int/double abs(7)returns 7
abs(-4.9)returns 4.9]]>
abs(7)returns 7
abs(-4.9)returns 4.9]]>
abs(7)returns 7
abs(-4.9)returns 4.9]]>
int/double true = 1, false = 0), or the number itself, if the input is a number]]> booleanToNumber(1<2)returns 1
booleanToNumber(2+2==5)returns 0
booleanToNumber(5*5)returns 25]]>
booleanToNumber(hasValenceError())returns 0 for molecules having no valence error]]> booleanToNumber(ringBond(reactant(0), bond(ratom(1), ratom(2))))returns 1 if reactant atoms matching maps 1 and 2 in the reaction equation are connected by a ring bond in the corresponding reactant, 0 otherwise]]>
int[] filter("charge() > 0") returns the indices of atoms with positive partial charge in the input molecule filter(6, 7, 8, 9, "match('[#8][C:1]=O', 1)") returns the carboxylic carbons out of atoms 6, 7, 8, 9 in the input molecule]]> filter(reactant(0), "charge() > 0") returns the indices of atoms with positive partial charge in the first reactant filter(patom(1), patom(2), "match('[#8][C:1]=O', 1)") returns the carboxylic carbons out of product atoms matching map 1 or 2 in the reaction equation (note, that these atoms are supposed to be in the same product molecule)]]> int[] array(2, 5, 6, 8)]]> array(2, 5, 6, 8)]]> array(ratom(2), ratom(5), ratom(6), ratom(8)) array(patom(2), patom(5), patom(6), patom(8))]]> boolean true if the array contains the specified integer, false otherwise]]> in(5, array(3, 5, 1)) returns true in(2, array(3, 5, 1)) returns false]]> in(3, maxatom("charge()", 2)) returns true if the partial charge 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]]> 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]]> int/double min(2, 8, 6) returns 2 max(3.4, 5.6, 1.2) returns 5.6]]> 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]]> 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]]> int/double min(2, 8, 6) returns 2 max(3.4, 5.6, 1.2) returns 5.6]]> 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]]> 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]]> int/int[] 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]]> 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]]> int/int[] 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]]> 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)]]> int/int[]/double/double[] minValue("charge('7.4')") returns the minimum partial charge in the major microspecies at pH 7.4 of the input molecule]]> minValue(reactant(0), "charge('7.4')") returns the minimum partial charge in the major microspecies at pH 7.4 of the first reactant]]> int/int[]/double/double[] 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]]> 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)]]> int[]/double[] sortAsc(array(3.4, 5.6, 1.2)) returns array(1.2, 3.4, 5.6)]]> sortAsc(charge()) returns the partial charge values in ascending order]]> sortAsc(charge(reactant(1))) returns the partial charge values of the second reactant in ascending order]]> int[]/double[] sortDesc(array(3.4, 5.6, 1.2)) returns array(5.6, 3.4, 1.2)]]> sortDesc(pka("basic")) returns the basic pKa values in descending order]]> sortDesc(pka(product(0), "basic")) returns the basic pKa values of the first product in descending order]]> int count(array(3.4, 5.6, 1.2)) returns 3]]> count(filter("charge() > 0")) returns the number of atoms with positive charge count(filter("match('[#8][C:1]=O', 1")) returns the number of carboxylic carbons]]> 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]]> int/double sum(array(3.4, 5.6, 1.2)) returns 10.2]]> sum(charge()) returns the sum of charge values sum(pol()) returns the sum of atom polarizability values]]> 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]]> int hCount(0) returns the hydrogen count of atom 0]]> hCount(patom(3)) returns the hydrogen count on the product atom matching map 3 in the reaction equation]]> int connections(2) returns the number of connections of atom 2]]> connections(ratom(1)) returns the number of connections of the reactant atom matching map 1 in the reaction equation]]> int valence(0) returns the valence of atom 0]]> valence(ratom(1)) returns the valence of the reactant atom matching map 1 in the reaction equation]]> int radicalCount(0) returns the radical count of atom 0]]> radicalCount(patom(3)) returns the radical count on the product atom matching map 3 in the reaction equation]]> atomicNumber int atno(0) returns the atomic number of atom 0]]> atno(ratom(1)) returns the atomic number of the reactant atom matching map 1]]> chemaxon.struc.MolAtom molAtom(6) returns a carbon atom]]> molAtom(6) returns a carbon atom]]> int map(3) returns the atom map number of atom 3]]> map(patom(3)) returns the atom map number on the product atom matching map 3 in the reaction equation]]> boolean true if the atom has an aromatic bond, false otherwise]]> arom(0) returns if the atom 0 has an aromatic bond]]> arom(patom(2)) returns true if the product atom matching map 2 in the reaction equation has an aromatic bond]]> property 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]]> 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]]> propertyAsString String fieldAsString('ID') returns the value of the ID property (SDF field)]]> field(reactant(0), 'ID') returns the value of the ID property field in first reactant]]> String bond (used for pairing atoms in shortestPath)]]> pair(2, 5) returns "3-6"]]> 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]]> totalCharge int formalCharge() returns the formal charge of the input molecule formalCharge(0) returns the formal charge of atom 0]]> formalCharge(ratom(1)) returns the formal charge of the reactant atom matching map 1]]> molFormat molConvert String
  • the molecule format (e.g. "mol", "sdf", "mrv", "smiles")
  • the clean dimension
  • ]]>
    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]]>
    molImage byte[] molImage("jpeg:w100,Q95,#ffff00") returns the 100x100 JPEG image of the input molecule with yellow background, 95% quality]]> Molecule importMol("c1ccccc1") returns benzene molecule]]> boolean true in case of valence error, false otherwise]]> hasValenceError() returns true if any atom in the molecule has valence error, false otherwise]]> hasValenceError(reactant(1)) returns true if any atom in the second reactant has valence error, false otherwise]]> int -1 if there is no valence error]]> -1 if there is no valence error]]> whereIsValenceError() returns the index of the first atom with valence error, or -1 if there is no valence error in the molecule]]> whereIsValenceError(reactant(1)) returns the index of the first atom with valence error in the second reactant, or -1 f there is no valence error in the second reactant]]> boolean true if there is an error in the aromatization of the molecule, false otherwise]]> hasAromatizationError() returns true if there is an error in the aromatization of the molecule, false otherwise]]> hasAromatizationError(reactant(0)) returns true if there is an error in the aromatization of the first reactant, false otherwise]]> boolean true if any atom in the molecule has radical, false otherwise]]> hasRadical() returns true if any atom in the molecule has radical, false otherwise]]> hasRadical(reactant(1)) returns true if any atom in the second reactant has radical, false otherwise]]> boolean true if any atom in the molecule is a specific isotope of the element, false otherwise]]> hasIsotope() returns true if any atom in the molecule is a specific isotope of the element, false otherwise]]> hasIsotope(reactant(1)) returns true if any atom in the second reactant is a specific isotope of the element, false otherwise]]> boolean true if the molecule does not contain any atoms, bonds, or non-empty S-groups, false otherwise]]> isQuery() returns true if the given molecule does not contain any atoms, bonds, or non-empty S-groups, false otherwise]]> isQuery(reactant(1)) returns true if the second reactant contains any atoms, bonds, or non-empty S-groups, false otherwise]]> boolean true if the molecule contains any query features, false otherwise]]> isQuery() returns true if the given molecule contains any query features, false otherwise]]> isQuery(reactant(1)) returns true if the second reactant contains any query features, false otherwise]]> boolean Markush true if the molecule contains any Markush features, false otherwise]]> isMarkush() returns true if the given molecule contains any Markush features, false otherwise]]> isMarkush(reactant(1)) returns true if the second reactant contains any Markush features, false otherwise]]> Molecule[] fragments() returns the disconnected fragments of the molecule]]> fragments(reactant(1)) returns the disconnected fragments of the second reactant]]> String Elemental Analysis
  • molecular formula
  • available functions:
    • atomCount
    • mass
    • massPrecision
    • exactMass
    • exactMassPrecision
    • formula
    • isotopeFormula
    • dotDisconnectedFormula
    • dotDisconnectedIsotopeFormula
  • ]]>
    elementalAnalysis('C12H25O', 'mass') returns the mass of molecule represented by formula]]>
    int Geometry bondCount() returns the number of bonds in the input molecule]]> bondCount(reactant(0)) returns the number of bonds in the first reactant bondCount(product(1)) returns the number of bonds in the second product]]> String Structure Checker
  • check("aromaticity..valence"), or
  • check('"<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"no\"?><checkers><AromaticityErrorChecker fixMode=\"fix\" fixerClassName=\"chemaxon.fixers.RearomatizeFixer\" type=\"general\"/><ValenceErrorChecker allowTraditionalNitrogen=\"false\" fixMode=\"fix\" fixerClassName=\"chemaxon.fixers.ValenceFixer\"/></checkers> "')
  • checks for aromaticity and valence errors, and returns the error report]]>
    check(reactant(0), "aromaticity..valence") checks for aromaticity and valence errors in first reactant, and returns the error report]]> http://www.chemaxon.com/marvin/help/structurechecker/checker.html
    Integer Structure Checker checkErrorCount('"<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"no\"?><checkers><AromaticityErrorChecker fixMode=\"fix\" fixerClassName=\"chemaxon.fixers.RearomatizeFixer\" type=\"general\"/><ValenceErrorChecker allowTraditionalNitrogen=\"false\" fixMode=\"fix\" fixerClassName=\"chemaxon.fixers.ValenceFixer\"/></checkers> "') or
    checkErrorCount("aromaticity..valence") checks for aromaticity and valence errors, and returns the total error count]]>
    check(reactant(0), "aromaticity..valence") checks for aromaticity and valence errors in first reactant, and returns the error report]]> http://www.chemaxon.com/marvin/help/structurechecker/checker.html
    boolean Structure Checker
  • isValid("aromaticity..valence"), or
  • isValid('"<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"no\"?><checkers><AromaticityErrorChecker fixMode=\"fix\" fixerClassName=\"chemaxon.fixers.RearomatizeFixer\" type=\"general\"/><ValenceErrorChecker allowTraditionalNitrogen=\"false\" fixMode=\"fix\" fixerClassName=\"chemaxon.fixers.ValenceFixer\"/></checkers> "')
  • checks for aromaticity and valence errors, and returns if the structure is valid]]>
    isValid(reactant(0), "aromaticity..valence") checks for aromaticity and valence errors in first reactant, and returns if it is valid]]> http://www.chemaxon.com/marvin/help/structurechecker/checker.html
    Molecule Structure Checker
  • fix("chiralflag..isotope->converttoelementalform"), or
  • fix('"<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"no\"?><checkers><ChiralFlagChecker fixMode=\"fix\" fixerClassName=\"chemaxon.fixers.RemoveChiralFlagFixer\"/><IsotopeChecker fixMode=\"fix\" fixerClassName=\"chemaxon.fixers.ConvertToElementalFormFixer\"/></checkers>"')
  • searches for ciral flags and isotopes, and removes them or converts them to elemental form]]>
    fix(product(1), "chiralflag..isotope->converttoelementalform") searches for ciral flags and isotopes in second product, and removes them or converts them to elemental form]]> http://www.chemaxon.com/marvin/help/structurechecker/checker.html
    int -1 if the the input (molecule) is not a reaction]]> 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.]]> 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.]]> int -1 if the the input (molecule) is not a reaction]]> 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.]]> 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.]]> int -1 if the the input (molecule) is not a reaction]]> 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.]]> 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.]]>
    majorMs Molecule Protonation
  • the pH value as string
  • ]]>
    majorMicrospecies("7.4") returns the major microspecies of the input molecule at pH 7.4]]> majorMicrospecies(reactant(0), "7.4") returns the major microspecies of the first reactant at pH 7.4 majorMicrospecies(product(1), "7.4") returns the major microspecies of the second product at pH 7.4]]> http://www.chemaxon.com/marvin/help/calculations/protonation.html#ms
    msCount int Protonation microspeciesCount() returns the number of microspecies of the input molecule]]> microspeciesCount(reactant(0)) returns the number of microspecies of the first reactant microspeciesCount(product(1)) returns the number of microspecies of the second product]]> http://www.chemaxon.com/marvin/help/calculations/protonation.html#ms ms Molecule Protonation
  • the pH value as string
  • the microspecies index by descending order of microspecies distributions
  • ]]>
    microspecies("7.4", 1) returns the microspecies of the input molecule with second largest distribution at pH 7.4]]> 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]]> http://www.chemaxon.com/marvin/help/calculations/protonation.html#ms
    msDistr double Protonation
  • the pH value as string
  • the microspecies index by descending order of microspecies distributions
  • ]]>
    microspeciesDistribution("5.4", 0) returns the largest microspecies distribution of the input molecule at pH 5.4]]> microspeciesDistribution(reactant(0), "5.4", 2) returns the third largest microspecies distribution of the first reactant at pH 5.4 microspeciesDistribution(product(1), "3.2", 1) returns the second largest microspecies distribution of the second product at pH 3.2]]> http://www.chemaxon.com/marvin/help/calculations/protonation.html#ms
    Isomers Molecule
  • the tautomer index (0-based)
  • ]]>
    tautomer(0) returns the first tautomer of the input molecule]]> tautomer(reactant(0), 1) returns the second tautomer of the first reactant]]>
    Molecule Isomers canonicalTautomer() returns the canonical tautomer structure of the input molecule]]> canonicalTautomer(reactant(0)) returns the canonical tautomer structure of the first reactant/td>]]> Molecule Isomers genericTautomer() returns the generic tautomer structure of the input molecule]]> genericTautomer(reactant(0)) returns the generic tautomer structure of the first reactant/td>]]> Molecule Isomers mostStableTautomer() returns the most stable tautomer structure of the input molecule]]> mostStableTautomer(reactant(0)) returns the most stable tautomer structure of the first reactant/td>]]> Molecule Isomers
  • the pH value as string (set if pH effect should be considered)
  • ]]>
    majorTautomer() returns the major tautomer structure of the input molecule]]> majorTautomer(reactant(0)) returns the major tautomer structure of the first reactant/td>]]>
    Molecule[] Isomers tautomers() returns all tautomers of the input molecule in an array]]> tautomers(reactant(0)) returns all tautomers of the first reactant in an array]]> int Isomers tautomerCount() returns the number of tautomers of the input molecule]]> tautomerCount(reactant(0)) returns the number of tautomers of the first reactant]]> tautomer Molecule Isomers ]]>
  • the dominant tautomer index (0-based)
  • the pH value as string (set if pH effect should be considered)
  • ]]>
    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 ]]> 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 ]]>
    tautomers Molecule[] Isomers
  • the pH value as string (set if pH effect should be considered)
  • ]]>
    dominantTautomers() returns all dominant tautomers of the input molecule in an array dominantTautomers("2.0") returns all dominant tautomers of the input molecule in an array, considering pH effect at pH 2.0 ]]> 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 ]]>
    int Isomers
  • the pH value as string (set if pH effect should be considered)
  • ]]>
    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]]> 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]]>
    Molecule Isomers resonant(0) returns the first resonant structure of the input molecule]]> resonant(reactant(0), 1) returns the second resonant structure of the first reactant]]> Molecule Isomers canonicalResonant() returns the canonical resonant structure of the input molecule]]> canonicalResonant(reactant(0)) returns the canonical resonant structure of the first reactant]]> Molecule[] Isomers resonants() returns all resonants of the input molecule in an array]]> resonants(reactant(0)) returns all resonants of the first reactant in an array]]> int Isomers resonantCount() returns the number of resonant structures of the input molecule]]> resonantCount(reactant(0)) returns the number of resonant structures of the first reactant]]> randomMarkushEnumeration randomEnumerations randomEnumeration Molecule[] Markush
  • the number of structures to be returned (default: 1)
  • the (1-based) atom indexes of the query atoms to be enumerated (default: all)
  • ]]>
    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) ]]> 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)]]>
    Markush
  • the number of structures to be returned (default: 1)
  • the (1-based) atom indexes of the query atoms to be enumerated (default: all)
  • ]]>
    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]]> 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]]>
    markushEnumeration enumerations enumeration Molecule[] Markush
  • the number of structures to be returned (default: all)
  • the (1-based) atom indexes of the query atoms to be enumerated (default: all)
  • ]]>
    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)]]> 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)]]>
    Molecule[] Markush
  • the number of structures to be returned (default: all)
  • the (1-based) atom indexes of the query atoms to be enumerated (default: all)
  • ]]>
    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 ]]> 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 ]]>
    enumerationCount Molecule[] Markush
  • the (1-based) atom indexes of the query atoms to be enumerated (default: all)
  • ]]>
    markushEnumerationCount() returns the number of Markush enumerated structures of the input molecule markushEnumerationCount('4,5') returns the number of Markush enumerated structures of the input molecule, enumerating only atoms 4, 5 (1-based)]]> 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)]]>
    int Markush
  • the (1-based) atom indexes of the query atoms to be enumerated (default: all)
  • ]]>
    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]]> 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)]]>
    String Markush
  • the (1-based) atom indexes of the query atoms to be enumerated (default: all)
  • ]]>
    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]]> 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)]]>
    int Markush
  • the (1-based) atom indexes of the query atoms to be enumerated (default: all)
  • ]]>
    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]]> 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)]]>
    double Charge 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 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)
  • ]]>
    charge(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 7.4]]> charge(ratom(1), "aromaticsystem") returns the sum of partial pi charges in the aromatic system containing the reactant atom matching map 1 in the reaction equation charge(patom(2), "aromaticring", "7.4") returns the sum of partial charges in the smallest aromatic ring containing the product atom matching map 2 in the major microspecies taken at pH 7.4]]>
    double Charge 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 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)
  • ]]>
    resonantCharge(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 effect]]> resonantCharge(ratom(1), "aromaticsystem") returns the sum of partial pi charges in the aromatic system containing the reactant atom matching map 1 in the reaction equation considering resonance 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]]>
    sOEN double Charge
  • the atom index / MolAtom object,
  • the major microspecies pH (takes the input molecule itself if omitted)
  • ]]>
    sigmaOrbitalElectronegativity(0) returns the sigma orbital electronegativity of atom 0 of the input molecule sigmaOrbitalElectronegativity(2, "7.4") returns the sigma orbital electronegativity of atom 2 of the major microspecies taken at pH 7.4]]> sOEN(ratom(1)) returns the sigma orbital electronegativity of reactant atom matching map 1 in the reaction equation sOEN(patom(2), "7.4") returns the sigma orbital electronegativity of the product atom matching map 2 of the major microspecies taken at pH 7.4]]>
    pOEN double Charge
  • the atom index / MolAtom object,
  • the major microspecies pH (takes the input molecule itself if omitted)
  • ]]>
    piOrbitalElectronegativity(0) returns the pi orbital electronegativity of atom 0 of the input molecule piOrbitalElectronegativity(2, "7.4") returns the pi orbital electronegativity of atom 2 of the major microspecies taken at pH 7.4]]> pOEN(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]]>
    polarizability atomPol pol double Charge
  • the atom index / MolAtom object,
  • the major microspecies pH (takes the input molecule itself if omitted)
  • ]]>
    atomicPolarizability(0) returns the polarizability of atom 0 of the input molecule atomicPolarizability(2, "7.4") returns the polarizability of atom 2 of the major microspecies taken at pH 7.4]]> atomicPolarizability(ratom(1)) returns the polarizability of reactant atom matching map 1 in the reaction equation atomicPolarizability(patom(2), "7.4") returns the polarizability of the product atom matching map 2 of the major microspecies taken at pH 7.4]]>
    molPol double Charge
  • the major microspecies pH (takes the input molecule itself if omitted)
  • ]]>
    molecularPolarizability() returns the molecular polarizability of the input molecule molecularPolarizability("7.4") returns the molecular polarizability of the major microspecies taken at pH 7.4]]> molecularPolarizability(reactant(1)) returns the molecular polarizability of the second reactant in the reaction equation molecularPolarizability(product(0), "7.4") returns the molecular polarizability of the first product major microspecies taken at pH 7.4]]>
    avgPol averagePol double Charge
  • the major microspecies pH (takes the input molecule itself if omitted)
  • ]]>
    averagePolarizability() returns the average polarizability component of the input molecule averagePolarizability("7.4") returns the average polarizability component of the major microspecies taken at pH 7.4]]> averagePolarizability(reactant(1)) returns the average polarizability component of the second reactant in the reaction equation averagePolarizability(product(0), "7.4") returns the average polarizability component of the first product major microspecies taken at pH 7.4]]>
    double Charge
  • the major microspecies pH (takes the input molecule itself if omitted)
  • ]]>
    axxPol() 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 7.4]]> axxPol(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]]>
    double Charge
  • the major microspecies pH (takes the input molecule itself if omitted)
  • ]]>
    ayyPol() 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 7.4]]> ayyPol(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]]>
    double Charge
  • the major microspecies pH (takes the input molecule itself if omitted)
  • ]]>
    azzPol() 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 7.4]]> azzPol(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]]>
    double/double[] Protonation Ka values]]> Ka values]]>
  • the atom index / MolAtom object,
  • the strength index as string (e.g., '1' for the strongest, '2' for the second strongest pKa),
  • 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 pKa values are acidic or basic (mixed!), depending on the acidic or basic character of the given atom. Acidic pKa is returned for an atom, if acidicpKa() ≤ 14.8-basicpKa(), otherwise basic pKa is returned. Specifying "acidic" or "basic" result type is required to get the acidic or basic pKa values only (also acidicpKa or basicpKa functions can be used alternatively).]]>
    pKa(0) returns the pKa of atom 0 of the input molecule pKa("acidic", "2") returns the second strongest acidic pKa value]]> pKa(ratom(1)) returns the pKa of reactant atom matching map 1 in the reaction equation pKa(product(0), "basic", "1") returns the strongest basic pKa value in the first product]]> http://www.chemaxon.com/marvin/help/calculations/protonation.html#pka
    double/double[] Protonation Ka values using the correction library]]> Ka values]]>
  • the atom index / MolAtom object,
  • the strength index as string (e.g. '1' for the strongest, '2' for the second strongest pKa),
  • 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 pKa values are acidic or basic (mixed!), depending on the acidic or basic character of the given atom. Acidic pKa is returned for an atom, if acidicpKa() ≤ 14.8-basicpKa(), otherwise basic pKa is returned. Specifying "acidic" or "basic" result type is required to get the acidic or basic pKa values only (also acidicpKaUseCorrection() or basicpKaUseCorrection() functions can be used alternatively).]]>
    pKaUseCorrection(0) returns the pKa of atom 0 of the input molecule pKaUseCorrection("acidic", "2") returns the second strongest acidic pKa value]]> pKaUseCorrection(ratom(1)) returns the pKa of reactant atom matching map 1 in the reaction equation pKaUseCorrection(product(0), "basic", "1") returns the strongest basic pKa value in the first product]]> http://www.chemaxon.com/marvin/help/calculations/protonation.html#pka
    apKa double/double[] Protonation Ka values]]> Ka values]]>
  • the atom index / MolAtom object,
  • the strength index as string (e.g. '1' for the strongest, '2' for the second strongest pKa),
  • Note, that the strength index is specified between quotation marks.]]>
    acidicpKa(0) returns the acidic pKa of atom 0 of the input molecule acidicpKa("2") returns the second strongest acidic pKa value]]> acidicpKa(ratom(1)) returns the acidic pKa of reactant atom matching map 1 in the reaction equation acidicpKa(product(0), "1") returns the strongest basic pKa value in the first product]]> http://www.chemaxon.com/marvin/help/calculations/protonation.html#pka
    bpKa double/double[] Protonation Ka values]]> Ka values]]>
  • the atom index / MolAtom object,
  • the strength index as string (e.g. '1' for the strongest, '2' for the second strongest pKa),
  • Note, that the strength index is specified between quotation marks.]]>
    basicpKa(0) returns the basic pKa of atom 0 of the input molecule basicpKa("2") returns the second strongest basic pKa value]]> basicpKa(ratom(1)) returns the basic pKa of reactant atom matching map 1 in the reaction equation basicpKa(product(0), "1") returns the strongest basic pKa value in the first product]]> http://www.chemaxon.com/marvin/help/calculations/protonation.html#pka
    double/double[] Protonation Ka values using the correction library]]> Ka values]]>
  • the atom index / MolAtom object,
  • the strength index as string (e.g. '1' for the strongest, '2' for the second strongest pKa),
  • Note, that the strength index is specified between quotation marks.]]>
    acidicpKaUseCorrection(0) returns the acidic pKa of atom 0 of the input molecule "acidicpKaUseCorrection"("2") returns the second strongest acidic pKa value]]> "acidicpKaUseCorrection"(ratom(1)) returns the acidic pKa of reactant atom matching map 1 in the reaction equation "acidicpKaUseCorrection"(product(0), "1") returns the strongest basic pKa value in the first product]]> http://www.chemaxon.com/marvin/help/calculations/protonation.html#pka
    double/double[] Protonation Ka values using the correction library]]> Ka values]]>
  • the atom index / MolAtom object,
  • the strength index as string (e.g. '1' for the strongest, '2' for the second strongest pKa),
  • Note, that the strength index is specified between quotation marks.]]>
    basicpKaUseCorrection(0) returns the basic pKa of atom 0 of the input molecule basicpKaUseCorrection("2") returns the second strongest basic pKa value]]> basicpKaUseCorrection(ratom(1)) returns the basic pKa of reactant atom matching map 1 in the reaction equation basicpKaUseCorrection(product(0), "1") returns the strongest basic pKa value in the first product]]> http://www.chemaxon.com/marvin/help/calculations/protonation.html#pka
    double/double[] Protonation Ka values using large model (this model is optimized for a large number of ionizable atoms)]]> Ka values]]>
  • the atom index / MolAtom object,
  • the strength index as string (e.g. '1' for the strongest, '2' for the second strongest pKa),
  • Note, that the strength index is specified between quotation marks.]]>
    acidicpKaLargeModel(0) returns the acidic pKa of atom 0 of the input molecule acidicpKaLargeModel("2") returns the second strongest acidic pKa value]]> acidicpKaLargeModel(ratom(1)) returns the acidic pKa of reactant atom matching map 1 in the reaction equation acidicpKaLargeModel(product(0), "1") returns the strongest basic pKa value in the first product]]> http://www.chemaxon.com/marvin/help/calculations/protonation.html#pka
    double/double[] Protonation Ka values using large model (this model is optimized for a large number of ionizable atoms)]]> Ka values]]>
  • the atom index / MolAtom object,
  • the strength index as string (e.g. '1' for the strongest, '2' for the second strongest pKa),
  • Note, that the strength index is specified between quotation marks.]]>
    basicpKaLargeModel(0) returns the basic pKa of atom 0 of the input molecule basicpKaLargeModel("2") returns the second strongest basic pKa value]]> basicpKaLargeModel(ratom(1)) returns the basic pKa of reactant atom matching map 1 in the reaction equation basicpKaLargeModel(product(0), "1") returns the strongest basic pKa value in the first product]]> http://www.chemaxon.com/marvin/help/calculations/protonation.html#pka
    double Partitioning D at specified pH]]> D value]]>
  • the pH value
  • ]]>
    logD('7.4') returns the logD at pH 7.4 of the input molecule]]> logD(reactant(1), '7.4') returns the logD at pH 7.4 of the second reactant]]> http://www.chemaxon.com/marvin/help/calculations/partitioning.html#logd
    double Partitioning D at specified pH using method "VG"]]> D value]]>
  • the pH value
  • ]]>
    logDVG('7.4') returns the logD at pH 7.4 of the input molecule]]> logDVG(reactant(1), '7.4') returns the logD at pH 7.4 of the second reactant]]> http://www.chemaxon.com/marvin/help/calculations/partitioning.html#logd
    double Partitioning D at specified pH using method "KLOP"]]> D value]]>
  • the pH value
  • ]]>
    logDKLOP('7.4') returns the logD at pH 7.4 of the input molecule]]> logDKLOP(reactant(1), '7.4') returns the logD at pH 7.4 of the second reactant]]> http://www.chemaxon.com/marvin/help/calculations/partitioning.html#logd
    double Partitioning D at specified pH using method "PHYS"]]> D value]]>
  • the pH value
  • ]]>
    logDPHYS('7.4') returns the logD at pH 7.4 of the input molecule]]> logDPHYS(reactant(1), '7.4') returns the logD at pH 7.4 of the second reactant]]> http://www.chemaxon.com/marvin/help/calculations/partitioning.html#logd
    double Partitioning D at specified pH using the user defined method]]> D value]]>
  • the pH value
  • ]]>
    logDUser('7.4') returns the logD at pH 7.4 of the input molecule]]> logDUser(reactant(1), '7.4') returns the logD at pH 7.4 of the second reactant]]> http://www.chemaxon.com/marvin/help/calculations/partitioning.html#logd
    double Partitioning D at specified pH using weighted method]]> D value]]>
  • the pH value
  • ]]>
    logDWeighted('7.4') returns the logD at pH 7.4 of the input molecule]]> logDWeighted(reactant(1), '7.4') returns the logD at pH 7.4 of the second reactant]]> http://www.chemaxon.com/marvin/help/calculations/partitioning.html#logd
    double Partitioning P]]> P value]]>
  • the result type:
    • "logPMicro": the logP of the input molecule itself
    • "logPNonionic": the logP of the nonionic species
    • "logDpI": logD at pI
    • "logPTrue": the most typical from the above (default)
  • ]]>
    logP() returns the most typical logP out of the input molecule logP, the logP of the nonionic species and logD at pI logP('logPMicro') returns the logP of the input molecule itself]]> logP(reactant(1), 'logDpI') returns the logD at pI of the second reactant logP(product(1), 'logPNonionic') returns logP of the nonionic species of the second product]]> http://www.chemaxon.com/marvin/help/calculations/partitioning.html#logp
    double Partitioning P using method "VG"]]> P value]]>
  • the result type:
    • "logPMicro": the logP of the input molecule itself
    • "logPNonionic": the logP of the nonionic species
    • "logDpI": logD at pI
    • "logPTrue": the most typical from the above (default)
  • ]]>
    logPVG() returns the most typical logP out of the input molecule logP, the logP of the nonionic species and logD at pI logPVG('logPMicro') returns the logP of the input molecule itself]]> logPVG(reactant(1), 'logDpI') returns the logD at pI of the second reactant logPVG(product(1), 'logPNonionic') returns logP of the nonionic species of the second product]]> http://www.chemaxon.com/marvin/help/calculations/partitioning.html#logp
    double Partitioning P using method "KLOP"]]> P value]]>
  • the result type:
    • "logPMicro": the logP of the input molecule itself
    • "logPNonionic": the logP of the nonionic species
    • "logDpI": logD at pI
    • "logPTrue": the most typical from the above (default)
  • ]]>
    logPKLOP() returns the most typical logP out of the input molecule logP, the logP of the nonionic species and logD at pI logPKLOP('logPMicro') returns the logP of the input molecule itself]]> logPKLOP(reactant(1), 'logDpI') returns the logD at pI of the second reactant logPKLOP(product(1), 'logPNonionic') returns logP of the nonionic species of the second product]]> http://www.chemaxon.com/marvin/help/calculations/partitioning.html#logp
    double Partitioning P using method "PHYS"]]> P value]]>
  • the result type:
    • "logPMicro": the logP of the input molecule itself
    • "logPNonionic": the logP of the nonionic species
    • "logDpI": logD at pI
    • "logPTrue": the most typical from the above (default)
  • ]]>
    logPPHYS() returns the most typical logP out of the input molecule logP, the logP of the nonionic species and logD at pI logPPHYS('logPMicro') returns the logP of the input molecule itself]]> logPPHYS(reactant(1), 'logDpI') returns the logD at pI of the second reactant logPPHYS(product(1), 'logPNonionic') returns logP of the nonionic species of the second product]]> http://www.chemaxon.com/marvin/help/calculations/partitioning.html#logp
    double Partitioning P using the user defined method]]> P value]]>
  • the result type:
    • "logPMicro": the logP of the input molecule itself
    • "logPNonionic": the logP of the nonionic species
    • "logDpI": logD at pI
    • "logPTrue": the most typical from the above (default)
  • ]]>
    logPUser() returns the most typical logP out of the input molecule logP, the logP of the nonionic species and logD at pI logPUser('logPMicro') returns the logP of the input molecule itself]]> logPUser(reactant(1), 'logDpI') returns the logD at pI of the second reactant logPUser(product(1), 'logPNonionic') returns logP of the nonionic species of the second product]]> http://www.chemaxon.com/marvin/help/calculations/partitioning.html#logp
    double Partitioning P using weighted method]]> P value]]>
  • the result type:
    • "logPMicro": the logP of the input molecule itself
    • "logPNonionic": the logP of the nonionic species
    • "logDpI": logD at pI
    • "logPTrue": the most typical from the above (default)
  • ]]>
    logPWeighted() returns the most typical logP out of the input molecule logP, the logP of the nonionic species and logD at pI logPWeighted('logPMicro') returns the logP of the input molecule itself]]> logPWeighted(reactant(1), 'logDpI') returns the logD at pI of the second reactant logPWeighted(product(1), 'logPNonionic') returns logP of the nonionic species of the second product]]> http://www.chemaxon.com/marvin/help/calculations/partitioning.html#logp
    logPi double[] Partitioning P increment]]> P increment]]>
  • the atom index / MolAtom object
  • ]]>
    logPincrement(2) returns the logP increment on atom 2 of the input molecule]]> logPincrement(ratom(1)) returns the logP increment on the reactant atom matching map 1 in the reaction equation]]> http://www.chemaxon.com/marvin/help/calculations/partitioning.html#logp
    double Solubility S0 value]]> logS0() returns the logS0 of the input molecule]]> logS0(reactant(1)) returns the logS0 of the second reactant]]> http://www.chemaxon.com/marvin/help/calculations/calculator-plugins.html double Solubility S value]]>
  • the pH value
  • ]]>
    logS('7.4') returns the logS at pH 7.4 of the input molecule]]> logS(reactant(1), '7.4') returns the logS at pH 7.4 of the second reactant]]> http://www.chemaxon.com/marvin/help/calculations/calculator-plugins.html
    String Solubility logSCategory() returns the solubilty category of the input molecule]]> logSCategory(reactant(1)) returns the solubility category of the second reactant]]> http://www.chemaxon.com/marvin/help/calculations/calculator-plugins.html String Isomers
  • -
  • the type of stereo descriptor: atrop, axial, cistrans, tetrahedral
  • ]]>
    stereoAnalysis() returns the stereo descriptors of the input molecule
    stereoAnalysis('tetrahedral') returns the tetrahedral stereo descriptors of the input molecule]]>
    stereoAnalysis(reactant(1)) returns the stereo descriptors of the second reactant
    stereoAnalysis(reactant(1), 'tetrahedral') returns the tetrahedral stereo descriptors of the second reactant]]>
    http://www.chemaxon.com/marvin/help/calculations/calculator-plugins.html
    orderE aromaticElectrophilicityOrder int[] Huckel (0, 1, 2, ...),
    ]]>
  • the atom index / MolAtom object
  • the major microspecies pH (takes the input molecule itself if omitted)
  • ]]>
    electrophilicityOrder(2) returns the E(+) order index of atom 2 of the input molecule, e.g. returns 0 if atom 2 is the most electrophilic atom, 1 if atom 2 is the second strongest electrophilic atom, etc.,]]> electrophilicityOrder(ratom(1)) returns the E(+) order index of the reactant atom matching map 1 in the reaction equation]]>
    hmoOrderE int[] Huckel (0, 1, 2, ...),
    ]]>
  • the atom index / MolAtom object
  • the major microspecies pH (takes the input molecule itself if omitted)
  • ]]>
    hmoElectrophilicityOrder(2) returns the E(+) order index of atom 2 of the input molecule, e.g. returns 0 if atom 2 is the most electrophilic atom, 1 if atom 2 is the second strongest electrophilic atom, etc.,]]> hmoElectrophilicityOrder(ratom(1)) returns the E(+) order index of the reactant atom matching map 1 in the reaction equation]]>
    orderNu aromaticNucleophilicityOrder int[] Huckel (0, 1, 2, ...),
    ]]>
  • the atom index / MolAtom object
  • the major microspecies pH (takes the input molecule itself if omitted)
  • ]]>
    nucleophilicityOrder(2) returns the Nu(-) order index of atom 2 of the input molecule, e.g. returns 0 if atom 2 is the most nucleophilic atom, 1 if atom 2 is the second strongest nucleophilic atom, etc., ]]> nucleophilicityOrder(ratom(1)) returns the Nu(-) order index of the reactant atom matching map 1 in the reaction equation]]>
    hmoOrderNu int[] Huckel (0, 1, 2, ...),
    ]]>
  • the atom index / MolAtom object
  • the major microspecies pH (takes the input molecule itself if omitted)
  • ]]>
    hmoNucleophilicityOrder(2) returns the Nu(-) order index of atom 2 of the input molecule, e.g. returns 0 if atom 2 is the most nucleophilic atom, 1 if atom 2 is the second strongest nucleophilic atom, etc., ]]> hmoNucleophilicityOrder(ratom(1)) returns the Nu(-) order index of the reactant atom matching map 1 in the reaction equation]]>
    electrophilicLocalizationEnergy energyE double[] Huckel NaN for non-aromatic atoms]]>
  • the atom index / MolAtom object
  • the major microspecies pH (takes the input molecule itself if omitted)
  • ]]>
    nucleophilicity(2) returns the nucleophilicity of atom 2 of the input molecule, NaN if atom 2 is non-aromatic]]> nucleophilicity(ratom(1)) returns the nucleophilicity of the reactant atom matching map 1 in the reaction equation]]>
    double[] Huckel NaN for non-aromatic atoms]]>
  • the atom index / MolAtom object
  • the major microspecies pH (takes the input molecule itself if omitted)
  • ]]>
    hmoElectrophilicLocalizationEnergy(2) returns the electrophilic L(+) localization energy of atom 2 of the input molecule, NaN if atom 2 is non-aromatic]]> hmoElectrophilicLocalizationEnergy(ratom(1)) returns the electrophilic L(+) localization energy of the reactant atom matching map 1 in the reaction equation]]>
    nucleophilicLocalizationEnergy energyNu double[] Huckel NaN for non-aromatic atoms]]>
  • the atom index / MolAtom object
  • the major microspecies pH (takes the input molecule itself if omitted)
  • ]]>
    electrophilicity(2) returns the electrophilicity of atom 2 of the input molecule, NaN if atom 2 is non-aromatic]]> electrophilicity(ratom(1)) returns the electrophilicity of the reactant atom matching map 1 in the reaction equation]]>
    double[] Huckel NaN for non-aromatic atoms]]>
  • the atom index / MolAtom object
  • the major microspecies pH (takes the input molecule itself if omitted)
  • ]]>
    hmoNucleophilicLocalizationEnergy(2) returns the nucleophilic L(-) localization energy of atom 2 of the input molecule, NaN if atom 2 is non-aromatic]]> hmoNucleophilicLocalizationEnergy(ratom(1)) returns the nucleophilic L(-) localization energy of the reactant atom matching map 1 in the reaction equation]]>
    double Huckel
  • the major microspecies pH (takes the input molecule itself if omitted)
  • ]]>
    piEnergy() returns the pi energy of the input molecule]]> piEnergy(product(1)) returns the pi energy of the second product]]>
    double Huckel
  • the major microspecies pH (takes the input molecule itself if omitted)
  • ]]>
    hmoPiEnergy() returns the pi energy of the input molecule]]> hmoPiEnergy(product(1)) returns the pi energy of the second product]]>
    piChargeDensity double[] Huckel NaN for non-existing values]]>
  • he atom index / MolAtom object
  • the major microspecies pH (takes the input molecule itself if omitted)
  • ]]>
    electronDensity(2) returns the electron density of atom 2 of the input molecule, NaN for non-existing value]]> electronDensity(ratom(1)) returns the electron density of the reactant atom matching map 1 in the reaction equation]]>
    double[] Huckel NaN for non-existing values]]>
  • he atom index / MolAtom object
  • the major microspecies pH (takes the input molecule itself if omitted)
  • ]]>
    hmoElectronDensity(2) returns the electron density of atom 2 of the input molecule, NaN for non-existing value]]> hmoElectronDensity(ratom(1)) returns the electron density of the reactant atom matching map 1 in the reaction equation]]>
    totalChargeDensity double[] Huckel NaN for non-existing values]]>
  • he atom index / MolAtom object
  • the major microspecies pH (takes the input molecule itself if omitted)
  • ]]>
    chargeDensity(2) returns the charge density of atom 2 of the input molecule, NaN for non-existing value]]> chargeDensity(ratom(1)) returns the charge density of the reactant atom matching map 1 in the reaction equation]]>
    double[] Huckel NaN for non-existing values]]>
  • he atom index / MolAtom object
  • the major microspecies pH (takes the input molecule itself if omitted)
  • ]]>
    hmoChargeDensity(2) returns the charge density of atom 2 of the input molecule, NaN for non-existing value]]> hmoChargeDensity(ratom(1)) returns the charge density of the reactant atom matching map 1 in the reaction equation]]>
    PSA double Geometry
  • the major microspecies pH (takes the input molecule itself if omitted)
  • ]]>
    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]]> 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]]>
    double Geometry
  • the major microspecies pH (takes the input molecule itself if omitted)
  • ]]>
    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]]> 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]]>
    ASA solventAccessibleSurfaceArea double Geometry
  • the major microspecies pH (takes the input molecule itself if omitted)
  • ]]>
    waterAccessibleSurfaceArea() returns the solvent accessible / water accessible surface area of the input molecule solventAccessibleSurfaceArea('7.4')returns the solvent accessible / water accessible surface area of the major microspecies taken at pH 7.4]]> 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]]>
    double Geometry
  • the major microspecies pH (takes the input molecule itself if omitted)
  • ]]>
    ASAPlus() returns the water accessible surface area of all atoms of the input molecule with positive partial charge ASAPlus('7.4')returns the water accessible surface area of all atoms with positive partial charge of the major microspecies taken at pH 7.4]]> ASAPlus(reactant(0)) returns the water accessible surface area of all atoms of the first reactant with positive partial charge ASAPlus(product(0), '7.4') returns the water accessible surface area of all atoms with positive partial charge of the major microspecies of the first product taken at pH 7.4]]>
    double Geometry
  • the major microspecies pH (takes the input molecule itself if omitted)
  • ]]>
    ASANegative() returns the water accessible surface area of all atoms of the input molecule with negative partial charge ASANegative('7.4')returns the water accessible surface area of all atoms with negative partial charge of the major microspecies taken at pH 7.4]]> ASANegative(reactant(0)) returns the water accessible surface area of all atoms of the first reactant with negative partial charge ASANegative(product(0), '7.4') returns the water accessible surface area of all atoms with negative partial charge of the major microspecies of the first product taken at pH 7.4]]>
    double Geometry
  • the major microspecies pH (takes the input molecule itself if omitted)
  • ]]>
    ASAHydrophobic() returns the water accessible surface area of all atoms of the input molecule with hydrophobic partial charge ASAHydrophobic('7.4')returns the water accessible surface area of all atoms with hydrophobic partial charge of the major microspecies taken at pH 7.4]]> ASAHydrophobic(reactant(0)) returns the water accessible surface area of all atoms of the first reactant with hydrophobic partial charge ASAHydrophobic(product(0), '7.4') returns the water accessible surface area of all atoms with hydrophobic partial charge of the major microspecies of the first product taken at pH 7.4]]>
    double Geometry
  • the major microspecies pH (takes the input molecule itself if omitted)
  • ]]>
    ASAPolar() returns the water accessible surface area of all atoms of the input molecule with polar partial charge ASAPolar('7.4')returns the water accessible surface area of all atoms with polar partial charge of the major microspecies taken at pH 7.4]]> 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]]>
    pI double Protonation isoelectricPoint() returns the isoelectric point of the input molecule]]> isoelectricPoint(reactant(1)) returns the isoelectric point of the second reactant]]> double Protonation
  • the major microspecies pH
  • ]]>
    averageMicrospeciesCharge() returns the average charge of the microspecies of the input molecule]]> averageMicrospeciesCharge(reactant(1)) returns the average charge of the microspecies of the second reactant]]>
    double Elemental Analysis mass() returns the mass of the input molecule]]> mass(reactant(0)) returns the mass of the first reactant]]> double Elemental Analysis exactMass() returns the exact mass of the input molecule]]> exactMass(product(1)) returns the exact mass of the second product]]> int Elemental Analysis
  • 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
  • ]]>
    atomCount() returns the number of atoms in the input molecule atomCount("6") returns the number of carbon atoms in the input molecule]]> atomCount(reactant(0), "7") returns the number of nitrogen atoms in the first reactant atomCount(product(1), "7.14") returns the number of nitrogen atoms with mass number 14 in the second product atomCount(product(1), "7.0") returns the number of non-isotope nitrogen atoms in the second product]]>
    String Elemental Analysis formula() returns the formula of the input molecule]]> String Elemental Analysis sortableFormula() returns the sortable formula of the input molecule; sortableFormula('digits:4') returns the 4 digit sortable formula of the input molecule]]> String Elemental Analysis isotopeFormula() returns the isotope formula of the input molecule]]> String Elemental Analysis dotDisconnectedFormula() returns the dot-disconnected formula of the input molecule]]> String Elemental Analysis dotDisconnectedIsotopeFormula() returns the dot-disconnected isotope formula of the input molecule]]> String Elemental Analysis composition() returns the composition of the input molecule]]> String Elemental Analysis isotopeComposition() returns the isotope composition of the input molecule]]> int Geometry aliphaticAtomCount() returns the number of aliphatic atoms in the input molecule]]> 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]]> int Geometry aliphaticBondCount() returns the number of bonds in the input molecule]]> 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]]> int Geometry aliphaticRingCount() returns the number of aliphatic rings in the input molecule]]> 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]]> int Geometry aliphaticRingCountOfSize(6) returns the number of aliphatic rings of size 6 in the input molecule]]> aliphaticRingCountOfSize(reactant(0), 5) returns the number of aliphatic rings of size 5 in the first reactant aliphaticRingCountOfSize(product(1), 5) returns the number of aliphatic rings of size 5 in the second product]]> int[][] Geometry aliphaticRings() returns the atom indexes of the aliphatic rings in the input molecule]]> 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]]> int[][] Geometry aliphaticRings() returns the atom indexes of the aliphatic rings in the input molecule having the given size]]> 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]]> int Geometry aromaticAtomCount() returns the number of aromatic atoms in the input molecule]]> 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]]> int Geometry aromaticBondCount() returns the number of aromatic bonds in the input molecule]]> 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]]> int Geometry aromaticRingCount() returns the number of aromatic rings in the input molecule]]> 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]]> int Geometry aromaticRingCountOfSize(6) returns the number of aromatic rings of size 6 in the input molecule]]> 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]]> int[][] Geometry aromaticRings() returns the atom indexes of the aromatic rings in the input molecule]]> 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]]> int[][] Geometry aromaticRings() returns the atom indexes of the aromatic rings in the input molecule having the given size]]> 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]]> int Geometry carboaliphaticRingCount() returns the number of carboaliphatic rings in the input molecule]]> 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]]> int Geometry carboaromaticRingCount() returns the number of carboaromatic rings in the input molecule]]> 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]]> int Geometry carboRingCount() returns the number of carbocyclic rings in the input molecule]]> 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]]> int Geometry carboRingCountOfSize(6) returns the number of carbocyclic rings of size 6 in the input molecule]]> carboRingCountOfSize(reactant(0), 5) returns the number of carbocyclic rings of size 5 in the first reactant carboRingCountOfSize(product(1), 5) returns the number of carbocyclic rings of size 5 in the second product]]> int[][] Geometry carboRings() returns the atom indexes of the carbocyclic rings in the input molecule]]> 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]]> int[][] Geometry carboRings() returns