Skip to content

Chemical Terms functions in alphabetic order

The alphabetical table contains only the molecule context example(s) of a function and does not contain the detailed description of its parameters. You can find all context examples and the detailed description of parameters in the category-based table.

Function name(s) Required Chemaxon license Description Return value Function parameters Molecule context example(s)
abs - returns the absolute value of a number the absolute value integer or real number abs(charge(1)) returns the absolute value of the charge of the 2nd atom in the molecule
  • acceptor
  • acc
 DGTK calculates atomic hydrogen bond acceptor multiplicity the atomic hydrogen bond acceptor multiplicity
  • the atom index/MolAtom object
  • the major microspecies pH (takes the input molecule if omitted)
 acceptor(2) returns the hydrogen bond acceptor multiplicity on atom 2 of the input molecule
acceptorCount DGTK calculates molecular hydrogen bond acceptor count (the number of acceptor atoms) the molecular hydrogen bond acceptor count the major microspecies pH (takes the input molecule if omitted) acceptorCount('7.4') returns the number of hydrogen bond acceptor atoms in the major microspecies of the input molecule at pH 7.4
  • acceptorSiteCount
  • accSiteCount
 DGTK calculates molecular hydrogen bond acceptor multiplicity (the sum of atomic multiplicities) the molecular hydrogen bond acceptor multiplicity the major microspecies pH (takes the input molecule if omitted) acceptorSiteCount() returns the hydrogen bond acceptor multiplicity of the input molecule
  • acidicpKa
  • apKa
 DGTK, SPTK calculates acidic pKa values the acidic pKa values
  • the atom index/MolAtom object
  • the strength index as a string (e.g. '1' for the strongest, '2' for the second strongest pKa)
  • acidicpKa(0) returns the acidic pKa of atom 0 of the input molecule
  • apKa('2') returns the second strongest acidic pKa value of the input molecule
acidicpKaLargeModel DGTK, SPTK calculates acidic pKa values using the Large model (this model is optimised for molecules with a higher number of ionizable atoms) the acidic pKa values the atom index/MolAtom object, the strength index as a string
  • acidicpKaLargeModel(0) returns the acidic pKa of atom 0 of the input molecule
  • acidicpKaLargeModel('2') returns the second strongest acidic pKa value of the input molecule
acidicpKaUseCorrection DGTK, SPTK calculates acidic pKa values using a pKa correction library the acidic pKa values
  • the atom index/MolAtom object
  • the strength index as a string
  • acidicpKaUseCorrection(0) returns the acidic pKa value of atom 0 of the input molecule
  • acidicpKaUseCorrection('2') returns the second strongest acidic pKa value of the input molecule
agentCount - counts the agents in the reaction the number of agents in the reaction or -1 if the input is not a reaction - agentCount() returns n if the input molecule is a reaction and contains n agents otherwise it returns -1
aliphaticAtom DGTK checks if an atom is aliphatic true for aliphatic atoms, false for non-aliphatic atoms the atom index/MolAtom object aliphaticAtom(2) returns true if atom 2 of the input molecule is aliphatic, false otherwise
aliphaticAtomCount DGTK calculates the aliphatic atom count the aliphatic atom count - aliphaticAtomCount() returns the number of aliphatic atoms in the input molecule
aliphaticBondCount DGTK calculates the aliphatic bond count the aliphatic bond count - aliphaticBondCount() returns the number of bonds in the input molecule
aliphaticRingCount DGTK calculates the aliphatic ring count the aliphatic ring count - aliphaticRingCount() returns the number of aliphatic rings in the input molecule
aliphaticRingCountOfSize DGTK calculates the number of aliphatic rings of a given size the number of aliphatic rings of the given size the ring size aliphaticRingCountOfSize(6) returns the number of aliphatic rings of size 6 in the input molecule
aliphaticRings DGTK identifies the aliphatic rings in the molecule atom indices of the aliphatic rings in the molecule (or null if the molecule does not contain aliphatic rings) - aliphaticRings() returns the atom indices of the aliphatic rings in the input molecule
aliphaticRingsOfSize DGTK identifies the aliphatic rings of a given size in the molecule atom indices of the aliphatic rings in the molecule having the given size (or null if the molecule does not contain aliphatic rings) the ring size aliphaticRings() returns the atom indices of the aliphatic rings in the input molecule having the given size
allTautomer DGTK, SPTK returns a tautomer from all tautomers the tautomer the tautomer index (0-based) allTautomer(0) returns the first tautomer of the input molecule
allTautomers DGTK, SPTK returns all tautomers in an array the tautomer array the normalization option normal (the default is false) allTautomers('normal:true') returns all normalised tautomers of the input molecule in an array
angle DGTK calculates the angle between three atoms the angle between three atoms the (1-based) atom indices of the three atoms in a string "index1-index2-index3" (e.g. '2-3-5') angle('1-2-3') and angle(atoms(0, 1, 2)) both return the angle between atoms 1, 2 and 3 of the input molecule
arom - returns if the atom has an aromatic bond true if the atom has an aromatic bond, false otherwise atom index or MolAtom object arom(0) returns if the atom 0 has an aromatic bond
aromaticAtom DGTK checks if an atom is aromatic true for aromatic atoms, false for non-aromatic atoms the atom index/MolAtom object aromaticAtom(2) returns true if atom 2 of the input molecule is aromatic, false otherwise
aromaticAtomCount DGTK calculates the aromatic atom count the aromatic atom count - aromaticAtomCount() returns the number of aromatic atoms in the input molecule
aromaticBondCount DGTK calculates the aromatic bond count the aromatic bond count - aromaticBondCount() returns the number of aromatic bonds in the input molecule
aromaticRingCount DGTK calculates the aromatic ring count the aromatic ring count - aromaticRingCount() returns the number of aromatic rings in the input molecule
aromaticRingCountOfSize DGTK calculates the number of aromatic rings of a given size the number of aromatic rings of the given size the ring size aromaticRingCountOfSize(6) returns the number of aromatic rings of size 6 in the input molecule
aromaticRings DGTK identifies the aromatic rings in the molecule atom indices of the aromatic rings in the molecule (or null if the molecule does not contain aromatic rings) - aromaticRings() returns the atom indices of the aromatic rings in the input molecule
aromaticRingsOfSize DGTK identifies the aromatic rings having a given size (number of atoms) in the molecule atom indices of the aromatic rings having the given size (or null if the molecule does not contain aromatic rings) the ring size aromaticRingsOfSize(6) returns the atom indices of the aromatic rings of size 6 in the input molecule
array - constructs an integer array from its arguments the integer array integers or MolAtom objects array(map(2), map(5), map(6), map(8)) creates an array from the mapped atoms 2, 5, 6, 8
ASAHydrophobic DGTK calculates the water accessible molecular surface area of all hydrophobic atoms in the molecule the molecular surface area the major microspecies pH (takes the input molecule if omitted)
  • 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
ASANegative DGTK calculates the water accessible molecular surface area of all atoms with negative partial charge the molecular surface area the major microspecies pH (takes the input molecule if omitted)
  • 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
ASAPlus DGTK calculates the water accessible molecular surface area of all atoms with positive partial charge the molecular surface area the major microspecies pH (takes the input molecule if omitted)
  • 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
ASAPolar DGTK calculates the water accessible molecular surface area of all polar atoms the molecular surface area the major microspecies pH (takes the input molecule if omitted)
  • 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
asymmetricAtom DGTK checks if the specified atom is an asymmetric atom true for asymmetric atoms, false for symmetric atoms the atom index/MolAtom object asymmetricAtom(2) returns true if atom 2 of the input molecule is an asymmetric atom, false otherwise
asymmetricAtomCount DGTK calculates the number of asymmetric atoms the asymmetric atom count - asymmetricAtomCount() returns the number of asymmetric atoms in the input molecule
asymmetricAtoms DGTK identifies the asymmetric atoms in the molecule indices of asymmetric atoms - asymmetricAtoms() returns the indices of asymmetric atoms in the input molecule
  • atno
  • atomicNumber
 - returns the atomic number of an atom the atomic number atom index or MolAtom object atno(0) returns the atomic number of atom 0
atomCount - calculates the number of atoms (all atoms or specific atoms) the atom count atomic number (optional) and mass number (optional) as a single string separated by "."
  • atomCount() returns the number of atoms in the input molecule
  • atomCount("6") returns the number of carbon atoms in the input molecule
  • atomicPolarizability
  • atomPol
  • pol
  • polarizability
 DGTK calculates atomic polarizability the polarizability values
  • atom index or MolAtom object
  • pH value
  • 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 at pH 7.4
averageMicrospeciesCharge DGTK, SPTK calculates the average microspecies charge (the weighted sum of the charges of all the microspecies of the molecule) at a given pH the average charge the major microspecies pH averageMicrospeciesCharge('7.4') returns the average charge of the microspecies of the input molecule at pH 7.4
  • averagePolarizability
  • averagePol
  • avgPol
 DGTK calculates average molecular polarizability component considering 3D geometry the polarizability value pH value
  • averagePolarizability() returns the average polarizability component of the input molecule
  • averagePolarizability("7.4") returns the average polarizability component of the major microspecies of the input molecule at pH 7.4
axxPol DGTK calculates the a(xx) principal component of the polarizability tensor (a(xx), a(yy), a(zz)) the a(xx) principal component of the polarizability tensor pH value axxPol() returns the principal component a(xx) of the polarizability tensor of the input molecule
ayyPol DGTK calculates the a(yy) principal component of the polarizability tensor (a(xx), a(yy), a(zz)) the a(yy) principal component of the polarizability tensor pH value ayyPol() returns the principal component a(yy) of the polarizability tensor of the input molecule
azzPol DGTK calculates the a(zz) principal component of the polarizability tensor (a(xx), a(yy), a(zz)) the a(zz) principal component of the polarizability tensor pH value azzPol() returns the principal component a(zz) of the polarizability tensor of the input molecule
balabanIndex DGTK calculates the Balaban index the Balaban index - balabanIndex() calculates the Balaban index of the input molecule
  • basicpKa
  • bpKa
 DGTK, SPTK calculates basic pKa values the basic pKa values
  • the atom index/MolAtom object
  • the strength index as a string
  • basicpKa(0) returns the basic pKa of atom 0 of the input molecule
  • basicpKa("2") returns the second most basic pKa value of the input molecule
basicpKaLargeModel DGTK, SPTK calculates basic pKa values using the Large model (this model is optimised for molecules with a higher number of ionisable atoms) the basic pKa values
  • the atom index/MolAtom object
  • the strength index as a string
  • basicpKaLargeModel(0) returns the basic pKa of atom 0 of the input molecule using the Large model
  • basicpKaLargeModel("2") returns the second strongest basic pKa value of the input molecule using the Large model
basicpKaUseCorrection DGTK, SPTK calculates basic pKa values using a correction library the basic pKa values
  • the atom index/MolAtom object
  • the strength index as a string
  • basicpKaUseCorrection(0) returns the basic pKa of atom 0 of the input molecule using the correction library
  • basicpKaUseCorrection("2") returns the second strongest basic pKa value of the input molecule using the correction library
bbb DGTK calculates the Blood Brain Barrier (BBB) Score the BBB Score - bbb() returns the BBB Score of the input molecule
  • bemisMurckoFrameworkLoose
  • bmfl
 DGTK generates the Bemis-Murcko Loose Framework (BMLF, which is generated from the BMF by removing side chains, keeping exocyclic non-single bonded atoms, while not changing the remaining atom and bond types) of the input molecule the BMLF - bmfl() returns the BMFL of the input molecule
  • bemisMurckoFrameworkLoosePruned
  • bmflp
 DGTK generates the Bemis-Murcko Loose Pruned Framework (BMFLP, which is generated from the BMF by removing side chains. Atom and bond types are generalised by replacing all atoms with carbon atoms and setting all bond types to single. Exocyclic non-single bonded atoms are kept as single bonded carbons.) the BMFLP - bmflp() returns the BMFLP of the input molecule
bmf DGTK generates the Bemis-Murcko Framework (BMF) of the input molecule the BMF - bmf() returns the BMF of the input molecule
bondCount - calculates the bond count the bond count - bondCount() returns the number of bonds in the input molecule
bondType DGTK returns the bond type between two atoms the bond type between two atoms or -1 if there is no bond between the two atoms the (1-based) atom indices of the two atoms in a string "index1-index2" (e.g. '2-3') bondType('2-3') and bondType(bond(1, 2)) both return the bond type between atoms 1 and 2 of the input molecule
booleanToNumber - returns the numerical representation of a boolean value (true = 1, false = 0) or the number itself if the input is a number the numerical representation of a boolean value boolean expression or number booleanToNumber(hasValenceError()) returns 0 for molecules having no valence error
canonicalResonant - generates the canonical resonant structure the canonical resonant structure - canonicalResonant() returns the canonical resonant structure of the input molecule
canonicalTautomer DGTK, SPTK generates the canonical tautomer structure the canonical tautomer the normalization option normal (the default is false) canonicalTautomer('normal:true') returns the normal canonical tautomer of the input molecule
carboaliphaticRingCount DGTK calculates the number of carboaliphatic rings in the molecule the number of carboaliphatic rings - carboaliphaticRingCount() returns the number of carboaliphatic rings in the input molecule
carboaromaticRingCount DGTK calculates the number of carboaromatic rings in the molecule the number of carboaromatic rings - carboaromaticRingCount() returns the number of carboaromatic rings in the input molecule
carboRingCount DGTK calculates the number of carbocyclic rings in the molecule the number of carbocyclic rings - carboRingCount() returns the number of carbocyclic rings in the input molecule
carboRingCountOfSize DGTK calculates the number of carbocyclic rings of a given size the number of carbocyclic rings of the given size the ring size carboRingCountOfSize(6) returns the number of carbocyclic rings of size 6 in the input molecule
carboRings DGTK identifies the carbocyclic rings in the molecule atom indices of the carbocyclic rings in the molecule (or null if the molecule does not contain carbocyclic rings) - carboRings() returns the atom indices of the carbocyclic rings in the input molecule
carboRingsOfSize DGTK identifies the carbocyclic rings in the molecule having a given size atom indices of the carbocyclic rings in the molecule having the given size (or null if the molecule does not carbocyclic rings) the ring size carboRingsOfSize(6) returns the atom indices of the carbocyclic rings of size 6 in the input molecule
chainAtom DGTK checks if the specified atom is a chain atom true for chain atoms, false for non-chain atoms the atom index/MolAtom object chainAtom(2) returns true if atom 2 of the input molecule is a chain atom, false otherwise
chainAtomCount DGTK calculates the chain atom count the chain atom count - chainAtomCount() returns the number of chain atoms in the input molecule
chainBond DGTK checks if two atoms are connected by a chain bond true if the two atoms are connected by a chain bond, false otherwise the (1-based) atom indices of the two atoms in a string "index1-index2" (e.g. '2-3') chainBond('2-3') and chainBond(bond(1, 2)) both return true if atoms 1 and 2 are connected by a chain bond in the input molecule
chainBondCount DGTK calculates the chain bond count the chain bond count - chainBondCount() returns the number of chain bonds in the input molecule
charge DGTK
  • calculates partial charges of atoms for the "aromaticsystem" and the "aromaticring" result types
  • calculates the sum of partial charges of the atoms in the aromatic system or the smallest aromatic ring containing the atom
 the partial charge values
  • atom index or MolAtom object
  • the result type ("total" (default), "pi", "sigma", "aromaticsystem", etc.)
