int/double
abs(7)returns 7
abs(-4.9)returns 4.9]]>
abs(7)returns 7
abs(-4.9)returns 4.9]]>
abs(7)returns 7
abs(-4.9)returns 4.9]]>
int/double
true = 1, false = 0),
or the number itself, if the input is a number]]>
booleanToNumber(1<2)returns 1
booleanToNumber(2+2==5)returns 0
booleanToNumber(5*5)returns 25]]>
booleanToNumber(hasValenceError())returns 0 for molecules having no valence error]]>
booleanToNumber(ringBond(reactant(0), bond(ratom(1), ratom(2))))returns 1 if reactant atoms
matching maps 1 and 2 in the reaction equation are connected by a ring bond in the corresponding reactant, 0 otherwise]]>
int[]
filter("charge() > 0") returns the indices of atoms with positive partial charge in the input
molecule filter(6, 7, 8, 9, "match('[#8][C:1]=O', 1)") returns the carboxylic carbons out of atoms 6,
7, 8, 9 in the input molecule]]>
filter(reactant(0), "charge() > 0") returns the indices of atoms with positive partial charge in
the first reactant filter(patom(1), patom(2), "match('[#8][C:1]=O', 1)") returns the carboxylic carbons out
of product atoms matching map 1 or 2 in the reaction equation (note, that these atoms are
supposed to be in the same product molecule)]]>
int[]
array(2, 5, 6, 8)]]>
array(2, 5, 6, 8)]]>
array(ratom(2), ratom(5), ratom(6), ratom(8)) array(patom(2), patom(5), patom(6), patom(8))]]>
boolean
true if the array contains the specified integer, false otherwise]]>
in(5, array(3, 5, 1)) returns true in(2, array(3, 5, 1)) returns false]]>
in(3, maxatom("charge()", 2)) returns true if the partial charge on atom 3
is within the first 2 largest partial charges in the input molecule in(3, minatom("pol()", 4))
returns true if the polarizability on atom 3 is within the first 4 smallest
polarizability values in the input molecule]]>
in(ratom(3), maxatom(reactant(0), "charge()", 2)) returns true if the partial charge
on reactant atom matching map 3 in the reaction equation is within the first 2 largest
partial charges in the first reactant in(patom(1), minatom(product(1), "pol()", 4)) returns true
if the polarizability on product atom matching map 1 in the reaction equation is within the first 4
smallest polarizability values in the second product]]>
int/double
min(2, 8, 6) returns 2 max(3.4, 5.6, 1.2) returns 5.6]]>
min(charge(0), charge(2)) returns the least of the partial charge values on atoms 0
and 2 max(charge()) returns the maximal partial charge value on the input molecule]]>
min(charge(ratom(2)), charge(ratom(3))) returns the least of the partial charge values on reactant
atoms matching maps 2 and 3 in the reaction equation max(charge(product(0)))
returns the maximal partial charge value on the first product]]>
int/double
min(2, 8, 6) returns 2 max(3.4, 5.6, 1.2) returns 5.6]]>
min(charge(0), charge(2)) returns the least of the partial charge values on atoms 0
and 2 max(charge()) returns the maximal partial charge value on the input molecule]]>
min(charge(ratom(2)), charge(ratom(3))) returns the least of the partial charge values on reactant
atoms matching maps 2 and 3 in the reaction equation max(charge(product(0)))
returns the maximal partial charge value on the first product]]>
int/int[]
minAtom("charge('7.4')") returns the atom index corresponding to minimum partial charge in the
major microspecies at pH 7.4 of the input molecule]]>
minAtom(reactant(0), "charge('7.4')") returns the atom index corresponding to minimum partial
charge in the major microspecies at pH 7.4 of the first reactant]]>
int/int[]
maxAtom(6, 7, 8, 9, "charge('7.4')", 2)
selects the two largest partial charges on atoms 6, 7, 8, 9 in the major microspecies at pH 7.4
of the input molecule and returns the corresponding indices]]>
maxAtom(patom(1), patom(2), patom(3), "charge('7.4')", 2)
selects the two largest partial charges on product atoms matching maps 1, 2, 3 in the major microspecies
at pH 7.4 of the product molecule of these atoms and returns the corresponding indices (note, that these
atoms are supposed to be in the same product molecule)]]>
int/int[]/double/double[]
minValue("charge('7.4')") returns the minimum partial charge in the major microspecies at pH 7.4
of the input molecule]]>
minValue(reactant(0), "charge('7.4')") returns the minimum partial charge in the major
microspecies at pH 7.4 of the first reactant]]>
int/int[]/double/double[]
maxValue(6, 7, 8, 9, "charge('7.4')", 2) returns the two largest partial charges on
atoms 6, 7, 8, 9 in the major microspecies at pH 7.4 of the input molecule]]>
maxValue(patom(1), patom(2), patom(3), "charge('7.4')", 2)
returns the two largest partial charges on product atoms matching maps 1, 2, 3 in the major microspecies
at pH 7.4 of the product molecule of these atoms (note, that these atoms are supposed to be in the same
product molecule)]]>
int[]/double[]
sortAsc(array(3.4, 5.6, 1.2)) returns array(1.2, 3.4, 5.6)]]>
sortAsc(charge()) returns the partial charge values in ascending order]]>
sortAsc(charge(reactant(1))) returns the partial charge values of the second reactant in ascending
order]]>
int[]/double[]
sortDesc(array(3.4, 5.6, 1.2)) returns array(5.6, 3.4, 1.2)]]>
sortDesc(pka("basic")) returns the basic pKa values in descending order]]>
sortDesc(pka(product(0), "basic")) returns the basic pKa values of the first
product in descending order]]>
int
count(array(3.4, 5.6, 1.2)) returns 3]]>
count(filter("charge() > 0")) returns the number of atoms with positive charge count(filter("match('[#8][C:1]=O', 1"))
returns the number of carboxylic carbons]]>
count(filter(reactant(1), "charge() > 0")) returns the number of atoms with positive charge in the
second reactant count(filter(product(0), "match('[#8][C:1]=O', 1")) returns the number of carboxylic
carbons in the first product]]>
int/double
sum(array(3.4, 5.6, 1.2)) returns 10.2]]>
sum(charge()) returns the sum of charge values sum(pol()) returns the sum of atom
polarizability values]]>
sum(charge(reactant(0))) returns the sum of charge values in the first reactant sum(pol(product(0)))
returns the sum of atom polarizability values in the first product]]>
int
hCount(0) returns the hydrogen count of atom 0]]>
hCount(patom(3)) returns the hydrogen count on the product atom matching map 3
in the reaction equation]]>
int
connections(2) returns the number of connections of atom 2]]>
connections(ratom(1)) returns the number of connections of the reactant atom matching map 1 in the
reaction equation]]>
int
valence(0) returns the valence of atom 0]]>
valence(ratom(1)) returns the valence of the reactant atom matching map 1 in the
reaction equation]]>
int
radicalCount(0) returns the radical count of atom 0]]>
radicalCount(patom(3)) returns the radical count on the product atom matching map 3
in the reaction equation]]>
atomicNumber
int
atno(0) returns the atomic number of atom 0]]>
atno(ratom(1)) returns the atomic number of the reactant atom matching map 1]]>
chemaxon.struc.MolAtom
molAtom(6) returns a carbon atom]]>
molAtom(6) returns a carbon atom]]>
int
map(3) returns the atom map number of atom 3]]>
map(patom(3)) returns the atom map number on the product atom matching map 3
in the reaction equation]]>
boolean
true if the atom has an aromatic bond, false otherwise]]>
arom(0) returns if the atom 0 has an aromatic bond]]>
arom(patom(2)) returns true if the product atom matching map 2
in the reaction equation has an aromatic bond]]>
property
field('ACTIVITY') returns the value of the ACTIVITY property (SDF field) field('ACTIVITY') > 2
returns 1 if the ACTIVITY value is bigger than 2, returns 0 otherwise]]>
field(reactant(1), 'ACTIVITY') returns the ACTIVITY property value of the second reactant field(product(0), 'ACTIVITY') > field(reactant(0), 'ACTIVITY')
returns 1 if the ACTIVITY value of the first product is bigger than that of the first reactant, returns 0
otherwise]]>
propertyAsString
String
fieldAsString('ID') returns the value of the ID property (SDF field)]]>
field(reactant(0), 'ID') returns the value of the ID property field in first reactant]]>
String
bond
(used for pairing atoms in shortestPath)]]>
pair(2, 5) returns "3-6"]]>
pair(ratom(1), ratom(2)) returns "index1-index2" where "index1" and "index2" are the 1-based atom
indexes of the reactant atoms matching map 1 and 2 in the reaction equation bond(patom(2), patom(5)
returns "index1-index2" where "index1" and "index2" are the 1-based atom indexes of the product atoms matching map 2
and 5 in the reaction equation]]>
totalCharge
int
formalCharge() returns the formal charge of the input molecule
formalCharge(0) returns the formal charge of atom 0]]>
formalCharge(ratom(1)) returns the formal charge of the reactant atom matching map 1]]>
molFormat
molConvert
String
the molecule format (e.g. "mol", "sdf", "mrv", "smiles")
the clean dimension
]]>
molFormat("mrv") returns the ChemAxon Marvin Document format representation of the input molecule
molFormat(tautomers(), "sdf", 2) returns the SDF format representation of the tautomers of the input molecule]]>
molImage
byte[]
molImage("jpeg:w100,Q95,#ffff00") returns the 100x100 JPEG image of the input molecule with yellow background, 95% quality]]>
Molecule
importMol("c1ccccc1") returns benzene molecule]]>
boolean
true in case of valence error, false otherwise]]>
hasValenceError() returns true if any atom in the molecule has valence error, false otherwise]]>
hasValenceError(reactant(1)) returns true if any atom in the second reactant has valence error,
false otherwise]]>
int
-1 if there is no valence error]]>
-1 if there is no valence error]]>
whereIsValenceError() returns the index of the first atom with valence error, or -1
if there is no valence error in the molecule]]>
whereIsValenceError(reactant(1)) returns the index of the first atom with valence error in the second reactant,
or -1 f there is no valence error in the second reactant]]>
boolean
true if there is an error in the aromatization of the molecule, false otherwise]]>
hasAromatizationError() returns true if there is an error in the aromatization of the molecule,
false otherwise]]>
hasAromatizationError(reactant(0)) returns true if there is an error in the aromatization of the first reactant,
false otherwise]]>
boolean
true if any atom in the molecule has radical, false otherwise]]>
hasRadical() returns true if any atom in the molecule has radical, false otherwise]]>
hasRadical(reactant(1)) returns true if any atom in the second reactant has radical,
false otherwise]]>
boolean
true if any atom in the molecule is a specific isotope of the element, false otherwise]]>
hasIsotope() returns true if any atom in the molecule is a specific isotope of the element, false otherwise]]>
hasIsotope(reactant(1)) returns true if any atom in the second reactant is a specific isotope of the element,
false otherwise]]>
boolean
true if the molecule does not contain any atoms, bonds, or non-empty S-groups, false otherwise]]>
isQuery() returns true if the given molecule does not contain any atoms, bonds, or non-empty S-groups, false otherwise]]>
isQuery(reactant(1)) returns true if the second reactant contains any atoms, bonds, or non-empty S-groups,
false otherwise]]>
boolean
true if the molecule contains any query features, false otherwise]]>
isQuery() returns true if the given molecule contains any query features, false otherwise]]>
isQuery(reactant(1)) returns true if the second reactant contains any query features,
false otherwise]]>
boolean
Markush
true if the molecule contains any Markush features, false otherwise]]>
isMarkush() returns true if the given molecule contains any Markush features, false otherwise]]>
isMarkush(reactant(1)) returns true if the second reactant contains any Markush features,
false otherwise]]>
Molecule[]
fragments() returns the disconnected fragments of the molecule]]>
fragments(reactant(1)) returns the disconnected fragments of the second reactant]]>
String
Elemental Analysis
molecular formula
available functions:
- atomCount
- mass
- massPrecision
- exactMass
- exactMassPrecision
- formula
- isotopeFormula
- dotDisconnectedFormula
- dotDisconnectedIsotopeFormula
]]>
elementalAnalysis('C12H25O', 'mass') returns the mass of molecule represented by formula]]>
int
Geometry
bondCount() returns the number of bonds in the input molecule]]>
bondCount(reactant(0)) returns the number of bonds in the first reactant bondCount(product(1))
returns the number of bonds in the second product]]>
String
Structure Checker
check("aromaticity..valence"), or check('"<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"no\"?><checkers><AromaticityErrorChecker fixMode=\"fix\" fixerClassName=\"chemaxon.fixers.RearomatizeFixer\" type=\"general\"/><ValenceErrorChecker allowTraditionalNitrogen=\"false\" fixMode=\"fix\" fixerClassName=\"chemaxon.fixers.ValenceFixer\"/></checkers>
"') checks for aromaticity and valence errors, and returns the error report]]>
check(reactant(0), "aromaticity..valence") checks for aromaticity and valence errors in first reactant, and returns the error report]]>
http://www.chemaxon.com/marvin/help/structurechecker/checker.html
Integer
Structure Checker
checkErrorCount('"<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"no\"?><checkers><AromaticityErrorChecker fixMode=\"fix\" fixerClassName=\"chemaxon.fixers.RearomatizeFixer\" type=\"general\"/><ValenceErrorChecker allowTraditionalNitrogen=\"false\" fixMode=\"fix\" fixerClassName=\"chemaxon.fixers.ValenceFixer\"/></checkers>
"') or
checkErrorCount("aromaticity..valence") checks for aromaticity and valence errors, and returns the total error count]]>
check(reactant(0), "aromaticity..valence") checks for aromaticity and valence errors in first reactant, and returns the error report]]>
http://www.chemaxon.com/marvin/help/structurechecker/checker.html
boolean
Structure Checker
isValid("aromaticity..valence"), or isValid('"<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"no\"?><checkers><AromaticityErrorChecker fixMode=\"fix\" fixerClassName=\"chemaxon.fixers.RearomatizeFixer\" type=\"general\"/><ValenceErrorChecker allowTraditionalNitrogen=\"false\" fixMode=\"fix\" fixerClassName=\"chemaxon.fixers.ValenceFixer\"/></checkers>
"') checks for aromaticity and valence errors, and returns if the structure is valid]]>
isValid(reactant(0), "aromaticity..valence") checks for aromaticity and valence errors in first reactant, and returns if it is valid]]>
http://www.chemaxon.com/marvin/help/structurechecker/checker.html
Molecule
Structure Checker
fix("chiralflag..isotope->converttoelementalform"), or
fix('"<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"no\"?><checkers><ChiralFlagChecker fixMode=\"fix\" fixerClassName=\"chemaxon.fixers.RemoveChiralFlagFixer\"/><IsotopeChecker fixMode=\"fix\" fixerClassName=\"chemaxon.fixers.ConvertToElementalFormFixer\"/></checkers>"') searches for ciral flags and isotopes, and removes them or converts them to elemental form]]>
fix(product(1), "chiralflag..isotope->converttoelementalform") searches for ciral flags and isotopes in second product, and removes them or converts them to elemental form]]>
http://www.chemaxon.com/marvin/help/structurechecker/checker.html
int
-1 if the the input (molecule) is not a reaction]]>
reactantCount() returns n if the given molecule is a reaction and contains n reactants.
