Contents

 
 

Charge Functions

Name

License

Description

Return value

Parameters

Examples

atomicPolarizability
atomPol
pol
polarizability

Structural Calculations License

calculates atomic polarizability

the polarizability values

  • the atom index / MolAtom object,
  • the major microspecies pH (takes the input molecule itself if omitted)

Molecule Context

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

Reaction Context

atomicPolarizability(ratom(1)) returns the polarizability of reactant atom matching map 1 in the reaction equation atomicPolarizability(patom(2), "7.4") returns the polarizability of the product atom matching map 2 of the major microspecies taken at pH 7.4

averagePolarizability
averagePol
avgPol

Structural Calculations License

calculates average molecular polarizability component considering 3D geometry

the polarizability value

  • the major microspecies pH (takes the input molecule itself if omitted)

Molecule Context

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

Reaction Context

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

axxPol

Structural Calculations License

calculates principal component of polarizability tensor (a(xx), a(yy), a(zz))

the principal component of polarizability tensor

  • the major microspecies pH (takes the input molecule itself if omitted)

Molecule Context

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

Reaction Context

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

ayyPol

Structural Calculations License

calculates principal component of polarizability tensor (a(xx), a(yy), a(zz))

the principal component of polarizability tensor

  • the major microspecies pH (takes the input molecule itself if omitted)

Molecule Context

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

Reaction Context

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

azzPol

Structural Calculations License

calculates principal component of polarizability tensor (a(xx), a(yy), a(zz))

the principal component of polarizability tensor

  • the major microspecies pH (takes the input molecule itself if omitted)

Molecule Context

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

Reaction Context

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

charge

Structural Calculations License

calculates partial charges on atoms
for result types "aromaticsystem" / "aromaticring", calculates the sum of partial charges of the atoms in the aromatic system / smallest aromatic ring containing the atom

the charge values

  • the atom index / MolAtom object,
  • the result type ("total" (default), "pi", "sigma", "aromaticsystem", "aromaticsystemsigma", "aromaticsystempi", "aromaticring", "aromaticringsigma", "aromaticringpi"),
  • the major microspecies pH (takes the input molecule itself if omitted)

Molecule Context

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

Reaction Context

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

molecularPolarizability
molPol

Structural Calculations License

calculates molecular polarizability

the polarizability value

  • the major microspecies pH (takes the input molecule itself if omitted)

Molecule Context

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

Reaction Context

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

piOrbitalElectronegativity
pOEN

Structural Calculations License

calculates atomic pi orbital electronegativity

the pi orbital electronegativity values

  • the atom index / MolAtom object,
  • the major microspecies pH (takes the input molecule itself if omitted)

Molecule Context

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

Reaction Context

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

resonantCharge

Structural Calculations License

calculates partial charges on atoms considering resonance effect
for result types "aromaticsystem" / "aromaticring", calculates the sum of partial charges of the atoms in the aromatic system / smallest aromatic ring containing the atom

the charge values

  • the atom index / MolAtom object,
  • the result type ("total" (default), "pi", "sigma", "aromaticsystem", "aromaticsystemsigma", "aromaticsystempi", "aromaticring", "aromaticringsigma", "aromaticringpi"),
  • the major microspecies pH (takes the input molecule itself if omitted)

Molecule Context

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

Reaction Context

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

sigmaOrbitalElectronegativity
sOEN

Structural Calculations License

calculates atomic sigma orbital electronegativity

the sigma orbital electronegativity values

  • the atom index / MolAtom object,
  • the major microspecies pH (takes the input molecule itself if omitted)

Molecule Context

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

Reaction Context

sOEN(ratom(1)) returns the sigma orbital electronegativity of reactant atom matching map 1 in the reaction equation sOEN(patom(2), "7.4") returns the sigma orbital electronegativity of the product atom matching map 2 of the major microspecies taken at pH 7.4

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Conformation Functions

Name

License

Description

Return value

Parameters

Examples

conformer

Structural Calculations License

calculates a conformer of the molecule

the conformer

  • the conformer index (0-based)

Molecule Context (All)

conformer(0) returns the first conformer of the input molecule

Reaction Context (All)

conformer(reactant(0), 1) returns the second conformer of the first reactant

conformerCount

Structural Calculations License

returns the number of calculated conformers

the number of calculated conformers

-

Molecule Context (All)

conformerCount() returns the number of calculated conformers of the input molecule

Reaction Context (All)

conformerCount(reactant(0)) returns the number of calculated conformers of the first reactant

conformers

Structural Calculations License

calculates conformers of the molecule (maximum number of conformers to be calculated can be set, default: 100)

the conformer array

-

Molecule Context (All)

conformers() returns conformers of the input molecule in an array

Reaction Context (All)

conformers(reactant(0)) returns conformers of the first reactant in an array

hasValidConformer

Structural Calculations License

returns true if the input molecule exist in 3D space (has a valid conformer)

true if the input molecule exist in 3D space

-

Molecule Context (All)

hasValidConformer() returns true if the input molecule exists in 3D space (has a valid conformer)

Reaction Context (All)

hasValidConformer(reactant(0)) returns true the if the first reactant exists in 3D space hasValidConformer(product(1)) returns true the if the second product exist in 3D space

lowestEnergyConformer
leconformer

Structural Calculations License

calculates the lowest energy conformer of the molecule

the lowest energy conformer

-

Molecule Context (All)

lowestEnergyConformer() returns the lowest energy conformer of the input molecule

Reaction Context (All)

lowestEnergyConformer(reactant(0)) returns the lowest energy conformer of the first reactant lowestEnergyConformer(product(1)) returns the lowest energy conformer of the second product

mmff94OptimizedStructure

Structural Calculations License

calculates the MMFF94 optimized lowest energy conformer

the MMFF94 optimized lowest energy conformer

-

Molecule Context (All)

mmff94OptimizedStructure() returns the MMFF94 optimized lowest energy conformer of the input molecule

Reaction Context (All)

mmff94OptimizedStructure(reactant(0)) returns the MMFF94 optimized lowest energy conformer of the first reactant mmff94OptimizedStructure(product(1)) returns the MMFF94 optimized lowest energy conformer of the second product

Conformation Functions

Name

License

Description

Return value

Parameters

Examples

conformer

Structural Calculations License

calculates a conformer of the molecule

the conformer

  • the conformer index (0-based)

Molecule Context
conformer(0) returns the first conformer of the input molecule
Reaction Context
conformer(reactant(0), 1) returns the second conformer of the first reactant

conformerCount

Structural Calculations License

returns the number of calculated conformers

the number of calculated conformers

-

Molecule Context
conformerCount() returns the number of calculated conformers of the input molecule
Reaction Context
conformerCount(reactant(0)) returns the number of calculated conformers of the first reactant

conformers

Structural Calculations License

calculates conformers of the molecule (maximum number of conformers to be calculated can be set, default: 100)

the conformer array

-

Molecule Context
conformers() returns conformers of the input molecule in an array
Reaction Context
conformers(reactant(0)) returns conformers of the first reactant in an array

hasValidConformer

Structural Calculations License

returns true if the input molecule exist in 3D space (has a valid conformer)

true if the input molecule exist in 3D space

-

Molecule Context
hasValidConformer() returns true if the input molecule exists in 3D space (has a valid conformer)
Reaction Context
hasValidConformer(reactant(0)) returns true the if the first reactant exists in 3D space hasValidConformer(product(1)) returns true the if the second product exist in 3D space

lowestEnergyConformer leconformer

Structural Calculations License

calculates the lowest energy conformer of the molecule

the lowest energy conformer

-

Molecule Context
lowestEnergyConformer() returns the lowest energy conformer of the input molecule
Reaction Context
lowestEnergyConformer(reactant(0)) returns the lowest energy conformer of the first reactant lowestEnergyConformer(product(1)) returns the lowest energy conformer of the second product

mmff94OptimizedStructure

Structural Calculations License

calculates the MMFF94 optimized lowest energy conformer

the MMFF94 optimized lowest energy conformer

-

Molecule Context
mmff94OptimizedStructure() returns the MMFF94 optimized lowest energy conformer of the input molecule
Reaction Context
mmff94OptimizedStructure(reactant(0)) returns the MMFF94 optimized lowest energy conformer of the first reactant mmff94OptimizedStructure(product(1)) returns the MMFF94 optimized lowest energy conformer of the second product

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Dissimilarity Functions

Name

License

Description

Return value

Parameters

Examples

dissimilarity

-

computes the dissimilarity value between two molecules Note 1: Dissimilarity function requires JChem. Note 2: The dissimilarity values returned by dissimilarity function and similarity search in JChem database may differ because of the applied fingerprints. Dissimilarity function uses the default options of the chemical fingerprints (length=1024, bonds=7, bits=2) optimized for similarity search. Database similarity search uses fingerprints specified during the generation of the given table, optimized for substructure (and related) search types.

the dissimilarity value

descriptor: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)

Molecule Context
dissimilarity("PF", "c1ccccc1", "C1CCCCC1") returns the dissimilarity value between the benzene ring and cyclohexane, computed with pharmacophore fingerprint and its default metric (Tanimoto) dissimilarity("c1ccccc1", "C1CCCCC1") returns the dissimilarity value between the benzene ring and cyclohexane, computed with default fingerprint and its default metric (chemical fingerprint with Tanimoto) dissimilarity("PF:Euclidean", "c1ccccc1") returns the dissimilarity value between the benzene ring and the input molecule, computed with pharmacophore fingerprint and Euclidean metric dissimilarity("LogD", "c1ccccc1") returns the dissimilarity value between the benzene ring and the input molecule, computed with the LogD descriptor and its default AbsDiff metric
Reaction Context
dissimilarity("CF:Euclidean", "c1ccccc1", reactant(0)) returns the dissimilarity value between the benzene ring and the first reactant, computed with chemical fingerprint and Euclidean metric dissimilarity(reactant(0), product(0)) returns the dissimilarity value between the first reactant and the first product, computed with default fingerprint and its default metric (chemical fingerprint with Tanimoto)

Dissimilarity descriptors and metrics

Descriptor

Metric

ChemicalFingerprint (or CF)

Tanimoto (default) Euclidean

PharmacophoreFingerprint (or PF)

Tanimoto (default) Euclidean

ECFP

Tanimoto (default) Euclidean

Burden eigenvalue descriptor (or BCUT) (BCUT is a trademark of Tripos, Inc., used with permission)

Euclidean

HDon

Euclidean

HAcc

AbsDiff

Heavy

AbsDiff

LogD

AbsDiff

LogP

AbsDiff

Mass

AbsDiff

TPSA

AbsDiff

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Elemental Analysis Functions

Name

License

Description

Return value

Parameters

Examples

atomCount

-

calculates the number of atoms (all atoms or specific atoms)

the atom count

  • atomic number (optional) and mass number (optional) as a single string, separated by "." (e.g. "6" for the number of carbon atoms, "6.12" for the number of carbon atoms with mass number 12) - if omitted, all atoms are counted, if the mass number is set to 0 then all non-isotope atoms are counted

Molecule Context
atomCount() returns the number of atoms in the input molecule atomCount("6") returns the number of carbon atoms in the input molecule
Reaction Context
atomCount(reactant(0), "7") returns the number of nitrogen atoms in the first reactant atomCount(product(1), "7.14") returns the number of nitrogen atoms with mass number 14 in the second product atomCount(product(1), "7.0") returns the number of non-isotope nitrogen atoms in the second product

composition

-

returns the composition

the composition

-

Molecule Context
composition() returns the composition of the input molecule
Reaction Context
N / A (reaction rules are numerical)

dotDisconnectedFormula

-

returns the dot-disconnected formula

the dot-disconnected formula

-

Molecule Context
dotDisconnectedFormula() returns the dot-disconnected formula of the input molecule
Reaction Context
N / A (reaction rules are numerical)

dotDisconnectedIsotopeFormula

-

returns the dot-disconnected isotope formula

the dot-disconnected isotope formula

-

Molecule Context
dotDisconnectedIsotopeFormula() returns the dot-disconnected isotope formula of the input molecule
Reaction Context
N / A (reaction rules are numerical)

dotDisconnectedFormulaWithGrouping

-

returns the grouped dot-disconnected formula

the grouped dot-disconnected formula

-

Molecule Context
dotDisconnectedFormulaWithGrouping() returns the grouped dot-disconnected formula of the input molecule
Reaction Context
N / A (reaction rules are numerical)

 

 

 

 

 

 

elementalAnalysis

-

performs elemental analysis on molecule represented by formula

the value calculated by the invoked function (e.g., mass)

  • molecular formula
  • available functions:
    • atomCount
    • mass
    • massPrecision
    • exactMass
    • exactMassPrecision
    • formula
    • isotopeFormula
    • dotDisconnectedFormula
    • dotDisconnectedIsotopeFormula
    • groupedDotDisconnectedFormula

Molecule Context
elementalAnalysis('mass','C12H25O') returns the mass of molecule represented by formula
Reaction Context
N / A

exactMass

-

calculates the exact mass of the molecule

the exact mass

-

Molecule Context
exactMass() returns the exact mass of the input molecule
Reaction Context
exactMass(product(1)) returns the exact mass of the second product

formula

-

returns the formula

the formula

-

Molecule Context
formula() returns the formula of the input molecule
Reaction Context
N / A (reaction rules are numerical)

isotopeComposition

-

returns the isotope composition

the isotope composition

-

Molecule Context
isotopeComposition() returns the isotope composition of the input molecule
Reaction Context
N / A (reaction rules are numerical)

isotopeFormula

-

returns the isotope formula

the isotope formula

-

Molecule Context
isotopeFormula() returns the isotope formula of the input molecule
Reaction Context
N / A (reaction rules are numerical)

mass

-

calculates the molecule mass

the mass

-

Molecule Context
mass() returns the mass of the input molecule
Reaction Context
mass(reactant(0)) returns the mass of the first reactant

massspectrum

-

calculates the mass spectrum, the m/z:relative abundance plot

the mass spectrum as a series of discrete values

-

Molecule Context
massspectrum() returns the mass spectrum of the input molecule
Reaction Context
massspectrum(reactant(0)) returns the mass spectrum of the first reactant

sortableFormula

-

returns the fixed digit sortable formula

fixed digit sortable molecular formula

-

Molecule Context
sortableFormula() returns the sortable formula of the input molecule; sortableFormula('digits:4') returns the 4 digit sortable formula of the input molecule
Reaction Context
N / A (reaction rules are numerical)

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General Functions

Name

License

Description

Return value

Parameters

Examples

abs

-

returns the absolute value of a number

the absolute value

integer or real number

General (All)
abs(7)returns 7 abs(-4.9)returns 4.9
Molecule Context
abs(7)returns 7abs(-4.9)returns 4.9
Reaction Context
abs(7)returns 7abs(-4.9)returns 4.9

agentCount

-

counts the agents in the reaction

the number of agents in the reaction, or -1 if the the input (molecule) is not a reaction

-

Molecule Context
agentCount() returns n if the given molecule is a reaction and contains n agents. agentCount() returns -1 if the given molecule is not a reaction.
Reaction Context
agentCount() returns n if the given molecule is a reaction and contains n agents. agentCount(reactant(0)) and agentCount(product(1)) calls does not make sense, and will return -1.

arom

-

returns if the atom has an aromatic bond

true if the atom has an aromatic bond, false otherwise

atom index or MolAtom object

Molecule Context
arom(0) returns if the atom 0 has an aromatic bond
Reaction Context
arom(patom(2)) returns true if the product atom matching map 2 in the reaction equation has an aromatic bond

array

-

constructs an integer array from its arguments

the integer array

integers or MolAtom objects

General (All)
array(2, 5, 6, 8)
Molecule Context
array(2, 5, 6, 8)
Reaction Context
array(ratom(2), ratom(5), ratom(6), ratom(8)) array(patom(2), patom(5), patom(6), patom(8))

atno atomicNumber

-

returns the atomic number

the atomic number

atom index or MolAtom object

Molecule Context
atno(0) returns the atomic number of atom 0
Reaction Context
atno(ratom(1)) returns the atomic number of the reactant atom matching map 1

atomProp

-

 

 

 

 

atoms

-

 

 

 

 

booleanToNumber

-

returns the number representation of a boolean value (true = 1, false = 0), or the number itself, if the input is a number

the number representation of a boolean value

boolean or number

General (All)
booleanToNumber(1<2)returns 1 booleanToNumber(2+2==5)returns 0 booleanToNumber(5*5)returns 25
Molecule Context
booleanToNumber(hasValenceError())returns 0 for molecules having no valence error
Reaction Context
booleanToNumber(ringBond(reactant(0), bond(ratom(1), ratom(2))))returns 1 if reactant atoms matching maps 1 and 2 in the reaction equation are connected by a ring bond in the corresponding reactant, 0 otherwise

connections

-

returns the bond plus implicit H count of an atom

the bond plus implicit H count

atom index or MolAtom object

Molecule Context
connections(2) returns the number of connections of atom 2
Reaction Context
connections(ratom(1)) returns the number of connections of the reactant atom matching map 1 in the reaction equation

count

-

determines the number of elements in an array

the number of array elements

integer array or real number array

General (All)
count(array(3.4, 5.6, 1.2)) returns 3
Molecule Context
<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="3d9c0d4d-8de7-4846-b07d-8748fb331d6c"><ac:plain-text-body><![CDATA[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
]]></ac:plain-text-body></ac:structured-macro>
Reaction Context
<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="825f8469-0816-4a2d-85a4-0979e3c49ae8"><ac:plain-text-body><![CDATA[count(filter(reactant(1), "charge() > 0")) returns the number of atoms with positive charge in the second reactant count(filter(product(0), "match('[#8][C:1]=O', 1")) returns the number of carboxylic carbons in the first product

