The following tables provide a summary of basic functions, structure based calculations and match functions using the built-in evaluator.xml configuration file.
Note, that 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.
Note: match, matchCount, disjointMatchCount and dissimilarity
functions are not available in Marvin, they can be used only if JChem software package is installed.
You can switch between corresponding descriptions and examples by clicking on the built-in names.
| Built-in name | Description | Return value | Parameters |
|---|---|---|---|
| abs | returns the absolute value of a number | the absolute value | integer or real number |
| array | constructs an integer array from its arguments | the integer array | integers or MolAtom objects |
| min max |
takes minimum / maximum of its array and/or numerical parameters | the minimum / maximum value | integers, real numbers, integer arrays, real number arrays |
| sum | computes the sum of array elements | the sum | integer array or real number array |
| count | determines the number of elements in an array | the number of array elements | integer array or real number array |
| sortAsc sortDesc |
sorts an array in ascending / descending order | the sorted array | integer array or real number array |
| formalCharge hCount connections valence radicalCount atno map arom |
|
various atomic properties | atom index or MolAtom object |
| field / property | returns a molecule property (SDF field value) | the molecule property | the property key (SDF field name) |
| 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 |
| 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) |
| minAtom maxAtom |
evaluates objective function for each atom, finds smallest / largest value(s) | the atom index / indices corresponding to the smallest / 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 smallest / largest values to be taken (optional, takes only one if omitted) |
| minValue maxValue |
evaluates objective function for each atom, finds smallest / largest value(s) | the smallest / 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 smallest / largest values to be taken (optional, takes only one if omitted) |
| 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 |
| dissimilarity | computes the dissimilarity value between two molecules
Note: Dissimilarity function is available only in JChem. |
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) |
| Built-in name | General example | Molecule context example | Reaction context example |
|---|---|---|---|
| abs | abs(7)returns 7abs(-4.9)returns 4.9 |
abs(7)returns 7abs(-4.9)returns 4.9 |
abs(7)returns 7abs(-4.9)returns 4.9 |
| array | array(2, 5, 6, 8) |
array(2, 5, 6, 8) |
array(ratom(2), ratom(5), ratom(6), ratom(8)) array(patom(2), patom(5), patom(6), patom(8)) |
| min max |
min(2, 8, 6)returns 2 max(3.4, 5.6, 1.2)returns 5.6 |
min(charge(0), charge(2))returns the least of the partial charge values on atoms 0
and 2 max(charge())returns the maximal partial charge value on the input molecule |
min(charge(ratom(2)), charge(ratom(3)))returns the least of the partial charge values on reactant atoms matching maps 2 and 3 in the reaction equation max(charge(product(0)))returns the maximal partial charge value on the first product |
| sum | sum(array(3.4, 5.6, 1.2))returns 10.2 |
sum(charge())returns the sum of charge values sum(pol())returns the sum of atom polarizability values |
sum(charge(reactant(0)))returns the sum of charge values in the first reactant sum(pol(product(0)))returns the sum of atom polarizability values in the first product |
| count | count(array(3.4, 5.6, 1.2))returns 3 |
count(filter("charge() > 0")) returns the number of atoms with positive charge count(filter("match('[#8][C:1]=O', 1"))
returns the number of carboxylic carbons |
count(filter(reactant(1), "charge() > 0"))returns the number of atoms with positive charge in the second reactant count(filter(product(0), "match('[#8][C:1]=O', 1")) returns the number of carboxylic
carbons in the first product |
| sortAsc sortDesc |
sortAsc(array(3.4, 5.6, 1.2))returns array(1.2, 3.4, 5.6) |
sortAsc(charge())returns the partial charge values in ascending order sortDesc(pka("basic"))
returns the basic pKa values in descending order |
sortAsc(charge(reactant(1)))returns the partial charge values of the second reactant in ascending order sortDesc(pka(product(0), "basic"))returns the basic pKa values of the first product in descending order |
| formalCharge hCount connections valence radicalCount atno map arom |
formalCharge(0)returns the formal charge of atom 0 map(3)returns the atom map number of atom 3 connections(2)returns the number of connections of atom 2
valence(0)returns the valence of atom 0
radicalCount(1)returns the radical count of atom 1 |
atno(ratom(1))returns the atomic number of the reactant atom matching map 1 in the
reaction equation hCount(patom(3))returns the hydrogen count on the product atom matching map 3
in the reaction equation arom(patom(2))returns true if the product atom matching map 2
in the reaction equation has an aromatic bond |
|
| field / property | field('ACTIVITY') returns the value of the ACTIVITY property (SDF field) field('ACTIVITY') > 2
returns 1 if the ACTIVITY value is bigger than 2, returns 0 otherwise |
field(reactant(1), 'ACTIVITY')returns the ACTIVITY property value of the second reactant field(product(0), 'ACTIVITY') > field(reactant(0), 'ACTIVITY')returns 1 if the ACTIVITY value of the first product is bigger than that of the first reactant, returns 0
otherwise |
|
| in | in(5, array(3, 5, 1))returns true in(2, array(3, 5, 1))returns false |
in(3, maxatom("charge()", 2)) returns true if the partial charge on atom 3
is within the first 2 largest partial charges in the input molecule in(3, minatom("pol()", 4))
returns true if the polarizability on atom 3 is within the first 4 smallest
polarizability values in the input molecule |
in(ratom(3), maxatom(reactant(0), "charge()", 2))returns true if the partial charge
on reactant atom matching map 3 in the reaction equation is within the first 2 largest
partial charges in the first reactant in(patom(1), minatom(product(1), "pol()", 4))returns true
if the polarizability on product atom matching map 1 in the reaction equation is within the first 4
smallest polarizability values in the second product |
| filter | filter("charge() > 0") returns the indices of atoms with positive partial charge in the input
molecule filter(6, 7, 8, 9, "match('[#8][C:1]=O', 1)") returns the carboxylic carbons out of atoms 6,
7, 8, 9 in the input molecule |
filter(reactant(0), "charge() > 0")returns the indices of atoms with positive partial charge in the first reactant filter(patom(1), patom(2), "match('[#8][C:1]=O', 1)") returns the carboxylic carbons out
of product atoms matching map 1 or 2 in the reaction equation (note, that these atoms are
supposed to be in the same product molecule) |
|
| minAtom maxAtom |
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 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 |
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 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) |
|
| minValue maxValue |
minValue("charge('7.4')") returns the minimum partial charge in the major microspecies at pH 7.4
of the input molecule 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 |
minValue(reactant(0), "charge('7.4')") returns the minimum partial charge in the major
microspecies at pH 7.4 of the first reactant 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) |
|
| pair / bond | pair(2, 5)returns "3-6" |
pair(ratom(1), ratom(2))returns "index1-index2" where "index1" and "index2" are the 1-based atom indexes of the reactant atoms matching map 1 and 2 in the reaction equation bond(patom(2), patom(5)returns "index1-index2" where "index1" and "index2" are the 1-based atom indexes of the product atoms matching map 2
and 5 in the reaction equation |
|
| dissimilarity | dissimilarity("PF", "c1ccccc1", "C1CCCCC1") returns the dissimilarity value between the benzene
ring and cyclohexane, computed with pharmacophore fingerprint and its default metric (Tanimoto) dissimilarity("c1ccccc1", "C1CCCCC1")
returns the dissimilarity value between the benzene ring and cyclohexane, computed with default fingerprint and its
default metric (chemical fingerprint with Tanimoto) |
dissimilarity("PF:Euclidean", "c1ccccc1") returns the dissimilarity value between the benzene ring
and the input molecule, computed with pharmacophore fingerprint and euclidean metric dissimilarity("LogD", "c1ccccc1")
returns the dissimilarity value between the benzene ring and the input molecule, computed with the LogD descriptor and
its default AbsDiff metric |
dissimilarity("CF:Euclidean", "c1ccccc1", reactant(0)) returns the dissimilarity value between the
benzene ring and the first reactant, computed with chemical fingerprint and euclidean metric dissimilarity(reactant(0), product(0))returns the dissimilarity value between the first reactant and the first product, computed with default fingerprint and its default metric (chemical fingerprint with Tanimoto) |
| Descriptor | Metric |
|---|---|
| ChemicalFingerprint (or CF) | Tanimoto (default) Euclidean |
| PharmacophoreFingerprint (or PF) | Tanimoto (default) Euclidean |
| Burden eigenvalue descriptor (or BCUTTM) (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 |
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).
| Built-in name | Description | Return Value | Parameters |
|---|---|---|---|
| majorMicrospecies majorMs |
calculates major microspecies at specified pH | the major microspecies |
|
| microspeciesCount msCount |
calculates the number of microspecies at specified pH | the number of microspecies | - |
| microspecies ms |
calculates microspecies at specified pH | the microspecies |
|
| microspeciesDistribution msDistr |
calculates microspecies distribution at specified pH | the microspecies distribution |
|
| tautomer | constructs a tautomeric form | the tautomer |
|
| tautomers | constructs all tautomeric forms | the tautomer array | - |
| tautomerCount | calculates the number of tautomers | the number of tautomers | - |
| dominantTautomer | returns the i-th dominant tautomeric form | the i-th dominant tautomer |
|
| dominantTautomers | constructs all dominant tautomeric forms | the dominant tautomer array |
|
| dominantTautomerCount | calculates the number of dominant tautomers | the number of dominant tautomers |
|
| canonicalTautomer | constructs the canonical tautomer structure | the canonical tautomer structure | - |
| genericTautomer | constructs the generic tautomer structure | the generic tautomer structure | - |
| mostStableTautomer | constructs the most stable tautomer structure | the most stable tautomer structure | - |
| resonantCount | calculates the number of resonant structures | the number of resonant structures | - |
| resonant | constructs a resonant structure | the resonant structure | - |
| canonicalResonant | constructs the canonical resonant structure | the canonical resonant structure | - |
| resonants | constructs all resonant structures | the resonant structure array | - |
| markushEnumerationCount | calculates the number of Markush enumerations | the number of Markush enumerations |
|
| randomMarkushEnumerations | constructs Markush enumerated structures randomly | the enumerated structures |
|
| randomMarkushEnumerationsDisplay | 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 |
|
| markushEnumerations | constructs Markush enumerated structures sequentially | the enumerated structures |
|
| markushEnumerationsDisplay | 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 |
|
| charge | 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 |
|
| resonantCharge | 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 |
|
| formalCahrge / totalCharge | calculates formal charge of molecule | the formal charge value | - |
| sigmaOrbitalElectronegativity sOEN |
calculates atomic sigma orbital electronegativity | the sigma orbital electronegativity values |
|
| piOrbitalElectronegativity pOEN |
calculates atomic pi orbital electronegativity | the pi orbital electronegativity values |
|
| atomicPolarizability polarizability pol atomPol |
calculates atomic polarizability | the polarizability values |
|
| molecularPolarizability molPol |
calculates molecular polarizability | the polarizability value |
|
| averagePolarizability averagePol avgPol |
calculates average molecular polarizability component considering 3D geometry | the polarizability value |
|
| axxPol ayyPol azzPol |
calculates principal component of polarizability tensor (a(xx), a(yy), a(zz)) |
the principal component of polarizability tensor |
|
| pKa | calculates pKa values | the pKa values |
In case of "pka"result type the returned pKa values are acidic or basic (mixed!), depending on the acidic or basic character of the given atom. Acidic pKa is returned for an atom, if acidicpKa() &le 14.8-basicpKa(), otherwise basic pKa is returned. Specifying "acidic" or "basic" result type is required to get the acidic or basic pKa values only (also acidicpKa or basicpKa functions can be used alternatively). |
| acidicpKa apKa |
calculates acidic pKa values | the acidic pKa values |
|
| basicpKa bpKa |
calculates basic pKa values | the basic pKa values |
|
| acidicpKaLargeModel | calculates acidic pKa values using large model (this model is optimized for a large number of ionizable atoms) | the acidic pKa values |
|
| basicpKaLargeModel | calculates basic pKa values using large model (this model is optimized for a large number of ionizable atoms) | the basic pKa values |
|
| logD
(logDVG, logDKLOP, logDPHYS, logDUser, logDWeighted refer to logD functions that use "VG", "KLOP", "PHYS", "user defined", and "weighted" methods) |
calculates logD at specified pH | the logD value |
|
| logP
(logPVG, logPKLOP, logPPHYS, logPUser, logPWeighted refer to logP functions that use "VG", "KLOP", "PHYS", "user defined", and "weighted" methods) |
calculates logP | the logP value |
|
| logPincrement logPi |
calculates the atomic logP increment | the atomic logP increment |
|
| solubility logS |
calculates solubility at specified pH | the logS value |
|
| solubilityAtIsoelectricPoint logSTrue |
calculates solubility at isoelectric point | the logS value | - |
| solubilityOfMicroSpecies logSMicro |
calculates solubility of the submitted microspecies | the logS value | - |
| solubilityOfNeutral logSNeutral |
calculates solubility of the neutral species | the logS value | - |
| electrophilicityOrder orderE |
calculates E(+) order of atoms | the E(+) order index of the atom ( 0, 1, 2, ...), |
|
| nucleophilicityOrder orderNu |
calculates Nu(-) order of atoms | the Nu(-) order index of the atom ( 0, 1, 2, ...), |
|
| electrophilicLocalizationEnergy energyE |
calculates localization energy L(+) of atoms | the localization energy L(+) of the atom,NaN for non-aromatic atoms |
|
| nucleophilicLocalizationEnergy energyNu |
calculates localization energy L(-) of atoms | the localization energy L(-) of the atom,NaN for non-aromatic atoms |
|
| piEnergy | calculates the pi energy of the molecule | the pi energy of the molecule |
|
| electronDensity piChargeDensity |
calculates the electron density of atoms | the electron density of the atom,NaN for non-existing values |
|
| chargeDensity totalChargeDensity |
calculates the charge density of atoms | the charge density of the atom,NaN for non-existing values |
|
| topologicalPolarSurfaceArea PSA |
calculates the topological polar surface area (2D) | the polar surface area (2D) |
|
| vanDerWaalsSurfaceArea | calculates the van der Waals surface area | the molecular surface area |
|
| solventAccessibleSurfaceArea / waterAccessibleSurfaceArea / ASA | calculates the solvent accessible / water accessible molecular surface area | the molecular surface area |
|
| ASAPlus | calculates the water accessible molecular surface area of all atoms with positive partial charge | the molecular surface area |
|
| ASANegative | calculates the water accessible molecular surface area of all atoms with negative partial charge | the molecular surface area |
|
| ASAPolar | calculates the water accessible molecular surface area of all polar atoms | the molecular surface area |
|
| ASAHydrophobic | calculates the water accessible molecular surface area of all hydrophobic atoms | the molecular surface area |
|
| mass / exactMass | calculates the molecule mass / exactmass | the mass / exactmass | - |
| formula | returns the formula | the formula | - |
| isotopeFormula | returns the isotope formula | the isotope formula | - |
| dotDisconnectedFormula | returns the dot-disconnected formula | the dot-disconnected formula | - |
| dotDisconnectedIsotopeFormula | returns the dot-disconnected isotope formula | the dot-disconnected isotope formula | - |
| composition | returns the composition | the composition | - |
| isotopeComposition | returns the isotope composition | the isotope composition | - |
| atomCount | calculates the number of atoms (all atoms or specific atoms) | the atom count |
|
| aliphaticAtomCount | calculates the aliphatic atom count | the aliphatic atom count | - |
| aromaticAtomCount | calculates the aromatic atom count | the aromatic atom count | - |
| bondCount | calculates the bond count | the bond count | - |
| aliphaticBondCount | calculates the aliphatic bond count | the aliphatic bond count | - |
| aromaticBondCount | calculates the aromatic bond count | the aromatic bond count | - |
| rotatableBondCount | calculates the rotatable bond count | the rotatable bond count | - |
| fragments | converts the molecule to its disconnected fragments | the disconnected fragments of the molecule | - |
| fragmentCount | returns the number of fragments (disconnected parts) | the fragment count | - |
| ringCount | calculates the ring count | the ring count | - |
| ringCountOfSize | calculates the number of rings of given size | the number of rings of given size | the ring size |
| aliphaticRingCount | calculates the aliphatic ring count | the aliphatic ring count | - |
| aliphaticRingCountOfSize | calculates the number of aliphatic rings of given size | the number of aliphatic rings of given size | the ring size |
| aromaticRingCount | calculates the aromatic ring count | the aromatic ring count | - |
| aromaticRingCountOfSize | calculates the number of aromatic rings of given size | the number of aromatic rings of given size | the ring size |
| heteroRingCount | calculates the hetero ring count | the hetero ring count | - |
| heteroaromaticRingCount | calculates the heteroaromatic ring count | the heteroaromatic ring count | - |
| carboRingCount | calculates the carbo ring count | the carbo ring count | - |
| carboaromaticRingCount | calculates the carboaromatic ring count | the carboaromatic ring count | - |
| ringAtomCount | calculates the ring atom count | the ring atom count | - |
| ringBondCount | calculates the ring bond count | the ring bond count | - |
| chainAtomCount | calculates the chain atom count | the chain atom count | - |
| chainBondCount | calculates the chain bond count | the chain bond count | - |
| smallestRingSize / largestRingSize | calculates the smallest / largest ring size | the smallest / largest ring size | - |
| fusedRingCount | calculates the number of fused rings (SSSR smallest set of smallest rings) |
the fused ring count | - |
| fusedAliphaticRingCount | calculates the number of fused aliphatic rings (SSSR smallest set of smallest aliphatic rings) |
the fused aliphatic ring count | - |
| fusedAromaticRingCount | calculates the number of fused aromatic rings (SSSR smallest set of smallest aromatic rings) |
the fused aromatic ring count | - |
| ringSystemCount | calculates the number of rings systems | the number of rings systems | - |
| ringSystemCountOfSize | calculates the number of rings systems of given size | the number of rings systems of given size | the ring system size |
| smallestRingSystemSize | calculates the size of the smallest ring system (number of rings) | the size of the smallest ring system | - |
| largestRingSystemSize | calculates the size of the largest ring system (number of rings) | the size of the largest ring system | - |
| asymmetricAtomCount | calculates the number of asymmetric atoms | the asymmetric atom count | - |
| chiralCenterCount | calculates the number of tetrahedral stereogenic center atoms | the tetrahedral stereogenic center count | - |
| aromaticAtom | checks if the specified atom is aromatic | true for aromatic atoms,false for non-aromatic atoms |
|
| aliphaticAtom | checks if the specified atom is aliphatic | true for aliphatic atoms,false for non-aliphatic atoms |
|
| chainAtom | checks if the specified atom is a chain atom | true for chain atoms,false for non-chain atoms |
|
| ringAtom | checks if the specified atom is a ring atom | true for ring atoms,false for non-ring atoms |
|
