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[] 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]]> int atno(0) returns the atomic number of atom 0]]> atno(ratom(1)) returns the atomic number of the reactant atom matching map 1]]> 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]]> atno(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]]> 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 String molFormat("mrv") returns the ChemAxon Marvin Document format representation 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]]> 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]]> boolean true if any atom in the molecule has radical, false otherwise]]> hasRadical() returns true if any atom in the molecule has radical, false othervise]]> 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 othervise]]> hasIsotope(reactant(1)) returns true if any atom in the second reactant is a specific isotope of the element, false otherwise]]> Molecule[] fragments() returns the disconnected fragments of the molecule]]> fragments(reactant(1)) returns the disconnected fragments of the second reactant]]> 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]]>     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]]>     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]]>     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]]>     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 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]]> 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 ]]>     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 data
    randomMarkushEnumerationsDisplay(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)]]>     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 effect
    resonantCharge(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 effect
    resonantCharge(patom(2), "aromaticring", "7.4")
    returns the sum of partial charges in the smallest aromatic ring containing the product atom matching map 2 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)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)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)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 strongness index as string (e.g. '1' for strongest, '2' for second strongest pKa),
  • the result type ("acidic", "basic", or "pka" for both (default))
    • Note, that the atom index and the strongness index are mutually exclusive, in the latter case the result type should 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]]>     apKa double/double[] Protonation Ka values]]> Ka values]]>
  • the atom index / MolAtom object,
  • the strongness index as string (e.g. '1' for strongest, '2' for second strongest pKa),
    • Note, that the atom index and the strongness index are mutually exclusive.]]>     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]]>     bpKa double/double[] Protonation Ka values]]> Ka values]]>
  • the atom index / MolAtom object,
  • the strongness index as string (e.g. '1' for strongest, '2' for second strongest pKa),
    • Note, that the atom index and the strongness index are mutually exclusive.]]>     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]]>     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 strongness index as string (e.g. '1' for strongest, '2' for second strongest pKa),
    • Note, that the atom index and the strongness index are mutually exclusive.]]>     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]]>     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 strongness index as string (e.g. '1' for strongest, '2' for second strongest pKa),
    • Note, that the atom index and the strongness index are mutually exclusive.]]>     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]]>     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]]>     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]]>     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]]>     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]]>     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]]>     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]]>     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]]>     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]]>     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]]>     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]]>     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]]>     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]]>     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]]>     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]]>     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]]>     energyE double[] Huckel NaN for non-aromatic atoms]]>
  • the atom index / MolAtom object
  • the major microspecies pH (takes the input molecule itself if omitted)
    • ]]>     electrophilicLocalizationEnergy(2) returns the electrophilic L(+) localization energy of atom 2 of the input molecule, NaN if atom 2 is non-aromatic]]> electrophilicLocalizationEnergy(ratom(1)) returns the electrophilic L(+) localization energy of the reactant atom matching map 1 in the reaction equation]]>     energyNu double[] Huckel NaN for non-aromatic atoms]]>
  • the atom index / MolAtom object
  • the major microspecies pH (takes the input molecule itself if omitted)
    • ]]>     nucleophilicLocalizationEnergy(2) returns the nucleophilic L(-) localization energy of atom 2 of the input molecule, NaN if atom 2 is non-aromatic]]> nucleophilicLocalizationEnergy(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]]>     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]]> 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]]> 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 reactant
    solventAccessibleSurfaceArea(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 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 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 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]]>     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]]>     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 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 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)