]]></ac:plain-text-body></ac:structured-macro>

elemanal

-

 

 

 

 

eval

-

 

 

 

 

field property

-

returns a molecule property (SDF field value)

the molecule property

the property key (SDF field name)

Molecule Context
field('ACTIVITY') returns the value of the ACTIVITY property (SDF field) field('ACTIVITY') > 2 returns 1 if the ACTIVITY value is bigger than 2, returns 0 otherwise
Reaction Context
field(reactant(1), 'ACTIVITY') returns the ACTIVITY property value of the second reactant field(product(0), 'ACTIVITY') > field(reactant(0), 'ACTIVITY') returns 1 if the ACTIVITY value of the first product is bigger than that of the first reactant, returns 0 otherwise

fieldAsString propertyAsString

-

returns a molecule property (SDF field value) as string

the molecule property as string

the property key (SDF field name)

Molecule Context
fieldAsString('ID') returns the value of the ID property (SDF field)
Reaction Context
field(reactant(0), 'ID') returns the value of the ID property field in first reactant

filter

-

filters target atoms by filtering condition

target atom indices satisfying the filtering condition

target atom indices / objects or index / atom object array (optional, all atoms taken if omitted), filtering condition (boolean expression)

Molecule Context
<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="060caeb3-8f40-46ad-a508-1aebced4275c"><ac:plain-text-body><![CDATA[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
]]></ac:plain-text-body></ac:structured-macro>
Reaction Context
<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="2639a0fc-8d39-4bd0-84aa-6a8d35a59641"><ac:plain-text-body><![CDATA[filter(reactant(0), "charge() > 0") returns the indices of atoms with positive partial charge in the first reactant filter(patom(1), patom(2), "match('[#8][C:1]=O', 1)") returns the carboxylic carbons out of product atoms matching map 1 or 2 in the reaction equation (note, that these atoms are supposed to be in the same product molecule)

]]></ac:plain-text-body></ac:structured-macro>

formalCharge totalCharge

-

calculates formal charge of molecule

the formal charge value

atom index or MolAtom object (optional)

Molecule Context
formalCharge() returns the formal charge of the input molecule formalCharge(0) returns the formal charge of atom 0
Reaction Context
formalCharge(reactant(0)) returns the formal charge of the first reactant formalCharge(ratom(1)) returns the formal charge of the reactant atom matching map 1

fragments

-

converts the molecule to its disconnected fragments

the disconnected fragments of the molecule

-

Molecule Context
fragments() returns the disconnected fragments of the molecule
Reaction Context
fragments(reactant(1)) returns the disconnected fragments of the second reactant

hasAromatizationError

-

determines if there is error in the aromatization of the molecule

true if there is an error in the aromatization of the molecule, false otherwise

-

Molecule Context
hasAromatizationError() returns true if there is an error in the aromatization of the molecule, false otherwise
Reaction Context
hasAromatizationError(reactant(0)) returns true if there is an error in the aromatization of the first reactant, false otherwise

hasIsotope

-

determines if any atom in the molecule is a specific isotope of the element

true if any atom in the molecule is a specific isotope of the element, false otherwise

-

Molecule Context
hasIsotope() returns true if any atom in the molecule is a specific isotope of the element, false otherwise
Reaction Context
hasIsotope(reactant(1)) returns true if any atom in the second reactant is a specific isotope of the element, false otherwise

hasRadical

-

determines if any atom in the molecule has radical

true if any atom in the molecule has radical, false otherwise

-

Molecule Context
hasRadical() returns true if any atom in the molecule has radical, false otherwise
Reaction Context
hasRadical(reactant(1)) returns true if any atom in the second reactant has radical, false otherwise

hasValenceError

-

determines if any atom in the molecule has valence error

true in case of valence error, false otherwise

-

Molecule Context
hasValenceError() returns true if any atom in the molecule has valence error, false otherwise
Reaction Context
hasValenceError(reactant(1)) returns true if any atom in the second reactant has valence error, false otherwise

HBDA

Structural Calculations License

 

 

 

 

hCount

-

returns the hydrogen count of an atom

the hydrogen count

atom index or array of atom indeces (separated by , or (wink) or MolAtom object

Molecule Context
hCount(0;2;3) returns the hydrogen count of atom 0,2,3
Reaction Context
hCount(patom(3)) returns the hydrogen count on the product atom matching map 3 in the reaction equation

importMol

-

imports and returns the molecule from its string representation

the string representation of the molecule

the molecule in string representation (e.g. "c1ccccc1")

Molecule Context
importMol("c1ccccc1") returns benzene molecule
Reaction Context
N / A (reaction rules are numerical)

in

-

determines whether an integer / atom index is contained in a given integer array

true if the array contains the specified integer, false otherwise

an integer or MolAtom object and an integer array

General (All)
in(5, array(3, 5, 1)) returns true in(2, array(3, 5, 1)) returns false
Molecule Context
in(3, maxatom("charge()", 2)) returns true if the partial charge on atom 3 is within the first 2 largest partial charges in the input molecule in(3, minatom("pol()", 4)) returns true if the polarizability on atom 3 is within the first 4 smallest polarizability values in the input molecule
Reaction Context
in(ratom(3), maxatom(reactant(0), "charge()", 2)) returns true if the partial charge on reactant atom matching map 3 in the reaction equation is within the first 2 largest partial charges in the first reactant in(patom(1), minatom(product(1), "pol()", 4)) returns true if the polarizability on product atom matching map 1 in the reaction equation is within the first 4 smallest polarizability values in the second product

ionCharge

Structural Calculations License

 

 

 

 

isEmpty

-

decides whether the given molecule is empty (does not contain any atoms, bonds, or non-empty S-groups)

true if the molecule does not contain any atoms, bonds, or non-empty S-groups, false otherwise

-

Molecule Context
isQuery() returns true if the given molecule does not contain any atoms, bonds, or non-empty S-groups, false otherwise
Reaction Context
isQuery(reactant(1)) returns true if the second reactant contains any atoms, bonds, or non-empty S-groups, false otherwise

isQuery

-

decides whether the given molecule contains any query features

true if the molecule contains any query features, false otherwise

-

Molecule Context
isQuery() returns true if the given molecule contains any query features, false otherwise
Reaction Context
isQuery(reactant(1)) returns true if the second reactant contains any query features, false otherwise

map

-

returns the atom map number

the atom map number

atom index or MolAtom object

Molecule Context
map(3) returns the atom map number of atom 3
Reaction Context
map(patom(3)) returns the atom map number on the product atom matching map 3 in the reaction equation

max

-

takes maximum of its array and/or numerical parameters

the maximum value

integers, real numbers, integer arrays, real number arrays

General (All)
min(2, 8, 6) returns 2 max(3.4, 5.6, 1.2) returns 5.6
Molecule Context
min(charge(0), charge(2)) returns the least of the partial charge values on atoms 0 and 2 max(charge()) returns the maximal partial charge value on the input molecule
Reaction Context
min(charge(ratom(2)), charge(ratom(3))) returns the least of the partial charge values on reactant atoms matching maps 2 and 3 in the reaction equation max(charge(product(0))) returns the maximal partial charge value on the first product

maxAtom

-

evaluates objective function for each atom, finds largest value(s)

the atom index / indices corresponding to the largest evaluation result(s)

target atom indices / objects or index / atom object array (optional, all atoms taken if omitted), the objective function (as inner expression string), the number of largest values to be taken (optional, takes only one if omitted)

Molecule Context
maxAtom(6, 7, 8, 9, "charge('7.4')", 2) selects the two largest partial charges on atoms 6, 7, 8, 9 in the major microspecies at pH 7.4 of the input molecule and returns the corresponding indices
Reaction Context
maxAtom(patom(1), patom(2), patom(3), "charge('7.4')", 2) selects the two largest partial charges on product atoms matching maps 1, 2, 3 in the major microspecies at pH 7.4 of the product molecule of these atoms and returns the corresponding indices (note, that these atoms are supposed to be in the same product molecule)

maxValue

-

evaluates objective function for each atom, finds largest value(s)

the largest evaluation result(s)

target atom indices / objects or index / atom object array (optional, all atoms taken if omitted), the objective function (as inner expression string), the number of largest values to be taken (optional, takes only one if omitted)

Molecule Context
maxValue(6, 7, 8, 9, "charge('7.4')", 2) returns the two largest partial charges on atoms 6, 7, 8, 9 in the major microspecies at pH 7.4 of the input molecule
Reaction Context
maxValue(patom(1), patom(2), patom(3), "charge('7.4')", 2) returns the two largest partial charges on product atoms matching maps 1, 2, 3 in the major microspecies at pH 7.4 of the product molecule of these atoms (note, that these atoms are supposed to be in the same product molecule)

min

-

takes minimum of its array and/or numerical parameters

the minimum value

integers, real numbers, integer arrays, real number arrays

General (All)
min(2, 8, 6) returns 2 max(3.4, 5.6, 1.2) returns 5.6
Molecule Context
min(charge(0), charge(2)) returns the least of the partial charge values on atoms 0 and 2 max(charge()) returns the maximal partial charge value on the input molecule
Reaction Context
min(charge(ratom(2)), charge(ratom(3))) returns the least of the partial charge values on reactant atoms matching maps 2 and 3 in the reaction equation max(charge(product(0))) returns the maximal partial charge value on the first product

minAtom

-

evaluates objective function for each atom, finds smallest value(s)

the atom index / indices corresponding to the smallest evaluation result(s)

target atom indices / objects or index / atom object array (optional, all atoms taken if omitted), the objective function (as inner expression string), the number of smallest values to be taken (optional, takes only one if omitted)

Molecule Context
minAtom("charge('7.4')") returns the atom index corresponding to minimum partial charge in the major microspecies at pH 7.4 of the input molecule
Reaction Context
minAtom(reactant(0), "charge('7.4')") returns the atom index corresponding to minimum partial charge in the major microspecies at pH 7.4 of the first reactant

minValue

-

evaluates objective function for each atom, finds smallest value(s)

the smallest evaluation result(s)

target atom indices / objects or index / atom object array (optional, all atoms taken if omitted), the objective function (as inner expression string), the number of smallest values to be taken (optional, takes only one if omitted)

Molecule Context
minValue("charge('7.4')") returns the minimum partial charge in the major microspecies at pH 7.4 of the input molecule
Reaction Context
minValue(reactant(0), "charge('7.4')") returns the minimum partial charge in the major microspecies at pH 7.4 of the first reactant

molAtom

-

creates a MolAtom

the MolAtom object

atomic number

Molecule Context
molAtom(6) returns a carbon atom
Reaction Context
molAtom(6) returns a carbon atom

molBinFormat molImage

-

returns the binary representation (image, pdf, GZIP compressed molecule file) of the molecule in specified format

the binary representation (image, pdf, GZIP compressed molecule file) of the molecule

the binary format with options (e.g. "jpeg", "png:w150,h150", "pdf", "gzip:sdf")

Molecule Context
molImage("jpeg:w100,Q95,#ffff00") returns the 100x100 JPEG image of the input molecule with yellow background, 95% quality
Reaction Context
N / A (reaction rules are numerical)

molString molConvert molFormat

-

returns the string representation of a molecule, or an array of molecules, in specified molecule format

the string representation of the molecule(s)

  • the molecule format (e.g. "mol", "sdf", "mrv", "smiles")
  • the clean dimension

Molecule Context
molFormat("mrv") returns the ChemAxon Marvin Document format representation of the input molecule molFormat(tautomers(), "sdf", 2) returns the SDF format representation of the tautomers of the input molecule
Reaction Context
N / A (reaction rules are numerical)

pair bond

-

converts two atoms or 0-based atom indexes into an "index1-index2" 1-based atom index setter string (used for pairing atoms in shortestPath )

the generated string

two atom indexes or two MolAtom objects

General (All)
pair(2, 5) returns "3-6"
Reaction Context
pair(ratom(1), ratom(2)) returns "index1-index2" where "index1" and "index2" are the 1-based atom indexes of the reactant atoms matching map 1 and 2 in the reaction equation bond(patom(2), patom(5) returns "index1-index2" where "index1" and "index2" are the 1-based atom indexes of the product atoms matching map 2 and 5 in the reaction equation

productCount

-

counts the products in the reaction

the number of products in the reaction, or -1 if the the input (molecule) is not a reaction

-

Molecule Context
productCount() returns n if the given molecule is a reaction and contains n products. productCount() returns -1 if the given molecule is not a reaction.
Reaction Context
productCount() returns n if the given molecule is a reaction and contains n products. productCount(product(0)) and productCount(product(1)) calls does not make sense, and will return -1.

radicalCount

-

returns the radical count of an atom

the radical count

atom index or MolAtom object

Molecule Context
radicalCount(0) returns the radical count of atom 0
Reaction Context
radicalCount(patom(3)) returns the radical count on the product atom matching map 3 in the reaction equation

reactantCount

-

counts the reactants in the reaction

the number of reactants in the reaction, or -1 if the the input (molecule) is not a reaction

-

Molecule Context
reactantCount() returns n if the given molecule is a reaction and contains n reactants. reactantCount() returns -1 if the given molecule is not a reaction.
Reaction Context
reactantCount() returns n if the given molecule is a reaction and contains n reactants. reactantCount(reactant(0)) and reactantCount(product(1)) calls does not make sense, and will return -1.

sortAsc

-

sorts an array in ascending order

the sorted array

integer array or real number array

General (All)
sortAsc(array(3.4, 5.6, 1.2)) returns array(1.2, 3.4, 5.6)
Molecule Context
sortAsc(charge()) returns the partial charge values in ascending order
Reaction Context
sortAsc(charge(reactant(1))) returns the partial charge values of the second reactant in ascending order

sortDesc

-

sorts an array in descending order

the sorted array

integer array or real number array

General (All)
sortDesc(array(3.4, 5.6, 1.2)) returns array(5.6, 3.4, 1.2)
Molecule Context
sortDesc(pka("basic")) returns the basic pK a values in descending order
Reaction Context
sortDesc(pka(product(0), "basic")) returns the basic pK a values of the first product in descending order

sum

-

computes the sum of array elements

the sum

integer array or real number array

General (All)
sum(array(3.4, 5.6, 1.2)) returns 10.2
Molecule Context
sum(charge()) returns the sum of charge values sum(pol()) returns the sum of atom polarizability values
Reaction Context
sum(charge(reactant(0))) returns the sum of charge values in the first reactant sum(pol(product(0))) returns the sum of atom polarizability values in the first product

topanal

Structural Calculations License

 

 

 

 

valence

-

returns the sum of bond orders and query H atoms of an atom

the sum of bond orders and query H atoms

atom index or MolAtom object

Molecule Context
valence(0) returns the valence of atom 0
Reaction Context
valence(ratom(1)) returns the valence of the reactant atom matching map 1 in the reaction equation

whereIsValenceError

-

returns the index of the first atom with valence error, or -1 if there is no valence error

the index of the first atom with valence error, or -1 if there is no valence error

-

Molecule Context
whereIsValenceError() returns the index of the first atom with valence error, or -1 if there is no valence error in the molecule
Reaction Context
whereIsValenceError(reactant(1)) returns the index of the first atom with valence error in the second reactant, or -1 f there is no valence error in the second reactant

Back to Contents
 
 

Geometry Functions

Name

License

Description

Return value

Parameters

Examples

aliphaticAtom

Structural Calculations License

checks if the specified atom is aliphatic

true for aliphatic atoms, false for non-aliphatic atoms

  • the atom index / MolAtom object

Molecule Context
aliphaticAtom(2) returns true if atom 2 of the input molecule is aliphatic, false otherwise
Reaction Context
aliphaticAtom(ratom(2)) returns true if the reactant atom matching map 2 in the reaction equation is aliphatic, false otherwise aliphaticAtom(patom(1)) returns true if the product atom matching map 1 in the reaction equation is aliphatic, false otherwise

aliphaticAtomCount

Structural Calculations License

calculates the aliphatic atom count

the aliphatic atom count

-

Molecule Context
aliphaticAtomCount() returns the number of aliphatic atoms in the input molecule
Reaction Context
aliphaticAtomCount(reactant(0)) returns the number of aliphatic atoms in the first reactant aliphaticAtomCount(product(1)) returns the number of aliphatic atoms in the second product

aliphaticBondCount

Structural Calculations License

calculates the aliphatic bond count

the aliphatic bond count

-

Molecule Context
aliphaticBondCount() returns the number of bonds in the input molecule
Reaction Context
aliphaticBondCount(reactant(0)) returns the number of aliphatic bonds in the first reactant aliphaticBondCount(product(1)) returns the number of aliphatic bonds in the second product

aliphaticRingCount

Structural Calculations License

calculates the aliphatic ring count

the aliphatic ring count

-

Molecule Context
aliphaticRingCount() returns the number of aliphatic rings in the input molecule
Reaction Context
aliphaticRingCount(reactant(0)) returns the number of aliphatic rings in the first reactant aliphaticRingCount(product(1)) returns the number of aliphatic rings in the second product

aliphaticRingCountOfSize

Structural Calculations License

calculates the number of aliphatic rings of given size

the number of aliphatic rings of given size

the ring size

Molecule Context
aliphaticRingCountOfSize(6) returns the number of aliphatic rings of size 6 in the input molecule
Reaction Context
aliphaticRingCountOfSize(reactant(0), 5) returns the number of aliphatic rings of size 5 in the first reactant aliphaticRingCountOfSize(product(1), 5) returns the number of aliphatic rings of size 5 in the second product

aliphaticRings

Structural Calculations License

identifies the aliphatic rings in the molecule

atom indexes of the aliphatic rings in the molecule (null if the molecule does not contain aliphatic rings)

-

Molecule Context
aliphaticRings() returns the atom indexes of the aliphatic rings in the input molecule
Reaction Context
aliphaticRings(reactant(0)) returns the atom indexes of the aliphatic rings in the first reactant aliphaticRings(product(1)) returns the atom indexes of the aliphatic rings in the second product

aliphaticRingsOfSize

Structural Calculations License

identifies the aliphatic rings in the molecule having a given size (number of atoms)

atom indexes of the aliphatic rings in the molecule having the given size (null if the molecule does not contain aliphatic rings)

the ring size

Molecule Context
aliphaticRings() returns the atom indexes of the aliphatic rings in the input molecule having the given size
Reaction Context
aliphaticRings(reactant(0)) returns the atom indexes of the aliphatic rings in the first reactant having the given size aliphaticRings(product(1)) returns the atom indexes of the aliphatic rings in the second product having the given size

angle

Structural Calculations License

calculates the angle between three atoms

the angle between three atoms

  • the (1-based) atom indexes of the three atoms in a string: "index1-index2-index3" (e.g. '2-3-5')

Molecule Context
angle('1-2-3') and angle(atoms(0, 1, 2)) both return the angle between atoms 1, 2 and 3 in the input molecule
Reaction Context
angle(reactant(0), atoms(ratom(1), ratom(2), ratom(3))) returns the angle between reactant atoms matching maps 1, 2 and 3 in the reaction equation (see note 1) angle(product(1), atoms(patom(2), patom(3), patom(4))) returns the angle between product atoms matching maps 2, 3 and 4 in the reaction equation (see note 1)

aromaticAtom

Structural Calculations License

checks if the specified atom is aromatic

true for aromatic atoms, false for non-aromatic atoms

  • the atom index / MolAtom object

Molecule Context
aromaticAtom(2) returns true if atom 2 of the input molecule is aromatic, false otherwise
Reaction Context
aromaticAtom(ratom(2)) returns true if the reactant atom matching map 2 in the reaction equation is aromatic, false otherwise aromaticAtom(patom(1)) returns true if the product atom matching map 1 in the reaction equation is aromatic, false otherwise

aromaticAtomCount

Structural Calculations License

calculates the aromatic atom count

the aromatic atom count

-

Molecule Context
aromaticAtomCount() returns the number of aromatic atoms in the input molecule
Reaction Context
aromaticAtomCount(reactant(0)) returns the number of aromatic atoms in the first reactant aromaticAtomCount(product(1)) returns the number of aromatic atoms in the second product

aromaticBondCount

Structural Calculations License

calculates the aromatic bond count

the aromatic bond count

-

Molecule Context
aromaticBondCount() returns the number of aromatic bonds in the input molecule
Reaction Context
aromaticBondCount(reactant(0)) returns the number of aromatic bonds in the first reactant aromaticBondCount(product(1)) returns the number of aromatic bonds in the second product

aromaticRingCount

Structural Calculations License

calculates the aromatic ring count

the aromatic ring count

-

Molecule Context
aromaticRingCount() returns the number of aromatic rings in the input molecule
Reaction Context
aromaticRingCount(reactant(0)) returns the number of aromatic rings in the first reactant aromaticRingCount(product(1)) returns the number of aromatic rings in the second product

aromaticRingCountOfSize

Structural Calculations License

calculates the number of aromatic rings of given size

the number of aromatic rings of given size

the ring size

Molecule Context
aromaticRingCountOfSize(6) returns the number of aromatic rings of size 6 in the input molecule
Reaction Context
aromaticRingCountOfSize(reactant(0), 5) returns the number of aromatic rings of size 5 in the first reactant aromaticRingCountOfSize(product(1), 5) returns the number of aromatic rings of size 5 in the second product

aromaticRings

Structural Calculations License

identifies the aromatic rings in the molecule

atom indexes of the aromatic rings in the molecule (null if the molecule does not contain aromatic rings)

-

Molecule Context
aromaticRings() returns the atom indexes of the aromatic rings in the input molecule
Reaction Context
aromaticRings(reactant(0)) returns the atom indexes of the aromatic rings in the first reactant aromaticRings(product(1)) returns the atom indexes of the aromatic rings in the second product

aromaticRingsOfSize

Structural Calculations License

identifies the aromatic rings in the molecule having a given size (number of atoms)

atom indexes of the aromatic rings in the molecule having the given size (null if the molecule does not contain aromatic rings)

the ring size

Molecule Context
aromaticRings() returns the atom indexes of the aromatic rings in the input molecule having the given size
Reaction Context
aromaticRings(reactant(0)) returns the atom indexes of the aromatic rings in the first reactant having the given size aromaticRings(product(1)) returns the atom indexes of the aromatic rings in the second product having the given size

ASAHydrophobic

Structural Calculations License

calculates the water accessible molecular surface area of all hydrophobic atoms

the molecular surface area

  • the major microspecies pH (takes the input molecule itself if omitted)

Molecule Context
ASAHydrophobic() returns the water accessible surface area of all atoms of the input molecule with hydrophobic partial charge ASAHydrophobic('7.4')returns the water accessible surface area of all atoms with hydrophobic partial charge of the major microspecies taken at pH 7.4
Reaction Context
ASAHydrophobic(reactant(0)) returns the water accessible surface area of all atoms of the first reactant with hydrophobic partial charge ASAHydrophobic(product(0), '7.4') returns the water accessible surface area of all atoms with hydrophobic partial charge of the major microspecies of the first product taken at pH 7.4

ASANegative

Structural Calculations License

calculates the water accessible molecular surface area of all atoms with negative partial charge

the molecular surface area

  • the major microspecies pH (takes the input molecule itself if omitted)

Molecule Context
ASANegative() returns the water accessible surface area of all atoms of the input molecule with negative partial charge ASANegative('7.4')returns the water accessible surface area of all atoms with negative partial charge of the major microspecies taken at pH 7.4
Reaction Context
ASANegative(reactant(0)) returns the water accessible surface area of all atoms of the first reactant with negative partial charge ASANegative(product(0), '7.4') returns the water accessible surface area of all atoms with negative partial charge of the major microspecies of the first product taken at pH 7.4

ASAPlus

Structural Calculations License

calculates the water accessible molecular surface area of all atoms with positive partial charge

the molecular surface area

  • the major microspecies pH (takes the input molecule itself if omitted)

Molecule Context
ASAPlus() returns the water accessible surface area of all atoms of the input molecule with positive partial charge ASAPlus('7.4')returns the water accessible surface area of all atoms with positive partial charge of the major microspecies taken at pH 7.4
Reaction Context
ASAPlus(reactant(0)) returns the water accessible surface area of all atoms of the first reactant with positive partial charge ASAPlus(product(0), '7.4') returns the water accessible surface area of all atoms with positive partial charge of the major microspecies of the first product taken at pH 7.4

ASAPolar

Structural Calculations License

calculates the water accessible molecular surface area of all polar atoms

the molecular surface area

  • the major microspecies pH (takes the input molecule itself if omitted)

Molecule Context
ASAPolar() returns the water accessible surface area of all atoms of the input molecule with polar partial charge ASAPolar('7.4')returns the water accessible surface area of all atoms with polar partial charge of the major microspecies taken at pH 7.4
Reaction Context
ASAPolar(reactant(0)) returns the water accessible surface area of all atoms of the first reactant with polar partial charge ASAPolar(product(0), '7.4') returns the water accessible surface area of all atoms with polar partial charge of the major microspecies of the first product taken at pH 7.4

asymmetricAtom

Structural Calculations License

checks if the specified atom is an asymmetric atom

true for asymmetric atoms, false for symmetric atoms

  • the atom index / MolAtom object

Molecule Context
asymmetricAtom(2) returns true if atom 2 of the input molecule is an asymmetric atom, false otherwise
Reaction Context
asymmetricAtom(ratom(2)) returns true if the reactant atom matching map 2 in the reaction equation is an asymmetric atom, false otherwise asymmetricAtom(patom(1)) returns true if the product atom matching map 1 in the reaction equation is an asymmetric atom, false otherwise

asymmetricAtomCount

Structural Calculations License

calculates the number of asymmetric atoms

the asymmetric atom count

-

Molecule Context
asymmetricAtomCount() returns the number of asymmetric atoms in the input molecule
Reaction Context
asymmetricAtomCount(reactant(0)) returns the number of asymmetric atoms in the first reactant asymmetricAtomCount(product(1)) returns the number of asymmetric atoms in the second product

asymmetricAtoms

Structural Calculations License

determines the asymmetric atoms

indexes of asymmetric atoms

-

Molecule Context
asymmetricAtoms() returns the indexes of asymmetric atoms in the input molecule
Reaction Context
asymmetricAtoms(reactant(0)) returns the indexes of asymmetric atoms in the first reactant asymmetricAtoms(product(1)) returns the indexes of asymmetric atoms in the second product

balabanIndex

Structural Calculations License

calculates the Balaban index

the Balaban index

-

Molecule Context
calculates the Balaban index
Reaction Context
the Balaban index

bondCount

-

calculates the bond count

the bond count

-

Molecule Context
bondCount() returns the number of bonds in the input molecule
Reaction Context
bondCount(reactant(0)) returns the number of bonds in the first reactant bondCount(product(1)) returns the number of bonds in the second product

bondType

Structural Calculations License

returns the bond type between two atoms

the bond type between two atoms, -1 if there is no bond between the two atoms

  • the (1-based) atom indexes of the two atoms in a string: "index1-index2" (e.g. '2-3')

Molecule Context
bondType('2-3') and bondType(bond(1, 2)) both return the bond type between atoms 1 and 2 in the input molecule
Reaction Context
bondType(reactant(0), bond(ratom(1), ratom(2))) returns the bond type between reactant atoms matching maps 1 and 2 in the reaction equation (see note 1) bondType(product(1), bond(patom(2), patom(3))) returns the bond type between product atoms matching maps 2 and 3 in the reaction equation (see note 1)

carboaliphaticRingCount

Structural Calculations License

calculates the number of carboaliphatic rings in the molecule (aliphatic rings containing carbon atoms only)

number of carboaliphatic rings

-

Molecule Context
carboaliphaticRingCount() returns the number of carboaliphatic rings in the input molecule
Reaction Context
carboaliphaticRingCount(reactant(0)) returns the number of carboaliphatic rings in the first reactant carboaliphaticRingCount(product(1)) returns the number of carboaliphatic rings in the second product

carboaromaticRingCount

Structural Calculations License

calculates the number of carboaromatic rings in the molecule (aromatic rings containing carbon atoms only)

number of carboaromatic rings

-

Molecule Context
carboaromaticRingCount() returns the number of carboaromatic rings in the input molecule
Reaction Context
carboaromaticRingCount(reactant(0)) returns the number of carboaromatic rings in the first reactant carboaromaticRingCount(product(1)) returns the number of carboaromatic rings in the second product

carboRingCount

Structural Calculations License

calculates the number of carbocyclic rings in the molecule (rings containing carbon atoms only)

number of carbocyclic rings

-

Molecule Context
carboRingCount() returns the number of carbocyclic rings in the input molecule
Reaction Context
carboRingCount(reactant(0)) returns the number of carbocyclic rings in the first reactant carboRingCount(product(1)) returns the number of carbocyclic rings in the second product

carboRingCountOfSize

Structural Calculations License

calculates the number of carbocyclic rings of given size (rings containing carbon atoms only)

the number of carbocyclic rings of given size

the ring size

Molecule Context
carboRingCountOfSize(6) returns the number of carbocyclic rings of size 6 in the input molecule
Reaction Context
carboRingCountOfSize(reactant(0), 5) returns the number of carbocyclic rings of size 5 in the first reactant carboRingCountOfSize(product(1), 5) returns the number of carbocyclic rings of size 5 in the second product

carboRings

Structural Calculations License

identifies the carbocyclic rings in the molecule (rings containing carbon atoms only)

atom indexes of the carbocyclic rings in the molecule (null if the molecule does not contain carbocyclic rings)

-

Molecule Context
carboRings() returns the atom indexes of the carbocyclic rings in the input molecule
Reaction Context
carboRings(reactant(0)) returns the atom indexes of the carbocyclic rings in the first reactant carboRings(product(1)) returns the atom indexes of the carbocyclic rings in the second product

carboRingsOfSize

Structural Calculations License

identifies the carbocyclic rings in the molecule having a given size (number of atoms)

atom indexes of the carbocyclic rings in the molecule having the given size (null if the molecule does not carbocyclic carbo rings)

the ring size

Molecule Context
carboRings() returns the atom indexes of the carbocyclic rings in the input molecule having the given size
Reaction Context
carboRings(reactant(0)) returns the atom indexes of the carbocyclic rings in the first reactant having the given size carboRings(product(1)) returns the atom indexes of the carbocyclic rings in the second product having the given size

chainAtom

Structural Calculations License

checks if the specified atom is a chain atom

true for chain atoms, false for non-chain atoms

  • the atom index / MolAtom object

Molecule Context
chainAtom(2) returns true if atom 2 of the input molecule is a chain atom, false otherwise
Reaction Context
chainAtom(ratom(2)) returns true if the reactant atom matching map 2 in the reaction equation is a chain atom, false otherwise chainAtom(patom(1)) returns true if the product atom matching map 1 in the reaction equation is a chain atom, false otherwise

chainAtomCount

Structural Calculations License

calculates the chain atom count

the chain atom count

-

Molecule Context
chainAtomCount() returns the number of chain atoms in the input molecule
Reaction Context
chainAtomCount(reactant(0)) returns the number of chain atoms in the first reactant chainAtomCount(product(1)) returns the number of chain atoms in the second product

chainBond

Structural Calculations License

checks if two atoms are connected by a chain bond

true if the two atoms are connected by a chain bond, false otherwise

  • the (1-based) atom indexes of the two atoms in a string: "index1-index2" (e.g. '2-3')

Molecule Context
chainBond('2-3') and chainBond(bond(1, 2)) both return true if atoms 1 and 2 are connected by a chain bond the input molecule
Reaction Context
chainBond(reactant(0), bond(ratom(1), ratom(2))) returns true if reactant atoms matching maps 1 and 2 in the reaction equation are connected by a chain bond in the corresponding reactant molecule (see note 1) chainBond(product(1), bond(patom(2), patom(3))) returns true if product atoms matching maps 2 and 3 in the reaction equation are connected by a chain bond in the corresponding product molecule (see note 1)

chainBondCount

Structural Calculations License

calculates the chain bond count

the chain bond count

-

Molecule Context
chainBondCount() returns the number of chain bonds in the input molecule
Reaction Context
chainBondCount(reactant(0)) returns the number of chain bonds in the first reactant chainBondCount(product(1)) returns the number of chain bonds in the second product

chiralCenter

Structural Calculations License

checks if the specified atom is a tetrahedral stereogenic center

true for tetrahedral stereogenic center atoms

  • the atom index / MolAtom object

Molecule Context
chiralCenter(2) returns true if atom 2 of the input molecule is a tetrahedral stereogenic center, false otherwise
Reaction Context
chiralCenter(ratom(2)) returns true if the reactant atom matching map 2 in the reaction equation is a tetrahedral stereogenic center, false otherwise chiralCenter(patom(1)) returns true if the product atom matching map 1 in the reaction equation is a tetrahedral stereogenic center, false otherwise

chiralCenterCount

Structural Calculations License

calculates the number of tetrahedral stereogenic center atoms

the tetrahedral stereogenic center count

-

Molecule Context
chiralCenterCount() returns the number of tetrahedral stereogenic centers in the input molecule
Reaction Context
chiralCenterCount(reactant(0)) returns the number of tetrahedral stereogenic centers in the first reactant chiralCenterCount(product(1)) returns the number of tetrahedral stereogenic centers in the second product

chiralCenters

Structural Calculations License

determines the chiral center atoms

indexes of chiral center atoms

-

Molecule Context
chiralCenters() returns the indexes of chiral center atoms in the input molecule
Reaction Context
chiralCenters(reactant(0)) returns the indexes of chiral center atoms in the first reactant chiralCenters(product(1)) returns the indexes of chiral center atoms in the second product

connected

Structural Calculations License

checks if two atoms are connected

true if the two atoms belong to the same connected component, false otherwise

  • the (1-based) atom indexes of the two atoms in a string: "index1-index2" (e.g. '2-3')

Molecule Context
connected('2-3') and connected(pair(1, 2)) both return true if atoms 1 and 2 are in the same connected component of the input molecule
Reaction Context
connected(reactant(0), pair(ratom(1), ratom(2))) returns true if reactant atoms matching maps 1 and 2 in the reaction equation are connected in the corresponding reactant molecule (see note 1) connected(product(1), pair(patom(2), patom(3))) returns true if product atoms matching maps 2 and 3 in the reaction equation are connected in the corresponding product molecule (see note 1)

connectedGraph

Structural Calculations License

checks whether the molecule graph is connected

true if the molecule graph is connected, false otherwise

-

Molecule Context
connectedGraph() returns true if the input molecule graph is connected
Reaction Context
connectedGraph(reactant(0)) returns true if the first reactant is connected connectedGraph(product(1)) returns true if the second product is connected

cyclomaticNumber

Structural Calculations License

calculates the cyclomatic number

the cyclomatic number

-

Molecule Context
cyclomaticNumber() returns the cyclomatic number of the input molecule
Reaction Context
cyclomaticNumber(reactant(0)) returns the cyclomatic number of the first reactant cyclomaticNumber(product(1)) returns the cyclomatic number of the second product

dihedral

Structural Calculations License

calculates the dihedral of four atoms

the dihedral of four atoms

  • the (1-based) atom indexes of the four atoms in a string: "index1-index2-index3-index4" (e.g. '2-3-7-4')

Molecule Context
dihedral('1-2-3-4') and dihedral(atoms(0, 1, 2, 3)) both return the dihedral of atoms 1, 2, 3 and 4 in the input molecule
Reaction Context
dihedral(reactant(0), atoms(ratom(1), ratom(2), ratom(3), ratom(4))) returns the dihedral of reactant atoms matching maps 1, 2, 3 and 4 in the reaction equation (see note 1) dihedral(product(1), atoms(patom(2), patom(3), patom(5), patom(6))) returns the dihedral of product atoms matching maps 2, 3, 5 and 6 in the reaction equation (see note 1)

distance

Structural Calculations License

calculates the distance between two atoms

the distance between two atoms

  • the (1-based) atom indexes of the two atoms in a string: "index1-index2" (e.g. '2-3')

Molecule Context
distance('1-2') and distance(pair(0, 1)) both return the distance between atoms 1 and 2 in the input molecule
Reaction Context
distance(reactant(0), pair(ratom(1), ratom(2))) returns the distance between reactant atoms matching maps 1 and 2 in the reaction equation (see note 1) distance(product(1), pair(patom(2), patom(3))) returns the distance between product atoms matching maps 2 and 3 in the reaction equation (see note 1)

distanceDegree

Structural Calculations License

calculates the distance degree of an atom

the distance degree

  • the atom index / MolAtom object

Molecule Context
distanceDegree(2) returns the distance degree of atom 2 of the input molecule
Reaction Context
distanceDegree(ratom(2)) returns the distance degree of the reactant atom matching map 2 in the reaction equation distanceDegree(patom(1)) returns the distance degree of the product atom matching map 1 in the reaction equation

dreidingEnergy

Structural Calculations License

returns the Dreiding energy of the input molecule (conformer)

the dreiding energy

-

Molecule Context
dreidingEnergy() returns the dreiding energy of the input molecule (conformer)
Reaction Context
dreidingEnergy(reactant(0)) returns the dreiding energy of the first reactant dreidingEnergy(product(1)) returns the dreiding energy of the second product

eccentricity

Structural Calculations License

calculates the eccentricity of an atom

the eccentricity of an atom

  • the atom index / MolAtom object

Molecule Context
eccentricity(2) returns the eccentricity of atom 2 of the input molecule
Reaction Context
eccentricity(ratom(2)) returns the eccentricity of the reactant atom matching map 2 in the reaction equation eccentricity(patom(1)) returns the distance degree of the product atom matching map 1 in the reaction equation

fragmentCount

Structural Calculations License

returns the number of fragments (disconnected parts)

the fragment count

-

Molecule Context
fragmentCount() returns the number of fragments in the input molecule
Reaction Context
fragmentCount(reactant(0)) returns the number of fragments in the first reactant fragmentCount(product(1)) returns the number of fragments in the second product

fsp3

Structural Calculations License

returns the fsp3 of the molecule

the fsp3 value

-

Molecule Context
fsp3() returns the fsp3 value of the input molecule
Reaction Context
fsp3(reactant(0)) returns the fsp3 value of the first reactant fsp3(product(1)) returns the fsp3 value of the second product

fusedAliphaticRingCount

Structural Calculations License

calculates the number of fused aliphatic rings (SSSR smallest set of smallest aliphatic rings)

the fused aliphatic ring count

-

Molecule Context
fusedAliphaticRingCount() returns the number of fused aliphatic rings in the input molecule
Reaction Context
fusedAliphaticRingCount(reactant(0)) returns the number of fused aliphatic rings in the first reactant fusedAliphaticRingCount(product(1)) returns the number of fused aliphatic rings in the second product

fusedAliphaticRingCountOfSize

Structural Calculations License

calculates the number of fused aliphatic rings of given size

the number of fused aliphatic rings of given size

the ring size

Molecule Context
fusedAliphaticRingCountOfSize(6) returns the number of fused aliphatic rings of size 6 in the input molecule
Reaction Context
fusedAliphaticRingCountOfSize(reactant(0), 5) returns the number of fused aliphatic rings of size 5 in the first reactant fusedAliphaticRingCountOfSize(product(1), 5) returns the number of fused aliphatic rings of size 5 in the second product

fusedAliphaticRings

Structural Calculations License

identifies the fused aliphatic rings in the molecule

atom indexes of the fused aliphatic rings in the molecule (null if the molecule does not contain fused aliphatic rings)

-

Molecule Context
fusedAliphaticRings() returns the atom indexes of the fused aliphatic rings in the input molecule
Reaction Context
fusedAliphaticRings(reactant(0)) returns the atom indexes of the fused aliphatic rings in the first reactant fusedAliphaticRings(product(1)) returns the atom indexes of the fused aliphatic rings in the second product

fusedAliphaticRingsOfSize

Structural Calculations License

identifies the fused aliphatic rings in the molecule having a given size (number of atoms)

atom indexes of the fused aliphatic rings in the molecule having the given size (null if the molecule does not contain fused aliphatic rings)

the ring size

Molecule Context
fusedAliphaticRings() returns the atom indexes of the fused aliphatic rings in the input molecule having the given size
Reaction Context
fusedAliphaticRings(reactant(0)) returns the atom indexes of the fused aliphatic rings in the first reactant having the given size fusedAliphaticRings(product(1)) returns the atom indexes of the fused aliphatic rings in the second product having the given size

fusedAromaticRingCount

Structural Calculations License

calculates the number of fused aromatic rings (SSSR smallest set of smallest aromatic rings)

the fused aromatic ring count

-

Molecule Context
fusedAromaticRingCount() returns the number of fused aromatic rings in the input molecule
Reaction Context
fusedAromaticRingCount(reactant(0)) returns the number of fused aromatic rings in the first reactant fusedAromaticRingCount(product(1)) returns the number of fused aromatic rings in the second product

fusedAromaticRingCountOfSize

Structural Calculations License

calculates the number of fused aromatic rings of given size

the number of fused aromatic rings of given size

the ring size

Molecule Context
fusedAromaticRingCountOfSize(6) returns the number of fused aromatic rings of size 6 in the input molecule
Reaction Context
fusedAromaticRingCountOfSize(reactant(0), 5) returns the number of fused aromatic rings of size 5 in the first reactant fusedAromaticRingCountOfSize(product(1), 5) returns the number of fused aromatic rings of size 5 in the second product

fusedAromaticRings

Structural Calculations License

identifies the fused aromatic rings in the molecule

atom indexes of the fused aromatic rings in the molecule (null if the molecule does not contain fused aromatic rings)

-

Molecule Context
fusedAromaticRings() returns the atom indexes of the fused aromatic rings in the input molecule
Reaction Context
fusedAromaticRings(reactant(0)) returns the atom indexes of the fused aromatic rings in the first reactant fusedAromaticRings(product(1)) returns the atom indexes of the fused aromatic rings in the second product

fusedAromaticRingsOfSize

Structural Calculations License

identifies the fused aromatic rings in the molecule having a given size (number of atoms)

atom indexes of the fused aromatic rings in the molecule having the given size (null if the molecule does not contain fused aromatic rings)

the ring size

Molecule Context
fusedAromaticRings() returns the atom indexes of the fused aromatic rings in the input molecule having the given size
Reaction Context
fusedAromaticRings(reactant(0)) returns the atom indexes of the fused aromatic rings in the first reactant having the given size fusedAromaticRings(product(1)) returns the atom indexes of the fused aromatic rings in the second product having the given size

fusedRingCount

Structural Calculations License

calculates the number of fused rings (SSSR smallest set of smallest rings)

the fused ring count

-

Molecule Context
fusedRingCount() returns the number of fused rings in the input molecule
Reaction Context
fusedRingCount(reactant(0)) returns the number of fused rings in the first reactant fusedRingCount(product(1)) returns the number of fused rings in the second product

hararyIndex

Structural Calculations License

calculates the Harary index

the Harary index

-

Molecule Context
calculates the Harary index
Reaction Context
the Harary index

heteroaliphaticRingCount

Structural Calculations License

calculates the number of aliphatic heterocyclic rings (SSSR smallest set of smallest aliphatic rings)

the aliphatic heterocyclic ring count

-

Molecule Context
heteroaliphaticRingCount() returns the number of aliphatic heterocyclic rings in the input molecule
Reaction Context
heteroaliphaticRingCount(reactant(0)) returns the number of aliphatic heterocyclic rings in the first reactant heteroaliphaticRingCount(product(1)) returns the number of aliphatic heterocyclic rings in the second product

heteroaliphaticRingCountOfSize

Structural Calculations License

calculates the number of aliphatic heterocyclic rings of given size

the number of aliphatic heterocyclic rings of given size

the ring size

Molecule Context
heteroaliphaticRingCountOfSize(6) returns the number of aliphatic heterocyclic rings of size 6 in the input molecule
Reaction Context
heteroaliphaticRingCountOfSize(reactant(0), 5) returns the number of aliphatic heterocyclic rings of size 5 in the first reactant heteroaliphaticRingCountOfSize(product(1), 5) returns the number of aliphatic heterocyclic rings of size 5 in the second product

heteroaliphaticRings

Structural Calculations License

identifies the aliphatic heterocyclic rings in the molecule

atom indexes of the aliphatic heterocyclic rings in the molecule (null if the molecule does not contain aliphatic heterocyclic rings)

-

Molecule Context
heteroaliphaticRings() returns the atom indexes of the aliphatic heterocyclic rings in the input molecule
Reaction Context
heteroaliphaticRings(reactant(0)) returns the atom indexes of the aliphatic heterocyclic rings in the first reactant heteroaliphaticRings(product(1)) returns the atom indexes of the aliphatic heterocyclic rings in the second product

heteroaliphaticRingsOfSize

Structural Calculations License

identifies the aliphatic heterocyclic rings in the molecule having a given size (number of atoms)

atom indexes of the aliphatic heterocyclic rings in the molecule having the given size (null if the molecule does not contain aliphatic heterocyclic rings)

the ring size

Molecule Context
heteroaliphaticRings() returns the atom indexes of the aliphatic heterocyclic rings in the input molecule having the given size
Reaction Context
heteroaliphaticRings(reactant(0)) returns the atom indexes of the aliphatic heterocyclic rings in the first reactant having the given size heteroaliphaticRings(product(1)) returns the atom indexes of the aliphatic heterocyclic rings in the second product having the given size

heteroaromaticRingCount

Structural Calculations License

calculates the number of aromatic heterocyclic rings (SSSR smallest set of smallest aromatic rings)

the aromatic heterocyclic ring count

-

Molecule Context
heteroaromaticRingCount() returns the number of aromatic heterocyclic rings in the input molecule
Reaction Context
heteroaromaticRingCount(reactant(0)) returns the number of aromatic heterocyclic rings in the first reactant heteroaromaticRingCount(product(1)) returns the number of aromatic heterocyclic rings in the second product

heteroaromaticRingCountOfSize

Structural Calculations License

calculates the number of aromatic heterocyclic rings of given size

the number of aromatic heterocyclic rings of given size

the ring size

Molecule Context
heteroaromaticRingCountOfSize(6) returns the number of aromatic heterocyclic rings of size 6 in the input molecule
Reaction Context
heteroaromaticRingCountOfSize(reactant(0), 5) returns the number of aromatic heterocyclic rings of size 5 in the first reactant heteroaromaticRingCountOfSize(product(1), 5) returns the number of aromatic heterocyclic rings of size 5 in the second product

heteroaromaticRings

Structural Calculations License

identifies the aromatic heterocyclic rings in the molecule

atom indexes of the aromatic heterocyclic rings in the molecule (null if the molecule does not contain aromatic heterocyclic rings)

-

Molecule Context
heteroaromaticRings() returns the atom indexes of the aromatic heterocyclic rings in the input molecule
Reaction Context
heteroaromaticRings(reactant(0)) returns the atom indexes of the aromatic heterocyclic rings in the first reactant heteroaromaticRings(product(1)) returns the atom indexes of the aromatic heterocyclic rings in the second product

heteroaromaticRingsOfSize

Structural Calculations License

identifies the aromatic heterocyclic rings in the molecule having a given size (number of atoms)

atom indexes of the aromatic heterocyclic rings in the molecule having the given size (null if the molecule does not contain aromatic heterocyclic rings)

the ring size

Molecule Context
heteroaromaticRings() returns the atom indexes of the aromatic heterocyclic rings in the input molecule having the given size
Reaction Context
heteroaromaticRings(reactant(0)) returns the atom indexes of the aromatic heterocyclic rings in the first reactant having the given size heteroaromaticRings(product(1)) returns the atom indexes of the aromatic heterocyclic rings in the second product having the given size

heteroRingCount

Structural Calculations License

calculates the number of heterocyclic rings (SSSR smallest set of smallest rings)

the heterocyclic ring count

-

Molecule Context
heteroRingCount() returns the number of heterocyclic rings in the input molecule
Reaction Context
heteroRingCount(reactant(0)) returns the number of heterocyclic rings in the first reactant heteroRingCount(product(1)) returns the number of heterocyclic rings in the second product

heteroRingCountOfSize

Structural Calculations License

calculates the number of heterocyclic rings of given size

the number of heterocyclic rings of given size

the ring size

Molecule Context
heteroRingCountOfSize(6) returns the number of heterocyclic rings of size 6 in the input molecule
Reaction Context
heteroRingCountOfSize(reactant(0), 5) returns the number of heterocyclic rings of size 5 in the first reactant heteroRingCountOfSize(product(1), 5) returns the number of heterocyclic rings of size 5 in the second product

heteroRings

Structural Calculations License

identifies the heterocyclic rings in the molecule

atom indexes of the heterocyclic rings in the molecule (null if the molecule does not contain heterocyclic rings)

-

Molecule Context
heteroRings() returns the atom indexes of the heterocyclic rings in the input molecule
Reaction Context
heteroRings(reactant(0)) returns the atom indexes of the heterocyclic rings in the first reactant heteroRings(product(1)) returns the atom indexes of the heterocyclic rings in the second product

heteroRingsOfSize

Structural Calculations License

identifies the heterocyclic rings in the molecule having a given size (number of atoms)

atom indexes of the heterocyclic rings in the molecule having the given size (null if the molecule does not contain heterocyclic rings)

the ring size

Molecule Context
heteroRings() returns the atom indexes of the heterocyclic rings in the input molecule having the given size
Reaction Context
heteroRings(reactant(0)) returns the atom indexes of the heterocyclic rings in the first reactant having the given size heteroRings(product(1)) returns the atom indexes of the heterocyclic rings in the second product having the given size

hyperWienerIndex

Structural Calculations License

calculates the Hyper Wiener index

the Hyper Wiener index

-

Molecule Context
calculates the Hyper Wiener index
Reaction Context
the Hyper Wiener index

largestAtomRingSize

Structural Calculations License

calculates the size of the largest ring containing the specified atom

the size of the largest ring containing the specified atom

  • the atom index / MolAtom object

Molecule Context
largestAtomRingSize(1) returns the size of the largest ring containing atom 1 in the input molecule
Reaction Context
largestAtomRingSize(patom(2)) returns the size of the largest ring containing product atom matching map 2 in the reaction equation

largestConjugatedSystem

Structural Calculations License

returns the atom list of the largest conjugated system in the molecule

-

 

Molecule Context
largestConjugatedSystem() returns the atom list of the largest conjugated system in the input molecule
Reaction Context
largestConjugatedSystem(product(1)) returns the atom list of the largest conjugated system in the 2nd product

largestConjugatedSystemSize

Structural Calculations License

returns the number of pi electron pairs in the largest conjugated system

-

 

Molecule Context
largestConjugatedSystemSize() returns the number of pi electron pairs in the largest conjugated system
Reaction Context
largestConjugatedSystemSize(product(1)) returns the number of pi electron pairs in the largest conjugated system of the 2nd product

largestConjugatedSystemMol

Structural Calculations License

returns the input molecule with the largest conjugated system coloured in green

This function should be used with the output option -f mrv to export colour in the output

 

Molecule Context
largestConjugatedSystemMol() returns the input molecule with the largest conjugated system coloured in green
Reaction Context
largestConjugatedSystemMol(product(1)) returns the 2nd product with the largest conjugated system coloured in green

largestRing

Structural Calculations License

identifies the atoms of the largest ring (number of atoms) in the molecule.

atom indexes of the largest ring in the molecule (null when acyclic)

-

Molecule Context
largestRingSize() returns the atom indexes of the largest ring in the input molecule
Reaction Context
largestRingSize(product(1)) returns the atom indexes of the largest ring in the second product

largestRingSize

Structural Calculations License

calculates the largest ring size

the largest ring size

-

Molecule Context
largestRingSize() returns the size of the largest ring in the input molecule
Reaction Context
largestRingSize(product(1)) returns the size of the largest ring in the second product

largestRingSystem

Structural Calculations License

identifies the atoms of the largest ring system (number of rings) in the molecule.

atom indexes of the largest ring system in the molecule (null when acyclic)

-

Molecule Context
largestRingSize() returns the atom indexes of the largest ring system in the input molecule
Reaction Context
largestRingSize(product(1)) returns the atom indexes of the largest ring system in the second product

largestRingSystemSize

Structural Calculations License

calculates the size of the largest ring system (number of rings)

the size of the largest ring system

-

Molecule Context
largestRingSystemSize() returns the size of the largest ring system in the input molecule
Reaction Context
largestRingSystemSize(reactant(0)) returns the size of the largest ring system in the first reactant largestringsystemsize(product(1)) returns the size of the largest ring system in the second product

maximalProjectionArea

Structural Calculations License

returns the maximal projection area

the maximal projection area

-

Molecule Context
maximalProjectionArea() returns the maximal projection area
Reaction Context
maximalProjectionArea((reactant(0)) returns the maximal projection area of the first reactant maximalProjectionArea(product(1)) returns the maximal projection area of the second product

maximalProjectionRadius

Structural Calculations License

returns the maximal projection radius

the maximal projection radius

-

Molecule Context
maximalProjectionRadius() returns the maximal projection radius
Reaction Context
maximalProjectionRadius((reactant(0)) returns the maximal projection radius of the first reactant maximalProjectionRadius(product(1)) returns the maximal projection radius of the second product

maximalProjectionSize

Structural Calculations License

returns the maximal distance in the molecule perpendicular to the maximal projection area

the maximal distance in the molecule (the actual conformer) perpendicular to its maximal projection area

-

Molecule Context
maximalProjectionSize() returns the maximal distance in the molecule perpendicular to the maximal projection area
Reaction Context
maximalProjectionSize((reactant(0)) returns the maximal distance of the first reactant perpendicular to the maximal projection area maximalProjectionSize(product(1)) returns the maximal distance of the second product perpendicular to the maximal projection area

minimalProjectionArea

Structural Calculations License

returns the minimal projection area

the minimal projection area

-

Molecule Context
minimalProjectionArea() returns the minimal projection area
Reaction Context
minimalProjectionArea((reactant(0)) returns the minimal projection area of the first reactant minimalProjectionArea(product(1)) returns the minimal projection area of the second product

minimalProjectionRadius

Structural Calculations License

returns the minimal projection radius

the minimal projection radius

-

Molecule Context
minimalProjectionRadius() returns the minimal projection radius
Reaction Context
minimalProjectionRadius((reactant(0)) returns the minimal projection radius of the first reactant minimalProjectionRadius(product(1)) returns the minimal projection radius of the second product

minimalProjectionSize

Structural Calculations License

returns the maximal distance in the molecule perpendicular to the minimal projection area

the maximal distance of the molecule (the actual conformer) perpendicular to its minimal projection area

-

Molecule Context
minimalProjectionSize() returns the maximal distance in the molecule perpendicular to the minimal projection area
Reaction Context
minimalProjectionSize((reactant(0)) returns the maximal distance of the first reactant perpendicular to the minimal projection area minimalProjectionSize(product(1)) returns the maximal distance of the second product perpendicular to the minimal projection area

 

 

 

 

 

 

mmff94Energy

Structural Calculations License

returns the MMFF94 energy of the input molecule (conformer)

the MMFF94 energy

-

Molecule Context
mmff94Energy() returns the MMFF94 energy of the input molecule (conformer)
Reaction Context
mmff94Energy(reactant(0)) returns the MMFF94 energy of the first reactant mmff94Energy(product(1)) returns the MMFF94 energy of the second product

plattIndex

Structural Calculations License

calculates the Platt index

the Platt index

-

Molecule Context
calculates the Platt index
Reaction Context
the Platt index

randicIndex

Structural Calculations License

calculates the Randic index

the Randic index

-

Molecule Context
calculates the Randic index
Reaction Context
the Randic index

ringAtom

Structural Calculations License

checks if the specified atom is a ring atom

true for ring atoms, false for non-ring atoms

  • the atom index / MolAtom object

Molecule Context
ringAtom(2) returns true if atom 2 of the input molecule is a ring atom, false otherwise
Reaction Context
ringAtom(ratom(2)) returns true if the reactant atom matching map 2 in the reaction equation is a ring atom, false otherwise ringAtom(patom(1)) returns true if the product atom matching map 1 in the reaction equation is a ring atom, false otherwise

ringAtomCount

Structural Calculations License

calculates the ring atom count

the ring atom count

-

Molecule Context
ringAtomCount() returns the number of ring atoms in the input molecule
Reaction Context
ringAtomCount(reactant(0)) returns the number of ring atoms in the first reactant ringAtomCount(product(1)) returns the number of ring atoms in the second product

ringBond

Structural Calculations License

checks if two atoms are connected by a ring bond

true if the two atoms are connected by a ring bond, false otherwise

  • the (1-based) atom indexes of the two atoms in a string: "index1-index2" (e.g. '2-3')

Molecule Context
ringBond('2-3') and ringBond(bond(1, 2)) both return true if atoms 1 and 2 are connected by a ring bond the input molecule
Reaction Context
ringBond(reactant(0), bond(ratom(1), ratom(2))) returns true if reactant atoms matching maps 1 and 2 in the reaction equation are connected by a ring bond in the corresponding reactant molecule (see note 1) ringBond(product(1), bond(patom(2), patom(3))) returns true if product atoms matching maps 2 and 3 in the reaction equation are connected by a ring bond in the corresponding product molecule (see note 1)

ringBondCount

Structural Calculations License

calculates the ring bond count

the ring bond count

-

Molecule Context
ringBondCount() returns the number of ring bonds in the input molecule
Reaction Context
ringBondCount(reactant(0)) returns the number of ring bonds in the first reactant ringBondCount(product(1)) returns the number of ring bonds in the second product

ringCount

Structural Calculations License

calculates the ring count

the ring count

-

Molecule Context
ringCount() returns the number of rings in the input molecule
Reaction Context
ringCount(reactant(0)) returns the number of rings in the first reactant ringCount(product(1)) returns the number of rings in the second product

ringCountOfAtom

Structural Calculations License

calculates the number of rings passing through an atom

the number of rings passing through an atom

  • the atom index / MolAtom object

Molecule Context
ringCountOfAtom(2) returns the number of rings passsing through atom 2 of the input molecule
Reaction Context
ringCountOfAtom(ratom(2)) returns the number of rings passsing through the reactant atom matching map 2 in the reaction equation ringCountOfAtom(patom(1)) returns the number of rings passsing through the product atom matching map 1 in the reaction equation

ringCountOfSize

Structural Calculations License

calculates the number of rings of given size

the number of rings of given size

the ring size

Molecule Context
ringCountOfSize(6) returns the number of rings of size 6 in the input molecule
Reaction Context
ringCountOfSize(reactant(0), 5) returns the number of rings of size 5 in the first reactant ringCountOfSize(product(1), 5) returns the number of rings of size 5 in the second product

rings

Structural Calculations License

identifies the rings in the molecule

atom indexes of the rings in the molecule (null if the molecule is acyclic)

-

Molecule Context
rings() returns the atom indexes of the rings in the input molecule
Reaction Context
rings(reactant(0)) returns the atom indexes of the rings in the first reactant rings(product(1)) returns the atom indexes of the rings in the second product

ringsOfSize

Structural Calculations License

identifies the rings in the molecule having a given size (number of atoms)

atom indexes of the rings in the molecule having the given size (null if the molecule is acyclic or contains different rings only)

the ring size

Molecule Context
rings() returns the atom indexes of the rings in the input molecule having the given size
Reaction Context
rings(reactant(0)) returns the atom indexes of the rings in the first reactant having the given size rings(product(1)) returns the atom indexes of the rings in the second product having the given size

ringSystemCount

Structural Calculations License

calculates the number of rings systems

the number of rings systems

-

Molecule Context
ringSystemCount() returns the number of ring systems in the input molecule
Reaction Context
ringSystemCount(reactant(0)) returns the number of ring systems in the first reactant ringsystemCount(product(1)) returns the number of ring systems in the second product

ringSystemCountOfSize

Structural Calculations License

calculates the number of rings systems of given size

the number of rings systems of given size

the ring system size

Molecule Context
ringSystemCountOfSize(4) returns the number of four-membered ring systems in the input molecule
Reaction Context
ringSystemCountOfSize(reactant(0),3) returns the number of three-membered ring systems in the first reactant ringsystemCountOfSize(product(1),3) returns the number of three-membered ring systems in the second product

ringSystems

Structural Calculations License

identifies the ring systems in the molecule (fused and spiro rings belong to one ring system)

atom indexes of the ring systems in the molecule (null if the molecule is acyclic)

-

Molecule Context
ringSystems() returns the atom indexes of the ring systems in the input molecule
Reaction Context
ringSystems(reactant(0)) returns the atom indexes of the ring systems in the first reactant ringSystems(product(1)) returns the atom indexes of the ring systems in the second product

ringSystemsOfSize

Structural Calculations License

identifies the ring systems in the molecule having a given size (number of atoms, fused and spiro rings belong to one ring system)

atom indexes of the ring systems in the molecule having the given size (null if the molecule is acyclic or contains different ringSystems only)

the ring size

Molecule Context
ringSystems() returns the atom indexes of the ring systems in the input molecule having the given size
Reaction Context
ringSystems(reactant(0)) returns the atom indexes of the ring systems in the first reactant having the given size ringSystems(product(1)) returns the atom indexes of the ring systems in the second product having the given size

rotatableBond

Structural Calculations License

checks if two atoms are connected by a rotatable bond

true if the two atoms are connected by a rotatable bond, false otherwise

  • the (1-based) atom indexes of the two atoms in a string: "index1-index2" (e.g. '2-3')

Molecule Context
rotatableBond('2-3') and rotatableBond(bond(1, 2)) both return true if atoms 1 and 2 are connected by a rotatable bond the input molecule
Reaction Context
rotatableBond(reactant(0), bond(ratom(1), ratom(2))) returns true if reactant atoms matching maps 1 and 2 in the reaction equation are connected by a rotatable bond in the corresponding reactant molecule (see note 1) rotatableBond(product(1), bond(patom(2), patom(3))) returns true if product atoms matching maps 2 and 3 in the reaction equation are connected by a rotatable bond in the corresponding product molecule (see note 1)

rotatableBondCount

Structural Calculations License

calculates the rotatable bond count

the rotatable bond count

-

Molecule Context
rotatableBondCount() returns the number of rotatable bonds in the input molecule
Reaction Context
rotatableBondCount(reactant(0)) returns the number of rotatable bonds in the first reactant rotatableBondCount(product(1)) returns the number of rotatable bonds in the second product

shortestPath

Structural Calculations License

calculates the length of the shortest path between two atoms

the length of the shortest path between two atoms, Integer.MAX_VALUE if disconnected

  • the (1-based) atom indexes of the two atoms in a string: "index1-index2" (e.g. '2-3')

Molecule Context
shortestPath('2-3') and shortestPath(pair(1, 2)) both return the shortest path length between atoms 1 and 2 in the input molecule
Reaction Context
shortestPath(reactant(0), pair(ratom(1), ratom(2))) returns the length of the shortest path between reactant atoms matching maps 1 and 2 in the reaction equation (see note 1) shortestPath(product(1), pair(patom(2), patom(3))) returns the length of the shortest path between product atoms matching maps 2 and 3 in the reaction equation (see note 1)

smallestAtomRingSize

Structural Calculations License

calculates the size of the smallest ring containing the specified atom

the size of the smallest ring containing the specified atom

  • the atom index / MolAtom object

Molecule Context
smallestAtomRingSize(0) returns the size of the smallest ring containing atom 0 in the input molecule
Reaction Context
smallestAtomRingSize(ratom(1)) returns the size of the smallest ring containing reactant atom matching map 1 in the reaction equation

smallestRing

Structural Calculations License

identifies the atoms of the smallest ring (number of atoms) in the molecule.

atom indexes of the smallest ring in the molecule (null when acyclic)

-

Molecule Context
smallestRingSize() returns the atom indexes of the smallest ring in the input molecule
Reaction Context
smallestRingSize(product(1)) returns the atom indexes of the smallest ring in the second product

smallestRingSize

Structural Calculations License

calculates the smallest ring size

the smallest ring size

-

Molecule Context
smallestRingSize() returns the size of the smallest ring in the input molecule
Reaction Context
smallestRingSize(reactant(0)) returns the size of the smallest ring in the first reactant

smallestRingSystem

Structural Calculations License

identifies the atoms of the smallest ring system (number of rings) in the molecule.

atom indexes of the smallest ring system in the molecule (null when acyclic)

-

Molecule Context
smallestRingSize() returns the atom indexes of the smallest ring system in the input molecule
Reaction Context
smallestRingSize(product(1)) returns the atom indexes of the smallest ring system in the second product

smallestRingSystemSize

Structural Calculations License

calculates the size of the smallest ring system (number of rings)

the size of the smallest ring system

-

Molecule Context
smallestRingSystemSize() returns the size of the smallest ring system in the input molecule
Reaction Context
smallestRingSystemSize(reactant(0)) returns the size of the smallest ring system in the first reactant smallestringsystemsize(product(1)) returns the size of the smallest ring system in the second product

stereoDoubleBondCount

Structural Calculations License

calculates the number of stereo double bonds

the stereo double bond count

-

Molecule Context
stereoDoubleBondCount() returns the number of stereo double bonds in the input molecule
Reaction Context
stereoDoubleBondCount(reactant(0)) returns the number of stereo double bonds in the first reactant stereoDoubleBondCount(product(1)) returns the number of stereo double bonds in the second product

stericEffectIndex

Structural Calculations License

calculates the steric effect index of an atom

the steric effect index of an atom

  • the atom index / MolAtom object

Molecule Context
calculates the steric effect index of an atom
Reaction Context
the steric effect index of an atom

stericHindrance

Structural Calculations License

calculates the steric hindrance of an atom

the steric hindrance of an atom

  • the atom index / MolAtom object

Molecule Context
stericHindrance(2) returns the steric hindrance of atom 2 of the input molecule
Reaction Context
stericHindrance(ratom(2)) returns the steric hindrance of the reactant atom matching map 2 in the reaction equation stericHindrance(patom(1)) returns the steric hindrance of the product atom matching map 1 in the reaction equation

szegedIndex

Structural Calculations License

calculates the Szeged index

the Szeged index

-

Molecule Context
calculates the Szeged index
Reaction Context
the Szeged index

topologicalPolarSurfaceArea PSA

-

calculates the topological polar surface area (2D)

the polar surface area (2D)

  • the major microspecies pH (takes the input molecule itself if omitted)

Molecule Context
topologicalPolarSurfaceArea() returns the polar surface area of the input molecule topologicalPolarSurfaceArea('7.4') returns the polar surface area of the major microspecies taken at pH 7.4
Reaction Context
topologicalPolarSurfaceArea(reactant(0)) returns the polar surface area of the first reactant topologicalPolarSurfaceArea(product(0), '7.4') returns the polar surface area of the major microspecies of the first product taken at pH 7.4

vanDerWaalsSurfaceArea

Structural Calculations License

calculates the van der Waals surface area

the molecular surface area

  • the major microspecies pH (takes the input molecule itself if omitted)

Molecule Context
vanDerWaalsSurfaceArea() returns the van der Waals surface area of the input molecule vanDerWaalsSurfaceArea('7.4') returns the van der Waals accessible surface area of the major microspecies taken at pH 7.4
Reaction Context
vanDerWaalsSurfaceArea(reactant(0)) returns the van der Waals surface area of the first reactant vanDerWaalsSurfaceArea(product(0), '7.4') returns the van der Waals surface area of the major microspecies of the first product taken at pH 7.4

waterAccessibleSurfaceArea ASA solventAccessibleSurfaceArea

Structural Calculations License

calculates the solvent accessible / water accessible molecular surface area

the molecular surface area

  • the major microspecies pH (takes the input molecule itself if omitted)

Molecule Context
waterAccessibleSurfaceArea() returns the solvent accessible / water accessible surface area of the input molecule solventAccessibleSurfaceArea('7.4')returns the solvent accessible / water accessible surface area of the major microspecies taken at pH 7.4
Reaction Context
waterAccessibleSurfaceArea(reactant(0)) returns the solvent accessible / water accessible surface area of the first reactantsolventAccessibleSurfaceArea(product(0), '7.4') returns the solvent accessible / water accessible surface area of the major microspecies of the first product taken at pH 7.4

wienerIndex

Structural Calculations License

calculates the Wiener index

the Wiener index

-

Molecule Context
wienerIndex() returns the Wiener index of the input molecule
Reaction Context
wienerIndex(reactant(0)) returns the Wiener index of the first reactant wienerIndex(product(1)) returns the Wiener index of the second product

wienerPolarity

Structural Calculations License

calculates the Wiener polarity

the Wiener polarity

-

Molecule Context
wienerPolarity() returns the Wiener polarity of the input molecule
Reaction Context
wienerPolarity(reactant(0)) returns the Wiener polarity of the first reactant wienerPolarity(product(1)) returns the Wiener polarity of the second product

