 |
|
|
|
|
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.
You can switch between corresponding descriptions and examples by clicking on the built-in names.
| Built-in name | Description | Return value | Parameters |
|---|---|---|---|
| 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 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 | 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 |
|---|---|---|---|
| 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 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 |
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 |
| 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 | - |
| 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 |
|
| markushEnumerations | constructs Markush enumerated structures sequentially | the enumerated structure |
|
| 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 |
|
| totalCharge | calculates total charge of molecule | the 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 | calculates logD at specified pH | the logD value |
|
| logP | 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 | - |
| aromaticElectrophilicityOrder orderE |
calculates aromatic E(+) order of atoms | the aromatic E(+) order index of the atom ( 0, 1, 2, ...),-1 for non-aromatic atoms -1 for non-aromatic atoms |
|
| aromaticNucleophilicityOrder orderNu |
calculates aromatic Nu(-) order of atoms | the aromatic Nu(-) order index of the atom ( 0, 1, 2, ...),-1 for non-aromatic atoms |
|
| 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 |
|
| piChargeDensity | calculates the pi charge density of atoms | the pi charge density of the atom,NaN for non-existing values |
|
| totalChargeDensity | calculates the total charge density of atoms | the total 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 | - |
| ringCount | calculates the ring count | the ring count | - |
| aliphaticRingCount | calculates the aliphatic ring count | the aliphatic ring count | - |
| aromaticRingCount | calculates the aromatic ring count | the aromatic ring count | - |
| 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 | - |
| 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 | - |
| 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 | - |
| 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 |
|
| 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> |
| 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) |
| 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) |
| 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 |
| totalCharge | totalCharge()returns the total charge of the input molecule totalCharge(majorms("7.4"))
returns the total charge of the major microspecies of the input molecule at pH 7.4 |
totalCharge(reactant(0))returns the total charge of the first reactant totalCharge(majorms(product(1), "7.4"))returns the total 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 | 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 | 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 |
| aromaticElectrophilicityOrder orderE |
aromaticElectrophilicityOrder(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., -1 if atom 2 is non-aromatic |
aromaticElectrophilicityOrder(ratom(1))returns the E(+) order index of the reactant atom matching map 1 in
the reaction equation |
| aromaticNucleophilicityOrder orderNu |
aromaticNucleophilicityOrder(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., -1 if atom 2 is non-aromatic |
aromaticNucleophilicityOrder(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 |
| piChargeDensity | piChargeDensity(2)returns the pi charge density of atom 2 of the input molecule, NaN
for non-existing value |
piChargeDensity(ratom(1))returns the pi charge density of the reactant atom matching map 1
in the reaction equation |
| totalChargeDensity | totalChargeDensity(2)returns the total charge density of atom 2 of the input
molecule, NaN for non-existing value |
totalChargeDensity(ratom(1))returns the total 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |