the input molecule Reaction Context carboRingCount(reactant(0)) returns the number of carbocyclic rings in the first reactant carboRingCount(product(1)) returns the number of carbocyclic rings in the second product
    carboRingCountOfSize Structural Calculations License calculates the number of carbocyclic rings of given size (rings containing carbon atoms only) the number of carbocyclic rings of given size the ring size Molecule Context carboRingCountOfSize(6) returns the number of carbocyclic rings of size 6 in the input molecule Reaction Context carboRingCountOfSize(reactant(0), 5) returns the number of carbocyclic rings of size 5 in the first reactant carboRingCountOfSize(product(1), 5) returns the number of carbocyclic rings of size 5 in the second product
    carboRings Structural Calculations License identifies the carbocyclic rings in the molecule (rings containing carbon atoms only) atom indexes of the carbocyclic rings in the molecule (null if the molecule does not contain carbocyclic rings) - Molecule Context carboRings() returns the atom indexes of the carbocyclic rings in the input molecule Reaction Context carboRings(reactant(0)) returns the atom indexes of the carbocyclic rings in the first reactant carboRings(product(1)) returns the atom indexes of the carbocyclic rings in the second product
    carboRingsOfSize Structural Calculations License identifies the carbocyclic rings in the molecule having a given size (number of atoms) atom indexes of the carbocyclic rings in the molecule having the given size (null if the molecule does not carbocyclic carbo rings) the ring size Molecule Context carboRings() returns the atom indexes of the carbocyclic rings in the input molecule having the given size Reaction Context carboRings(reactant(0)) returns the atom indexes of the carbocyclic rings in the first reactant having the given size carboRings(product(1)) returns the atom indexes of the carbocyclic rings in the second product having the given size
    chainAtom Structural Calculations License checks if the specified atom is a chain atom true for chain atoms, false for non-chain atoms * the atom index / MolAtom object Molecule Context chainAtom(2) returns true if atom 2 of the input molecule is a chain atom, false otherwise Reaction Context chainAtom(ratom(2)) returns true if the reactant atom matching map 2 in the reaction equation is a chain atom, false otherwise chainAtom(patom(1)) returns true if the product atom matching map 1 in the reaction equation is a chain atom, false otherwise
    chainAtomCount Structural Calculations License calculates the chain atom count the chain atom count - Molecule Context chainAtomCount() returns the number of chain atoms in the input molecule Reaction Context chainAtomCount(reactant(0)) returns the number of chain atoms in the first reactant chainAtomCount(product(1)) returns the number of chain atoms in the second product
    chainBond Structural Calculations License checks if two atoms are connected by a chain bond true if the two atoms are connected by a chain bond, false otherwise * the (1-based) atom indexes of the two atoms in a string: "index1-index2" (e.g. '2-3') Molecule Context chainBond('2-3') and chainBond(bond(1, 2)) both return true if atoms 1 and 2 are connected by a chain bond the input molecule Reaction Context chainBond(reactant(0), bond(ratom(1), ratom(2))) returns true if reactant atoms matching maps 1 and 2 in the reaction equation are connected by a chain bond in the corresponding reactant molecule (see note 1) chainBond(product(1), bond(patom(2), patom(3))) returns true if product atoms matching maps 2 and 3 in the reaction equation are connected by a chain bond in the corresponding product molecule (see note 1)
    chainBondCount Structural Calculations License calculates the chain bond count the chain bond count - Molecule Context chainBondCount() returns the number of chain bonds in the input molecule Reaction Context chainBondCount(reactant(0)) returns the number of chain bonds in the first reactant chainBondCount(product(1)) returns the number of chain bonds in the second product
    chiralCenter Structural Calculations License checks if the specified atom is a tetrahedral stereogenic center true for tetrahedral stereogenic center atoms * the atom index / MolAtom object Molecule Context chiralCenter(2) returns true if atom 2 of the input molecule is a tetrahedral stereogenic center, false otherwise Reaction Context chiralCenter(ratom(2)) returns true if the reactant atom matching map 2 in the reaction equation is a tetrahedral stereogenic center, false otherwise chiralCenter(patom(1)) returns true if the product atom matching map 1 in the reaction equation is a tetrahedral stereogenic center, false otherwise
    chiralCenterCount Structural Calculations License calculates the number of tetrahedral stereogenic center atoms the tetrahedral stereogenic center count - Molecule Context chiralCenterCount() returns the number of tetrahedral stereogenic centers in the input molecule Reaction Context chiralCenterCount(reactant(0)) returns the number of tetrahedral stereogenic centers in the first reactant chiralCenterCount(product(1)) returns the number of tetrahedral stereogenic centers in the second product
    chiralCenters Structural Calculations License determines the chiral center atoms indexes of chiral center atoms - Molecule Context chiralCenters() returns the indexes of chiral center atoms in the input molecule Reaction Context chiralCenters(reactant(0)) returns the indexes of chiral center atoms in the first reactant chiralCenters(product(1)) returns the indexes of chiral center atoms in the second product
    connected Structural Calculations License checks if two atoms are connected true if the two atoms belong to the same connected component, false otherwise * the (1-based) atom indexes of the two atoms in a string: "index1-index2" (e.g. '2-3') Molecule Context connected('2-3') and connected(pair(1, 2)) both return true if atoms 1 and 2 are in the same connected component of the input molecule Reaction Context connected(reactant(0), pair(ratom(1), ratom(2))) returns true if reactant atoms matching maps 1 and 2 in the reaction equation are connected in the corresponding reactant molecule ( see note 1) connected(product(1), pair(patom(2), patom(3))) returns true if product atoms matching maps 2 and 3 in the reaction equation are connected in the corresponding product molecule (see note 1)
    connectedGraph Structural Calculations License checks whether the molecule graph is connected true if the molecule graph is connected, false otherwise - Molecule Context connectedGraph() returns true if the input molecule graph is connected Reaction Context connectedGraph(reactant(0)) returns true if the first reactant is connected connectedGraph(product(1)) returns true if the second product is connected
    cyclomaticNumber Structural Calculations License calculates the cyclomatic number the cyclomatic number - Molecule Context cyclomaticNumber() returns the cyclomatic number of the input molecule Reaction Context cyclomaticNumber(reactant(0)) returns the cyclomatic number of the first reactant cyclomaticNumber(product(1)) returns the cyclomatic number of the second product
    dihedral Structural Calculations License calculates the dihedral of four atoms the dihedral of four atoms * the (1-based) atom indexes of the four atoms in a string: "index1-index2-index3-index4" (e.g. '2-3-7-4') Molecule Context dihedral('1-2-3-4') and dihedral(atoms(0, 1, 2, 3)) both return the dihedral of atoms 1, 2, 3 and 4 in the input molecule Reaction Context dihedral(reactant(0), atoms(ratom(1), ratom(2), ratom(3), ratom(4))) returns the dihedral of reactant atoms matching maps 1, 2, 3 and 4 in the reaction equation (see note 1) dihedral(product(1), atoms(patom(2), patom(3), patom(5), patom(6))) returns the dihedral of product atoms matching maps 2, 3, 5 and 6 in the reaction equation (see note 1)
    distance Structural Calculations License calculates the distance between two atoms the distance between two atoms * the (1-based) atom indexes of the two atoms in a string: "index1-index2" (e.g. '2-3') Molecule Context distance('1-2') and distance(pair(0, 1)) both return the distance between atoms 1 and 2 in the input molecule Reaction Context distance(reactant(0), pair(ratom(1), ratom(2))) returns the distance between reactant atoms matching maps 1 and 2 in the reaction equation (see note 1) distance(product(1), pair(patom(2), patom(3))) returns the distance between product atoms matching maps 2 and 3 in the reaction equation (see note 1)
    distanceDegree Structural Calculations License calculates the distance degree of an atom the distance degree * the atom index / MolAtom object Molecule Context distanceDegree(2) returns the distance degree of atom 2 of the input molecule Reaction Context distanceDegree(ratom(2)) returns the distance degree of the reactant atom matching map 2 in the reaction equation distanceDegree(patom(1)) returns the distance degree of the product atom matching map 1 in the reaction equation
    dreidingEnergy Structural Calculations License returns the Dreiding energy of the input molecule (conformer) the dreiding energy - Molecule Context dreidingEnergy() returns the dreiding energy of the input molecule (conformer) Reaction Context dreidingEnergy(reactant(0)) returns the dreiding energy of the first reactant dreidingEnergy(product(1)) returns the dreiding energy of the second product
    eccentricity Structural Calculations License calculates the eccentricity of an atom the eccentricity of an atom * the atom index / MolAtom object Molecule Context eccentricity(2) returns the eccentricity of atom 2 of the input molecule Reaction Context eccentricity(ratom(2)) returns the eccentricity of the reactant atom matching map 2 in the reaction equation eccentricity(patom(1)) returns the distance degree of the product atom matching map 1 in the reaction equation
    fragmentCount Structural Calculations License returns the number of fragments (disconnected parts) the fragment count - Molecule Context fragmentCount() returns the number of fragments in the input molecule Reaction Context fragmentCount(reactant(0)) returns the number of fragments in the first reactant fragmentCount(product(1)) returns the number of fragments in the second product
    fsp3 Structural Calculations License returns the fsp3 of the molecule the fsp3 value - Molecule Context fsp3() returns the fsp3 value of the input molecule Reaction Context fsp3(reactant(0)) returns the fsp3 value of the first reactant fsp3(product(1)) returns the fsp3 value of the second product
    fusedAliphaticRingCount Structural Calculations License calculates the number of fused aliphatic rings (SSSR smallest set of smallest aliphatic rings) the fused aliphatic ring count - Molecule Context fusedAliphaticRingCount() returns the number of fused aliphatic rings in the input molecule Reaction Context fusedAliphaticRingCount(reactant(0)) returns the number of fused aliphatic rings in the first reactant fusedAliphaticRingCount(product(1)) returns the number of fused aliphatic rings in the second product
    fusedAliphaticRingCountOfSize Structural Calculations License calculates the number of fused aliphatic rings of given size the number of fused aliphatic rings of given size the ring size Molecule Context fusedAliphaticRingCountOfSize(6) returns the number of fused aliphatic rings of size 6 in the input molecule Reaction Context fusedAliphaticRingCountOfSize(reactant(0), 5) returns the number of fused aliphatic rings of size 5 in the first reactant fusedAliphaticRingCountOfSize(product(1), 5) returns the number of fused aliphatic rings of size 5 in the second product
    fusedAliphaticRings Structural Calculations License identifies the fused aliphatic rings in the molecule atom indexes of the fused aliphatic rings in the molecule (null if the molecule does not contain fused aliphatic rings) - Molecule Context fusedAliphaticRings() returns the atom indexes of the fused aliphatic rings in the input molecule Reaction Context fusedAliphaticRings(reactant(0)) returns the atom indexes of the fused aliphatic rings in the first reactant fusedAliphaticRings(product(1)) returns the atom indexes of the fused aliphatic rings in the second product
    fusedAliphaticRingsOfSize Structural Calculations License identifies the fused aliphatic rings in the molecule having a given size (number of atoms) atom indexes of the fused aliphatic rings in the molecule having the given size (null if the molecule does not contain fused aliphatic rings) the ring size Molecule Context fusedAliphaticRings() returns the atom indexes of the fused aliphatic rings in the input molecule having the given size Reaction Context fusedAliphaticRings(reactant(0)) returns the atom indexes of the fused aliphatic rings in the first reactant having the given size fusedAliphaticRings(product(1)) returns the atom indexes of the fused aliphatic rings in the second product having the given size
    fusedAromaticRingCount Structural Calculations License calculates the number of fused aromatic rings (SSSR smallest set of smallest aromatic rings) the fused aromatic ring count - Molecule Context fusedAromaticRingCount() returns the number of fused aromatic rings in the input molecule Reaction Context fusedAromaticRingCount(reactant(0)) returns the number of fused aromatic rings in the first reactant fusedAromaticRingCount(product(1)) returns the number of fused aromatic rings in the second product
    fusedAromaticRingCountOfSize Structural Calculations License calculates the number of fused aromatic rings of given size the number of fused aromatic rings of given size the ring size Molecule Context fusedAromaticRingCountOfSize(6) returns the number of fused aromatic rings of size 6 in the input molecule Reaction Context fusedAromaticRingCountOfSize(reactant(0), 5) returns the number of fused aromatic rings of size 5 in the first reactant fusedAromaticRingCountOfSize(product(1), 5) returns the number of fused aromatic rings of size 5 in the second product
    fusedAromaticRings Structural Calculations License identifies the fused aromatic rings in the molecule atom indexes of the fused aromatic rings in the molecule (null if the molecule does not contain fused aromatic rings) - Molecule Context fusedAromaticRings() returns the atom indexes of the fused aromatic rings in the input molecule Reaction Context fusedAromaticRings(reactant(0)) returns the atom indexes of the fused aromatic rings in the first reactant fusedAromaticRings(product(1)) returns the atom indexes of the fused aromatic rings in the second product
    fusedAromaticRingsOfSize Structural Calculations License identifies the fused aromatic rings in the molecule having a given size (number of atoms) atom indexes of the fused aromatic rings in the molecule having the given size (null if the molecule does not contain fused aromatic rings) the ring size Molecule Context fusedAromaticRings() returns the atom indexes of the fused aromatic rings in the input molecule having the given size Reaction Context fusedAromaticRings(reactant(0)) returns the atom indexes of the fused aromatic rings in the first reactant having the given size fusedAromaticRings(product(1)) returns the atom indexes of the fused aromatic rings in the second product having the given size
    fusedRingCount Structural Calculations License calculates the number of fused rings (SSSR smallest set of smallest rings) the fused ring count - Molecule Context fusedRingCount() returns the number of fused rings in the input molecule Reaction Context fusedRingCount(reactant(0)) returns the number of fused rings in the first reactant fusedRingCount(product(1)) returns the number of fused rings in the second product
    hararyIndex Structural Calculations License calculates the Harary index the Harary index - Molecule Context calculates the Harary index Reaction Context the Harary index
    heteroaliphaticRingCount Structural Calculations License calculates the number of aliphatic heterocyclic rings (SSSR smallest set of smallest aliphatic rings) the aliphatic heterocyclic ring count - Molecule Context heteroaliphaticRingCount() returns the number of aliphatic heterocyclic rings in the input molecule Reaction Context heteroaliphaticRingCount(reactant(0)) returns the number of aliphatic heterocyclic rings in the first reactant heteroaliphaticRingCount(product(1)) returns the number of aliphatic heterocyclic rings in the second product
    heteroaliphaticRingCountOfSize Structural Calculations License calculates the number of aliphatic heterocyclic rings of given size the number of aliphatic heterocyclic rings of given size the ring size Molecule Context heteroaliphaticRingCountOfSize(6) returns the number of aliphatic heterocyclic rings of size 6 in the input molecule Reaction Context heteroaliphaticRingCountOfSize(reactant(0), 5) returns the number of aliphatic heterocyclic rings of size 5 in the first reactant heteroaliphaticRingCountOfSize(product(1), 5) returns the number of aliphatic heterocyclic rings of size 5 in the second product
    heteroaliphaticRings Structural Calculations License identifies the aliphatic heterocyclic rings in the molecule atom indexes of the aliphatic heterocyclic rings in the molecule (null if the molecule does not contain aliphatic heterocyclic rings) - Molecule Context heteroaliphaticRings() returns the atom indexes of the aliphatic heterocyclic rings in the input molecule Reaction Context heteroaliphaticRings(reactant(0)) returns the atom indexes of the aliphatic heterocyclic rings in the first reactant heteroaliphaticRings(product(1)) returns the atom indexes of the aliphatic heterocyclic rings in the second product
    heteroaliphaticRingsOfSize Structural Calculations License identifies the aliphatic heterocyclic rings in the molecule having a given size (number of atoms) atom indexes of the aliphatic heterocyclic rings in the molecule having the given size (null if the molecule does not contain aliphatic heterocyclic rings) the ring size Molecule Context heteroaliphaticRings() returns the atom indexes of the aliphatic heterocyclic rings in the input molecule having the given size Reaction Context heteroaliphaticRings(reactant(0)) returns the atom indexes of the aliphatic heterocyclic rings in the first reactant having the given size heteroaliphaticRings(product(1)) returns the atom indexes of the aliphatic heterocyclic rings in the second product having the given size
    heteroaromaticRingCount Structural Calculations License calculates the number of aromatic heterocyclic rings (SSSR smallest set of smallest aromatic rings) the aromatic heterocyclic ring count - Molecule Context heteroaromaticRingCount() returns the number of aromatic heterocyclic rings in the input molecule Reaction Context heteroaromaticRingCount(reactant(0)) returns the number of aromatic heterocyclic rings in the first reactant heteroaromaticRingCount(product(1)) returns the number of aromatic heterocyclic rings in the second product
    heteroaromaticRingCountOfSize Structural Calculations License calculates the number of aromatic heterocyclic rings of given size the number of aromatic heterocyclic rings of given size the ring size Molecule Context heteroaromaticRingCountOfSize(6) returns the number of aromatic heterocyclic rings of size 6 in the input molecule Reaction Context heteroaromaticRingCountOfSize(reactant(0), 5) returns the number of aromatic heterocyclic rings of size 5 in the first reactant heteroaromaticRingCountOfSize(product(1), 5) returns the number of aromatic heterocyclic rings of size 5 in the second product
    heteroaromaticRings Structural Calculations License identifies the aromatic heterocyclic rings in the molecule atom indexes of the aromatic heterocyclic rings in the molecule (null if the molecule does not contain aromatic heterocyclic rings) - Molecule Context heteroaromaticRings() returns the atom indexes of the aromatic heterocyclic rings in the input molecule Reaction Context heteroaromaticRings(reactant(0)) returns the atom indexes of the aromatic heterocyclic rings in the first reactant heteroaromaticRings(product(1)) returns the atom indexes of the aromatic heterocyclic rings in the second product
    heteroaromaticRingsOfSize Structural Calculations License identifies the aromatic heterocyclic rings in the molecule having a given size (number of atoms) atom indexes of the aromatic heterocyclic rings in the molecule having the given size (null if the molecule does not contain aromatic heterocyclic rings) the ring size Molecule Context heteroaromaticRings() returns the atom indexes of the aromatic heterocyclic rings in the input molecule having the given size Reaction Context heteroaromaticRings(reactant(0)) returns the atom indexes of the aromatic heterocyclic rings in the first reactant having the given size heteroaromaticRings(product(1)) returns the atom indexes of the aromatic heterocyclic rings in the second product having the given size
    heteroRingCount Structural Calculations License calculates the number of heterocyclic rings (SSSR smallest set of smallest rings) the heterocyclic ring count - Molecule Context heteroRingCount() returns the number of heterocyclic rings in the input molecule Reaction Context heteroRingCount(reactant(0)) returns the number of heterocyclic rings in the first reactant heteroRingCount(product(1)) returns the number of heterocyclic rings in the second product
    heteroRingCountOfSize Structural Calculations License calculates the number of heterocyclic rings of given size the number of heterocyclic rings of given size the ring size Molecule Context heteroRingCountOfSize(6) returns the number of heterocyclic rings of size 6 in the input molecule Reaction Context heteroRingCountOfSize(reactant(0), 5) returns the number of heterocyclic rings of size 5 in the first reactant heteroRingCountOfSize(product(1), 5) returns the number of heterocyclic rings of size 5 in the second product
    heteroRings Structural Calculations License identifies the heterocyclic rings in the molecule atom indexes of the heterocyclic rings in the molecule (null if the molecule does not contain heterocyclic rings) - Molecule Context heteroRings() returns the atom indexes of the heterocyclic rings in the input molecule Reaction Context heteroRings(reactant(0)) returns the atom indexes of the heterocyclic rings in the first reactant heteroRings(product(1)) returns the atom indexes of the heterocyclic rings in the second product