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HBDA Functions

Name

License

Description

Return value

Parameters

Examples

acceptor acc

Structural Calculations License

calculates atomic hydrogen bond acceptor multiplicity

the atomic hydrogen bond acceptor multiplicity

  • the atom index / MolAtom object
  • the major microspecies pH (takes the input molecule itself if omitted)

Molecule Context
acceptor(2) returns the hydrogen bond acceptor multiplicity on atom 2 of the input molecule
Reaction Context
acceptor(ratom(2)) returns the hydrogen bond acceptor multiplicity on the reactant atom matching map 2 in the reaction equation

acceptorCount

Structural Calculations License

calculates molecular hydrogen bond acceptor count (the number of acceptor atoms)

the molecular hydrogen bond acceptor count

  • the major microspecies pH (takes the input molecule itself if omitted)

Molecule Context
acceptorCount() returns the number of hydrogen bond acceptor atoms in the input molecule
Reaction Context
acceptorCount(reactant(0)) returns the number of hydrogen bond acceptor atoms in the first reactant

acceptorSiteCount accSiteCount

Structural Calculations License

calculates molecular hydrogen bond acceptor multiplicity (the sum of atomic multiplicities)

the molecular hydrogen bond acceptor multiplicity

  • the major microspecies pH (takes the input molecule itself if omitted)

Molecule Context
acceptorSiteCount() returns the hydrogen bond acceptor multiplicity of the input molecule
Reaction Context
acceptorSiteCount(reactant(0)) returns the hydrogen bond acceptor multiplicity of the first reactant

donor don

Structural Calculations License

calculates atomic hydrogen bond donor multiplicity

the atomic hydrogen bond donor multiplicity

  • the atom index / MolAtom object
  • the major microspecies pH (takes the input molecule itself if omitted)

Molecule Context
donor(1, "7.4") returns the hydrogen bond donor multiplicity on atom 1 of the major microspecies at pH 7.4
Reaction Context
returns the hydrogen bond donor multiplicity on the product atom matching map 3 in the reaction equation, taking the major microspecies of the corresponding product at pH 7.4

donorCount

Structural Calculations License

calculates molecular hydrogen bond donor count (the number of donor atoms)

the molecular hydrogen bond donor count

  • the major microspecies pH (takes the input molecule itself if omitted)

Molecule Context
donorCount("7.4") returns the number of hydrogen bond donor atoms in the major microspecies at pH 7.4
Reaction Context
donorCount(product(1), "7.4") returns the number of hydrogen bond donor atoms in the major microspecies of the first product taken at pH 7.4

donorSiteCount donSiteCount

Structural Calculations License

calculates molecular hydrogen bond acceptor / donor multiplicity (the sum of atomic multiplicities)

the molecular hydrogen bond acceptor / donor multiplicity

  • the major microspecies pH (takes the input molecule itself if omitted)

Molecule Context
donorSiteCount("7.4") returns the hydrogen bond donor multiplicity of the major microspecies at pH 7.4
Reaction Context
donorSiteCount(product(1), "7.4") returns the hydrogen bond donor multiplicity of the major microspecies of the first product taken at pH 7.4

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Huckel Functions

Name

License

Description

Return value

Parameters

Examples

chargeDensity totalChargeDensity

Structural Calculations License

calculates the charge density of atoms

the charge density of the atom, NaN for non-existing values

  • he atom index / MolAtom object
  • the major microspecies pH (takes the input molecule itself if omitted)

Molecule Context
chargeDensity(2) returns the charge density of atom 2 of the input molecule, NaN for non-existing value
Reaction Context
chargeDensity(ratom(1)) returns the charge density of the reactant atom matching map 1 in the reaction equation

electronDensity piChargeDensity

Structural Calculations License

calculates the electron density of atoms

the electron density of the atom, NaN for non-existing values

  • he atom index / MolAtom object
  • the major microspecies pH (takes the input molecule itself if omitted)

Molecule Context
electronDensity(2) returns the electron density of atom 2 of the input molecule, NaN for non-existing value
Reaction Context
electronDensity(ratom(1)) returns the electron density of the reactant atom matching map 1 in the reaction equation

electrophilicity energyNu nucleophilicLocalizationEnergy

Structural Calculations License

calculates electrophilicity of atoms

the electrophilicity of the atom, NaN for non-aromatic atoms

  • the atom index / MolAtom object
  • the major microspecies pH (takes the input molecule itself if omitted)

Molecule Context
electrophilicity(2) returns the electrophilicity of atom 2 of the input molecule, NaN if atom 2 is non-aromatic
Reaction Context
electrophilicity(ratom(1)) returns the electrophilicity of the reactant atom matching map 1 in the reaction equation

electrophilicityOrder aromaticElectrophilicityOrder orderE

Structural Calculations License

calculates E(plus) order of atoms

the E(plus) order index of the atom (0, 1, 2, ...),

  • the atom index / MolAtom object
  • the major microspecies pH (takes the input molecule itself if omitted)

Molecule Context
electrophilicityOrder(2) returns the E(plus) order index of atom 2 of the input molecule, e.g. returns 0 if atom 2 is the most electrophilic atom, 1 if atom 2 is the second strongest electrophilic atom, etc.,
Reaction Context
electrophilicityOrder(ratom(1)) returns the E(plus) order index of the reactant atom matching map 1 in the reaction equation

hmoChargeDensity

Structural Calculations License

calculates the HMO charge density of atoms

the charge density of the atom, NaN for non-existing values

  • he atom index / MolAtom object
  • the major microspecies pH (takes the input molecule itself if omitted)

Molecule Context
hmoChargeDensity(2) returns the charge density of atom 2 of the input molecule, NaN for non-existing value
Reaction Context
hmoChargeDensity(ratom(1)) returns the charge density of the reactant atom matching map 1 in the reaction equation

hmoElectronDensity

Structural Calculations License

calculates the HMO electron density of atoms

the electron density of the atom, NaN for non-existing values

  • he atom index / MolAtom object
  • the major microspecies pH (takes the input molecule itself if omitted)

Molecule Context
hmoElectronDensity(2) returns the electron density of atom 2 of the input molecule, NaN for non-existing value
Reaction Context
hmoElectronDensity(ratom(1)) returns the electron density of the reactant atom matching map 1 in the reaction equation

hmoElectrophilicityOrder hmoOrderE

Structural Calculations License

calculates HMO E(plus) order of atoms

the E(plus) order index of the atom (0, 1, 2, ...),

  • the atom index / MolAtom object
  • the major microspecies pH (takes the input molecule itself if omitted)

Molecule Context
hmoElectrophilicityOrder(2) returns the E(plus) order index of atom 2 of the input molecule, e.g. returns 0 if atom 2 is the most electrophilic atom, 1 if atom 2 is the second strongest electrophilic atom, etc.,
Reaction Context
hmoElectrophilicityOrder(ratom(1)) returns the E(plus) order index of the reactant atom matching map 1 in the reaction equation

hmoElectrophilicLocalizationEnergy

Structural Calculations License

calculates HMO localization energy L(plus) of atoms

the localization energy L(plus) of the atom, NaN for non-aromatic atoms

  • the atom index / MolAtom object
  • the major microspecies pH (takes the input molecule itself if omitted)

Molecule Context
hmoElectrophilicLocalizationEnergy(2) returns the electrophilic L(plus) localization energy of atom 2 of the input molecule, NaN if atom 2 is non-aromatic
Reaction Context
hmoElectrophilicLocalizationEnergy(ratom(1)) returns the electrophilic L(plus) localization energy of the reactant atom matching map 1 in the reaction equation

hmoNucleophilicityOrder hmoOrderNu

Structural Calculations License

calculates HMO Nu(minus) order of atoms

the Nu(minus) order index of the atom (0, 1, 2, ...),

  • the atom index / MolAtom object
  • the major microspecies pH (takes the input molecule itself if omitted)

Molecule Context
hmoNucleophilicityOrder(2) returns the Nu(minus) order index of atom 2 of the input molecule, e.g. returns 0 if atom 2 is the most nucleophilic atom, 1 if atom 2 is the second strongest nucleophilic atom, etc.,
Reaction Context
hmoNucleophilicityOrder(ratom(1)) returns the Nu(minus) order index of the reactant atom matching map 1 in the reaction equation

hmoNucleophilicLocalizationEnergy

Structural Calculations License

calculates HMO localization energy L(minus) of atoms

the localization energy L(minus) of the atom, NaN for non-aromatic atoms

  • the atom index / MolAtom object
  • the major microspecies pH (takes the input molecule itself if omitted)

Molecule Context
hmoNucleophilicLocalizationEnergy(2) returns the nucleophilic L(minus) localization energy of atom 2 of the input molecule, NaN if atom 2 is non-aromatic
Reaction Context
hmoNucleophilicLocalizationEnergy(ratom(1)) returns the nucleophilic L(minus) localization energy of the reactant atom matching map 1 in the reaction equation

hmoPiEnergy

Structural Calculations License

calculates the HMO pi energy of the molecule

the pi energy of the molecule

  • the major microspecies pH (takes the input molecule itself if omitted)

Molecule Context
hmoPiEnergy() returns the pi energy of the input molecule
Reaction Context
hmoPiEnergy(product(1)) returns the pi energy of the second product

nucleophilicity electrophilicLocalizationEnergy energyE

Structural Calculations License

calculates nucleophilicity of atoms

the nucleophilicity of the atom, NaN for non-aromatic atoms

  • the atom index / MolAtom object
  • the major microspecies pH (takes the input molecule itself if omitted)

Molecule Context
nucleophilicity(2) returns the nucleophilicity of atom 2 of the input molecule, NaN if atom 2 is non-aromatic
Reaction Context
nucleophilicity(ratom(1)) returns the nucleophilicity of the reactant atom matching map 1 in the reaction equation

nucleophilicityOrder aromaticNucleophilicityOrder orderNu

Structural Calculations License

calculates Nu(minus) order of atoms

the Nu(minus) order index of the atom (0, 1, 2, ...),

  • the atom index / MolAtom object
  • the major microspecies pH (takes the input molecule itself if omitted)

Molecule Context
nucleophilicityOrder(2) returns the Nu(minus) order index of atom 2 of the input molecule, e.g. returns 0 if atom 2 is the most nucleophilic atom, 1 if atom 2 is the second strongest nucleophilic atom, etc.,
Reaction Context
nucleophilicityOrder(ratom(1)) returns the Nu(minus) order index of the reactant atom matching map 1 in the reaction equation

piEnergy

Structural Calculations License

calculates the pi energy of the molecule. Deprecated.

the pi energy of the molecule

  • the major microspecies pH (takes the input molecule itself if omitted)

Molecule Context
piEnergy() returns the pi energy of the input molecule
Reaction Context
piEnergy(product(1)) returns the pi energy of the second product

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Isomers Functions

Name

License

Description

Return value

Parameters

Examples

allTautomer

Isomers License

returns a tautomeric form from all tautomers

the tautomer

  • the tautomer index (0-based)

Molecule Context
allTautomer(0) returns the first tautomer of the input molecule
Reaction Context
allTautomer(reactant(0), 1) returns the second tautomer of the first reactant

allTautomers

Isomers License

returns all tautomer forms in an array

the tautomer array

the normalization option (default is false)

Molecule Context
allTautomers('normal:true') returns all normal tautomers of the input molecule in an array
Reaction Context
allTautomers(reactant(0)) returns all tautomers of the first reactant in an array

canonicalResonant

-

constructs the canonical resonant structure

the canonical resonant structure

-

Molecule Context
canonicalResonant() returns the canonical resonant structure of the input molecule
Reaction Context
canonicalResonant(reactant(0)) returns the canonical resonant structure of the first reactant

canonicalTautomer

Isomers License

generates the canonical tautomer structure

the canonical tautomer

option that switches on the normalization (defaults is false)

Molecule Context
canonicalTautomer('normal:true') returns the normal canonical tautomer structure of the input molecule
Reaction Context
canonicalTautomer(reactant(0)) returns the canonical tautomer structure of the first reactant/td>

dominantTautomer tautomer

Isomers License

returns the i-th dominant tautomeric form

the i-th dominant tautomer

  • the dominant tautomer index (0-based)
  • the pH value as string (set if pH effect should be considered)

Molecule Context
dominantTautomer(0) returns the first dominant tautomer of the input molecule dominantTautomer(1, "2.0") returns the second dominant tautomer of the input molecule, considering pH effect at pH 2.0
Reaction Context
dominantTautomer(reactant(0), 1) returns the second dominant tautomer of the first reactant dominantTautomer(product(1), 0, "7.4") returns the first dominant tautomer of the second product, considering pH effect at pH 7.4

dominantTautomerCount

Isomers License

calculates the number of dominant tautomers

the number of dominant tautomers

  • the pH value as string (set if pH effect should be considered)

Molecule Context
dominantTautomerCount() returns the number of dominant tautomers of the input molecule dominantTautomerCount("7.4") returns the number of dominant tautomers of the input molecule, considering pH effect at pH 7.4
Reaction Context
dominantTautomerCount(reactant(0)) returns the number of dominant tautomers of the first reactant dominantTautomerCount(product(1), "2.5") returns the number of dominant tautomers of the second product, considering pH effect at pH 2.5

dominantTautomers tautomers

Isomers License

constructs all dominant tautomeric forms (ordered by distribution)

the dominant tautomer array

  • the pH value as string (set if pH effect should be considered)

Molecule Context
dominantTautomers() returns all dominant tautomers of the input molecule in an array dominantTautomers("2.0") returns all dominant tautomers of the input molecule in an array, considering pH effect at pH 2.0
Reaction Context
dominantTautomers(reactant(0)) returns all dominant tautomers of the first reactant in an array dominantTautomers(product(1), "7.4") returns all dominant tautomers of the second product in an array, considering pH effect at pH 7.4

doubleBondStereoisomer

Isomers License

generates a double bond stereoisomer of the molecule

the double bond stereoisomer

  • the double bond stereoisomer index (0-based)

Molecule Context
doubleBondStereoisomer(0) returns the first double bond stereoisomer of the input molecule
Reaction Context
doubleBondStereoisomer(reactant(0), 1) returns the second double bond stereoisomer of the first reactant

doubleBondStereoisomerCount

Isomers License

returns the number of generated double bond stereoisomers

the number of generated double bond stereoisomers

-

Molecule Context
doubleBondStereoisomerCount() returns the number of generated double bond stereoisomers of the input molecule
Reaction Context
doubleBondStereoisomerCount(reactant(0)) returns the number of calculated double bond stereoisomers of the first reactant

doubleBondStereoisomers

Isomers License

generates double bond stereoisomers of the molecule (maximum number of double bond stereoisomers to be generated can be set, default: all)

the double bond stereoisomer array

-

Molecule Context
doubleBondStereoisomers() returns double bond stereoisomers of the input molecule in an array
Reaction Context
doubleBondStereoisomers(reactant(0)) returns double bond stereoisomers of the first reactant in an array

genericTautomer

Isomers License

constructs the generic tautomer structure

the generic tautomer structure

-

Molecule Context
genericTautomer() returns the generic tautomer structure of the input molecule
Reaction Context
genericTautomer(reactant(0)) returns the generic tautomer structure of the first reactant/td>

majorTautomer

Isomers License

constructs the major tautomer structure

the major tautomer structure

  • the pH value as string (set if pH effect should be considered)

Molecule Context
majorTautomer() returns the major tautomer structure of the input molecule
Reaction Context
majorTautomer(reactant(0)) returns the major tautomer structure of the first reactant/td>

mostStableTautomer

Isomers License

deprecated, use majorTautomer instead. constructs the most stable tautomer structure

the most stable tautomer structure

-

Molecule Context
mostStableTautomer() returns the most stable tautomer structure of the input molecule
Reaction Context
mostStableTautomer(reactant(0)) returns the most stable tautomer structure of the first reactant/td>

resonant

-

constructs a resonant structure

the resonant structure

-

Molecule Context
resonant(0) returns the first resonant structure of the input molecule
Reaction Context
resonant(reactant(0), 1) returns the second resonant structure of the first reactant

resonantCount

-

calculates the number of resonant structures

the number of resonant structures

-

Molecule Context
resonantCount() returns the number of resonant structures of the input molecule
Reaction Context
resonantCount(reactant(0)) returns the number of resonant structures of the first reactant

resonants

-

constructs all resonant structures

the resonant structure array

-

Molecule Context
resonants() returns all resonants of the input molecule in an array
Reaction Context
resonants(reactant(0)) returns all resonants of the first reactant in an array

stereoAnalysis

-

calculates stereo descriptors of molecule

list of stereo descriptors

  • -
  • the type of stereo descriptor: see the API function names

Molecule Context
stereoAnalysis() returns the stereo descriptors of the input molecule as a string stereoAnalysis('tetrahedralStereoCenters') returns the array of tetrahedral stereo descriptors of the input molecule
Reaction Context
stereoAnalysis(reactant(1)) returns the stereo descriptors of the second reactant stereoAnalysis(reactant(1), 'tetrahedral') returns the tetrahedral stereo descriptors of the second reactant

stereoisomer

Isomers License

generates a stereoisomer of the molecule

the stereoisomer

  • the stereoisomer index (0-based)

Molecule Context
stereoisomer(0) returns the first stereoisomer of the input molecule
Reaction Context
stereoisomer(reactant(0), 1) returns the second stereoisomer of the first reactant

stereoisomerCount

Isomers License

returns the number of generated stereoisomers

the number of generated stereoisomers

-

Molecule Context
stereoisomerCount() returns the number of generated stereoisomers of the input molecule
Reaction Context
stereoisomerCount(reactant(0)) returns the number of calculated stereoisomers of the first reactant

stereoisomers

Isomers License

generates stereoisomers of the molecule (maximum number of stereoisomers to be generated can be set, default: all)

the stereoisomer array

-

Molecule Context
stereoisomers() returns stereoisomers of the input molecule in an array
Reaction Context
stereoisomers(reactant(0)) returns stereoisomers of the first reactant in an array

tautomerCount

Isomers License

calculates the number of tautomers

the number of tautomers

-

Molecule Context
tautomerCount() returns the number of tautomers of the input molecule
Reaction Context
tautomerCount(reactant(0)) returns the number of tautomers of the first reactant

tetrahedralStereoisomer

Isomers License

generates a tetrahedral stereoisomer of the molecule

the tetrahedral stereoisomer

-

Molecule Context
tetrahedralStereoisomer(0) returns the first tetrahedral stereoisomer of the input molecule
Reaction Context
tetrahedralStereoisomer(reactant(0), 1) returns the second tetrahedral stereoisomer of the first reactant

tetrahedralStereoisomerCount

Isomers License

returns the number of generated tetrahedral stereoisomers

the number of generated tetrahedral stereoisomers

-

Molecule Context
tetrahedralStereoisomerCount() returns the number of generated tetrahedral stereoisomers of the input molecule
Reaction Context
tetrahedralStereoisomerCount(reactant(0)) returns the number of calculated tetrahedral stereoisomers of the first reactant

tetrahedralStereoisomers

Isomers License

generates tetrahedral stereoisomers of the molecule (maximum number of tetrahedral stereoisomers to be generated can be set, default: all)

the tetrahedral stereoisomer array

-

Molecule Context
tetrahedralStereoisomers() returns tetrahedral stereoisomers of the input molecule in an array
Reaction Context
tetrahedralStereoisomers(reactant(0)) returns tetrahedral stereoisomers of the first reactant in an array

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Markush Functions

Name

License

Description

Return value

Parameters

Examples

isMarkush

-

decides whether the given molecule contains any Markush features

true if the molecule contains any Markush features, false otherwise

-

Molecule Context
isMarkush() returns true if the given molecule contains any Markush features, false otherwise
Reaction Context
isMarkush(reactant(1)) returns true if the second reactant contains any Markush features, false otherwise

markushEnumerationCount enumerationCount

Markush Enumeration Plugin

calculates the number of Markush enumerations

the number of Markush enumerations

  • the (1-based) atom indexes of the query atoms to be enumerated (default: all)

Molecule Context
markushEnumerationCount() returns the number of Markush enumerated structures of the input molecule markushEnumerationCount('4,5') returns the number of Markush enumerated structures of the input molecule, enumerating only atoms 4, 5 (1-based)
Reaction Context
markushEnumerationCount(reactant(0)) returns the number of Markush enumerated structures of the first reactant markushEnumerationCount(product(1), atoms(3,4)) returns the number of Markush enumerated structures of the second product, enumerating only atoms 4, 5 (1-based) (the atoms() function converts 0-based indexes to a '-'-separated 1-based atom index string)

markushEnumerations enumeration enumerations markushEnumeration

Markush Enumeration Plugin

constructs Markush enumerated structures sequentially

the enumerated structures

  • the number of structures to be returned (default: all)
  • the (1-based) atom indexes of the query atoms to be enumerated (default: all)

Molecule Context
markushEnumerations() returns all Markush enumerated structures of the input molecule markushEnumerations(1, '2,3') returns one Markush enumerated structure of the input molecule, enumerating atoms 2, 3 (1-based)
Reaction Context
markushEnumerations(reactant(0), 1) returns one Markush enumerated structure of the first reactant markushEnumerations(product(1), 2, '2,3') returns two Markush enumerated structures of the second product, enumerating atoms 2, 3 (1-based)

markushEnumerationsDisplay

Markush Enumeration Plugin

constructs Markush enumerated structures sequentially with scaffold alignment and scaffold/R-group coloring and enumeration ID

the enumerated structures with alignment and coloring data and enumeration ID

  • the number of structures to be returned (default: all)
  • the (1-based) atom indexes of the query atoms to be enumerated (default: all)

Molecule Context
markushEnumerationsDisplay() returns all Markush enumerated structures of the input molecule, with scaffold alignment and coloring data markushEnumerationsDisplay(1, '2,3') returns one Markush enumerated structure of the input molecule, enumerating atoms 2, 3 (1-based), with scaffold alignment and coloring data
Reaction Context
markushEnumerationsDisplay(reactant(0), 1) returns one Markush enumerated structure of the first reactant, with scaffold alignment and coloring data with scaffold alignment and coloring data markushEnumerationsDisplay(product(1), 2, '2,3') returns two Markush enumerated structures of the second product, enumerating atoms 2, 3 (1-based), with scaffold alignment and coloring data

markushLibraryMagnitude

Markush Enumeration Plugin

calculates the Markush library magnitude, no enumeration is done

the Markush library magnitude

  • the (1-based) atom indexes of the query atoms to be enumerated (default: all)

Molecule Context
markushLibraryMagnitude() returns the Markush library magnitude for the input molecule markushLibraryMagnitude('4,5') returns the Markush library magnitude for the input molecule, presuming only atoms 4, 5 (1-based) are enumerated
Reaction Context
markushLibraryMagnitude(reactant(0)) returns the Markush library magnitude for the first reactant markushLibraryMagnitude(product(1), atoms(3,4)) returns the Markush library magnitude for the second product, presuming only atoms 4, 5 (1-based) are enumerated (the atoms() function converts 0-based indexes to a '-'-separated 1-based atom index string)

markushLibrarySize

Markush Enumeration Plugin

calculates the Markush library size, no enumeration is done

the Markush library size

  • the (1-based) atom indexes of the query atoms to be enumerated (default: all)

Molecule Context
markushLibrarySize() returns the Markush library size for the input molecule markushLibrarySize('4,5') returns the Markush library size for the input molecule, presuming only atoms 4, 5 (1-based) are enumerated
Reaction Context
markushLibrarySize(reactant(0)) returns the Markush library size for the first reactant markushLibrarySize(product(1), atoms(3,4)) returns the Markush library size for the second product, presuming only atoms 4, 5 (1-based) are enumerated (the atoms() function converts 0-based indexes to a '-'-separated 1-based atom index string)

markushLibrarySizeAsString

Markush Enumeration Plugin

calculates the Markush library size and returns it as string, no enumeration is done

the Markush library size

  • the (1-based) atom indexes of the query atoms to be enumerated (default: all)

Molecule Context
markushLibrarySize() returns the Markush library size as string for the input molecule markushLibrarySize('4,5') returns the Markush library size as string for the input molecule, presuming only atoms 4, 5 (1-based) are enumerated
Reaction Context
markushLibrarySize(reactant(0)) returns the Markush library size as string for the first reactant markushLibrarySize(product(1), atoms(3,4)) returns the Markush library size as string for the second product, presuming only atoms 4, 5 (1-based) are enumerated (the atoms() function converts 0-based indexes to a '-'-separated 1-based atom index string)

randomMarkushEnumerations randomEnumeration randomEnumerations randomMarkushEnumeration

Markush Enumeration Plugin

constructs Markush enumerated structures randomly

the enumerated structures

  • the number of structures to be returned (default: 1)
  • the (1-based) atom indexes of the query atoms to be enumerated (default: all)

Molecule Context
randomMarkushEnumerations() returns a randomly constructed enumerated structure of the input molecule randomMarkushEnumerations(4, '2,3') returns 4 randomly constructed enumerated structures of the input molecule, enumerating only atoms 2, 3 (1-based)
Reaction Context
randomMarkushEnumerations(reactant(0), 100) returns 100 randomly constructed enumerated structures of the first reactant randomMarkushEnumerations(product(1), '3,4,5') returns a randomly constructed enumerated structure of the second product, enumerating atoms 3, 4, 5 (1-based)

randomMarkushEnumerationsDisplay

Markush Enumeration Plugin

constructs Markush enumerated structures randomly with scaffold alignment and scaffold/R-group coloring and enumeration ID

the enumerated structures with alignment and coloring data and enumeration ID

  • the number of structures to be returned (default: 1)
  • the (1-based) atom indexes of the query atoms to be enumerated (default: all)

Molecule Context
randomMarkushEnumerationsDisplay() returns a randomly constructed enumerated structure of the input molecule, with scaffold alignment and scaffold/R-group coloring datarandomMarkushEnumerationsDisplay(4, '2,3') returns 4 randomly constructed enumerated structures of the input molecule, enumerating only atoms 2, 3 (1-based), with scaffold alignment and coloring data
Reaction Context
randomMarkushEnumerationsDisplay(reactant(0), 100) returns 100 randomly constructed enumerated structures of the first reactant, with scaffold alignment and coloring data randomMarkushEnumerationsDisplay(product(1), '3,4,5') returns a randomly constructed enumerated structure of the second product, enumerating atoms 3, 4, 5 (1-based), with scaffold alignment and coloring data

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Match Functions

Name

License

Description

Return value

Parameters

Examples

disjointMatchCount

-

performs substructure search, returns the maximal number of pairwise disjoint search hits

the maximal number of pairwise disjoint search hits

  • target atom index / MolAtom object (optional)
  • query Molecule object / SMARTS string
  • query atom map(s) (optional)
    The function returns the maximal number of pairwise disjoint query structures found in the target molecule. Warning: if the target atom index and optionally query atom maps are specified then the return value can only be 0 or 1, therefore the result is similar to the result of the match function.

Molecule Context
<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="32063639-03ca-4f1c-9f87-82aa66315fac"><ac:plain-text-body><![CDATA[disjointMatchCount("[#8]C=O") counts the maximal number of pairwise disjoint carboxylic groups in the input molecule
]]></ac:plain-text-body></ac:structured-macro>
Reaction Context
<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="c7696101-9696-47e1-89e4-bd6f6914fb9b"><ac:plain-text-body><![CDATA[disjointMatchCount(reactant(0), "[#8]C=O") counts the maximal number of pairwise disjoint carboxylic groups in the first reactant

]]></ac:plain-text-body></ac:structured-macro>

match

-

performs substructure search and optionally checks for atom matching

true if matching substructure found, false otherwise

  • target atom index / MolAtom object (optional)
  • query Molecule object / SMARTS string
  • query atom map(s) (optional)
    The function returns true if the query structure is found in the target molecule, the hit is required to include the target atom if specified, furthermore if query atom map(s) are specified then these mapped atoms should match the target atom.

Molecule Context
<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="e12cb441-0b95-4bd7-b3b7-825793aa9439"><ac:plain-text-body><![CDATA[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
]]></ac:plain-text-body></ac:structured-macro>
Reaction Context
<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="f39f6396-975c-4b7b-ae76-24f463898f0f"><ac:plain-text-body><![CDATA[match(reactant(0), "[#8]C=O") performs substructure search without atom matching requirement, the target is the first reactant, the query is the carboxylic group given in the string parameter match(patom(2), "[#8]C=O") performs substructure search, checks if product atom matching map 2 in the reaction equation matches any atom of the carboxylic group query match(ratom(1), "[#8:1]C=[O:2]", 1, 2) performs substructure search, checks if reactant atom matching map 1 in the reaction equation is a carboxylic oxygen

]]></ac:plain-text-body></ac:structured-macro>

matchCount

-

performs substructure search and optionally checks for atom matching, counts search hits

the number of search hits

  • target atom index / MolAtom object (optional)
  • query Molecule object / SMARTS string
  • query atom map(s) (optional)
    The function returns the number of query structures found in the target molecule, the hit is required to include the target atom if specified, furthermore if query atom map(s) are specified then these mapped atoms should match the target atom.

Molecule Context
<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="8a943b00-ca03-44ba-8942-d5b1a2c43197"><ac:plain-text-body><![CDATA[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
]]></ac:plain-text-body></ac:structured-macro>
Reaction Context
<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="c77d67a8-f859-48a3-a482-c99ca63b1d49"><ac:plain-text-body><![CDATA[matchCount(reactant(0), "[#8]C=O") counts search hits without atom matching requirement, the target is the first reactant, the query is the carboxylic group given in the string parameter matchCount(patom(2), "[#8]C=O") counts search hits, checks if product atom matching map 2 in the reaction equation matches any atom of the carboxylic group query matchCount(ratom(1), "[#8:1]C=[O:2]", 1, 2) counts search hits with reactant atom matching map 1 in the reaction equation being a carboxylic oxygen

]]></ac:plain-text-body></ac:structured-macro>

matchFirst

-

performs substructure search and optionally checks for atom matching

index of the first matching substructure (1-based indexing)

  • target atom index / MolAtom object (optional)
  • query Molecule objects / SMARTS strings in collection (e.g. {amine,amide,"[#8][C:1]=O"})
  • query atom map(s) (optional)
The function returns the index of the first matching query structure found in the target molecule, the hit is required to include the target atom if specified, furthermore if query atom map(s) are specified then these mapped atoms should match the target atom.

Molecule Context
matchFirst({amine,amide,alcohol}) performs substructure search without atom matching requirement, the target is the input molecule, the queries are the amine, amide, and alcohol groups given in the string parameter. Function returns 1 if there is an amine group in the input molecule, 2 if there is no amine, but there is an amide group in the input molecule, and returns 3 if there is no amine or amide group, but there is an alcohol group in the input molecule. Returns 0 if none of the listed groups is found in input molecule. matchFirst(6, {"[#8][C:1]=O","[NX3:2][CX3:1]=[OX1:3]"}, 1) performs substructure search, checks if target atom 6 matches the carbon (atom with map 1) of the carboxylic or amide group in query. Returns the index of the query if match found, 0 otherwise. matchFirst(6, {"[#8:1]C=[O:2]","[#6][OX2:1][CX3](=[O:2])[#6]"}, 1, 2) performs substructure search, checks if target atom 6 of the input molecule is a carboxylic oxygen or an oxigen in an ester group. Returns the index of the query if match found, 0 otherwise.
Reaction Context
matchFirst(reactant(0), {amine,amide,alcohol}) performs substructure search without atom matching requirement, the target is the first reactant, the queries are the amine, amide, and alcohol groups given in the string parameter. Function returns 1 if there is an amine group in the first reactant, 2 if there is no amine group, but there is an amide group in the first reactant, and returns 3 if there is no amine or amide group, but there is an alcohol group in the first reactant. Returns 0 if none of the listed groups is found in first reactant. matchFirst(patom(2), {"[#8][C]=O","[NX3][CX3]=[OX1]"}) performs substructure search, checks if product atom matching map 2 in the reaction equation matches any atom of the carboxylic or amide group query. Returns the index of mathing query, or 0 if no match found. matchFirst(ratom(1), {"[#8:1]C=[O:2]","[#6][OX2:1][CX3](=[O:2])[#6]"}, 1, 2) performs substructure search, checks if reactant atom matching map 1 in the reaction equation is a carboxylic oxygen or an oxigen in an ester group. Returns the index of the query if match found, 0 otherwise.