the atom indexes of the carbocyclic rings in the input molecule having the given size]]> 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]]> int Geometry rotatableBondCount() returns the number of rotatable bonds in the input molecule]]> 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]]> int Geometry fragmentCount() returns the number of fragments in the input molecule]]> fragmentCount(reactant(0)) returns the number of fragments in the first reactant fragmentCount(product(1)) returns the number of fragments in the second product]]> double Geometry fsp3() returns the fsp3 value of the input molecule]]> fsp3(reactant(0)) returns the fsp3 value of the first reactant fsp3(product(1)) returns the fsp3 value of the second product]]> int Geometry (SSSR smallest set of smallest aliphatic rings)]]> fusedAliphaticRingCount() returns the number of fused aliphatic rings in the input molecule]]> fusedAliphaticRingCount(reactant(0)) returns the number of fused aliphatic rings in the first reactant fusedAliphaticRingCount(product(1)) returns the number of fused aliphatic rings in the second product]]> int Geometry fusedAliphaticRingCountOfSize(6) returns the number of fused aliphatic rings of size 6 in the input molecule]]> fusedAliphaticRingCountOfSize(reactant(0), 5) returns the number of fused aliphatic rings of size 5 in the first reactant fusedAliphaticRingCountOfSize(product(1), 5) returns the number of fused aliphatic rings of size 5 in the second product]]> int[][] Geometry fusedAliphaticRings() returns the atom indexes of the fused aliphatic rings in the input molecule]]> 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]]> int[][] Geometry fusedAliphaticRings() returns the atom indexes of the fused aliphatic rings in the input molecule having the given size]]> 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]]> int Geometry (SSSR smallest set of smallest aromatic rings)]]> fusedAromaticRingCount() returns the number of fused aromatic rings in the input molecule]]> fusedAromaticRingCount(reactant(0)) returns the number of fused aromatic rings in the first reactant fusedAromaticRingCount(product(1)) returns the number of fused aromatic rings in the second product]]> int Geometry fusedAromaticRingCountOfSize(6) returns the number of fused aromatic rings of size 6 in the input molecule]]> fusedAromaticRingCountOfSize(reactant(0), 5) returns the number of fused aromatic rings of size 5 in the first reactant fusedAromaticRingCountOfSize(product(1), 5) returns the number of fused aromatic rings of size 5 in the second product]]> int[][] Geometry fusedAromaticRings() returns the atom indexes of the fused aromatic rings in the input molecule]]> 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]]> int[][] Geometry fusedAromaticRings() returns the atom indexes of the fused aromatic rings in the input molecule having the given size]]> 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]]> int Geometry (SSSR smallest set of smallest aliphatic rings)]]> heteroaliphaticRingCount() returns the number of aliphatic heterocyclic rings in the input molecule]]> heteroaliphaticRingCount(reactant(0)) returns the number of aliphatic heterocyclic rings in the first reactant heteroaliphaticRingCount(product(1)) returns the number of aliphatic heterocyclic rings in the second product]]> int Geometry heteroaliphaticRingCountOfSize(6) returns the number of aliphatic heterocyclic rings of size 6 in the input molecule]]> 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]]> int[][] Geometry heteroaliphaticRings() returns the atom indexes of the aliphatic heterocyclic rings in the input molecule]]> 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]]> int[][] Geometry heteroaliphaticRings() returns the atom indexes of the aliphatic heterocyclic rings in the input molecule having the given size]]> 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]]> int Geometry (SSSR smallest set of smallest aromatic rings)]]> heteroaromaticRingCount() returns the number of aromatic heterocyclic rings in the input molecule]]> heteroaromaticRingCount(reactant(0)) returns the number of aromatic heterocyclic rings in the first reactant heteroaromaticRingCount(product(1)) returns the number of aromatic heterocyclic rings in the second product]]> int Geometry heteroaromaticRingCountOfSize(6) returns the number of aromatic heterocyclic rings of size 6 in the input molecule]]> 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]]> int[][] Geometry heteroaromaticRings() returns the atom indexes of the aromatic heterocyclic rings in the input molecule]]> 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]]> int[][] Geometry heteroaromaticRings() returns the atom indexes of the aromatic heterocyclic rings in the input molecule having the given size]]> 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]]> int Geometry (SSSR smallest set of smallest rings)]]> heteroRingCount() returns the number of heterocyclic rings in the input molecule]]> 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]]> int Geometry heteroRingCountOfSize(6) returns the number of heterocyclic rings of size 6 in the input molecule]]> heteroRingCountOfSize(reactant(0), 5) returns the number of heterocyclic rings of size 5 in the first reactant heteroRingCountOfSize(product(1), 5) returns the number of heterocyclic rings of size 5 in the second product]]> int[][] Geometry heteroRings() returns the atom indexes of the heterocyclic rings in the input molecule]]> 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]]> int[][] Geometry heteroRings() returns the atom indexes of the heterocyclic rings in the input molecule having the given size]]> 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]]> int[] Geometry largestRingSize() returns the atom indexes of the largest ring in the input molecule]]> largestRingSize(product(1)) returns the atom indexes of the largest ring in the second product]]> int Geometry largestRingSize() returns the size of the largest ring in the input molecule]]> largestRingSize(product(1)) returns the size of the largest ring in the second product]]> int[][] Geometry largestRingSize() returns the atom indexes of the largest ring system in the input molecule]]> largestRingSize(product(1)) returns the atom indexes of the largest ring system in the second product]]> int Geometry largestRingSystemSize() returns the size of the largest ring system in the input molecule]]> largestRingSystemSize(reactant(0)) returns the size of the largest ring system in the first reactant largestringsystemsize(product(1)) returns the size of the largest ring system in the second product]]> int Geometry ringAtomCount() returns the number of ring atoms in the input molecule]]> 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]]> ringAtomCount() returns the number of ring atoms in the input molecule]]> 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]]> int Geometry ringBondCount() returns the number of ring bonds in the input molecule]]> 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]]> int Geometry ringCount() returns the number of rings in the input molecule]]> ringCount(reactant(0)) returns the number of rings in the first reactant ringCount(product(1)) returns the number of rings in the second product]]> int Geometry ringCountOfSize(6) returns the number of rings of size 6 in the input molecule]]> ringCountOfSize(reactant(0), 5) returns the number of rings of size 5 in the first reactant ringCountOfSize(product(1), 5) returns the number of rings of size 5 in the second product]]> int[][] Geometry rings() returns the atom indexes of the rings in the input molecule]]> 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]]> int[][] Geometry rings() returns the atom indexes of the rings in the input molecule having the given size]]> 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]]> int[][] Geometry ringSystems() returns the atom indexes of the ring systems in the input molecule]]> 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]]> int[][] Geometry ringSystems() returns the atom indexes of the ring systems in the input molecule having the given size]]> 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]]> int[] Geometry smallestRingSize() returns the atom indexes of the smallest ring in the input molecule]]> smallestRingSize(product(1)) returns the atom indexes of the smallest ring in the second product]]> int Geometry smallestRingSize() returns the size of the smallest ring in the input molecule]]> smallestRingSize(reactant(0)) returns the size of the smallest ring in the first reactant]]> int[][] Geometry smallestRingSize() returns the atom indexes of the smallest ring system in the input molecule]]> smallestRingSize(product(1)) returns the atom indexes of the smallest ring system in the second product]]> int Geometry smallestRingSystemSize() returns the size of the smallest ring system in the input molecule]]> smallestRingSystemSize(reactant(0)) returns the size of the smallest ring system in the first reactant smallestringsystemsize(product(1)) returns the size of the smallest ring system in the second product]]> int Geometry chainAtomCount() returns the number of chain atoms in the input molecule]]> 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]]> int Geometry chainBondCount() returns the number of chain bonds in the input molecule]]> 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]]> int Geometry (SSSR smallest set of smallest rings)]]> fusedRingCount() returns the number of fused rings in the input molecule]]> 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]]> int Geometry ringSystemCount() returns the number of ring systems in the input molecule]]> 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]]> int Geometry ringSystemCountOfSize(4) returns the number of four-membered ring systems in the input molecule]]> 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]]> int Geometry asymmetricAtomCount() returns the number of asymmetric atoms in the input molecule]]> 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]]> int[] Geometry asymmetricAtoms() returns the indexes of asymmetric atoms in the input molecule]]> 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]]> int Geometry chiralCenterCount() returns the number of tetrahedral stereogenic centers in the input molecule]]> 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]]> int[] Geometry chiralCenters() returns the indexes of chiral center atoms in the input molecule]]> 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]]> int Geometry stereoDoubleBondCount() returns the number of stereo double bonds in the input molecule]]> 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]]> boolean Geometry true for aromatic atoms,
    false for non-aromatic atoms]]>
  • the atom index / MolAtom object
  • ]]>
    aromaticAtom(2) returns true if atom 2 of the input molecule is aromatic, false otherwise]]> aromaticAtom(ratom(2)) returns true if the reactant atom matching map 2 in the reaction equation is aromatic, false otherwise aromaticAtom(patom(1)) returns true if the product atom matching map 1 in the reaction equation is aromatic, false otherwise]]>
    boolean Geometry true for aliphatic atoms,
    false for non-aliphatic atoms]]>
  • the atom index / MolAtom object
  • ]]>
    aliphaticAtom(2) returns true if atom 2 of the input molecule is aliphatic, false otherwise]]> aliphaticAtom(ratom(2)) returns true if the reactant atom matching map 2 in the reaction equation is aliphatic, false otherwise aliphaticAtom(patom(1)) returns true if the product atom matching map 1 in the reaction equation is aliphatic, false otherwise]]>
    boolean Geometry true for chain atoms,
    false for non-chain atoms]]>
  • the atom index / MolAtom object
  • ]]>
    chainAtom(2) returns true if atom 2 of the input molecule is a chain atom, false otherwise]]> chainAtom(ratom(2)) returns true if the reactant atom matching map 2 in the reaction equation is a chain atom, false otherwise chainAtom(patom(1)) returns true if the product atom matching map 1 in the reaction equation is a chain atom, false otherwise]]>
    boolean Geometry true for ring atoms,
    false for non-ring atoms]]>
  • the atom index / MolAtom object
  • ]]>
    ringAtom(2) returns true if atom 2 of the input molecule is a ring atom, false otherwise]]> ringAtom(ratom(2)) returns true if the reactant atom matching map 2 in the reaction equation is a ring atom, false otherwise ringAtom(patom(1)) returns true if the product atom matching map 1 in the reaction equation is a ring atom, false otherwise]]>
    boolean Geometry true for asymmetric atoms,
    false for symmetric atoms]]>
  • the atom index / MolAtom object
  • ]]>
    asymmetricAtom(2) returns true if atom 2 of the input molecule is an asymmetric atom, false otherwise]]> asymmetricAtom(ratom(2)) returns true if the reactant atom matching map 2 in the reaction equation is an asymmetric atom, false otherwise asymmetricAtom(patom(1)) returns true if the product atom matching map 1 in the reaction equation is an asymmetric atom, false otherwise]]>
    boolean Geometry true for tetrahedral stereogenic center atoms]]>
  • the atom index / MolAtom object
  • ]]>
    chiralCenter(2) returns true if atom 2 of the input molecule is a tetrahedral stereogenic center, false otherwise]]> chiralCenter(ratom(2)) returns true if the reactant atom matching map 2 in the reaction equation is a tetrahedral stereogenic center, false otherwise chiralCenter(patom(1)) returns true if the product atom matching map 1 in the reaction equation is a tetrahedral stereogenic center, false otherwise]]>
    int Geometry cyclomaticNumber() returns the cyclomatic number of the input molecule]]> cyclomaticNumber(reactant(0)) returns the cyclomatic number of the first reactant cyclomaticNumber(product(1)) returns the cyclomatic number of the second product]]> int Geometry plattIndex() returns the Platt index of the input molecule]]> plattIndex(reactant(0)) returns the Platt index of the first reactant plattIndex(product(1)) returns the Platt index of the second product]]> double Geometry randicIndex() returns the Randic index of the input molecule]]> randicIndex(reactant(0)) returns the Randic index of the first reactant randicIndex(product(1)) returns the Randic index of the second product]]> double Geometry balabanIndex() returns the Balaban index of the input molecule]]> balabanIndex(reactant(0)) returns the Balaban index of the first reactant balabanIndex(product(1)) returns the Balaban index of the second product]]> double[] Geometry
  • the atom index / MolAtom object
  • ]]>
    distanceDegree(2) returns the distance degree of atom 2 of the input molecule]]> distanceDegree(ratom(2)) returns the distance degree of the reactant atom matching map 2 in the reaction equation distanceDegree(patom(1)) returns the distance degree of the product atom matching map 1 in the reaction equation]]>
    int[] Geometry
  • the atom index / MolAtom object
  • ]]>
    eccentricity(2) returns the eccentricity of atom 2 of the input molecule]]> 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]]>
    double Geometry hararyIndex() returns the Harary index of the input molecule]]> hararyIndex(reactant(0)) returns the Harary index of the first reactant hararyIndex(product(1)) returns the Harary index of the second product]]> int Geometry hyperWienerIndex() returns the Hyper Wiener index of the input molecule]]> hyperWienerIndex(reactant(0)) returns the Hyper Wiener index of the first reactant hyperWienerIndex(product(1)) returns the Hyper Wiener index of the second product]]> int Geometry szegedIndex() returns the Szeged index of the input molecule]]> szegedIndex(reactant(0)) returns the Szeged index of the first reactant szegedIndex(product(1)) returns the Szeged index of the second product]]> int Geometry wienerIndex() returns the Wiener index of the input molecule]]> wienerIndex(reactant(0)) returns the Wiener index of the first reactant wienerIndex(product(1)) returns the Wiener index of the second product]]> int Geometry wienerPolarity() returns the Wiener polarity of the input molecule]]> wienerPolarity(reactant(0)) returns the Wiener polarity of the first reactant wienerPolarity(product(1)) returns the Wiener polarity of the second product]]> double/double[] Geometry
  • the atom index / MolAtom object
  • ]]>
    stericEffectIndex(2) returns the steric effect index of atom 2 of the input molecule]]> stericEffectIndex(ratom(2)) returns the steric effect index of the reactant atom matching map 2 in the reaction equation stericEffectIndex(patom(1)) returns the steric effect index of the product atom matching map 1 in the reaction equation]]>
    int Geometry
  • the atom index / MolAtom object
  • ]]>
    smallestAtomRingSize(0) returns the size of the smallest ring containing atom 0 in the input molecule]]> smallestAtomRingSize(ratom(1)) returns the size of the smallest ring containing reactant atom matching map 1 in the reaction equation]]>
    int Geometry
  • the atom index / MolAtom object
  • ]]>
    largestAtomRingSize(1) returns the size of the largest ring containing atom 1 in the input molecule]]> largestAtomRingSize(patom(2)) returns the size of the largest ring containing product atom matching map 2 in the reaction equation]]>
    int Geometry Integer.MAX_VALUE if disconnected]]>
  • the (1-based) atom indexes of the two atoms in a string: "index1-index2" (e.g. '2-3')
  • ]]>
    shortestPath('2-3') and shortestPath(pair(1, 2)) both return the shortest path length between atoms 1 and 2 in the input molecule]]> shortestPath(reactant(0), pair(ratom(1), ratom(2))) returns the length of the shortest path 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)]]>
    boolean Geometry 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')
  • ]]>
    connected('2-3') and connected(pair(1, 2)) both return true if atoms 1 and 2 are in the same connected component of the input molecule]]> connected(reactant(0), pair(ratom(1), ratom(2))) returns true if reactant atoms matching maps 1 and 2 in the reaction equation are connected in the corresponding reactant molecule (see note 1) connected(product(1), pair(patom(2), patom(3))) returns true if product atoms matching maps 2 and 3 in the reaction equation are connected in the corresponding product molecule (see note 1)]]>
    boolean Geometry true if the molecule graph is connected, false otherwise]]> connectedGraph() returns true if the input molecule graph is connected]]> connectedGraph(reactant(0)) returns true if the first reactant is connected connectedGraph(product(1)) returns true if the second product is connected]]> int Geometry -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')
  • ]]>
    bondType('2-3') and bondType(bond(1, 2)) both return the bond type between atoms 1 and 2 in the input molecule]]> bondType(reactant(0), bond(ratom(1), ratom(2))) returns the bond type between reactant atoms matching maps 1 and 2 in the reaction equation (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)]]>
    boolean Geometry 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')
  • ]]>
    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]]> 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)]]>
    boolean Geometry 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')
  • ]]>
    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]]> 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)]]>
    boolean Geometry 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')
  • ]]>
    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]]> 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)]]>
    int Geometry
  • the atom index / MolAtom object
  • ]]>
    ringCountOfAtom(2) returns the number of rings passsing through atom 2 of the input molecule]]> ringCountOfAtom(ratom(2)) returns the number of rings 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]]>
    acc int HBDA
  • the atom index / MolAtom object
  • the major microspecies pH (takes the input molecule itself if omitted)
  • ]]>
    acceptor(2) returns the hydrogen bond acceptor multiplicity on atom 2 of the input molecule]]> acceptor(ratom(2)) returns the hydrogen bond acceptor multiplicity on the reactant atom matching map 2 in the reaction equation]]>
    don int HBDA
  • the atom index / MolAtom object
  • the major microspecies pH (takes the input molecule itself if omitted)
  • ]]>
    donor(1, "7.4") returns the hydrogen bond donor multiplicity on atom 1 of the major microspecies at pH 7.4]]> 3 in the reaction equation, taking the major microspecies of the corresponding product at pH 7.4]]>
    accSiteCount int HBDA
  • the major microspecies pH (takes the input molecule itself if omitted)
  • ]]>
    acceptorSiteCount() returns the hydrogen bond acceptor multiplicity of the input molecule]]> acceptorSiteCount(reactant(0)) returns the hydrogen bond acceptor multiplicity of the first reactant]]>
    donSiteCount int HBDA
  • the major microspecies pH (takes the input molecule itself if omitted)
  • ]]>
    donorSiteCount("7.4") returns the hydrogen bond donor multiplicity of the major microspecies at pH 7.4]]> donorSiteCount(product(1), "7.4") returns the hydrogen bond donor multiplicity of the major microspecies of the first product taken at pH 7.4]]>