  • pH value
  • charge(0) returns the partial charge of atom 0 of the input molecule
  • charge(2, "pi", "7.4") returns the partial "pi" charge of atom 2 of the major microspecies taken at pH 7.4
  • chargeDensity
  • totalChargeDensity
 DGTK calculates the charge density of atoms the charge density of the atom or NaN for non-existing values
  • the atom index/MolAtom object
  • the major microspecies pH
 chargeDensity(2) returns the charge density of atom 2 of the input molecule or NaN for non-existing value
check - checks a structure for errors according to a configuration and returns an error report the error report the structure checker/fixer configuration as an action string or an XML string check("aromaticity..valence") checks aromaticity and valence errors in the input molecule and returns an error report
checkErrorCount - checks a structure for errors according to a configuration and returns the total error count the total error count the structure checker/fixer configuration as an action string or an XML string checkErrorCount("aromaticity..valence") checks aromaticity and valence errors in the input molecule and returns the total error count
chiralCenter DGTK checks if the specified atom is a tetrahedral stereogenic center true for tetrahedral stereogenic center atoms the atom index/MolAtom object chiralCenter(2) returns true if atom 2 of the input molecule is a tetrahedral stereogenic center, false otherwise
chiralCenterCount DGTK calculates the number of tetrahedral stereogenic center atoms the tetrahedral stereogenic center count - chiralCenterCount() returns the number of tetrahedral stereogenic centers in the input molecule
chiralCenters DGTK determines the chiral center atoms indices of chiral center atoms - chiralCenters() returns the indices of the chiral center atoms in the input molecule
composition - returns the composition the composition - composition() returns the composition of the input molecule
conformer DGTK generates a conformer of the molecule the conformer the conformer index (0-based) conformer(0) returns the first conformer of the input molecule
conformerCount DGTK returns the number of generated conformers the number of generated conformers - conformerCount() returns the number of generated conformers of the input molecule
conformers DGTK generates conformers of the molecule (maximum number of conformers to be generated can be set, default: 100) the conformer array - conformers() generates conformers of the input molecule in an array
connected DGTK checks if two atoms are connected true if the two atoms belong to the same connected component, false otherwise the (1-based) atom indices of the two atoms in a string "index1-index2" (e.g. '2-3') 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
connectedGraph DGTK checks whether the molecule graph is connected true if the molecule graph is connected, false otherwise - connectedGraph() returns true if the input molecule graph is connected
connections - returns the bond plus implicit H count of an atom the bond plus implicit H count atom index or MolAtom object connections(2) returns the number of connections of atom 2
count - determines the number of elements in an array the number of elements in the array integer or real number array count(filter("charge() > 0")) returns the number of positively charged atoms of the molecule
cyclomaticNumber DGTK calculates the cyclomatic number the cyclomatic number - cyclomaticNumber() returns the cyclomatic number of the input molecule
dihedral DGTK calculates the dihedral angle of four atoms the dihedral angle of four atoms the (1-based) atom indices of the four atoms in a string "index1-index2-index3-index4" (e.g. '2-3-7-4') dihedral('1-2-3-4') and dihedral(atoms(0, 1, 2, 3)) both return the dihedral angle of atoms 1, 2, 3 and 4 in the input molecule
disjointMatchCount Structure Search performs substructure search and returns the maximal number of pairwise disjoint search hits the maximal number of pairwise disjoint search hits
  • target atom index/MolAtom object (optional)
  • query Molecule object/SMARTS string
  • query atom map(s) (optional)
 disjointMatchCount("[#8]C=O") counts the maximal number of pairwise disjoint carboxylic groups in the input molecule
dissimilarity - calculates the dissimilarity value between two molecules (see the Notes below the table) the dissimilarity value
  • descriptor:metric or descriptor (optional)
  • one or two molecules
  • 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 the default fingerprint (Chemical Fingerprint with Tanimoto metric)
distance DGTK calculates the distance between two atoms the distance between the two atoms the (1-based) atom indices of the two atoms in a string "index1-index2" (e.g. '2-3') distance('1-2') and distance(pair(0, 1)) both return the distance between atoms 1 and 2 in the input molecule
distanceDegree DGTK calculates the distance degree of an atom the distance degree the atom index/MolAtom object distanceDegree(2) returns the distance degree of atom 2 of the input molecule
  • dominantTautomer
  • tautomer
 DGTK, SPTK returns a dominant tautomeric form the dominant tautomer
  • the dominant tautomer index (0-based)
  • the pH value
  • dominantTautomer(0) returns the first dominant tautomer of the input molecule with no pH effect considered
  • dominantTautomer(1, "2.0") returns the second dominant tautomer of the input molecule at pH 2.0
dominantTautomerCount DGTK, SPTK calculates the number of dominant tautomers the number of dominant tautomers the pH value as string dominantTautomerCount("7.4") returns the number of dominant tautomers of the input molecule at pH 7.4
  • dominantTautomers
  • tautomers
 DGTK, SPTK generates all dominant tautomers ordered by distribution % the dominant tautomers in an array the pH value as a string
  • dominantTautomers() returns all dominant tautomers of the input molecule in an array
  • dominantTautomers("2.0") returns all dominant tautomers of the input molecule at pH 2.0 in an array
  • donor
  • don
 DGTK calculates atomic hydrogen bond donor multiplicity the atomic hydrogen bond donor multiplicity
  • the atom index/MolAtom object
  • the major microspecies pH
 donor(1, "7.4") returns the hydrogen bond donor multiplicity on atom 1 of the major microspecies at pH 7.4
donorCount DGTK calculates molecular hydrogen bond donor count the molecular hydrogen bond donor count the major microspecies pH donorCount("7.4") returns the number of hydrogen bond donor atoms in the major microspecies of the input molecule at pH 7.4
  • donorSiteCount
  • donSiteCount
 DGTK calculates the molecular hydrogen bond donor multiplicity the molecular hydrogen bond donor multiplicity the major microspecies pH donorSiteCount("7.4") returns the hydrogen bond donor multiplicity of the major microspecies at pH 7.4
dotDisconnectedFormula - returns the dot-disconnected formula the dot-disconnected formula - dotDisconnectedFormula() returns the dot-disconnected formula of the input molecule
dotDisconnectedIsotopeFormula - returns the dot-disconnected isotope formula the dot-disconnected isotope formula - dotDisconnectedIsotopeFormula() returns the dot-disconnected isotope formula of the input molecule
doubleBondStereoisomer DGTK, SPTK generates a double bond stereoisomer of the molecule the double bond stereoisomer the double bond stereoisomer index (0-based) doubleBondStereoisomer(0) returns the first double bond stereoisomer of the input molecule
doubleBondStereoisomerCount DGTK, SPTK returns the number of generated double bond stereoisomers the number of generated double bond stereoisomers - doubleBondStereoisomerCount() returns the number of generated double bond stereoisomers of the input molecule
doubleBondStereoisomers DGTK, SPTK generates double bond stereoisomers of the molecule the double bond stereoisomer array the maximum number of stereoisomers to be generated doubleBondStereoisomers(100) returns at most 100 double bond stereoisomers of the input molecule in an array
dreidingEnergy DGTK returns the Dreiding energy of the input molecule (conformer) the dreiding energy - dreidingEnergy() returns the Dreiding energy of the input molecule (conformer)
eccentricity DGTK calculates the eccentricity of an atom the eccentricity of the atom the atom index/MolAtom object eccentricity(2) returns the eccentricity of atom 2 of the input molecule
  • electronDensity
  • piChargeDensity
 DGTK calculates the electron density of an atom the electron density of the atom or NaN for non-existing values
  • the atom index/MolAtom object
  • the major microspecies pH
 electronDensity(2) returns the electron density of atom 2 of the input molecule or NaN for non-existing values
  • electrophilicity
  • energyNu
  • nucleophilicLocalizationEnergy
 DGTK calculates the electrophilicity of an atom the electrophilicity of the atom or NaN for non-aromatic atoms
  • the atom index/MolAtom object
  • the major microspecies pH
 electrophilicity(2) returns the electrophilicity of atom 2 of the input molecule or NaN if atom 2 is non-aromatic
  • electrophilicityOrder
  • aromaticElectrophilicityOrder
  • orderEA
 DGTK calculates the electrophilicity (E+) order of an atom the E+ order of the atom
  • the atom index/MolAtom object
  • the major microspecies pH
 electrophilicityOrder(2) returns the E+ order of atom 2 of the input molecule
  • elementalAnalysis
  • elemanal
 - performs elemental analysis on the molecule represented by its formula the property calculated by the function parameter (e.g. mass)
  • molecular formula
  • available function parameters: atomCount, mass, massPrecision, exactMass, exactMassPrecision, formula, isotopeFormula, dotDisconnectedFormula, dotDisconnectedIsotopeFormula, groupedDotDisconnectedFormula
 elementalAnalysis('mass','C12H25O') returns the mass of molecule represented by its formula
eval - evaluates a boolean expression the evaluation result (0 or 1) boolean expression eval('charge() > 0') determines if the atoms of a molecule are positively charged
exactMass - calculates the exact mass of the molecule the exact mass - exactMass() returns the exact mass of the input molecule
field - returns a molecule property (SDF field value) the molecule property the property key (SDF field name)
  • field('ACTIVITY') returns the value of the ACTIVITY property (SDF field)
  • field('ACTIVITY') > 2 returns 1 if the ACTIVITY property value is bigger than 2, 0 otherwise
  • fieldAsString
  • propertyAsString
 - returns a molecule property (SDF field value) as string the molecule property as string the property key (SDF field name) fieldAsString('ID') returns the value of the ID property (SDF field)
filter - filters target atoms by a 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)
 filter("charge() > 0") returns the indices of atoms with positive partial charge of the molecule
fix - checks a structure for errors according to a configuration and fixes them the fixed structure the structure checker/fixer configuration as an action string or an XML string fix("chiralflag..isotope->converttoelementalform") searches for chiral flags and isotopes and then removes them or converts them to elemental form
  • formalCharge
  • totalCharge
 - calculates the formal charge of the molecule the formal charge value atom index or MolAtom object (optional)
  • formalCharge() returns the formal charge of the input molecule
  • formalCharge(0) returns the formal charge of atom 0
formula - returns the formula the formula - formula() returns the formula of the input molecule
fragmentCount DGTK returns the number of fragments (disconnected parts) of a molecule the fragment count - fragmentCount() returns the number of fragments in the input molecule
fragments - converts the molecule into its disconnected fragments the disconnected fragments of the molecule - fragments() returns the disconnected fragments of the molecule
fsp3 DGTK returns the fsp3 of the molecule the fsp3 value - fsp3() returns the fsp3 value of the input molecule
fusedAliphaticRingCount DGTK calculates the number of fused aliphatic rings (SSSR = smallest set of smallest aliphatic rings) the fused aliphatic ring count - fusedAliphaticRingCount() returns the number of fused aliphatic rings in the input molecule
fusedAliphaticRingCountOfSize DGTK calculates the number of fused aliphatic rings of a given size the number of fused aliphatic rings of the given size the ring size fusedAliphaticRingCountOfSize(6) returns the number of fused aliphatic rings of size 6 in the input molecule
fusedAliphaticRings DGTK identifies the fused aliphatic rings in the molecule the atom indices of the fused aliphatic rings in the molecule (or null if the molecule does not contain fused aliphatic rings) - fusedAliphaticRings() returns the atom indices of the fused aliphatic rings in the input molecule
fusedAliphaticRingsOfSize DGTK identifies the fused aliphatic rings having a given size (number of atoms) in the molecule the atom indices of the fused aliphatic rings having the given size (or null if the molecule does not contain fused aliphatic rings) the ring size fusedAliphaticRings() returns the atom indices of the fused aliphatic rings having the given size in the input molecule
fusedAromaticRingCount DGTK calculates the number of fused aromatic rings (SSSR = smallest set of smallest aromatic rings) the fused aromatic ring count - fusedAromaticRingCount() returns the number of fused aromatic rings in the input molecule
fusedAromaticRingCountOfSize DGTK calculates the number of fused aromatic rings of a given size the number of fused aromatic rings of the given size the ring size fusedAromaticRingCountOfSize(6) returns the number of fused aromatic rings of size 6 in the input molecule
fusedAromaticRings DGTK identifies the fused aromatic rings in the molecule the atom indices of the fused aromatic rings in the molecule (or null if the molecule does not contain fused aromatic rings) - fusedAromaticRings() returns the atom indices of the fused aromatic rings in the input molecule
fusedAromaticRingsOfSize DGTK identifies the fused aromatic rings having a given size (number of atoms) the atom indices of the fused aromatic rings having the given size in the molecule (or null if the molecule does not contain fused aromatic rings) the ring size fusedAromaticRings() returns the atom indices of the fused aromatic rings having the given size in the input molecule
fusedRingCount DGTK calculates the number of fused rings (SSSR = smallest set of smallest rings) the fused ring count - fusedRingCount() returns the number of fused rings in the input molecule
genericTautomer DGTK, SPTK generates the generic tautomer structure the generic tautomer structure - genericTautomer() returns the generic tautomer structure of the input molecule
groupedDotDisconnectedFormula - returns the grouped dot-disconnected formula the grouped dot-disconnected formula - groupedDotDisconnectedFormula() returns the grouped dot-disconnected formula of the input molecule
hararyIndex DGTK calculates the Harary index the Harary index - hararyIndex() calculates the Harary index of the input molecule
hasAromatizationError - determines if there is error in the aromatization of the molecule true if there is an error, false otherwise - hasAromatizationError() returns true if there is an error in the aromatization of the molecule, false otherwise
hasIsotope - determines if any atom of the molecule is a specific isotope of the element true if any atom is a specific isotope, false otherwise - hasIsotope() returns true if any atom in the molecule is a specific isotope of the element, false otherwise
hasRadical - determines if any atom in the molecule has a radical true if any atom has a radical, false otherwise - hasRadical() returns true if any atom in the molecule has a radical, false otherwise
hasValenceError - determines if the molecule has a valence error true if the molecule has a valence error, false otherwise - hasValenceError() returns true if the molecule has a valence error, false otherwise
hasValidConformer DGTK checks if the input molecule is in 3D space (has a valid conformer) true if the input molecule is in 3D space - hasValidConformer() returns true if the input molecule is in 3D space
hCount - returns the hydrogen count of an atom the hydrogen count atom index, an array of atom indices or MolAtom object hCount(0,2,3) returns the hydrogen count of atom 0, 2 and 3
herg DGTK predicts hERG activity and returns the pActivity value the pActivity value - herg() returns the predicted hERG pActivity value of the input molecule
hergActivity DGTK predicts hERG activity (as pActivity) the pActivity value - hergActivity() returns the predicted hERG pActivity of the input molecule
hergClass DGTK predicts the hERG classification class the classification class (SAFE or TOXIC) - hergClass() returns the predicted hERG classification class of the input molecule
heteroaliphaticRingCount DGTK calculates the number of aliphatic heterocyclic rings (SSSR = smallest set of smallest aliphatic rings) the aliphatic heterocyclic ring count - heteroaliphaticRingCount() returns the number of aliphatic heterocyclic rings in the input molecule
heteroaliphaticRingCountOfSize DGTK calculates the number of aliphatic heterocyclic rings of a given size the number of aliphatic heterocyclic rings of the given size the ring size heteroaliphaticRingCountOfSize(6) returns the number of aliphatic heterocyclic rings of size 6 in the input molecule
heteroaliphaticRings DGTK identifies the aliphatic heterocyclic rings in the molecule atom indices of the aliphatic heterocyclic rings in the molecule (or null if the molecule does not contain aliphatic heterocyclic rings) - heteroaliphaticRings() returns the atom indices of the aliphatic heterocyclic rings in the input molecule
heteroaliphaticRingsOfSize DGTK identifies the aliphatic heterocyclic rings having a given size atom indices of the aliphatic heterocyclic rings having the given size (or null if the molecule does not contain aliphatic heterocyclic rings) the ring size heteroaliphaticRingsOfSize() returns the atom indices of the aliphatic heterocyclic rings having the given size in the input molecule
heteroaromaticRingCount DGTK calculates the number of aromatic heterocyclic rings (SSSR = smallest set of smallest aromatic rings) the aromatic heterocyclic ring count - heteroaromaticRingCount() returns the number of aromatic heterocyclic rings in the input molecule
heteroaromaticRingCountOfSize DGTK calculates the number of aromatic heterocyclic rings of a given size the number of aromatic heterocyclic rings of the given size the ring size heteroaromaticRingCountOfSize(6) returns the number of aromatic heterocyclic rings of size 6 in the input molecule
heteroaromaticRings DGTK identifies the aromatic heterocyclic rings in the molecule atom indices of the aromatic heterocyclic rings in the molecule (or null if the molecule does not contain aromatic heterocyclic rings) - heteroaromaticRings() returns the atom indices of the aromatic heterocyclic rings in the input molecule
heteroaromaticRingsOfSize DGTK identifies the aromatic heterocyclic rings in the molecule having a given size atom indices of the aromatic heterocyclic rings having the given size (or null if the molecule does not contain aromatic heterocyclic rings) the ring size heteroaromaticRingsOfSize() returns the atom indices of the aromatic heterocyclic rings in the input molecule having the given size
heteroRingCount DGTK calculates the number of heterocyclic rings (SSSR = smallest set of smallest rings) the heterocyclic ring count - heteroRingCount() returns the number of heterocyclic rings in the input molecule
heteroRingCountOfSize DGTK calculates the number of heterocyclic rings of a given size the number of heterocyclic rings of the given size the ring size heteroRingCountOfSize(6) returns the number of heterocyclic rings of size 6 in the input molecule
heteroRings DGTK identifies the heterocyclic rings in the molecule atom indices of the heterocyclic rings in the molecule (or null if the molecule does not contain heterocyclic rings) - heteroRings() returns the atom indices of the heterocyclic rings in the input molecule
heteroRingsOfSize DGTK identifies the heterocyclic rings in the molecule having a given size atom indices of the heterocyclic rings having the given size (or null if the molecule does not contain heterocyclic rings) the ring size heteroRingsOfSize(6) returns the atom indices of the heterocyclic rings in the input molecule having size of 6
hlb DGTK calculates the HLB number the HLB number the HLB method (chemaxon, davies, griffin, required; default: chemaxon)
  • hlb() returns the HLB number of the input molecule calculated by the ChemAxon method
  • hlb('davies') returns the HLB number of the input molecule calculated by the Davies method
hmoChargeDensity DGTK calculates the HMO charge density of an atom the charge density of the atom or NaN for non-existing values
  • the atom index/MolAtom object
  • the major microspecies pH
 hmoChargeDensity(2) returns the charge density of atom 2 of the input molecule or NaN for non-existing values
hmoElectronDensity DGTK calculates the HMO electron density of an atom the electron density of the atom or NaN for non-existing values
  • the atom index/MolAtom object
  • the major microspecies pH
 hmoElectronDensity(2) returns the electron density of atom 2 of the input molecule or NaN for non-existing values
  • hmoElectrophilicityOrder
  • hmoOrderE
 DGTK calculates HMO electrophilic (HMO E+) order of an atom the HMO E+ order index of the atom (0, 1, 2, ...)
  • the atom index/MolAtom object
  • the major microspecies pH
 hmoElectrophilicityOrder(2) returns the HMO E+ order index of atom 2 of the input molecule
hmoElectrophilicLocalizationEnergy DGTK calculates the HMO localization energy (L+) of an atom the localization energy (L+) of the atom or NaN for non-aromatic atoms
  • the atom index/MolAtom object
  • the major microspecies pH
 hmoElectrophilicLocalizationEnergy(2) returns the L+ energy of atom 2 of the input molecule or NaN if atom 2 is non-aromatic
  • hmoNucleophilicityOrder
  • hmoOrderNu
 DGTK calculates the HMO nucleophilic (HMO Nu-) order index of the atom the HMO Nu- order index of the atom (0, 1, 2, ...)
  • the atom index/MolAtom object
  • the major microspecies pH
 hmoNucleophilicityOrder(2, '7.4') returns the Nu- order index of atom 2 of the major microspecies of the input molecule at pH 7.4
hmoNucleophilicLocalizationEnergy DGTK calculates the HMO nucleophilic (HMO L-) localization energy of an atom the HMO L- energy of the atom or NaN for non-aromatic atoms
  • the atom index/MolAtom object
  • the major microspecies pH
 hmoNucleophilicLocalizationEnergy(2) returns the nucleophilic localization energy of atom 2 of the input molecule or NaN if atom 2 is non-aromatic
hmoPiEnergy DGTK calculates the HMO pi energy of the molecule the HMO pi energy of the molecule
  • the atom index/MolAtom object
  • the major microspecies pH
 hmoPiEnergy('7.4') returns the pi energy of the major microspecies of the input molecule at pH 7.4
hyperWienerIndex DGTK calculates the Hyper Wiener index the Hyper Wiener index - hyperWienerIndex() calculates the Hyper Wiener index of the input molecule
importMol - imports and returns the molecule from its string representation the string representation of the molecule the molecule imported importMol("c1ccccc1") returns the benzene molecule
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, a MolAtom object or an integer array
  • in(3, maxatom("charge()", 2)) returns true if the partial charge of atom 3 is in the first 2 largest partial charges of the input molecule
  • in(3, minatom("pol()", 4)) returns true if the polarizability of atom 3 is in the first 4 smallest polarizability values of the input molecule
isEmpty - decides whether a molecule is empty true if the molecule is empty - isEmpty() returns true if the molecule is empty, false otherwise
isMarkush - decides whether a molecule contains any Markush features true if the molecule contains any Markush features, false otherwise - isMarkush() returns true if the given molecule contains any Markush features, false otherwise
  • isoelectricPoint
  • pI
 DGTK, SPTK calculates the isoelectric point the isoelectric point - isoelectricPoint() returns the isoelectric point of the input molecule
isotopeComposition - returns the isotope composition the isotope composition - isotopeComposition() returns the isotope composition of the input molecule
isotopeFormula - returns the isotope formula the isotope formula - isotopeFormula() returns the isotope formula of the input molecule
isQuery - decides whether a molecule contains any query features true if the molecule contains any query features, false otherwise - isQuery() returns true if the molecule contains any query features, false otherwise
isValid - checks if a structure is valid (has no errors) according to a configuration true if the structure is valid, false otherwise the structure checker/fixer configuration as an action string or an XML string isValid("aromaticity..valence") checks for aromaticity and valence errors and returns if the structure is valid
largestAtomRingSize DGTK calculates the size of the largest ring containing a specified atom the size of the largest ring containing the specified atom the atom index/MolAtom object largestAtomRingSize(1) returns the size of the largest ring containing atom 1 in the input molecule
largestConjugatedSystem DGTK returns the atom list of the largest conjugated system of the molecule the atom list of the largest conjugated system - largestConjugatedSystem() returns the atom list of the largest conjugated system in the input molecule
largestConjugatedSystemMol DGTK returns the input molecule with its largest conjugated system coloured in green the input molecule with its largest conjugated system coloured in green - largestConjugatedSystemMol() returns the input molecule with its largest conjugated system coloured in green
largestConjugatedSystemSize DGTK returns the number of pi electron pairs in the largest conjugated system of the molecule the number of pi electron pairs in the largest conjugated system - largestConjugatedSystemSize() returns the number of pi electron pairs in the largest conjugated system of the input molecule
largestRing DGTK identifies the atoms of the largest ring in the molecule the atom indices of the largest ring in the molecule (or null if the input molecule is acyclic) - largestRingSize() returns the atom indices of the largest ring in the input molecule
largestRingSize DGTK calculates the largest ring size in the molecule the largest ring size - largestRingSize() returns the size of the largest ring in the input molecule
largestRingSystem DGTK identifies the atoms of the largest ring system in the molecule atom indices of the largest ring system (or null if the molecule is acyclic) - largestRingSystem() returns the atom indices of the largest ring system in the input molecule
largestRingSystemSize DGTK calculates the size of the largest ring system (=number of rings) the size of the largest ring system - largestRingSystemSize() returns the size of the largest ring system in the input molecule
logD DGTK calculates logD at a specified pH value using the ChemAxon method the logD value the pH value logD('7.4') returns the logD value of the input molecule at pH 7.4
logDKLOP DGTK calculates logD at a specified pH value using the Klopman method the logD value the pH value logDKLOP('7.4') returns the logD at pH 7.4 of the input molecule
logDPHYS DGTK calculates logD at a specified pH value using the PhysProp method the logD value the pH value logDPHYS('7.4') returns the logD at pH 7.4 of the input molecule
logDUser DGTK calculates logD at a specified pH value using the user defined method the logD value the pH value logDUser('7.4') returns the logD value at pH 7.4 of the input molecule
logDVG DGTK calculates logD at a specified pH value using the VG method the logD value the pH value logDVG('7.4') returns the logD at pH 7.4 of the input molecule
logDWeighted DGTK calculates logD at a specified pH value using the weighted method the logD value the pH value logDWeighted('7.4') returns the logD at pH 7.4 of the input molecule
logP DGTK calculates the logP the logP value the value type: logPMicro, logPNonionic, logDpI, logPTrue (default) logP() returns the most typical logP of the input molecule
  • logPincrement
  • logPi
 DGTK calculates atomic logP increments the atomic logP increment the atom index/MolAtom object logPincrement(2) returns the logP increment on atom 2 of the input molecule
logPKLOP DGTK calculates logP using the Klopman method the logP value the value type: logPMicro, logPNonionic, logDpI, logPTrue (default)
  • logPKLOP() returns the most typical logP value of the input molecule
  • logPKLOP('logPMicro') returns the logP of the input molecule itself
logPPHYS DGTK calculates logP using the PhysProp method the logP value the value type: logPMicro, logPNonionic, logDpI, logPTrue (default)
  • logPPHYS('logPNonionic') returns the non-ionic logP of the input molecule
  • logPPHYS('logPMicro') returns the logP of the input molecule itself
logPUser DGTK calculates logP using the user defined method the logP value the value type: logPMicro, logPNonionic, logDpI, logPTrue (default) logPUser() returns the most typical logP of the input molecule
logPVG DGTK calculates the logP using the VG method the logP value the value type: logPMicro, logPNonionic, logDpI, logPTrue (default)
  • logPVG() returns the most typical logP value of the input molecule
  • logPVG('logPMicro') returns the logP of the input molecule itself
logPWeighted DGTK calculates the logP using the weighted method the logP value the value type: logPMicro, logPNonionic, logDpI, logPTrue (default)
  • logPWeighted() returns the most typical logP value of the input molecule
  • logPWeighted('logPMicro') returns the logP of the input molecule itself
logS DGTK calculates intrinsic or pH-dependent solubility (logS) the logS value
  • the pH value (for pH-dependent logS)
  • the solubility unit: logS, mol/l, mg/ml or category (default: logS)
  • logS('mol/l') returns the intrinsic solubility of the input molecule in mol/l unit
  • logS('7.4', 'category') returns the solubility category of the input molecule at pH 7.4
  • lowestEnergyConformer
  • leconformer
 DGTK generates the lowest energy conformer of the molecule the lowest energy conformer - lowestEnergyConformer() returns the lowest energy conformer of the input molecule
  • majorMicrospecies
  • majorMs
 DGTK, SPTK calculates the major microspecies at a specified pH value the major microspecies the pH value as a string majorMicrospecies("7.4") returns the major microspecies of the input molecule at pH 7.4
majorTautomer DGTK, SPTK generates the major tautomer structure the major tautomer structure the pH value as a string majorTautomer('7.4') returns the major tautomer structure of the input molecule at pH 7.4
map - returns the atom map number the atom map number atom index or MolAtom object map(3) returns the atom map number of atom 3
  • markushEnumeration
  • markushEnumerations
  • enumeration
  • enumerations
 SETK enumerates Markush structures sequentially the enumerated structures
  • the number of structures to be enumerated
  • the (1-based) atom indices of the query atoms to be enumerated
  • markushEnumerations() returns all Markush enumerated structures of the input molecule
  • markushEnumerations(5, '2,3') returns five Markush enumerated structures of the input molecule, enumerating atoms 2, 3
  • markushEnumerationCount
  • enumerationCount
 SETK calculates the number of Markush enumerations the number of Markush enumerations the (1-based) atom indices of the query atoms to be enumerated
  • 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
markushEnumerationsDisplay SETK generates Markush enumerated structures sequentially with scaffold alignment and scaffold/R-group colouring and enumeration ID the enumerated structures with alignment, colouring data and enumeration ID
  • the number of structures to be returned
  • the (1-based) atom indices of the query atoms to be enumerated
  • markushEnumerationsDisplay() returns all Markush enumerated structures of the input molecule with scaffold alignment and colouring data
  • markushEnumerationsDisplay(10, '2,3') returns ten Markush enumerated structures of the input molecule, enumerating atoms 2, 3
markushLibraryMagnitude SETK calculates the Markush library magnitude with no enumeration the Markush library magnitude the (1-based) atom indices of the query atoms to be enumerated
  • markushLibraryMagnitude() returns the Markush library magnitude for the input molecule
  • markushLibraryMagnitude('4,5') returns the Markush library magnitude for the input molecule with only atoms 4, 5 being enumerated
markushLibrarySize SETK calculates the Markush library size with no enumeration the Markush library size the (1-based) atom indices of the query atoms to be enumerated
  • markushLibrarySize() returns the Markush library size for the input molecule
  • markushLibrarySize('4,5') returns the Markush library size for the input molecule with only atoms 4, 5 being enumerated
markushLibrarySizeAsString SETK calculates the Markush library size and returns it as a string with no enumeration done the Markush library size the (1-based) atom indices of the query atoms to be enumerated
  • markushLibrarySize() returns the Markush library size as string for the input molecule
  • markushLibrarySize('4,5') returns the Markush library size as a string for the input molecule with only atoms 4, 5 being enumerated
mass - calculates the molecule mass the mass - mass() returns the mass of the input molecule
massspectrum - calculates the mass spectrum (the m/z:relative abundance plot) the mass spectrum as a series of discrete values - massspectrum() returns the mass spectrum of the input molecule
match Structure Search performs substructure search and optionally checks for atom matching true if a matching substructure found, false otherwise
  • target atom index/MolAtom object (optional)
  • query Molecule object/SMARTS string
  • query atom map(s) (optional)
 match("[#8]C=O") performs substructure search without atom matching requirement
matchCount Structure Search performs substructure search and counts search hits the number of search hits
  • target atom index/MolAtom object (optional)
  • query Molecule object/SMARTS string
  • query atom map(s) (optional)
 matchCount("[#8]C=O") counts search hits without atom matching requirement
matchFirst Structure Search performs substructure search and optionally checks for atom matching the (1-based) index of the first matching substructure
  • target atom index/MolAtom object (optional)
  • query Molecule objects/SMARTS strings in collection
  • query atom map(s) (optional)
  • matchFirst({amine,amide,alcohol}) performs substructure search without atom matching requirement
  • matchFirst(6, {"[#8][C:1]=O","[NX3:2][CX3:1]=[OX1:3]"}, 1) checks if target atom 6 matches the carbon atom with map 1 of the carboxylic or amide group
max - takes the maximum of numerical values and arrays the maximum value integers, real numbers, integer arrays, real number arrays
  • max(charge(0), charge(2)) returns the maximum of the partial charge values of atoms 0 and 2
  • max(charge()) returns the maximal atomic partial charge value of the input molecule
maxAtom - evaluates an objective function for atoms and finds largest value(s) the atom index/indices corresponding to the largest evaluation result(s) target atom indices/objects or index/atom object array; the function (as inner expression string); the number of largest values maxAtom(6, 7, 8, 9, "charge('7.4')", 2) selects the two largest partial charges of atoms 6, 7, 8, 9 in the major microspecies at pH 7.4
maximalProjectionArea DGTK returns the maximal projection area the maximal projection area - maximalProjectionArea() returns the maximal projection area of the input molecule
maximalProjectionRadius DGTK returns the maximal projection radius the maximal projection radius - maximalProjectionRadius() returns the maximal projection radius of the input molecule
maximalProjectionSize DGTK returns the maximal distance in the molecule perpendicular to its maximal projection area the maximal distance - maximalProjectionSize() returns the maximal distance in the input molecule perpendicular to its maximal projection area
maxValue - evaluates an objective function for atoms and finds largest value(s) the largest evaluation value(s) target atom indices/objects or index/atom object array; the function (as inner expression string); the number of largest values maxValue(6, 7, 8, 9, "charge('7.4')", 2) returns the two largest partial charges of atoms 6, 7, 8, 9 in the major microspecies at pH 7.4
  • microspecies
  • ms
 DGTK, SPTK returns microspecies ranked based on their distribution % at a specified pH the microspecies
  • the pH value as a string
  • the (0-based) microspecies index
 microspecies('7.4', 1) returns the microspecies with the second largest distribution of the input molecule at pH 7.4
  • microspeciesCount
  • msCount
 DGTK, SPTK calculates the number of microspecies at a specified pH the number of microspecies the pH value as a string microspeciesCount('7.4') returns the number of microspecies of the input molecule at pH 7.4
  • microspeciesDistribution
  • msDistr
 DGTK, SPTK calculates microspecies distribution (in %) at a specified pH the microspecies distribution
  • the pH value as a string
  • the (0-based) microspecies index
 microspeciesDistribution("5.4", 0) returns the largest microspecies distribution of the input molecule at pH 5.4
min - takes the minimum of numerical values and arrays the minimum value integers, real numbers, integer arrays, real number arrays
  • min(charge(0), charge(2)) returns the least of the partial charge values of atoms 0 and 2
  • min(charge()) returns the minimal partial charge value on the input molecule
minAtom - evaluates an objective function for atoms and finds smallest value(s) the atom index/indices corresponding to the smallest evaluation result(s) target atom indices/objects or index/atom object array; the function (as inner expression string); the number of smallest values minAtom("charge('7.4')") returns the atom index corresponding to smallest atomic partial charge in the major microspecies at pH 7.4
minimalProjectionArea DGTK returns the minimal projection area the minimal projection area - minimalProjectionArea() returns the minimal projection area of the input molecule
minimalProjectionRadius DGTK returns the minimal projection radius the minimal projection radius - minimalProjectionRadius() returns the minimal projection radius of the input molecule
minimalProjectionSize DGTK returns the maximal distance in the molecule perpendicular to its minimal projection area the maximal distance - minimalProjectionSize() returns the maximal distance in the input molecule perpendicular to its minimal projection area
minValue - evaluates objective function for each atom and finds smallest value(s) the smallest evaluation result(s) target atom indices/objects or index/atom object array; the function (as inner expression string); the number of smallest values minValue("charge('7.4')") returns the smallest atomic partial charge in the major microspecies at pH 7.4
mmff94Energy DGTK returns the MMFF94 energy of the input molecule (conformer) the MMFF94 energy - mmff94Energy() returns the MMFF94 energy of the input molecule (conformer)