| asymmetricAtom | checks if the specified atom is an asymmetric atom | true for asymmetric atoms,false for symmetric atoms |
|
| chiralCenter | checks if the specified atom is a tetrahedral stereogenic center | true for tetrahedral stereogenic center atoms |
|
| cyclomaticNumber | calculates the cyclomatic number | the cyclomatic number | - |
| plattIndex | calculates the Platt index | the Platt index | - |
| randicIndex | calculates the Randic index | the Randic index | - |
| balabanIndex | calculates the Balaban index | the Balaban index | - |
| distanceDegree | calculates the distance degree of an atom | the distance degree |
|
| eccentricity | calculates the eccentricity of an atom | the eccentricity of an atom |
|
| hararyIndex | calculates the Harary index | the Harary index | - |
| hyperWienerIndex | calculates the Hyper Wiener index | the Hyper Wiener index | - |
| szegedIndex | calculates the Szeged index | the Szeged index | - |
| wienerIndex | calculates the Wiener index | the Wiener index | - |
| wienerPolarity | calculates the Wiener polarity | the Wiener polarity | - |
| stericEffectIndex | calculates the steric effect index of an atom | the steric effect index of an atom |
|
| smallestAtomRingSize / largestAtomRingSize | calculates the size of the smallest / largest ring containing the specified atom | the size of the smallest / largest ring containing the specified atom |
|
| shortestPath | calculates the length of the shortest path between two atoms | the length of the shortest path between two atoms, Integer.MAX_VALUE if disconnected |
|
| connected | checks if two atoms are connected | true if the two atoms belong to the same connected component, false otherwise |
|
| connectedGraph | checks whether the molecule graph is connected | true if the molecule graph is connected, false otherwise |
- |
| bondType | returns the bond type between two atoms | the bond type between two atoms, -1 if there is no bond between the two atoms |
|
| chainBond | checks if two atoms are connected by a chain bond | true if the two atoms are connected by a chain bond, false otherwise |
|
| ringBond | checks if two atoms are connected by a ring bond | true if the two atoms are connected by a ring bond, false otherwise |
|
| rotatableBond | checks if two atoms are connected by a rotatable bond | true if the two atoms are connected by a rotatable bond, false otherwise |
|
| ringCountOfAtom | calculates the number of rings passing through an atom | the number of rings passing through an atom |
|
| hasValenceError() | determines if any atom in the molecule has valence error | true in case of valence error, false otherwise | - |
| hasRadical() | determines if any atom in the molecule has radical | true if any atom in the molecule has radical, 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 |
- |
| acceptor / donor acc / don |
calculates atomic hydrogen bond acceptor / donor multiplicity | the atomic hydrogen bond acceptor / donor multiplicity |
|
| acceptorSiteCount / donorSiteCount accSiteCount / donSiteCount |
calculates molecular hydrogen bond acceptor / donor multiplicity (the sum of atomic multiplicities) | the molecular hydrogen bond acceptor / donor multiplicity |
|
| acceptorCount / donorCount | calculates molecular hydrogen bond acceptor / donor count (the number of acceptor / donor atoms) | the molecular hydrogen bond acceptor / donor count |
|
| refractivity refrac |
calculates molar refractivity | the refractivity value | - |
| refractivityIncrements refraci |
calculates atomic refractivity increments | the atomic refractivity increment |
|
| isoelectricPoint pI |
calculates isoelectric point | the isoelectric point | - |
| stereoisomerCount | returns the number of generated stereoisomers | the number of generated stereoisomers |
|
| stereoisomer | generates a stereoisomer of the molecule | the stereoisomer |
|
| stereoisomers | generates stereoisomers of the molecule (maximum number of stereoisomers to be generated can be set, default: all) | the stereoisomer array |
|
| doubleBondStereoisomerCount | returns the number of generated double bond stereoisomers | the number of generated double bond stereoisomers |
|
| doubleBondStereoisomer | generates a double bond stereoisomer of the molecule | the double bond stereoisomer |
|
| doubleBondStereoisomers | 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 |
|
| tetrahedralStereoisomerCount | returns the number of generated tetrahedral stereoisomers | the number of generated tetrahedral stereoisomers |
|
| tetrahedralStereoisomer | generates a tetrahedral stereoisomer of the molecule | the tetrahedral stereoisomer |
|
| tetrahedralStereoisomers | generates tetrahedral stereoisomers of the molecule (maximum number of tetrahedral stereoisomers to be generated can be set, default: all) | the tetrahedral stereoisomer array |
|
| conformerCount | returns the number of calculated conformers | the number of calculated conformers |
|
| conformer | calculates a conformer of the molecule | the conformer |
|
| conformers | calculates conformers of the molecule (maximum number of conformers to be calculated can be set, default: 100) | the conformer array |
|
| lowestEnergyConformer leconformer |
calculates the lowest energy conformer of the molecule | the lowest energy conformer | - |
| hasValidConformer | returns true if the input molecule exist in 3D space (has a valid conformer) | true if the input molecule exist in 3D space | - |
| dreidingEnergy | returns the Dreiding energy of the input molecule (conformer) | the dreiding energy | - |
| minimalProjectionArea | returns the minimal projection area | the minimal projection area | - |
| maximalProjectionArea | returns the maximal projection area | the maximal projection area | - |
| minimalProjectionRadius | returns the minimal projection radius | the minimal projection radius | - |
| maximalProjectionRadius | returns the maximal projection radius | the maximal projection radius | - |
| distance | calculates the distance between two atoms | the distance between two atoms |
|
| angle | calculates the angle between three atoms | the angle between three atoms |
|
| dihedral | calculates the dihedral of four atoms | the dihedral of four atoms |
|
| stericHindrance | calculates the steric hindrance of an atom | the steric hindrance of an atom |
|
| name | returns the preferred IUPAC name of the molecule | the preferred IUPAC name of the molecule | - |
| traditionalName | returns the traditional name of the molecule | the traditional name of the molecule | - |
| molFormat molString |
returns the string representation of the molecule in specified molecule format | the string representation of the molecule |
|
| 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 |
|
| bmf | Returns the Bemis-Murcko framework of the input structure | BMF of the input structure | - |
| Built-in name | Molecule Context Example | Reaction Context Example |
|---|---|---|
| majorMicrospecies majorMs |
majorMicrospecies("7.4") returns the major microspecies of the input molecule at pH 7.4 |
majorMicrospecies(reactant(0), "7.4")returns the major microspecies of the first reactant at pH 7.4
majorMicrospecies(product(1), "7.4")returns the major microspecies of the second product at pH 7.4 |
| microspeciesCount msCount |
microspeciesCount()returns the number of microspecies of the input molecule |
microspeciesCount(reactant(0))returns the number of microspecies of the first reactant microspeciesCount(product(1))returns the number of microspecies of the second product |
| microspecies ms |
microspecies("7.4", 1) returns the microspecies of the input molecule with second largest distribution at pH
7.4 |
microspecies(reactant(0), "7.4", 2)returns the microspecies of the first reactant with third largest distribution at pH 7.4 microspecies(product(1), "7.4", 1)returns the microspecies of the second product with second largest distribution at pH 7.4 |
| microspeciesDistribution msDistr |
microspeciesDistribution("5.4", 0) returns the largest microspecies distribution of the input molecule at pH 5.4 |
microspeciesDistribution(reactant(0), "5.4", 2)returns the third largest microspecies distribution of the first reactant at pH 5.4 microspeciesDistribution(product(1), "3.2", 1)returns the second largest microspecies distribution of the second product at pH 3.2 |
| tautomer | tautomer(0)returns the first tautomer of the input molecule |
tautomer(reactant(0), 1)returns the second tautomer of the first reactant |
| tautomers | tautomers()returns all tautomers of the input molecule in an array |
tautomers(reactant(0))returns all tautomers of the first reactant in an array |
| tautomerCount | tautomerCount()returns the number of tautomers of the input molecule |
tautomerCount(reactant(0))returns the number of tautomers of the first reactant |
| dominantTautomer | dominantTautomer(0)returns the first dominant tautomer of the input molecule dominantTautomer(1, "2.0")returns the second dominant tautomer of the input molecule, considering pH effect at pH 2.0 |
dominantTautomer(reactant(0), 1)returns the second dominant tautomer of the first reactant dominantTautomer(product(1), 0, "7.4")returns the first dominant tautomer of the second product, considering pH effect at pH 7.4 |
| dominantTautomers | dominantTautomers()returns all dominant tautomers of the input molecule in an array dominantTautomers("2.0")
returns all dominant tautomers of the input molecule in an array, considering pH effect at pH 2.0 |
dominantTautomers(reactant(0))returns all dominant tautomers of the first reactant in an array dominantTautomers(product(1), "7.4")returns all dominant tautomers of the second product in an array, considering pH effect at pH 7.4 |
| dominantTautomerCount | dominantTautomerCount()returns the number of dominant tautomers of the input molecule dominantTautomerCount("7.4")
returns the number of dominant tautomers of the input molecule, considering pH effect at pH 7.4 |
dominantTautomerCount(reactant(0))returns the number of dominant tautomers of the first reactant dominantTautomerCount(product(1), "2.5")returns the number of dominant tautomers of the second product, considering pH effect at pH 2.5 |
| canonicalTautomer | canonicalTautomer()returns the canonical tautomer structure of the input molecule |
canonicalTautomer(reactant(0))returns the canonical tautomer structure of the first reactant/td> |
| genericTautomer | genericTautomer()returns the generic tautomer structure of the input molecule |
genericTautomer(reactant(0))returns the generic tautomer structure of the first reactant/td> |
| mostStableTautomer | mostStableTautomer()returns the most stable tautomer structure of the input molecule |
mostStableTautomer(reactant(0))returns the most stable tautomer structure of the first reactant/td> |
| resonantCount | resonantCount()returns the number of resonant structures of the input molecule |
resonantCount(reactant(0))returns the number of resonant structures of the first reactant |
| resonant | resonant(0)returns the first resonant structure of the input molecule |
resonant(reactant(0), 1)returns the second resonant structure of the first reactant |
| canonicalResonant | canonicalResonant()returns the canonical resonant structure of the input molecule |
canonicalResonant(reactant(0))returns the canonical resonant structure of the first reactant |
| resonants | resonants()returns all resonants of the input molecule in an array |
resonants(reactant(0))returns all resonants of the first reactant in an array |