  • the maximum number of conformers to calculate (optional, default: 100) as a string in format: "max-" , where max is an integer followed by a minus sign (e.g. '250-')
    • Note: the number of calculated conformers is smaller or equal then the maximum number of conformers set in the option string.]]>     conformer(0) returns the first conformer of the input molecule 
    conformer(2, "250-")
    returns the third of 250 conformers (or less, if there are no 250 conformers) of the input molecule]]>     conformer(reactant(0), 1) returns the second conformer of the first reactant 
    conformer(product(1), 0, "250-")
    returns the third of 250 conformers (or less, if there are no 250 conformers) of the second product]]>     Molecule[] Conformation
  • the maximum number of conformers to calculate (optional, default: 100) as a string in format: "max-" , where max is an integer followed by a minus sign (e.g. '250-')
    • Note: the number of calculated conformers is smaller or equal then the maximum number of conformers set in the option string.]]>     conformers() returns conformers of the input molecule in an array 
    conformers("250-")
    returns 250 conformers (or less, if there are no 250 conformers) of the input molecule in an array]]>     conformers(reactant(0)) returns conformers of the first reactant in an array 
    conformers(product(1), "250-")
    returns 250 conformers (or less, if there are no 250 conformers) of the the second product]]>     int Conformation
  • the maximum number of conformers to calculate (optional, default: 100) as a string in format: "max-" , where max is an integer followed by a minus sign (e.g. '250-')
    • Note: the returned conformerCount is smaller or equal then the maximum number of conformers set in the option string.]]>     conformerCount() returns the number of calculated conformers of the input molecule 
    conformerCount("250-")
    returns the number of calculated conformers of the input molecule; the maximum number of conformers to calculate is set to 250, so it returns 250 or - if there are no 250 conformers of the input molecule - less then 250]]>     conformerCount(reactant(0)) returns the number of calculated conformers of the first reactant 
    conformerCount(product(1), "250-")
    returns the number of calculated conformers of the the second product; the maximum number of conformers to calculate is set to 250, so it returns 250 or - if there are no 250 conformers of the second product - less then 250]]>     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]]>     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)
  • the maximum number of stereoisomers to generate (optional, default: all) as a string in format: "max-" , where max is an integer followed by a minus sign (e.g. '250-')
    • Note: the number of generated stereoisomers is smaller or equal then the maximum number of stereoisomers set in the option string.]]>     stereoisomer(0) returns the first stereoisomer of the input molecule 
    stereoisomer(2, "250-")
    returns the third of 250 stereoisomers (or less, if there are no 250 stereoisomers) of the input molecule]]>     stereoisomer(reactant(0), 1) returns the second stereoisomer of the first reactant 
    stereoisomer(product(1), 0, "250-")
    returns the third of 250 stereoisomers (or less, if there are no 250 stereoisomers) of the second product]]>     Molecule[] Isomers
  • the maximum number of stereoisomers to generate (optional, default: all) as a string in format: "max-" , where max is an integer followed by a minus sign (e.g. '250-')
    • Note: the number of generated stereoisomers is smaller or equal then the maximum number of stereoisomers set in the option string.]]>     stereoisomers() returns stereoisomers of the input molecule in an array 
    stereoisomers("250-")
    returns 250 stereoisomers (or less, if there are no 250 stereoisomers) of the input molecule in an array]]>     stereoisomers(reactant(0)) returns stereoisomers of the first reactant in an array 
    stereoisomers(product(1), "250-")
    returns 250 stereoisomers (or less, if there are no 250 stereoisomers) of the the second product]]>     int Isomers
  • the maximum number of stereoisomers to generate (optional, default: all) as a string in format: "max-" , where max is an integer followed by a minus sign (e.g. '250-')
    • Note: the returned stereoisomerCount is smaller or equal then the maximum number of stereoisomers set in the option string.]]>     stereoisomerCount() returns the number of generated stereoisomers of the input molecule 
    stereoisomerCount("250-")
    returns the number of geneated stereoisomers of the input molecule; the maximum number of stereoisomers to generate is set to 250, so it returns 250 or - if there are no 250 stereoisomers of the input molecule - less then 250]]>     stereoisomerCount(reactant(0)) returns the number of calculated stereoisomers of the first reactant 
    stereoisomerCount(product(1), "250-")
    returns the number of calculated stereoisomers of the the second product; the maximum number of stereoisomers to generate is set to 250, so it returns 250 or - if there are no 250 stereoisomers of the second product - less then 250]]>     Molecule Isomers
  • the double bond stereoisomer index (0-based)
  • the maximum number of double bond stereoisomers to generate (optional, default: all) as a string in format: "max-" , where max is an integer followed by a minus sign (e.g. '250-')
    • Note: the number of generated double bond stereoisomers is smaller or equal then the maximum number of double bond stereoisomers set in the option string.]]>     doubleBondStereoisomer(0) returns the first double bond stereoisomer of the input molecule 
    doubleBondStereoisomer(2, "250-")
    returns the third of 250 double bond stereoisomers (or less, if there are no 250 double bond stereoisomers) of the input molecule]]>     doubleBondStereoisomer(reactant(0), 1) returns the second double bond stereoisomer of the first reactant 
    doubleBondStereoisomer(product(1), 0, "250-")
    returns the third of 250 double bond stereoisomers (or less, if there are no 250 double bond stereoisomers) of the second product]]>     Molecule[] Isomers
  • the maximum number of double bond stereoisomers to generate (optional, default: all) as a string in format: "max-" , where max is an integer followed by a minus sign (e.g. '250-')
    • Note: the number of generated double bond stereoisomers is smaller or equal then the maximum number of double bond stereoisomers set in the option string.]]>     doubleBondStereoisomers() returns double bond stereoisomers of the input molecule in an array 
    doubleBondStereoisomers("250-")
    returns 250 double bond stereoisomers (or less, if there are no 250 double bond stereoisomers) of the input molecule in an array]]>     doubleBondStereoisomers(reactant(0)) returns double bond stereoisomers of the first reactant in an array 
    doubleBondStereoisomers(product(1), "250-")
    returns 250 double bond stereoisomers (or less, if there are no 250 double bond stereoisomers) of the the second product]]>     int Isomers
  • the maximum number of double bond stereoisomers to generate (optional, default: all) as a string in format: "max-" , where max is an integer followed by a minus sign (e.g. '250-')
    • Note: the returned doubleBondStereoisomerCount is smaller or equal then the maximum number of double bond stereoisomers set in the option string.]]>     doubleBondStereoisomerCount() returns the number of generated double bond stereoisomers of the input molecule 
    doubleBondStereoisomerCount("250-")
    returns the number of geneated double bond stereoisomers of the input molecule; the maximum number of double bond stereoisomers to generate is set to 250, so it returns 250 or - if there are no 250 double bond stereoisomers of the input molecule - less then 250]]>     doubleBondStereoisomerCount(reactant(0)) returns the number of calculated double bond stereoisomers of the first reactant 
    doubleBondStereoisomerCount(product(1), "250-")
    returns the number of calculated double bond stereoisomers of the the second product; the maximum number of double bond stereoisomers to generate is set to 250, so it returns 250 or - if there are no 250 double bond stereoisomers of the second product - less then 250]]>     Molecule Isomers
  • the tetrahedral stereoisomer index (0-based)
  • the maximum number of tetrahedral stereoisomers to generate (optional, default: all) as a string in format: "max-" , where max is an integer followed by a minus sign (e.g. '250-')
    • Note: the number of generated tetrahedral stereoisomers is smaller or equal then the maximum number of tetrahedral stereoisomers set in the option string.]]>     tetrahedralStereoisomer(0) returns the first tetrahedral stereoisomer of the input molecule 
    tetrahedralStereoisomer(2, "250-")
    returns the third of 250 tetrahedral stereoisomers (or less, if there are no 250 tetrahedral stereoisomers) of the input molecule]]>     tetrahedralStereoisomer(reactant(0), 1) returns the second tetrahedral stereoisomer of the first reactant 
    tetrahedralStereoisomer(product(1), 0, "250-")
    returns the third of 250 tetrahedral stereoisomers (or less, if there are no 250 tetrahedral stereoisomers) of the second product]]>     Molecule[] Isomers
  • the maximum number of tetrahedral stereoisomers to generate (optional, default: all) as a string in format: "max-" , where max is an integer followed by a minus sign (e.g. '250-')
    • Note: the number of generated tetrahedral stereoisomers is smaller or equal then the maximum number of tetrahedral stereoisomers set in the option string.]]>     tetrahedralStereoisomers() returns tetrahedral stereoisomers of the input molecule in an array 
    tetrahedralStereoisomers("250-")
    returns 250 tetrahedral stereoisomers (or less, if there are no 250 tetrahedral stereoisomers) of the input molecule in an array]]>     tetrahedralStereoisomers(reactant(0)) returns tetrahedral stereoisomers of the first reactant in an array 
    tetrahedralStereoisomers(product(1), "250-")
    returns 250 tetrahedral stereoisomers (or less, if there are no 250 tetrahedral stereoisomers) of the the second product]]>     int Isomers
  • the maximum number of tetrahedral stereoisomers to generate (optional, default: all) as a string in format: "max-" , where max is an integer followed by a minus sign (e.g. '250-')
    • Note: the returned tetrahedralStereoisomerCount is smaller or equal then the maximum number of tetrahedral stereoisomers set in the option string.]]>     tetrahedralStereoisomerCount() returns the number of generated tetrahedral stereoisomers of the input molecule 
    tetrahedralStereoisomerCount("250-")
    returns the number of geneated tetrahedral stereoisomers of the input molecule; the maximum number of tetrahedral stereoisomers to generate is set to 250, so it returns 250 or - if there are no 250 tetrahedral stereoisomers of the input molecule - less then 250]]>     tetrahedralStereoisomerCount(reactant(0)) returns the number of calculated tetrahedral stereoisomers of the first reactant 
    tetrahedralStereoisomerCount(product(1), "250-")
    returns the number of calculated tetrahedral stereoisomers of the the second product; the maximum number of tetrahedral stereoisomers to generate is set to 250, so it returns 250 or - if there are no 250 tetrahedral stereoisomers of the second product - less then 250]]>     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 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]]>     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.]]> counts the maximal number of pairwise disjoint carboxylic groups in the input molecule]]> counts the maximal number of pairwise disjoint carboxylic groups in the first reactant]]> double Dissimilarity

    Note: Dissimilarity function is available only in JChem.]]> 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)]]>