    heteroRingsOfSize Structural Calculations License identifies the heterocyclic rings in the molecule having a given size (number of atoms) atom indexes of the heterocyclic rings in the molecule having the given size (null if the molecule does not contain heterocyclic rings) the ring size Molecule Context heteroRings() returns the atom indexes of the heterocyclic rings in the input molecule having the given size Reaction Context heteroRings(reactant(0)) returns the atom indexes of the heterocyclic rings in the first reactant having the given size heteroRings(product(1)) returns the atom indexes of the heterocyclic rings in the second product having the given size
    hyperWienerIndex Structural Calculations License calculates the Hyper Wiener index the Hyper Wiener index - Molecule Context calculates the Hyper Wiener index Reaction Context the Hyper Wiener index
    largestAtomRingSize Structural Calculations License calculates the size of the largest ring containing the specified atom the size of the largest ring containing the specified atom * the atom index / MolAtom object Molecule Context largestAtomRingSize(1) returns the size of the largest ring containing atom 1 in the input molecule Reaction Context largestAtomRingSize(patom(2)) returns the size of the largest ring containing product atom matching map 2 in the reaction equation
    largestConjugatedSystem Structural Calculations License returns the atom list of the largest conjugated system in the molecule - Molecule Context largestConjugatedSystem() returns the atom list of the largest conjugated system in the input molecule Reaction Context largestConjugatedSystem(product(1)) returns the atom list of the largest conjugated system in the 2nd product
    largestConjugatedSystemSize Structural Calculations License returns the number of pi electron pairs in the largest conjugated system - Molecule Context largestConjugatedSystemSize() returns the number of pi electron pairs in the largest conjugated system Reaction Context largestConjugatedSystemSize(product(1)) returns the number of pi electron pairs in the largest conjugated system of the 2nd product
    largestConjugatedSystemMol Structural Calculations License returns the input molecule with the largest conjugated system coloured in green This function should be used with the output option -f mrv to export colour in the output Molecule Context largestConjugatedSystemMol() returns the input molecule with the largest conjugated system coloured in green Reaction Context largestConjugatedSystemMol(product(1)) returns the 2nd product with the largest conjugated system coloured in green
    largestRing Structural Calculations License identifies the atoms of the largest ring (number of atoms) in the molecule. atom indexes of the largest ring in the molecule (null when acyclic) - Molecule Context largestRingSize() returns the atom indexes of the largest ring in the input molecule Reaction Context largestRingSize(product(1)) returns the atom indexes of the largest ring in the second product
    largestRingSize Structural Calculations License calculates the largest ring size the largest ring size - Molecule Context largestRingSize() returns the size of the largest ring in the input molecule Reaction Context largestRingSize(product(1)) returns the size of the largest ring in the second product
    largestRingSystem Structural Calculations License identifies the atoms of the largest ring system (number of rings) in the molecule. atom indexes of the largest ring system in the molecule (null when acyclic) - Molecule Context largestRingSize() returns the atom indexes of the largest ring system in the input molecule Reaction Context largestRingSize(product(1)) returns the atom indexes of the largest ring system in the second product
    largestRingSystemSize Structural Calculations License calculates the size of the largest ring system (number of rings) the size of the largest ring system - Molecule Context largestRingSystemSize() returns the size of the largest ring system in the input molecule Reaction Context largestRingSystemSize(reactant(0)) returns the size of the largest ring system in the first reactant largestringsystemsize(product(1)) returns the size of the largest ring system in the second product
    maximalProjectionArea Structural Calculations License returns the maximal projection area the maximal projection area - Molecule Context maximalProjectionArea() returns the maximal projection area Reaction Context maximalProjectionArea((reactant(0)) returns the maximal projection area of the first reactant maximalProjectionArea(product(1)) returns the maximal projection area of the second product
    maximalProjectionRadius Structural Calculations License returns the maximal projection radius the maximal projection radius - Molecule Context maximalProjectionRadius() returns the maximal projection radius Reaction Context maximalProjectionRadius((reactant(0)) returns the maximal projection radius of the first reactant maximalProjectionRadius(product(1)) returns the maximal projection radius of the second product
    maximalProjectionSize Structural Calculations License returns the maximal distance in the molecule perpendicular to the maximal projection area the maximal distance in the molecule (the actual conformer) perpendicular to its maximal projection area - Molecule Context maximalProjectionSize() returns the maximal distance in the molecule perpendicular to the maximal projection area Reaction Context maximalProjectionSize((reactant(0)) returns the maximal distance of the first reactant perpendicular to the maximal projection area maximalProjectionSize(product(1)) returns the maximal distance of the second product perpendicular to the maximal projection area
    minimalProjectionArea Structural Calculations License returns the minimal projection area the minimal projection area - Molecule Context minimalProjectionArea() returns the minimal projection area Reaction Context minimalProjectionArea((reactant(0)) returns the minimal projection area of the first reactant minimalProjectionArea(product(1)) returns the minimal projection area of the second product
    minimalProjectionRadius Structural Calculations License returns the minimal projection radius the minimal projection radius - Molecule Context minimalProjectionRadius() returns the minimal projection radius Reaction Context minimalProjectionRadius((reactant(0)) returns the minimal projection radius of the first reactant minimalProjectionRadius(product(1)) returns the minimal projection radius of the second product
    minimalProjectionSize Structural Calculations License returns the maximal distance in the molecule perpendicular to the minimal projection area the maximal distance of the molecule (the actual conformer) perpendicular to its minimal projection area - Molecule Context minimalProjectionSize() returns the maximal distance in the molecule perpendicular to the minimal projection area Reaction Context minimalProjectionSize((reactant(0)) returns the maximal distance of the first reactant perpendicular to the minimal projection area minimalProjectionSize(product(1)) returns the maximal distance of the second product perpendicular to the minimal projection area
    mmff94Energy Structural Calculations License returns the MMFF94 energy of the input molecule (conformer) the MMFF94 energy - Molecule Context mmff94Energy() returns the MMFF94 energy of the input molecule (conformer) Reaction Context mmff94Energy(reactant(0)) returns the MMFF94 energy of the first reactant mmff94Energy(product(1)) returns the MMFF94 energy of the second product
    plattIndex Structural Calculations License calculates the Platt index the Platt index - Molecule Context calculates the Platt index Reaction Context the Platt index
    randicIndex Structural Calculations License calculates the Randic index the Randic index - Molecule Context calculates the Randic index Reaction Context the Randic index
    ringAtom Structural Calculations License checks if the specified atom is a ring atom true for ring atoms, false for non-ring atoms * the atom index / MolAtom object Molecule Context ringAtom(2) returns true if atom 2 of the input molecule is a ring atom, false otherwise Reaction Context ringAtom(ratom(2)) returns true if the reactant atom matching map 2 in the reaction equation is a ring atom, false otherwise ringAtom(patom(1)) returns true if the product atom matching map 1 in the reaction equation is a ring atom, false otherwise
    ringAtomCount Structural Calculations License calculates the ring atom count the ring atom count - Molecule Context ringAtomCount() returns the number of ring atoms in the input molecule Reaction Context ringAtomCount(reactant(0)) returns the number of ring atoms in the first reactant ringAtomCount(product(1)) returns the number of ring atoms in the second product
    ringBond Structural Calculations License checks if two atoms are connected by a ring bond true if the two atoms are connected by a ring bond, false otherwise * the (1-based) atom indexes of the two atoms in a string: "index1-index2" (e.g. '2-3') Molecule Context ringBond('2-3') and ringBond(bond(1, 2)) both return true if atoms 1 and 2 are connected by a ring bond the input molecule Reaction Context ringBond(reactant(0), bond(ratom(1), ratom(2))) returns true if reactant atoms matching maps 1 and 2 in the reaction equation are connected by a ring bond in the corresponding reactant molecule (see note 1) ringBond(product(1), bond(patom(2), patom(3))) returns true if product atoms matching maps 2 and 3 in the reaction equation are connected by a ring bond in the corresponding product molecule (see note 1)
    ringBondCount Structural Calculations License calculates the ring bond count the ring bond count - Molecule Context ringBondCount() returns the number of ring bonds in the input molecule Reaction Context ringBondCount(reactant(0)) returns the number of ring bonds in the first reactant ringBondCount(product(1)) returns the number of ring bonds in the second product
    ringCount Structural Calculations License calculates the ring count the ring count - Molecule Context ringCount() returns the number of rings in the input molecule Reaction Context ringCount(reactant(0)) returns the number of rings in the first reactant ringCount(product(1)) returns the number of rings in the second product
    ringCountOfAtom Structural Calculations License calculates the number of rings passing through an atom the number of rings passing through an atom * the atom index / MolAtom object Molecule Context ringCountOfAtom(2) returns the number of rings passsing through atom 2 of the input molecule Reaction Context ringCountOfAtom(ratom(2)) returns the number of rings passsing through the reactant atom matching map 2 in the reaction equation ringCountOfAtom(patom(1)) returns the number of rings passsing through the product atom matching map 1 in the reaction equation
    ringCountOfSize Structural Calculations License calculates the number of rings of given size the number of rings of given size the ring size Molecule Context ringCountOfSize(6) returns the number of rings of size 6 in the input molecule Reaction Context ringCountOfSize(reactant(0), 5) returns the number of rings of size 5 in the first reactant ringCountOfSize(product(1), 5) returns the number of rings of size 5 in the second product
    rings Structural Calculations License identifies the rings in the molecule atom indexes of the rings in the molecule (null if the molecule is acyclic) - Molecule Context rings() returns the atom indexes of the rings in the input molecule Reaction Context rings(reactant(0)) returns the atom indexes of the rings in the first reactant rings(product(1)) returns the atom indexes of the rings in the second product
    ringsOfSize Structural Calculations License identifies the rings in the molecule having a given size (number of atoms) atom indexes of the rings in the molecule having the given size (null if the molecule is acyclic or contains different rings only) the ring size Molecule Context rings() returns the atom indexes of the rings in the input molecule having the given size Reaction Context rings(reactant(0)) returns the atom indexes of the rings in the first reactant having the given size rings(product(1)) returns the atom indexes of the rings in the second product having the given size
    ringSystemCount Structural Calculations License calculates the number of rings systems the number of rings systems - Molecule Context ringSystemCount() returns the number of ring systems in the input molecule Reaction Context ringSystemCount(reactant(0)) returns the number of ring systems in the first reactant ringsystemCount(product(1)) returns the number of ring systems in the second product
    ringSystemCountOfSize Structural Calculations License calculates the number of rings systems of given size the number of rings systems of given size the ring system size Molecule Context ringSystemCountOfSize(4) returns the number of four-membered ring systems in the input molecule Reaction Context ringSystemCountOfSize(reactant(0),3) returns the number of three-membered ring systems in the first reactant ringsystemCountOfSize(product(1),3) returns the number of three-membered ring systems in the second product
    ringSystems Structural Calculations License identifies the ring systems in the molecule (fused and spiro rings belong to one ring system) atom indexes of the ring systems in the molecule (null if the molecule is acyclic) - Molecule Context ringSystems() returns the atom indexes of the ring systems in the input molecule Reaction Context ringSystems(reactant(0)) returns the atom indexes of the ring systems in the first reactant ringSystems(product(1)) returns the atom indexes of the ring systems in the second product
    ringSystemsOfSize Structural Calculations License identifies the ring systems in the molecule having a given size (number of atoms, fused and spiro rings belong to one ring system) atom indexes of the ring systems in the molecule having the given size (null if the molecule is acyclic or contains different ringSystems only) the ring size Molecule Context ringSystems() returns the atom indexes of the ring systems in the input molecule having the given size Reaction Context ringSystems(reactant(0)) returns the atom indexes of the ring systems in the first reactant having the given size ringSystems(product(1)) returns the atom indexes of the ring systems in the second product having the given size
    rotatableBond Structural Calculations License checks if two atoms are connected by a rotatable bond true if the two atoms are connected by a rotatable bond, false otherwise * the (1-based) atom indexes of the two atoms in a string: "index1-index2" (e.g. '2-3') Molecule Context rotatableBond('2-3') and rotatableBond(bond(1, 2)) both return true if atoms 1 and 2 are connected by a rotatable bond the input molecule Reaction Context rotatableBond(reactant(0), bond(ratom(1), ratom(2))) returns true if reactant atoms matching maps 1 and 2 in the reaction equation are connected by a rotatable bond in the corresponding reactant molecule (see note 1) rotatableBond(product(1), bond(patom(2), patom(3))) returns true if product atoms matching maps 2 and 3 in the reaction equation are connected by a rotatable bond in the corresponding product molecule (see note 1)
    rotatableBondCount Structural Calculations License calculates the rotatable bond count the rotatable bond count - Molecule Context rotatableBondCount() returns the number of rotatable bonds in the input molecule Reaction Context rotatableBondCount(reactant(0)) returns the number of rotatable bonds in the first reactant rotatableBondCount(product(1)) returns the number of rotatable bonds in the second product
    shortestPath Structural Calculations License calculates the length of the shortest path between two atoms the length of the shortest path between two atoms, Integer.MAX_VALUE if disconnected * the (1-based) atom indexes of the two atoms in a string: "index1-index2" (e.g. '2-3') Molecule Context shortestPath('2-3') and shortestPath(pair(1, 2)) both return the shortest path length between atoms 1 and 2 in the input molecule Reaction Context shortestPath(reactant(0), pair(ratom(1), ratom(2))) returns the length of the shortest path between reactant atoms matching maps 1 and 2 in the reaction equation (see note 1) shortestPath(product(1), pair(patom(2), patom(3))) returns the length of the shortest path between product atoms matching maps 2 and 3 in the reaction equation (see note 1)
    smallestAtomRingSize Structural Calculations License calculates the size of the smallest ring containing the specified atom the size of the smallest ring containing the specified atom * the atom index / MolAtom object Molecule Context smallestAtomRingSize(0) returns the size of the smallest ring containing atom 0 in the input molecule Reaction Context smallestAtomRingSize(ratom(1)) returns the size of the smallest ring containing reactant atom matching map 1 in the reaction equation
    smallestRing Structural Calculations License identifies the atoms of the smallest ring (number of atoms) in the molecule. atom indexes of the smallest ring in the molecule (null when acyclic) - Molecule Context smallestRingSize() returns the atom indexes of the smallest ring in the input molecule Reaction Context smallestRingSize(product(1)) returns the atom indexes of the smallest ring in the second product
    smallestRingSize Structural Calculations License calculates the smallest ring size the smallest ring size - Molecule Context smallestRingSize() returns the size of the smallest ring in the input molecule Reaction Context smallestRingSize(reactant(0)) returns the size of the smallest ring in the first reactant
    smallestRingSystem Structural Calculations License identifies the atoms of the smallest ring system (number of rings) in the molecule. atom indexes of the smallest ring system in the molecule (null when acyclic) - Molecule Context smallestRingSize() returns the atom indexes of the smallest ring system in the input molecule Reaction Context smallestRingSize(product(1)) returns the atom indexes of the smallest ring system in the second product
    smallestRingSystemSize Structural Calculations License calculates the size of the smallest ring system (number of rings) the size of the smallest ring system - Molecule Context smallestRingSystemSize() returns the size of the smallest ring system in the input molecule Reaction Context smallestRingSystemSize(reactant(0)) returns the size of the smallest ring system in the first reactant smallestringsystemsize(product(1)) returns the size of the smallest ring system in the second product
    stereoDoubleBondCount Structural Calculations License calculates the number of stereo double bonds the stereo double bond count - Molecule Context stereoDoubleBondCount() returns the number of stereo double bonds in the input molecule Reaction Context stereoDoubleBondCount(reactant(0)) returns the number of stereo double bonds in the first reactant stereoDoubleBondCount(product(1)) returns the number of stereo double bonds in the second product
    stericEffectIndex Structural Calculations License calculates the steric effect index of an atom the steric effect index of an atom * the atom index / MolAtom object Molecule Context calculates the steric effect index of an atom Reaction Context the steric effect index of an atom
    stericHindrance Structural Calculations License calculates the steric hindrance of an atom the steric hindrance of an atom * the atom index / MolAtom object Molecule Context stericHindrance(2) returns the steric hindrance of atom 2 of the input molecule Reaction Context stericHindrance(ratom(2)) returns the steric hindrance of the reactant atom matching map 2 in the reaction equation stericHindrance(patom(1)) returns the steric hindrance of the product atom matching map 1 in the reaction equation
    szegedIndex Structural Calculations License calculates the Szeged index the Szeged index - Molecule Context calculates the Szeged index Reaction Context the Szeged index
    topologicalPolarSurfaceArea PSA - calculates the topological polar surface area (2D) the polar surface area (2D) * the major microspecies pH (takes the input molecule itself if omitted) Molecule Context topologicalPolarSurfaceArea() returns the polar surface area of the input molecule topologicalPolarSurfaceArea('7.4') returns the polar surface area of the major microspecies taken at pH 7.4 Reaction Context topologicalPolarSurfaceArea(reactant(0)) returns the polar surface area of the first reactant topologicalPolarSurfaceArea(product(0), '7.4') returns the polar surface area of the major microspecies of the first product taken at pH 7.4
    vanDerWaalsSurfaceArea Structural Calculations License calculates the van der Waals surface area the molecular surface area * the major microspecies pH (takes the input molecule itself if omitted) Molecule Context vanDerWaalsSurfaceArea() returns the van der Waals surface area of the input molecule vanDerWaalsSurfaceArea('7.4') returns the van der Waals accessible surface area of the major microspecies taken at pH 7.4 Reaction Context vanDerWaalsSurfaceArea(reactant(0)) returns the van der Waals surface area of the first reactant vanDerWaalsSurfaceArea(product(0), '7.4') returns the van der Waals surface area of the major microspecies of the first product taken at pH 7.4
    waterAccessibleSurfaceArea ASA solventAccessibleSurfaceArea Structural Calculations License calculates the solvent accessible / water accessible molecular surface area the molecular surface area * the major microspecies pH (takes the input molecule itself if omitted) Molecule Context waterAccessibleSurfaceArea() returns the solvent accessible / water accessible surface area of the input molecule solventAccessibleSurfaceArea('7.4')returns the solvent accessible / water accessible surface area of the major microspecies taken at pH 7.4 Reaction Context waterAccessibleSurfaceArea(reactant(0)) returns the solvent accessible / water accessible surface area of the first reactantsolventAccessibleSurfaceArea(product(0), '7.4') returns the solvent accessible / water accessible surface area of the major microspecies of the first product taken at pH 7.4
    wienerIndex Structural Calculations License calculates the Wiener index the Wiener index - Molecule Context wienerIndex() returns the Wiener index of the input molecule Reaction Context wienerIndex(reactant(0)) returns the Wiener index of the first reactant wienerIndex(product(1)) returns the Wiener index of the second product
    wienerPolarity Structural Calculations License calculates the Wiener polarity the Wiener polarity - Molecule Context wienerPolarity() returns the Wiener polarity of the input molecule Reaction Context wienerPolarity(reactant(0)) returns the Wiener polarity of the first reactant wienerPolarity(product(1)) returns the Wiener polarity of the second product

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    HBDA Functions

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

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    Huckel Functions

    Name License Description Return value Parameters Examples
    chargeDensity totalChargeDensity Structural Calculations License calculates the charge density of atoms the charge density of the atom, NaN for non-existing values he atom index / MolAtom object the major microspecies pH (takes the input molecule itself if omitted) Molecule Context chargeDensity(2) returns the charge density of atom 2 of the input molecule, NaN for non-existing value Reaction Context chargeDensity(ratom(1)) returns the charge density of the reactant atom matching map 1 in the reaction equation
    electronDensity piChargeDensity Structural Calculations License calculates the electron density of atoms the electron density of the atom, NaN for non-existing values he atom index / MolAtom object the major microspecies pH (takes the input molecule itself if omitted) Molecule Context electronDensity(2) returns the electron density of atom 2 of the input molecule, NaN for non-existing value Reaction Context electronDensity(ratom(1)) returns the electron density of the reactant atom matching map 1 in the reaction equation
    electrophilicity energyNu nucleophilicLocalizationEnergy Structural Calculations License calculates electrophilicity of atoms the electrophilicity of the atom, NaN for non-aromatic atoms the atom index / MolAtom object the major microspecies pH (takes the input molecule itself if omitted) Molecule Context electrophilicity(2) returns the electrophilicity of atom 2 of the input molecule, NaN if atom 2 is non-aromatic Reaction Context electrophilicity(ratom(1)) returns the electrophilicity of the reactant atom matching map 1 in the reaction equation
    electrophilicityOrder aromaticElectrophilicityOrder orderE Structural Calculations License calculates Eimages/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/add.svg order of atoms the Eimages/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/add.svg order index of the atom (0, 1, 2, ...), the atom index / MolAtom object the major microspecies pH (takes the input molecule itself if omitted) Molecule Context electrophilicityOrder(2) returns the Eimages/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/add.svg order index of atom 2 of the input molecule, e.g. returns 0 if atom 2 is the most electrophilic atom, 1 if atom 2 is the second strongest electrophilic atom, etc., Reaction Context electrophilicityOrder(ratom(1)) returns the Eimages/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/add.svg order index of the reactant atom matching map 1 in the reaction equation
    hmoChargeDensity Structural Calculations License calculates the HMO charge density of atoms the charge density of the atom, NaN for non-existing values he atom index / MolAtom object the major microspecies pH (takes the input molecule itself if omitted) Molecule Context hmoChargeDensity(2) returns the charge density of atom 2 of the input molecule, NaN for non-existing value Reaction Context hmoChargeDensity(ratom(1)) returns the charge density of the reactant atom matching map 1 in the reaction equation
    hmoElectronDensity Structural Calculations License calculates the HMO electron density of atoms the electron density of the atom, NaN for non-existing values he atom index / MolAtom object the major microspecies pH (takes the input molecule itself if omitted) Molecule Context hmoElectronDensity(2) returns the electron density of atom 2 of the input molecule, NaN for non-existing value Reaction Context hmoElectronDensity(ratom(1)) returns the electron density of the reactant atom matching map 1 in the reaction equation
    hmoElectrophilicityOrder hmoOrderE Structural Calculations License calculates HMO Eimages/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/add.svg order of atoms the Eimages/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/add.svg order index of the atom (0, 1, 2, ...), the atom index / MolAtom object the major microspecies pH (takes the input molecule itself if omitted) Molecule Context hmoElectrophilicityOrder(2) returns the Eimages/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/add.svg order index of atom 2 of the input molecule, e.g. returns 0 if atom 2 is the most electrophilic atom, 1 if atom 2 is the second strongest electrophilic atom, etc., Reaction Context hmoElectrophilicityOrder(ratom(1)) returns the Eimages/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/add.svg order index of the reactant atom matching map 1 in the reaction equation
    hmoElectrophilicLocalizationEnergy Structural Calculations License calculates HMO localization energy Limages/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/add.svg of atoms the localization energy Limages/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/add.svg of the atom, NaN for non-aromatic atoms the atom index / MolAtom object the major microspecies pH (takes the input molecule itself if omitted) Molecule Context hmoElectrophilicLocalizationEnergy(2) returns the electrophilic Limages/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/add.svg localization energy of atom 2 of the input molecule, NaN if atom 2 is non-aromatic Reaction Context hmoElectrophilicLocalizationEnergy(ratom(1)) returns the electrophilic Limages/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/add.svg localization energy of the reactant atom matching map 1 in the reaction equation
    hmoNucleophilicityOrder hmoOrderNu Structural Calculations License calculates HMO Nuimages/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/forbidden.svg order of atoms the Nuimages/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/forbidden.svg order index of the atom (0, 1, 2, ...), the atom index / MolAtom object the major microspecies pH (takes the input molecule itself if omitted) Molecule Context hmoNucleophilicityOrder(2) returns the Nuimages/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/forbidden.svg order index of atom 2 of the input molecule, e.g. returns 0 if atom 2 is the most nucleophilic atom, 1 if atom 2 is the second strongest nucleophilic atom, etc., Reaction Context hmoNucleophilicityOrder(ratom(1)) returns the Nuimages/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/forbidden.svg order index of the reactant atom matching map 1 in the reaction equation
    hmoNucleophilicLocalizationEnergy Structural Calculations License calculates HMO localization energy Limages/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/forbidden.svg of atoms the localization energy Limages/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/forbidden.svg of the atom, NaN for non-aromatic atoms the atom index / MolAtom object the major microspecies pH (takes the input molecule itself if omitted) Molecule Context hmoNucleophilicLocalizationEnergy(2) returns the nucleophilic Limages/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/forbidden.svg localization energy of atom 2 of the input molecule, NaN if atom 2 is non-aromatic Reaction Context hmoNucleophilicLocalizationEnergy(ratom(1)) returns the nucleophilic Limages/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/forbidden.svg localization energy of the reactant atom matching map 1 in the reaction equation
    hmoPiEnergy Structural Calculations License calculates the HMO pi energy of the molecule the pi energy of the molecule * the major microspecies pH (takes the input molecule itself if omitted) Molecule Context hmoPiEnergy() returns the pi energy of the input molecule Reaction Context hmoPiEnergy(product(1)) returns the pi energy of the second product
    nucleophilicity electrophilicLocalizationEnergy energyE Structural Calculations License calculates nucleophilicity of atoms the nucleophilicity of the atom, NaN for non-aromatic atoms the atom index / MolAtom object the major microspecies pH (takes the input molecule itself if omitted) Molecule Context nucleophilicity(2) returns the nucleophilicity of atom 2 of the input molecule, NaN if atom 2 is non-aromatic Reaction Context nucleophilicity(ratom(1)) returns the nucleophilicity of the reactant atom matching map 1 in the reaction equation
    nucleophilicityOrder aromaticNucleophilicityOrder orderNu Structural Calculations License calculates Nuimages/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/forbidden.svg order of atoms the Nuimages/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/forbidden.svg order index of the atom (0, 1, 2, ...), the atom index / MolAtom object the major microspecies pH (takes the input molecule itself if omitted) Molecule Context nucleophilicityOrder(2) returns the Nuimages/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/forbidden.svg order index of atom 2 of the input molecule, e.g. returns 0 if atom 2 is the most nucleophilic atom, 1 if atom 2 is the second strongest nucleophilic atom, etc., Reaction Context nucleophilicityOrder(ratom(1)) returns the Nuimages/s/en_US/8100/6512c1e2a41cdf14570641b46bd2fe3eaeb38d03/_/images/icons/emoticons/forbidden.svg order index of the reactant atom matching map 1 in the reaction equation
    piEnergy Structural Calculations License calculates the pi energy of the molecule. Deprecated. the pi energy of the molecule * the major microspecies pH (takes the input molecule itself if omitted) Molecule Context piEnergy() returns the pi energy of the input molecule Reaction Context piEnergy(product(1)) returns the pi energy of the second product