| markushEnumerationCount | markushEnumerationCount()returns the number of Markush enumerated structures of the input molecule markushEnumerationCount('4,5')
returns the number of Markush enumerated structures of the input molecule, enumerating only atoms 4, 5 (1-based) |
markushEnumerationCount(reactant(0))returns the number of Markush enumerated structures of the first reactant markushEnumerationCount(product(1), atoms(3,4))returns the number of Markush enumerated structures of the second product, enumerating only atoms 4, 5 (1-based) (the atoms() function converts 0-based indexes to a '-'-separated 1-based atom index string) |
| randomMarkushEnumerations | randomMarkushEnumerations()returns a randomly constructed enumerated structure of the input molecule randomMarkushEnumerations(4, '2,3')returns 4 randomly constructed enumerated structures of the input molecule, enumerating only atoms 2, 3 (1-based) |
randomMarkushEnumerations(reactant(0), 100)returns 100 randomly constructed enumerated structures of the first reactant randomMarkushEnumerations(product(1), '3,4,5')returns a randomly constructed enumerated structure of the second product, enumerating atoms 3, 4, 5 (1-based) |
| randomMarkushEnumerationsDisplay | randomMarkushEnumerationsDisplay()returns a randomly constructed enumerated structure of the input molecule, with scaffold alignment and scaffold/R-group coloring data randomMarkushEnumerationsDisplay(4, '2,3')returns 4 randomly constructed enumerated structures of the input molecule, enumerating only atoms 2, 3 (1-based), with scaffold alignment and coloring data |
randomMarkushEnumerationsDisplay(reactant(0), 100)returns 100 randomly constructed enumerated structures of the first reactant, with scaffold alignment and coloring data randomMarkushEnumerationsDisplay(product(1), '3,4,5')returns a randomly constructed enumerated structure of the second product, enumerating atoms 3, 4, 5 (1-based), with scaffold alignment and coloring data |
| markushEnumerations | markushEnumerations()returns all Markush enumerated structures of the input molecule markushEnumerations(1, '2,3')returns one Markush enumerated structure of the input molecule, enumerating atoms 2, 3 (1-based) |
markushEnumerations(reactant(0), 1)returns one Markush enumerated structure of the first reactant markushEnumerations(product(1), 2, '2,3')returns two Markush enumerated structures of the second product, enumerating atoms 2, 3 (1-based) |
| markushEnumerationsDisplay | markushEnumerationsDisplay()returns all Markush enumerated structures of the input molecule, with scaffold alignment and coloring data markushEnumerationsDisplay(1, '2,3')returns one Markush enumerated structure of the input molecule, enumerating atoms 2, 3 (1-based), with scaffold alignment and coloring data |
markushEnumerationsDisplay(reactant(0), 1)returns one Markush enumerated structure of the first reactant, with scaffold alignment and coloring data with scaffold alignment and coloring data markushEnumerationsDisplay(product(1), 2, '2,3')returns two Markush enumerated structures of the second product, enumerating atoms 2, 3 (1-based), with scaffold alignment and coloring data |
| charge | charge(0)returns the partial charge on atom 0 of the input molecule charge(2, "pi", "7.4")returns the partial "pi" charge on atom 2 of the major microspecies taken at pH 7.4 |
charge(ratom(1), "aromaticsystem")returns the sum of partial pi charges in the aromatic system containing the reactant atom matching map 1 in the reaction equation charge(patom(2), "aromaticring", "7.4")returns the sum of partial charges in the smallest aromatic ring containing the product atom matching map 2
in the major microspecies taken at pH 7.4 |
| resonantCharge | resonantCharge(0)returns the partial charge on atom 0 of the input molecule considering resonance effectresonantCharge(2, "pi", "7.4")returns the partial "pi" charge on atom 2 of the major microspecies taken at pH 7.4 considering resonance effect |
resonantCharge(ratom(1), "aromaticsystem")returns the sum of partial pi charges in the aromatic system containing the reactant atom matching map 1 in the reaction equation considering resonance effectresonantCharge(patom(2), "aromaticring", "7.4")returns the sum of partial charges in the smallest aromatic ring containing the product atom matching map 2
in the major microspecies taken at pH 7.4 considering resonance effect |
| formalCharge / totalCharge | formalCharge()returns the formal charge of the input molecule formalCharge(majorms("7.4"))
returns the formal charge of the major microspecies of the input molecule at pH 7.4 |
formalCharge(reactant(0))returns the formal charge of the first reactant formalCharge(majorms(product(1), "7.4"))returns the formal charge of the major microspecies of the second product at pH 7.4 |
| sigmaOrbitalElectronegativity sOEN |
sigmaOrbitalElectronegativity(0)returns the sigma orbital electronegativity of atom 0
of the input molecule sigmaOrbitalElectronegativity(2, "7.4")returns the sigma orbital electronegativity of atom 2 of the major microspecies taken at pH 7.4 |
sOEN(ratom(1))returns the sigma orbital electronegativity of reactant atom matching map 1
in the reaction equation sOEN(patom(2), "7.4")returns the sigma orbital electronegativity of the product atom matching map 2 of the major microspecies taken at pH 7.4 |
| piOrbitalElectronegativity sOEN |
piOrbitalElectronegativity(0)returns the pi orbital electronegativity of atom 0 of
the input molecule piOrbitalElectronegativity(2, "7.4")returns the pi orbital electronegativity of atom 2
of the major microspecies taken at pH 7.4 |
pOEN(ratom(1))returns the pi orbital electronegativity of reactant atom matching map 1
in the reaction equation pOEN(patom(2), "7.4")returns the pi orbital electronegativity of the product atom matching map 2 of the major microspecies taken at pH 7.4 |
| atomicPolarizability polarizability pol atomPol |
atomicPolarizability(0)returns the polarizability of atom 0 of the input molecule atomicPolarizability(2, "7.4")returns the polarizability of atom 2 of the major microspecies taken at pH 7.4 |
atomicPolarizability(ratom(1))returns the polarizability of reactant atom matching map 1 in the
reaction equation atomicPolarizability(patom(2), "7.4")returns the polarizability of the product atom matching map 2
of the major microspecies taken at pH 7.4 |
| molecularPolarizability molPol |
molecularPolarizability()returns the molecular polarizability of the input molecule molecularPolarizability("7.4")
returns the molecular polarizability of the major microspecies taken at pH 7.4 |
molecularPolarizability(reactant(1))returns the molecular polarizability of the second reactant in the reaction equation molecularPolarizability(product(0), "7.4")returns the molecular polarizability of the first product major microspecies taken at pH 7.4 |
| averagePolarizability averagePol avgPol |
averagePolarizability()returns the average polarizability component of the input molecule averagePolarizability("7.4")
returns the average polarizability component of the major microspecies taken at pH 7.4 |
averagePolarizability(reactant(1))returns the average polarizability component of the second reactant in the reaction equation averagePolarizability(product(0), "7.4")returns the average polarizability component of the first product major microspecies taken at pH 7.4 |
| axxPol ayyPol azzPol |
axxPol()returns the principal component a(xx) 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 |
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 |
| pKa | pKa(0)returns the pKa of atom 0 of the input molecule pKa("acidic", "2")
returns the second strongest acidic pKa value |
pKa(ratom(1))returns the pKa of reactant atom matching map 1 in
the reaction equation pKa(product(0), "basic", "1")returns the strongest basic pKa value in the first product |
| acidicpKa() apKa |
acidicpKa(0)returns the acidic pKa of atom 0 of the input molecule acidicpKa("2")
returns the second strongest acidic pKa value |
acidicpKa(ratom(1))returns the acidic pKa of reactant atom matching map 1
in the reaction equation acidicpKa(product(0), "1")returns the strongest basic pKa value in the first product |
| basicpKa bpKa |
basicpKa(0)returns the basic pKa of atom 0 of the input molecule
basicpKa("2") returns the second strongest basic pKa value |
basicpKa(ratom(1))returns the basic pKa of reactant atom matching map 1
in the reaction equation basicpKa(product(0), "1")returns the strongest basic pKa value in the first product |
| acidicpKaLargeModel | acidicpKaLargeModel(0)returns the acidic pKa of atom 0 of the input molecule
acidicpKaLargeModel("2") returns the second strongest acidic pKa value |
acidicpKaLargeModel(ratom(1))returns the acidic pKa of reactant atom matching map 1
in the reaction equation acidicpKaLargeModel(product(0), "1")returns the strongest basic pKa value in the first product |
| basicpKaLargeModel | basicpKaLargeModel(0)returns the basic pKa of atom 0 of the input molecule
basicpKaLargeModel("2") returns the second strongest basic pKa value |
basicpKaLargeModel(ratom(1))returns the basic pKa of reactant atom matching map 1
in the reaction equation basicpKaLargeModel(product(0), "1")returns the strongest basic pKa value in the first product |
| logD
(logDVG, logDKLOP, logDPHYS, logDUser, logDWeighted refer to logD functions that use "VG", "KLOP", "PHYS", "user defined", and "weighted" methods) |
logD('7.4') returns the logD at pH 7.4 of the input molecule |
logD(reactant(1), '7.4')returns the logD at pH 7.4 of the second reactant |
| logP
(logPVG, logPKLOP, logPPHYS, logPUser, logPWeighted refer to logP functions that use "VG", "KLOP", "PHYS", "user defined", and "weighted" methods) |
logP()returns the most typical logP out of the input molecule logP, the logP of the nonionic species and logD at pI logP('logPMicro') returns the logP of the input
molecule itself |
logP(reactant(1), 'logDpI')returns the logD at pI of the second reactant logP(product(1), 'logPNonionic')returns logP of the nonionic species of the second product |
| logPincrement logPi |
logPincrement(2)returns the logP increment on atom 2 of the input molecule |
logPincrement(ratom(1))returns the logP increment on the reactant atom matching map 1
in the reaction equation |
| solubility logS |
solubility('7.4') returns the logS at pH 7.4 of the input molecule |
solubility(reactant(1), '7.4')returns the logS at pH 7.4 of the second reactant |
| solubilityAtIsoelectricPoint logSTue |
solubilityAtIsoelectricPoint()returns the logS at isoelectric point of the input molecule |
solubilityAtIsoelectricPoint(reactant(1))returns the logS at isoelectric point of the second reactant |
| solubilityOfMicroSpecies logSMicro |
solubilityOfMicroSpecies()returns the logS of the input molecule |
solubilityOfMicroSpecies(reactant(1))returns the logS of the second reactant |
| solubilityOfNeutral logSNeutral |
solubilityOfNeutral()returns the logS of the neutralized form of the input molecule |
solubilityOfNeutral(reactant(1))returns the logS of the neutralized form of the second reactant |
| electrophilicityOrder orderE |
electrophilicityOrder(2)returns the E(+) order index of atom 2 of the input molecule, e.g. returns
0 if atom 2 is the most electrophilic atom, 1 if atom 2 is the
second strongest electrophilic atom, etc., |
electrophilicityOrder(ratom(1))returns the E(+) order index of the reactant atom matching map 1 in
the reaction equation |
| nucleophilicityOrder orderNu |
nucleophilicityOrder(2)returns the Nu(-) order index of atom 2 of the input molecule, e.g.
returns 0 if atom 2 is the most nucleophilic atom, 1 if atom 2 is
the second strongest nucleophilic atom, etc., |
nucleophilicityOrder(ratom(1))returns the Nu(-) order index of the reactant atom matching map 1
in the reaction equation |
| electrophilicLocalizationEnergy energyE |
electrophilicLocalizationEnergy(2)returns the electrophilic L(+) localization energy of atom 2 of the input
molecule, NaN if atom 2 is non-aromatic |
electrophilicLocalizationEnergy(ratom(1))returns the electrophilic L(+) localization energy of the reactant atom matching map 1 in the reaction equation |
| nucleophilicLocalizationEnergy energyNu |
nucleophilicLocalizationEnergy(2)returns the nucleophilic L(-) localization energy of atom 2 of the input
molecule, NaN if atom 2 is non-aromatic |
nucleophilicLocalizationEnergy(ratom(1))returns the nucleophilic L(-) localization energy of the reactant atom matching map 1 in the reaction equation |
| piEnergy | piEnergy()returns the pi energy of the input molecule |
piEnergy(product(1))returns the pi energy of the second product |
| electronDensity piChargeDensity |
electronDensity(2)returns the electron density of atom 2 of the input molecule, NaN
for non-existing value |
electronDensity(ratom(1))returns the electron density of the reactant atom matching map 1
in the reaction equation |
| chargeDensity totalChargeDensity |
chargeDensity(2)returns the charge density of atom 2 of the input
molecule, NaN for non-existing value |
chargeDensity(ratom(1))returns the charge density of the reactant atom matching map 1
in the reaction equation |
| topologicalPolarSurfaceArea PSA |
topologicalPolarSurfaceArea()returns the polar surface area of the input molecule topologicalPolarSurfaceArea('7.4') returns the polar surface area of the major microspecies taken at pH 7.4 |
topologicalPolarSurfaceArea(reactant(0))returns the polar surface area of the first reactant topologicalPolarSurfaceArea(product(0), '7.4')returns the polar surface area of the major microspecies of the first product taken at pH 7.4 |
| vanDerWaalsSurfaceArea | vanDerWaalsSurfaceArea()returns the van der Waals surface area of the input molecule vanDerWaalsSurfaceArea('7.4')
returns the van der Waals accessible surface area of the major microspecies taken at pH 7.4 |
vanDerWaalsSurfaceArea(reactant(0))returns the van der Waals surface area of the first reactant vanDerWaalsSurfaceArea(product(0), '7.4')returns the van der Waals surface area of the major microspecies of the first product taken at pH 7.4 |
| solventAccessibleSurfaceArea / waterAccessibleSurfaceArea / ASA | waterAccessibleSurfaceArea()returns the solvent accessible / water accessible surface area of the input molecule solventAccessibleSurfaceArea('7.4')returns the solvent accessible / water accessible surface area of the major microspecies taken at
pH 7.4 |
waterAccessibleSurfaceArea(reactant(0))returns the solvent accessible / water accessible surface area of the first reactant solventAccessibleSurfaceArea(product(0), '7.4')returns the solvent accessible / water accessible surface area of the major microspecies of the first product taken at pH 7.4 |
| ASAPlus | ASAPlus()returns the water accessible surface area of all atoms of the input molecule with positive partial charge ASAPlus('7.4')returns the water accessible surface area of all atoms with positive partial charge of the major microspecies taken at
pH 7.4 |
ASAPlus(reactant(0))returns the water accessible surface area of all atoms of the first reactant with positive partial charge ASAPlus(product(0), '7.4')returns the water accessible surface area of all atoms with positive partial charge of the major microspecies of the first product taken at pH 7.4 |
| ASANegative | ASANegative()returns the water accessible surface area of all atoms of the input molecule with negative partial charge ASANegative('7.4')returns the water accessible surface area of all atoms with negative partial charge of the major microspecies taken at
pH 7.4 |
ASANegative(reactant(0))returns the water accessible surface area of all atoms of the first reactant with negative partial charge ASANegative(product(0), '7.4')returns the water accessible surface area of all atoms with negative partial charge of the major microspecies of the first product taken at pH 7.4 |
| ASAHydrophobic | ASAHydrophobic()returns the water accessible surface area of all atoms of the input molecule with hydrophobic partial charge ASAHydrophobic('7.4')returns the water accessible surface area of all atoms with hydrophobic partial charge of the major microspecies taken at
pH 7.4 |
ASAHydrophobic(reactant(0))returns the water accessible surface area of all atoms of the first reactant with hydrophobic partial charge ASAHydrophobic(product(0), '7.4')returns the water accessible surface area of all atoms with hydrophobic partial charge of the major microspecies of the first product taken at pH 7.4 |
| ASAPolar | ASAPolar()returns the water accessible surface area of all atoms of the input molecule with polar partial charge ASAPolar('7.4')returns the water accessible surface area of all atoms with polar partial charge of the major microspecies taken at
pH 7.4 |
ASAPolar(reactant(0))returns the water accessible surface area of all atoms of the first reactant with polar partial charge ASAPolar(product(0), '7.4')returns the water accessible surface area of all atoms with polar partial charge of the major microspecies of the first product taken at pH 7.4 |
| mass / exactMass | mass()returns the mass of the input molecule exactMass()returns the exact mass of the input molecule |
mass(reactant(0))returns the mass of the first reactant exactMass(product(1))returns the exact mass of the second product |
| formula | formula()returns the formula of the input molecule |
N / A (reaction rules are numerical) |
| isotopeFormula | isotopeFormula()returns the isotope formula of the input molecule |
N / A (reaction rules are numerical) |
| dotDisconnectedFormula | dotDisconnectedFormula()returns the dot-disconnected formula of the input molecule |
N / A (reaction rules are numerical) |
| dotDisconnectedIsotopeFormula | dotDisconnectedIsotopeFormula()returns the dot-disconnected isotope formula of the input molecule |
N / A (reaction rules are numerical) |
| composition | composition()returns the composition of the input molecule |
N / A (reaction rules are numerical) |
| isotopeComposition | isotopeComposition()returns the isotope composition of the input molecule |
N / A (reaction rules are numerical) |
| atomCount | atomCount()returns the number of atoms in the input molecule atomCount("6") returns
the number of carbon atoms in the input molecule |
atomCount(reactant(0), "7")returns the number of nitrogen atoms in the first reactant atomCount(product(1), "7.14")returns the number of nitrogen atoms with mass number 14 in the second product atomCount(product(1), "7.0")returns the number of non-isotope nitrogen atoms in the second product |
| aliphaticAtomCount | aliphaticAtomCount()returns the number of aliphatic atoms in the input molecule |
aliphaticAtomCount(reactant(0))returns the number of aliphatic atoms in the first reactant aliphaticAtomCount(product(1))returns the number of aliphatic atoms in the second product |
| aromaticAtomCount | aromaticAtomCount()returns the number of aromatic atoms in the input molecule |
aromaticAtomCount(reactant(0))returns the number of aromatic atoms in the first reactant aromaticAtomCount(product(1))returns the number of aromatic atoms in the second product |
| bondCount | bondCount()returns the number of bonds in the input molecule |
bondCount(reactant(0))returns the number of bonds in the first reactant bondCount(product(1))returns the number of bonds in the second product |
| aliphaticBondCount | aliphaticBondCount()returns the number of bonds in the input molecule |
aliphaticBondCount(reactant(0))returns the number of aliphatic bonds in the first reactant aliphaticBondCount(product(1))returns the number of aliphatic bonds in the second product |
| aromaticBondCount | aromaticBondCount()returns the number of aromatic bonds in the input molecule |
aromaticBondCount(reactant(0))returns the number of aromatic bonds in the first reactant aromaticBondCount(product(1))returns the number of aromatic bonds in the second product |
| rotatableBondCount | rotatableBondCount()returns the number of rotatable bonds in the input molecule |
rotatableBondCount(reactant(0))returns the number of rotatable bonds in the first reactant rotatableBondCount(product(1))returns the number of rotatable bonds in the second product |
| fragments | fragments()returns the disconnected fragments of the molecule |
fragments(reactant(1))returns the disconnected fragments of the second reactant |
| ringCount | ringCount()returns the number of rings in the input molecule |
ringCount(reactant(0))returns the number of rings in the first reactant ringCount(product(1))returns the number of rings in the second product |
| ringCountOfSize | ringCountOfSize(6)returns the number of rings of size 6 in the input molecule |
ringCountOfSize(reactant(0), 5)returns the number of rings of size 5 in the first reactant ringCountOfSize(product(1), 5)returns the number of rings of size 5 in the second product |
| aliphaticRingCount | aliphaticRingCount()returns the number of aliphatic rings in the input molecule |
aliphaticRingCount(reactant(0))returns the number of aliphatic rings in the first reactant aliphaticRingCount(product(1))returns the number of aliphatic rings in the second product |
| aliphaticRingCountOfSize | aliphaticRingCountOfSize(6)returns the number of aliphatic rings of size 6 in the input molecule |
aliphaticRingCountOfSize(reactant(0), 5)returns the number of aliphatic rings of size 5 in the first reactant aliphaticRingCountOfSize(product(1), 5)returns the number of aliphatic rings of size 5 in the second product |
| aromaticRingCount | aromaticRingCount()returns the number of aromatic rings in the input molecule |
aromaticRingCount(reactant(0))returns the number of aromatic rings in the first reactant aromaticRingCount(product(1))returns the number of aromatic rings in the second product |
| aromaticRingCountOfSize | aromaticRingCountOfSize(6)returns the number of aromatic rings of size 6 in the input molecule |
aromaticRingCountOfSize(reactant(0), 5)returns the number of aromatic rings of size 5 in the first reactant aromaticRingCountOfSize(product(1), 5)returns the number of aromatic rings of size 5 in the second product |
| heteroRingCount | heteroRingCount()returns the number of hetero rings in the input molecule |
heteroRingCount(reactant(0))returns the number of hetero rings in the first reactant heteroRingCount(product(1))returns the number of hetero rings in the second product |
| heteroaromaticRingCount | heteroaromaticRingCount()returns the number of heteroaromatic rings in the input molecule |
heteroaromaticRingCount(reactant(0))returns the number of heteroaromatic rings in the first reactant heteroaromaticRingCount(product(1))returns the number of heteroaromatic rings in the second product |
| carboRingCount | carboRingCount()returns the number of carbo rings in the input molecule |
carboRingCount(reactant(0))returns the number of carbo rings in the first reactant carboRingCount(product(1))returns the number of carbo rings in the second product |
| carboaromaticRingCount | carboaromaticRingCount()returns the number of carboaromatic rings in the input molecule |
carboaromaticRingCount(reactant(0))returns the number of carboaromatic rings in the first reactant carboaromaticRingCount(product(1))returns the number of carboaromatic rings in the second product |
| ringAtomCount | ringAtomCount()returns the number of ring atoms in the input molecule |
ringAtomCount(reactant(0))returns the number of ring atoms in the first reactant ringAtomCount(product(1))returns the number of ring atoms in the second product |
| ringBondCount | ringBondCount()returns the number of ring bonds in the input molecule |
ringBondCount(reactant(0))returns the number of ring bonds in the first reactant ringBondCount(product(1))returns the number of ring bonds in the second product |
| chainAtomCount | chainAtomCount()returns the number of chain atoms in the input molecule |
chainAtomCount(reactant(0))returns the number of chain atoms in the first reactant chainAtomCount(product(1))returns the number of chain atoms in the second product |
| chainBondCount | chainBondCount()returns the number of chain bonds in the input molecule |
chainBondCount(reactant(0))returns the number of chain bonds in the first reactant chainBondCount(product(1))returns the number of chain bonds in the second product |
| ringAtomCount | ringAtomCount()returns the number of ring atoms in the input molecule |
ringAtomCount(reactant(0))returns the number of ring atoms in the first reactant ringAtomCount(product(1))returns the number of ring atoms in the second product |
| smallestRingSize / largestRingSize | smallestRingSize()returns the size of the smallest ring in the input molecule largestRingSize()returns the size of the largest ring in the input molecule |
smallestRingSize(reactant(0))returns the size of the smallest ring in the first reactant largestRingSize(product(1))returns the size of the largest ring in the second product |
| fusedRingCount | fusedRingCount()returns the number of fused rings in the input molecule |
fusedRingCount(reactant(0))returns the number of fused rings in the first reactant fusedRingCount(product(1))returns the number of fused rings in the second product |
| fusedAliphaticRingCount | fusedAliphaticRingCount()returns the number of fused aliphatic rings in the input molecule |
fusedAliphaticRingCount(reactant(0))returns the number of fused aliphatic rings in the first reactant fusedAliphaticRingCount(product(1))returns the number of fused aliphatic rings in the second product |
| fusedAromaticRingCount | fusedAromaticRingCount()returns the number of fused aromatic rings in the input molecule |
fusedAromaticRingCount(reactant(0))returns the number of fused aromatic rings in the first reactant fusedAromaticRingCount(product(1))returns the number of fused aromatic rings in the second product |
| ringSystemCountOfSize | ringSystemCountOfSize(4)returns the number of four-membered ring systems in the input molecule |
ringSystemCountOfSize(reactant(0),3)returns the number of three-membered ring systems in the first reactant ringsystemCountOfSize(product(1),3)returns the number of three-membered ring systems in the second product |
| ringSystemCount | ringSystemCount()returns the number of ring systems in the input molecule |
ringSystemCount(reactant(0))returns the number of ring systems in the first reactant ringsystemCount(product(1))returns the number of ring systems in the second product |
| smallestRingSystemSize | smallestRingSystemSize()returns the size of the smallest ring system in the input molecule |
smallestRingSystemSize(reactant(0))returns the size of the smallest ring system in the first reactant smallestringsystemsize(product(1))returns the size of the smallest ring system in the second product |
| largestRingSystemSize | largestRingSystemSize()returns the size of the largest ring system in the input molecule |
largestRingSystemSize(reactant(0))returns the size of the largest ring system in the first reactant largestringsystemsize(product(1))returns the size of the largest ring system in the second product |
| asymmetricAtomCount | asymmetricAtomCount()returns the number of asymmetric atoms in the input molecule |
asymmetricAtomCount(reactant(0))returns the number of asymmetric atoms in the first reactant asymmetricAtomCount(product(1))returns the number of asymmetric atoms in the second product |
| chiralCenterCount | chiralCenterCount()returns the number of tetrahedral stereogenic centers in the input molecule |
chiralCenterCount(reactant(0))returns the number of tetrahedral stereogenic centers in the first reactant chiralCenterCount(product(1))returns the number of tetrahedral stereogenic centers in the second product |
| aromaticAtom | aromaticAtom(2)returns true if atom 2 of the input molecule is
aromatic, false otherwise |
aromaticAtom(ratom(2))returns true if the reactant atom matching map 2
in the reaction equation is aromatic, false otherwise aromaticAtom(patom(1))returns true
if the product atom matching map 1 in the reaction equation is aromatic, false otherwise |
| aliphaticAtom | aliphaticAtom(2)returns true if atom 2 of the input molecule is
aliphatic, false otherwise |
aliphaticAtom(ratom(2))returns true if the reactant atom matching map 2
in the reaction equation is aliphatic, false otherwise aliphaticAtom(patom(1))returns true
if the product atom matching map 1 in the reaction equation is aliphatic, false otherwise |
| chainAtom | chainAtom(2)returns true if atom 2 of the input molecule is a chain
atom, false otherwise |
chainAtom(ratom(2))returns true if the reactant atom matching map 2 in
the reaction equation is a chain atom, false otherwise chainAtom(patom(1))returns true
if the product atom matching map 1 in the reaction equation is a chain atom, false otherwise |
| ringAtom | ringAtom(2)returns true if atom 2 of the input molecule is a ring atom,
false otherwise |
ringAtom(ratom(2))returns true if the reactant atom matching map 2 in
the reaction equation is a ring atom, false otherwise ringAtom(patom(1))returns true
if the product atom matching map 1 in the reaction equation is a ring atom, false otherwise |
| asymmetricAtom | asymmetricAtom(2)returns true if atom 2 of the input molecule is an
asymmetric atom, false otherwise |
asymmetricAtom(ratom(2))returns true if the reactant atom matching map 2
in the reaction equation is an asymmetric atom, false otherwise asymmetricAtom(patom(1))returns true if the product atom matching map 1 in the reaction equation is an asymmetric
atom, false otherwise |
| chiralCenter | chiralCenter(2)returns true if atom 2 of the input molecule is a
tetrahedral stereogenic center, false otherwise |
chiralCenter(ratom(2))returns true if the reactant atom matching map 2
in the reaction equation is a tetrahedral stereogenic center, false otherwise chiralCenter(patom(1))returns true if the product atom matching map 1 in the reaction equation is a tetrahedral
stereogenic center, false otherwise |
| cyclomaticNumber | cyclomaticNumber()returns the cyclomatic number of the input molecule |
cyclomaticNumber(reactant(0))returns the cyclomatic number of the first reactant cyclomaticNumber(product(1))returns the cyclomatic number of the second product |
| plattIndex | plattIndex()returns the Platt index of the input molecule |
plattIndex(reactant(0))returns the Platt index of the first reactant plattIndex(product(1))returns the Platt index of the second product |
| randicIndex | randicIndex()returns the Randic index of the input molecule |
randicIndex(reactant(0))returns the Randic index of the first reactant randicIndex(product(1))returns the Randic index of the second product |
| balabanIndex | balabanIndex()returns the Balaban index of the input molecule |
balabanIndex(reactant(0))returns the Balaban index of the first reactant balabanIndex(product(1))returns the Balaban index of the second product |
| distanceDegree | distanceDegree(2)returns the distance degree of atom 2 of the input molecule |
distanceDegree(ratom(2))returns the distance degree of the reactant atom matching map 2
in the reaction equation distanceDegree(patom(1))returns the distance degree of the product atom matching map 1 in the reaction equation |
| eccentricity | eccentricity(2)returns the eccentricity of atom 2 of the input molecule |
eccentricity(ratom(2))returns the eccentricity of the reactant atom matching map 2
in the reaction equation eccentricity(patom(1))returns the distance degree of the product atom matching map 1 in the reaction equation |
| hararyIndex | hararyIndex()returns the Harary index of the input molecule |
hararyIndex(reactant(0))returns the Harary index of the first reactant hararyIndex(product(1))returns the Harary index of the second product |
| hyperWienerIndex | hyperWienerIndex()returns the Hyper Wiener index of the input molecule |
hyperWienerIndex(reactant(0))returns the Hyper Wiener index of the first reactant hyperWienerIndex(product(1))returns the Hyper Wiener index of the second product |
| szegedIndex | szegedIndex()returns the Szeged index of the input molecule |
szegedIndex(reactant(0))returns the Szeged index of the first reactant szegedIndex(product(1))returns the Szeged index of the second product |
| wienerIndex | wienerIndex()returns the Wiener index of the input molecule |
wienerIndex(reactant(0))returns the Wiener index of the first reactant wienerIndex(product(1))returns the Wiener index of the second product |
| wienerPolarity | wienerPolarity()returns the Wiener polarity of the input molecule |
wienerPolarity(reactant(0))returns the Wiener polarity of the first reactant wienerPolarity(product(1))returns the Wiener polarity of the second product |
| stericEffectIndex | stericEffectIndex(2)returns the steric effect index of atom 2 of the input molecule |
stericEffectIndex(ratom(2))returns the steric effect index of the reactant atom matching map 2
in the reaction equation stericEffectIndex(patom(1))returns the steric effect index of the product atom matching map 1 in the reaction equation |
| smallestAtomRingSize / largestAtomRingSize | smallestAtomRingSize(0)returns the size of the smallest ring containing atom 0 in
the input molecule largestAtomRingSize(1)returns the size of the largest ring containing atom 1
in the input molecule |
smallestAtomRingSize(ratom(1))returns the size of the smallest ring containing reactant atom matching map 1 in the reaction equation largestRingSize(patom(2))returns the size of the largest ring containing product atom matching map 2 in the reaction equation |
| shortestPath | shortestPath('2-3') and shortestPath(pair(1, 2))both return the shortest path length between atoms 1 and 2 in the input molecule |
shortestPath(reactant(0), pair(ratom(1), ratom(2)))returns the length of the shortest path between reactant atoms matching maps 1 and 2 in the reaction equation (see note 1)
shortestPath(product(1), pair(patom(2), patom(3)))returns the length of the shortest path between product atoms matching maps 2 and 3 in the reaction equation (see note 1) |
| connected | connected('2-3') and connected(pair(1, 2))both return true if atoms 1
and 2 are in the same connected component of the input molecule |
connected(reactant(0), pair(ratom(1), ratom(2)))returns true if reactant atoms matching maps 1
and 2 in the reaction equation are connected in the corresponding reactant molecule (see note 1)
connected(product(1), pair(patom(2), patom(3)))returns true if product atoms matching maps 2
and 3 in the reaction equation are connected in the corresponding product molecule (see note 1) |
| conenctedGraph | connectedGraph()returns true if the input molecule graph is connected |
connectedGraph(reactant(0))returns true if the first reactant is connected connectedGraph(product(1))returns true if the second product is connected |
| bondType | bondType('2-3') and bondType(bond(1, 2))both return the bond type between atoms 1
and 2 in the input molecule |
bondType(reactant(0), bond(ratom(1), ratom(2)))returns the bond type between reactant atoms matching maps 1
and 2 in the reaction equation (see note 1)bondType(product(1), bond(patom(2), patom(3)))returns the bond type between product atoms matching maps 2 and 3 in the reaction equation
(see note 1) |
| chainBond | chainBond('2-3') and chainBond(bond(1, 2))both return true if atoms 1
and 2 are connected by a chain bond the input molecule |
chainBond(reactant(0), bond(ratom(1), ratom(2)))returns true if reactant atoms matching maps 1
and 2 in the reaction equation are connected by a chain bond in the corresponding reactant molecule (see note 1)
chainBond(product(1), bond(patom(2), patom(3)))returns true if product atoms matching maps 2 and 3 in the
reaction equation are connected by a chain bond in the corresponding product molecule (see note 1) |
| ringBond | ringBond('2-3') and ringBond(bond(1, 2))both return true if atoms 1
and 2 are connected by a ring bond the input molecule |
ringBond(reactant(0), bond(ratom(1), ratom(2)))returns true if reactant atoms matching maps 1
and 2 in the reaction equation are connected by a ring bond in the corresponding reactant molecule (see note 1)
ringBond(product(1), bond(patom(2), patom(3)))returns true if product atoms matching maps 2 and 3
in the reaction equation are connected by a ring bond in the corresponding product molecule (see note 1) |
| rotatableBond | rotatableBond('2-3') and rotatableBond(bond(1, 2))both return true if
atoms 1 and 2 are connected by a rotatable bond the input molecule |
rotatableBond(reactant(0), bond(ratom(1), ratom(2)))returns true if reactant atoms matching maps
1 and 2 in the reaction equation are connected by a rotatable bond in the corresponding
reactant molecule (see note 1)
rotatableBond(product(1), bond(patom(2), patom(3)))returns true if product atoms
matching maps 2 and 3 in the reaction equation are connected by a rotatable bond in the
corresponding product molecule (see note 1) |
| ringCountOfAtom | ringCountOfAtom(2)returns the number of rings passsing through atom 2 of the input
molecule |
ringCountOfAtom(ratom(2))returns the number of rings passsing through the reactant atom matching map 2 in the reaction equation ringCountOfAtom(patom(1))returns the number of rings passsing through the product atom matching map 1 in the reaction equation |
| hasValenceError | hasValenceError()returns true if any atom in the molecule has valence error,
false othervise |
hasValenceError(reactant(1))returns true if any atom in the second reactant has valence error,
false otherwise hasValenceError(product(0)returns true if any atom in the first
product has valence error, false otherwise |
| hasRadical | hasRadical()returns true if any atom in the molecule has radical, false otherwise |
hasRadical(reactant(1))returns true if any atom in the second reactant has radical,
false otherwise |
| hasIsotope | hasIsotope()returns true if any atom in the molecule is a specific isotope of the element,
false othervise |
hasIsotope(reactant(1))returns true if any atom in the second reactant is a specific isotope of the element,
false otherwise |
| acceptor / donor acc / don |
acceptor(2)returns the hydrogen bond acceptor multiplicity on atom 2 of the input molecule donor(1, "7.4")returns the hydrogen bond donor multiplicity on atom 1 of the major microspecies at pH 7.4 |
acceptor(ratom(2))returns the hydrogen bond acceptor multiplicity on the reactant atom matching map 2
in the reaction equation donor(patom(3), "7.4")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 |
| acceptorSiteCount / donorSiteCount accSiteCount / donSiteCount |
acceptorSiteCount()returns the hydrogen bond acceptor multiplicity of the input molecule donorSiteCount("7.4")
returns the hydrogen bond donor multiplicity of the major microspecies at pH 7.4 |
acceptorSiteCount(reactant(0))returns the hydrogen bond acceptor multiplicity of the first reactant donorSiteCount(product(1), "7.4")returns the hydrogen bond donor multiplicity of the major microspecies of the first product taken at pH 7.4 |
| acceptorCount / donorCount | acceptorCount()returns the number of hydrogen bond acceptor atoms in the input molecule donorCount("7.4")
returns the number of hydrogen bond donor atoms in the major microspecies at pH 7.4 |
acceptorCount(reactant(0))returns the number of hydrogen bond acceptor atoms in the first reactant 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 |
| refractivity refrac |
refractivity()returns the molar refractivity of the input molecule |
refractivity(reactant(1))returns the molar refractivity of the second reactant |
| refractivityIncrements refraci |
refractivityIncrements(2)returns the refractivity increment on atom 2 of the input molecule |
refractivityIncrements(ratom(1))returns the refractivity increment on the reactant atom matching map 1
in the reaction equation |
| isoelectricPoint pI |
isoelectricPoint()returns the isoelectric point of the input molecule |
isoelectricPoint(reactant(1))returns the isoelectric point of the second reactant |
| stereoisomerCount | stereoisomerCount()returns the number of generated stereoisomers of the input molecule stereoisomerCount("250-")
returns the number of geneated stereoisomers of the input molecule; the maximum number of stereoisomers to generate is
set to 250, so it returns 250 or - if there are no 250 stereoisomers of the input molecule - less then 250 |
stereoisomerCount(reactant(0))returns the number of calculated stereoisomers of the first reactant stereoisomerCount(product(1), "250-")returns the number of calculated stereoisomers of the the second product; the maximum number of stereoisomers to generate is set to 250, so it returns 250 or - if there are no 250 stereoisomers of the second product - less then 250 |
| stereoisomer | stereoisomer(0)returns the first stereoisomer of the input molecule stereoisomer(2, "250-")returns the third of 250 stereoisomers (or less, if there are no 250 stereoisomers) of the input molecule |
stereoisomer(reactant(0), 1)returns the second stereoisomer of the first reactant stereoisomer(product(1), 0, "250-")returns the third of 250 stereoisomers (or less, if there are no 250 stereoisomers) of the second product |
| stereoisomers | stereoisomers()returns stereoisomers of the input molecule in an array stereoisomers("250-")
returns 250 stereoisomers (or less, if there are no 250 stereoisomers) of the input molecule in an array |
stereoisomers(reactant(0))returns stereoisomers of the first reactant in an array stereoisomers(product(1), "250-")returns 250 stereoisomers (or less, if there are no 250 stereoisomers) of the the second product |
| doubleBondStereoisomerCount | doubleBondStereoisomerCount()returns the number of generated double bond stereoisomers of the input molecule doubleBondStereoisomerCount("250-") returns the number of geneated double bond stereoisomers
of the input molecule; the maximum number of double bond stereoisomers to generate is set to 250, so it returns 250 or
- if there are no 250 double bond stereoisomers of the input molecule - less then 250 |
doubleBondStereoisomerCount(reactant(0))returns the number of calculated double bond stereoisomers of the first reactant doubleBondStereoisomerCount(product(1), "250-")returns the number of calculated double bond stereoisomers of the the second product; the maximum number of double bond stereoisomers to generate is set to 250, so it returns 250 or - if there are no 250 double bond stereoisomers of the second product - less then 250 |
| doubleBondStereoisomer | doubleBondStereoisomer(0)returns the first double bond stereoisomer of the input molecule doubleBondStereoisomer(2, "250-")returns the third of 250 double bond stereoisomers (or less, if there are no 250 double bond stereoisomers) of the input molecule |
doubleBondStereoisomer(reactant(0), 1)returns the second double bond stereoisomer of the first reactant doubleBondStereoisomer(product(1), 0, "250-")returns the third of 250 double bond stereoisomers (or less, if there are no 250 double bond stereoisomers) of the second product |
| doubleBondStereoisomers | doubleBondStereoisomers()returns double bond stereoisomers of the input molecule in an array doubleBondStereoisomers("250-")
returns 250 double bond stereoisomers (or less, if there are no 250 double bond stereoisomers) of the input molecule
in an array |
doubleBondStereoisomers(reactant(0))returns double bond stereoisomers of the first reactant in an array doubleBondStereoisomers(product(1), "250-")returns 250 double bond stereoisomers (or less, if there are no 250 double bond stereoisomers) of the the second product |
| tetrahedralStereoisomerCount | tetrahedralStereoisomerCount()returns the number of generated tetrahedral stereoisomers of the input molecule tetrahedralStereoisomerCount("250-") returns the number of geneated tetrahedral
stereoisomers of the input molecule; the maximum number of tetrahedral stereoisomers to generate is set to 250, so it
returns 250 or - if there are no 250 tetrahedral stereoisomers of the input molecule - less then 250 |
tetrahedralStereoisomerCount(reactant(0))returns the number of calculated tetrahedral stereoisomers of the first reactant tetrahedralStereoisomerCount(product(1), "250-")returns the number of calculated tetrahedral stereoisomers of the the second product; the maximum number of tetrahedral stereoisomers to generate is set to 250, so it returns 250 or - if there are no 250 tetrahedral stereoisomers of the second product - less then 250 |
| tetrahedralStereoisomer | tetrahedralStereoisomer(0)returns the first tetrahedral stereoisomer of the input molecule tetrahedralStereoisomer(2, "250-")returns the third of 250 tetrahedral stereoisomers (or less, if there are no 250 tetrahedral stereoisomers) of the input molecule |
tetrahedralStereoisomer(reactant(0), 1)returns the second tetrahedral stereoisomer of the first reactant tetrahedralStereoisomer(product(1), 0, "250-")returns the third of 250 tetrahedral stereoisomers (or less, if there are no 250 tetrahedral stereoisomers) of the second product |
| tetrahedralStereoisomers | tetrahedralStereoisomers()returns tetrahedral stereoisomers of the input molecule in an array tetrahedralStereoisomers("250-")
returns 250 tetrahedral stereoisomers (or less, if there are no 250 tetrahedral stereoisomers) of the input molecule
in an array |
tetrahedralStereoisomers(reactant(0))returns tetrahedral stereoisomers of the first reactant in an array tetrahedralStereoisomers(product(1), "250-")returns 250 tetrahedral stereoisomers (or less, if there are no 250 tetrahedral stereoisomers) of the the second product |
| conformerCount | conformerCount()returns the number of calculated conformers of the input molecule conformerCount("250-")
returns the number of calculated conformers of the input molecule; the maximum number of conformers to calculate is
set to 250, so it returns 250 or - if there are no 250 conformers of the input molecule - less then 250 |
conformerCount(reactant(0))returns the number of calculated conformers of the first reactant conformerCount(product(1), "250-")returns the number of calculated conformers of the the second product; the maximum number of conformers to calculate is set to 250, so it returns 250 or - if there are no 250 conformers of the second product - less then 250 |
| conformer | conformer(0)returns the first conformer of the input molecule conformer(2, "250-")returns the third of 250 conformers (or less, if there are no 250 conformers) of the input molecule |
conformer(reactant(0), 1)returns the second conformer of the first reactant conformer(product(1), 0, "250-")returns the third of 250 conformers (or less, if there are no 250 conformers) of the second product |
| conformers | conformers()returns conformers of the input molecule in an array conformers("250-")
returns 250 conformers (or less, if there are no 250 conformers) of the input molecule in an array |
conformers(reactant(0))returns conformers of the first reactant in an array conformers(product(1), "250-")returns 250 conformers (or less, if there are no 250 conformers) of the the second product |
| lowestEnergyConformer leconformer |
lowestEnergyConformer()returns the lowest energy conformer of the input molecule |
lowestEnergyConformer(reactant(0))returns the lowest energy conformer of the first reactant lowestEnergyConformer(product(1))returns the lowest energy conformer of the second product |
| hasValidConformer | hasValidConformer()returns true if the input molecule exists in 3D space (has a valid conformer) |
hasValidConformer(reactant(0))returns true the if the first reactant exists in 3D space hasValidConformer(product(1))returns true the if the second product exist in 3D space |
| dreidingEnergy | dreidingEnergy()returns the dreiding energy of the input molecule (conformer) |
dreidingEnergy(reactant(0))returns the dreiding energy of the first reactant dreidingEnergy(product(1))returns the dreiding energy of the second product |
| minimalProjectionArea | minimalProjectionArea()returns the minimal projection area |
minimalProjectionArea((reactant(0))returns the minimal projection area of the first reactant minimalProjectionArea(product(1))returns the minimal projection area of the second product |
| maximalProjectionArea | maximalProjectionArea()returns the maximal projection area |
maximalProjectionArea((reactant(0))returns the maximal projection area of the first reactant maximalProjectionArea(product(1))returns the maximal projection area of the second product |
| minimalProjectionRadius | minimalProjectionRadius()returns the minimal projection radius |
minimalProjectionRadius((reactant(0))returns the minimal projection radius of the first reactant minimalProjectionRadius(product(1))returns the minimal projection radius of the second product |
| maximalProjectionRadius | maximalProjectionRadius()returns the maximal projection radius |
maximalProjectionRadius((reactant(0))returns the maximal projection radius of the first reactant maximalProjectionRadius(product(1))returns the maximal projection radius of the second product |
| distance | distance('1-2') and distance(pair(0, 1))both return the distance between atoms 1
and 2 in the input molecule |
distance(reactant(0), pair(ratom(1), ratom(2)))returns the distance between reactant atoms matching maps 1
and 2 in the reaction equation (see note 1)
distance(product(1), pair(patom(2), patom(3)))returns the distance between product atoms matching maps 2 and 3
in the reaction equation (see note 1) |
| angle | angle('1-2-3') and angle(atoms(0, 1, 2))both return the angle between atoms 1,
2 and 3 in the input molecule |
angle(reactant(0), atoms(ratom(1), ratom(2), ratom(3)))returns the angle between reactant atoms matching maps 1, 2 and 3 in the reaction equation (see note 1)
angle(product(1), atoms(patom(2), patom(3), patom(4)))returns the angle between product atoms matching maps 2,
3 and 4 in the reaction equation (see note 1) |
| dihedral | dihedral('1-2-3-4') and dihedral(atoms(0, 1, 2, 3))both return the dihedral of atoms 1,
2, 3 and 4 in the input molecule |
dihedral(reactant(0), atoms(ratom(1), ratom(2), ratom(3), ratom(4)))returns the dihedral of reactant atoms matching maps 1, 2, 3 and 4 in the reaction equation (see note 1)
dihedral(product(1), atoms(patom(2), patom(3), patom(5), patom(6)))returns the dihedral of product atoms matching maps 2,
3, 5 and 6 in the reaction equation (see note 1) |
| stericHindrance | stericHindrance(2)returns the steric hindrance of atom 2 of the input molecule |
stericHindrance(ratom(2))returns the steric hindrance of the reactant atom matching map 2
in the reaction equation stericHindrance(patom(1))returns the steric hindrance of the product atom matching map 1 in the reaction equation |
| name | name()returns the preferred IUPAC name of the input molecule |
N / A (reaction rules are numerical) |
| traditionalName | traditionalName()returns the traditional name of the input molecule |
N / A (reaction rules are numerical) |
| molFormat molString |
molFormat("mrv") returns the ChemAxon Marvin Document format representation of the input molecule |
N / A (reaction rules are numerical) |
| molBinFormat molImage |
molImage("jpeg:w100,Q95,#ffff00") returns the 100x100 JPEG image of the input molecule with yellow background, 95% quality |
N / A (reaction rules are numerical) |
| bmf | bmf()returns the Bemis-Murcko framework of the input molecule |
bmf(reactant(0))returns the Bemis-Murcko framework of the first reactant |
Note: Match functions are available only in JChem.
| Built-in name | Description | Return value | Parameters |
|---|---|---|---|
| match | performs substructure search and optionally checks for atom matching | true if matching substructure found, false otherwise |
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. |
| matchCount | performs substructure search and optionally checks for atom matching, counts search hits | the number of search hits |
|
| disjointMatchCount | performs substructure search, returns the maximal number of pairwise disjoint search hits | the maximal number of pairwise disjoint search hits |
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. |
| Built-in name | Molecule Context Example | Reaction Context Example |
|---|---|---|
| match | match("[#8]C=O") performs substructure search without atom matching requirement, the target is the
input molecule, the query is the carboxylic group given in the string parameter match(6, "[#8][C:1]=O", 1)performs substructure search, checks if target atom 6 matches the carbon (atom with map 1)
of the carboxylic group query match(6, "[#8:1]C=[O:2]", 1, 2)performs substructure search, checks if target atom 6 of the input molecule is a carboxylic oxygen |
match(reactant(0), "[#8]C=O")performs substructure search without atom matching requirement, the target is the first reactant, the query is the carboxylic group given in the string parameter match(patom(2), "[#8]C=O")performs substructure search, checks if product atom matching map 2 in the reaction equation matches any
atom of the carboxylic group query match(ratom(1), "[#8:1]C=[O:2]", 1, 2)performs substructure search, checks if reactant atom matching map 1 in the reaction equation is a carboxylic oxygen |
| matchCount | matchCount("[#8]C=O") counts search hits without atom matching requirement, the target is the
input molecule, the query is the carboxylic group given in the string parameter matchCount(6, "[#8]C=O")counts search hits with target atom 6 matching any atom in a carboxylic group matchCount(6, "[#8:1]C=[O:2]", 1, 2)counts search hits with target atom 6 of the input molecule being a carboxylic oxygen |
matchCount(reactant(0), "[#8]C=O")counts search hits without atom matching requirement, the target is the first reactant, the query is the carboxylic group given in the string parameter matchCount(patom(2), "[#8]C=O")counts search hits, checks if product atom matching map 2 in the reaction equation matches any atom of
the carboxylic group query matchCount(ratom(1), "[#8:1]C=[O:2]", 1, 2)counts search hits with reactant atom matching map 1 in the reaction equation being a carboxylic oxygen |
| disjointMatchCount | disjointMatchCount("[#8]C=O") counts the maximal number of pairwise disjoint carboxylic groups in the input molecule
| disjointMatchCount(reactant(0), "[#8]C=O")counts the maximal number of pairwise disjoint carboxylic groups in the first reactant |
shortestPath(reactant(0), pair(ratom(1), ratom(2)))) and must contain all the
atoms referred by atom indexes.