]]></ac:plain-text-body></ac:structured-macro>

Predefined Molecules and Molecule Sets

It is sometimes easier to refer molecules by names rather than explicit SMARTS strings or molecule file paths. For example, you may want to write nitro or carboxyl as query in a match function. Frequently used queries are pre-defined in the built-in functional groups file (chemaxon/marvin/templates/functionalgroups.cxsmi within MarvinBeans-templates.jar).
You can also define your favourite query SMARTS in marvin/config/marvin/templates/functionalgroups.cxsmi file and in $HOME\chemaxon\marvin\templates\functionalgroups.cxsmi (Windows) or $HOME/.chemaxon/marvin/templates/functionalgroups.cxsmi (UNIX / Linux) file where marvin is the Marvin istallation directory, $HOME is your user home directory.
  Back to Contents
 
 

Name Functions

Name

License

Description

Return value

Parameters

Examples

name

Structure To Name License

returns the name(s) of the molecule specified by the export option

the name(s) of the molecule

either empty (IUPAC export option) or the specified name export option

Molecule Context
name() returns the preferred IUPAC name of the input molecule
name('CAS#') returns CAS Registry Number(s) of the input molecule
Reaction Context
N / A (reaction rules are numerical)

traditionalName

Structure To Name License

returns the traditional name of the molecule

the traditional name of the molecule

-

Molecule Context
traditionalName() returns the traditional name of the input molecule
Reaction Context
N / A (reaction rules are numerical)

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Partitioning Functions

Name

License

Description

Return value

Parameters

Examples

HLB number

Partitioning License

calculates the HLB number

the HLB number

  • the calculation method or empty

Molecule Context
hlb() returns the HLB number of the input molecule using the default calculation method hlb('davies') returns the HLB number of the input molecule using the Davies calculation method
Reaction Context
hlb(reactant(1), 'griffin') returns the HLB number of the second reactant using the Griffin method

logD

Partitioning License

calculates logD at specified pH

the logD value

  • the pH value

Molecule Context
logD('7.4') returns the logD at pH 7.4 of the input molecule
Reaction Context
logD(reactant(1), '7.4') returns the logD at pH 7.4 of the second reactant

logDKLOP

Partitioning License

calculates logD at specified pH using method "KLOP"

the logD value

  • the pH value

Molecule Context
logDKLOP('7.4') returns the logD at pH 7.4 of the input molecule
Reaction Context
logDKLOP(reactant(1), '7.4') returns the logD at pH 7.4 of the second reactant

logDPHYS

Partitioning License

calculates logD at specified pH using method "PHYS"

the logD value

  • the pH value

Molecule Context
logDPHYS('7.4') returns the logD at pH 7.4 of the input molecule
Reaction Context
logDPHYS(reactant(1), '7.4') returns the logD at pH 7.4 of the second reactant

logDUser

Partitioning License

calculates logD at specified pH using the user defined method

the logD value

  • the pH value

Molecule Context
logDUser('7.4') returns the logD at pH 7.4 of the input molecule
Reaction Context
logDUser(reactant(1), '7.4') returns the logD at pH 7.4 of the second reactant

logDVG

Partitioning License

calculates logD at specified pH using method "VG"

the logD value

  • the pH value

Molecule Context
logDVG('7.4') returns the logD at pH 7.4 of the input molecule
Reaction Context
logDVG(reactant(1), '7.4') returns the logD at pH 7.4 of the second reactant

logDWeighted

Partitioning License

calculates logD at specified pH using weighted method

the logD value

  • the pH value

Molecule Context
logDWeighted('7.4') returns the logD at pH 7.4 of the input molecule
Reaction Context
logDWeighted(reactant(1), '7.4') returns the logD at pH 7.4 of the second reactant

logP

Partitioning License

calculates logP

the logP 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)

Molecule Context
logP() returns the most typical logP 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
Reaction Context
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

logPincrement logPi

Partitioning License

calculates the atomic logP increment

the atomic logP increment

  • the atom index / MolAtom object

Molecule Context
logPincrement(2) returns the logP increment on atom 2 of the input molecule
Reaction Context
logPincrement(ratom(1)) returns the logP increment on the reactant atom matching map 1 in the reaction equation

logPKLOP

Partitioning License

calculates logP using method "KLOP"

the logP 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)

Molecule Context
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
Reaction Context
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

logPPHYS

Partitioning License

calculates logP using method "PHYS"

the logP 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)

Molecule Context
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
Reaction Context
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

logPUser

Partitioning License

calculates logP using the user defined method

the logP 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)

Molecule Context
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
Reaction Context
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

logPVG

Partitioning License

calculates logP using method "VG"

the logP 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)

Molecule Context
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
Reaction Context
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

logPWeighted

Partitioning License

calculates logP using weighted method

the logP 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)

Molecule Context
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
Reaction Context
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

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Protonation Functions

Name

License

Description

Return value

Parameters

Examples

acidicpKa apKa

Protonation License

calculates acidic pK a values

the acidic pK a values

  • the atom index / MolAtom object,
  • the strength index as string (e.g. '1' for the strongest, '2' for the second strongest pK a),
    Note, that the strength index is specified between quotation marks.

Molecule Context
acidicpKa(0) returns the acidic pK a of atom 0 of the input molecule acidicpKa("2") returns the second strongest acidic pK a value
Reaction Context
acidicpKa(ratom(1)) returns the acidic pK a of reactant atom matching map 1 in the reaction equation acidicpKa(product(0), "1") returns the strongest basic pK a value in the first product

acidicpKaLargeModel

Protonation License

calculates acidic pK a values using large model (this model is optimized for a large number of ionizable atoms)

the acidic pK a values

  • the atom index / MolAtom object,
  • the strength index as string (e.g. '1' for the strongest, '2' for the second strongest pK a),
    Note, that the strength index is specified between quotation marks.

Molecule Context
acidicpKaLargeModel(0) returns the acidic pK a of atom 0 of the input molecule acidicpKaLargeModel("2") returns the second strongest acidic pK a value
Reaction Context
acidicpKaLargeModel(ratom(1)) returns the acidic pK a of reactant atom matching map 1 in the reaction equation acidicpKaLargeModel(product(0), "1") returns the strongest basic pK a value in the first product

acidicpKaUseCorrection

Protonation License

calculates acidic pK a values using the correction library

the acidic pK a values

  • the atom index / MolAtom object,
  • the strength index as string (e.g. '1' for the strongest, '2' for the second strongest pK a),
    Note, that the strength index is specified between quotation marks.

Molecule Context
acidicpKaUseCorrection(0) returns the acidic pK a of atom 0 of the input molecule "acidicpKaUseCorrection"("2") returns the second strongest acidic pK a value
Reaction Context
"acidicpKaUseCorrection"(ratom(1)) returns the acidic pK a of reactant atom matching map 1 in the reaction equation "acidicpKaUseCorrection"(product(0), "1") returns the strongest basic pK a value in the first product

averageMicrospeciesCharge

Protonation License

calculates the average microspecies charge (weighted sum of charges of all the microspecies of the molecule) at the given pH

the average charge

  • the major microspecies pH

Molecule Context
averageMicrospeciesCharge() returns the average charge of the microspecies of the input molecule
Reaction Context
averageMicrospeciesCharge(reactant(1)) returns the average charge of the microspecies of the second reactant

basicpKa bpKa

Protonation License

calculates basic pK a values

the basic pK a values

  • the atom index / MolAtom object,
  • the strength index as string (e.g. '1' for the strongest, '2' for the second strongest pK a),
    Note, that the strength index is specified between quotation marks.

Molecule Context
basicpKa(0) returns the basic pK a of atom 0 of the input molecule basicpKa("2") returns the second strongest basic pK a value
Reaction Context
basicpKa(ratom(1)) returns the basic pK a of reactant atom matching map 1 in the reaction equation basicpKa(product(0), "1") returns the strongest basic pK a value in the first product

basicpKaLargeModel

Protonation License

calculates basic pK a values using large model (this model is optimized for a large number of ionizable atoms)

the basic pK a values

  • the atom index / MolAtom object,
  • the strength index as string (e.g. '1' for the strongest, '2' for the second strongest pK a),
    Note, that the strength index is specified between quotation marks.

Molecule Context
basicpKaLargeModel(0) returns the basic pK a of atom 0 of the input molecule basicpKaLargeModel("2") returns the second strongest basic pK a value
Reaction Context
basicpKaLargeModel(ratom(1)) returns the basic pK a of reactant atom matching map 1 in the reaction equation basicpKaLargeModel(product(0), "1") returns the strongest basic pK a value in the first product

basicpKaUseCorrection

Protonation License

calculates basic pK a values using the correction library

the basic pK a values

  • the atom index / MolAtom object,
  • the strength index as string (e.g. '1' for the strongest, '2' for the second strongest pK a),
    Note, that the strength index is specified between quotation marks.

Molecule Context
basicpKaUseCorrection(0) returns the basic pK a of atom 0 of the input molecule basicpKaUseCorrection("2") returns the second strongest basic pK a value
Reaction Context
basicpKaUseCorrection(ratom(1)) returns the basic pK a of reactant atom matching map 1 in the reaction equation basicpKaUseCorrection(product(0), "1") returns the strongest basic pK a value in the first product

isoelectricPoint pI

Protonation License

calculates isoelectric point

the isoelectric point

-

Molecule Context
isoelectricPoint() returns the isoelectric point of the input molecule
Reaction Context
isoelectricPoint(reactant(1)) returns the isoelectric point of the second reactant

majorMicrospecies majorMs

Protonation License

calculates major microspecies at specified pH

the major microspecies

  • the pH value as string

Molecule Context
majorMicrospecies("7.4") returns the major microspecies of the input molecule at pH 7.4
Reaction Context
majorMicrospecies(reactant(0), "7.4") returns the major microspecies of the first reactant at pH 7.4 majorMicrospecies(product(1), "7.4") returns the major microspecies of the second product at pH 7.4

microspecies ms

Protonation License

calculates microspecies at specified pH

the microspecies

  • the pH value as string
  • the microspecies index by descending order of microspecies distributions

Molecule Context
microspecies("7.4", 1) returns the microspecies of the input molecule with second largest distribution at pH 7.4
Reaction Context
microspecies(reactant(0), "7.4", 2) returns the microspecies of the first reactant with third largest distribution at pH 7.4 microspecies(product(1), "7.4", 1) returns the microspecies of the second product with second largest distribution at pH 7.4

microspeciesCount msCount

Protonation License

calculates the number of microspecies at specified pH

the number of microspecies

-

Molecule Context
microspeciesCount() returns the number of microspecies of the input molecule
Reaction Context
microspeciesCount(reactant(0)) returns the number of microspecies of the first reactant microspeciesCount(product(1)) returns the number of microspecies of the second product

microspeciesDistribution msDistr

Protonation License

calculates microspecies distribution at specified pH

the microspecies distribution

  • the pH value as string
  • the microspecies index by descending order of microspecies distributions

Molecule Context
microspeciesDistribution("5.4", 0) returns the largest microspecies distribution of the input molecule at pH 5.4
Reaction Context
microspeciesDistribution(reactant(0), "5.4", 2) returns the third largest microspecies distribution of the first reactant at pH 5.4 microspeciesDistribution(product(1), "3.2", 1) returns the second largest microspecies distribution of the second product at pH 3.2

pKa

Protonation License

calculates pK a values

the pK a values

  • the atom index / MolAtom object,
  • the strength index as string (e.g., '1' for the strongest, '2' for the second strongest pK a),
  • the result type ("acidic", "basic", or "pka" for both (default))
    Note, that the strength index is specified between quotation marks. In case of strength index the result type can be specified as "acidic" or "basic". In case of "pka"result type the returned pK a values are acidic or basic (mixed!), depending on the acidic or basic character of the given atom. Acidic pK a is returned for an atom, if acidicpKa() ≤ 14.8-basicpKa(), otherwise basic pK a is returned. Specifying "acidic" or "basic" result type is required to get the acidic or basic pK a values only (also acidicpKa or basicpKa functions can be used alternatively).

Molecule Context
pKa(0) returns the pK a of atom 0 of the input molecule pKa("acidic", "2") returns the second strongest acidic pK a value
Reaction Context
pKa(ratom(1)) returns the pK a of reactant atom matching map 1 in the reaction equation pKa(product(0), "basic", "1") returns the strongest basic pK a value in the first product

pKaUseCorrection

Protonation License

calculates pK a values using the correction library

the pK a values

  • the atom index / MolAtom object,
  • the strength index as string (e.g. '1' for the strongest, '2' for the second strongest pK a),
  • the result type ("acidic", "basic", or "pka" for both (default))
    Note, that the strength index is specified between quotation marks. In case of strength index the result type can be specified as "acidic" or "basic". In case of "pka"result type the returned pK a values are acidic or basic (mixed!), depending on the acidic or basic character of the given atom. Acidic pK a is returned for an atom, if acidicpKa() ≤ 14.8-basicpKa(), otherwise basic pK a is returned. Specifying "acidic" or "basic" result type is required to get the acidic or basic pK a values only (also acidicpKaUseCorrection() or basicpKaUseCorrection() functions can be used alternatively).

Molecule Context
pKaUseCorrection(0) returns the pK a of atom 0 of the input molecule pKaUseCorrection("acidic", "2") returns the second strongest acidic pK a value
Reaction Context
pKaUseCorrection(ratom(1)) returns the pK a of reactant atom matching map 1 in the reaction equation pKaUseCorrection(product(0), "basic", "1") returns the strongest basic pK a value in the first product

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Refractivity Functions

Name

License

Description

Return value

Parameters

Examples

refractivity refrac

Structural Calculations License

calculates molar refractivity

the refractivity value

-

Molecule Context
refractivity() returns the molar refractivity of the input molecule
Reaction Context
refractivity(reactant(1)) returns the molar refractivity of the second reactant

refractivityIncrements refraci

Structural Calculations License

calculates atomic refractivity increments

the atomic refractivity increment

  • the atom index / MolAtom object

Molecule Context
refractivityIncrements(2) returns the refractivity increment on atom 2 of the input molecule
Reaction Context
refractivityIncrements(ratom(1)) returns the refractivity increment on the reactant atom matching map 1 in the reaction equation

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Solubility Functions

Name

License

Description

Return value

Parameters

Examples

logS

Solubility License

Calculates intrinsic solubility or solubility at a specified pH

the logS value

  • the pH value
  • the solubility unit: logS, mol/l, mg/ml, category

Molecule Context
logS() returns the intrinsic solubility of the input molecule in logS unit (default)
logS('7.4', 'category') returns the qualitative logS at pH 7.4 of the input molecule
logS('7.4', 'mol/l') returns the logS at pH 7.4 of the input molecule in mol/l unit

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StructuralFrameworks Functions

Name

License

Description

Return value

Parameters

Examples

bmf

Structural Calculations License

Returns the Bemis-Murcko framework of the input structure

BMF of the input structure

-

Molecule Context
bmf() returns the Bemis-Murcko framework of the input molecule
Reaction Context
bmf(reactant(0)) returns the Bemis-Murcko framework of the first reactant

bmfl bemisMurckoFrameworkLoose

Structural Calculations License

Returns the Bemis-Murcko loose framework of the input structure. Calculated by removing side chains. Exocyclic non single bonded atoms are kept. Remaining atom and bond types are not changed.

Loose BMF of the input structure

-

Molecule Context
bmfl() returns the loose Bemis-Murcko framework of the input molecule
Reaction Context
bmfl(reactant(0)) returns the loose Bemis-Murcko framework of the first reactant

bmflp bemisMurckoFrameworkLoosePruned

Structural Calculations License

Returns the Bemis-Murcko loose framework of the input structure. Calculated by removing side cains. Atom and bond types are generalized by replacing all atoms with carbons and setting all bond types to single. Exocyclic non single bonded atoms are kept as single bonded carbons.

Generalized loose BMF of the input structure

-

Molecule Context
bmflp() returns the generalized loose Bemis-Murcko framework of the input molecule
Reaction Context
bmflp(reactant(0)) returns the generalized loose Bemis-Murcko framework of the first reactant

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Structure Checker Functions

Name

License

Description

Return value

Parameters

Examples

check

-

checks the structure for errors, according to the configuration

the error report

Structure checker/fixer configuration as action string or XML string

Molecule Context (All)

  • check("aromaticity..valence"), or
  • check('"<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"no\"?><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
    Reaction Context
    check(reactant(0), "aromaticity..valence") checks for aromaticity and valence errors in first reactant, and returns the error report

checkErrorCount

-

checks the structure for errors, according to the configuration

the total error count

Structure checker/fixer configuration as XML or action string

Molecule Context
checkErrorCount('"<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"no\"?><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
Reaction Context
check(reactant(0), "aromaticity..valence") checks for aromaticity and valence errors in first reactant, and returns the error report

fix

-

checks the structure for errors, according to the configuration, and then fixes the errors

the fixed molecule

Structure checker/fixer configuration as action string or XML string

Molecule Context (All)

  • fix("chiralflag..isotope->converttoelementalform"), or
  • fix('"<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"no\"?><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
    Reaction Context
    fix(product(1), "chiralflag..isotope->converttoelementalform") searches for ciral flags and isotopes in second product, and removes them or converts them to elemental form

isValid

-

checks the structure for errors, according to the configuration

true, if the structure is valid (has no errors), false otherwise

Structure checker/fixer configuration as action string or XML string

Molecule Context (All)

  • isValid("aromaticity..valence"), or
  • isValid('"<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"no\"?><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
    Reaction Context
    isValid(reactant(0), "aromaticity..valence") checks for aromaticity and valence errors in first reactant, and returns if it is valid

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Notes

  1. If in reaction context in the parameter list of a Chemical Terms function atoms are referred by atom index - including cases when a Chemical Terms function is used to convert reactant or product atom maps to atom indexes - then the molecule (reactant / product) parameter always have to be specified (e.g. shortestPath(reactant(0), pair(ratom(1), ratom(2)))) and must contain all the atoms referred by atom indexes.
  2. Although the function/calculation names are case-sensitive, the lowercase versions are always accepted. For example, aromaticAtomCount() is equivalent to aromaticatomcount(), but AromaticAtomCount() and AROMATICATOMCOUNT() are not recognized by the parser.
  3. match, matchCount, disjointMatchCount and dissimilarity functions are not available in Marvin, they can be used only if JChem software package is installed.
  4. Structure based calculations are performed using Calculator Plugins (these calculations are also referred as "plugin calculations").Since Marvin 5.2, all of these functions can have an additional string argument that specifies plugin parameters in "key1:value1 key2:value2 key3:value3 ..." fashion. For example: charge(8, "type:pi pH:3.5") will compute the pi charge of atom 8 in the major microspecies at pH=3.5 of the input molecule, markushEnumerations("code:true max:4","1,2") will generate maximum 4 enumerated structures with enumeration ID, enumerating only atoms 1 and 2 of the input Markush structure. Note, that this feature cannot be combined with the former possibility of specifying the pH in a string argument, for example: charge(8, "type:pi pH:3.5") cannot be written in the form charge(8, "type:pi", "3.5"), while charge("pi", 8, "3.5") is accepted (backward compatibility).