"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">Chemical Terms Reference Tables

Molecule Context(All)
acidicpKa(0) returns the acidic pK_a of atom 0 of the input molecule acidicpKa("2")returns the second strongest acidic pK_a valueReaction Context(All)
acidicpKa(ratom(1)) returns the acidic pK_a of reactant atom matching map 1in 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(All)
acidicpKaLargeModel(0) returns the acidic pK_a of atom 0 of the input moleculeacidicpKaLargeModel("2") returns the second strongest acidic pK_a valueReaction Context(All)
acidicpKaLargeModel(ratom(1)) returns the acidic pK_a of reactant atom matching map 1in 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(All)
acidicpKaUseCorrection(0) returns the acidic pK_a of atom 0 of the input molecule"acidicpKaUseCorrection"("2") returns the second strongest acidic pK_a valueReaction Context(All)
"acidicpKaUseCorrection"(ratom(1)) returns the acidic pK_a of reactant atom matching map 1in the reaction equation "acidicpKaUseCorrection"(product(0), "1") returns the strongest basic pK_a value in the first product

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(All)
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(All)
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.

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(All)
aliphaticAtom(2) returns true if atom 2 of the input molecule is aliphatic, false otherwiseReaction Context(All)
aliphaticAtom(ratom(2)) returns true if the reactant atom matching map 2in the reaction equation is aliphatic, false otherwise aliphaticAtom(patom(1)) returns trueif 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(All)
aliphaticAtomCount() returns the number of aliphatic atoms in the input moleculeReaction Context(All)
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(All)
aliphaticBondCount() returns the number of bonds in the input moleculeReaction Context(All)
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(All)
aliphaticRingCount() returns the number of aliphatic rings in the input moleculeReaction Context(All)
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(All)
aliphaticRingCountOfSize(6) returns the number of aliphatic rings of size 6 in the input moleculeReaction Context(All)
aliphaticRingCountOfSize(reactant(0), 5) returns the number of aliphatic rings of size 5 in the first reactantaliphaticRingCountOfSize(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(All)
aliphaticRings() returns the atom indexes of the aliphatic rings in the input moleculeReaction Context(All)
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(All)
aliphaticRings() returns the atom indexes of the aliphatic rings in the input molecule having the given sizeReaction Context(All)
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

allTautomer

Isomers License

constructs a tautomeric form

the tautomer

the tautomer index (0-based)

Molecule Context(All)
tautomer(0) returns the first tautomer of the input moleculeReaction Context(All)
tautomer(reactant(0), 1) returns the second tautomer of the first reactant

allTautomers

Isomers License

constructs all tautomeric forms

the tautomer array

-

Molecule Context(All)
tautomers() returns all tautomers of the input molecule in an arrayReaction Context(All)
tautomers(reactant(0)) returns all tautomers of the first reactant in an array

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(All)
angle('1-2-3') and angle(atoms(0, 1, 2)) both return the angle between atoms 1,2 and 3 in the input moleculeReaction Context(All)
angle(reactant(0), atoms(ratom(1), ratom(2), ratom(3))) returns the angle between reactant atoms matching maps1, 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)

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

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(All)
aromaticAtom(2) returns true if atom 2 of the input molecule is aromatic, false otherwiseReaction Context(All)
aromaticAtom(ratom(2)) returns true if the reactant atom matching map 2in the reaction equation is aromatic, false otherwise aromaticAtom(patom(1)) returns trueif 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(All)
aromaticAtomCount() returns the number of aromatic atoms in the input moleculeReaction Context(All)
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(All)
aromaticBondCount() returns the number of aromatic bonds in the input moleculeReaction Context(All)
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(All)
aromaticRingCount() returns the number of aromatic rings in the input moleculeReaction Context(All)
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(All)
aromaticRingCountOfSize(6) returns the number of aromatic rings of size 6 in the input moleculeReaction Context(All)
aromaticRingCountOfSize(reactant(0), 5) returns the number of aromatic rings of size 5 in the first reactantaromaticRingCountOfSize(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(All)
aromaticRings() returns the atom indexes of the aromatic rings in the input moleculeReaction Context(All)
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(All)
aromaticRings() returns the atom indexes of the aromatic rings in the input molecule having the given sizeReaction Context(All)
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

array

-

constructs an integer array from its arguments

the integer array

integers or MolAtom objects

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

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(All)
ASAHydrophobic() returns the water accessible surface area of all atoms of the input molecule with hydrophobic partial chargeASAHydrophobic('7.4')returns the water accessible surface area of all atoms with hydrophobic partial charge of the major microspecies taken at pH 7.4Reaction Context(All)
ASAHydrophobic(reactant(0)) returns the water accessible surface area of all atoms of the first reactant with hydrophobic partial chargeASAHydrophobic(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(All)
ASANegative() returns the water accessible surface area of all atoms of the input molecule with negative partial chargeASANegative('7.4')returns the water accessible surface area of all atoms with negative partial charge of the major microspecies taken at pH 7.4Reaction Context(All)
ASANegative(reactant(0)) returns the water accessible surface area of all atoms of the first reactant with negative partial chargeASANegative(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(All)
ASAPlus() returns the water accessible surface area of all atoms of the input molecule with positive partial chargeASAPlus('7.4')returns the water accessible surface area of all atoms with positive partial charge of the major microspecies taken at pH 7.4Reaction Context(All)
ASAPlus(reactant(0)) returns the water accessible surface area of all atoms of the first reactant with positive partial chargeASAPlus(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(All)
ASAPolar() returns the water accessible surface area of all atoms of the input molecule with polar partial chargeASAPolar('7.4')returns the water accessible surface area of all atoms with polar partial charge of the major microspecies taken at pH 7.4Reaction Context(All)
ASAPolar(reactant(0)) returns the water accessible surface area of all atoms of the first reactant with polar partial chargeASAPolar(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(All)
asymmetricAtom(2) returns true if atom 2 of the input molecule is an asymmetric atom, false otherwiseReaction Context(All)
asymmetricAtom(ratom(2)) returns true if the reactant atom matching map 2in 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(All)
asymmetricAtomCount() returns the number of asymmetric atoms in the input moleculeReaction Context(All)
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(All)
asymmetricAtoms() returns the indexes of asymmetric atoms in the input moleculeReaction Context(All)
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

atno
atomicNumber

-

returns the atomic number

the atomic number

atom index or MolAtom object

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

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(All)
atomCount() returns the number of atoms in the input molecule atomCount("6") returns the number of carbon atoms in the input moleculeReaction Context(All)
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

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(All)
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 7.4Reaction Context(All)
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 2of the major microspecies taken at pH 7.4

atomProp

-

atoms

-

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(All)
averageMicrospeciesCharge() returns the average charge of the microspecies of the input moleculeReaction Context(All)
averageMicrospeciesCharge(reactant(1)) returns the average charge of the microspecies of the second reactant

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(All)
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 7.4Reaction Context(All)
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(All)
axxPol() returns the principal component a(xx) of polarizability tensor of the input moleculeaxxPol("7.4") returns the principal component a(xx) of polarizability tensor of the major microspecies taken at pH 7.4Reaction Context(All)
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(All)
ayyPol() returns the principal component a(yy) of polarizability tensor of the input moleculeayyPol("7.4") returns the principal component a(yy) of polarizability tensor of the major microspecies taken at pH 7.4Reaction Context(All)
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(All)
azzPol() returns the principal component a(zz) of polarizability tensor of the input moleculeazzPol("7.4") returns the principal component a(zz) of polarizability tensor of the major microspecies taken at pH 7.4Reaction Context(All)
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

balabanIndex

Structural Calculations License

calculates the Balaban index

the Balaban index

-

Molecule Context(All)
calculates the Balaban indexReaction Context(All)
the Balaban index

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(All)
basicpKa(0) returns the basic pK_a of atom 0 of the input moleculebasicpKa("2") returns the second strongest basic pK_a valueReaction Context(All)
basicpKa(ratom(1)) returns the basic pK_a of reactant atom matching map 1in 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(All)
basicpKaLargeModel(0) returns the basic pK_a of atom 0 of the input moleculebasicpKaLargeModel("2") returns the second strongest basic pK_a valueReaction Context(All)
basicpKaLargeModel(ratom(1)) returns the basic pK_a of reactant atom matching map 1in 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(All)
basicpKaUseCorrection(0) returns the basic pK_a of atom 0 of the input moleculebasicpKaUseCorrection("2") returns the second strongest basic pK_a valueReaction Context(All)
basicpKaUseCorrection(ratom(1)) returns the basic pK_a of reactant atom matching map 1in the reaction equation basicpKaUseCorrection(product(0), "1") returns the strongest basic pK_a value in the first product

bmf

Structural Calculations License

Returns the Bemis-Murcko framework of the input structure

BMF of the input structure

-

Molecule Context(All)
bmf() returns the Bemis-Murcko framework of the input moleculeReaction Context(All)
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(All)
bmfl() returns the loose Bemis-Murcko framework of the input moleculeReaction Context(All)
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(All)
bmflp() returns the generalized loose Bemis-Murcko framework of the input moleculeReaction Context(All)
bmflp(reactant(0)) returns the generalized loose Bemis-Murcko framework of the first reactant

bondCount

-

calculates the bond count

the bond count

-

Molecule Context(All)
bondCount() returns the number of bonds in the input moleculeReaction Context(All)
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(All)
bondType('2-3') and bondType(bond(1, 2)) both return the bond type between atoms 1and 2 in the input moleculeReaction Context(All)
bondType(reactant(0), bond(ratom(1), ratom(2))) returns the bond type between reactant atoms matching maps 1and 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)

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 25Molecule Context(All)
booleanToNumber(hasValenceError())returns 0 for molecules having no valence errorReaction Context(All)
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

canonicalResonant

-

constructs the canonical resonant structure

the canonical resonant structure

-

Molecule Context(All)
canonicalResonant() returns the canonical resonant structure of the input moleculeReaction Context(All)
canonicalResonant(reactant(0)) returns the canonical resonant structure of the first reactant

canonicalTautomer

Isomers License

constructs the canonical tautomer structure

the canonical tautomer structure

-

Molecule Context(All)
canonicalTautomer() returns the canonical tautomer structure of the input moleculeReaction Context(All)
canonicalTautomer(reactant(0)) returns the canonical tautomer structure of the first reactant/td>

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(All)
carboaliphaticRingCount() returns the number of carboaliphatic rings in the input moleculeReaction Context(All)
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(All)
carboaromaticRingCount() returns the number of carboaromatic rings in the input moleculeReaction Context(All)
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(All)
carboRingCount() returns the number of carbocyclic rings in the input moleculeReaction Context(All)
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(All)
carboRingCountOfSize(6) returns the number of carbocyclic rings of size 6 in the input moleculeReaction Context(All)
carboRingCountOfSize(reactant(0), 5) returns the number of carbocyclic rings of size 5 in the first reactantcarboRingCountOfSize(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(All)
carboRings() returns the atom indexes of the carbocyclic rings in the input moleculeReaction Context(All)
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(All)
carboRings() returns the atom indexes of the carbocyclic rings in the input molecule having the given sizeReaction Context(All)
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(All)
chainAtom(2) returns true if atom 2 of the input molecule is a chain atom, false otherwiseReaction Context(All)
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 trueif 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(All)
chainAtomCount() returns the number of chain atoms in the input moleculeReaction Context(All)
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(All)
chainBond('2-3') and chainBond(bond(1, 2)) both return true if atoms 1and 2 are connected by a chain bond the input moleculeReaction Context(All)
chainBond(reactant(0), bond(ratom(1), ratom(2))) returns true if reactant atoms matching maps 1and 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(All)
chainBondCount() returns the number of chain bonds in the input moleculeReaction Context(All)
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

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(All)
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 7.4Reaction Context(All)
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 2in the major microspecies taken at pH 7.4