reactantCount() returns -1 if the given molecule is not a reaction.]]>
reactantCount() returns n if the given molecule is a reaction and contains n reactants.
reactantCount(reactant(0)) and reactantCount(product(1)) calls does not make sense, and will return -1.]]>
int
-1 if the the input (molecule) is not a reaction]]>
productCount() returns n if the given molecule is a reaction and contains n products.
productCount() returns -1 if the given molecule is not a reaction.]]>
productCount() returns n if the given molecule is a reaction and contains n products.
productCount(product(0)) and productCount(product(1)) calls does not make sense, and will return -1.]]>
int
-1 if the the input (molecule) is not a reaction]]>
agentCount() returns n if the given molecule is a reaction and contains n agents.
agentCount() returns -1 if the given molecule is not a reaction.]]>
agentCount() returns n if the given molecule is a reaction and contains n agents.
agentCount(reactant(0)) and agentCount(product(1)) calls does not make sense, and will return -1.]]>
majorMs
Molecule
Protonation
the pH value as string
]]>
majorMicrospecies("7.4") returns the major microspecies of the input molecule at pH 7.4]]>
majorMicrospecies(reactant(0), "7.4") returns the major microspecies of the first reactant at pH 7.4
majorMicrospecies(product(1), "7.4") returns the major microspecies of the second product at pH 7.4]]>
http://www.chemaxon.com/marvin/help/calculations/protonation.html#ms
msCount
int
Protonation
microspeciesCount() returns the number of microspecies of the input molecule]]>
microspeciesCount(reactant(0)) returns the number of microspecies of the first reactant microspeciesCount(product(1))
returns the number of microspecies of the second product]]>
http://www.chemaxon.com/marvin/help/calculations/protonation.html#ms
ms
Molecule
Protonation
the pH value as string
the microspecies index by descending order of microspecies distributions
]]>
microspecies("7.4", 1) returns the microspecies of the input molecule with second largest distribution at pH
7.4]]>
microspecies(reactant(0), "7.4", 2) returns the microspecies of the first reactant with third largest
distribution at pH 7.4 microspecies(product(1), "7.4", 1) returns the microspecies of the second product
with second largest distribution at pH 7.4]]>
http://www.chemaxon.com/marvin/help/calculations/protonation.html#ms
msDistr
double
Protonation
the pH value as string
the microspecies index by descending order of microspecies distributions
]]>
microspeciesDistribution("5.4", 0) returns the largest microspecies distribution of the input molecule at pH 5.4]]>
microspeciesDistribution(reactant(0), "5.4", 2) returns the third largest microspecies distribution of the first
reactant at pH 5.4 microspeciesDistribution(product(1), "3.2", 1) returns the second largest microspecies
distribution of the second product at pH 3.2]]>
http://www.chemaxon.com/marvin/help/calculations/protonation.html#ms
Isomers
Molecule
the tautomer index (0-based)
]]>
tautomer(0) returns the first tautomer of the input molecule]]>
tautomer(reactant(0), 1) returns the second tautomer of the first reactant]]>
Molecule
Isomers
canonicalTautomer() returns the canonical tautomer structure of the input molecule]]>
canonicalTautomer(reactant(0)) returns the canonical tautomer structure of the first reactant/td>]]>
Molecule
Isomers
genericTautomer() returns the generic tautomer structure of the input molecule]]>
genericTautomer(reactant(0)) returns the generic tautomer structure of the first reactant/td>]]>
Molecule
Isomers
mostStableTautomer() returns the most stable tautomer structure of the input molecule]]>
mostStableTautomer(reactant(0)) returns the most stable tautomer structure of the first reactant/td>]]>
Molecule
Isomers
the pH value as string (set if pH effect should be considered)
]]>
majorTautomer() returns the major tautomer structure of the input molecule]]>
majorTautomer(reactant(0)) returns the major tautomer structure of the first reactant/td>]]>
Molecule[]
Isomers
tautomers() returns all tautomers of the input molecule in an array]]>
tautomers(reactant(0)) returns all tautomers of the first reactant in an array]]>
int
Isomers
tautomerCount() returns the number of tautomers of the input molecule]]>
tautomerCount(reactant(0)) returns the number of tautomers of the first reactant]]>
tautomer
Molecule
Isomers
]]>
the dominant tautomer index (0-based)
the pH value as string (set if pH effect should be considered)
]]>
dominantTautomer(0) returns the first dominant tautomer of the input molecule dominantTautomer(1, "2.0") returns
the second dominant tautomer of the input molecule, considering pH effect at pH 2.0 ]]>
dominantTautomer(reactant(0), 1) returns the second dominant tautomer of the first reactant dominantTautomer(product(1), 0, "7.4")
returns the first dominant tautomer of the second product, considering pH effect at pH 7.4 ]]>
tautomers
Molecule[]
Isomers
the pH value as string (set if pH effect should be considered)
]]>
dominantTautomers() returns all dominant tautomers of the input molecule in an array dominantTautomers("2.0")
returns all dominant tautomers of the input molecule in an array, considering pH effect at pH 2.0 ]]>
dominantTautomers(reactant(0)) returns all dominant tautomers of the first reactant in an array dominantTautomers(product(1), "7.4")
returns all dominant tautomers of the second product in an array, considering pH effect at pH 7.4 ]]>
int
Isomers
the pH value as string (set if pH effect should be considered)
]]>
dominantTautomerCount() returns the number of dominant tautomers of the input molecule dominantTautomerCount("7.4")
returns the number of dominant tautomers of the input molecule, considering pH effect at pH 7.4]]>
dominantTautomerCount(reactant(0)) returns the number of dominant tautomers of the first reactant dominantTautomerCount(product(1), "2.5")
returns the number of dominant tautomers of the second product, considering pH effect at pH 2.5]]>
Molecule
Isomers
resonant(0) returns the first resonant structure of the input molecule]]>
resonant(reactant(0), 1) returns the second resonant structure of the first reactant]]>
Molecule
Isomers
canonicalResonant() returns the canonical resonant structure of the input molecule]]>
canonicalResonant(reactant(0)) returns the canonical resonant structure of the first reactant]]>
Molecule[]
Isomers
resonants() returns all resonants of the input molecule in an array]]>
resonants(reactant(0)) returns all resonants of the first reactant in an array]]>
int
Isomers
resonantCount() returns the number of resonant structures of the input molecule]]>
resonantCount(reactant(0)) returns the number of resonant structures of the first reactant]]>
randomMarkushEnumeration
randomEnumerations
randomEnumeration
Molecule[]
Markush
the number of structures to be returned (default: 1)
the (1-based) atom indexes of the query atoms to be enumerated (default: all)
]]>
randomMarkushEnumerations()
returns a randomly constructed enumerated structure of the input molecule randomMarkushEnumerations(4, '2,3') returns 4 randomly constructed enumerated structures of the input molecule, enumerating only atoms 2, 3 (1-based) ]]>
randomMarkushEnumerations(reactant(0), 100) returns 100 randomly constructed enumerated structures of the first reactant randomMarkushEnumerations(product(1), '3,4,5')
returns a randomly constructed enumerated structure of the second product, enumerating atoms 3, 4, 5 (1-based)]]>
Markush
the number of structures to be returned (default: 1)
the (1-based) atom indexes of the query atoms to be enumerated (default: all)
]]>
randomMarkushEnumerationsDisplay()
returns a randomly constructed enumerated structure of the input molecule, with scaffold alignment and scaffold/R-group coloring datarandomMarkushEnumerationsDisplay(4, '2,3') returns 4 randomly constructed enumerated structures of the input molecule, enumerating only atoms 2, 3 (1-based), with scaffold alignment and coloring data]]>
randomMarkushEnumerationsDisplay(reactant(0), 100) returns 100 randomly constructed enumerated structures of the first reactant, with scaffold alignment and coloring data randomMarkushEnumerationsDisplay(product(1), '3,4,5')
returns a randomly constructed enumerated structure of the second product, enumerating atoms 3, 4, 5 (1-based), with scaffold alignment and coloring data]]>
markushEnumeration
enumerations
enumeration
Molecule[]
Markush
the number of structures to be returned (default: all)
the (1-based) atom indexes of the query atoms to be enumerated (default: all)
]]>
markushEnumerations() returns all Markush enumerated structures of the input molecule markushEnumerations(1, '2,3')
returns one Markush enumerated structure of the input molecule, enumerating atoms 2, 3 (1-based)]]>
markushEnumerations(reactant(0), 1) returns one Markush enumerated structure of the first reactant markushEnumerations(product(1), 2, '2,3')
returns two Markush enumerated structures of the second product, enumerating atoms 2, 3 (1-based)]]>
Molecule[]
Markush
the number of structures to be returned (default: all)
the (1-based) atom indexes of the query atoms to be enumerated (default: all)
]]>
markushEnumerationsDisplay() returns all Markush enumerated structures of the input molecule, with scaffold alignment and coloring data markushEnumerationsDisplay(1, '2,3')
returns one Markush enumerated structure of the input molecule, enumerating atoms 2, 3 (1-based), with scaffold alignment and coloring data ]]>
markushEnumerationsDisplay(reactant(0), 1) returns one Markush enumerated structure of the first reactant, with scaffold alignment and coloring data with scaffold alignment and coloring data markushEnumerationsDisplay(product(1), 2, '2,3')
returns two Markush enumerated structures of the second product, enumerating atoms 2, 3 (1-based), with scaffold alignment and coloring data ]]>
enumerationCount
Molecule[]
Markush
the (1-based) atom indexes of the query atoms to be enumerated (default: all)
]]>
markushEnumerationCount() returns the number of Markush enumerated structures of the input molecule markushEnumerationCount('4,5')
returns the number of Markush enumerated structures of the input molecule, enumerating only atoms 4, 5 (1-based)]]>
markushEnumerationCount(reactant(0)) returns the number of Markush enumerated structures of the first reactant markushEnumerationCount(product(1), atoms(3,4))
returns the number of Markush enumerated structures of the second product, enumerating only atoms 4, 5 (1-based) (the atoms() function converts 0-based indexes to a '-'-separated 1-based atom index string)]]>
int
Markush
the (1-based) atom indexes of the query atoms to be enumerated (default: all)
]]>
markushLibrarySize() returns the Markush library size for the input molecule markushLibrarySize('4,5')
returns the Markush library size for the input molecule, presuming only atoms 4, 5 (1-based) are enumerated]]>
markushLibrarySize(reactant(0)) returns the Markush library size for the first reactant markushLibrarySize(product(1), atoms(3,4))
returns the Markush library size for the second product, presuming only atoms 4, 5 (1-based) are enumerated (the atoms() function converts 0-based indexes to a '-'-separated 1-based atom index string)]]>
String
Markush
the (1-based) atom indexes of the query atoms to be enumerated (default: all)
]]>
markushLibrarySize() returns the Markush library size as string for the input molecule markushLibrarySize('4,5')
returns the Markush library size as string for the input molecule, presuming only atoms 4, 5 (1-based) are enumerated]]>
markushLibrarySize(reactant(0)) returns the Markush library size as string for the first reactant markushLibrarySize(product(1), atoms(3,4))
returns the Markush library size as string for the second product, presuming only atoms 4, 5 (1-based) are enumerated (the atoms() function converts 0-based indexes to a '-'-separated 1-based atom index string)]]>
int
Markush
the (1-based) atom indexes of the query atoms to be enumerated (default: all)
]]>
markushLibraryMagnitude() returns the Markush library magnitude for the input molecule markushLibraryMagnitude('4,5')
returns the Markush library magnitude for the input molecule, presuming only atoms 4, 5 (1-based) are enumerated]]>
markushLibraryMagnitude(reactant(0)) returns the Markush library magnitude for the first reactant markushLibraryMagnitude(product(1), atoms(3,4))
returns the Markush library magnitude for the second product, presuming only atoms 4, 5 (1-based) are enumerated (the atoms() function converts 0-based indexes to a '-'-separated 1-based atom index string)]]>
double
Charge
for result types "aromaticsystem" / "aromaticring", calculates the sum of partial charges of the atoms in the aromatic
system / smallest aromatic ring containing the atom]]>
the atom index / MolAtom object,
the result type ("total" (default), "pi", "sigma", "aromaticsystem", "aromaticsystemsigma",
"aromaticsystempi", "aromaticring", "aromaticringsigma", "aromaticringpi"),
the major microspecies pH (takes the input molecule itself if omitted)
]]>
charge(0) returns the partial charge on atom 0 of the input molecule charge(2, "pi", "7.4")
returns the partial "pi" charge on atom 2 of the major microspecies taken at pH 7.4]]>
charge(ratom(1), "aromaticsystem") returns the sum of partial pi charges in the aromatic system
containing the reactant atom matching map 1 in the reaction equation charge(patom(2), "aromaticring", "7.4")
returns the sum of partial charges in the smallest aromatic ring containing the product atom matching map 2
in the major microspecies taken at pH 7.4]]>
double
Charge
for result types "aromaticsystem" / "aromaticring", calculates the sum of partial charges of the atoms in the aromatic
system / smallest aromatic ring containing the atom]]>
the atom index / MolAtom object,
the result type ("total" (default), "pi", "sigma", "aromaticsystem", "aromaticsystemsigma",
"aromaticsystempi", "aromaticring", "aromaticringsigma", "aromaticringpi"),
the major microspecies pH (takes the input molecule itself if omitted)
]]>
resonantCharge(0) returns the partial charge on atom 0 of the input molecule considering resonance effectresonantCharge(2, "pi", "7.4")
returns the partial "pi" charge on atom 2 of the major microspecies taken at pH 7.4 considering resonance effect]]>
resonantCharge(ratom(1), "aromaticsystem") returns the sum of partial pi charges in the aromatic system
containing the reactant atom matching map 1 in the reaction equation considering resonance effectresonantCharge(patom(2), "aromaticring", "7.4")
returns the sum of partial charges in the smallest aromatic ring containing the product atom matching map 2
in the major microspecies taken at pH 7.4 considering resonance effect]]>
sOEN
double
Charge
the atom index / MolAtom object,
the major microspecies pH (takes the input molecule itself if omitted)
]]>
sigmaOrbitalElectronegativity(0) returns the sigma orbital electronegativity of atom 0
of the input molecule sigmaOrbitalElectronegativity(2, "7.4") returns the sigma orbital electronegativity
of atom 2 of the major microspecies taken at pH 7.4]]>
sOEN(ratom(1)) returns the sigma orbital electronegativity of reactant atom matching map 1
in the reaction equation sOEN(patom(2), "7.4") returns the sigma orbital electronegativity of the product
atom matching map 2 of the major microspecies taken at pH 7.4]]>
pOEN
double
Charge
the atom index / MolAtom object,
the major microspecies pH (takes the input molecule itself if omitted)
]]>
piOrbitalElectronegativity(0) returns the pi orbital electronegativity of atom 0 of
the input molecule piOrbitalElectronegativity(2, "7.4") returns the pi orbital electronegativity of atom 2
of the major microspecies taken at pH 7.4]]>
pOEN(ratom(1)) returns the pi orbital electronegativity of reactant atom matching map 1
in the reaction equation pOEN(patom(2), "7.4") returns the pi orbital electronegativity of the product atom
matching map 2 of the major microspecies taken at pH 7.4]]>
polarizability
atomPol
pol
double
Charge
the atom index / MolAtom object,
the major microspecies pH (takes the input molecule itself if omitted)
]]>
atomicPolarizability(0) returns the polarizability of atom 0 of the input molecule atomicPolarizability(2, "7.4")
returns the polarizability of atom 2 of the major microspecies taken at pH 7.4]]>
atomicPolarizability(ratom(1)) returns the polarizability of reactant atom matching map 1 in the
reaction equation atomicPolarizability(patom(2), "7.4") returns the polarizability of the product atom matching map 2
of the major microspecies taken at pH 7.4]]>
molPol
double
Charge
the major microspecies pH (takes the input molecule itself if omitted)
]]>
molecularPolarizability() returns the molecular polarizability of the input molecule molecularPolarizability("7.4")
returns the molecular polarizability of the major microspecies taken at pH 7.4]]>
molecularPolarizability(reactant(1)) returns the molecular polarizability of the second reactant in the reaction
equation molecularPolarizability(product(0), "7.4") returns the molecular polarizability of the first product major
microspecies taken at pH 7.4]]>
avgPol
averagePol
double
Charge
the major microspecies pH (takes the input molecule itself if omitted)
]]>
averagePolarizability() returns the average polarizability component of the input molecule averagePolarizability("7.4")
returns the average polarizability component of the major microspecies taken at pH 7.4]]>
averagePolarizability(reactant(1)) returns the average polarizability component of the second reactant in the
reaction equation averagePolarizability(product(0), "7.4") returns the average polarizability component of the first
product major microspecies taken at pH 7.4]]>
double
Charge
the major microspecies pH (takes the input molecule itself if omitted)
]]>
axxPol() returns the principal component a(xx) of polarizability tensor of the input molecule
axxPol("7.4") returns the principal component a(xx) of polarizability tensor of the major microspecies taken
at pH 7.4]]>
axxPol(reactant(1)) returns the principal component a(xx) of polarizability tensor of the second
reactant in the reaction equation axxPol(product(0), "7.4") returns the principal component a(xx) of polarizability
tensor of the first product major microspecies taken at pH 7.4]]>
double
Charge
the major microspecies pH (takes the input molecule itself if omitted)
]]>
ayyPol() returns the principal component a(yy) of polarizability tensor of the input molecule
ayyPol("7.4") returns the principal component a(yy) of polarizability tensor of the major microspecies taken
at pH 7.4]]>
ayyPol(reactant(1)) returns the principal component a(yy) of polarizability tensor of the second
reactant in the reaction equation ayyPol(product(0), "7.4") returns the principal component a(yy) of polarizability
tensor of the first product major microspecies taken at pH 7.4]]>
double
Charge
the major microspecies pH (takes the input molecule itself if omitted)
]]>
azzPol() returns the principal component a(zz) of polarizability tensor of the input molecule
azzPol("7.4") returns the principal component a(zz) of polarizability tensor of the major microspecies taken
at pH 7.4]]>
azzPol(reactant(1)) returns the principal component a(zz) of polarizability tensor of the second
reactant in the reaction equation azzPol(product(0), "7.4") returns the principal component a(zz) of polarizability
tensor of the first product major microspecies taken at pH 7.4]]>
double/double[]
Protonation
Ka values]]>
Ka values]]>
the atom index / MolAtom object,
the strength index as string (e.g., '1' for the strongest, '2' for the second strongest pKa),
the result type ("acidic", "basic", or "pka" for both (default))
Note, that the strength index is specified between quotation marks.
In case of strength index the result type can be specified as "acidic" or "basic".
In case of "pka"result type the returned pKa values are
acidic or basic (mixed!), depending on the acidic or basic character of the given atom. Acidic pKa
is returned for an atom, if acidicpKa() ≤ 14.8-basicpKa(), otherwise basic pKa is returned.
Specifying "acidic" or "basic" result type is required to get the acidic or basic pKa values only
(also acidicpKa or basicpKa functions can be used alternatively).]]>
pKa(0) returns the pKa of atom 0 of the input molecule pKa("acidic", "2")
returns the second strongest acidic pKa value]]>
pKa(ratom(1)) returns the pKa of reactant atom matching map 1 in
the reaction equation pKa(product(0), "basic", "1") returns the strongest basic pKa value
in the first product]]>
http://www.chemaxon.com/marvin/help/calculations/protonation.html#pka
double/double[]
Protonation
Ka values using the correction library]]>
Ka values]]>
the atom index / MolAtom object,
the strength index as string (e.g. '1' for the strongest, '2' for the second strongest pKa),
the result type ("acidic", "basic", or "pka" for both (default))
Note, that the strength index is specified between quotation marks.
In case of strength index the result type can be specified as "acidic" or "basic".
In case of "pka"result type the returned pKa values are
acidic or basic (mixed!), depending on the acidic or basic character of the given atom. Acidic pKa
is returned for an atom, if acidicpKa() ≤ 14.8-basicpKa(), otherwise basic pKa is returned.
Specifying "acidic" or "basic" result type is required to get the acidic or basic pKa values only
(also acidicpKaUseCorrection() or basicpKaUseCorrection() functions can be used alternatively).]]>
pKaUseCorrection(0) returns the pKa of atom 0 of the input molecule
pKaUseCorrection("acidic", "2") returns the second strongest acidic pKa value]]>
pKaUseCorrection(ratom(1)) returns the pKa of reactant atom matching map 1 in
the reaction equation pKaUseCorrection(product(0), "basic", "1") returns the strongest basic pKa value
in the first product]]>
http://www.chemaxon.com/marvin/help/calculations/protonation.html#pka
apKa
double/double[]
Protonation
Ka values]]>
Ka values]]>
the atom index / MolAtom object,
the strength index as string (e.g. '1' for the strongest, '2' for the second strongest pKa),
Note, that the strength index is specified between quotation marks.]]>
acidicpKa(0) returns the acidic pKa of atom 0 of the input molecule acidicpKa("2")
returns the second strongest acidic pKa value]]>
acidicpKa(ratom(1)) returns the acidic pKa of reactant atom matching map 1
in the reaction equation acidicpKa(product(0), "1") returns the strongest basic pKa value in
the first product]]>
http://www.chemaxon.com/marvin/help/calculations/protonation.html#pka
bpKa
double/double[]
Protonation
Ka values]]>
Ka values]]>
the atom index / MolAtom object,
the strength index as string (e.g. '1' for the strongest, '2' for the second strongest pKa),
Note, that the strength index is specified between quotation marks.]]>
basicpKa(0) returns the basic pKa of atom 0 of the input molecule
basicpKa("2") returns the second strongest basic pKa value]]>
basicpKa(ratom(1)) returns the basic pKa of reactant atom matching map 1
in the reaction equation basicpKa(product(0), "1") returns the strongest basic pKa value in
the first product]]>
http://www.chemaxon.com/marvin/help/calculations/protonation.html#pka
double/double[]
Protonation
Ka values using the correction library]]>
Ka values]]>
the atom index / MolAtom object,
the strength index as string (e.g. '1' for the strongest, '2' for the second strongest pKa),
Note, that the strength index is specified between quotation marks.]]>
acidicpKaUseCorrection(0) returns the acidic pKa of atom 0 of the input molecule
"acidicpKaUseCorrection"("2") returns the second strongest acidic pKa value]]>
"acidicpKaUseCorrection"(ratom(1)) returns the acidic pKa of reactant atom matching map 1
in the reaction equation "acidicpKaUseCorrection"(product(0), "1") returns the strongest basic pKa value in
the first product]]>
http://www.chemaxon.com/marvin/help/calculations/protonation.html#pka
double/double[]
Protonation
Ka values using the correction library]]>
Ka values]]>
the atom index / MolAtom object,
the strength index as string (e.g. '1' for the strongest, '2' for the second strongest pKa),
Note, that the strength index is specified between quotation marks.]]>
basicpKaUseCorrection(0) returns the basic pKa of atom 0 of the input molecule
basicpKaUseCorrection("2") returns the second strongest basic pKa value]]>
basicpKaUseCorrection(ratom(1)) returns the basic pKa of reactant atom matching map 1
in the reaction equation basicpKaUseCorrection(product(0), "1") returns the strongest basic pKa value in
the first product]]>
http://www.chemaxon.com/marvin/help/calculations/protonation.html#pka
double/double[]
Protonation
Ka values using large model (this model is optimized for a large number of ionizable atoms)]]>
Ka values]]>
the atom index / MolAtom object,
the strength index as string (e.g. '1' for the strongest, '2' for the second strongest pKa),
Note, that the strength index is specified between quotation marks.]]>
acidicpKaLargeModel(0) returns the acidic pKa of atom 0 of the input molecule
acidicpKaLargeModel("2") returns the second strongest acidic pKa value]]>
acidicpKaLargeModel(ratom(1)) returns the acidic pKa of reactant atom matching map 1
in the reaction equation acidicpKaLargeModel(product(0), "1") returns the strongest basic pKa value in
the first product]]>
http://www.chemaxon.com/marvin/help/calculations/protonation.html#pka
double/double[]
Protonation
Ka values using large model (this model is optimized for a large number of ionizable atoms)]]>
Ka values]]>
the atom index / MolAtom object,
the strength index as string (e.g. '1' for the strongest, '2' for the second strongest pKa),
Note, that the strength index is specified between quotation marks.]]>
basicpKaLargeModel(0) returns the basic pKa of atom 0 of the input molecule
basicpKaLargeModel("2") returns the second strongest basic pKa value]]>
basicpKaLargeModel(ratom(1)) returns the basic pKa of reactant atom matching map 1
in the reaction equation basicpKaLargeModel(product(0), "1") returns the strongest basic pKa value in
the first product]]>
http://www.chemaxon.com/marvin/help/calculations/protonation.html#pka
double
Partitioning
D at specified pH]]>
D value]]>
the pH value
]]>
logD('7.4') returns the logD at pH 7.4 of the input molecule]]>
logD(reactant(1), '7.4') returns the logD at pH 7.4 of the second reactant]]>
http://www.chemaxon.com/marvin/help/calculations/partitioning.html#logd
double
Partitioning
D at specified pH using method "VG"]]>
D value]]>
the pH value
]]>
logDVG('7.4') returns the logD at pH 7.4 of the input molecule]]>
logDVG(reactant(1), '7.4') returns the logD at pH 7.4 of the second reactant]]>
http://www.chemaxon.com/marvin/help/calculations/partitioning.html#logd
double
Partitioning
D at specified pH using method "KLOP"]]>
D value]]>
the pH value
]]>
logDKLOP('7.4') returns the logD at pH 7.4 of the input molecule]]>
logDKLOP(reactant(1), '7.4') returns the logD at pH 7.4 of the second reactant]]>
http://www.chemaxon.com/marvin/help/calculations/partitioning.html#logd
double
Partitioning
D at specified pH using method "PHYS"]]>
D value]]>
the pH value
]]>
logDPHYS('7.4') returns the logD at pH 7.4 of the input molecule]]>
logDPHYS(reactant(1), '7.4') returns the logD at pH 7.4 of the second reactant]]>
http://www.chemaxon.com/marvin/help/calculations/partitioning.html#logd
double
Partitioning
D at specified pH using the user defined method]]>
D value]]>
the pH value
]]>
logDUser('7.4') returns the logD at pH 7.4 of the input molecule]]>
logDUser(reactant(1), '7.4') returns the logD at pH 7.4 of the second reactant]]>