    int HBDA
  • the major microspecies pH (takes the input molecule itself if omitted)
  • ]]>
    acceptorCount() returns the number of hydrogen bond acceptor atoms in the input molecule]]> acceptorCount(reactant(0)) returns the number of hydrogen bond acceptor atoms in the first reactant]]>
    int HBDA
  • the major microspecies pH (takes the input molecule itself if omitted)
  • ]]>
    donorCount("7.4") returns the number of hydrogen bond donor atoms in the major microspecies at pH 7.4]]> donorCount(product(1), "7.4") returns the number of hydrogen bond donor atoms in the major microspecies of the first product taken at pH 7.4]]>
    refrac double Refractivity refractivity() returns the molar refractivity of the input molecule]]> refractivity(reactant(1)) returns the molar refractivity of the second reactant]]> refraci double/double[] Refractivity
  • the atom index / MolAtom object
  • ]]>
    refractivityIncrements(2) returns the refractivity increment on atom 2 of the input molecule]]> refractivityIncrements(ratom(1)) returns the refractivity increment on the reactant atom matching map 1 in the reaction equation]]>
    Molecule Conformation
  • the conformer index (0-based)
  • ]]>
    conformer(0) returns the first conformer of the input molecule]]> conformer(reactant(0), 1) returns the second conformer of the first reactant]]>
    Molecule[] Conformation conformers() returns conformers of the input molecule in an array]]> conformers(reactant(0)) returns conformers of the first reactant in an array]]> int Conformation conformerCount() returns the number of calculated conformers of the input molecule]]> conformerCount(reactant(0)) returns the number of calculated conformers of the first reactant]]> leconformer Molecule Conformation lowestEnergyConformer() returns the lowest energy conformer of the input molecule]]> lowestEnergyConformer(reactant(0)) returns the lowest energy conformer of the first reactant lowestEnergyConformer(product(1)) returns the lowest energy conformer of the second product]]> Molecule Conformation mmff94OptimizedStructure() returns the MMFF94 optimized lowest energy conformer of the input molecule]]> mmff94OptimizedStructure(reactant(0)) returns the MMFF94 optimized lowest energy conformer of the first reactant mmff94OptimizedStructure(product(1)) returns the MMFF94 optimized lowest energy conformer of the second product]]> boolean Conformation hasValidConformer() returns true if the input molecule exists in 3D space (has a valid conformer)]]> 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]]> Molecule Isomers
  • the stereoisomer index (0-based)
  • ]]>
    stereoisomer(0) returns the first stereoisomer of the input molecule]]> stereoisomer(reactant(0), 1) returns the second stereoisomer of the first reactant]]>
    Molecule[] Isomers stereoisomers() returns stereoisomers of the input molecule in an array ]]> stereoisomers(reactant(0)) returns stereoisomers of the first reactant in an array]]> int Isomers stereoisomerCount() returns the number of generated stereoisomers of the input molecule]]> stereoisomerCount(reactant(0)) returns the number of calculated stereoisomers of the first reactant]]> Molecule Isomers
  • the double bond stereoisomer index (0-based)
  • ]]>
    doubleBondStereoisomer(0) returns the first double bond stereoisomer of the input molecule]]> doubleBondStereoisomer(reactant(0), 1) returns the second double bond stereoisomer of the first reactant]]>
    Molecule[] Isomers doubleBondStereoisomers() returns double bond stereoisomers of the input molecule in an array]]> doubleBondStereoisomers(reactant(0)) returns double bond stereoisomers of the first reactant in an array]]> int Isomers doubleBondStereoisomerCount() returns the number of generated double bond stereoisomers of the input molecule]]> doubleBondStereoisomerCount(reactant(0)) returns the number of calculated double bond stereoisomers of the first reactant]]> Molecule Isomers tetrahedralStereoisomer(0) returns the first tetrahedral stereoisomer of the input molecule]]> tetrahedralStereoisomer(reactant(0), 1) returns the second tetrahedral stereoisomer of the first reactant]]> Molecule[] Isomers tetrahedralStereoisomers() returns tetrahedral stereoisomers of the input molecule in an array]]> tetrahedralStereoisomers(reactant(0)) returns tetrahedral stereoisomers of the first reactant in an array]]> int Isomers tetrahedralStereoisomerCount() returns the number of generated tetrahedral stereoisomers of the input molecule]]> tetrahedralStereoisomerCount(reactant(0)) returns the number of calculated tetrahedral stereoisomers of the first reactant]]> double Geometry dreidingEnergy() returns the dreiding energy of the input molecule (conformer)]]> dreidingEnergy(reactant(0)) returns the dreiding energy of the first reactant dreidingEnergy(product(1)) returns the dreiding energy of the second product]]> double Geometry mmff94Energy() returns the MMFF94 energy of the input molecule (conformer)]]> mmff94Energy(reactant(0)) returns the MMFF94 energy of the first reactant mmff94Energy(product(1)) returns the MMFF94 energy of the second product]]> double Geometry minimalProjectionArea() returns the minimal projection area]]> minimalProjectionArea((reactant(0)) returns the minimal projection area of the first reactant minimalProjectionArea(product(1)) returns the minimal projection area of the second product]]> double Geometry maximalProjectionArea() returns the maximal projection area]]> maximalProjectionArea((reactant(0)) returns the maximal projection area of the first reactant maximalProjectionArea(product(1)) returns the maximal projection area of the second product]]> double Geometry minimalProjectionRadius() returns the minimal projection radius]]> minimalProjectionRadius((reactant(0)) returns the minimal projection radius of the first reactant minimalProjectionRadius(product(1)) returns the minimal projection radius of the second product]]> double Geometry maximalProjectionRadius() returns the maximal projection radius]]> maximalProjectionRadius((reactant(0)) returns the maximal projection radius of the first reactant maximalProjectionRadius(product(1)) returns the maximal projection radius of the second product]]> double Geometry
  • the (1-based) atom indexes of the two atoms in a string: "index1-index2" (e.g. '2-3')
  • ]]>
    distance('1-2') and distance(pair(0, 1)) both return the distance between atoms 1 and 2 in the input molecule]]> distance(reactant(0), pair(ratom(1), ratom(2))) returns the distance between reactant atoms matching maps 1 and 2 in the reaction equation (see note 1) distance(product(1), pair(patom(2), patom(3))) returns the distance between product atoms matching maps 2 and 3 in the reaction equation (see note 1)]]>
    double Geometry
  • the (1-based) atom indexes of the three atoms in a string: "index1-index2-index3" (e.g. '2-3-5')
  • ]]>
    angle('1-2-3') and angle(atoms(0, 1, 2)) both return the angle between atoms 1, 2 and 3 in the input molecule]]> angle(reactant(0), atoms(ratom(1), ratom(2), ratom(3))) returns the angle between reactant atoms matching maps 1, 2 and 3 in the reaction equation (see note 1) angle(product(1), atoms(patom(2), patom(3), patom(4))) returns the angle between product atoms matching maps 2, 3 and 4 in the reaction equation (see note 1)]]>
    double Geometry
  • the (1-based) atom indexes of the four atoms in a string: "index1-index2-index3-index4" (e.g. '2-3-7-4')
  • ]]>
    dihedral('1-2-3-4') and dihedral(atoms(0, 1, 2, 3)) both return the dihedral of atoms 1, 2, 3 and 4 in the input molecule]]> dihedral(reactant(0), atoms(ratom(1), ratom(2), ratom(3), ratom(4))) returns the dihedral 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)]]>
    double/double[] Geometry
  • the atom index / MolAtom object
  • ]]>
    stericHindrance(2) returns the steric hindrance of atom 2 of the input molecule]]> 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]]>
    String Name name() returns the preferred IUPAC name of the input molecule]]> String Name traditionalName() returns the traditional name of the input molecule]]> Molecule StructuralFrameworks bmf() returns the Bemis-Murcko framework of the input molecule]]> bmf(reactant(0)) returns the Bemis-Murcko framework of the first reactant]]> bemisMurckoFrameworkLoose Molecule StructuralFrameworks bmfl() returns the loose Bemis-Murcko framework of the input molecule]]> bmfl(reactant(0)) returns the loose Bemis-Murcko framework of the first reactant]]> bemisMurckoFrameworkLoosePruned Molecule StructuralFrameworks bmflp() returns the generalized loose Bemis-Murcko framework of the input molecule]]> bmflp(reactant(0)) returns the generalized loose Bemis-Murcko framework of the first reactant]]>
    boolean Match 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.]]>
    match("[#8]C=O") performs substructure search without atom matching requirement, the target is the input molecule, the query is the carboxylic group given in the string parameter match(6, "[#8][C:1]=O", 1) performs substructure search, checks if target atom 6 matches the carbon (atom with map 1) of the carboxylic group query match(6, "[#8:1]C=[O:2]", 1, 2) performs substructure search, checks if target atom 6 of the input molecule is a carboxylic oxygen]]> 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]]>
    int Match
  • 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.]]>
    matchCount("[#8]C=O") counts search hits without atom matching requirement, the target is the input molecule, the query is the carboxylic group given in the string parameter matchCount(6, "[#8]C=O") counts search hits with target atom 6 matching any atom in a carboxylic group matchCount(6, "[#8:1]C=[O:2]", 1, 2) counts search hits with target atom 6 of the input molecule being a carboxylic oxygen]]> 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]]>
    int Match
  • 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.]]>
    disjointMatchCount("[#8]C=O") counts the maximal number of pairwise disjoint carboxylic groups in the input molecule]]> disjointMatchCount(reactant(0), "[#8]C=O") counts the maximal number of pairwise disjoint carboxylic groups in the first reactant]]>
    int Match
  • 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.]]>
    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.]]> 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.]]>
    double Dissimilarity 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.]]>
    descriptor:metric or 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)]]> 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]]> 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)]]>