| abs |
- |
returns the absolute value of a number |
the absolute value |
the integer or real number |
- abs(7) returns 7
- abs(-4.5) returns 4.5
|
| acceptor, acc |
Structural Calculations |
returns the H-bond acceptor multiplicity of an atom |
the H-bond acceptor multiplicity of the atom |
pH value (used for calculating the major microspecies if specified) |
acceptor(4, '7.4') returns the H-bond acceptor multiplicity of atom 4 of the major microspecies of the molecule at pH 7.4 |
| acceptorCount |
Structural Calculations |
returns the total number of H-bond acceptor atoms in a molecule |
the H-bond acceptor atom count of the molecule |
pH value (used for calculating the major microspecies if specified) |
acceptorCount('7.4') returns the total number of H-bond acceptor atoms in the major microspecies of the molecule at pH 7.4 |
| acceptorSiteCount, accSiteCount |
Structural Calculations |
returns the molecular H-bond acceptor multiplicity (the sum of atomic multiplicities) of a molecule |
the molecular H-bond acceptor multiplicity |
pH value (used for calculating the major microspecies if specified) |
- acceptorSiteCount('7.4') returns the H-bond acceptor multiplicity of the major microspecies of the molecule at pH 7.4
- accSiteCount() returns the H-bond acceptor multiplicity of the molecule
|
| acidicpKa, apKa |
Protonation |
returns acidic pKa value(s) |
the acidic pKa value(s) |
- atom index or MolAtom object
- strength index (an integer given between ' marks e.g. '2' denotes the 2nd strongest acidic pKa value)
|
- acidicpKa() returns all acidic pKa values of the molecule
- apKa(1) returns the acidic pKa value of atom 1 of the molecule
- acidicpKa('1') returns the strongest acidic pKa value of the molecule
- acidicpKa(1, '1') returns the strongest acidic pKa value of atom 1 of the molecule
|
| acidicpKaLargeModel |
Protonation |
returns the acidic pKa value(s) using the LARGE calculation model (optimised for molecules with a large number of ionisable atoms) |
the acidic pKa values |
- atom index or MolAtom object
- strength index (an integer given between ' marks e.g. '2' denotes the 2nd strongest acidic pKa value)
|
- acidicpKaLargeModel(2) returns the acidic pKa value of atom 2 of the molecule using the LARGE model
- acidicpKaLargeModel('2') returns the 2nd strongest acidic pKa value of the molecule using the LARGE model
|
| acidicpKaUseCorrection |
Protonation |
returns the acidic pKa value(s) using a specified pKa correction library |
the acidic pKa values |
- atom index or MolAtom object
- strength index (an integer given between ' marks e.g. '2' denotes the 2nd strongest acidic pKa value)
- the pKacorrection (training) library specified in the format of correctionlibrary:name , generated by the cxtrain command line tool
|
acidicpKaUseCorrection(‘correctionlibrary:mypka’, '1') calculates the strongest acidic pKa value of the molecule taking into account the mypka correction library for training |
| agentCount |
- |
counts the agents in a reaction |
the number of agents in a reaction or -1 if the input is not a reaction |
- |
agentCount() returns n for a reaction of n agents |
| aliphaticAtom |
Structural Calculations |
checks if a specified atom is aliphatic |
true for aliphatic, false for non-aliphatic atoms |
the atom index or MolAtom object |
aliphaticAtom(3) returns true if atom 3 is aliphatic, false otherwise |
| aliphaticAtomCount() |
Structural Calculations |
calculates the number of aliphatic atoms in a molecule |
the aliphatic atom count |
- |
aliphaticAtomCount() returns the number of aliphatic atoms in the molecule |
| aliphaticBondCount |
Structural Calculations |
calculates the number of aliphatic bonds in the molecule |
the aliphatic bond count |
- |
aliphaticBondCount() returns the number of aliphatic bonds in the molecule |
| aliphaticRingCount |
Structural Calculations |
calculates the number of aliphatic rings in the molecule |
the aliphatic ring count |
- |
aliphaticRingCount() returns the number of aliphatic rings in the molecule |
| aliphaticRingCountOfSize |
Structural Calculations |
calculates the number of aliphatic rings of a given size in a molecule |
the number of aliphatic rings of a given size |
- |
aliphaticRingCountOfSize(5) returns the number of aliphatic five-member rings in a molecule |
| aliphaticRings |
Structural Calculations |
identifies the aliphatic rings in a molecule |
the list of atom indices of the aliphatic rings in the molecule (or null if the molecule doesn't have aliphatic rings) |
- |
aliphaticRings() returns the atom indices of the aliphatic rings |
| aliphaticRingsOfSize |
Structural Calculations |
identifies the aliphatic rings of a given size in a molecule |
the list of atom indices of the aliphatic rings of a given size in the molecule (or null if the molecule doesn't have aliphatic rings) |
- |
aliphaticRingsOfSize() returns the atom indices of the aliphatic rings of a given size |
| allTautomer |
Isomers |
returns a given tautomer of all the tautomers of the input molecule |
the tautomer |
tautomer index |
allTautomer(1) returns the 2nd tautomer of all tautomers |
| allTautomers |
Isomers |
returns all tautomers of the input molecule in an array |
the array of tautomers |
normal (for normal tautomerization option, default is false ) |
allTautomers('normal:true') returns all normal tautomer forms in an array |
| angle |
Structural Calculations |
calculates the angle between 3 atoms |
the angle between the 3 atoms |
(1-based) atom indexes of the 3 atoms in an "index1-index2-index3" format OR an atom defined by an array of indexes (index1, index2, index3) |
- angle('1-2-3') returns the angle between atoms 1, 2 and 3
- angle(atoms(2, 3, 4)) returns the angle between atoms 2, 3 and 4
|
| arom |
- |
returns if an atom has an aromatic bond |
true if the atom has an aromatic bond, false otherwise |
the atom index or MolAtom object |
arom(0) returns if the 1st atom in the array of all atoms has an aromatic bond |
| aromaticAtom |
Structural Calculations |
checks if a specified atom is aromatic |
true for aromatic atoms, false otherwise |
the atom index or MolAtom object |
aromaticAtom(1) * decides if the 2nd atom of the molecule is aromatic |
| aromaticAtomCount |
Structural Calculations |
calculates the number of aromatic atoms in the molecule |
the number of aromatic atoms in the molecule |
- |
aromaticAtomCount()* returns the number of aromatic atoms in the molecule |
| aromaticBondCount |
Structural Calculations |
calculates the number of aromatic bonds in the molecule |
the number of aromatic bonds in the molecule |
- |
aromaticBondCount()* returns the number of aromatic bonds in the molecule |
| aromaticRingCount |
Structural Calculations |
calculates the number of aromatic rings in the molecule |
the number of aromatic rings in the molecule |
- |
aromaticRingCount()* returns the number of aromatic rings in the molecule |
| aromaticRingCountOfSize |
Structural Calculations |
calculates the number of aromatic rings of a given size in the molecule |
the number of aromatic rings of a given size in the molecule |
the ring size |
aromaticRingCountOfSize(5)* returns the number of 5-member aromatic rings in the molecule |