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(All)
chargeDensity(2) returns the charge density of atom 2 of the input molecule, NaNfor non-existing valueReaction Context(All)
chargeDensity(ratom(1)) returns the charge density of the reactant atom matching map 1in the reaction equation

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 reportReaction Context(All)
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(All)
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 countReaction Context(All)
check(reactant(0), "aromaticity..valence") checks for aromaticity and valence errors in first reactant, and returns the error report

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(All)
chiralCenter(2) returns true if atom 2 of the input molecule is a tetrahedral stereogenic center, false otherwiseReaction Context(All)
chiralCenter(ratom(2)) returns true if the reactant atom matching map 2in 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(All)
chiralCenterCount() returns the number of tetrahedral stereogenic centers in the input moleculeReaction Context(All)
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(All)
chiralCenters() returns the indexes of chiral center atoms in the input moleculeReaction Context(All)
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

composition

-

returns the composition

the composition

-

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

conformer

Structural Calculations License

calculates a conformer of the molecule

the conformer

the conformer index (0-based)

Molecule Context(All)
conformer(0) returns the first conformer of the input moleculeReaction Context(All)
conformer(reactant(0), 1) returns the second conformer of the first reactant

conformerCount

Structural Calculations License

returns the number of calculated conformers

the number of calculated conformers

-

Molecule Context(All)
conformerCount() returns the number of calculated conformers of the input moleculeReaction Context(All)
conformerCount(reactant(0)) returns the number of calculated conformers of the first reactant

conformers

Structural Calculations License

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

the conformer array

-

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

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(All)
connected('2-3') and connected(pair(1, 2)) both return true if atoms 1and 2 are in the same connected component of the input moleculeReaction Context(All)
connected(reactant(0), pair(ratom(1), ratom(2))) returns true if reactant atoms matching maps 1and 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 2and 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(All)
connectedGraph() returns true if the input molecule graph is connectedReaction Context(All)
connectedGraph(reactant(0)) returns true if the first reactant is connected connectedGraph(product(1))returns true if the second product is connected

connections

-

returns the bond plus implicit H count of an atom

the bond plus implicit H count

atom index or MolAtom object

Molecule Context(All)
connections(2) returns the number of connections of atom 2Reaction Context(All)
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 3Molecule Context(All)
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 carbonsReaction Context(All)
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

cyclomaticNumber

Structural Calculations License

calculates the cyclomatic number

the cyclomatic number

-

Molecule Context(All)
cyclomaticNumber() returns the cyclomatic number of the input moleculeReaction Context(All)
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(All)
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 moleculeReaction Context(All)
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)

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 thematch function.

Molecule Context(All)
disjointMatchCount("[#8]C=O") counts the maximal number of pairwise disjoint carboxylic groups in the input moleculeReaction Context(All)
disjointMatchCount(reactant(0), "[#8]C=O") counts the maximal number of pairwise disjoint carboxylic groups in the first reactant

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(All)
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 metricReaction Context(All)
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)

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(All)
distance('1-2') and distance(pair(0, 1)) both return the distance between atoms 1and 2 in the input moleculeReaction Context(All)
distance(reactant(0), pair(ratom(1), ratom(2))) returns the distance between reactant atoms matching maps 1and 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 3in 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(All)
distanceDegree(2) returns the distance degree of atom 2 of the input moleculeReaction Context(All)
distanceDegree(ratom(2)) returns the distance degree of the reactant atom matching map 2in the reaction equation distanceDegree(patom(1)) returns the distance degree of the product atom matching map 1 in the reaction equation

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(All)
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(All)
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(All)
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 7.4Reaction Context(All)
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(All)
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(All)
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

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

dotDisconnectedFormula

-

returns the dot-disconnected formula

the dot-disconnected formula

-

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

dotDisconnectedIsotopeFormula

-

returns the dot-disconnected isotope formula

the dot-disconnected isotope formula

-

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

dotDisconnectedFormulaWithGrouping

-

returns the grouped dot-disconnected formula

the grouped dot-disconnected formula

-

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

doubleBondStereoisomer

Isomers License

generates a double bond stereoisomer of the molecule

the double bond stereoisomer

the double bond stereoisomer index (0-based)

Molecule Context(All)
doubleBondStereoisomer(0) returns the first double bond stereoisomer of the input moleculeReaction Context(All)
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(All)
doubleBondStereoisomerCount() returns the number of generated double bond stereoisomers of the input moleculeReaction Context(All)
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(All)
doubleBondStereoisomers() returns double bond stereoisomers of the input molecule in an arrayReaction Context(All)
doubleBondStereoisomers(reactant(0)) returns double bond stereoisomers of the first reactant in an array

dreidingEnergy

Structural Calculations License

returns the Dreiding energy of the input molecule (conformer)

the dreiding energy

-

Molecule Context(All)
dreidingEnergy() returns the dreiding energy of the input molecule (conformer)Reaction Context(All)
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(All)
eccentricity(2) returns the eccentricity of atom 2 of the input moleculeReaction Context(All)
eccentricity(ratom(2)) returns the eccentricity of the reactant atom matching map 2in the reaction equation eccentricity(patom(1)) returns the distance degree of the product 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(All)
electronDensity(2) returns the electron density of atom 2 of the input molecule, NaNfor non-existing valueReaction Context(All)
electronDensity(ratom(1)) returns the electron density of the reactant atom matching map 1in 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(All)
electrophilicity(2) returns the electrophilicity of atom 2 of the input molecule, NaN if atom 2 is non-aromaticReaction Context(All)
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(+) order of atoms

the E(+) 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(All)
electrophilicityOrder(2) returns the E(+) order index of atom 2 of the input molecule, e.g. returns0 if atom 2 is the most electrophilic atom, 1 if atom 2 is the second strongest electrophilic atom, etc.,Reaction Context(All)
electrophilicityOrder(ratom(1)) returns the E(+) order index of the reactant atom matching map 1 in the reaction equation

elemanal

-

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

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

eval

-

exactMass

-

calculates the exact mass of the molecule

the exact mass

-

Molecule Context(All)
exactMass() returns the exact mass of the input moleculeReaction Context(All)
exactMass(product(1)) returns the exact mass of the second product

field
property

-

returns a molecule property (SDF field value)

the molecule property

the property key (SDF field name)

Molecule Context(All)
field('ACTIVITY') returns the value of the ACTIVITY property (SDF field) field('ACTIVITY') > 2returns 1 if the ACTIVITY value is bigger than 2, returns 0 otherwiseReaction Context(All)
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 0otherwise

fieldAsString
propertyAsString

-

returns a molecule property (SDF field value) as string

the molecule property as string

the property key (SDF field name)

Molecule Context(All)
fieldAsString('ID') returns the value of the ID property (SDF field)Reaction Context(All)
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(All)
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 moleculeReaction Context(All)
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)

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 formReaction Context(All)
fix(product(1), "chiralflag..isotope->converttoelementalform") searches for ciral flags and isotopes in second product, and removes them or converts them to elemental form

formalCharge
totalCharge

-

calculates formal charge of molecule

the formal charge value

atom index or MolAtom object (optional)

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

formula

-

returns the formula

the formula

-

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

fragmentCount

Structural Calculations License

returns the number of fragments (disconnected parts)

the fragment count

-

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

fragments

-

converts the molecule to its disconnected fragments

the disconnected fragments of the molecule

-

Molecule Context(All)
fragments() returns the disconnected fragments of the moleculeReaction Context(All)
fragments(reactant(1)) returns the disconnected fragments of the second reactant

fsp3

Structural Calculations License

returns the fsp3 of the molecule

the fsp3 value

-

Molecule Context(All)
fsp3() returns the fsp3 value of the input moleculeReaction Context(All)
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(All)
fusedAliphaticRingCount() returns the number of fused aliphatic rings in the input moleculeReaction Context(All)
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(All)
fusedAliphaticRingCountOfSize(6) returns the number of fused aliphatic rings of size 6 in the input moleculeReaction Context(All)
fusedAliphaticRingCountOfSize(reactant(0), 5) returns the number of fused aliphatic rings of size 5 in the first reactantfusedAliphaticRingCountOfSize(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(All)
fusedAliphaticRings() returns the atom indexes of the fused aliphatic rings in the input moleculeReaction Context(All)
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(All)
fusedAliphaticRings() returns the atom indexes of the fused aliphatic rings in the input molecule having the given sizeReaction Context(All)
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(All)
fusedAromaticRingCount() returns the number of fused aromatic rings in the input moleculeReaction Context(All)
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(All)
fusedAromaticRingCountOfSize(6) returns the number of fused aromatic rings of size 6 in the input moleculeReaction Context(All)
fusedAromaticRingCountOfSize(reactant(0), 5) returns the number of fused aromatic rings of size 5 in the first reactantfusedAromaticRingCountOfSize(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(All)
fusedAromaticRings() returns the atom indexes of the fused aromatic rings in the input moleculeReaction Context(All)
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(All)
fusedAromaticRings() returns the atom indexes of the fused aromatic rings in the input molecule having the given sizeReaction Context(All)
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(All)
fusedRingCount() returns the number of fused rings in the input moleculeReaction Context(All)
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

genericTautomer

Isomers License

constructs the generic tautomer structure

the generic tautomer structure

-

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

hararyIndex

Structural Calculations License

calculates the Harary index

the Harary index

-

Molecule Context(All)
calculates the Harary indexReaction Context(All)
the Harary index

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(All)
hasAromatizationError() returns true if there is an error in the aromatization of the molecule,false otherwiseReaction Context(All)
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(All)
hasIsotope() returns true if any atom in the molecule is a specific isotope of the element, false otherwiseReaction Context(All)
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(All)
hasRadical() returns true if any atom in the molecule has radical, false otherwiseReaction Context(All)
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(All)
hasValenceError() returns true if any atom in the molecule has valence error, false otherwiseReaction Context(All)
hasValenceError(reactant(1)) returns true if any atom in the second reactant has valence error,false otherwise

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

HBDA

Structural Calculations License

hCount

-

returns the hydrogen count of an atom

the hydrogen count

atom index or MolAtom object

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

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(All)
heteroaliphaticRingCount() returns the number of aliphatic heterocyclic rings in the input moleculeReaction Context(All)
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(All)
heteroaliphaticRingCountOfSize(6) returns the number of aliphatic heterocyclic rings of size 6 in the input moleculeReaction Context(All)
heteroaliphaticRingCountOfSize(reactant(0), 5) returns the number of aliphatic heterocyclic rings of size 5 in the first reactantheteroaliphaticRingCountOfSize(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(All)
heteroaliphaticRings() returns the atom indexes of the aliphatic heterocyclic rings in the input moleculeReaction Context(All)
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(All)
heteroaliphaticRings() returns the atom indexes of the aliphatic heterocyclic rings in the input molecule having the given sizeReaction Context(All)
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(All)
heteroaromaticRingCount() returns the number of aromatic heterocyclic rings in the input moleculeReaction Context(All)
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(All)
heteroaromaticRingCountOfSize(6) returns the number of aromatic heterocyclic rings of size 6 in the input moleculeReaction Context(All)
heteroaromaticRingCountOfSize(reactant(0), 5) returns the number of aromatic heterocyclic rings of size 5 in the first reactantheteroaromaticRingCountOfSize(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(All)
heteroaromaticRings() returns the atom indexes of the aromatic heterocyclic rings in the input moleculeReaction Context(All)
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(All)
heteroaromaticRings() returns the atom indexes of the aromatic heterocyclic rings in the input molecule having the given sizeReaction Context(All)
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(All)
heteroRingCount() returns the number of heterocyclic rings in the input moleculeReaction Context(All)
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(All)
heteroRingCountOfSize(6) returns the number of heterocyclic rings of size 6 in the input moleculeReaction Context(All)
heteroRingCountOfSize(reactant(0), 5) returns the number of heterocyclic rings of size 5 in the first reactantheteroRingCountOfSize(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(All)
heteroRings() returns the atom indexes of the heterocyclic rings in the input moleculeReaction Context(All)
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(All)
heteroRings() returns the atom indexes of the heterocyclic rings in the input molecule having the given sizeReaction Context(All)
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

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(All)
hmoChargeDensity(2) returns the charge density of atom 2 of the input molecule, NaNfor non-existing valueReaction Context(All)
hmoChargeDensity(ratom(1)) returns the charge density of the reactant atom matching map 1in 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(All)
hmoElectronDensity(2) returns the electron density of atom 2 of the input molecule, NaNfor non-existing valueReaction Context(All)
hmoElectronDensity(ratom(1)) returns the electron density of the reactant atom matching map 1in the reaction equation

hmoElectrophilicityOrder
hmoOrderE

Structural Calculations License

calculates HMO E(+) order of atoms

the E(+) 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(All)
hmoElectrophilicityOrder(2) returns the E(+) order index of atom 2 of the input molecule, e.g. returns0 if atom 2 is the most electrophilic atom, 1 if atom 2 is the second strongest electrophilic atom, etc.,Reaction Context(All)
hmoElectrophilicityOrder(ratom(1)) returns the E(+) order index of the reactant atom matching map 1 in the reaction equation

hmoElectrophilicLocalizationEnergy

Structural Calculations License

calculates HMO localization energy L(+) of atoms

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

hmoNucleophilicityOrder
hmoOrderNu

Structural Calculations License

calculates HMO Nu(-) order of atoms

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

hmoNucleophilicLocalizationEnergy

Structural Calculations License

calculates HMO localization energy L(-) of atoms

the localization energy L(-) 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(All)
hmoNucleophilicLocalizationEnergy(2) returns the nucleophilic L(-) localization energy of atom 2 of the input molecule, NaN if atom 2 is non-aromaticReaction Context(All)
hmoNucleophilicLocalizationEnergy(ratom(1)) returns the nucleophilic L(-) 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(All)
hmoPiEnergy() returns the pi energy of the input moleculeReaction Context(All)
hmoPiEnergy(product(1)) returns the pi energy of the second product

hyperWienerIndex

Structural Calculations License

calculates the Hyper Wiener index

the Hyper Wiener index

-

Molecule Context(All)
calculates the Hyper Wiener indexReaction Context(All)
the Hyper Wiener index

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(All)
importMol("c1ccccc1") returns benzene moleculeReaction Context(All)
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 falseMolecule Context(All)
in(3, maxatom("charge()", 2)) returns true if the partial charge on atom 3is 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 moleculeReaction Context(All)
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 trueif the polarizability on product atom matching map 1 in the reaction equation is within the first 4smallest 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(All)
isQuery() returns true if the given molecule does not contain any atoms, bonds, or non-empty S-groups, false otherwiseReaction Context(All)
isQuery(reactant(1)) returns true if the second reactant contains any atoms, bonds, or non-empty S-groups,false otherwise

isMarkush

-

decides whether the given molecule contains any Markush features

true if the molecule contains any Markush features, false otherwise

-

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

isoelectricPoint
pI

Protonation License

calculates isoelectric point

the isoelectric point

-

Molecule Context(All)
isoelectricPoint() returns the isoelectric point of the input moleculeReaction Context(All)
isoelectricPoint(reactant(1)) returns the isoelectric point of the second reactant

isotopeComposition

-

returns the isotope composition

the isotope composition

-

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

isotopeFormula

-

returns the isotope formula

the isotope formula

-

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

isQuery

-

decides whether the given molecule contains any query features

true if the molecule contains any query features, false otherwise

-

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

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 validReaction Context(All)
isValid(reactant(0), "aromaticity..valence") checks for aromaticity and valence errors in first reactant, and returns if it is valid

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

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(All)
largestRingSize() returns the atom indexes of the largest ring in the input moleculeReaction Context(All)
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(All)
largestRingSize() returns the size of the largest ring in the input moleculeReaction Context(All)
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(All)
largestRingSize() returns the atom indexes of the largest ring system in the input moleculeReaction Context(All)
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(All)
largestRingSystemSize() returns the size of the largest ring system in the input moleculeReaction Context(All)
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

logD

Partitioning License

calculates logD at specified pH

the logD value

the pH value

Molecule Context(All)
logD('7.4') returns the logD at pH 7.4 of the input moleculeReaction Context(All)
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(All)
logDKLOP('7.4') returns the logD at pH 7.4 of the input moleculeReaction Context(All)
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(All)
logDPHYS('7.4') returns the logD at pH 7.4 of the input moleculeReaction Context(All)
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(All)
logDUser('7.4') returns the logD at pH 7.4 of the input moleculeReaction Context(All)
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(All)
logDVG('7.4') returns the logD at pH 7.4 of the input moleculeReaction Context(All)
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(All)
logDWeighted('7.4') returns the logD at pH 7.4 of the input moleculeReaction Context(All)
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(All)
logP() returns the most typical logP out of the input molecule logP, the logPof the nonionic species and logD at pI logP('logPMicro') returns the logP of the input molecule itselfReaction Context(All)
logP(reactant(1), 'logDpI') returns the logD at pI of the second reactantlogP(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(All)
logPincrement(2) returns the logP increment on atom 2 of the input moleculeReaction Context(All)
logPincrement(ratom(1)) returns the logP increment on the reactant atom matching map 1in 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(All)
logPKLOP() returns the most typical logP out of the input molecule logP, the logPof the nonionic species and logD at pI logPKLOP('logPMicro') returns the logP of the input molecule itselfReaction Context(All)
logPKLOP(reactant(1), 'logDpI') returns the logD at pI of the second reactantlogPKLOP(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(All)
logPPHYS() returns the most typical logP out of the input molecule logP, the logPof the nonionic species and logD at pI logPPHYS('logPMicro') returns the logP of the input molecule itselfReaction Context(All)
logPPHYS(reactant(1), 'logDpI') returns the logD at pI of the second reactantlogPPHYS(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(All)
logPUser() returns the most typical logP out of the input molecule logP, the logPof the nonionic species and logD at pI logPUser('logPMicro') returns the logP of the input molecule itselfReaction Context(All)
logPUser(reactant(1), 'logDpI') returns the logD at pI of the second reactantlogPUser(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(All)
logPVG() returns the most typical logP out of the input molecule logP, the logPof the nonionic species and logD at pI logPVG('logPMicro') returns the logP of the input molecule itselfReaction Context(All)
logPVG(reactant(1), 'logDpI') returns the logD at pI of the second reactantlogPVG(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(All)
logPWeighted() returns the most typical logP out of the input molecule logP, the logPof the nonionic species and logD at pI logPWeighted('logPMicro') returns the logP of the input molecule itselfReaction Context(All)
logPWeighted(reactant(1), 'logDpI') returns the logD at pI of the second reactantlogPWeighted(product(1), 'logPNonionic') returns logP of the nonionic species of the second product

logS

Solubility License

calculates the aqueous solubility (either intrinsic or pH-dependent) of the molecule

solubility value in a given unit or solubility category

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

Molecule Context(All)
logS() returns the intrinsic solubility value of the input molecule in logS unitlogS('7.4', 'mg/ml') returns the solubility at pH 7.4 in mg/ml unitlogS('7.4', 'category') returns the qualitative solubility at pH 7.4

lowestEnergyConformer
leconformer

Structural Calculations License

calculates the lowest energy conformer of the molecule

the lowest energy conformer

-

Molecule Context(All)
lowestEnergyConformer() returns the lowest energy conformer of the input moleculeReaction Context(All)
lowestEnergyConformer(reactant(0)) returns the lowest energy conformer of the first reactantlowestEnergyConformer(product(1)) returns the lowest energy conformer of the second product

majorMicrospecies
majorMs

Protonation License

calculates major microspecies at specified pH

the major microspecies

the pH value as string

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

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(All)
majorTautomer() returns the major tautomer structure of the input moleculeReaction Context(All)
majorTautomer(reactant(0)) returns the major tautomer structure of the first reactant/td>

map

-

returns the atom map number

the atom map number

atom index or MolAtom object

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

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(All)
markushEnumerationCount() returns the number of Markush enumerated structures of the input molecule markushEnumerationCount('4,5')returns the number of Markush enumerated structures of the input molecule, enumerating only atoms 4, 5 (1-based)Reaction Context(All)
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(All)
markushEnumerations() returns all Markush enumerated structures of the input molecule markushEnumerations(1, '2,3')returns one Markush enumerated structure of the input molecule, enumerating atoms 2, 3 (1-based)Reaction Context(All)
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(All)
markushEnumerationsDisplay() returns all Markush enumerated structures of the input molecule, with scaffold alignment and coloring data markushEnumerationsDisplay(1, '2,3')returns one Markush enumerated structure of the input molecule, enumerating atoms 2, 3 (1-based), with scaffold alignment and coloring dataReaction Context(All)
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(All)
markushLibraryMagnitude() returns the Markush library magnitude for the input molecule markushLibraryMagnitude('4,5')returns the Markush library magnitude for the input molecule, presuming only atoms 4, 5 (1-based) are enumeratedReaction Context(All)
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(All)
markushLibrarySize() returns the Markush library size for the input molecule markushLibrarySize('4,5')returns the Markush library size for the input molecule, presuming only atoms 4, 5 (1-based) are enumeratedReaction Context(All)
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(All)
markushLibrarySize() returns the Markush library size as string for the input molecule markushLibrarySize('4,5')returns the Markush library size as string for the input molecule, presuming only atoms 4, 5 (1-based) are enumeratedReaction Context(All)
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)

mass

-

calculates the molecule mass

the mass

-

Molecule Context(All)
mass() returns the mass of the input moleculeReaction Context(All)
mass(reactant(0)) returns the mass of the first reactant

massspectrum

-

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

the mass spectrum as a series of discrete values

-

Molecule Context(All)
massspectrum() returns the mass spectrum of the input moleculeReaction Context(All)
massspectrum(reactant(0)) returns the mass spectrum of the first reactant

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(All)
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 oxygenReaction Context(All)
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

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(All)
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 oxygenReaction Context(All)
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

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(All)
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(All)
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.

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 5.6Molecule Context(All)
min(charge(0), charge(2)) returns the least of the partial charge values on atoms 0and 2 max(charge()) returns the maximal partial charge value on the input moleculeReaction Context(All)
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(All)
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 7.4of the input molecule and returns the corresponding indicesReaction Context(All)
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)

maximalProjectionArea

Structural Calculations License

returns the maximal projection area

the maximal projection area

-

Molecule Context(All)
maximalProjectionArea() returns the maximal projection areaReaction Context(All)
maximalProjectionArea((reactant(0)) returns the maximal projection area of the first reactantmaximalProjectionArea(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(All)
maximalProjectionRadius() returns the maximal projection radiusReaction Context(All)
maximalProjectionRadius((reactant(0)) returns the maximal projection radius of the first reactantmaximalProjectionRadius(product(1)) returns the maximal projection radius of the second product

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(All)
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 moleculeReaction Context(All)
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)

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(All)
microspecies("7.4", 1) returns the microspecies of the input molecule with second largest distribution at pH7.4Reaction Context(All)
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(All)
microspeciesCount() returns the number of microspecies of the input moleculeReaction Context(All)
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(All)
microspeciesDistribution("5.4", 0) returns the largest microspecies distribution of the input molecule at pH 5.4Reaction Context(All)
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

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 5.6Molecule Context(All)
min(charge(0), charge(2)) returns the least of the partial charge values on atoms 0and 2 max(charge()) returns the maximal partial charge value on the input moleculeReaction Context(All)
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(All)
minAtom("charge('7.4')") returns the atom index corresponding to minimum partial charge in the major microspecies at pH 7.4 of the input moleculeReaction Context(All)
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

minimalProjectionArea

Structural Calculations License

returns the minimal projection area

the minimal projection area

-

Molecule Context(All)
minimalProjectionArea() returns the minimal projection areaReaction Context(All)
minimalProjectionArea((reactant(0)) returns the minimal projection area of the first reactantminimalProjectionArea(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(All)
minimalProjectionRadius() returns the minimal projection radiusReaction Context(All)
minimalProjectionRadius((reactant(0)) returns the minimal projection radius of the first reactantminimalProjectionRadius(product(1)) returns the minimal projection radius of the second product

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

mmff94Energy

Structural Calculations License

returns the MMFF94 energy of the input molecule (conformer)

the MMFF94 energy

-

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

mmff94OptimizedStructure

Structural Calculations License

calculates the MMFF94 optimized lowest energy conformer

the MMFF94 optimized lowest energy conformer

-

Molecule Context(All)
mmff94OptimizedStructure() returns the MMFF94 optimized lowest energy conformer of the input moleculeReaction Context(All)
mmff94OptimizedStructure(reactant(0)) returns the MMFF94 optimized lowest energy conformer of the first reactantmmff94OptimizedStructure(product(1)) returns the MMFF94 optimized lowest energy conformer of the second product

molAtom

-

creates a MolAtom

the MolAtom object

atomic number

Molecule Context(All)
molAtom(6) returns a carbon atomReaction Context(All)
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(All)
molImage("jpeg:w100,Q95,#ffff00") returns the 100x100 JPEG image of the input molecule with yellow background, 95% qualityReaction Context(All)
N / A (reaction rules are numerical)

molecularPolarizability
molPol

Structural Calculations License

calculates molecular polarizability

the polarizability value

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

Molecule Context(All)
molecularPolarizability() returns the molecular polarizability of the input molecule molecularPolarizability("7.4")returns the molecular polarizability of the major microspecies taken at pH 7.4Reaction Context(All)
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

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

mostStableTautomer

Isomers License

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

the most stable tautomer structure

-

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

name

Structure To Name License

returns the preferred IUPAC name of the molecule

the preferred IUPAC name of the molecule

-

Molecule Context(All)
name() returns the preferred IUPAC name of the input moleculeReaction Context(All)
N / A (reaction rules are numerical)

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(All)
nucleophilicity(2) returns the nucleophilicity of atom 2 of the input molecule, NaN if atom 2 is non-aromaticReaction Context(All)
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(-) order of atoms

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

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(All)
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 2and 5 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(All)
piEnergy() returns the pi energy of the input moleculeReaction Context(All)
piEnergy(product(1)) returns the pi energy of the second product

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(All)
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 2of the major microspecies taken at pH 7.4Reaction Context(All)
pOEN(ratom(1)) returns the pi orbital electronegativity of reactant atom matching map 1in 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

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_ais 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(All)
pKa(0) returns the pK_a of atom 0 of the input molecule pKa("acidic", "2")returns the second strongest acidic pK_a valueReaction Context(All)
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_ais 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(All)
pKaUseCorrection(0) returns the pK_a of atom 0 of the input moleculepKaUseCorrection("acidic", "2") returns the second strongest acidic pK_a valueReaction Context(All)
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

plattIndex

Structural Calculations License

calculates the Platt index

the Platt index

-

Molecule Context(All)
calculates the Platt indexReaction Context(All)
the Platt index

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

randicIndex

Structural Calculations License

calculates the Randic index

the Randic index

-

Molecule Context(All)
calculates the Randic indexReaction Context(All)
the Randic index

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(All)
randomMarkushEnumerations()returns a randomly constructed enumerated structure of the input molecule randomMarkushEnumerations(4, '2,3') returns 4 randomly constructed enumerated structures of the input molecule, enumerating only atoms 2, 3 (1-based)Reaction Context(All)
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(All)
randomMarkushEnumerationsDisplay()returns a randomly constructed enumerated structure of the input molecule, with scaffold alignment and scaffold/R-group coloring datarandomMarkushEnumerationsDisplay(4, '2,3') returns 4 randomly constructed enumerated structures of the input molecule, enumerating only atoms 2, 3 (1-based), with scaffold alignment and coloring dataReaction Context(All)
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

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(All)
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(All)
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.

refractivity
refrac

Structural Calculations License

calculates molar refractivity

the refractivity value

-

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

resonant

-

constructs a resonant structure

the resonant structure

-

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

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(All)
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 effectReaction Context(All)
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 2in the major microspecies taken at pH 7.4 considering resonance effect

resonantCount

-

calculates the number of resonant structures

the number of resonant structures

-

Molecule Context(All)
resonantCount() returns the number of resonant structures of the input moleculeReaction Context(All)
resonantCount(reactant(0)) returns the number of resonant structures of the first reactant

resonants

-

constructs all resonant structures

the resonant structure array

-

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

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(All)
ringAtom(2) returns true if atom 2 of the input molecule is a ring atom,false otherwiseReaction Context(All)
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 trueif 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(All)
ringAtomCount() returns the number of ring atoms in the input moleculeReaction Context(All)
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(All)
ringBond('2-3') and ringBond(bond(1, 2)) both return true if atoms 1and 2 are connected by a ring bond the input moleculeReaction Context(All)
ringBond(reactant(0), bond(ratom(1), ratom(2))) returns true if reactant atoms matching maps 1and 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 3in 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(All)
ringBondCount() returns the number of ring bonds in the input moleculeReaction Context(All)
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(All)
ringCount() returns the number of rings in the input moleculeReaction Context(All)
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(All)
ringCountOfAtom(2) returns the number of rings passsing through atom 2 of the input moleculeReaction Context(All)
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(All)
ringCountOfSize(6) returns the number of rings of size 6 in the input moleculeReaction Context(All)
ringCountOfSize(reactant(0), 5) returns the number of rings of size 5 in the first reactantringCountOfSize(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(All)
rings() returns the atom indexes of the rings in the input moleculeReaction Context(All)
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(All)
rings() returns the atom indexes of the rings in the input molecule having the given sizeReaction Context(All)
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(All)
ringSystemCount() returns the number of ring systems in the input moleculeReaction Context(All)
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(All)
ringSystemCountOfSize(4) returns the number of four-membered ring systems in the input moleculeReaction Context(All)
ringSystemCountOfSize(reactant(0),3) returns the number of three-membered ring systems in the first reactantringsystemCountOfSize(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(All)
ringSystems() returns the atom indexes of the ring systems in the input moleculeReaction Context(All)
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(All)
ringSystems() returns the atom indexes of the ring systems in the input molecule having the given sizeReaction Context(All)
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(All)
rotatableBond('2-3') and rotatableBond(bond(1, 2)) both return true if atoms 1 and 2 are connected by a rotatable bond the input moleculeReaction Context(All)
rotatableBond(reactant(0), bond(ratom(1), ratom(2))) returns true if reactant atoms matching maps1 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(All)
rotatableBondCount() returns the number of rotatable bonds in the input moleculeReaction Context(All)
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(All)
shortestPath('2-3') and shortestPath(pair(1, 2)) both return the shortest path length between atoms 1 and 2 in the input moleculeReaction Context(All)
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)

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(All)
sigmaOrbitalElectronegativity(0) returns the sigma orbital electronegativity of atom 0of the input molecule sigmaOrbitalElectronegativity(2, "7.4") returns the sigma orbital electronegativity of atom 2 of the major microspecies taken at pH 7.4Reaction Context(All)
sOEN(ratom(1)) returns the sigma orbital electronegativity of reactant atom matching map 1in 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

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(All)
smallestAtomRingSize(0) returns the size of the smallest ring containing atom 0 in the input moleculeReaction Context(All)
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(All)
smallestRingSize() returns the atom indexes of the smallest ring in the input moleculeReaction Context(All)
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(All)
smallestRingSize() returns the size of the smallest ring in the input moleculeReaction Context(All)
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(All)
smallestRingSize() returns the atom indexes of the smallest ring system in the input moleculeReaction Context(All)
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(All)
smallestRingSystemSize() returns the size of the smallest ring system in the input moleculeReaction Context(All)
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

sortableFormula

-

returns the fixed digit sortable formula

fixed digit sortable molecular formula

-

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

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(All)
sortAsc(charge()) returns the partial charge values in ascending orderReaction Context(All)
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(All)
sortDesc(pka("basic")) returns the basic pK_a values in descending orderReaction Context(All)
sortDesc(pka(product(0), "basic")) returns the basic pK_a values of the first product in descending order

stereoAnalysis

-

calculates stereo descriptors of molecule

a list of stereo descriptors

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

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

stereoDoubleBondCount

Structural Calculations License

calculates the number of stereo double bonds

the stereo double bond count

-

Molecule Context(All)
stereoDoubleBondCount() returns the number of stereo double bonds in the input moleculeReaction Context(All)
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

stereoisomer

Isomers License

generates a stereoisomer of the molecule

the stereoisomer

the stereoisomer index (0-based)

Molecule Context(All)
stereoisomer(0) returns the first stereoisomer of the input moleculeReaction Context(All)
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(All)
stereoisomerCount() returns the number of generated stereoisomers of the input moleculeReaction Context(All)
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(All)
stereoisomers() returns stereoisomers of the input molecule in an arrayReaction Context(All)
stereoisomers(reactant(0)) returns stereoisomers of the first reactant in an array

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(All)
calculates the steric effect index of an atomReaction Context(All)
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(All)
stericHindrance(2) returns the steric hindrance of atom 2 of the input moleculeReaction Context(All)
stericHindrance(ratom(2)) returns the steric hindrance of the reactant atom matching map 2in the reaction equation stericHindrance(patom(1)) returns the steric hindrance of the product atom matching map 1 in the reaction equation

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 10.2Molecule Context(All)
sum(charge()) returns the sum of charge values sum(pol()) returns the sum of atom polarizability valuesReaction Context(All)
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

szegedIndex

Structural Calculations License

calculates the Szeged index

the Szeged index

-

Molecule Context(All)
calculates the Szeged indexReaction Context(All)
the Szeged index

tautomerCount

Isomers License

calculates the number of tautomers

the number of tautomers

-

Molecule Context(All)
tautomerCount() returns the number of tautomers of the input moleculeReaction Context(All)
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(All)
tetrahedralStereoisomer(0) returns the first tetrahedral stereoisomer of the input moleculeReaction Context(All)
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(All)
tetrahedralStereoisomerCount() returns the number of generated tetrahedral stereoisomers of the input moleculeReaction Context(All)
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(All)
tetrahedralStereoisomers() returns tetrahedral stereoisomers of the input molecule in an arrayReaction Context(All)
tetrahedralStereoisomers(reactant(0)) returns tetrahedral stereoisomers of the first reactant in an array

topanal

Structural Calculations License

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

traditionalName

Structure To Name License

returns the traditional name of the molecule

the traditional name of the molecule

-

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

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

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(All)
vanDerWaalsSurfaceArea() returns the van der Waals surface area of the input moleculevanDerWaalsSurfaceArea('7.4') returns the van der Waals accessible surface area of the major microspecies taken at pH 7.4Reaction Context(All)
vanDerWaalsSurfaceArea(reactant(0)) returns the van der Waals surface area of the first reactantvanDerWaalsSurfaceArea(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(All)
waterAccessibleSurfaceArea() returns the solvent accessible / water accessible surface area of the input moleculesolventAccessibleSurfaceArea('7.4')returns the solvent accessible / water accessible surface area of the major microspecies taken at pH 7.4Reaction Context(All)
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

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(All)
whereIsValenceError() returns the index of the first atom with valence error, or -1if there is no valence error in the moleculeReaction Context(All)
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

wienerIndex

Structural Calculations License

calculates the Wiener index

the Wiener index

-

Molecule Context(All)
wienerIndex() returns the Wiener index of the input moleculeReaction Context(All)
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(All)
wienerPolarity() returns the Wiener polarity of the input moleculeReaction Context(All)
wienerPolarity(reactant(0)) returns the Wiener polarity of the first reactant wienerPolarity(product(1))returns the Wiener polarity of the second product

Back to Contents

Appendix

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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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.

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Notes

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

Functions in Alphabetic Order

Contents

Function list

Appendix

Dissimilarity descriptors and metrics

Predefined Molecules and Molecule Sets

Notes

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