mmff94OptimizedStructure DGTK generates the MMFF94-optimized lowest energy conformer the MMFF94-optimized lowest energy conformer - mmff94OptimizedStructure() returns the MMFF94-optimized lowest energy conformer of the input molecule
molAtom - creates a MolAtom the MolAtom object atomic number molAtom(6) returns a carbon atom
  • molBinFormat
  • molImage
 - returns the binary representation of the molecule in the specified format the binary representation of the molecule the binary format with options (e.g. "jpeg", "png:w150,h150", "pdf", "gzip:sdf") molImage("jpeg:w100,Q95,#ffff00") returns the 100x100 JPEG image of the input molecule with yellow background with 95% quality
  • molecularPolarizability
  • molPol
 DGTK calculates molecular polarizability the polarizability value pH value
  • molecularPolarizability() returns the molecular polarizability of the input molecule
  • molecularPolarizability("7.4") returns the molecular polarizability of the major microspecies of the input molecule taken at pH 7.4
  • molString
  • molConvert
  • molFormat
 - returns the string representation of a molecule in a specified format the string representation of the molecule(s) the molecule format (e.g. "mol", "sdf", "mrv", "smiles"); the clean dimension
  • molFormat("mrv") returns the Chemaxon Marvin Document format representation of the input molecule
  • molFormat(tautomers(), "sdf", 2) returns the 2D-cleaned representation of the tautomers of the input molecule in SD format
mpo DGTK calculates the CNS Multiparameter Optimisation (MPO) Score the MPO score - mpo() returns the MPO score of the input molecule
name NTK returns the name(s) of a molecule specified by the export option the name(s) of the molecule either empty (the IUPAC export option) or the specified name export option
  • name() returns the preferred IUPAC name of the input molecule
  • name('CAS#') returns CAS Registry Number(s) of the input molecule
  • nucleophilicity
  • electrophilicLocalizationEnergy
  • energyE
 DGTK calculates nucleophilicity of an atom the nucleophilicity of the atom or NaN for non-aromatic atoms
  • the atom index/MolAtom object
  • the major microspecies pH
 nucleophilicity(2) returns the nucleophilicity of atom 2 of the input molecule or NaN if atom 2 is non-aromatic
  • nucleophilicityOrder
  • aromaticNucleophilicityOrder
  • orderNu
 DGTK calculates the nucleophilic (Nu-) order index of an atom the Nu- order index of the atom
  • the atom index/MolAtom object
  • the major microspecies pH
 nucleophilicityOrder(2) returns the Nu- order index of atom 2 of the input molecule
  • pair
  • bond
 - converts two atoms or 0-based atom indices into an "index1-index2" 1-based atom index setter string the generated string the two atom indices or the two MolAtom objects N/A
piEnergy DGTK calculates the pi energy of a molecule the pi energy of the molecule the major microspecies pH piEnergy() returns the pi energy of the input molecule
  • piOrbitalElectronegativity
  • pOEN
 DGTK calculates atomic pi orbital electronegativity the pi orbital electronegativity values
  • atom index or MolAtom object
  • pH value
  • 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 at pH 7.4
pKa DGTK, SPTK calculates pKa values the pKa values
  • the atom index/MolAtom object
  • the strength index as a string
  • the pKa result type ('acidic', 'basic' or 'pka')
  • pKa(0) returns the pKa values of atom 0 of the input molecule
  • pKa('acidic', '2') returns the second strongest acidic pKa value of the input molecule
  • pKa(2, 'basic', '1') returns the strongest basic pKa value of atom 2 of the input molecule
pKaUseCorrection DGTK, SPTK calculates pKa values using a correction library the pKa values
  • the atom index/MolAtom object
  • the strength index as a string
  • the pKa result type ('acidic', 'basic' or 'pka')
  • pKaUseCorrection(0) returns the pKa of atom 0 of the input molecule using the correction library
  • pKaUseCorrection('acidic', '2') returns the second strongest acidic pKa value using the correction library
plattIndex DGTK calculates the Platt index the Platt index - plattIndex() returns the Platt index of the input molecule
productCount - counts the products in a reaction the number of products in the reaction or -1 if the input is not a reaction - productCount() returns n if the input molecule is a reaction and contains n products
radicalCount - returns the radical count of an atom the radical count atom index or MolAtom object radicalCount(0) returns the radical count of atom 0
randicIndex DGTK calculates the Randic index the Randic index - randicIndex() calculates the Randic index of the input molecule
  • randomMarkushEnumeration
  • randomMarkushEnumerations
  • randomEnumeration
  • randomEnumerations
 SETK enumerates Markush structures randomly the enumerated structures
  • the number of structures to be enumerated (default is 1)
  • the (1-based) atom indices of the query atoms to be enumerated
  • randomMarkushEnumeration() returns a randomly enumerated Markush structure of the input molecule
  • randomMarkushEnumerations(4, '2,3') returns 4 randomly enumerated structures of the input molecule, enumerating only atoms 2, 3
randomMarkushEnumerationsDisplay SETK generates Markush enumerated structures randomly with scaffold alignment and scaffold/R-group colouring and enumeration ID the enumerated structures with alignment, colouring data and enumeration ID
  • the number of structures to be returned (default is 1)
  • the (1-based) atom indices of the query atoms to be enumerated
  • randomMarkushEnumerationsDisplay() returns a randomly enumerated Markush structure of the input molecule with scaffold alignment and scaffold/R-group colouring
  • randomMarkushEnumerationsDisplay(4, '2,3') returns 4 randomly enumerated structures of the input molecule, enumerating only atoms 2, 3 with scaffold alignment and colouring data
reactantCount - counts the reactants of a reaction the number of reactants of the reaction or -1 if the input is not a reaction - reactantCount() returns n if the given molecule is a reaction and contains n reactants else it returns -1
  • refractivity
  • refrac
 DGTK calculates molar refractivity the refractivity value - refractivity() returns the molar refractivity of the input molecule
  • refractivityIncrements
  • refraci
 DGTK calculates atomic refractivity increments the atomic refractivity increment the atom index/MolAtom object refractivityIncrements(2) returns the refractivity increment of atom 2 of the input molecule
resonant - generates a resonant structure of the molecule the resonant structure the resonant index (0-based) resonant(0) returns the first resonant structure of the input molecule
resonantCharge DGTK
  • calculates partial charges of atoms considering resonance effect for the "aromaticsystem" and the "aromaticring" result types
  • calculates the sum of partial charges of the atoms in the aromatic system or the smallest aromatic ring containing the atom
 the resonant charge values
  • atom index or MolAtom object
  • the result type
  • pH value
  • resonantCharge(0) returns the partial charge on atom 0 of the input molecule considering resonance effect
  • resonantCharge(2, "pi", "7.4") returns the partial "pi" charge on atom 2 of the major microspecies at pH 7.4 considering resonance effect
resonantCount - calculates the number of resonant structures of the input molecule the number of resonant structures - resonantCount() returns the number of resonant structures of the input molecule
resonants - generates all resonant structures of the input molecule the array of resonant structures - resonants() returns all resonant structures of the input molecule in an array
ringAtom DGTK checks if a specified atom is a ring atom true for ring atoms, false for non-ring atoms the atom index/MolAtom object ringAtom(2) returns true if atom 2 of the input molecule is a ring atom, false otherwise
ringAtomCount DGTK calculates the ring atom count the ring atom count - ringAtomCount() returns the number of ring atoms in the input molecule
ringBond DGTK checks if two atoms are connected by a ring bond true if the two atoms are connected by a ring bond, false otherwise the (1-based) atom indices of the two atoms in a string "index1-index2" (e.g. '2-3') ringBond('2-3') and ringBond(bond(1, 2)) both return true if atoms 1 and 2 are connected by a ring bond in the input molecule
ringBondCount DGTK calculates the ring bond count the ring bond count - ringBondCount() returns the number of ring bonds in the input molecule
ringCount DGTK calculates the ring count the ring count - ringCount() returns the number of rings in the input molecule
ringCountOfAtom DGTK calculates the number of rings passing through an atom the number of rings passing through the atom the atom index/MolAtom object ringCountOfAtom(2) returns the number of rings passing through atom 2 of the input molecule
ringCountOfSize DGTK calculates the number of rings of a given size the number of rings of the given size the ring size ringCountOfSize(6) returns the number of rings of size 6 in the input molecule
rings DGTK identifies the rings in the molecule atom indices of the rings in the molecule (or null if the molecule is acyclic) - rings() returns the atom indices of the rings in the input molecule
ringsOfSize DGTK identifies the rings in the molecule having a given size atom indices of the rings having the given size in the molecule the ring size ringsOfSize(6) returns the atom indices of the rings of size 6 in the input molecule
ringSystemCount DGTK calculates the number of ring systems the number of ring systems - ringSystemCount() returns the number of ring systems in the input molecule
ringSystemCountOfSize DGTK calculates the number of ring systems of a given size the number of ring systems of the given size the ring system size ringSystemCountOfSize(10) returns the number of 10-membered ring systems in the input molecule
ringSystems DGTK identifies the ring systems in the molecule atom indices of the ring systems in the molecule (or null if the molecule is acyclic) - ringSystems() returns the atom indices of the ring systems in the input molecule
ringSystemsOfSize DGTK identifies the ring systems in the molecule having a given size atom indices of the ring systems in the molecule having the given size the ring size ringSystemsOfSize(10) returns the atom indices of the 10-membered ring systems in the input molecule
rotatableBond DGTK checks if two atoms are connected by a rotatable bond true if the two atoms are connected by a rotatable bond, false otherwise the (1-based) atom indices of the two atoms in a string "index1-index2" (e.g. '2-3') rotatableBond('2-3') and rotatableBond(bond(1, 2)) both return true if atoms 1 and 2 are connected by a rotatable bond in the input molecule
rotatableBondCount DGTK calculates the rotatable bond count the rotatable bond count - rotatableBondCount() returns the number of rotatable bonds in the input molecule
shortestPath DGTK calculates the length of the shortest path between two atoms the length of the shortest path between two atoms (returns Integer.MAX_VALUE if the two atoms are disconnected) the (1-based) atom indices of the two atoms in a string "index1-index2" (e.g. '2-3') shortestPath('2-3') and shortestPath(pair(1, 2)) both return the shortest path length between atoms 1 and 2 in the input molecule
  • sigmaOrbitalElectronegativity
  • sOEN
 DGTK calculates atomic sigma orbital electronegativity the sigma orbital electronegativity values
  • atom index or MolAtom object
  • pH value
  • 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 at pH 7.4
smallestAtomRingSize DGTK calculates the size of the smallest ring containing a specified atom the size of the smallest ring containing the specified atom the atom index/MolAtom object smallestAtomRingSize(0) returns the size of the smallest ring containing atom 0 in the input molecule
smallestRing DGTK identifies the atoms of the smallest ring in the molecule atom indices of the smallest ring in the molecule (null when the molecule is acyclic) - smallestRing() returns the atom indices of the smallest ring in the input molecule
smallestRingSize DGTK calculates the smallest ring size the smallest ring size - smallestRingSize() returns the size of the smallest ring in the input molecule
smallestRingSystem DGTK identifies the atoms of the smallest ring system in the molecule atom indices of the smallest ring system in the molecule (null when the molecule is acyclic) - smallestRingSystem() returns the atom indices of the smallest ring system in the input molecule
smallestRingSystemSize DGTK calculates the size of the smallest ring system the size of the smallest ring system - smallestRingSystemSize() returns the size of the smallest ring system in the input molecule
sortableFormula - returns the fixed digit sortable molecular formula the fixed digit sortable molecular formula the number of digits (default is 4) sortableFormula('digits:2') returns the 2-digit sortable formula of the input molecule
sortAsc - sorts an array in ascending order the sorted array integer array or real number array sortAsc(charge()) returns the atomic partial charge values in ascending order
sortDesc - sorts an array in descending order the sorted array integer array or real number array sortDesc(pka("basic")) returns the basic pKa values in descending order
stereoAnalysis - recognises stereo descriptors in a molecule the list of stereo descriptors the stereo descriptor type
  • stereoAnalysis() returns all stereo descriptors of the input molecule
  • stereoAnalysis('tetrahedralStereoCenters') returns the array of tetrahedral stereocenters of the input molecule
stereoDoubleBondCount DGTK calculates the number of stereo double bonds the stereo double bond count - stereoDoubleBondCount() returns the number of stereo double bonds in the input molecule
stereoisomer DGTK, SPTK generates a stereoisomer of the molecule the stereoisomer the stereoisomer index (0-based) stereoisomer(0) returns the first stereoisomer of the input molecule
stereoisomerCount DGTK, SPTK returns the number of generated stereoisomers the number of generated stereoisomers - stereoisomerCount() returns the number of generated stereoisomers of the input molecule
stereoisomers DGTK, SPTK generates stereoisomers for a molecule the array of stereoisomers generated the maximum number of stereoisomers to be generated stereoisomers(10) returns maximum 10 stereoisomers of the input molecule in an array
stericEffectIndex DGTK calculates the steric effect index of an atom the steric effect index of the atom the atom index/MolAtom object stericEffectIndex(1) returns the steric effect index of atom 1
stericHindrance DGTK calculates the steric hindrance of an atom the steric hindrance of the atom the atom index/MolAtom object stericHindrance(2) returns the steric hindrance of atom 2 in the input molecule
sum - calculates the sum of elements in an array the sum integer array or real number array sum(charge()) returns the sum of the atomic partial charges
szegedIndex DGTK calculates the Szeged index the Szeged index - szegedIndex() calculates the Szeged index of the input molecule
tautomerCount DGTK, SPTK calculates the number of tautomers for a molecule the number of tautomers - tautomerCount() returns the number of tautomers of the input molecule
tetrahedralStereoisomer DGTK, SPTK generates a tetrahedral stereoisomer of a molecule the tetrahedral stereoisomer the stereoisomer index (0-based) tetrahedralStereoisomer(0) returns the first tetrahedral stereoisomer of the input molecule
tetrahedralStereoisomerCount DGTK, SPTK returns the number of generated tetrahedral stereoisomers the number of generated tetrahedral stereoisomers - tetrahedralStereoisomerCount() returns the number of generated tetrahedral stereoisomers of the input molecule
tetrahedralStereoisomers DGTK, SPTK generates tetrahedral stereoisomers for a molecule the tetrahedral stereoisomers in an array the maximum number of tetrahedral stereoisomers to be generated tetrahedralStereoisomers() returns all tetrahedral stereoisomers of the input molecule in an array
  • topologicalPolarSurfaceArea
  • PSA
 - calculates the (2D) topological polar surface area the polar surface area the major microspecies pH
  • topologicalPolarSurfaceArea() returns the polar surface area of the input molecule
  • topologicalPolarSurfaceArea('7.4') returns the polar surface area of the major microspecies at pH 7.4 of the input molecule
traditionalName NTK returns the traditional name of a molecule the traditional name of the molecule - traditionalName() returns the traditional name of the input molecule
valence - returns the sum of bond orders and query H atoms of an atom the sum of bond orders and query H atoms atom index or MolAtom object valence(0) returns the valence of atom 0
vanDerWaalsSurfaceArea DGTK calculates the van der Waals surface area the van der Waals surface area the major microspecies pH
  • vanDerWaalsSurfaceArea() returns the van der Waals surface area of the input molecule
  • vanDerWaalsSurfaceArea('7.4') returns the van der Waals surface area of the major microspecies of the input molecule at pH 7.4
  • waterAccessibleSurfaceArea
  • ASA
  • solventAccessibleSurfaceArea
 DGTK calculates the solvent accessible/water accessible molecular surface area the water accessible molecular surface area the major microspecies pH
  • 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 of the input molecule at pH 7.4
whereIsValenceError - returns the index of the first atom with valence error or -1 if there is no valence error the index of the first atom with valence error or -1 if there is no valence error - whereIsValenceError() returns the index of the first atom with valence error or -1 if there is no valence error in the molecule
wienerIndex DGTK calculates the Wiener index the Wiener index - wienerIndex() returns the Wiener index of the input molecule
wienerPolarity DGTK calculates the Wiener polarity the Wiener polarity - wienerPolarity() returns the Wiener polarity of the input molecule