| aromaticRings |
Structural Calculations |
identifies the aromatic rings in the molecule |
atom indexes of the aromatic rings in the molecule (or null if the molecule does not contain aromatic rings) |
- |
aromaticRings()* returns the atom indexes of the aromatic rings in the molecule |
| aromaticRingsOfSize |
Structural Calculations |
identifies the aromatic rings of a given size in the molecule (number of atoms) |
atom indexes of the aromatic rings of a given size in the molecule (or null if the molecule does not contain aromatic rings) |
the ring size |
aromaticRingsOfSize(6)* returns the atom indexes of the 6-member aromatic rings in the input molecule |
| array |
- |
constructs an integer array from its integer arguments |
the integer array |
the integers or MolAtom objects |
array(2, 3, 4, 5)* |
| ASAHydrophobic |
Structural Calculations |
calculates the water accessible molecular surface area of all hydrophobic atoms |
the molecular surface area |
pH value (used for calculating the major microspecies if specified) |
ASAHydrophobic() calculates the hydrophobic water accessible surface area for the input molecule ASAHydrophobic('7.4') calculates the hydrophobic water accessible surface area for the major microspecies form of the input molecule at pH 7.4 |
| ASANegative |
Structural Calculations |
calculates the water accessible molecular surface area of all atoms with negative partial charge |
the molecular surface area |
pH value (used for calculating the major microspecies if specified) |
ASANegative() calculates the water accessible surface area for the atoms of negative partial charge of the input molecule ASANegative('7.4') calculates the water accessible surface area for the atoms of negative partial charge of the major microspecies form of the input molecule at pH 7.4 |
| ASAPlus |
Structural Calculations |
calculates the water accessible molecular surface area of all atoms with positive partial charge |
the molecular surface area |
pH value (used for calculating the major microspecies if specified) |
ASAPlus() calculates the water accessible surface area for the atoms of positive partial charge of the input molecule ASAPlus('7.4') calculates the water accessible surface area for the atoms of positive partial charge of the major microspecies form of the input molecule at pH 7.4 |
| ASAPolar |
Structural Calculations |
calculates the water accessible molecular surface area of all polar atoms |
the molecular surface area |
pH value (used for calculating the major microspecies if specified) |
ASAPolar() calculates the water accessible surface area of all polar atoms ASAPolar('7.4') calculates the water accessible surface area of all polar atoms in the major microform of the molecule at pH 7.4 |
| asymmetricAtom |
Structural Calculations |
checks if a specified atom is asymmetric |
true for asymmetric atoms, false for symmetric atoms |
atom index or MolAtom object |
asymmetricAtom(3)* checks if the atom with the index 3 in the molecule is asymmetric |
| asymmetricAtomCount |
Structural Calculations |
calculates the number of asymmetric atoms |
the asymmetric atom count |
- |
asymmetricAtomCount()* returns the number of asymmetric atoms in the input molecule |
| asymmetricAtoms |
Structural Calculations |
determines the asymmetric atoms |
the indexes of asymmetric atoms |
- |
asymmetricAtoms()* returns the array of asymmetric atoms in the molecule |
| atomicNumber, atno |
- |
returns the atomic number of an atom |
the atomic number |
atom index or MolAtom object |
atomicNumber(1) returns the atomic number of the 2nd atom in the molecule atno(2) returns the atomic number of the 3rd atom in the molecule |
| atomCount |
- |
returns the number of (specified) atoms in the molecule |
the (specified) atom count with the given parameters |
no parameter means all atoms are counted "x.y", where x is the atomic number and y is the isotope mass (if y is not given, all atoms of that given atomic number are counted) |
atomCount() returns the total number of atoms in the molecule atomCount('6') returns the total number of carbon atoms in the molecule atomCount('6.14')* returns the total number of carbon 14 isotope atoms |
| atomicPolarizability, atomPol, pol, polarizability |
Structural Calculations |
calculates the atomic polarizability |
the atomic polarizability |
atom index or MolAtom object pH value (used for calculating the major microspecies if specified) |
atomicPolarizability(0) returns the polarizability of atom 0 of the input molecule atomPol(2, '7.4') returns the polarizability of atom 2 of the major microspecies form of the molecule taken at pH 7.4 |
| atomProp |
|
|
|
|
|
| atoms |
|
|
|
|
|
| averageMicrospeciesCharge |
Protonation |
calculates the average microspecies charge (the weighted sum of charges of all microspecies of the molecule) at a given pH value |
the average charge |
pH value (used for calculating the major microspecies if specified) |
averageMicrospeciesCharge('7.4')* calculates the average charge of the microspecies at pH 7.4 |
| averagePolarizability, averagePol, avgPol |
Structural Calculations |
calculates the average molecular polarizability considering the 3D geometry |
the polarizability value |
pH value (used for calculating the major microspecies if specified) |
averagePol('7.4')* calculates the average polarizability of the major microspecies form of the molecule at pH 7.4 |
| axxPol |
Structural Calculations |
calculates the 1st principal component of the polarizability tensor (Axx, Ayy, Azz) |
the 1st principal component |
pH value (used for calculating the major microspecies if specified) |
axxPol()* calculates the 1st principal component of the polarizability tensor of the molecule |
| ayyPol |
Structural Calculations |
calculates the 2nd principal component of the polarizability tensor (Axx, Ayy, Azz) |
the 2nd principal component |
pH value (used for calculating the major microspecies if specified) |
ayyPol()* calculates the 2nd principal component of the polarizability tensor of the molecule |
| azzPol |
Structural Calculations |
calculates the 3rd principal component of the polarizability tensor (Axx, Ayy, Azz) |
the 3rd principal component |
pH value (used for calculating the major microspecies if specified) |
azzPol()* calculates the 3rd principal component of the polarizability tensor of the molecule |
| balabanIndex |
Structural Calculations |
calculates the Balaban index |
the Balaban index |
- |
balabanIndex()* calculates the Balaban index of the molecule |
| basicpKa, bpKa |
Protonation |
returns basic pKa value(s) (if any) |
the basic pKa value(s) |
atom index or MolAtom object strength index (an integer given between ' marks e.g. '2' denotes the 2nd strongest basic pKa value) |
basicpKa() returns all basic pKa values of the molecule bpKa(1) returns the basic pKa value of the 2nd atom basicpKa('1') returns the strongest basic pKa value of the molecule basicpKa(1, '1') returns the strongest basic pKa value of the 2nd atom |
| basicpKaLargeModel |
Protonation |
returns the basic pKa value(s) using the Large calculation model (optimised for molecules with a large number of ionisable atoms) |
the basic pKa value(s) |
atom index or MolAtom object strength index (an integer given between ' marks e.g. '2' denotes the 2nd strongest acidic pKa value) |
basicpKaLargeModel(2) returns the basic pKa value of the 3rd atom basicpKaLargeModel('2') returns the 2nd strongest basic pKa value of the molecule |
| basicpKaUseCorrection |
Protonation |
returns the basic pKa value(s) using a specified pKa correction library |
the basic pKa values |
atom index or MolAtom object strength index (an integer given between ' marks e.g. '2' denotes the 2nd strongest basic pKa value) pKa correction (training) library specified in the format of correctionlibrary:name* , generated by the cxtrain command line tool |
basicpKaUseCorrection(‘correctionlibrary:mypka’, '1') calculates the strongest basic pKa value of the molecule taking into account the mypka* correction library for training |
| bmf |
Structural Calculations |
calculates the Bemis-Murcko framework of the molecule |
the BMF for the input structure |
- |
bmf()* returns the Bemis-Murcko framework of the input molecule |
| bemisMurckoFrameworkLoose, bmfl |
Structural Calculations |
calculates the loose Bemis-Murcko framework of the molecule (by removing side chains; exocyclic non-single bonded atoms are kept; the remaining atom and bond types are not changed) |
the loose BMF for the input structure |
- |
bmfl()* returns the loose Bemis-Murcko framework of the input molecule |
| bmflp, bemisMurckoFrameworkLoosePruned |
Structural Calculations |
returns the Bemis-Murcko loose framework of the input structure (by removing side cains; atom and bond types are generalized by replacing all atoms with carbons and setting all bond types to single; exocyclic non single bonded atoms are kept as single bonded carbons) |
the generalized loose BMF of the input structure |
- |
bmflp() * returns the generalized loose Bemis-Murcko framework of the input molecule |
| bondCount |
- |
calculates the bond count |
the bound count |
- |
bondCount() * returns the number of bonds in the molecules |
| bondType |
Structural Calculations |
returns the bond type between two atoms |
the bond type or -1 if there is no bond between the two atoms |
the (1-based) atom indexes of the two atoms in a string "index1-index2" (e.g. '2-3') |
bondType('2-3') and bondType(bond(1, 2))* both return the bond type between atoms 1 and 2 in the input molecule |
| booleanToNumber |
- |
returns the numerical representation of a boolean expression (true = 1, false = 0) or the number itself if the input is a number (or an expression) |
the number representation of a boolean value |
boolean expression or number/numerical expression |
booleanToNumber(1<2) returns 1 booleanToNumber(55) returns 25 booleanToNumber(hasValenceError()) returns 0 for molecules with no valence error |
| canonicalResonant |
Isomers |
generates the canonical resonant form of the molecule |
the canonical resonant form |
- |
canonicalResonant()* generates the canonical resonant form of the input molecule |
| canonicalTautomer |
Structural Calculations |
generates the canonical tautomer form of the molecule |
the canonical tautomer form |
normalization option (to generate the normal canonical tautomer) |
canonicalTautomer('normal:true')* generates the normal canonical tautomer of the input molecule |
| carboAliphaticRingCount |
Structural Calculations |
calculates the number of carbo-aliphatic (containing only aliphatic C atoms) rings in the molecule |
the number of carbo-aliphatic rings in the molecule |
- |
carboAliphaticRingCount() * calculates the number of carboaliphatic rings of the input molecule |
| carboAromaticRingCount |
Structural Calculations |
calculates the number of carbo-aromatic (containing only aromatic C atoms) rings in the molecule |
the number of carbo-aromatic rings in the molecule |
- |
carboAromaticRingCount() * calculates the number of carbo-aromatic rings of the input molecule |
| carboRingCount |
Structural Calculations |
calculates the number of C (containing only C atoms) rings in the molecule |
the number of C rings in the molecule |
- |
carboRingCount() * calculates the number of C rings of the input molecule |
| carboRingCountOfSize |
Structural Calculations |
calculates the number of C (containing only C atoms) rings of a given size in the molecule |
the number of C rings of a given size in the molecule |
ring size |
carboRingCountOfSize(5) * calculates the number of 5-membered C rings of the input molecule |
| carboRings |
Structural Calculations |
identifies the C (containing only C atoms) rings in the molecule |
atom indexes of the C rings in the molecule (or null if the molecule does not contain C rings) |
- |
carboRings()* returns the atom indexes of the C rings in the input molecule |
| carboRingsOfSize |
Structural Calculations |
identifies the C (containing only C atoms) rings in the molecule of a given size |
atom indexes of the C rings in the molecule having the given size (or null if the molecule does not contain C rings) |
ring size |
carboRingsOfSize(6)* returns the atom indexes of the 6-membered C rings of the input molecule |
| chainAtom |
Structural Calculations |
checks if a specified atom is a chain atom |
true for chain atoms ( false otherwise) |
atom index or MolAtom object |
chainAtom(2) returns true if atom 2 is a chain atom, false * otherwise |
| chainAtomCount |
Structural Calculations |
calculates the number of chain atoms in the molecule |
the number of chain atoms |
- |
chainAtomCount() * returns the number of chain atoms in the molecule |
| chainBond |
Structural Calculations |
checks if two atoms are connected by a chain bond |
true if two atoms are connected by a chain bond |
(1-based) atom indexes of the two atoms in a string: "index1-index2" (e.g. '2-3') |
chainBond('2-3') and chainBond(bond(2, 3)) both return true if the bond between atom 2 and 3 is a chain bond, false * otherwise |
| chainBondCount |
Structural Calculations |
calculates the chain bond count |
the chain bond count |
- |
chainBondCount()* returns the number of chain bonds in the input molecule |
| charge |
Structural Calculations |
calculates atomic partial charges of a given type |
the partial charge values |
atom index or MolAtom object charge type that can be: total (default) pi sigma aromaticsystem aromaticsystemsigma aromaticsystempi aromaticring aromaticringsigma aromaticringpi pH value (used for calculating the major microspecies if specified) |
charge(1, "pi") calculates the pi partial charge of atom 1 in the molecule charge(2, "sigma", "7.4") calculates the sigma partial charge of atom 2 of the major microspecies of the input molecule at pH 7.4 |
| chargeDensity, totalChargeDensity |
Structural Calculations |
calculates the charge density of atoms |
the charge density (NaN for non-existing values) |
atom index or MolAtom object pH value (used for calculating the major microspecies if specified) |
chargeDensity(2)* calculates the charge density of atom 2 of the input molecule |
| check |
- |
checks the molecule for errors based on a configuration string |
the error report |
structure checker/fixer configuration as an action string or XML string |
check("aromaticity..valence") check('"<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"no\"?><checkers><AromaticityErrorChecker fixMode=\"fix\" fixerClassName=\"chemaxon.fixers.RearomatizeFixer\" type=\"general\"/><ValenceErrorChecker allowTraditionalNitrogen=\"false\" fixMode=\"fix\" fixerClassName=\"chemaxon.fixers.ValenceFixer\"/> "') Both checkers check for aromaticity and valence errors in the molecule and returns them. |
| checkErrorCount |
- |
checks the molecule for errors based on a configuration string and returns the error count |
the total error count |
structure checker/fixer configuration as an action string or XML string |
checkErrorCount("aromaticity..valence") checkErrorCount('"<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"no\"?><checkers><AromaticityErrorChecker fixMode=\"fix\" fixerClassName=\"chemaxon.fixers.RearomatizeFixer\" type=\"general\"/><ValenceErrorChecker allowTraditionalNitrogen=\"false\" fixMode=\"fix\" fixerClassName=\"chemaxon.fixers.ValenceFixer\"/> "') Both checkers check for aromaticity and valence errors and returns the error count. |
| chiralCenter |
Structural Calculations |
checks if a specified atom is a chiral center in the molecule |
true for a chiral center, false otherwise |
atom index or the MolAtom object |
chiralCenter(2) returns true* if atom 2 of the input molecule is a chiral center |
| chiralCenterCount |
Structural Calculations |
calculates the number of chiral centers in the molecule |
the number of chiral centers |
- |
chiralCenterCount()* returns the number of chiral centers of the input molecule |
| chiralCenters |
Structural Calculations |
lists the chiral centers of the molecule |
indexes of the chiral centers of the molecule |
- |
chiralCenters()* returns the indexes of the chiral centers of the input molecule |
| composition |
- |
calculates the elemental composition of the molecule |
the elemental composition |
- |
composition() * returns the elemental composition of the molecule |
| conformer |
Structural Calculations |
returns a given conformer of the molecule |
the conformer |
(0-based) conformer index |
conformer(1) * the 2nd conformer of the molecule |
| conformerCount |
Structural Calculations |
returns the number of generated conformers for the molecule (default is 100) |
the number of conformers |
- |
conformerCount() * returns the number of generated conformers of the input molecule |
| conformers |
Structural Calculations |
generates conformers of the molecule |
the set of conformers generated |
forcefield (MMFF94 or Dreiding, the default is Dreiding) maxconformers (default is 100) diversity (default is 0.1) hyperfine (default is false ) prehydrogenize (default is true ) timelimit (in secs, default is 900) * optimization (from 0 to 3, default is 1) |
conformers('forcefield:mmff94 maxconformers:50 optimization:2') * generates at most 50 conformers using the MMFF94 forcefield and a strict optimization level |
| connected |
Structural Calculations |
checks if two atoms are connected by bonds in the molecule |
true if the two atoms belong to the same connected component, false otherwise |
(1-based) atom indexes of the two atoms in a string "index1-index2" (e.g. '2-3') |
connected('2-3') or connected(pair(2, 3)) both return true* if atoms 2 and 3 are in the same connected component of the input molecule |
| connectedGraph |
Structural Calculations |
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 the implicit H count of an atom in the molecule |
the bond plus implicit H count |
the atom index or MolAtom object |
connections(2) * returns the number of connections of atom 2 in the molecule |
| count |
- |
determines the number of elements in an array |
the number of elements in the array |
the integer/real number array |
count(array(3.4, 5.6, 1.2)) returns 3 count(filter('charge()>0')) returns the number of atoms with positive partial charge in the molecule |
| cyclomaticNumber |
Structural Calculations |
calculates the cyclomatic number of the molecule graph |
the cyclomatic number |
- |
cyclomaticNumber() * returns the cyclomatic number of the molecule |
| dihedral |
Structural Calculations |
calculates the dihedral angle of 4 atoms in the molecule |
the dihedral angle |
the (1-based) atom indexes of the four atoms in a string "index1-index2-index3-index4" (e.g. '2-3-7-4') |
dihedral('1-2-3-4') calculates the dihedral angle between atom 1,2,3 and 4 dihedral(atoms(0,1,2,3)) calculates the dihedral angle between atoms defined by atom indices 0,1,2 and 3 |
| disjointMatchCount |
Structure Search |
performs sub and returns the maximal number of pairwise disjoint search hits |
the maximal number of pairwise disjoint query search hits found in the target molecule |
target atom index or MolAtom object (optional) query molecule object or SMARTS string * query atom mapping(s) (optional)If the target atom index and the query atom mappings are specified, the return value can only be 0 or 1. |
disjointMatchCount('[#8]C=O') calculates the number of pairwise disjoint carboxylic groups in the molecule disjointMatchCount(2, '[#8]C=O') calculates the number of pairwise disjoint carboxylic groups in the molecule with the target atom 2 (either 0 or 1) |
| dissimilarity |
- |
calculates the dissimilarity between two molecules using a given fingerprint and metric |
the dissimilarity value |
the descriptor and/or metric options given as descriptor:metric or descriptor (optional, the chemical (hashed) fingerprint with Tanimoto metric is used as default) 1 or 2 molecules (if only 1 molecule is specified then the other one is taken from the context) |
dissimilarity("c1ccccc1", "C1CCCCC1") calculates the dissimilarity between benzene and cyclohexane using the chemical (hashed) fingerprint with Tanimoto metric dissimilarity("PF", "c1ccccc1", "C1CCCCC1") calculates the dissimilarity between the benzene and cyclohexane molecules using the pharmacophore fingerprint with the (default) Tanimoto metric dissimilarity("PF:Euclidean", "c1ccccc1") calculates the dissimilarity between benzene and the input molecule using pharmacophore fingerprint with Euclidean metric dissimilarity("LogD", "c1ccccc1") calculates the dissimilarity between benzene and the input molecule using logD with the absolute difference (AbsDiff) metric |
| distance |
Structural Calculations |
calculates the distance between two atoms |
the distance between the two atoms |
the (1-based) atom indexes 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 molecule |
| distanceDegree |
Structural Calculations |
calculates the distance degree of an atom |
the distance degree |
the atom index or MolAtom object |
distanceDegree(2)* returns the distance degree of atom 2 of the input molecule |
| dominantTautomer, tautomer |
Isomers |
returns a dominant tautomer of the molecule |
the dominant tautomer |
dominant tautomer index (0-based) pH value (set if pH effect should be considered) |
dominantTautomer(0) returns the most dominant tautomer form of the input molecule dominantTautomer(1, "7.4") returns the 2nd most dominant tautomer form of the input molecule at pH 7.4 |
| dominantTautomerCount |
Isomers |
calculates the number of dominant tautomers |
the number of dominant tautomers |
* pH value (set if pH effect should be considered) |
dominantTautomerCount() returns the number of dominant tautomers of the input molecule dominantTautomerCount('7.4') returns the number of dominant tautomers of the input molecule at pH 7.4 |
| dominantTautomers, tautomers |
Isomers |
generates all dominant tautomer forms (ordered by distribution) |
the array of generated dominant tautomers |
* pH value (set if pH effect should be considered) |
dominantTautomers() returns the array of dominant tautomers of the input molecule dominantTautomers('7.4') returns the array of dominant tautomers of the input molecule at pH 7.4 |
| donor, don |
Structural Calculations |
calculates the atomic H bond donor multiplicity |
the atomic hydrogen bond donor multiplicity |
atom index or MolAtom object pH value (used for calculating the major microspecies if specified) |
donor(1, '7.4')* returns the hydrogen bond donor multiplicity of atom 1 for the major microspecies of the input molecule at pH 7.4 |
| donorCount |
Structural Calculations |
calculates the hydrogen bond donor count (the number of donor atoms) for the molecule |
the molecular hydrogen bond donor count |
* pH value (used for calculating the major microspecies if specified) |
donorCount("7.4")* returns the number of hydrogen bond donor atoms for the major microspecies of the input molecule at pH 7.4 |
| donorSiteCount, donSiteCount |
Structural Calculations |
calculates the molecular hydrogen bond donor multiplicity (the sum of atomic multiplicities) |
the molecular hydrogen bond donor multiplicity |
* pH value (used for calculating the major microspecies if specified) |
donorSiteCount('7.4')* returns the hydrogen bond donor multiplicity for the major microspecies of the input molecule 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 |
| dotDisconnectedFormulaWithGrouping |
- |
returns the grouped form of the dot-disconnected formula |
the grouped form of the dot-disconnected formula |
- |
dotDisconnectedIsotopeFormulaWithGrouping()* returns the grouped form of the dot-disconnected isotope formula of the input molecule |
| doubleBondStereoIsomer |
Isomers |
generates a double bond stereoisomer of the molecule |
the double bond stereoisomer |
the stereoisomer index (0-based) |
doubleBondStereoIsomer(0) * generates the first double bond stereoisomer of the input molecule |
| doubleBondStereoIsomerCount |
Isomers |
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 |
Isomers |
generates double bond stereoisomers of the molecule |
the array of generated isomers |
maxstereoisomers (sets the maximal number of stereoisomers to be generated, default is all) |
doubleBondStereoIsomers() returns all double bond stereoisomers of the input molecule doubleBondStereoIsomers('maxstereoisomers:10') returns at most 10 double bond stereoisomers of the input molecule |
| dreidingEnergy |
Structural Calculations |
returns the Dreiding forcefield energy of the input molecule (for the input if it is a 3D molecule or a generated lowest energy conformer) |
the Dreiding energy |
optimization level strictness (from 0 to 3, 1 default is 1) lowest energy conformer generation option (never, if2D (default), always) |
dreidingEnergy('optimization:2 calcforleconformer:always') calculates the Dreiding energy of the input molecule using level 2* (strict) optimization and always generating a lowest energy conformer for the input |
| eccentricity |
Structural Calculations |
calculates the eccentricity of an atom |
the eccentricity of the atom |
the atom index or MolAtom object |
eccentricity(2)* returns the eccentricity of atom 2 in the molecule |
| electronDensity, piChargeDensity |
Structural Calculations |
calculates the pi electron density of the atoms in the molecule (if exists) |
the electron density (returns NaN for non-existing values) |
the atom index or MolAtom object pH value (used for calculating the major microspecies if specified) |
electrondensity(2, '7.5')* calculates the electron density of atom 2 for the major microform of the input molecule at pH 7.5 |
| electrophilicity, energyNu, nucleophilicLocalizationEnergy |
Structural Calculations |
calculates the electrophilicity of aromatic centers (by calculating localization energies for nucleophilic attack) |
the electrophilicity of the aromatic atom (or NaN if the atom is non-aromatic) |
the atom index or MolAtom object pH value (used for calculating the major microspecies if specified) |
electrophilicity(2)* calculates the eletrophilicity of atom 2 in the input molecule |
| electrophilicityOrder, aromaticElectrophilicityOrder, orderE |
Structural Calculations |
calculates the order of electrophilicity (for nucleophilic attack) for atoms (the E(+) order) |
the E(+) order of atoms (index numbers starting from 0, smallest is the most reactive) |
the atom index or MolAtom object pH value (used for calculating the major microspecies if specified) |
electrophilicityOrder(1)* calculates the E(+) order of atom 1 |
| elemanal |
- |
calculates basic (elemental) chemical properties of the molecule |
the calculated property |
the available properties: atomCount mass massPrecision exactMass exactMassPrecision formula isotopeFormula dotDisconnectedFormula dotDisconnectedIsotopeFormula |
elemanal('exactmass')* calculates the exact mass of the molecule |
| elementalAnalysis |
- |
calculates basic (elemental) chemical properties for a molecule represented by its formula |
the calculated property |
the molecular formula of the input molecule (must be given) the available properties: atomCount mass massPrecision exactMass exactMassPrecision formula isotopeFormula dotDisconnectedFormula * dotDisconnectedIsotopeFormula |
elementalAnalysis('C12H25O', 'mass')* returns the mass of molecule represented by its formula |
| eval |
|
|
|
|
|
| exactMass |
- |
calculates the exact mass of the molecule |
the exact mass |
- |
exactmass()* returns the exact mass of the molecule |
| field |
- |
returns a molecule property value from an SD field as a number |
the SD property value |
the property key (the SD file field name) |
field('LOGP') returns the value of the LOGP property in the SD file field('LOGP') > 1.5 returns 1 if the value of the LOGP property is > 1.5, 0 otherwise |
| fieldAsString, propertyAsString |
- |
returns a molecule property value from an SD field as a string |
the SD property value as a string |
the property key (the SD file field name) |
fieldAsString('LOGP')* returns the value of the LOGP property in the SD file as a string |
| filter |
- |
filters target atoms by filtering condition |
target atom indices satisfying the filtering condition |
target atom indices, MolAtom objects or an array of MolAtom objects (optional, default is all) filtering condition (as a boolean expression) |
filter('charge()>0') returns the list of indices of atoms with positive partial charge in the input molecule filter(6, 7, 8, 9, "match('[#8][C:1]=O', 1)") returns the list of carboxylic atoms from atom 6, 7, 8 and 9 of the input molecule |
| fix |
- |
checks the structure for errors using the configuration and then fixes the errors |
the fixed molecule |
the structure checker/fixer configuration as an action string or XML string |
fix("chiralflag..isotope→converttoelementalform") fix('"<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"no\"?><checkers><ChiralFlagChecker fixMode=\"fix\" fixerClassName=\"chemaxon.fixers.RemoveChiralFlagFixer\"/><IsotopeChecker fixMode=\"fix\" fixerClassName=\"chemaxon.fixers.ConvertToElementalFormFixer\"/>"') Both functions search for chiral flags and isotopes and removes them or converts them to elemental form. |
| formalCharge, totalCharge |
|
calculates the formal charge of the molecule |
the formal charge of the input molecule |
the atom index or MolAtom object |
formalCharge() returns the formal charge of the input molecule formalCharge(0) returns the formal charge of atom 0 of the input molecule |
| formula |
- |
returns the molecular formula as a string in Hill notation |
the molecular formula |
- |
formula()* returns the molecular formula of the input molecule |
| fragmentCount |
Structural Calculations |
returns the number of disconnected fragments in the molecule |
the fragment count |
- |
fragmentCount()* returns the number of disconnected fragments in the molecule |
| fragments |
- |
splits and lists the molecule into its disconnected fragments |
the disconnected fragments of the molecule |
- |
fragments()* returns the disconnected fragments of the molecule |
| fsp3 |
Structural Calculations |
returns the fraction of sp3 C atoms in the molecule (fsp3) |
the fsp3 value |
- |
fsp3()* returns the fsp3 value of the molecule |
| fusedAliphaticRingCount |
Structural Calculations |
calculates the number of fused aliphatic rings (the number of rings in the smallest set of smallest aliphatic rings, SSSR) |
the number of fused aliphatic rings |
- |
fusedAliphaticRingCount()* returns the number of fused aliphatic rings in the input molecule |
| fusedAliphaticRingCountOfSize |
Structural Calculations |
calculates the number of fused aliphatic rings of given size |
the number of fused aliphatic rings of given size |
the ring size |
fusedAliphaticRingCountOfSize(6)* returns the number of fused 6-membered aliphatic rings in the input molecule |
| fusedAliphaticRings |
Structural Calculations |
identifies the fused aliphatic rings in the molecule |
atom indexes of the fused aliphatic rings in the molecule (or null if the molecule does not contain fused aliphatic rings) |
- |
fusedAliphaticRings()* returns the atom indexes of the fused aliphatic rings in the input molecule |
| fusedAliphaticRingsOfSize |
Structural Calculations |
identifies the fused aliphatic rings in the molecule having a given size (number of atoms) |
atom indexes of the fused aliphatic rings in the molecule of the given size (or null if the molecule does not contain fused aliphatic rings) |
the ring size |
fusedAliphaticRingsOfSize(5)* returns the atom indexes of the 5-membered fused aliphatic rings in the input molecule |
| fusedAromaticRingCount |
Structural Calculations |
calculates the number of fused aromatic rings (the number of rings in the smallest set of smallest aromatic rings, SSSR) |
the number of fused aromatic rings |
- |
fusedAromaticRingCount()* returns the number of fused aromatic rings in the input molecule |
| fusedAromaticRingCountOfSize |
Structural Calculations |
calculates the number of fused aromatic rings of a given size |
the number of fused aromatic rings of a given size |
the ring size |
fusedAromaticRingCountOfSize(6)* returns the number of 6-membered fused aromatic rings in the input molecule |
| fusedAromaticRings |
Structural Calculations |
identifies the fused aromatic rings in the molecule |
atom indexes 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 molecule |
| fusedAromaticRingsOfSize |
Structural Calculations |
identifies the fused aromatic rings of a given size in the molecule |
atom indexes of the fused aromatic rings in the molecule of a given size (or null if the molecule does not contain fused aromatic rings) |
the ring size |
fusedAromaticRingsOfSize(5)* returns the atom indices of the fused aromatic rings of size of 5 in the molecule |
| fusedRingCount |
Structural Calculations |
calculates the number of fused rings (the number of rings in the smallest set of smallest rings, SSSR) |
the fused ring count |
- |
fusedRingCount()* returns the number of fused rings in the molecule |
| genericTautomer |
Isomers |
generates the generic tautomer form of the input molecule |
the generic tautomer form |
- |
generictautomer()* returns the generic tautomer form of the input molecule |
| hararyIndex |
Structural Calculations |
calculates the Harary index for the graph of input the molecule |
the Harary index |
- |
hararyIndex()* calculates the Harary index of the input molecule |
| hasAromatizationError |
- |
determines if there is an aromatization error in input the molecule |
true if there is any aromatization error in the input molecule, false otherwise |
- |
hasAromatizationError() returns true there is an aromatization error in the input molecule, false* otherwise |
| hasIsotope |
- |
determines if there is an isotopic atom /element in the input molecule |
true if there is an isotopic element in the input molecule, false otherwise |
- |
hasIsotope() returns true if there is an isotopic element in the input molecule, false* otherwise |
| hasRadical |
- |
determines if there is any atom with a radical in the molecule |
true if there is any atom in the molecule with a radical, false otherwise |
- |
hasRadical() returns true if there is an atom in the molecule with a radical, false* otherwise |
| hasValenceError |
- |
determines if there is a valence error in the input molecule |
true if there is a valence error in the molecule, false otherwise |
- |
hasValenceError() returns true if there is a valence error in the molecule, false* otherwise |
| hasValidConformer |
Structural Calculations |
determines if the input molecule is in 3D (has a valid conformer) |
true if the molecule is in 3D, false otherwise |
- |
hasValidConformer() returns true if the molecule is in 3D, false* otherwise |
| HBDA |
Structural Calculations |
calculates H-bond donor and acceptor properties for the atoms in the input molecule or for the molecule |
a list of the calculated HBDA properties |
type, these can be acc: acceptor multiplicity on atoms don: donor multiplicity on atoms accsitecount: acceptor multiplicity in the molecule donsitecount: donor multiplicity in the molecule acceptorcount: number of acceptor atoms in the molecule donorcount: number of donor atoms in the molecule msacc: average acceptor multiplicity over microspecies at a given pH msdon : average donor multiplicity over microspecies at a given pH (default: acceptorcount, donorcount, accsitecount, donorsitecount) options related to pH, these can be pH: calculate for the microspecies at that given pH value instead of the input molecule (default is no pH) upper: upper pH limit (default is 14) lower : lower pH limit (default is 0) step: pH step size (default is 1) excluding certain atoms from acceptors, these can be excludesulfur : excludes S atoms from the acceptors (default is true) excludehalogens: excludes halogen atoms from the acceptors (default is true ) precision: floating point precision for numbers (default is 2) |
hbda('type:acc,don', 'pH:7.4', 'precision:1') lists donor and acceptor multiplicity on atoms of the major microform of the input molecule at pH 7.4 hbda('type:donorcount', 'pH:7.4') calculates the donor count of the major microform of the input molecule at pH 7.4 |
| hCount |
- |
calculates the H atom count of an atom |
the H atom count |
the atom index or MolAtom object |
hCount(1)* returns the H count of the atom with index 1 |
| hergBeta |
ADMET |
predicts hERG activity and returns the pActivity using Chemaxon's hERG activity model |
the pActivity value |
- |
hergBeta() returns the predicted hERG pActivity of the input molecule |
| hergActivityBeta |
ADMET |
predicts hERG activity (as pActivity) using Chemaxon's hERG activity model |
the pActivity value |
- |
hergActivityBeta() returns the predicted hERG pActivity of the input molecule |
| hergClassBeta |
ADMET |
predicts hERG classification class using Chemaxon's hERG classification model |
the classification class (SAFE or TOXIC) |
- |
hergClassBeta() returns the predicted hERG classification class of the input molecule |
| heteroAliphaticRingCount |
Structural Calculations |
calculates the number of aliphatic heterocyclic rings (the number of rings in the smallest set of smallest aliphatic heterocyclic rings, SSSR) in the input molecule |
the aliphatic heterocyclic ring count |
- |
heteroAliphaticRingCount() * returns the number of aliphatic heterocyclic rings in the input molecule |
| heteroAliphaticRingCountOfSize |
Structural Calculations |
calculates the number of aliphatic heterocyclic rings of a given size (the number of rings of a given size in the smallest set of smallest aliphatic heterocyclic rings, SSSR) in the input molecule |
the number of aliphatic heterocyclic rings of a given size |
the ring size |
heteroAliphaticRingCountOfSize(8) * returns the number of 8-membered aliphatic heterocyclic rings in the input molecule |
| heteroAliphaticRings |
Structural Calculations |
identifies the aliphatic heterocyclic rings in the input molecule |
atom indexes of the aliphatic heterocyclic rings in the input molecule (or null if the molecule does not have aliphatic heterocyclic rings) |
- |
heteroAliphaticRings() * returns the atom indexes of the aliphatic heterocyclic rings in the input molecule |
| heteroAliphaticRingsOfSize |
Structural Calculations |
identifies the aliphatic heterocyclic rings of a given size in the input molecule |
atom indexes of the aliphatic heterocyclic rings of a given size in the input molecule (or null if the molecule does not have aliphatic heterocyclic rings of the given size) |
the ring size |
heteroAliphaticRingsOfSize(6) * returns the atom indexes of the 6-membered aliphatic heterocyclic rings in the input molecule |
| heteroaromaticRingCount |
Structural Calculations |
calculates the number of aromatic heterocyclic rings (the number of rings in the smallest set of smallest aromatic heterocyclic rings, SSSR) in the input molecule |
the aromatic heterocyclic ring count |
- |
heteroaromaticRingCount() * returns the number of aromatic heterocyclic rings in the input molecule |
| heteroaromaticRingCountOfSize |
Structural Calculations |
calculates the number of aromatic heterocyclic rings of a given size (the number of rings of a given size in the smallest set of smallest aromatic heterocyclic rings, SSSR) in the input molecule |
the number of aromatic heterocyclic rings of a given size |
the ring size |
heteroaromaticRingCountOfSize(8) * returns the number of 8-membered aromatic heterocyclic rings in the input molecule |
| heteroaromaticRings |
Structural Calculations |
identifies the aromatic heterocyclic rings in the input molecule |
atom indexes of the aromatic heterocyclic rings in the input molecule (or null if the molecule does not have aromatic heterocyclic rings) |
- |
heteroAromaticRings() * returns the atom indexes of the aromatic heterocyclic rings in the input molecule |
| heteroaromaticRingsOfSize |
Structural Calculations |
identifies the aromatic heterocyclic rings of a given size in the input molecule |
atom indexes of the aromatic heterocyclic rings of a given size in the input molecule (or null if the molecule does not have aromatic heterocyclic rings of that given size) |
the ring size |
heteroaromaticRingsOfSize(6) * returns the atom indexes of the 6-membered aromatic heterocyclic rings in the input molecule |
| heteroRingCount |
Structural Calculations |
calculates the number of heterocyclic rings (the number of rings in the smallest set of smallest heterocyclic rings, SSSR) in the input molecule |
the number of heterocyclic rings |
- |
heteroRingCount() * returns the number of heterocyclic rings in the input molecule |
| heteroRingCountOfSize |
Structural Calculations |
calculates the number of heterocyclic rings of a given size (the number of rings of a given size in the smallest set of smallest heterocyclic rings, SSSR) in the input molecule |
the number of heterocyclic rings of a given size |
the ring size |
heteroRingCountOfSize(5) * returns the number of 5-membered heterocyclic rings in the input molecule |
| heteroRings |
Structural Calculations |
identifies the heterocyclic rings in the input molecule |
atom indexes of the heterocyclic rings in the input molecule (or null if the molecule does not have heterocyclic rings) |
- |
heteroRings() * returns the atom indexes of the heterocyclic rings in the input molecule |
| heteroRingsOfSize |
Structural Calculations |
identifies the heterocyclic rings of a given size in the input molecule |
atom indexes of the heterocyclic rings of a given size in the input molecule (or null if the molecule does not have heterocyclic rings of that given size) |
the ring size |
heteroRingsOfSize(6) * returns the atom indexes of the 6-membered heterocyclic rings in the input molecule |
| hlb |
Partitioning |
predicts the hydrophil-lipophil balance (HLB) number |
the HLB number |
the calculation method that can be: davies griffin required chemaxon (default) precision (number of digits, default is 8) |
hlb('davies') * returns the HLB number calculated using the Davies method |
| hmoElectronDensity |
Structural Calculations |
calculates the electron density of atoms based on the Hückel Molecular Orbital (HMO) method |
the electron density of the atom or NaN for non-existing values |
atom index or MolAtom object pH value (used for calculating the major microspecies if specified) |
hmoElectronDensity(2, '6.5') * returns the electron density of the atom of index 2 for the major microspecies of the input molecule at pH 6.5 |
| hmoChargeDensity |
Structural Calculations |
calculates the charge density of atoms based on the Hückel Molecular Orbital (HMO) method |
the charge density of the atom or NaN for non-existing values |
atom index or MolAtom object pH value (used for calculating the major microspecies if specified) |
hmoChargeDensity(2, '6.5') * returns the charge density of the atom of index 2 for the major microspecies of the input molecule at pH 6.5 |
| hmoElectrophilicityOrder, hmoOrderE |