http://www.chemaxon.com/marvin/help/calculations/partitioning.html#logd
double
Partitioning
D at specified pH using weighted method]]>
D value]]>
the pH value
]]>
logDWeighted('7.4') returns the logD at pH 7.4 of the input molecule]]>
logDWeighted(reactant(1), '7.4') returns the logD at pH 7.4 of the second reactant]]>
http://www.chemaxon.com/marvin/help/calculations/partitioning.html#logd
double
Partitioning
P]]>
P value]]>
the result type:
- "logPMicro": the logP of the input molecule itself
- "logPNonionic": the logP of the nonionic species
- "logDpI": logD at pI
- "logPTrue": the most typical from the above (default)
]]>
logP() returns the most typical logP out of the input molecule logP, the logP
of the nonionic species and logD at pI logP('logPMicro') returns the logP of the input
molecule itself]]>
logP(reactant(1), 'logDpI') returns the logD at pI of the second reactant
logP(product(1), 'logPNonionic') returns logP of the nonionic species of the second product]]>
http://www.chemaxon.com/marvin/help/calculations/partitioning.html#logp
double
Partitioning
P using method "VG"]]>
P value]]>
the result type:
- "logPMicro": the logP of the input molecule itself
- "logPNonionic": the logP of the nonionic species
- "logDpI": logD at pI
- "logPTrue": the most typical from the above (default)
]]>
logPVG() returns the most typical logP out of the input molecule logP, the logP
of the nonionic species and logD at pI logPVG('logPMicro') returns the logP of the input
molecule itself]]>
logPVG(reactant(1), 'logDpI') returns the logD at pI of the second reactant
logPVG(product(1), 'logPNonionic') returns logP of the nonionic species of the second product]]>
http://www.chemaxon.com/marvin/help/calculations/partitioning.html#logp
double
Partitioning
P using method "KLOP"]]>
P value]]>
the result type:
- "logPMicro": the logP of the input molecule itself
- "logPNonionic": the logP of the nonionic species
- "logDpI": logD at pI
- "logPTrue": the most typical from the above (default)
]]>
logPKLOP() returns the most typical logP out of the input molecule logP, the logP
of the nonionic species and logD at pI logPKLOP('logPMicro') returns the logP of the input
molecule itself]]>
logPKLOP(reactant(1), 'logDpI') returns the logD at pI of the second reactant
logPKLOP(product(1), 'logPNonionic') returns logP of the nonionic species of the second product]]>
http://www.chemaxon.com/marvin/help/calculations/partitioning.html#logp
double
Partitioning
P using method "PHYS"]]>
P value]]>
the result type:
- "logPMicro": the logP of the input molecule itself
- "logPNonionic": the logP of the nonionic species
- "logDpI": logD at pI
- "logPTrue": the most typical from the above (default)
]]>
logPPHYS() returns the most typical logP out of the input molecule logP, the logP
of the nonionic species and logD at pI logPPHYS('logPMicro') returns the logP of the input
molecule itself]]>
logPPHYS(reactant(1), 'logDpI') returns the logD at pI of the second reactant
logPPHYS(product(1), 'logPNonionic') returns logP of the nonionic species of the second product]]>
http://www.chemaxon.com/marvin/help/calculations/partitioning.html#logp
double
Partitioning
P using the user defined method]]>
P value]]>
the result type:
- "logPMicro": the logP of the input molecule itself
- "logPNonionic": the logP of the nonionic species
- "logDpI": logD at pI
- "logPTrue": the most typical from the above (default)
]]>
logPUser() returns the most typical logP out of the input molecule logP, the logP
of the nonionic species and logD at pI logPUser('logPMicro') returns the logP of the input
molecule itself]]>
logPUser(reactant(1), 'logDpI') returns the logD at pI of the second reactant
logPUser(product(1), 'logPNonionic') returns logP of the nonionic species of the second product]]>
http://www.chemaxon.com/marvin/help/calculations/partitioning.html#logp
double
Partitioning
P using weighted method]]>
P value]]>
the result type:
- "logPMicro": the logP of the input molecule itself
- "logPNonionic": the logP of the nonionic species
- "logDpI": logD at pI
- "logPTrue": the most typical from the above (default)
]]>
logPWeighted() returns the most typical logP out of the input molecule logP, the logP
of the nonionic species and logD at pI logPWeighted('logPMicro') returns the logP of the input
molecule itself]]>
logPWeighted(reactant(1), 'logDpI') returns the logD at pI of the second reactant
logPWeighted(product(1), 'logPNonionic') returns logP of the nonionic species of the second product]]>
http://www.chemaxon.com/marvin/help/calculations/partitioning.html#logp
logPi
double[]
Partitioning
P increment]]>
P increment]]>
the atom index / MolAtom object
]]>
logPincrement(2) returns the logP increment on atom 2 of the input molecule]]>
logPincrement(ratom(1)) returns the logP increment on the reactant atom matching map 1
in the reaction equation]]>
http://www.chemaxon.com/marvin/help/calculations/partitioning.html#logp
double
Solubility
S0 value]]>
logS0() returns the logS0 of the input molecule]]>
logS0(reactant(1)) returns the logS0 of the second reactant]]>
http://www.chemaxon.com/marvin/help/calculations/calculator-plugins.html
double
Solubility
S value]]>
the pH value
]]>
logS('7.4') returns the logS at pH 7.4 of the input molecule]]>
logS(reactant(1), '7.4') returns the logS at pH 7.4 of the second reactant]]>
http://www.chemaxon.com/marvin/help/calculations/calculator-plugins.html
String
Solubility
logSCategory() returns the solubilty category of the input molecule]]>
logSCategory(reactant(1)) returns the solubility category of the second reactant]]>
http://www.chemaxon.com/marvin/help/calculations/calculator-plugins.html
String
Isomers
-
the type of stereo descriptor: atrop, axial, cistrans, tetrahedral
]]>
stereoAnalysis() returns the stereo descriptors of the input molecule
stereoAnalysis('tetrahedral') returns the tetrahedral stereo descriptors of the input molecule]]>
stereoAnalysis(reactant(1)) returns the stereo descriptors of the second reactant
stereoAnalysis(reactant(1), 'tetrahedral') returns the tetrahedral stereo descriptors of the second reactant]]>
http://www.chemaxon.com/marvin/help/calculations/calculator-plugins.html
orderE
aromaticElectrophilicityOrder
int[]
Huckel
(0, 1, 2, ...),
]]>
the atom index / MolAtom object
the major microspecies pH (takes the input molecule itself if omitted)
]]>
electrophilicityOrder(2) returns the E(+) order index of atom 2 of the input molecule, e.g. returns
0 if atom 2 is the most electrophilic atom, 1 if atom 2 is the
second strongest electrophilic atom, etc.,]]>
electrophilicityOrder(ratom(1)) returns the E(+) order index of the reactant atom matching map 1 in
the reaction equation]]>
hmoOrderE
int[]
Huckel
(0, 1, 2, ...),
]]>
the atom index / MolAtom object
the major microspecies pH (takes the input molecule itself if omitted)
]]>
hmoElectrophilicityOrder(2) returns the E(+) order index of atom 2 of the input molecule, e.g. returns
0 if atom 2 is the most electrophilic atom, 1 if atom 2 is the
second strongest electrophilic atom, etc.,]]>
hmoElectrophilicityOrder(ratom(1)) returns the E(+) order index of the reactant atom matching map 1 in
the reaction equation]]>
orderNu
aromaticNucleophilicityOrder
int[]
Huckel
(0, 1, 2, ...),
]]>
the atom index / MolAtom object
the major microspecies pH (takes the input molecule itself if omitted)
]]>
nucleophilicityOrder(2) returns the Nu(-) order index of atom 2 of the input molecule, e.g.
returns 0 if atom 2 is the most nucleophilic atom, 1 if atom 2 is
the second strongest nucleophilic atom, etc., ]]>
nucleophilicityOrder(ratom(1)) returns the Nu(-) order index of the reactant atom matching map 1
in the reaction equation]]>
hmoOrderNu
int[]
Huckel
(0, 1, 2, ...),
]]>
the atom index / MolAtom object
the major microspecies pH (takes the input molecule itself if omitted)
]]>
hmoNucleophilicityOrder(2) returns the Nu(-) order index of atom 2 of the input molecule, e.g.
returns 0 if atom 2 is the most nucleophilic atom, 1 if atom 2 is
the second strongest nucleophilic atom, etc., ]]>
hmoNucleophilicityOrder(ratom(1)) returns the Nu(-) order index of the reactant atom matching map 1
in the reaction equation]]>
electrophilicLocalizationEnergy
energyE
double[]
Huckel
NaN for non-aromatic atoms]]>
the atom index / MolAtom object
the major microspecies pH (takes the input molecule itself if omitted)
]]>
nucleophilicity(2) returns the nucleophilicity of atom 2 of the input
molecule, NaN if atom 2 is non-aromatic]]>
nucleophilicity(ratom(1)) returns the nucleophilicity of the reactant atom matching
map 1 in the reaction equation]]>
double[]
Huckel
NaN for non-aromatic atoms]]>
the atom index / MolAtom object
the major microspecies pH (takes the input molecule itself if omitted)
]]>
hmoElectrophilicLocalizationEnergy(2) returns the electrophilic L(+) localization energy of atom 2 of the input
molecule, NaN if atom 2 is non-aromatic]]>
hmoElectrophilicLocalizationEnergy(ratom(1)) returns the electrophilic L(+) localization energy of the reactant atom matching
map 1 in the reaction equation]]>
nucleophilicLocalizationEnergy
energyNu
double[]
Huckel
NaN for non-aromatic atoms]]>
the atom index / MolAtom object
the major microspecies pH (takes the input molecule itself if omitted)
]]>
electrophilicity(2) returns the electrophilicity of atom 2 of the input
molecule, NaN if atom 2 is non-aromatic]]>
electrophilicity(ratom(1)) returns the electrophilicity of the reactant atom matching
map 1 in the reaction equation]]>
double[]
Huckel
NaN for non-aromatic atoms]]>
the atom index / MolAtom object
the major microspecies pH (takes the input molecule itself if omitted)
]]>
hmoNucleophilicLocalizationEnergy(2) returns the nucleophilic L(-) localization energy of atom 2 of the input
molecule, NaN if atom 2 is non-aromatic]]>
hmoNucleophilicLocalizationEnergy(ratom(1)) returns the nucleophilic L(-) localization energy of the reactant atom matching
map 1 in the reaction equation]]>
double
Huckel
the major microspecies pH (takes the input molecule itself if omitted)
]]>
piEnergy() returns the pi energy of the input molecule]]>
piEnergy(product(1)) returns the pi energy of the second product]]>
double
Huckel
the major microspecies pH (takes the input molecule itself if omitted)
]]>
hmoPiEnergy() returns the pi energy of the input molecule]]>
hmoPiEnergy(product(1)) returns the pi energy of the second product]]>
piChargeDensity
double[]
Huckel
NaN for non-existing values]]>
he atom index / MolAtom object
the major microspecies pH (takes the input molecule itself if omitted)
]]>
electronDensity(2) returns the electron density of atom 2 of the input molecule, NaN
for non-existing value]]>
electronDensity(ratom(1)) returns the electron density of the reactant atom matching map 1
in the reaction equation]]>
double[]
Huckel
NaN for non-existing values]]>
he atom index / MolAtom object
the major microspecies pH (takes the input molecule itself if omitted)
]]>
hmoElectronDensity(2) returns the electron density of atom 2 of the input molecule, NaN
for non-existing value]]>
hmoElectronDensity(ratom(1)) returns the electron density of the reactant atom matching map 1
in the reaction equation]]>
totalChargeDensity
double[]
Huckel
NaN for non-existing values]]>
he atom index / MolAtom object
the major microspecies pH (takes the input molecule itself if omitted)
]]>
chargeDensity(2) returns the charge density of atom 2 of the input molecule, NaN
for non-existing value]]>
chargeDensity(ratom(1)) returns the charge density of the reactant atom matching map 1
in the reaction equation]]>
double[]
Huckel
NaN for non-existing values]]>
he atom index / MolAtom object
the major microspecies pH (takes the input molecule itself if omitted)
]]>
hmoChargeDensity(2) returns the charge density of atom 2 of the input molecule, NaN
for non-existing value]]>
hmoChargeDensity(ratom(1)) returns the charge density of the reactant atom matching map 1
in the reaction equation]]>
PSA
double
Geometry
the major microspecies pH (takes the input molecule itself if omitted)
]]>
topologicalPolarSurfaceArea() returns the polar surface area of the input molecule
topologicalPolarSurfaceArea('7.4') returns the polar surface area of the major microspecies taken at pH 7.4]]>
topologicalPolarSurfaceArea(reactant(0)) returns the polar surface area of the first reactant
topologicalPolarSurfaceArea(product(0), '7.4')
returns the polar surface area of the major microspecies of the first product taken at pH 7.4]]>
double
Geometry
the major microspecies pH (takes the input molecule itself if omitted)
]]>
vanDerWaalsSurfaceArea() returns the van der Waals surface area of the input molecule
vanDerWaalsSurfaceArea('7.4') returns the van der Waals accessible surface area of the major microspecies taken at
pH 7.4]]>
vanDerWaalsSurfaceArea(reactant(0)) returns the van der Waals surface area of the first reactant
vanDerWaalsSurfaceArea(product(0), '7.4') returns the van der Waals surface area of the major microspecies of the
first product taken at pH 7.4]]>
ASA
solventAccessibleSurfaceArea
double
Geometry
the major microspecies pH (takes the input molecule itself if omitted)
]]>
waterAccessibleSurfaceArea() returns the solvent accessible / water accessible surface area of the input molecule
solventAccessibleSurfaceArea('7.4')returns the solvent accessible / water accessible surface area of the major microspecies taken at
pH 7.4]]>
waterAccessibleSurfaceArea(reactant(0)) returns the solvent accessible / water accessible surface area of the first
reactantsolventAccessibleSurfaceArea(product(0), '7.4') returns the solvent accessible / water accessible surface area of the major
microspecies of the first product taken at pH 7.4]]>
double
Geometry
the major microspecies pH (takes the input molecule itself if omitted)
]]>