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    Isomers Functions

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

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    Markush Functions

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

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    Match Functions

    Name License Description Return value Parameters Examples
    disjointMatchCount - performs substructure search, returns the maximal number of pairwise disjoint search hits the maximal number of pairwise disjoint search hits target atom index / MolAtom object (optional) query Molecule object / SMARTS string * query atom map(s) (optional) The function returns the maximal number of pairwise disjoint query structures found in the target molecule. Warning: if the target atom index and optionally query atom maps are specified then the return value can only be 0 or 1, therefore the result is similar to the result of the match function. Molecule Context </ac:plain-text-body></ac:structured-macro> Reaction Context <![CDATA[disjointMatchCount(reactant(0), "[#8]C=O") counts the maximal number of pairwise disjoint carboxylic groups in the first reactant ]]></ac:plain-text-body></ac:structured-macro>
    match - performs substructure search and optionally checks for atom matching true if matching substructure found, false otherwise target atom index / MolAtom object (optional) query Molecule object / SMARTS string * query atom map(s) (optional) The function returns true if the query structure is found in the target molecule, the hit is required to include the target atom if specified, furthermore if query atom map(s) are specified then these mapped atoms should match the target atom. Molecule Context </ac:plain-text-body></ac:structured-macro> Reaction Context <![CDATA[match(reactant(0), "[#8]C=O") performs substructure search without atom matching requirement, the target is the first reactant, the query is the carboxylic group given in the string parameter match(patom(2), "[#8]C=O") performs substructure search, checks if product atom matching map 2 in the reaction equation matches any atom of the carboxylic group query match(ratom(1), "[#8:1]C=[O:2]", 1, 2) performs substructure search, checks if reactant atom matching map 1 in the reaction equation is a carboxylic oxygen ]]></ac:plain-text-body></ac:structured-macro>
    matchCount - performs substructure search and optionally checks for atom matching, counts search hits the number of search hits target atom index / MolAtom object (optional) query Molecule object / SMARTS string * query atom map(s) (optional) The function returns the number of query structures found in the target molecule, the hit is required to include the target atom if specified, furthermore if query atom map(s) are specified then these mapped atoms should match the target atom. Molecule Context </ac:plain-text-body></ac:structured-macro> Reaction Context <![CDATA[matchCount(reactant(0), "[#8]C=O") counts search hits without atom matching requirement, the target is the first reactant, the query is the carboxylic group given in the string parameter matchCount(patom(2), "[#8]C=O") counts search hits, checks if product atom matching map 2 in the reaction equation matches any atom of the carboxylic group query matchCount(ratom(1), "[#8:1]C=[O:2]", 1, 2) counts search hits with reactant atom matching map 1 in the reaction equation being a carboxylic oxygen ]]></ac:plain-text-body></ac:structured-macro>
    matchFirst - performs substructure search and optionally checks for atom matching index of the first matching substructure (1-based indexing) target atom index / MolAtom object (optional) query Molecule objects / SMARTS strings in collection (e.g. {amine,amide,"[#8][C:1]=O"}) * query atom map(s) (optional)The function returns the index of the first matching query structure found in the target molecule, the hit is required to include the target atom if specified, furthermore if query atom map(s) are specified then these mapped atoms should match the target atom. Molecule Context matchFirst({amine,amide,alcohol}) performs substructure search without atom matching requirement, the target is the input molecule, the queries are the amine, amide, and alcohol groups given in the string parameter. Function returns 1 if there is an amine group in the input molecule, 2 if there is no amine, but there is an amide group in the input molecule, and returns 3 if there is no amine or amide group, but there is an alcohol group in the input molecule. Returns 0 if none of the listed groups is found in input molecule. matchFirst(6, {"[#8][C:1]=O","[NX3:2][CX3:1]=[OX1:3]"}, 1) performs substructure search, checks if target atom 6 matches the carbon (atom with map 1) of the carboxylic or amide group in query. Returns the index of the query if match found, 0 otherwise. matchFirst(6, {"[#8:1]C=[O:2]","[#6][OX2:1][CX3](o-2)[#6]"}, 1, 2) performs substructure search, checks if target atom 6 of the input molecule is a carboxylic oxygen or an oxigen in an ester group. Returns the index of the query if match found, 0 otherwise. Reaction Context matchFirst(reactant(0), {amine,amide,alcohol}) performs substructure search without atom matching requirement, the target is the first reactant, the queries are the amine, amide, and alcohol groups given in the string parameter. Function returns 1 if there is an amine group in the first reactant, 2 if there is no amine group, but there is an amide group in the first reactant, and returns 3 if there is no amine or amide group, but there is an alcohol group in the first reactant. Returns 0 if none of the listed groups is found in first reactant. matchFirst(patom(2), {"[#8][C]=O","[NX3][CX3]=[OX1]"}) performs substructure search, checks if product atom matching map 2 in the reaction equation matches any atom of the carboxylic or amide group query. Returns the index of mathing query, or 0 if no match found. matchFirst(ratom(1), {"[#8:1]C=[O:2]","[#6][OX2:1][CX3](o-2)[#6]"}, 1, 2) performs substructure search, checks if reactant atom matching map 1 in the reaction equation is a carboxylic oxygen or an oxigen in an ester group. Returns the index of the query if match found, 0 otherwise. ]]></ac:plain-text-body></ac:structured-macro>

    Predefined Molecules and Molecule Sets

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

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

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    Name Functions

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

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    Partitioning Functions

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

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    Protonation Functions

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

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    Refractivity Functions

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

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    Solubility Functions

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

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    StructuralFrameworks Functions

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

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    Structure Checker Functions

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

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    Notes

    1. If in reaction context in the parameter list of a Chemical Terms function atoms are referred by atom index - including cases when a Chemical Terms function is used to convert reactant or product atom maps to atom indexes - then the molecule (reactant / product) parameter always have to be specified (e.g. shortestPath(reactant(0), pair(ratom(1), ratom(2)))) and must contain all the atoms referred by atom indexes.

    2. Although the function/calculation names are case-sensitive, the lowercase versions are always accepted. For example, aromaticAtomCount() is equivalent to aromaticatomcount(), but AromaticAtomCount() and AROMATICATOMCOUNT() are not recognized by the parser.

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

    4. Structure based calculations are performed using Calculator Plugins (these calculations are also referred as "plugin calculations").Since Marvin 5.2, all of these functions can have an additional string argument that specifies plugin parameters in "key1:value1 key2:value2 key3:value3 ..." fashion. For example: charge(8, "type:pi pH:3.5") will compute the pi charge of atom 8 in the major microspecies at pH=3.5 of the input molecule, markushEnumerations("code:true max:4","1,2") will generate maximum 4 enumerated structures with enumeration ID, enumerating only atoms 1 and 2 of the input Markush structure. Note, that this feature cannot be combined with the former possibility of specifying the pH in a string argument, for example: charge(8, "type:pi pH:3.5") cannot be written in the form charge(8, "type:pi", "3.5"), while charge("pi", 8, "3.5") is accepted (backward compatibility).