Chemical Terms Reference Tables

Contents

Function list

Name	License	Description	Return value	Parameters	Examples
abs	-	returns the absolute value of a number	the absolute value	integer or real number	General (All) `abs(7)`returns `7` `abs(-4.9)`returns `4.9` Molecule Context (All) `abs(7)`returns `7` `abs(-4.9)`returns `4.9` Reaction Context (All) `abs(7)`returns `7` `abs(-4.9)`returns `4.9`
acceptor acc	HBDA Plugin	calculates atomic hydrogen bond acceptor multiplicity	the atomic hydrogen bond acceptor multiplicity	the atom index / MolAtom object the major microspecies pH (takes the input molecule itself if omitted)	Molecule Context (All) `acceptor(2)` returns the hydrogen bond acceptor multiplicity on atom `2` of the input molecule Reaction Context (All) `acceptor(ratom(2))` returns the hydrogen bond acceptor multiplicity on the reactant atom matching map `2` in the reaction equation
acceptorCount	HBDA Plugin	calculates molecular hydrogen bond acceptor count (the number of acceptor atoms)	the molecular hydrogen bond acceptor count	the major microspecies pH (takes the input molecule itself if omitted)	Molecule Context (All) `acceptorCount()` returns the number of hydrogen bond acceptor atoms in the input molecule Reaction Context (All) `acceptorCount(reactant(0))` returns the number of hydrogen bond acceptor atoms in the first reactant
acceptorSiteCount accSiteCount	HBDA Plugin	calculates molecular hydrogen bond acceptor multiplicity (the sum of atomic multiplicities)	the molecular hydrogen bond acceptor multiplicity	the major microspecies pH (takes the input molecule itself if omitted)	Molecule Context (All) `acceptorSiteCount()` returns the hydrogen bond acceptor multiplicity of the input molecule Reaction Context (All) `acceptorSiteCount(reactant(0))` returns the hydrogen bond acceptor multiplicity of the first reactant
acidicpKa apKa	Protonation Plugin Group	calculates acidic pK_a values	the acidic pK_a values	the atom index / MolAtom object, the strength index as string (e.g. '1' for the strongest, '2' for the second strongest pK_a), Note, that the strength index is specified between quotation marks.	Molecule Context (All) `acidicpKa(0)` returns the acidic pK_a of atom `0` of the input molecule `acidicpKa("2")` returns the second strongest acidic pK_a value Reaction Context (All) `acidicpKa(ratom(1))` returns the acidic pK_a of reactant atom matching map `1` in the reaction equation `acidicpKa(product(0), "1")` returns the strongest basic pK_a value in the first product
acidicpKaLargeModel	Protonation Plugin Group	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 molecule `acidicpKaLargeModel("2")` returns the second strongest acidic pK_a value Reaction Context (All) `acidicpKaLargeModel(ratom(1))` returns the acidic pK_a of reactant atom matching map `1` in the reaction equation `acidicpKaLargeModel(product(0), "1")` returns the strongest basic pK_a value in the first product
acidicpKaUseCorrection	Protonation Plugin Group	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 value Reaction Context (All) `"acidicpKaUseCorrection"(ratom(1))` returns the acidic pK_a of reactant atom matching map `1` in the reaction equation `"acidicpKaUseCorrection"(product(0), "1")` returns the strongest basic pK_a value in the first product
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	Geometry Plugin Group	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` otherwise Reaction Context (All) `aliphaticAtom(ratom(2))` returns `true` if the reactant atom matching map `2` in the reaction equation is aliphatic, `false` otherwise `aliphaticAtom(patom(1))` returns `true` if the product atom matching map `1` in the reaction equation is aliphatic, `false` otherwise
aliphaticAtomCount	Geometry Plugin Group	calculates the aliphatic atom count	the aliphatic atom count	-	Molecule Context (All) `aliphaticAtomCount()` returns the number of aliphatic atoms in the input molecule Reaction 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	Geometry Plugin Group	calculates the aliphatic bond count	the aliphatic bond count	-	Molecule Context (All) `aliphaticBondCount()` returns the number of bonds in the input molecule Reaction 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	Geometry Plugin Group	calculates the aliphatic ring count	the aliphatic ring count	-	Molecule Context (All) `aliphaticRingCount()` returns the number of aliphatic rings in the input molecule Reaction 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	Geometry Plugin Group	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 molecule Reaction Context (All) `aliphaticRingCountOfSize(reactant(0), 5)` returns the number of aliphatic rings of size 5 in the first reactant `aliphaticRingCountOfSize(product(1), 5)` returns the number of aliphatic rings of size 5 in the second product
aliphaticRings	Geometry Plugin Group	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 molecule Reaction 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	Geometry Plugin Group	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 size Reaction 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 Plugin Group	constructs a tautomeric form	the tautomer	the tautomer index (0-based)	Molecule Context (All) `tautomer(0)` returns the first tautomer of the input molecule Reaction Context (All) `tautomer(reactant(0), 1)` returns the second tautomer of the first reactant
allTautomers	Isomers Plugin Group	constructs all tautomeric forms	the tautomer array	-	Molecule Context (All) `tautomers()` returns all tautomers of the input molecule in an array Reaction Context (All) `tautomers(reactant(0))` returns all tautomers of the first reactant in an array
angle	Geometry Plugin Group	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 molecule Reaction Context (All) `angle(reactant(0), atoms(ratom(1), ratom(2), ratom(3)))` returns the angle between reactant atoms matching maps `1`, `2` and `3` in the reaction equation (see note 1) `angle(product(1), atoms(patom(2), patom(3), patom(4)))` returns the angle between product atoms matching maps `2`, `3` and `4` in the reaction equation (see note 1)
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 bond Reaction Context (All) `arom(patom(2))` returns `true` if the product atom matching map `2` in the reaction equation has an aromatic bond
aromaticAtom	Geometry Plugin Group	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` otherwise Reaction Context (All) `aromaticAtom(ratom(2))` returns `true` if the reactant atom matching map `2` in the reaction equation is aromatic, `false` otherwise `aromaticAtom(patom(1))` returns `true` if the product atom matching map `1` in the reaction equation is aromatic, `false` otherwise
aromaticAtomCount	Geometry Plugin Group	calculates the aromatic atom count	the aromatic atom count	-	Molecule Context (All) `aromaticAtomCount()` returns the number of aromatic atoms in the input molecule Reaction 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	Geometry Plugin Group	calculates the aromatic bond count	the aromatic bond count	-	Molecule Context (All) `aromaticBondCount()` returns the number of aromatic bonds in the input molecule Reaction 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	Geometry Plugin Group	calculates the aromatic ring count	the aromatic ring count	-	Molecule Context (All) `aromaticRingCount()` returns the number of aromatic rings in the input molecule Reaction 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	Geometry Plugin Group	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 molecule Reaction Context (All) `aromaticRingCountOfSize(reactant(0), 5)` returns the number of aromatic rings of size 5 in the first reactant `aromaticRingCountOfSize(product(1), 5)` returns the number of aromatic rings of size 5 in the second product
aromaticRings	Geometry Plugin Group	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 molecule Reaction 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	Geometry Plugin Group	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 size Reaction 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	Geometry Plugin Group	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 charge `ASAHydrophobic('7.4')`returns the water accessible surface area of all atoms with hydrophobic partial charge of the major microspecies taken at pH `7.4` Reaction Context (All) `ASAHydrophobic(reactant(0))` returns the water accessible surface area of all atoms of the first reactant with hydrophobic partial charge `ASAHydrophobic(product(0), '7.4')` returns the water accessible surface area of all atoms with hydrophobic partial charge of the major microspecies of the first product taken at pH `7.4`
ASANegative	Geometry Plugin Group	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 charge `ASANegative('7.4')`returns the water accessible surface area of all atoms with negative partial charge of the major microspecies taken at pH `7.4` Reaction Context (All) `ASANegative(reactant(0))` returns the water accessible surface area of all atoms of the first reactant with negative partial charge `ASANegative(product(0), '7.4')` returns the water accessible surface area of all atoms with negative partial charge of the major microspecies of the first product taken at pH `7.4`
ASAPlus	Geometry Plugin Group	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 charge `ASAPlus('7.4')`returns the water accessible surface area of all atoms with positive partial charge of the major microspecies taken at pH `7.4` Reaction Context (All) `ASAPlus(reactant(0))` returns the water accessible surface area of all atoms of the first reactant with positive partial charge `ASAPlus(product(0), '7.4')` returns the water accessible surface area of all atoms with positive partial charge of the major microspecies of the first product taken at pH `7.4`
ASAPolar	Geometry Plugin Group	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 charge `ASAPolar('7.4')`returns the water accessible surface area of all atoms with polar partial charge of the major microspecies taken at pH `7.4` Reaction Context (All) `ASAPolar(reactant(0))` returns the water accessible surface area of all atoms of the first reactant with polar partial charge `ASAPolar(product(0), '7.4')` returns the water accessible surface area of all atoms with polar partial charge of the major microspecies of the first product taken at pH `7.4`
asymmetricAtom	Geometry Plugin Group	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` otherwise Reaction Context (All) `asymmetricAtom(ratom(2))` returns `true` if the reactant atom matching map `2` in the reaction equation is an asymmetric atom, `false` otherwise `asymmetricAtom(patom(1))` returns `true` if the product atom matching map `1` in the reaction equation is an asymmetric atom, `false` otherwise
asymmetricAtomCount	Geometry Plugin Group	calculates the number of asymmetric atoms	the asymmetric atom count	-	Molecule Context (All) `asymmetricAtomCount()` returns the number of asymmetric atoms in the input molecule Reaction 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	Geometry Plugin Group	determines the asymmetric atoms	indexes of asymmetric atoms	-	Molecule Context (All) `asymmetricAtoms()` returns the indexes of asymmetric atoms in the input molecule Reaction 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 `0` Reaction 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 molecule Reaction 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	Charge Plugin Group	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 `7.4` Reaction 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 `2` of the major microspecies taken at pH `7.4`
atomProp	-
atoms	-
averageMicrospeciesCharge	Protonation Plugin Group	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 molecule Reaction Context (All) `averageMicrospeciesCharge(reactant(1))` returns the average charge of the microspecies of the second reactant
averagePolarizability averagePol avgPol	Charge Plugin Group	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 `7.4` Reaction 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	Charge Plugin Group	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 molecule `axxPol("7.4")` returns the principal component `a(xx)` of polarizability tensor of the major microspecies taken at pH `7.4` Reaction 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	Charge Plugin Group	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 molecule `ayyPol("7.4")` returns the principal component `a(yy)` of polarizability tensor of the major microspecies taken at pH `7.4` Reaction 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	Charge Plugin Group	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 molecule `azzPol("7.4")` returns the principal component `a(zz)` of polarizability tensor of the major microspecies taken at pH `7.4` Reaction 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	Geometry Plugin Group	calculates the Balaban index	the Balaban index	-	Molecule Context (All) calculates the Balaban index Reaction Context (All) the Balaban index
basicpKa bpKa	Protonation Plugin Group	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 molecule `basicpKa("2")` returns the second strongest basic pK_a value Reaction Context (All) `basicpKa(ratom(1))` returns the basic pK_a of reactant atom matching map `1` in the reaction equation `basicpKa(product(0), "1")` returns the strongest basic pK_a value in the first product
basicpKaLargeModel	Protonation Plugin Group	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 molecule `basicpKaLargeModel("2")` returns the second strongest basic pK_a value Reaction Context (All) `basicpKaLargeModel(ratom(1))` returns the basic pK_a of reactant atom matching map `1` in the reaction equation `basicpKaLargeModel(product(0), "1")` returns the strongest basic pK_a value in the first product
basicpKaUseCorrection	Protonation Plugin Group	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 molecule `basicpKaUseCorrection("2")` returns the second strongest basic pK_a value Reaction Context (All) `basicpKaUseCorrection(ratom(1))` returns the basic pK_a of reactant atom matching map `1` in the reaction equation `basicpKaUseCorrection(product(0), "1")` returns the strongest basic pK_a value in the first product
bmf	Structural Frameworks Plugin	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 molecule Reaction Context (All) `bmf(reactant(0))` returns the Bemis-Murcko framework of the first reactant
bmfl bemisMurckoFrameworkLoose	Structural Frameworks Plugin	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 molecule Reaction Context (All) `bmfl(reactant(0))` returns the loose Bemis-Murcko framework of the first reactant
bmflp bemisMurckoFrameworkLoosePruned	Structural Frameworks Plugin	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 molecule Reaction 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 molecule Reaction 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	Geometry Plugin Group	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 `1` and `2` in the input molecule Reaction Context (All) `bondType(reactant(0), bond(ratom(1), ratom(2)))` returns the bond type between reactant atoms matching maps `1` and `2` in the reaction equation (see note 1)`bondType(product(1), bond(patom(2), patom(3)))` returns the bond type between product atoms matching maps `2` and `3` in the reaction equation (see note 1)
booleanToNumber	-	returns the number representation of a boolean value (`true` = `1`, `false` = `0`), or the number itself, if the input is a number	the number representation of a boolean value	boolean or number	General (All) `booleanToNumber(1<2)`returns `1` `booleanToNumber(2+2==5)`returns `0` `booleanToNumber(5*5)`returns `25` Molecule Context (All) `booleanToNumber(hasValenceError())`returns `0` for molecules having no valence error Reaction 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 molecule Reaction Context (All) `canonicalResonant(reactant(0))` returns the canonical resonant structure of the first reactant
canonicalTautomer	Isomers Plugin Group	constructs the canonical tautomer structure	the canonical tautomer structure	-	Molecule Context (All) `canonicalTautomer()` returns the canonical tautomer structure of the input molecule Reaction Context (All) `canonicalTautomer(reactant(0))` returns the canonical tautomer structure of the first reactant/td>
carboaliphaticRingCount	Geometry Plugin Group	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 molecule Reaction 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	Geometry Plugin Group	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 molecule Reaction 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	Geometry Plugin Group	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 molecule Reaction 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	Geometry Plugin Group	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 molecule Reaction Context (All) `carboRingCountOfSize(reactant(0), 5)` returns the number of carbocyclic rings of size 5 in the first reactant `carboRingCountOfSize(product(1), 5)` returns the number of carbocyclic rings of size 5 in the second product
carboRings	Geometry Plugin Group	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 molecule Reaction 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	Geometry Plugin Group	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 size Reaction 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	Geometry Plugin Group	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` otherwise Reaction 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 `true` if the product atom matching map `1` in the reaction equation is a chain atom, `false` otherwise
chainAtomCount	Geometry Plugin Group	calculates the chain atom count	the chain atom count	-	Molecule Context (All) `chainAtomCount()` returns the number of chain atoms in the input molecule Reaction 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	Geometry Plugin Group	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 `1` and `2` are connected by a chain bond the input molecule Reaction Context (All) `chainBond(reactant(0), bond(ratom(1), ratom(2)))` returns `true` if reactant atoms matching maps `1` and `2` in the reaction equation are connected by a chain bond in the corresponding reactant molecule (see note 1) `chainBond(product(1), bond(patom(2), patom(3)))` returns `true` if product atoms matching maps `2` and `3` in the reaction equation are connected by a chain bond in the corresponding product molecule (see note 1)
chainBondCount	Geometry Plugin Group	calculates the chain bond count	the chain bond count	-	Molecule Context (All) `chainBondCount()` returns the number of chain bonds in the input molecule Reaction 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	Charge Plugin Group	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 `7.4` Reaction 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 `2` in the major microspecies taken at pH `7.4`
chargeDensity totalChargeDensity	Huckel Analysis Plugin	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, `NaN` for non-existing value Reaction Context (All) `chargeDensity(ratom(1))` returns the charge density of the reactant atom matching map `1` in 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 report Reaction 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 count Reaction Context (All) `check(reactant(0), "aromaticity..valence")` checks for aromaticity and valence errors in first reactant, and returns the error report
chiralCenter	Geometry Plugin Group	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` otherwise Reaction Context (All) `chiralCenter(ratom(2))` returns `true` if the reactant atom matching map `2` in the reaction equation is a tetrahedral stereogenic center, `false` otherwise `chiralCenter(patom(1))` returns `true` if the product atom matching map `1` in the reaction equation is a tetrahedral stereogenic center, `false` otherwise
chiralCenterCount	Geometry Plugin Group	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 molecule Reaction 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	Geometry Plugin Group	determines the chiral center atoms	indexes of chiral center atoms	-	Molecule Context (All) `chiralCenters()` returns the indexes of chiral center atoms in the input molecule Reaction 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 molecule Reaction Context (All) N / A (reaction rules are numerical)
conformer	Conformation Plugin Group	calculates a conformer of the molecule	the conformer	the conformer index (0-based)	Molecule Context (All) `conformer(0)` returns the first conformer of the input molecule Reaction Context (All) `conformer(reactant(0), 1)` returns the second conformer of the first reactant
conformerCount	Conformation Plugin Group	returns the number of calculated conformers	the number of calculated conformers	-	Molecule Context (All) `conformerCount()` returns the number of calculated conformers of the input molecule Reaction Context (All) `conformerCount(reactant(0))` returns the number of calculated conformers of the first reactant
conformers	Conformation Plugin Group	calculates conformers of the molecule (maximum number of conformers to be calculated can be set, default: 100)	the conformer array	-	Molecule Context (All) `conformers()` returns conformers of the input molecule in an array Reaction Context (All) `conformers(reactant(0))` returns conformers of the first reactant in an array
connected	Geometry Plugin Group	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 `1` and `2` are in the same connected component of the input molecule Reaction Context (All) `connected(reactant(0), pair(ratom(1), ratom(2)))` returns `true` if reactant atoms matching maps `1` and `2` in the reaction equation are connected in the corresponding reactant molecule (see note 1) `connected(product(1), pair(patom(2), patom(3)))` returns `true` if product atoms matching maps `2` and `3` in the reaction equation are connected in the corresponding product molecule (see note 1)
connectedGraph	Geometry Plugin Group	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 connected Reaction 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 `2` Reaction 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 `3` Molecule 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 carbons Reaction 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	Geometry Plugin Group	calculates the cyclomatic number	the cyclomatic number	-	Molecule Context (All) `cyclomaticNumber()` returns the cyclomatic number of the input molecule Reaction 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	Geometry Plugin Group	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 molecule Reaction 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 the match function.	Molecule Context (All) `disjointMatchCount("[#8]C=O")` counts the maximal number of pairwise disjoint carboxylic groups in the input molecule Reaction 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` metric Reaction 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	Geometry Plugin Group	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 `1` and `2` in the input molecule Reaction Context (All) `distance(reactant(0), pair(ratom(1), ratom(2)))` returns the distance between reactant atoms matching maps `1` and `2` in the reaction equation (see note 1) `distance(product(1), pair(patom(2), patom(3)))` returns the distance between product atoms matching maps `2` and `3` in the reaction equation (see note 1)
distanceDegree	Geometry Plugin Group	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 molecule Reaction Context (All) `distanceDegree(ratom(2))` returns the distance degree of the reactant atom matching map `2` in the reaction equation `distanceDegree(patom(1))` returns the distance degree of the product atom matching map `1` in the reaction equation
dominantTautomer tautomer	Isomers Plugin Group	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 Plugin Group	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 `7.4` Reaction 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 Plugin Group	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	HBDA Plugin	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 `7.4` Reaction 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	HBDA Plugin	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 `7.4` Reaction 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	HBDA Plugin	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 `7.4` Reaction 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 molecule Reaction 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 molecule Reaction Context (All) N / A (reaction rules are numerical)
doubleBondStereoisomer	Isomers Plugin Group	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 molecule Reaction Context (All) `doubleBondStereoisomer(reactant(0), 1)` returns the second double bond stereoisomer of the first reactant
doubleBondStereoisomerCount	Isomers Plugin Group	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 molecule Reaction Context (All) `doubleBondStereoisomerCount(reactant(0))` returns the number of calculated double bond stereoisomers of the first reactant
doubleBondStereoisomers	Isomers Plugin Group	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 array Reaction Context (All) `doubleBondStereoisomers(reactant(0))` returns double bond stereoisomers of the first reactant in an array
dreidingEnergy	Geometry Plugin Group	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	Geometry Plugin Group	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 molecule Reaction Context (All) `eccentricity(ratom(2))` returns the eccentricity of the reactant atom matching map `2` in the reaction equation `eccentricity(patom(1))` returns the distance degree of the product atom matching map `1` in the reaction equation
electronDensity piChargeDensity	Huckel Analysis Plugin	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, `NaN` for non-existing value Reaction Context (All) `electronDensity(ratom(1))` returns the electron density of the reactant atom matching map `1` in the reaction equation
electrophilicity energyNu nucleophilicLocalizationEnergy	Huckel Analysis Plugin	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-aromatic Reaction Context (All) `electrophilicity(ratom(1))` returns the electrophilicity of the reactant atom matching map `1` in the reaction equation
electrophilicityOrder aromaticElectrophilicityOrder orderE	Huckel Analysis Plugin	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. returns `0` 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 formula Reaction 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 molecule Reaction 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') > 2` returns `1` if the ACTIVITY value is bigger than `2`, returns `0` otherwise Reaction 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 `0` otherwise
fieldAsString propertyAsString	-	returns a molecule property (SDF field value) as string	the molecule property as string	the property key (SDF field name)	Molecule Context (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 molecule Reaction 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 form Reaction 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 molecule `formalCharge(0)` returns the formal charge of atom `0` Reaction Context (All) formalCharge(reactant(0)) returns the formal charge of the first reactant `formalCharge(ratom(1))` returns the formal charge of the reactant atom matching map `1`
formula	-	returns the formula	the formula	-	Molecule Context (All) `formula()` returns the formula of the input molecule Reaction Context (All) N / A (reaction rules are numerical)
fragmentCount	Geometry Plugin Group	returns the number of fragments (disconnected parts)	the fragment count	-	Molecule Context (All) `fragmentCount()` returns the number of fragments in the input molecule Reaction 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 molecule Reaction Context (All) `fragments(reactant(1))` returns the disconnected fragments of the second reactant
fsp3	Geometry Plugin Group	returns the fsp3 of the molecule	the fsp3 value	-	Molecule Context (All) `fsp3()` returns the fsp3 value of the input molecule Reaction 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	Geometry Plugin Group	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 molecule Reaction 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	Geometry Plugin Group	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 molecule Reaction Context (All) `fusedAliphaticRingCountOfSize(reactant(0), 5)` returns the number of fused aliphatic rings of size 5 in the first reactant `fusedAliphaticRingCountOfSize(product(1), 5)` returns the number of fused aliphatic rings of size 5 in the second product
fusedAliphaticRings	Geometry Plugin Group	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 molecule Reaction 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	Geometry Plugin Group	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 size Reaction 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	Geometry Plugin Group	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 molecule Reaction 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	Geometry Plugin Group	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 molecule Reaction Context (All) `fusedAromaticRingCountOfSize(reactant(0), 5)` returns the number of fused aromatic rings of size 5 in the first reactant `fusedAromaticRingCountOfSize(product(1), 5)` returns the number of fused aromatic rings of size 5 in the second product
fusedAromaticRings	Geometry Plugin Group	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 molecule Reaction 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	Geometry Plugin Group	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 size Reaction 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	Geometry Plugin Group	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 molecule Reaction 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 Plugin Group	constructs the generic tautomer structure	the generic tautomer structure	-	Molecule Context (All) `genericTautomer()` returns the generic tautomer structure of the input molecule Reaction Context (All) `genericTautomer(reactant(0))` returns the generic tautomer structure of the first reactant/td>
groupedDotDisconnectedFormula	-	returns the grouped dot-disconnected formula	the grouped dot-disconnected formula	-	Molecule Context (All) `groupedDotDisconnectedFormula()` returns the grouped dot-disconnected formula of the input molecule Reaction Context (All) N / A (reaction rules are numerical)
hararyIndex	Geometry Plugin Group	calculates the Harary index	the Harary index	-	Molecule Context (All) calculates the Harary index Reaction 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` otherwise Reaction 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` otherwise Reaction 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` otherwise Reaction 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` otherwise Reaction Context (All) `hasValenceError(reactant(1))` returns `true` if any atom in the second reactant has valence error, `false` otherwise
hasValidConformer	Conformation Plugin Group	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	HBDA Plugin
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 `0` Reaction Context (All) `hCount(patom(3))` returns the hydrogen count on the product atom matching map `3` in the reaction equation
heteroaliphaticRingCount	Geometry Plugin Group	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 molecule Reaction 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	Geometry Plugin Group	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 molecule Reaction Context (All) `heteroaliphaticRingCountOfSize(reactant(0), 5)` returns the number of aliphatic heterocyclic rings of size 5 in the first reactant `heteroaliphaticRingCountOfSize(product(1), 5)` returns the number of aliphatic heterocyclic rings of size 5 in the second product
heteroaliphaticRings	Geometry Plugin Group	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 molecule Reaction 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	Geometry Plugin Group	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 size Reaction 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	Geometry Plugin Group	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 molecule Reaction 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	Geometry Plugin Group	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 molecule Reaction Context (All) `heteroaromaticRingCountOfSize(reactant(0), 5)` returns the number of aromatic heterocyclic rings of size 5 in the first reactant `heteroaromaticRingCountOfSize(product(1), 5)` returns the number of aromatic heterocyclic rings of size 5 in the second product
heteroaromaticRings	Geometry Plugin Group	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 molecule Reaction 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	Geometry Plugin Group	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 size Reaction 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	Geometry Plugin Group	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 molecule Reaction 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	Geometry Plugin Group	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 molecule Reaction Context (All) `heteroRingCountOfSize(reactant(0), 5)` returns the number of heterocyclic rings of size 5 in the first reactant `heteroRingCountOfSize(product(1), 5)` returns the number of heterocyclic rings of size 5 in the second product
heteroRings	Geometry Plugin Group	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 molecule Reaction 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	Geometry Plugin Group	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 size Reaction 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	Huckel Analysis Plugin	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, `NaN` for non-existing value Reaction Context (All) `hmoChargeDensity(ratom(1))` returns the charge density of the reactant atom matching map `1` in the reaction equation
hmoElectronDensity	Huckel Analysis Plugin	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, `NaN` for non-existing value Reaction Context (All) `hmoElectronDensity(ratom(1))` returns the electron density of the reactant atom matching map `1` in the reaction equation
hmoElectrophilicityOrder hmoOrderE	Huckel Analysis Plugin	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. returns `0` 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	Huckel Analysis Plugin	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-aromatic Reaction Context (All) `hmoElectrophilicLocalizationEnergy(ratom(1))` returns the electrophilic L(+) localization energy of the reactant atom matching map `1` in the reaction equation
hmoNucleophilicityOrder hmoOrderNu	Huckel Analysis Plugin	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 `1` in the reaction equation
hmoNucleophilicLocalizationEnergy	Huckel Analysis Plugin	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-aromatic Reaction Context (All) `hmoNucleophilicLocalizationEnergy(ratom(1))` returns the nucleophilic L(-) localization energy of the reactant atom matching map `1` in the reaction equation
hmoPiEnergy	Huckel Analysis Plugin	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 molecule Reaction Context (All) `hmoPiEnergy(product(1))` returns the pi energy of the second product
hyperWienerIndex	Geometry Plugin Group	calculates the Hyper Wiener index	the Hyper Wiener index	-	Molecule Context (All) calculates the Hyper Wiener index Reaction 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 molecule Reaction 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 `false` Molecule Context (All) `in(3, maxatom("charge()", 2))` returns `true` if the partial charge on atom `3` is within the first `2` largest partial charges in the input molecule `in(3, minatom("pol()", 4))` returns `true` if the polarizability on atom `3` is within the first `4` smallest polarizability values in the input molecule Reaction Context (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 `true` if the polarizability on product atom matching map `1` in the reaction equation is within the first `4` smallest polarizability values in the second product
ionCharge	Charge Plugin Group
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` otherwise Reaction 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` otherwise Reaction Context (All) `isMarkush(reactant(1))` returns `true` if the second reactant contains any Markush features, `false` otherwise
isoelectricPoint pI	Protonation Plugin Group	calculates isoelectric point	the isoelectric point	-	Molecule Context (All) `isoelectricPoint()` returns the isoelectric point of the input molecule Reaction 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 molecule Reaction 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 molecule Reaction 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` otherwise Reaction 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 valid Reaction Context (All) `isValid(reactant(0), "aromaticity..valence")` checks for aromaticity and valence errors in first reactant, and returns if it is valid
largestAtomRingSize	Geometry Plugin Group	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 `1` in the input molecule Reaction Context (All) `largestAtomRingSize(patom(2))` returns the size of the largest ring containing product atom matching map `2` in the reaction equation
largestRing	Geometry Plugin Group	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 molecule Reaction Context (All) `largestRingSize(product(1))` returns the atom indexes of the largest ring in the second product
largestRingSize	Geometry Plugin Group	calculates the largest ring size	the largest ring size	-	Molecule Context (All) `largestRingSize()` returns the size of the largest ring in the input molecule Reaction Context (All) `largestRingSize(product(1))` returns the size of the largest ring in the second product
largestRingSystem	Geometry Plugin Group	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 molecule Reaction Context (All) `largestRingSize(product(1))` returns the atom indexes of the largest ring system in the second product
largestRingSystemSize	Geometry Plugin Group	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 molecule Reaction 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 Plugin Group	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 molecule Reaction Context (All) `logD(reactant(1), '7.4')` returns the logD at pH `7.4` of the second reactant
logDKLOP	Partitioning Plugin Group	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 molecule Reaction Context (All) `logDKLOP(reactant(1), '7.4')` returns the logD at pH `7.4` of the second reactant
logDPHYS	Partitioning Plugin Group	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 molecule Reaction Context (All) `logDPHYS(reactant(1), '7.4')` returns the logD at pH `7.4` of the second reactant
logDUser	Partitioning Plugin Group	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 molecule Reaction Context (All) `logDUser(reactant(1), '7.4')` returns the logD at pH `7.4` of the second reactant
logDVG	Partitioning Plugin Group	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 molecule Reaction Context (All) `logDVG(reactant(1), '7.4')` returns the logD at pH `7.4` of the second reactant
logDWeighted	Partitioning Plugin Group	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 molecule Reaction Context (All) `logDWeighted(reactant(1), '7.4')` returns the logD at pH `7.4` of the second reactant
logP	Partitioning Plugin Group	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 logP of the nonionic species and logD at pI `logP('logPMicro')` returns the logP of the input molecule itself Reaction Context (All) `logP(reactant(1), 'logDpI')` returns the logD at pI of the second reactant `logP(product(1), 'logPNonionic')` returns logP of the nonionic species of the second product
logPincrement logPi	Partitioning Plugin Group	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 molecule Reaction Context (All) `logPincrement(ratom(1))` returns the logP increment on the reactant atom matching map `1` in the reaction equation
logPKLOP	Partitioning Plugin Group	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 logP of the nonionic species and logD at pI `logPKLOP('logPMicro')` returns the logP of the input molecule itself Reaction Context (All) `logPKLOP(reactant(1), 'logDpI')` returns the logD at pI of the second reactant `logPKLOP(product(1), 'logPNonionic')` returns logP of the nonionic species of the second product
logPPHYS	Partitioning Plugin Group	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 logP of the nonionic species and logD at pI `logPPHYS('logPMicro')` returns the logP of the input molecule itself Reaction Context (All) `logPPHYS(reactant(1), 'logDpI')` returns the logD at pI of the second reactant `logPPHYS(product(1), 'logPNonionic')` returns logP of the nonionic species of the second product
logPUser	Partitioning Plugin Group	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 logP of the nonionic species and logD at pI `logPUser('logPMicro')` returns the logP of the input molecule itself Reaction Context (All) `logPUser(reactant(1), 'logDpI')` returns the logD at pI of the second reactant `logPUser(product(1), 'logPNonionic')` returns logP of the nonionic species of the second product
logPVG	Partitioning Plugin Group	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 logP of the nonionic species and logD at pI `logPVG('logPMicro')` returns the logP of the input molecule itself Reaction Context (All) `logPVG(reactant(1), 'logDpI')` returns the logD at pI of the second reactant `logPVG(product(1), 'logPNonionic')` returns logP of the nonionic species of the second product
logPWeighted	Partitioning Plugin Group	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 logP of the nonionic species and logD at pI `logPWeighted('logPMicro')` returns the logP of the input molecule itself Reaction Context (All) `logPWeighted(reactant(1), 'logDpI')` returns the logD at pI of the second reactant `logPWeighted(product(1), 'logPNonionic')` returns logP of the nonionic species of the second product
logS	Solubility Plugin	calculates solubility at specified pH	the logS value	the pH value	Molecule Context (All) `logS('7.4')` returns the logS at pH `7.4` of the input molecule Reaction Context (All) `logS(reactant(1), '7.4')` returns the logS at pH `7.4` of the second reactant
logS0	Solubility Plugin	calculates intrinsic solubility	the logS₀ value	-	Molecule Context (All) `logS0()` returns the logS₀ of the input molecule Reaction Context (All) `logS0(reactant(1))` returns the logS₀ of the second reactant
logSCategory	Solubility Plugin	calculates solubility category	the solubility category	-	Molecule Context (All) `logSCategory()` returns the solubilty category of the input molecule Reaction Context (All) `logSCategory(reactant(1))` returns the solubility category of the second reactant
lowestEnergyConformer leconformer	Conformation Plugin Group	calculates the lowest energy conformer of the molecule	the lowest energy conformer	-	Molecule Context (All) `lowestEnergyConformer()` returns the lowest energy conformer of the input molecule Reaction Context (All) `lowestEnergyConformer(reactant(0))` returns the lowest energy conformer of the first reactant `lowestEnergyConformer(product(1))` returns the lowest energy conformer of the second product
majorMicrospecies majorMs	Protonation Plugin Group	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 `7.4` Reaction Context (All) `majorMicrospecies(reactant(0), "7.4")` returns the major microspecies of the first reactant at pH `7.4` `majorMicrospecies(product(1), "7.4")` returns the major microspecies of the second product at pH `7.4`
majorTautomer	Isomers Plugin Group	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 molecule Reaction 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 `3` Reaction Context (All) `map(patom(3))` returns the atom map number on the product atom matching map `3` in 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 data Reaction 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 enumerated Reaction 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 enumerated Reaction 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 enumerated Reaction 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 molecule Reaction Context (All) `mass(reactant(0))` returns the mass of the first reactant
massSpectrum	-	returns the mass spectrum	the mass spectrum	-	Molecule Context (All) `massSpectrum()` returns the mass spectrum of the input molecule Reaction Context (All) N / A (reaction rules are numerical)
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 oxygen Reaction 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 oxygen Reaction 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 `5.6` Molecule Context (All) `min(charge(0), charge(2))` returns the least of the partial charge values on atoms `0` and `2` `max(charge())` returns the maximal partial charge value on the input molecule Reaction Context (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 `7.4` of the input molecule and returns the corresponding indices Reaction 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	Geometry Plugin Group	returns the maximal projection area	the maximal projection area	-	Molecule Context (All) `maximalProjectionArea()` returns the maximal projection area Reaction Context (All) `maximalProjectionArea((reactant(0))` returns the maximal projection area of the first reactant `maximalProjectionArea(product(1))` returns the maximal projection area of the second product
maximalProjectionRadius	Geometry Plugin Group	returns the maximal projection radius	the maximal projection radius	-	Molecule Context (All) `maximalProjectionRadius()` returns the maximal projection radius Reaction Context (All) `maximalProjectionRadius((reactant(0))` returns the maximal projection radius of the first reactant `maximalProjectionRadius(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 molecule Reaction 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 Plugin Group	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 pH `7.4` Reaction 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 Plugin Group	calculates the number of microspecies at specified pH	the number of microspecies	-	Molecule Context (All) `microspeciesCount()` returns the number of microspecies of the input molecule Reaction 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 Plugin Group	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 `5.4` Reaction 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 `5.6` Molecule Context (All) `min(charge(0), charge(2))` returns the least of the partial charge values on atoms `0` and `2` `max(charge())` returns the maximal partial charge value on the input molecule Reaction Context (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 molecule Reaction 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	Geometry Plugin Group	returns the minimal projection area	the minimal projection area	-	Molecule Context (All) `minimalProjectionArea()` returns the minimal projection area Reaction Context (All) `minimalProjectionArea((reactant(0))` returns the minimal projection area of the first reactant `minimalProjectionArea(product(1))` returns the minimal projection area of the second product
minimalProjectionRadius	Geometry Plugin Group	returns the minimal projection radius	the minimal projection radius	-	Molecule Context (All) `minimalProjectionRadius()` returns the minimal projection radius Reaction Context (All) `minimalProjectionRadius((reactant(0))` returns the minimal projection radius of the first reactant `minimalProjectionRadius(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 `7.4` of the input molecule Reaction 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	Geometry Plugin Group	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	Conformation Plugin Group	calculates the MMFF94 optimized lowest energy conformer	the MMFF94 optimized lowest energy conformer	-	Molecule Context (All) `mmff94OptimizedStructure()` returns the MMFF94 optimized lowest energy conformer of the input molecule Reaction Context (All) `mmff94OptimizedStructure(reactant(0))` returns the MMFF94 optimized lowest energy conformer of the first reactant `mmff94OptimizedStructure(product(1))` returns the MMFF94 optimized lowest energy conformer of the second product
molAtom	-	creates a MolAtom	the MolAtom object	atomic number	Molecule Context (All) `molAtom(6)` returns a carbon atom Reaction 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% quality Reaction Context (All) N / A (reaction rules are numerical)
molecularPolarizability molPol	Charge Plugin Group	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 `7.4` Reaction 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 molecule `molFormat(tautomers(), "sdf", 2)` returns the SDF format representation of the tautomers of the input molecule Reaction Context (All) N / A (reaction rules are numerical)
mostStableTautomer	Isomers Plugin Group	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 molecule Reaction Context (All) `mostStableTautomer(reactant(0))` returns the most stable tautomer structure of the first reactant/td>
name	IUPAC Naming Plugin	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 molecule Reaction Context (All) N / A (reaction rules are numerical)
nucleophilicity electrophilicLocalizationEnergy energyE	Huckel Analysis Plugin	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-aromatic Reaction Context (All) `nucleophilicity(ratom(1))` returns the nucleophilicity of the reactant atom matching map `1` in the reaction equation
nucleophilicityOrder aromaticNucleophilicityOrder orderNu	Huckel Analysis Plugin	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 `1` in 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 `2` and `5` in the reaction equation
piEnergy	Huckel Analysis Plugin	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 molecule Reaction Context (All) `piEnergy(product(1))` returns the pi energy of the second product
piOrbitalElectronegativity pOEN	Charge Plugin Group	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 `2` of the major microspecies taken at pH `7.4` Reaction Context (All) `pOEN(ratom(1))` returns the pi orbital electronegativity of reactant atom matching map `1` in the reaction equation `pOEN(patom(2), "7.4")` returns the pi orbital electronegativity of the product atom matching map `2` of the major microspecies taken at pH `7.4`
pKa	Protonation Plugin Group	calculates pK_a values	the pK_a values	the atom index / MolAtom object, the strength index as string (e.g., '1' for the strongest, '2' for the second strongest pK_a), the result type ("acidic", "basic", or "pka" for both (default)) Note, that the strength index is specified between quotation marks. In case of strength index the result type can be specified as "acidic" or "basic". In case of "pka"result type the returned pK_a values are acidic or basic (mixed!), depending on the acidic or basic character of the given atom. Acidic pK_a is returned for an atom, if acidicpKa() ≤ 14.8-basicpKa(), otherwise basic pK_a is returned. Specifying "acidic" or "basic" result type is required to get the acidic or basic pK_a values only (also `acidicpKa` or `basicpKa` functions can be used alternatively).	Molecule Context (All) `pKa(0)` returns the pK_a of atom `0` of the input molecule `pKa("acidic", "2")` returns the second strongest acidic pK_a value Reaction Context (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 Plugin Group	calculates pK_a values using the correction library	the pK_a values	the atom index / MolAtom object, the strength index as string (e.g. '1' for the strongest, '2' for the second strongest pK_a), the result type ("acidic", "basic", or "pka" for both (default)) Note, that the strength index is specified between quotation marks. In case of strength index the result type can be specified as "acidic" or "basic". In case of "pka"result type the returned pK_a values are acidic or basic (mixed!), depending on the acidic or basic character of the given atom. Acidic pK_a is returned for an atom, if acidicpKa() ≤ 14.8-basicpKa(), otherwise basic pK_a is returned. Specifying "acidic" or "basic" result type is required to get the acidic or basic pK_a values only (also `acidicpKaUseCorrection()` or `basicpKaUseCorrection()` functions can be used alternatively).	Molecule Context (All) `pKaUseCorrection(0)` returns the pK_a of atom `0` of the input molecule `pKaUseCorrection("acidic", "2")` returns the second strongest acidic pK_a value Reaction Context (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	Geometry Plugin Group	calculates the Platt index	the Platt index	-	Molecule Context (All) calculates the Platt index Reaction 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 `0` Reaction Context (All) `radicalCount(patom(3))` returns the radical count on the product atom matching map `3` in the reaction equation
randicIndex	Geometry Plugin Group	calculates the Randic index	the Randic index	-	Molecule Context (All) calculates the Randic index Reaction 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 data`randomMarkushEnumerationsDisplay(4, '2,3')` returns 4 randomly constructed enumerated structures of the input molecule, enumerating only atoms 2, 3 (1-based), with scaffold alignment and coloring data Reaction 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	Refractivity Plugin	calculates molar refractivity	the refractivity value	-	Molecule Context (All) `refractivity()` returns the molar refractivity of the input molecule Reaction Context (All) `refractivity(reactant(1))` returns the molar refractivity of the second reactant
refractivityIncrements refraci	Refractivity Plugin	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 molecule Reaction Context (All) `refractivityIncrements(ratom(1))` returns the refractivity increment on the reactant atom matching map `1` in the reaction equation
resonant	-	constructs a resonant structure	the resonant structure	-	Molecule Context (All) `resonant(0)` returns the first resonant structure of the input molecule Reaction Context (All) `resonant(reactant(0), 1)` returns the second resonant structure of the first reactant
resonantCharge	Charge Plugin Group	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 effect`resonantCharge(2, "pi", "7.4")` returns the partial "pi" charge on atom `2` of the major microspecies taken at pH `7.4` considering resonance effect Reaction 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 effect`resonantCharge(patom(2), "aromaticring", "7.4")` returns the sum of partial charges in the smallest aromatic ring containing the product atom matching map `2` in the major microspecies taken at pH `7.4` considering resonance effect
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 molecule Reaction 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 array Reaction Context (All) `resonants(reactant(0))` returns all resonants of the first reactant in an array
ringAtom	Geometry Plugin Group	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` otherwise Reaction 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 `true` if the product atom matching map `1` in the reaction equation is a ring atom, `false` otherwise
ringAtomCount	Geometry Plugin Group	calculates the ring atom count	the ring atom count	-	Molecule Context (All) `ringAtomCount()` returns the number of ring atoms in the input molecule Reaction 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	Geometry Plugin Group	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 `1` and `2` are connected by a ring bond the input molecule Reaction Context (All) `ringBond(reactant(0), bond(ratom(1), ratom(2)))` returns `true` if reactant atoms matching maps `1` and `2` in the reaction equation are connected by a ring bond in the corresponding reactant molecule (see note 1) `ringBond(product(1), bond(patom(2), patom(3)))` returns `true` if product atoms matching maps `2` and `3` in the reaction equation are connected by a ring bond in the corresponding product molecule (see note 1)
ringBondCount	Geometry Plugin Group	calculates the ring bond count	the ring bond count	-	Molecule Context (All) `ringBondCount()` returns the number of ring bonds in the input molecule Reaction 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	Geometry Plugin Group	calculates the ring count	the ring count	-	Molecule Context (All) `ringCount()` returns the number of rings in the input molecule Reaction 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	Geometry Plugin Group	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 molecule Reaction 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	Geometry Plugin Group	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 molecule Reaction Context (All) `ringCountOfSize(reactant(0), 5)` returns the number of rings of size 5 in the first reactant `ringCountOfSize(product(1), 5)` returns the number of rings of size 5 in the second product
rings	Geometry Plugin Group	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 molecule Reaction 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	Geometry Plugin Group	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 size Reaction 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	Geometry Plugin Group	calculates the number of rings systems	the number of rings systems	-	Molecule Context (All) `ringSystemCount()` returns the number of ring systems in the input molecule Reaction 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	Geometry Plugin Group	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 molecule Reaction Context (All) `ringSystemCountOfSize(reactant(0),3)` returns the number of three-membered ring systems in the first reactant `ringsystemCountOfSize(product(1),3)` returns the number of three-membered ring systems in the second product
ringSystems	Geometry Plugin Group	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 molecule Reaction 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	Geometry Plugin Group	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 size Reaction 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	Geometry Plugin Group	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 molecule Reaction Context (All) `rotatableBond(reactant(0), bond(ratom(1), ratom(2)))` returns `true` if reactant atoms matching maps `1` and `2` in the reaction equation are connected by a rotatable bond in the corresponding reactant molecule (see note 1) `rotatableBond(product(1), bond(patom(2), patom(3)))` returns `true` if product atoms matching maps `2` and `3` in the reaction equation are connected by a rotatable bond in the corresponding product molecule (see note 1)
rotatableBondCount	Geometry Plugin Group	calculates the rotatable bond count	the rotatable bond count	-	Molecule Context (All) `rotatableBondCount()` returns the number of rotatable bonds in the input molecule Reaction 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	Geometry Plugin Group	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 molecule Reaction 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	Charge Plugin Group	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 `0` of the input molecule `sigmaOrbitalElectronegativity(2, "7.4")` returns the sigma orbital electronegativity of atom `2` of the major microspecies taken at pH `7.4` Reaction Context (All) `sOEN(ratom(1))` returns the sigma orbital electronegativity of reactant atom matching map `1` in the reaction equation `sOEN(patom(2), "7.4")` returns the sigma orbital electronegativity of the product atom matching map `2` of the major microspecies taken at pH `7.4`
smallestAtomRingSize	Geometry Plugin Group	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 molecule Reaction Context (All) `smallestAtomRingSize(ratom(1))` returns the size of the smallest ring containing reactant atom matching map `1` in the reaction equation
smallestRing	Geometry Plugin Group	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 molecule Reaction Context (All) `smallestRingSize(product(1))` returns the atom indexes of the smallest ring in the second product
smallestRingSize	Geometry Plugin Group	calculates the smallest ring size	the smallest ring size	-	Molecule Context (All) `smallestRingSize()` returns the size of the smallest ring in the input molecule Reaction Context (All) `smallestRingSize(reactant(0))` returns the size of the smallest ring in the first reactant
smallestRingSystem	Geometry Plugin Group	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 molecule Reaction Context (All) `smallestRingSize(product(1))` returns the atom indexes of the smallest ring system in the second product
smallestRingSystemSize	Geometry Plugin Group	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 molecule Reaction 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 molecule Reaction 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 order Reaction 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 order Reaction 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	list of stereo descriptors	- the type of stereo descriptor: atrop, axial, cistrans, tetrahedral	Molecule Context (All) `stereoAnalysis()` returns the stereo descriptors of the input molecule `stereoAnalysis('tetrahedral')` returns the tetrahedral stereo descriptors of the input molecule Reaction 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	Geometry Plugin Group	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 molecule Reaction 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 Plugin Group	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 molecule Reaction Context (All) `stereoisomer(reactant(0), 1)` returns the second stereoisomer of the first reactant
stereoisomerCount	Isomers Plugin Group	returns the number of generated stereoisomers	the number of generated stereoisomers	-	Molecule Context (All) `stereoisomerCount()` returns the number of generated stereoisomers of the input molecule Reaction Context (All) `stereoisomerCount(reactant(0))` returns the number of calculated stereoisomers of the first reactant
stereoisomers	Isomers Plugin Group	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 array Reaction Context (All) `stereoisomers(reactant(0))` returns stereoisomers of the first reactant in an array
stericEffectIndex	Geometry Plugin Group	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 atom Reaction Context (All) the steric effect index of an atom
stericHindrance	Geometry Plugin Group	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 molecule Reaction Context (All) `stericHindrance(ratom(2))` returns the steric hindrance of the reactant atom matching map `2` in the reaction equation `stericHindrance(patom(1))` returns the steric hindrance of the product atom matching map `1` in the reaction equation
sum	-	computes the sum of array elements	the sum	integer array or real number array	General (All) `sum(array(3.4, 5.6, 1.2))` returns `10.2` Molecule Context (All) `sum(charge())` returns the sum of charge values `sum(pol())` returns the sum of atom polarizability values Reaction 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	Geometry Plugin Group	calculates the Szeged index	the Szeged index	-	Molecule Context (All) calculates the Szeged index Reaction Context (All) the Szeged index
tautomerCount	Isomers Plugin Group	calculates the number of tautomers	the number of tautomers	-	Molecule Context (All) `tautomerCount()` returns the number of tautomers of the input molecule Reaction Context (All) `tautomerCount(reactant(0))` returns the number of tautomers of the first reactant
tetrahedralStereoisomer	Isomers Plugin Group	generates a tetrahedral stereoisomer of the molecule	the tetrahedral stereoisomer	-	Molecule Context (All) `tetrahedralStereoisomer(0)` returns the first tetrahedral stereoisomer of the input molecule Reaction Context (All) `tetrahedralStereoisomer(reactant(0), 1)` returns the second tetrahedral stereoisomer of the first reactant
tetrahedralStereoisomerCount	Isomers Plugin Group	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 molecule Reaction Context (All) `tetrahedralStereoisomerCount(reactant(0))` returns the number of calculated tetrahedral stereoisomers of the first reactant
tetrahedralStereoisomers	Isomers Plugin Group	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 array Reaction Context (All) `tetrahedralStereoisomers(reactant(0))` returns tetrahedral stereoisomers of the first reactant in an array
topanal	Geometry Plugin Group
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 molecule `topologicalPolarSurfaceArea('7.4')` returns the polar surface area of the major microspecies taken at pH `7.4` Reaction Context (All) `topologicalPolarSurfaceArea(reactant(0))` returns the polar surface area of the first reactant `topologicalPolarSurfaceArea(product(0), '7.4')` returns the polar surface area of the major microspecies of the first product taken at pH `7.4`
traditionalName	IUPAC Naming Plugin	returns the traditional name of the molecule	the traditional name of the molecule	-	Molecule Context (All) `traditionalName()` returns the traditional name of the input molecule Reaction 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 `0` Reaction Context (All) `valence(ratom(1))` returns the valence of the reactant atom matching map `1` in the reaction equation
vanDerWaalsSurfaceArea	Geometry Plugin Group	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 molecule `vanDerWaalsSurfaceArea('7.4')` returns the van der Waals accessible surface area of the major microspecies taken at pH `7.4` Reaction Context (All) `vanDerWaalsSurfaceArea(reactant(0))` returns the van der Waals surface area of the first reactant `vanDerWaalsSurfaceArea(product(0), '7.4')` returns the van der Waals surface area of the major microspecies of the first product taken at pH `7.4`
waterAccessibleSurfaceArea ASA solventAccessibleSurfaceArea	Geometry Plugin Group	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 molecule `solventAccessibleSurfaceArea('7.4')`returns the solvent accessible / water accessible surface area of the major microspecies taken at pH `7.4` Reaction Context (All) `waterAccessibleSurfaceArea(reactant(0))` returns the solvent accessible / water accessible surface area of the first reactant`solventAccessibleSurfaceArea(product(0), '7.4')` returns the solvent accessible / water accessible surface area of the major microspecies of the first product taken at pH `7.4`
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 `-1` if there is no valence error in the molecule Reaction 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	Geometry Plugin Group	calculates the Wiener index	the Wiener index	-	Molecule Context (All) `wienerIndex()` returns the Wiener index of the input molecule Reaction 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	Geometry Plugin Group	calculates the Wiener polarity	the Wiener polarity	-	Molecule Context (All) `wienerPolarity()` returns the Wiener polarity of the input molecule Reaction Context (All) `wienerPolarity(reactant(0))` returns the Wiener polarity of the first reactant `wienerPolarity(product(1))` returns the Wiener polarity of the second product

Name

License

Description

Return value

Parameters

Examples

abs

returns the absolute value of a number

the absolute value

integer or real number

General (All)

abs(7)returns 7
abs(-4.9)returns 4.9

Molecule Context (All)

abs(7)returns 7
abs(-4.9)returns 4.9

Reaction Context (All)

abs(7)returns 7
abs(-4.9)returns 4.9

acceptor
acc

HBDA Plugin

calculates atomic hydrogen bond acceptor multiplicity

the atomic hydrogen bond acceptor multiplicity

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

Molecule Context (All)

acceptor(2) returns the hydrogen bond acceptor multiplicity on atom 2 of the input molecule

Reaction Context (All)

acceptor(ratom(2)) returns the hydrogen bond acceptor multiplicity on the reactant atom matching map 2 in the reaction equation

acceptorCount

HBDA Plugin

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

the molecular hydrogen bond acceptor count

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

Molecule Context (All)

acceptorCount() returns the number of hydrogen bond acceptor atoms in the input molecule

Reaction Context (All)

acceptorCount(reactant(0)) returns the number of hydrogen bond acceptor atoms in the first reactant

acceptorSiteCount
accSiteCount

HBDA Plugin

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

the molecular hydrogen bond acceptor multiplicity

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

Molecule Context (All)

acceptorSiteCount() returns the hydrogen bond acceptor multiplicity of the input molecule

Reaction Context (All)

acceptorSiteCount(reactant(0)) returns the hydrogen bond acceptor multiplicity of the first reactant

acidicpKa
apKa

Protonation Plugin Group

calculates acidic pK_a values

the acidic pK_a values

the atom index / MolAtom object,
the strength index as string (e.g. '1' for the strongest, '2' for the second strongest pK_a),

Note, that the strength index is specified between quotation marks.

Molecule Context (All)

acidicpKa(0) returns the acidic pK_a of atom 0 of the input molecule acidicpKa("2") returns the second strongest acidic pK_a value

Reaction Context (All)

acidicpKa(ratom(1)) returns the acidic pK_a of reactant atom matching map 1 in the reaction equation acidicpKa(product(0), "1") returns the strongest basic pK_a value in the first product

acidicpKaLargeModel

Protonation Plugin Group

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 molecule acidicpKaLargeModel("2") returns the second strongest acidic pK_a value

Reaction Context (All)

acidicpKaLargeModel(ratom(1)) returns the acidic pK_a of reactant atom matching map 1 in the reaction equation acidicpKaLargeModel(product(0), "1") returns the strongest basic pK_a value in the first product

acidicpKaUseCorrection

Protonation Plugin Group

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 value

Reaction Context (All)

"acidicpKaUseCorrection"(ratom(1)) returns the acidic pK_a of reactant atom matching map 1 in the reaction equation "acidicpKaUseCorrection"(product(0), "1") returns the strongest basic pK_a value in the first product

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

Geometry Plugin Group

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 otherwise

Reaction Context (All)

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

aliphaticAtomCount

Geometry Plugin Group

calculates the aliphatic atom count

the aliphatic atom count

Molecule Context (All)

aliphaticAtomCount() returns the number of aliphatic atoms in the input molecule

Reaction 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

Geometry Plugin Group

calculates the aliphatic bond count

the aliphatic bond count

Molecule Context (All)

aliphaticBondCount() returns the number of bonds in the input molecule

Reaction 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

Geometry Plugin Group

calculates the aliphatic ring count

the aliphatic ring count

Molecule Context (All)

aliphaticRingCount() returns the number of aliphatic rings in the input molecule

Reaction 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

Geometry Plugin Group

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 molecule

Reaction Context (All)

aliphaticRingCountOfSize(reactant(0), 5) returns the number of aliphatic rings of size 5 in the first reactant aliphaticRingCountOfSize(product(1), 5) returns the number of aliphatic rings of size 5 in the second product

aliphaticRings

Geometry Plugin Group

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 molecule

Reaction 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

Geometry Plugin Group

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 size

Reaction 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 Plugin Group

constructs a tautomeric form

the tautomer

the tautomer index (0-based)

Molecule Context (All)

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

Reaction Context (All)

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

allTautomers

Isomers Plugin Group

constructs all tautomeric forms

the tautomer array

Molecule Context (All)

tautomers() returns all tautomers of the input molecule in an array

Reaction Context (All)

tautomers(reactant(0)) returns all tautomers of the first reactant in an array

angle

Geometry Plugin Group

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 molecule

Reaction Context (All)

angle(reactant(0), atoms(ratom(1), ratom(2), ratom(3))) returns the angle between reactant atoms matching maps 1, 2 and 3 in the reaction equation (see note 1) angle(product(1), atoms(patom(2), patom(3), patom(4))) returns the angle between product atoms matching maps 2, 3 and 4 in the reaction equation (see note 1)

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 bond

Reaction Context (All)

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

aromaticAtom

Geometry Plugin Group

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 otherwise

Reaction Context (All)

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

aromaticAtomCount

Geometry Plugin Group

calculates the aromatic atom count

the aromatic atom count

Molecule Context (All)

aromaticAtomCount() returns the number of aromatic atoms in the input molecule

Reaction 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

Geometry Plugin Group

calculates the aromatic bond count

the aromatic bond count

Molecule Context (All)

aromaticBondCount() returns the number of aromatic bonds in the input molecule

Reaction 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

Geometry Plugin Group

calculates the aromatic ring count

the aromatic ring count

Molecule Context (All)

aromaticRingCount() returns the number of aromatic rings in the input molecule

Reaction 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

Geometry Plugin Group

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 molecule

Reaction Context (All)

aromaticRingCountOfSize(reactant(0), 5) returns the number of aromatic rings of size 5 in the first reactant aromaticRingCountOfSize(product(1), 5) returns the number of aromatic rings of size 5 in the second product

aromaticRings

Geometry Plugin Group

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 molecule

Reaction 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

Geometry Plugin Group

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 size

Reaction 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

Geometry Plugin Group

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 charge ASAHydrophobic('7.4')returns the water accessible surface area of all atoms with hydrophobic partial charge of the major microspecies taken at pH 7.4

Reaction Context (All)

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

ASANegative

Geometry Plugin Group

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 charge ASANegative('7.4')returns the water accessible surface area of all atoms with negative partial charge of the major microspecies taken at pH 7.4

Reaction Context (All)

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

ASAPlus

Geometry Plugin Group

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 charge ASAPlus('7.4')returns the water accessible surface area of all atoms with positive partial charge of the major microspecies taken at pH 7.4

Reaction Context (All)

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

ASAPolar

Geometry Plugin Group

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 charge ASAPolar('7.4')returns the water accessible surface area of all atoms with polar partial charge of the major microspecies taken at pH 7.4

Reaction Context (All)

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

asymmetricAtom

Geometry Plugin Group

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 otherwise

Reaction Context (All)

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

asymmetricAtomCount

Geometry Plugin Group

calculates the number of asymmetric atoms

the asymmetric atom count

Molecule Context (All)

asymmetricAtomCount() returns the number of asymmetric atoms in the input molecule

Reaction 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

Geometry Plugin Group

determines the asymmetric atoms

indexes of asymmetric atoms

Molecule Context (All)

asymmetricAtoms() returns the indexes of asymmetric atoms in the input molecule

Reaction 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 0

Reaction 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 molecule

Reaction 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

Charge Plugin Group

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 7.4

Reaction 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 2 of the major microspecies taken at pH 7.4

atomProp

atoms

averageMicrospeciesCharge

Protonation Plugin Group

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 molecule

Reaction Context (All)

averageMicrospeciesCharge(reactant(1)) returns the average charge of the microspecies of the second reactant

averagePolarizability
averagePol
avgPol

Charge Plugin Group

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 7.4

Reaction 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

Charge Plugin Group

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 molecule axxPol("7.4") returns the principal component a(xx) of polarizability tensor of the major microspecies taken at pH 7.4

Reaction 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

Charge Plugin Group

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 molecule ayyPol("7.4") returns the principal component a(yy) of polarizability tensor of the major microspecies taken at pH 7.4

Reaction 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

Charge Plugin Group

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 molecule azzPol("7.4") returns the principal component a(zz) of polarizability tensor of the major microspecies taken at pH 7.4

Reaction 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

Geometry Plugin Group

calculates the Balaban index

the Balaban index

Molecule Context (All)

calculates the Balaban index

Reaction Context (All)

basicpKa
bpKa

Protonation Plugin Group

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 molecule basicpKa("2") returns the second strongest basic pK_a value

Reaction Context (All)

basicpKa(ratom(1)) returns the basic pK_a of reactant atom matching map 1 in the reaction equation basicpKa(product(0), "1") returns the strongest basic pK_a value in the first product

basicpKaLargeModel

Protonation Plugin Group

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 molecule basicpKaLargeModel("2") returns the second strongest basic pK_a value

Reaction Context (All)

basicpKaLargeModel(ratom(1)) returns the basic pK_a of reactant atom matching map 1 in the reaction equation basicpKaLargeModel(product(0), "1") returns the strongest basic pK_a value in the first product

basicpKaUseCorrection

Protonation Plugin Group

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 molecule basicpKaUseCorrection("2") returns the second strongest basic pK_a value

Reaction Context (All)

basicpKaUseCorrection(ratom(1)) returns the basic pK_a of reactant atom matching map 1 in the reaction equation basicpKaUseCorrection(product(0), "1") returns the strongest basic pK_a value in the first product

bmf

Structural Frameworks Plugin

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 molecule

Reaction Context (All)

bmf(reactant(0)) returns the Bemis-Murcko framework of the first reactant

bmfl
bemisMurckoFrameworkLoose

Structural Frameworks Plugin

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 molecule

Reaction Context (All)

bmfl(reactant(0)) returns the loose Bemis-Murcko framework of the first reactant

bmflp
bemisMurckoFrameworkLoosePruned

Structural Frameworks Plugin

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 molecule

Reaction 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 molecule

Reaction 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

Geometry Plugin Group

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 1 and 2 in the input molecule

Reaction Context (All)

bondType(reactant(0), bond(ratom(1), ratom(2))) returns the bond type between reactant atoms matching maps 1 and 2 in the reaction equation (see note 1)bondType(product(1), bond(patom(2), patom(3))) returns the bond type between product atoms matching maps 2 and 3 in the reaction equation (see note 1)

booleanToNumber

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

the number representation of a boolean value

boolean or number

General (All)

booleanToNumber(1<2)returns 1
booleanToNumber(2+2==5)returns 0
booleanToNumber(5*5)returns 25

Molecule Context (All)

booleanToNumber(hasValenceError())returns 0 for molecules having no valence error

Reaction 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 molecule

Reaction Context (All)

canonicalResonant(reactant(0)) returns the canonical resonant structure of the first reactant

canonicalTautomer

Isomers Plugin Group

constructs the canonical tautomer structure

the canonical tautomer structure

Molecule Context (All)

canonicalTautomer() returns the canonical tautomer structure of the input molecule

Reaction Context (All)

canonicalTautomer(reactant(0)) returns the canonical tautomer structure of the first reactant/td>

carboaliphaticRingCount

Geometry Plugin Group

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 molecule

Reaction 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

Geometry Plugin Group

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 molecule

Reaction 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

Geometry Plugin Group

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 molecule

Reaction 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

Geometry Plugin Group

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 molecule

Reaction Context (All)

carboRingCountOfSize(reactant(0), 5) returns the number of carbocyclic rings of size 5 in the first reactant carboRingCountOfSize(product(1), 5) returns the number of carbocyclic rings of size 5 in the second product

carboRings

Geometry Plugin Group

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 molecule

Reaction 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

Geometry Plugin Group

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 size

Reaction 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

Geometry Plugin Group

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 otherwise

Reaction 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 true if the product atom matching map 1 in the reaction equation is a chain atom, false otherwise

chainAtomCount

Geometry Plugin Group

calculates the chain atom count

the chain atom count

Molecule Context (All)

chainAtomCount() returns the number of chain atoms in the input molecule

Reaction 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

Geometry Plugin Group

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 1 and 2 are connected by a chain bond the input molecule

Reaction Context (All)

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

chainBondCount

Geometry Plugin Group

calculates the chain bond count

the chain bond count

Molecule Context (All)

chainBondCount() returns the number of chain bonds in the input molecule

Reaction 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

Charge Plugin Group

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 7.4

Reaction 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 2 in the major microspecies taken at pH 7.4

chargeDensity
totalChargeDensity

Huckel Analysis Plugin

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, NaN for non-existing value

Reaction Context (All)

chargeDensity(ratom(1)) returns the charge density of the reactant atom matching map 1 in 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 report

Reaction 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 count

Reaction Context (All)

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

chiralCenter

Geometry Plugin Group

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 otherwise

Reaction Context (All)

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

chiralCenterCount

Geometry Plugin Group

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 molecule

Reaction 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

Geometry Plugin Group

determines the chiral center atoms

indexes of chiral center atoms

Molecule Context (All)

chiralCenters() returns the indexes of chiral center atoms in the input molecule

Reaction 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 molecule

Reaction Context (All)

conformer

Conformation Plugin Group

calculates a conformer of the molecule

the conformer

the conformer index (0-based)

Molecule Context (All)

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

Reaction Context (All)

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

conformerCount

Conformation Plugin Group

returns the number of calculated conformers

the number of calculated conformers

Molecule Context (All)

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

Reaction Context (All)

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

conformers

Conformation Plugin Group

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

the conformer array

Molecule Context (All)

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

Reaction Context (All)

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

connected

Geometry Plugin Group

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 1 and 2 are in the same connected component of the input molecule

Reaction Context (All)

connected(reactant(0), pair(ratom(1), ratom(2))) returns true if reactant atoms matching maps 1 and 2 in the reaction equation are connected in the corresponding reactant molecule (see note 1) connected(product(1), pair(patom(2), patom(3))) returns true if product atoms matching maps 2 and 3 in the reaction equation are connected in the corresponding product molecule (see note 1)

connectedGraph

Geometry Plugin Group

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 connected

Reaction 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 2

Reaction 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 3

Molecule 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 carbons

Reaction 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

Geometry Plugin Group

calculates the cyclomatic number

the cyclomatic number

Molecule Context (All)

cyclomaticNumber() returns the cyclomatic number of the input molecule

Reaction 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

Geometry Plugin Group

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 molecule

Reaction 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 the match function.

Molecule Context (All)

disjointMatchCount("[#8]C=O") counts the maximal number of pairwise disjoint carboxylic groups in the input molecule

Reaction 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 metric

Reaction 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

Geometry Plugin Group

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 1 and 2 in the input molecule

Reaction Context (All)

distance(reactant(0), pair(ratom(1), ratom(2))) returns the distance between reactant atoms matching maps 1 and 2 in the reaction equation (see note 1) distance(product(1), pair(patom(2), patom(3))) returns the distance between product atoms matching maps 2 and 3 in the reaction equation (see note 1)

distanceDegree

Geometry Plugin Group

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 molecule

Reaction Context (All)

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

dominantTautomer
tautomer

Isomers Plugin Group

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 Plugin Group

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 7.4

Reaction 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 Plugin Group

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

HBDA Plugin

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 7.4

Reaction 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

HBDA Plugin

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 7.4

Reaction 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

HBDA Plugin

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 7.4

Reaction 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 molecule

Reaction Context (All)

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 molecule

Reaction Context (All)

doubleBondStereoisomer

Isomers Plugin Group

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 molecule

Reaction Context (All)

doubleBondStereoisomer(reactant(0), 1) returns the second double bond stereoisomer of the first reactant

doubleBondStereoisomerCount

Isomers Plugin Group

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 molecule

Reaction Context (All)

doubleBondStereoisomerCount(reactant(0)) returns the number of calculated double bond stereoisomers of the first reactant

doubleBondStereoisomers

Isomers Plugin Group

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 array

Reaction Context (All)

doubleBondStereoisomers(reactant(0)) returns double bond stereoisomers of the first reactant in an array

dreidingEnergy

Geometry Plugin Group

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

Geometry Plugin Group

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 molecule

Reaction Context (All)

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

electronDensity
piChargeDensity

Huckel Analysis Plugin

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, NaN for non-existing value

Reaction Context (All)

electronDensity(ratom(1)) returns the electron density of the reactant atom matching map 1 in the reaction equation

electrophilicity
energyNu
nucleophilicLocalizationEnergy

Huckel Analysis Plugin

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-aromatic

Reaction Context (All)

electrophilicity(ratom(1)) returns the electrophilicity of the reactant atom matching map 1 in the reaction equation

electrophilicityOrder
aromaticElectrophilicityOrder
orderE

Huckel Analysis Plugin

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. returns 0 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 formula

Reaction Context (All)

eval

exactMass

calculates the exact mass of the molecule

the exact mass

Molecule Context (All)

exactMass() returns the exact mass of the input molecule

Reaction 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') > 2 returns 1 if the ACTIVITY value is bigger than 2, returns 0 otherwise

Reaction 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 0 otherwise

fieldAsString
propertyAsString

returns a molecule property (SDF field value) as string

the molecule property as string

the property key (SDF field name)

Molecule Context (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 molecule

Reaction 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 form

Reaction 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 molecule formalCharge(0) returns the formal charge of atom 0

Reaction Context (All)

formalCharge(reactant(0)) returns the formal charge of the first reactant formalCharge(ratom(1)) returns the formal charge of the reactant atom matching map 1

formula

returns the formula

the formula

Molecule Context (All)

formula() returns the formula of the input molecule

Reaction Context (All)

fragmentCount

Geometry Plugin Group

returns the number of fragments (disconnected parts)

the fragment count

Molecule Context (All)

fragmentCount() returns the number of fragments in the input molecule

Reaction 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 molecule

Reaction Context (All)

fragments(reactant(1)) returns the disconnected fragments of the second reactant

fsp3

Geometry Plugin Group

returns the fsp3 of the molecule

the fsp3 value

Molecule Context (All)

fsp3() returns the fsp3 value of the input molecule

Reaction 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

Geometry Plugin Group

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 molecule

Reaction 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

Geometry Plugin Group

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 molecule

Reaction Context (All)

fusedAliphaticRingCountOfSize(reactant(0), 5) returns the number of fused aliphatic rings of size 5 in the first reactant fusedAliphaticRingCountOfSize(product(1), 5) returns the number of fused aliphatic rings of size 5 in the second product

fusedAliphaticRings

Geometry Plugin Group

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 molecule

Reaction 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

Geometry Plugin Group

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 size

Reaction 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

Geometry Plugin Group

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 molecule

Reaction 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

Geometry Plugin Group

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 molecule

Reaction Context (All)

fusedAromaticRingCountOfSize(reactant(0), 5) returns the number of fused aromatic rings of size 5 in the first reactant fusedAromaticRingCountOfSize(product(1), 5) returns the number of fused aromatic rings of size 5 in the second product

fusedAromaticRings

Geometry Plugin Group

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 molecule

Reaction 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

Geometry Plugin Group

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 size

Reaction 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

Geometry Plugin Group

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 molecule

Reaction 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 Plugin Group

constructs the generic tautomer structure

the generic tautomer structure

Molecule Context (All)

genericTautomer() returns the generic tautomer structure of the input molecule

Reaction Context (All)

genericTautomer(reactant(0)) returns the generic tautomer structure of the first reactant/td>

groupedDotDisconnectedFormula

returns the grouped dot-disconnected formula

the grouped dot-disconnected formula

Molecule Context (All)

groupedDotDisconnectedFormula() returns the grouped dot-disconnected formula of the input molecule

Reaction Context (All)

hararyIndex

Geometry Plugin Group

calculates the Harary index

the Harary index

Molecule Context (All)

calculates the Harary index

Reaction Context (All)

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 otherwise

Reaction 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 otherwise

Reaction 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 otherwise

Reaction 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 otherwise

Reaction Context (All)

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

hasValidConformer

Conformation Plugin Group

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

HBDA Plugin

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 0

Reaction Context (All)

hCount(patom(3)) returns the hydrogen count on the product atom matching map 3 in the reaction equation

heteroaliphaticRingCount

Geometry Plugin Group

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 molecule

Reaction 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

Geometry Plugin Group

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 molecule

Reaction Context (All)

heteroaliphaticRingCountOfSize(reactant(0), 5) returns the number of aliphatic heterocyclic rings of size 5 in the first reactant heteroaliphaticRingCountOfSize(product(1), 5) returns the number of aliphatic heterocyclic rings of size 5 in the second product

heteroaliphaticRings

Geometry Plugin Group

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 molecule

Reaction 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

Geometry Plugin Group

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 size

Reaction 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

Geometry Plugin Group

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 molecule

Reaction 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

Geometry Plugin Group

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 molecule

Reaction Context (All)

heteroaromaticRingCountOfSize(reactant(0), 5) returns the number of aromatic heterocyclic rings of size 5 in the first reactant heteroaromaticRingCountOfSize(product(1), 5) returns the number of aromatic heterocyclic rings of size 5 in the second product

heteroaromaticRings

Geometry Plugin Group

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 molecule

Reaction 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

Geometry Plugin Group

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 size

Reaction 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

Geometry Plugin Group

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 molecule

Reaction 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

Geometry Plugin Group

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 molecule

Reaction Context (All)

heteroRingCountOfSize(reactant(0), 5) returns the number of heterocyclic rings of size 5 in the first reactant heteroRingCountOfSize(product(1), 5) returns the number of heterocyclic rings of size 5 in the second product

heteroRings

Geometry Plugin Group

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 molecule

Reaction 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

Geometry Plugin Group

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 size

Reaction 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

Huckel Analysis Plugin

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, NaN for non-existing value

Reaction Context (All)

hmoChargeDensity(ratom(1)) returns the charge density of the reactant atom matching map 1 in the reaction equation

hmoElectronDensity

Huckel Analysis Plugin

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, NaN for non-existing value

Reaction Context (All)

hmoElectronDensity(ratom(1)) returns the electron density of the reactant atom matching map 1 in the reaction equation

hmoElectrophilicityOrder
hmoOrderE

Huckel Analysis Plugin

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. returns 0 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

Huckel Analysis Plugin

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-aromatic

Reaction Context (All)

hmoElectrophilicLocalizationEnergy(ratom(1)) returns the electrophilic L(+) localization energy of the reactant atom matching map 1 in the reaction equation

hmoNucleophilicityOrder
hmoOrderNu

Huckel Analysis Plugin

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 1 in the reaction equation

hmoNucleophilicLocalizationEnergy

Huckel Analysis Plugin

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-aromatic

Reaction Context (All)

hmoNucleophilicLocalizationEnergy(ratom(1)) returns the nucleophilic L(-) localization energy of the reactant atom matching map 1 in the reaction equation

hmoPiEnergy

Huckel Analysis Plugin

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 molecule

Reaction Context (All)

hmoPiEnergy(product(1)) returns the pi energy of the second product

hyperWienerIndex

Geometry Plugin Group

calculates the Hyper Wiener index

the Hyper Wiener index

Molecule Context (All)

calculates the Hyper Wiener index

Reaction Context (All)

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 molecule

Reaction Context (All)

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

true if the array contains the specified integer, false otherwise

an integer or MolAtom object and an integer array

General (All)

in(5, array(3, 5, 1)) returns true in(2, array(3, 5, 1)) returns false

Molecule Context (All)

in(3, maxatom("charge()", 2)) returns true if the partial charge on atom 3 is within the first 2 largest partial charges in the input molecule in(3, minatom("pol()", 4)) returns true if the polarizability on atom 3 is within the first 4 smallest polarizability values in the input molecule

Reaction Context (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 true if the polarizability on product atom matching map 1 in the reaction equation is within the first 4 smallest polarizability values in the second product

ionCharge

Charge Plugin Group

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 otherwise

Reaction 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 otherwise

Reaction Context (All)

isMarkush(reactant(1)) returns true if the second reactant contains any Markush features, false otherwise

isoelectricPoint
pI

Protonation Plugin Group

calculates isoelectric point

the isoelectric point

Molecule Context (All)

isoelectricPoint() returns the isoelectric point of the input molecule

Reaction 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 molecule

Reaction Context (All)

isotopeFormula

returns the isotope formula

the isotope formula

Molecule Context (All)

isotopeFormula() returns the isotope formula of the input molecule

Reaction Context (All)

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 otherwise

Reaction 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 valid

Reaction Context (All)

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

largestAtomRingSize

Geometry Plugin Group

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 1 in the input molecule

Reaction Context (All)

largestAtomRingSize(patom(2)) returns the size of the largest ring containing product atom matching map 2 in the reaction equation

largestRing

Geometry Plugin Group

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 molecule

Reaction Context (All)

largestRingSize(product(1)) returns the atom indexes of the largest ring in the second product

largestRingSize

Geometry Plugin Group

calculates the largest ring size

the largest ring size

Molecule Context (All)

largestRingSize() returns the size of the largest ring in the input molecule

Reaction Context (All)

largestRingSize(product(1)) returns the size of the largest ring in the second product

largestRingSystem

Geometry Plugin Group

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 molecule

Reaction Context (All)

largestRingSize(product(1)) returns the atom indexes of the largest ring system in the second product

largestRingSystemSize

Geometry Plugin Group

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 molecule

Reaction 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 Plugin Group

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 molecule

Reaction Context (All)

logD(reactant(1), '7.4') returns the logD at pH 7.4 of the second reactant

logDKLOP

Partitioning Plugin Group

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 molecule

Reaction Context (All)

logDKLOP(reactant(1), '7.4') returns the logD at pH 7.4 of the second reactant

logDPHYS

Partitioning Plugin Group

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 molecule

Reaction Context (All)

logDPHYS(reactant(1), '7.4') returns the logD at pH 7.4 of the second reactant

logDUser

Partitioning Plugin Group

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 molecule

Reaction Context (All)

logDUser(reactant(1), '7.4') returns the logD at pH 7.4 of the second reactant

logDVG

Partitioning Plugin Group

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 molecule

Reaction Context (All)

logDVG(reactant(1), '7.4') returns the logD at pH 7.4 of the second reactant

logDWeighted

Partitioning Plugin Group

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 molecule

Reaction Context (All)

logDWeighted(reactant(1), '7.4') returns the logD at pH 7.4 of the second reactant

logP

Partitioning Plugin Group

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 logP of the nonionic species and logD at pI logP('logPMicro') returns the logP of the input molecule itself

Reaction Context (All)

logP(reactant(1), 'logDpI') returns the logD at pI of the second reactant logP(product(1), 'logPNonionic') returns logP of the nonionic species of the second product

logPincrement
logPi

Partitioning Plugin Group

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 molecule

Reaction Context (All)

logPincrement(ratom(1)) returns the logP increment on the reactant atom matching map 1 in the reaction equation

logPKLOP

Partitioning Plugin Group

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 logP of the nonionic species and logD at pI logPKLOP('logPMicro') returns the logP of the input molecule itself

Reaction Context (All)

logPKLOP(reactant(1), 'logDpI') returns the logD at pI of the second reactant logPKLOP(product(1), 'logPNonionic') returns logP of the nonionic species of the second product

logPPHYS

Partitioning Plugin Group

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 logP of the nonionic species and logD at pI logPPHYS('logPMicro') returns the logP of the input molecule itself

Reaction Context (All)

logPPHYS(reactant(1), 'logDpI') returns the logD at pI of the second reactant logPPHYS(product(1), 'logPNonionic') returns logP of the nonionic species of the second product

logPUser

Partitioning Plugin Group

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 logP of the nonionic species and logD at pI logPUser('logPMicro') returns the logP of the input molecule itself

Reaction Context (All)

logPUser(reactant(1), 'logDpI') returns the logD at pI of the second reactant logPUser(product(1), 'logPNonionic') returns logP of the nonionic species of the second product

logPVG

Partitioning Plugin Group

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 logP of the nonionic species and logD at pI logPVG('logPMicro') returns the logP of the input molecule itself

Reaction Context (All)

logPVG(reactant(1), 'logDpI') returns the logD at pI of the second reactant logPVG(product(1), 'logPNonionic') returns logP of the nonionic species of the second product

logPWeighted

Partitioning Plugin Group

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 logP of the nonionic species and logD at pI logPWeighted('logPMicro') returns the logP of the input molecule itself

Reaction Context (All)

logPWeighted(reactant(1), 'logDpI') returns the logD at pI of the second reactant logPWeighted(product(1), 'logPNonionic') returns logP of the nonionic species of the second product

logS

Solubility Plugin

calculates solubility at specified pH

the logS value

the pH value

Molecule Context (All)

logS('7.4') returns the logS at pH 7.4 of the input molecule

Reaction Context (All)

logS(reactant(1), '7.4') returns the logS at pH 7.4 of the second reactant

logS0

Solubility Plugin

calculates intrinsic solubility

the logS₀ value

Molecule Context (All)

logS0() returns the logS₀ of the input molecule

Reaction Context (All)

logS0(reactant(1)) returns the logS₀ of the second reactant

logSCategory

Solubility Plugin

calculates solubility category

the solubility category

Molecule Context (All)

logSCategory() returns the solubilty category of the input molecule

Reaction Context (All)

logSCategory(reactant(1)) returns the solubility category of the second reactant

lowestEnergyConformer
leconformer

Conformation Plugin Group

calculates the lowest energy conformer of the molecule

the lowest energy conformer

Molecule Context (All)

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

Reaction Context (All)

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

majorMicrospecies
majorMs

Protonation Plugin Group

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 7.4

Reaction Context (All)

majorMicrospecies(reactant(0), "7.4") returns the major microspecies of the first reactant at pH 7.4 majorMicrospecies(product(1), "7.4") returns the major microspecies of the second product at pH 7.4

majorTautomer

Isomers Plugin Group

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 molecule

Reaction 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 3

Reaction Context (All)

map(patom(3)) returns the atom map number on the product atom matching map 3 in 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 data

Reaction 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 enumerated

Reaction 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 enumerated

Reaction 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 enumerated

Reaction 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 molecule

Reaction Context (All)

mass(reactant(0)) returns the mass of the first reactant

massSpectrum

returns the mass spectrum

the mass spectrum

Molecule Context (All)

massSpectrum() returns the mass spectrum of the input molecule

Reaction Context (All)

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 oxygen

Reaction 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 oxygen

Reaction 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 5.6

Molecule Context (All)

min(charge(0), charge(2)) returns the least of the partial charge values on atoms 0 and 2 max(charge()) returns the maximal partial charge value on the input molecule

Reaction Context (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 7.4 of the input molecule and returns the corresponding indices

Reaction 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

Geometry Plugin Group

returns the maximal projection area

the maximal projection area

Molecule Context (All)

maximalProjectionArea() returns the maximal projection area

Reaction Context (All)

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

maximalProjectionRadius

Geometry Plugin Group

returns the maximal projection radius

the maximal projection radius

Molecule Context (All)

maximalProjectionRadius() returns the maximal projection radius

Reaction Context (All)

maximalProjectionRadius((reactant(0)) returns the maximal projection radius of the first reactant maximalProjectionRadius(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)

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 molecule

Reaction 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 Plugin Group

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 pH 7.4

Reaction 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 Plugin Group

calculates the number of microspecies at specified pH

the number of microspecies

Molecule Context (All)

microspeciesCount() returns the number of microspecies of the input molecule

Reaction 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 Plugin Group

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 5.4

Reaction 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 5.6

Molecule Context (All)

min(charge(0), charge(2)) returns the least of the partial charge values on atoms 0 and 2 max(charge()) returns the maximal partial charge value on the input molecule

Reaction Context (All)

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 molecule

Reaction 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

Geometry Plugin Group

returns the minimal projection area

the minimal projection area

Molecule Context (All)

minimalProjectionArea() returns the minimal projection area

Reaction Context (All)

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

minimalProjectionRadius

Geometry Plugin Group

returns the minimal projection radius

the minimal projection radius

Molecule Context (All)

minimalProjectionRadius() returns the minimal projection radius

Reaction Context (All)

minimalProjectionRadius((reactant(0)) returns the minimal projection radius of the first reactant minimalProjectionRadius(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)

Molecule Context (All)

minValue("charge('7.4')") returns the minimum partial charge in the major microspecies at pH 7.4 of the input molecule

Reaction 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

Geometry Plugin Group

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

Conformation Plugin Group

calculates the MMFF94 optimized lowest energy conformer

the MMFF94 optimized lowest energy conformer

Molecule Context (All)

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

Reaction Context (All)

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

molAtom

creates a MolAtom

the MolAtom object

atomic number

Molecule Context (All)

molAtom(6) returns a carbon atom

Reaction 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% quality

Reaction Context (All)

molecularPolarizability
molPol

Charge Plugin Group

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 7.4

Reaction 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 molecule molFormat(tautomers(), "sdf", 2) returns the SDF format representation of the tautomers of the input molecule

Reaction Context (All)

mostStableTautomer

Isomers Plugin Group

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 molecule

Reaction Context (All)

mostStableTautomer(reactant(0)) returns the most stable tautomer structure of the first reactant/td>

name

IUPAC Naming Plugin

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 molecule

Reaction Context (All)

nucleophilicity
electrophilicLocalizationEnergy
energyE

Huckel Analysis Plugin

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-aromatic

Reaction Context (All)

nucleophilicity(ratom(1)) returns the nucleophilicity of the reactant atom matching map 1 in the reaction equation

nucleophilicityOrder
aromaticNucleophilicityOrder
orderNu

Huckel Analysis Plugin

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 1 in 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 2 and 5 in the reaction equation

piEnergy

Huckel Analysis Plugin

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 molecule

Reaction Context (All)

piEnergy(product(1)) returns the pi energy of the second product

piOrbitalElectronegativity
pOEN

Charge Plugin Group

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 2 of the major microspecies taken at pH 7.4

Reaction Context (All)

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

pKa

Protonation Plugin Group

calculates pK_a values

the pK_a values

the atom index / MolAtom object,
the strength index as string (e.g., '1' for the strongest, '2' for the second strongest pK_a),
the result type ("acidic", "basic", or "pka" for both (default))

Note, that the strength index is specified between quotation marks.
In case of strength index the result type can be specified as "acidic" or "basic".

In case of "pka"result type the returned pK_a values are acidic or basic (mixed!), depending on the acidic or basic character of the given atom. Acidic pK_a is returned for an atom, if acidicpKa() ≤ 14.8-basicpKa(), otherwise basic pK_a is returned. Specifying "acidic" or "basic" result type is required to get the acidic or basic pK_a values only (also acidicpKa or basicpKa functions can be used alternatively).

Molecule Context (All)

pKa(0) returns the pK_a of atom 0 of the input molecule pKa("acidic", "2") returns the second strongest acidic pK_a value

Reaction Context (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 Plugin Group

calculates pK_a values using the correction library

the pK_a values

the atom index / MolAtom object,
the strength index as string (e.g. '1' for the strongest, '2' for the second strongest pK_a),
the result type ("acidic", "basic", or "pka" for both (default))

Note, that the strength index is specified between quotation marks.
In case of strength index the result type can be specified as "acidic" or "basic".

In case of "pka"result type the returned pK_a values are acidic or basic (mixed!), depending on the acidic or basic character of the given atom. Acidic pK_a is returned for an atom, if acidicpKa() ≤ 14.8-basicpKa(), otherwise basic pK_a is returned. Specifying "acidic" or "basic" result type is required to get the acidic or basic pK_a values only (also acidicpKaUseCorrection() or basicpKaUseCorrection() functions can be used alternatively).

Molecule Context (All)

pKaUseCorrection(0) returns the pK_a of atom 0 of the input molecule pKaUseCorrection("acidic", "2") returns the second strongest acidic pK_a value

Reaction Context (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

Geometry Plugin Group

calculates the Platt index

the Platt index

Molecule Context (All)

calculates the Platt index

Reaction Context (All)

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 0

Reaction Context (All)

radicalCount(patom(3)) returns the radical count on the product atom matching map 3 in the reaction equation

randicIndex

Geometry Plugin Group

calculates the Randic index

the Randic index

Molecule Context (All)

calculates the Randic index

Reaction Context (All)

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 data

Reaction 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

Refractivity Plugin

calculates molar refractivity

the refractivity value

Molecule Context (All)

refractivity() returns the molar refractivity of the input molecule

Reaction Context (All)

refractivity(reactant(1)) returns the molar refractivity of the second reactant

refractivityIncrements
refraci

Refractivity Plugin

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 molecule

Reaction Context (All)

refractivityIncrements(ratom(1)) returns the refractivity increment on the reactant atom matching map 1 in the reaction equation

resonant

constructs a resonant structure

the resonant structure

Molecule Context (All)

resonant(0) returns the first resonant structure of the input molecule

Reaction Context (All)

resonant(reactant(0), 1) returns the second resonant structure of the first reactant

resonantCharge

Charge Plugin Group

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 effect

Reaction 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 2 in 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 molecule

Reaction 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 array

Reaction Context (All)

resonants(reactant(0)) returns all resonants of the first reactant in an array

ringAtom

Geometry Plugin Group

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 otherwise

Reaction 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 true if the product atom matching map 1 in the reaction equation is a ring atom, false otherwise

ringAtomCount

Geometry Plugin Group

calculates the ring atom count

the ring atom count

Molecule Context (All)

ringAtomCount() returns the number of ring atoms in the input molecule

Reaction 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

Geometry Plugin Group

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 1 and 2 are connected by a ring bond the input molecule

Reaction Context (All)

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

ringBondCount

Geometry Plugin Group

calculates the ring bond count

the ring bond count

Molecule Context (All)

ringBondCount() returns the number of ring bonds in the input molecule

Reaction 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

Geometry Plugin Group

calculates the ring count

the ring count

Molecule Context (All)

ringCount() returns the number of rings in the input molecule

Reaction 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

Geometry Plugin Group

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 molecule

Reaction 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

Geometry Plugin Group

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 molecule

Reaction Context (All)

ringCountOfSize(reactant(0), 5) returns the number of rings of size 5 in the first reactant ringCountOfSize(product(1), 5) returns the number of rings of size 5 in the second product

rings

Geometry Plugin Group

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 molecule

Reaction 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

Geometry Plugin Group

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 size

Reaction 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

Geometry Plugin Group

calculates the number of rings systems

the number of rings systems

Molecule Context (All)

ringSystemCount() returns the number of ring systems in the input molecule

Reaction 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

Geometry Plugin Group

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 molecule

Reaction Context (All)

ringSystemCountOfSize(reactant(0),3) returns the number of three-membered ring systems in the first reactant ringsystemCountOfSize(product(1),3) returns the number of three-membered ring systems in the second product

ringSystems

Geometry Plugin Group

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 molecule

Reaction 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

Geometry Plugin Group

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 size

Reaction 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

Geometry Plugin Group

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 molecule

Reaction Context (All)

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

rotatableBondCount

Geometry Plugin Group

calculates the rotatable bond count

the rotatable bond count

Molecule Context (All)

rotatableBondCount() returns the number of rotatable bonds in the input molecule

Reaction 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

Geometry Plugin Group

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 molecule

Reaction 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

Charge Plugin Group

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 0 of the input molecule sigmaOrbitalElectronegativity(2, "7.4") returns the sigma orbital electronegativity of atom 2 of the major microspecies taken at pH 7.4

Reaction Context (All)

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

smallestAtomRingSize

Geometry Plugin Group

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 molecule

Reaction Context (All)

smallestAtomRingSize(ratom(1)) returns the size of the smallest ring containing reactant atom matching map 1 in the reaction equation

smallestRing

Geometry Plugin Group

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 molecule

Reaction Context (All)

smallestRingSize(product(1)) returns the atom indexes of the smallest ring in the second product

smallestRingSize

Geometry Plugin Group

calculates the smallest ring size

the smallest ring size

Molecule Context (All)

smallestRingSize() returns the size of the smallest ring in the input molecule

Reaction Context (All)

smallestRingSize(reactant(0)) returns the size of the smallest ring in the first reactant

smallestRingSystem

Geometry Plugin Group

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 molecule

Reaction Context (All)

smallestRingSize(product(1)) returns the atom indexes of the smallest ring system in the second product

smallestRingSystemSize

Geometry Plugin Group

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 molecule

Reaction 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 molecule

Reaction Context (All)

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 order

Reaction 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 order

Reaction 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

list of stereo descriptors

-
the type of stereo descriptor: atrop, axial, cistrans, tetrahedral

Molecule Context (All)

stereoAnalysis() returns the stereo descriptors of the input molecule
stereoAnalysis('tetrahedral') returns the tetrahedral stereo descriptors of the input molecule

Reaction 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

Geometry Plugin Group

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 molecule

Reaction 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 Plugin Group

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 molecule

Reaction Context (All)

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

stereoisomerCount

Isomers Plugin Group

returns the number of generated stereoisomers

the number of generated stereoisomers

Molecule Context (All)

stereoisomerCount() returns the number of generated stereoisomers of the input molecule

Reaction Context (All)

stereoisomerCount(reactant(0)) returns the number of calculated stereoisomers of the first reactant

stereoisomers

Isomers Plugin Group

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 array

Reaction Context (All)

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

stericEffectIndex

Geometry Plugin Group

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 atom

Reaction Context (All)

stericHindrance

Geometry Plugin Group

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 molecule

Reaction Context (All)

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

sum

computes the sum of array elements

the sum

integer array or real number array

General (All)

sum(array(3.4, 5.6, 1.2)) returns 10.2

Molecule Context (All)

sum(charge()) returns the sum of charge values sum(pol()) returns the sum of atom polarizability values

Reaction 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

Geometry Plugin Group

calculates the Szeged index

the Szeged index

Molecule Context (All)

calculates the Szeged index

Reaction Context (All)

tautomerCount

Isomers Plugin Group

calculates the number of tautomers

the number of tautomers

Molecule Context (All)

tautomerCount() returns the number of tautomers of the input molecule

Reaction Context (All)

tautomerCount(reactant(0)) returns the number of tautomers of the first reactant

tetrahedralStereoisomer

Isomers Plugin Group

generates a tetrahedral stereoisomer of the molecule

the tetrahedral stereoisomer

Molecule Context (All)

tetrahedralStereoisomer(0) returns the first tetrahedral stereoisomer of the input molecule

Reaction Context (All)

tetrahedralStereoisomer(reactant(0), 1) returns the second tetrahedral stereoisomer of the first reactant

tetrahedralStereoisomerCount

Isomers Plugin Group

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 molecule

Reaction Context (All)

tetrahedralStereoisomerCount(reactant(0)) returns the number of calculated tetrahedral stereoisomers of the first reactant

tetrahedralStereoisomers

Isomers Plugin Group

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 array

Reaction Context (All)

tetrahedralStereoisomers(reactant(0)) returns tetrahedral stereoisomers of the first reactant in an array

topanal

Geometry Plugin Group

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 molecule topologicalPolarSurfaceArea('7.4') returns the polar surface area of the major microspecies taken at pH 7.4

Reaction Context (All)

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

traditionalName

IUPAC Naming Plugin

returns the traditional name of the molecule

the traditional name of the molecule

Molecule Context (All)

traditionalName() returns the traditional name of the input molecule

Reaction Context (All)

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 0

Reaction Context (All)

valence(ratom(1)) returns the valence of the reactant atom matching map 1 in the reaction equation

vanDerWaalsSurfaceArea

Geometry Plugin Group

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 molecule vanDerWaalsSurfaceArea('7.4') returns the van der Waals accessible surface area of the major microspecies taken at pH 7.4

Reaction Context (All)

vanDerWaalsSurfaceArea(reactant(0)) returns the van der Waals surface area of the first reactant vanDerWaalsSurfaceArea(product(0), '7.4') returns the van der Waals surface area of the major microspecies of the first product taken at pH 7.4

waterAccessibleSurfaceArea
ASA
solventAccessibleSurfaceArea

Geometry Plugin Group

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 molecule solventAccessibleSurfaceArea('7.4')returns the solvent accessible / water accessible surface area of the major microspecies taken at pH 7.4

Reaction 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 -1 if there is no valence error in the molecule

Reaction 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

Geometry Plugin Group

calculates the Wiener index

the Wiener index

Molecule Context (All)

wienerIndex() returns the Wiener index of the input molecule

Reaction 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

Geometry Plugin Group

calculates the Wiener polarity

the Wiener polarity

Molecule Context (All)

wienerPolarity() returns the Wiener polarity of the input molecule

Reaction Context (All)

wienerPolarity(reactant(0)) returns the Wiener polarity of the first reactant wienerPolarity(product(1)) returns the Wiener polarity of the second product

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

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

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.

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).

Chemical Terms Reference Tables

Version 14.9.29.0

Contents

Function list

Appendix

Dissimilarity descriptors and metrics

Predefined Molecules and Molecule Sets

Notes