ASAPlus() returns the water accessible surface area of all atoms of the input molecule with positive partial charge
ASAPlus('7.4')returns the water accessible surface area of all atoms with positive partial charge of the major microspecies taken at
pH 7.4]]>
ASAPlus(reactant(0)) returns the water accessible surface area of all atoms of the first reactant with positive partial charge
ASAPlus(product(0), '7.4') returns the water accessible surface area of all atoms with positive partial charge of the major
microspecies of the first product taken at pH 7.4]]>
double
Geometry
the major microspecies pH (takes the input molecule itself if omitted)
]]>
ASANegative() returns the water accessible surface area of all atoms of the input molecule with negative partial charge
ASANegative('7.4')returns the water accessible surface area of all atoms with negative partial charge of the major microspecies taken at
pH 7.4]]>
ASANegative(reactant(0)) returns the water accessible surface area of all atoms of the first reactant with negative partial charge
ASANegative(product(0), '7.4') returns the water accessible surface area of all atoms with negative partial charge of the major
microspecies of the first product taken at pH 7.4]]>
double
Geometry
the major microspecies pH (takes the input molecule itself if omitted)
]]>
ASAHydrophobic() returns the water accessible surface area of all atoms of the input molecule with hydrophobic partial charge
ASAHydrophobic('7.4')returns the water accessible surface area of all atoms with hydrophobic partial charge of the major microspecies taken at
pH 7.4]]>
ASAHydrophobic(reactant(0)) returns the water accessible surface area of all atoms of the first reactant with hydrophobic partial charge
ASAHydrophobic(product(0), '7.4') returns the water accessible surface area of all atoms with hydrophobic partial charge of the major
microspecies of the first product taken at pH 7.4]]>
double
Geometry
the major microspecies pH (takes the input molecule itself if omitted)
]]>
ASAPolar() returns the water accessible surface area of all atoms of the input molecule with polar partial charge
ASAPolar('7.4')returns the water accessible surface area of all atoms with polar partial charge of the major microspecies taken at
pH 7.4]]>
ASAPolar(reactant(0)) returns the water accessible surface area of all atoms of the first reactant with polar partial charge
ASAPolar(product(0), '7.4') returns the water accessible surface area of all atoms with polar partial charge of the major
microspecies of the first product taken at pH 7.4]]>
pI
double
Protonation
isoelectricPoint() returns the isoelectric point of the input molecule]]>
isoelectricPoint(reactant(1)) returns the isoelectric point of the second reactant]]>
double
Protonation
the major microspecies pH
]]>
averageMicrospeciesCharge() returns the average charge of the microspecies of the input molecule]]>
averageMicrospeciesCharge(reactant(1)) returns the average charge of the microspecies of the second reactant]]>
double
Elemental Analysis
mass() returns the mass of the input molecule]]>
mass(reactant(0)) returns the mass of the first reactant]]>
double
Elemental Analysis
exactMass() returns the exact mass of the input molecule]]>
exactMass(product(1)) returns the exact mass of the second product]]>
int
Elemental Analysis
atomic number (optional) and mass number (optional) as a single string, separated by "." (e.g. "6" for the
number of carbon atoms, "6.12" for the number of carbon atoms with mass number 12) - if omitted, all
atoms are counted, if the mass number is set to 0 then all non-isotope atoms are counted
]]>
atomCount() returns the number of atoms in the input molecule atomCount("6") returns
the number of carbon atoms in the input molecule]]>
atomCount(reactant(0), "7") returns the number of nitrogen atoms in the first reactant atomCount(product(1), "7.14")
returns the number of nitrogen atoms with mass number 14 in the second product atomCount(product(1), "7.0")
returns the number of non-isotope nitrogen atoms in the second product]]>
String
Elemental Analysis
formula() returns the formula of the input molecule]]>
String
Elemental Analysis
sortableFormula() returns the sortable formula of the input molecule; sortableFormula('digits:4')
returns the 4 digit sortable formula of the input molecule]]>
String
Elemental Analysis
isotopeFormula() returns the isotope formula of the input molecule]]>
String
Elemental Analysis
dotDisconnectedFormula() returns the dot-disconnected formula of the input molecule]]>
String
Elemental Analysis
dotDisconnectedIsotopeFormula() returns the dot-disconnected isotope formula of the input molecule]]>
String
Elemental Analysis
composition() returns the composition of the input molecule]]>
String
Elemental Analysis
isotopeComposition() returns the isotope composition of the input molecule]]>
int
Geometry
aliphaticAtomCount() returns the number of aliphatic atoms in the input molecule]]>
aliphaticAtomCount(reactant(0)) returns the number of aliphatic atoms in the first reactant aliphaticAtomCount(product(1))
returns the number of aliphatic atoms in the second product]]>
int
Geometry
aliphaticBondCount() returns the number of bonds in the input molecule]]>
aliphaticBondCount(reactant(0)) returns the number of aliphatic bonds in the first reactant aliphaticBondCount(product(1))
returns the number of aliphatic bonds in the second product]]>
int
Geometry
aliphaticRingCount() returns the number of aliphatic rings in the input molecule]]>
aliphaticRingCount(reactant(0)) returns the number of aliphatic rings in the first reactant aliphaticRingCount(product(1))
returns the number of aliphatic rings in the second product]]>
int
Geometry
aliphaticRingCountOfSize(6) returns the number of aliphatic rings of size 6 in the input molecule]]>
aliphaticRingCountOfSize(reactant(0), 5) returns the number of aliphatic rings of size 5 in the first reactant
aliphaticRingCountOfSize(product(1), 5) returns the number of aliphatic rings of size 5 in the second product]]>
int[][]
Geometry
aliphaticRings() returns the atom indexes of the aliphatic rings in the input molecule]]>
aliphaticRings(reactant(0)) returns the atom indexes of the aliphatic rings in the first reactant aliphaticRings(product(1))
returns the atom indexes of the aliphatic rings in the second product]]>
int[][]
Geometry
aliphaticRings() returns the atom indexes of the aliphatic rings in the input molecule having the given size]]>
aliphaticRings(reactant(0)) returns the atom indexes of the aliphatic rings in the first reactant having the given size aliphaticRings(product(1))
returns the atom indexes of the aliphatic rings in the second product having the given size]]>
int
Geometry
aromaticAtomCount() returns the number of aromatic atoms in the input molecule]]>
aromaticAtomCount(reactant(0)) returns the number of aromatic atoms in the first reactant aromaticAtomCount(product(1))
returns the number of aromatic atoms in the second product]]>
int
Geometry
aromaticBondCount() returns the number of aromatic bonds in the input molecule]]>
aromaticBondCount(reactant(0)) returns the number of aromatic bonds in the first reactant aromaticBondCount(product(1))
returns the number of aromatic bonds in the second product]]>
int
Geometry
aromaticRingCount() returns the number of aromatic rings in the input molecule]]>
aromaticRingCount(reactant(0)) returns the number of aromatic rings in the first reactant aromaticRingCount(product(1))
returns the number of aromatic rings in the second product]]>
int
Geometry
aromaticRingCountOfSize(6) returns the number of aromatic rings of size 6 in the input molecule]]>
aromaticRingCountOfSize(reactant(0), 5) returns the number of aromatic rings of size 5 in the first reactant
aromaticRingCountOfSize(product(1), 5) returns the number of aromatic rings of size 5 in the second product]]>
int[][]
Geometry
aromaticRings() returns the atom indexes of the aromatic rings in the input molecule]]>
aromaticRings(reactant(0)) returns the atom indexes of the aromatic rings in the first reactant aromaticRings(product(1))
returns the atom indexes of the aromatic rings in the second product]]>
int[][]
Geometry
aromaticRings() returns the atom indexes of the aromatic rings in the input molecule having the given size]]>
aromaticRings(reactant(0)) returns the atom indexes of the aromatic rings in the first reactant having the given size aromaticRings(product(1))
returns the atom indexes of the aromatic rings in the second product having the given size]]>
int
Geometry
carboaliphaticRingCount() returns the number of carboaliphatic rings in the input molecule]]>
carboaliphaticRingCount(reactant(0)) returns the number of carboaliphatic rings in the first
reactant carboaliphaticRingCount(product(1)) returns the number of carboaliphatic rings in the second product]]>
int
Geometry
carboaromaticRingCount() returns the number of carboaromatic rings in the input molecule]]>
carboaromaticRingCount(reactant(0)) returns the number of carboaromatic rings in the first
reactant carboaromaticRingCount(product(1)) returns the number of carboaromatic rings in the second product]]>
int
Geometry
carboRingCount() returns the number of carbocyclic rings in the input molecule]]>
carboRingCount(reactant(0)) returns the number of carbocyclic rings in the first reactant carboRingCount(product(1))
returns the number of carbocyclic rings in the second product]]>
int
Geometry
carboRingCountOfSize(6) returns the number of carbocyclic rings of size 6 in the input molecule]]>
carboRingCountOfSize(reactant(0), 5) returns the number of carbocyclic rings of size 5 in the first reactant
carboRingCountOfSize(product(1), 5) returns the number of carbocyclic rings of size 5 in the second product]]>
int[][]
Geometry
carboRings() returns the atom indexes of the carbocyclic rings in the input molecule]]>
carboRings(reactant(0)) returns the atom indexes of the carbocyclic rings in the first reactant carboRings(product(1))
returns the atom indexes of the carbocyclic rings in the second product]]>
int[][]
Geometry
carboRings() returns the atom indexes of the carbocyclic rings in the input molecule having the given size]]>
carboRings(reactant(0)) returns the atom indexes of the carbocyclic rings in the first reactant having the given size carboRings(product(1))
returns the atom indexes of the carbocyclic rings in the second product having the given size]]>
int
Geometry
rotatableBondCount() returns the number of rotatable bonds in the input molecule]]>
rotatableBondCount(reactant(0)) returns the number of rotatable bonds in the first reactant rotatableBondCount(product(1))
returns the number of rotatable bonds in the second product]]>
int
Geometry
fragmentCount() returns the number of fragments in the input molecule]]>
fragmentCount(reactant(0)) returns the number of fragments in the first reactant fragmentCount(product(1))
returns the number of fragments in the second product]]>
double
Geometry
fsp3() returns the fsp3 value of the input molecule]]>
fsp3(reactant(0)) returns the fsp3 value of the first reactant fsp3(product(1))
returns the fsp3 value of the second product]]>
int
Geometry
(SSSR smallest set of smallest aliphatic rings)]]>
fusedAliphaticRingCount() returns the number of fused aliphatic rings in the input molecule]]>
fusedAliphaticRingCount(reactant(0)) returns the number of fused aliphatic rings in the first
reactant fusedAliphaticRingCount(product(1)) returns the number of fused aliphatic rings in the second
product]]>
int
Geometry
fusedAliphaticRingCountOfSize(6) returns the number of fused aliphatic rings of size 6 in the input molecule]]>
fusedAliphaticRingCountOfSize(reactant(0), 5) returns the number of fused aliphatic rings of size 5 in the first reactant
fusedAliphaticRingCountOfSize(product(1), 5) returns the number of fused aliphatic rings of size 5 in the second product]]>
int[][]
Geometry
fusedAliphaticRings() returns the atom indexes of the fused aliphatic rings in the input molecule]]>
fusedAliphaticRings(reactant(0)) returns the atom indexes of the fused aliphatic rings in the first reactant fusedAliphaticRings(product(1))
returns the atom indexes of the fused aliphatic rings in the second product]]>
int[][]
Geometry
fusedAliphaticRings() returns the atom indexes of the fused aliphatic rings in the input molecule having the given size]]>
fusedAliphaticRings(reactant(0)) returns the atom indexes of the fused aliphatic rings in the first reactant having the given size fusedAliphaticRings(product(1))
returns the atom indexes of the fused aliphatic rings in the second product having the given size]]>
int
Geometry
(SSSR smallest set of smallest aromatic rings)]]>
fusedAromaticRingCount() returns the number of fused aromatic rings in the input molecule]]>
fusedAromaticRingCount(reactant(0)) returns the number of fused aromatic rings in the first
reactant fusedAromaticRingCount(product(1)) returns the number of fused aromatic rings in the second
product]]>
int
Geometry
fusedAromaticRingCountOfSize(6) returns the number of fused aromatic rings of size 6 in the input molecule]]>
fusedAromaticRingCountOfSize(reactant(0), 5) returns the number of fused aromatic rings of size 5 in the first reactant
fusedAromaticRingCountOfSize(product(1), 5) returns the number of fused aromatic rings of size 5 in the second product]]>
int[][]
Geometry
fusedAromaticRings() returns the atom indexes of the fused aromatic rings in the input molecule]]>
fusedAromaticRings(reactant(0)) returns the atom indexes of the fused aromatic rings in the first reactant fusedAromaticRings(product(1))
returns the atom indexes of the fused aromatic rings in the second product]]>
int[][]
Geometry
fusedAromaticRings() returns the atom indexes of the fused aromatic rings in the input molecule having the given size]]>
fusedAromaticRings(reactant(0)) returns the atom indexes of the fused aromatic rings in the first reactant having the given size fusedAromaticRings(product(1))
returns the atom indexes of the fused aromatic rings in the second product having the given size]]>
int
Geometry
(SSSR smallest set of smallest aliphatic rings)]]>
heteroaliphaticRingCount() returns the number of aliphatic heterocyclic rings in the input molecule]]>
heteroaliphaticRingCount(reactant(0)) returns the number of aliphatic heterocyclic rings in the first
reactant heteroaliphaticRingCount(product(1)) returns the number of aliphatic heterocyclic rings in the second
product]]>
int
Geometry
heteroaliphaticRingCountOfSize(6) returns the number of aliphatic heterocyclic rings of size 6 in the input molecule]]>
heteroaliphaticRingCountOfSize(reactant(0), 5) returns the number of aliphatic heterocyclic rings of size 5 in the first reactant
heteroaliphaticRingCountOfSize(product(1), 5) returns the number of aliphatic heterocyclic rings of size 5 in the second product]]>
int[][]
Geometry
heteroaliphaticRings() returns the atom indexes of the aliphatic heterocyclic rings in the input molecule]]>
heteroaliphaticRings(reactant(0)) returns the atom indexes of the aliphatic heterocyclic rings in the first reactant heteroaliphaticRings(product(1))
returns the atom indexes of the aliphatic heterocyclic rings in the second product]]>
int[][]
Geometry
heteroaliphaticRings() returns the atom indexes of the aliphatic heterocyclic rings in the input molecule having the given size]]>
heteroaliphaticRings(reactant(0)) returns the atom indexes of the aliphatic heterocyclic rings in the first reactant having the given size heteroaliphaticRings(product(1))
returns the atom indexes of the aliphatic heterocyclic rings in the second product having the given size]]>
int
Geometry
(SSSR smallest set of smallest aromatic rings)]]>
heteroaromaticRingCount() returns the number of aromatic heterocyclic rings in the input molecule]]>
heteroaromaticRingCount(reactant(0)) returns the number of aromatic heterocyclic rings in the first
reactant heteroaromaticRingCount(product(1)) returns the number of aromatic heterocyclic rings in the second
product]]>
int
Geometry
heteroaromaticRingCountOfSize(6) returns the number of aromatic heterocyclic rings of size 6 in the input molecule]]>
heteroaromaticRingCountOfSize(reactant(0), 5) returns the number of aromatic heterocyclic rings of size 5 in the first reactant
heteroaromaticRingCountOfSize(product(1), 5) returns the number of aromatic heterocyclic rings of size 5 in the second product]]>
int[][]
Geometry
heteroaromaticRings() returns the atom indexes of the aromatic heterocyclic rings in the input molecule]]>
heteroaromaticRings(reactant(0)) returns the atom indexes of the aromatic heterocyclic rings in the first reactant heteroaromaticRings(product(1))
returns the atom indexes of the aromatic heterocyclic rings in the second product]]>
int[][]
Geometry
heteroaromaticRings() returns the atom indexes of the aromatic heterocyclic rings in the input molecule having the given size]]>
heteroaromaticRings(reactant(0)) returns the atom indexes of the aromatic heterocyclic rings in the first reactant having the given size heteroaromaticRings(product(1))
returns the atom indexes of the aromatic heterocyclic rings in the second product having the given size]]>
int
Geometry
(SSSR smallest set of smallest rings)]]>
heteroRingCount() returns the number of heterocyclic rings in the input molecule]]>
heteroRingCount(reactant(0)) returns the number of heterocyclic rings in the first
reactant heteroRingCount(product(1)) returns the number of heterocyclic rings in the second
product]]>
int
Geometry
heteroRingCountOfSize(6) returns the number of heterocyclic rings of size 6 in the input molecule]]>
heteroRingCountOfSize(reactant(0), 5) returns the number of heterocyclic rings of size 5 in the first reactant
heteroRingCountOfSize(product(1), 5) returns the number of heterocyclic rings of size 5 in the second product]]>
int[][]
Geometry
heteroRings() returns the atom indexes of the heterocyclic rings in the input molecule]]>
heteroRings(reactant(0)) returns the atom indexes of the heterocyclic rings in the first reactant heteroRings(product(1))
returns the atom indexes of the heterocyclic rings in the second product]]>
int[][]
Geometry
heteroRings() returns the atom indexes of the heterocyclic rings in the input molecule having the given size]]>
heteroRings(reactant(0)) returns the atom indexes of the heterocyclic rings in the first reactant having the given size heteroRings(product(1))
returns the atom indexes of the heterocyclic rings in the second product having the given size]]>
int[]
Geometry
largestRingSize() returns the atom indexes of the largest ring in the input molecule]]>
largestRingSize(product(1)) returns the atom indexes of the largest ring in the second product]]>
int
Geometry
largestRingSize() returns the size of the largest ring in the input molecule]]>
largestRingSize(product(1)) returns the size of the largest ring in the second product]]>
int[][]
Geometry
largestRingSize() returns the atom indexes of the largest ring system in the input molecule]]>
largestRingSize(product(1)) returns the atom indexes of the largest ring system in the second product]]>
int
Geometry
largestRingSystemSize() returns the size of the largest ring system in the input molecule]]>
largestRingSystemSize(reactant(0)) returns the size of the largest ring system in the first reactant largestringsystemsize(product(1))
returns the size of the largest ring system in the second product]]>
int
Geometry
ringAtomCount() returns the number of ring atoms in the input molecule]]>
ringAtomCount(reactant(0)) returns the number of ring atoms in the first reactant ringAtomCount(product(1))
returns the number of ring atoms in the second product]]>
ringAtomCount() returns the number of ring atoms in the input molecule]]>
ringAtomCount(reactant(0)) returns the number of ring atoms in the first reactant ringAtomCount(product(1))
returns the number of ring atoms in the second product]]>
int
Geometry
ringBondCount() returns the number of ring bonds in the input molecule]]>
ringBondCount(reactant(0)) returns the number of ring bonds in the first reactant ringBondCount(product(1))
returns the number of ring bonds in the second product]]>
int
Geometry
ringCount() returns the number of rings in the input molecule]]>
ringCount(reactant(0)) returns the number of rings in the first reactant ringCount(product(1))
returns the number of rings in the second product]]>
int
Geometry
ringCountOfSize(6) returns the number of rings of size 6 in the input molecule]]>
ringCountOfSize(reactant(0), 5) returns the number of rings of size 5 in the first reactant
ringCountOfSize(product(1), 5) returns the number of rings of size 5 in the second product]]>
int[][]
Geometry
rings() returns the atom indexes of the rings in the input molecule]]>
rings(reactant(0)) returns the atom indexes of the rings in the first reactant rings(product(1))
returns the atom indexes of the rings in the second product]]>
int[][]
Geometry
rings() returns the atom indexes of the rings in the input molecule having the given size]]>
rings(reactant(0)) returns the atom indexes of the rings in the first reactant having the given size rings(product(1))
returns the atom indexes of the rings in the second product having the given size]]>
int[][]
Geometry
ringSystems() returns the atom indexes of the ring systems in the input molecule]]>
ringSystems(reactant(0)) returns the atom indexes of the ring systems in the first reactant ringSystems(product(1))
returns the atom indexes of the ring systems in the second product]]>
int[][]
Geometry
ringSystems() returns the atom indexes of the ring systems in the input molecule having the given size]]>
ringSystems(reactant(0)) returns the atom indexes of the ring systems in the first reactant having the given size ringSystems(product(1))
returns the atom indexes of the ring systems in the second product having the given size]]>
int[]
Geometry
smallestRingSize() returns the atom indexes of the smallest ring in the input molecule]]>
smallestRingSize(product(1)) returns the atom indexes of the smallest ring in the second product]]>
int
Geometry
smallestRingSize() returns the size of the smallest ring in the input molecule]]>
smallestRingSize(reactant(0)) returns the size of the smallest ring in the first reactant]]>
int[][]
Geometry
smallestRingSize() returns the atom indexes of the smallest ring system in the input molecule]]>
smallestRingSize(product(1)) returns the atom indexes of the smallest ring system in the second product]]>
int
Geometry
smallestRingSystemSize() returns the size of the smallest ring system in the input molecule]]>
smallestRingSystemSize(reactant(0)) returns the size of the smallest ring system in the first reactant smallestringsystemsize(product(1))
returns the size of the smallest ring system in the second product]]>
int
Geometry
chainAtomCount() returns the number of chain atoms in the input molecule]]>
chainAtomCount(reactant(0)) returns the number of chain atoms in the first reactant chainAtomCount(product(1))
returns the number of chain atoms in the second product]]>
int
Geometry
chainBondCount() returns the number of chain bonds in the input molecule]]>
chainBondCount(reactant(0)) returns the number of chain bonds in the first reactant chainBondCount(product(1))
returns the number of chain bonds in the second product]]>
int
Geometry
(SSSR smallest set of smallest rings)]]>
fusedRingCount() returns the number of fused rings in the input molecule]]>
fusedRingCount(reactant(0)) returns the number of fused rings in the first reactant fusedRingCount(product(1))
returns the number of fused rings in the second product]]>
int
Geometry
ringSystemCount() returns the number of ring systems in the input molecule]]>
ringSystemCount(reactant(0)) returns the number of ring systems in the first reactant ringsystemCount(product(1))
returns the number of ring systems in the second product]]>
int
Geometry
ringSystemCountOfSize(4) returns the number of four-membered ring systems in the input molecule]]>
ringSystemCountOfSize(reactant(0),3) returns the number of three-membered ring systems in the first reactant
ringsystemCountOfSize(product(1),3) returns the number of three-membered ring systems in the second product]]>
int
Geometry
asymmetricAtomCount() returns the number of asymmetric atoms in the input molecule]]>
asymmetricAtomCount(reactant(0)) returns the number of asymmetric atoms in the first reactant asymmetricAtomCount(product(1))
returns the number of asymmetric atoms in the second product]]>
int[]
Geometry
asymmetricAtoms() returns the indexes of asymmetric atoms in the input molecule]]>
asymmetricAtoms(reactant(0)) returns the indexes of asymmetric atoms in the first reactant asymmetricAtoms(product(1))
returns the indexes of asymmetric atoms in the second product]]>
int
Geometry
chiralCenterCount() returns the number of tetrahedral stereogenic centers in the input molecule]]>
chiralCenterCount(reactant(0)) returns the number of tetrahedral stereogenic centers in the first
reactant chiralCenterCount(product(1)) returns the number of tetrahedral stereogenic centers in the second
product]]>
int[]
Geometry
chiralCenters() returns the indexes of chiral center atoms in the input molecule]]>
chiralCenters(reactant(0)) returns the indexes of chiral center atoms in the first
reactant chiralCenters(product(1)) returns the indexes of chiral center atoms in the second
product]]>
int
Geometry
stereoDoubleBondCount() returns the number of stereo double bonds in the input molecule]]>
stereoDoubleBondCount(reactant(0)) returns the number of stereo double bonds in the first
reactant stereoDoubleBondCount(product(1)) returns the number of stereo double bonds in the second product]]>
boolean
Geometry
true for aromatic atoms,
false for non-aromatic atoms]]>
the atom index / MolAtom object
]]>
aromaticAtom(2) returns true if atom 2 of the input molecule is
aromatic, false otherwise]]>
aromaticAtom(ratom(2)) returns true if the reactant atom matching map 2
in the reaction equation is aromatic, false otherwise aromaticAtom(patom(1)) returns true
if the product atom matching map 1 in the reaction equation is aromatic, false otherwise]]>
boolean
Geometry
true for aliphatic atoms,
false for non-aliphatic atoms]]>
the atom index / MolAtom object
]]>
aliphaticAtom(2) returns true if atom 2 of the input molecule is
aliphatic, false otherwise]]>
aliphaticAtom(ratom(2)) returns true if the reactant atom matching map 2
in the reaction equation is aliphatic, false otherwise aliphaticAtom(patom(1)) returns true
if the product atom matching map 1 in the reaction equation is aliphatic, false otherwise]]>
boolean
Geometry
true for chain atoms,
false for non-chain atoms]]>
the atom index / MolAtom object
]]>
chainAtom(2) returns true if atom 2 of the input molecule is a chain
atom, false otherwise]]>
chainAtom(ratom(2)) returns true if the reactant atom matching map 2 in
the reaction equation is a chain atom, false otherwise chainAtom(patom(1)) returns true
if the product atom matching map 1 in the reaction equation is a chain atom, false otherwise]]>
boolean
Geometry
true for ring atoms,
false for non-ring atoms]]>
the atom index / MolAtom object
]]>
ringAtom(2) returns true if atom 2 of the input molecule is a ring atom,
false otherwise]]>
ringAtom(ratom(2)) returns true if the reactant atom matching map 2 in
the reaction equation is a ring atom, false otherwise ringAtom(patom(1)) returns true
if the product atom matching map 1 in the reaction equation is a ring atom, false otherwise]]>
boolean
Geometry
true for asymmetric atoms,
false for symmetric atoms]]>
the atom index / MolAtom object
]]>
asymmetricAtom(2) returns true if atom 2 of the input molecule is an
asymmetric atom, false otherwise]]>
asymmetricAtom(ratom(2)) returns true if the reactant atom matching map 2
in the reaction equation is an asymmetric atom, false otherwise asymmetricAtom(patom(1))
returns true if the product atom matching map 1 in the reaction equation is an asymmetric
atom, false otherwise]]>
boolean
Geometry
true for tetrahedral stereogenic center atoms]]>
the atom index / MolAtom object
]]>
chiralCenter(2) returns true if atom 2 of the input molecule is a
tetrahedral stereogenic center, false otherwise]]>
chiralCenter(ratom(2)) returns true if the reactant atom matching map 2
in the reaction equation is a tetrahedral stereogenic center, false otherwise chiralCenter(patom(1))
returns true if the product atom matching map 1 in the reaction equation is a tetrahedral
stereogenic center, false otherwise]]>
int
Geometry
cyclomaticNumber() returns the cyclomatic number of the input molecule]]>
cyclomaticNumber(reactant(0)) returns the cyclomatic number of the first reactant cyclomaticNumber(product(1))
returns the cyclomatic number of the second product]]>
int
Geometry
plattIndex() returns the Platt index of the input molecule]]>
plattIndex(reactant(0)) returns the Platt index of the first reactant plattIndex(product(1))
returns the Platt index of the second product]]>
double
Geometry
randicIndex() returns the Randic index of the input molecule]]>
randicIndex(reactant(0)) returns the Randic index of the first reactant randicIndex(product(1))
returns the Randic index of the second product]]>
double
Geometry
balabanIndex() returns the Balaban index of the input molecule]]>
balabanIndex(reactant(0)) returns the Balaban index of the first reactant balabanIndex(product(1))
returns the Balaban index of the second product]]>
double[]
Geometry
the atom index / MolAtom object
]]>
distanceDegree(2) returns the distance degree of atom 2 of the input molecule]]>
distanceDegree(ratom(2)) returns the distance degree of the reactant atom matching map 2
in the reaction equation distanceDegree(patom(1)) returns the distance degree of the product atom matching
map 1 in the reaction equation]]>
int[]
Geometry
the atom index / MolAtom object
]]>
eccentricity(2) returns the eccentricity of atom 2 of the input molecule]]>
eccentricity(ratom(2)) returns the eccentricity of the reactant atom matching map 2
in the reaction equation eccentricity(patom(1)) returns the distance degree of the product atom matching
map 1 in the reaction equation]]>
double
Geometry
hararyIndex() returns the Harary index of the input molecule]]>
hararyIndex(reactant(0)) returns the Harary index of the first reactant hararyIndex(product(1))
returns the Harary index of the second product]]>
int
Geometry
hyperWienerIndex() returns the Hyper Wiener index of the input molecule]]>
hyperWienerIndex(reactant(0)) returns the Hyper Wiener index of the first reactant hyperWienerIndex(product(1))
returns the Hyper Wiener index of the second product]]>
int
Geometry
szegedIndex() returns the Szeged index of the input molecule]]>
szegedIndex(reactant(0)) returns the Szeged index of the first reactant szegedIndex(product(1))
returns the Szeged index of the second product]]>
int
Geometry
wienerIndex() returns the Wiener index of the input molecule]]>
wienerIndex(reactant(0)) returns the Wiener index of the first reactant wienerIndex(product(1))
returns the Wiener index of the second product]]>
int
Geometry
wienerPolarity() returns the Wiener polarity of the input molecule]]>
wienerPolarity(reactant(0)) returns the Wiener polarity of the first reactant wienerPolarity(product(1))
returns the Wiener polarity of the second product]]>
double/double[]
Geometry
the atom index / MolAtom object
]]>
stericEffectIndex(2) returns the steric effect index of atom 2 of the input molecule]]>
stericEffectIndex(ratom(2)) returns the steric effect index of the reactant atom matching map 2
in the reaction equation stericEffectIndex(patom(1)) returns the steric effect index of the product atom
matching map 1 in the reaction equation]]>
int
Geometry
the atom index / MolAtom object
]]>
smallestAtomRingSize(0) returns the size of the smallest ring containing atom 0 in
the input molecule]]>
smallestAtomRingSize(ratom(1)) returns the size of the smallest ring containing reactant atom
matching map 1 in the reaction equation]]>
int
Geometry
the atom index / MolAtom object
]]>
largestAtomRingSize(1) returns the size of the largest ring containing atom 1
in the input molecule]]>
largestAtomRingSize(patom(2)) returns the size of the largest ring containing product atom
matching map 2 in the reaction equation]]>
int
Geometry
Integer.MAX_VALUE if disconnected]]>
the (1-based) atom indexes of the two atoms in a string: "index1-index2" (e.g. '2-3')
]]>
shortestPath('2-3') and shortestPath(pair(1, 2)) both return the shortest path length
between atoms 1 and 2 in the input molecule]]>
shortestPath(reactant(0), pair(ratom(1), ratom(2))) returns the length of the shortest path between reactant
atoms matching maps 1 and 2 in the reaction equation (see note 1)
shortestPath(product(1), pair(patom(2), patom(3))) returns the length of the shortest path between product
atoms matching maps 2 and 3 in the reaction equation (see note 1)]]>
boolean
Geometry
true if the two atoms belong to the same connected component, false otherwise]]>
the (1-based) atom indexes of the two atoms in a string: "index1-index2" (e.g. '2-3')
]]>
connected('2-3') and connected(pair(1, 2)) both return true if atoms 1
and 2 are in the same connected component of the input molecule]]>
connected(reactant(0), pair(ratom(1), ratom(2))) returns true if reactant atoms matching maps 1
and 2 in the reaction equation are connected in the corresponding reactant molecule (see note 1)
connected(product(1), pair(patom(2), patom(3))) returns true if product atoms matching maps 2
and 3 in the reaction equation are connected in the corresponding product molecule (see note 1)]]>
boolean
Geometry
true if the molecule graph is connected, false otherwise]]>
connectedGraph() returns true if the input molecule graph is connected]]>
connectedGraph(reactant(0)) returns true if the first reactant is connected connectedGraph(product(1))
returns true if the second product is connected]]>
int
Geometry
-1 if there is no bond between the two atoms]]>
the (1-based) atom indexes of the two atoms in a string: "index1-index2" (e.g. '2-3')
]]>
bondType('2-3') and bondType(bond(1, 2)) both return the bond type between atoms 1
and 2 in the input molecule]]>
bondType(reactant(0), bond(ratom(1), ratom(2))) returns the bond type between reactant atoms matching maps 1
and 2 in the reaction equation (see note 1)bondType(product(1), bond(patom(2), patom(3)))
returns the bond type between product atoms matching maps 2 and 3 in the reaction equation
(see note 1)]]>
boolean
Geometry
true if the two atoms are connected by a chain bond, false otherwise]]>
the (1-based) atom indexes of the two atoms in a string: "index1-index2" (e.g. '2-3')
]]>
chainBond('2-3') and chainBond(bond(1, 2)) both return true if atoms 1
and 2 are connected by a chain bond the input molecule]]>
chainBond(reactant(0), bond(ratom(1), ratom(2))) returns true if reactant atoms matching maps 1
and 2 in the reaction equation are connected by a chain bond in the corresponding reactant molecule (see note 1)
chainBond(product(1), bond(patom(2), patom(3))) returns true if product atoms matching maps 2 and 3 in the
reaction equation are connected by a chain bond in the corresponding product molecule (see note 1)]]>
boolean
Geometry
true if the two atoms are connected by a ring bond, false otherwise]]>
the (1-based) atom indexes of the two atoms in a string: "index1-index2" (e.g. '2-3')
]]>
ringBond('2-3') and ringBond(bond(1, 2)) both return true if atoms 1
and 2 are connected by a ring bond the input molecule]]>
ringBond(reactant(0), bond(ratom(1), ratom(2))) returns true if reactant atoms matching maps 1
and 2 in the reaction equation are connected by a ring bond in the corresponding reactant molecule (see note 1)
ringBond(product(1), bond(patom(2), patom(3))) returns true if product atoms matching maps 2 and 3
in the reaction equation are connected by a ring bond in the corresponding product molecule (see note 1)]]>
boolean
Geometry
true if the two atoms are connected by a rotatable bond, false otherwise]]>
the (1-based) atom indexes of the two atoms in a string: "index1-index2" (e.g. '2-3')
]]>
rotatableBond('2-3') and rotatableBond(bond(1, 2)) both return true if
atoms 1 and 2 are connected by a rotatable bond the input molecule]]>
rotatableBond(reactant(0), bond(ratom(1), ratom(2))) returns true if reactant atoms matching maps
1 and 2 in the reaction equation are connected by a rotatable bond in the corresponding
reactant molecule (see note 1)
rotatableBond(product(1), bond(patom(2), patom(3))) returns true if product atoms
matching maps 2 and 3 in the reaction equation are connected by a rotatable bond in the
corresponding product molecule (see note 1)]]>
int
Geometry
the atom index / MolAtom object
]]>
ringCountOfAtom(2) returns the number of rings passsing through atom 2 of the input
molecule]]>
ringCountOfAtom(ratom(2)) returns the number of rings passsing through the reactant atom matching
map 2 in the reaction equation ringCountOfAtom(patom(1)) returns the number of rings passsing
through the product atom matching map 1 in the reaction equation]]>
acc
int
HBDA
the atom index / MolAtom object
the major microspecies pH (takes the input molecule itself if omitted)
]]>
acceptor(2) returns the hydrogen bond acceptor multiplicity on atom 2 of the input molecule]]>
acceptor(ratom(2)) returns the hydrogen bond acceptor multiplicity on the reactant atom matching map
2 in the reaction equation]]>
don
int
HBDA
the atom index / MolAtom object
the major microspecies pH (takes the input molecule itself if omitted)
]]>
donor(1, "7.4") returns the hydrogen bond donor multiplicity on atom 1 of the major microspecies
at pH 7.4]]>
3 in the reaction equation,
taking the major microspecies of the corresponding product at pH 7.4]]>
accSiteCount
int
HBDA
the major microspecies pH (takes the input molecule itself if omitted)
]]>
acceptorSiteCount() returns the hydrogen bond acceptor multiplicity of the input molecule]]>
acceptorSiteCount(reactant(0)) returns the hydrogen bond acceptor multiplicity of the first reactant]]>
donSiteCount
int
HBDA
the major microspecies pH (takes the input molecule itself if omitted)
]]>
donorSiteCount("7.4") returns the hydrogen bond donor multiplicity of the major microspecies
at pH 7.4]]>
donorSiteCount(product(1), "7.4") returns the hydrogen bond donor multiplicity of the major microspecies
of the first product taken at pH 7.4]]>
int
HBDA
the major microspecies pH (takes the input molecule itself if omitted)
]]>
acceptorCount() returns the number of hydrogen bond acceptor atoms in the input molecule]]>
acceptorCount(reactant(0)) returns the number of hydrogen bond acceptor atoms in the first reactant]]>
int
HBDA
the major microspecies pH (takes the input molecule itself if omitted)
]]>
donorCount("7.4") returns the number of hydrogen bond donor atoms in the major microspecies
at pH 7.4]]>
donorCount(product(1), "7.4") returns the number of hydrogen bond donor atoms in the major microspecies
of the first product taken at pH 7.4]]>
refrac
double
Refractivity
refractivity() returns the molar refractivity of the input molecule]]>
refractivity(reactant(1)) returns the molar refractivity of the second reactant]]>
refraci
double/double[]
Refractivity
the atom index / MolAtom object
]]>
refractivityIncrements(2) returns the refractivity increment on atom 2 of the input molecule]]>
refractivityIncrements(ratom(1)) returns the refractivity increment on the reactant atom matching map 1
in the reaction equation]]>
Molecule
Conformation
the conformer index (0-based)
]]>
conformer(0) returns the first conformer of the input molecule]]>
conformer(reactant(0), 1) returns the second conformer of the first reactant]]>
Molecule[]
Conformation
conformers() returns conformers of the input molecule in an array]]>
conformers(reactant(0)) returns conformers of the first reactant in an array]]>
int
Conformation
conformerCount() returns the number of calculated conformers of the input molecule]]>
conformerCount(reactant(0)) returns the number of calculated conformers of the first reactant]]>
leconformer
Molecule
Conformation
lowestEnergyConformer() returns the lowest energy conformer of the input molecule]]>
lowestEnergyConformer(reactant(0)) returns the lowest energy conformer of the first reactant
lowestEnergyConformer(product(1)) returns the lowest energy conformer of the second product]]>
Molecule
Conformation
mmff94OptimizedStructure() returns the MMFF94 optimized lowest energy conformer of the input molecule]]>
mmff94OptimizedStructure(reactant(0)) returns the MMFF94 optimized lowest energy conformer of the first reactant
mmff94OptimizedStructure(product(1)) returns the MMFF94 optimized lowest energy conformer of the second product]]>
boolean
Conformation
hasValidConformer() returns true if the input molecule exists in 3D space (has a valid conformer)]]>
hasValidConformer(reactant(0)) returns true the if the first reactant exists in 3D space hasValidConformer(product(1))
returns true the if the second product exist in 3D space]]>
Molecule
Isomers
the stereoisomer index (0-based)]]>
stereoisomer(0) returns the first stereoisomer of the input molecule]]>
stereoisomer(reactant(0), 1) returns the second stereoisomer of the first reactant]]>
Molecule[]
Isomers
stereoisomers() returns stereoisomers of the input molecule in an array ]]>
stereoisomers(reactant(0)) returns stereoisomers of the first reactant in an array]]>
int
Isomers
stereoisomerCount() returns the number of generated stereoisomers of the input molecule]]>
stereoisomerCount(reactant(0)) returns the number of calculated stereoisomers of the first
reactant]]>
Molecule
Isomers
the double bond stereoisomer index (0-based)]]>
doubleBondStereoisomer(0) returns the first double bond stereoisomer of the input molecule]]>
doubleBondStereoisomer(reactant(0), 1) returns the second double bond stereoisomer of the first
reactant]]>
Molecule[]
Isomers
doubleBondStereoisomers() returns double bond stereoisomers of the input molecule in an array]]>
doubleBondStereoisomers(reactant(0)) returns double bond stereoisomers of the first reactant in an array]]>
int
Isomers
doubleBondStereoisomerCount() returns the number of generated double bond stereoisomers of the
input molecule]]>
doubleBondStereoisomerCount(reactant(0)) returns the number of calculated double bond
stereoisomers of the first reactant]]>
Molecule
Isomers
tetrahedralStereoisomer(0) returns the first tetrahedral stereoisomer of the input molecule]]>
tetrahedralStereoisomer(reactant(0), 1) returns the second tetrahedral stereoisomer of the first
reactant]]>
Molecule[]
Isomers
tetrahedralStereoisomers() returns tetrahedral stereoisomers of the input molecule in an array]]>
tetrahedralStereoisomers(reactant(0)) returns tetrahedral stereoisomers of the first reactant in
an array]]>
int
Isomers
tetrahedralStereoisomerCount() returns the number of generated tetrahedral stereoisomers of the
input molecule]]>
tetrahedralStereoisomerCount(reactant(0)) returns the number of calculated tetrahedral
stereoisomers of the first reactant]]>
double
Geometry
dreidingEnergy() returns the dreiding energy of the input molecule (conformer)]]>
dreidingEnergy(reactant(0)) returns the dreiding energy of the first reactant dreidingEnergy(product(1))
returns the dreiding energy of the second product]]>
double
Geometry
mmff94Energy() returns the MMFF94 energy of the input molecule (conformer)]]>
mmff94Energy(reactant(0)) returns the MMFF94 energy of the first reactant mmff94Energy(product(1))
returns the MMFF94 energy of the second product]]>
double
Geometry
minimalProjectionArea() returns the minimal projection area]]>
minimalProjectionArea((reactant(0)) returns the minimal projection area of the first reactant
minimalProjectionArea(product(1)) returns the minimal projection area of the second product]]>
double
Geometry
maximalProjectionArea() returns the maximal projection area]]>
maximalProjectionArea((reactant(0)) returns the maximal projection area of the first reactant
maximalProjectionArea(product(1)) returns the maximal projection area of the second product]]>
double
Geometry
minimalProjectionRadius() returns the minimal projection radius]]>
minimalProjectionRadius((reactant(0)) returns the minimal projection radius of the first reactant
minimalProjectionRadius(product(1)) returns the minimal projection radius of the second product]]>
double
Geometry
maximalProjectionRadius() returns the maximal projection radius]]>
maximalProjectionRadius((reactant(0)) returns the maximal projection radius of the first reactant
maximalProjectionRadius(product(1)) returns the maximal projection radius of the second product]]>
double
Geometry
the (1-based) atom indexes of the two atoms in a string: "index1-index2" (e.g. '2-3')
]]>
distance('1-2') and distance(pair(0, 1)) both return the distance between atoms 1
and 2 in the input molecule]]>
distance(reactant(0), pair(ratom(1), ratom(2))) returns the distance between reactant atoms matching maps 1
and 2 in the reaction equation (see note 1)
distance(product(1), pair(patom(2), patom(3))) returns the distance between product atoms matching maps 2 and 3
in the reaction equation (see note 1)]]>
double
Geometry
the (1-based) atom indexes of the three atoms in a string: "index1-index2-index3" (e.g. '2-3-5')
]]>
angle('1-2-3') and angle(atoms(0, 1, 2)) both return the angle between atoms 1,
2 and 3 in the input molecule]]>
angle(reactant(0), atoms(ratom(1), ratom(2), ratom(3))) returns the angle between reactant atoms matching maps
1, 2 and 3 in the reaction equation (see note 1)
angle(product(1), atoms(patom(2), patom(3), patom(4))) returns the angle between product atoms matching maps 2,
3 and 4 in the reaction equation (see note 1)]]>
double
Geometry
the (1-based) atom indexes of the four atoms in a string: "index1-index2-index3-index4" (e.g. '2-3-7-4')
]]>
dihedral('1-2-3-4') and dihedral(atoms(0, 1, 2, 3)) both return the dihedral of atoms 1,
2, 3 and 4 in the input molecule]]>
dihedral(reactant(0), atoms(ratom(1), ratom(2), ratom(3), ratom(4))) returns the dihedral of reactant atoms
matching maps 1, 2, 3 and 4 in the reaction equation (see note 1)
dihedral(product(1), atoms(patom(2), patom(3), patom(5), patom(6))) returns the dihedral of product atoms matching maps 2,
3, 5 and 6 in the reaction equation (see note 1)]]>
double/double[]
Geometry
the atom index / MolAtom object
]]>
stericHindrance(2) returns the steric hindrance of atom 2 of the input molecule]]>
stericHindrance(ratom(2)) returns the steric hindrance of the reactant atom matching map 2
in the reaction equation stericHindrance(patom(1)) returns the steric hindrance of the product atom
matching map 1 in the reaction equation]]>
String
Name
name() returns the preferred IUPAC name of the input molecule]]>
String
Name
traditionalName() returns the traditional name of the input molecule]]>
Molecule
StructuralFrameworks
bmf() returns the Bemis-Murcko framework of the input molecule]]>
bmf(reactant(0)) returns the Bemis-Murcko framework of the first reactant]]>
bemisMurckoFrameworkLoose
Molecule
StructuralFrameworks
bmfl() returns the loose Bemis-Murcko framework of the input molecule]]>
bmfl(reactant(0)) returns the loose Bemis-Murcko framework of the first reactant]]>
bemisMurckoFrameworkLoosePruned
Molecule
StructuralFrameworks
bmflp() returns the generalized loose Bemis-Murcko framework of the input molecule]]>
bmflp(reactant(0)) returns the generalized loose Bemis-Murcko framework of the first reactant]]>
boolean
Match
true if matching substructure found, false otherwise]]>
target atom index / MolAtom object (optional)
query Molecule object / SMARTS string
query atom map(s) (optional)
The function returns true if the query structure is found in the target molecule, the hit is required
to include the target atom if specified, furthermore if query atom map(s) are specified then these mapped atoms should
match the target atom.]]>
match("[#8]C=O") performs substructure search without atom matching requirement, the target is the
input molecule, the query is the carboxylic group given in the string parameter match(6, "[#8][C:1]=O", 1)
performs substructure search, checks if target atom 6 matches the carbon (atom with map 1)
of the carboxylic group query match(6, "[#8:1]C=[O:2]", 1, 2) performs substructure search, checks if
target atom 6 of the input molecule is a carboxylic oxygen]]>
match(reactant(0), "[#8]C=O") performs substructure search without atom matching requirement, the
target is the first reactant, the query is the carboxylic group given in the string parameter match(patom(2), "[#8]C=O")
performs substructure search, checks if product atom matching map 2 in the reaction equation matches any
atom of the carboxylic group query match(ratom(1), "[#8:1]C=[O:2]", 1, 2) performs substructure search,
checks if reactant atom matching map 1 in the reaction equation is a carboxylic oxygen]]>
int
Match
target atom index / MolAtom object (optional)
query Molecule object / SMARTS string
query atom map(s) (optional)
The function returns the number of query structures found in the target molecule, the hit is required to include
the target atom if specified, furthermore if query atom map(s) are specified then these mapped atoms should match the
target atom.]]>
matchCount("[#8]C=O") counts search hits without atom matching requirement, the target is the
input molecule, the query is the carboxylic group given in the string parameter matchCount(6, "[#8]C=O")
counts search hits with target atom 6 matching any atom in a carboxylic group matchCount(6, "[#8:1]C=[O:2]", 1, 2)
counts search hits with target atom 6 of the input molecule being a carboxylic oxygen]]>
matchCount(reactant(0), "[#8]C=O") counts search hits without atom matching requirement, the
target is the first reactant, the query is the carboxylic group given in the string parameter matchCount(patom(2), "[#8]C=O")
counts search hits, checks if product atom matching map 2 in the reaction equation matches any atom of
the carboxylic group query matchCount(ratom(1), "[#8:1]C=[O:2]", 1, 2) counts search hits with reactant
atom matching map 1 in the reaction equation being a carboxylic oxygen]]>
int
Match
target atom index / MolAtom object (optional)
query Molecule object / SMARTS string
query atom map(s) (optional)
The function returns the maximal number of pairwise disjoint query structures found in the target molecule.
Warning: if the target atom index and optionally query atom maps are specified then the return value
can only be 0 or 1, therefore the result is similar to the result of the
match function.]]>
disjointMatchCount("[#8]C=O") counts the maximal number of pairwise disjoint carboxylic groups in the input molecule]]>
disjointMatchCount(reactant(0), "[#8]C=O") counts the maximal number of pairwise disjoint carboxylic groups in the first reactant]]>
int
Match
target atom index / MolAtom object (optional)
query Molecule objects / SMARTS strings in collection (e.g. {amine,amide,"[#8][C:1]=O"})
query atom map(s) (optional)
The function returns the index of the first matching query structure found in the target molecule, the hit is required
to include the target atom if specified, furthermore if query atom map(s) are specified then these mapped atoms should
match the target atom.]]>
matchFirst({amine,amide,alcohol}) performs substructure search without atom matching requirement,
the target is the input molecule, the queries are the amine, amide, and alcohol groups given in the string parameter. Function
returns 1 if there is an amine group in the input molecule, 2 if there is no amine, but there is an amide
group in the input molecule, and returns 3 if there is no amine or amide group, but there is an alcohol group in the
input molecule. Returns 0 if none of the listed groups is found in input molecule.
matchFirst(6, {"[#8][C:1]=O","[NX3:2][CX3:1]=[OX1:3]"}, 1) performs substructure search, checks if target
atom 6 matches the carbon (atom with map 1) of the carboxylic or amide group in query. Returns the index
of the query if match found, 0 otherwise.
matchFirst(6, {"[#8:1]C=[O:2]","[#6][OX2:1][CX3](=[O:2])[#6]"}, 1, 2) performs substructure search, checks if
target atom 6 of the input molecule is a carboxylic oxygen or an oxigen in an ester group. Returns the index
of the query if match found, 0 otherwise.]]>
matchFirst(reactant(0), {amine,amide,alcohol}) performs substructure search without atom matching requirement,
the target is the first reactant, the queries are the amine, amide, and alcohol groups given in the string parameter. Function
returns 1 if there is an amine group in the first reactant, 2 if there is no amine group, but there is an amide
group in the first reactant, and returns 3 if there is no amine or amide group, but there is an alcohol group in the
first reactant. Returns 0 if none of the listed groups is found in first reactant.
matchFirst(patom(2), {"[#8][C]=O","[NX3][CX3]=[OX1]"}) performs substructure search, checks if product atom matching map
2 in the reaction equation matches any atom of the carboxylic or amide group query. Returns the index of mathing query,
or 0 if no match found.
matchFirst(ratom(1), {"[#8:1]C=[O:2]","[#6][OX2:1][CX3](=[O:2])[#6]"}, 1, 2) performs substructure search, checks if reactant
atom matching map 1 in the reaction equation is a carboxylic oxygen or an oxigen in an ester group. Returns the index of the
query if match found, 0 otherwise.]]>
double
Dissimilarity
Note 1: Dissimilarity function requires JChem.
Note 2: The dissimilarity values returned by dissimilarity function and similarity search in JChem database may differ because of the applied fingerprints. Dissimilarity function uses the default options of the chemical
fingerprints (length=1024, bonds=7, bits=2) optimized for similarity search. Database
similarity search uses fingerprints specified during the generation of the given table, optimized for substructure (and related) search types.]]>
descriptor:metric or descriptor (with default metric) (optional, chemical
fingerprint with Tanimoto metric is taken by default), one or two molecules (if only one is specified then the other
one is taken from the context)]]>
dissimilarity("PF", "c1ccccc1", "C1CCCCC1") returns the dissimilarity value between the benzene
ring and cyclohexane, computed with pharmacophore fingerprint and its default metric (Tanimoto) dissimilarity("c1ccccc1", "C1CCCCC1")
returns the dissimilarity value between the benzene ring and cyclohexane, computed with default fingerprint and its
default metric (chemical fingerprint with Tanimoto)
dissimilarity("PF:Euclidean", "c1ccccc1") returns the dissimilarity value between the benzene ring
and the input molecule, computed with pharmacophore fingerprint and Euclidean metric dissimilarity("LogD", "c1ccccc1")
returns the dissimilarity value between the benzene ring and the input molecule, computed with the LogD descriptor and
its default AbsDiff metric]]>
dissimilarity("CF:Euclidean", "c1ccccc1", reactant(0)) returns the dissimilarity value between the
benzene ring and the first reactant, computed with chemical fingerprint and Euclidean metric dissimilarity(reactant(0), product(0))
returns the dissimilarity value between the first reactant and the first product, computed with default fingerprint
and its default metric (chemical fingerprint with Tanimoto)]]>