Structural Calculations |
calculates the electrophilic order (E(+) order) of atoms based on electrophilic localization energy calculations using the Hückel Molecular Orbital (HMO) method |
the electrophilic order of the atom ( 0, 1, 2, ..., 0 is the most electrophilic atom) or -1 if the atom is not aromatic |
atom index or MolAtom object pH value (used for calculating the major microspecies if specified) |
hmoOrderE(2) * returns the electrophilic order of atom with index 2 |
| hmoElectrophilicLocalizationEnergy |
Structural Calculations |
calculates the electrophilic localization energy (L(+)) for the atoms of the molecule based on the Hückel Molecular Orbital (HMO) method |
the electrophilic localization energy or NaN if the atom is not aromatic |
atom index or MolAtom object pH value (used for calculating the major microspecies if specified) |
hmoElectrophilicLocalizationEnergy(1, '7.4') * returns the electrophilic localization energy of atom 1 for the major microspecies of the input molecule at pH 7.4 |
| hmoNucleophilicityOrder, hmoOrderN |
Structural Calculations |
calculates the nucleophilic order (Nu(-) order) of atoms based on nucleophilic localization energy calculations using the Hückel Molecular Orbital (HMO) method |
the nucleophilic order of the atom ( 0, 1, 2, ..., 0 is the most nucleophilic atom) or -1 if the atom is not aromatic |
atom index or MolAtom object pH value (used for calculating the major microspecies if specified) |
hmoOrderN(2) * returns the nucleophilic order of atom with index 2 |
| hmoNucleophilicLocalizationEnergy |
Structural Calculations |
calculates the nucleophilic localization energy (L(-)) for the atoms of the molecule based on the Hückel Molecular Orbital (HMO) method |
the nucleophilic localization energy or NaN if the atom is not aromatic |
atom index or MolAtom object pH value (used for calculating the major microspecies if specified) |
hmoNucleophilicLocalizationEnergy(1, '7.4') * returns the nucleophilic localization energy of atom 1 for the major microspecies of the input molecule at pH 7.4 |
| hmoPiEnergy |
Structural Calculations |
calculates the pi energy of the molecule based on the Hückel Molecular Orbital (HMO) method |
the pi energy of the molecule |
pH value (used for calculating the major microspecies if specified) |
hmoPiEnergy('7.4')* calculates the pi energy of the major microspecies of the input molecule at pH 7.4 |
| hybridization |
Structural Calculations |
returns the atoms (indices) of a given hybridization state in the molecule |
the list of atoms of a given hybridization state |
the hybridization state, can be sp3 sp2 sp(optional parameter, the function returns the list of hybridization states for all atoms if not specified) |
hybridization() returns the list of hybridization states for all atoms of the input molecule hybridization('sp3') returns the list of atoms (indices) of sp3 hybridization state |
| hyperWienerIndex |
Structural Calculations |
calculates the hyper Wiener index of the molecule |
the hyper Wiener index |
the fragment option (single) for multi-fragment molecules (takes the largest fragment if true , otherwise the whole molecule (default)) |
hyperWienerIndex()* calculates the hyper Wiener index of the molecule |
| importMol |
- |
imports and returns the input molecule from its string representation, the output format can be set at evaluation (conversion) |
the imported molecule as a string (default is SMILES code) |
the string representation of the input molecule (e.g. SMILES, name) |
importMol('aspirine') imports the aspirine molecule and returns its string representation in the format defined at evaluation importMol('CCCN') imports the CCCN molecule and returns its string representation in the format defined at evaluation |
| in |
- |
determines if an integer (atom index) is in a given array |
true if the array contains the integer, false otherwise |
atom index or MolAtom object the integer array |
in(2, array(1,2,3)) returns true in(4, array(1,2,3)) returns false in(3, maxatom('charge()', 2)) * checks if atom 3 is one of the two atoms with the largest partial charge value in the molecule |
| ionCharge |
Structural Calculations |
calculates the partial charge distribution of atoms of specific microspecies |
the partial distribution of atoms |
minpercent, min (minimum percentage): the minimal % of distribution of a microspecies to be considered for calculation (optional, only the microspecies with the max. distribution % is considered if not given) maxions (maximum number of ionizable atoms, default is 9) pH value charge type (single or accumulated, the accumulated adds the charges of the attached Hs, default is single) * precision (default is 2) |
ioncharge('minpercent:50', '7.0') * calculates the single ionic charge distribution using the microspecies that has at least 50% distribution at pH 7.0 |
| isEmpty |
- |
determines if the input molecule is an empty object (that is it does not contain any atoms, bonds, or non-empty S groups) |
true if the molecule is empty, false otherwise |
- |
isEmpty() * determines if the input molecule is an empty object |
| isMarkush |
- |
determines if the input molecule has any Markush features |
true if the molecule has Markush features, false otherwise |
- |
isMarkush()* determines if the input molecule has any Markush features |
| isoelectricPoint, pI |
Protonation |
calculates the isoelectric point of the input molecule |
the isoelectric point |
precision (default is 2) |
isoelectricPoint()* calculates the isoelectric point of the input molecule with 2-digit precision |
| isotopeComposition |
- |
calculates the isotope composition of the input molecule |
the isotope composition |
single (takes the largest connected fragment of a multi-fragment input molecule if true, otherwise the whole molecule, default is false ) precision (default is 2) |
isotopeComposition('single:true') * calculates the isotope composition of the largest connected fragment of the input molecule |
| isotopeFormula |
- |
returns the isotope formula of the input molecule |
the isotope formula |
symbolD (uses the D and T notation for deuterium and tritium atoms, respectively, default is true ) single (takes the largest connected fragment of a multi-fragment input molecule if true, otherwise the whole molecule, default is false ) |
isotopeFormula() * returns the isotope formula for the whole input molecule without using the D and T notation |
| isQuery |
- |
determines if the input molecule has any query features |
true if the molecule has any query features, false otherwise |
- |
isQuery()* determines if the input molecule has any query features |
| isValid |
- |
checks the input structure for errors using a configuration file (string) |
true if the structure is valid, false otherwise |
structure checker/fixer configuration as an action/XML string |
isValid('aromaticity..valence') checks the molecule for aromaticity or valence errors isValid( '"<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"no\"?><checkers><AromaticityErrorChecker fixMode=\"fix\" fixerClassName=\"chemaxon.fixers.RearomatizeFixer\" type=\"general\"/><ValenceErrorChecker allowTraditionalNitrogen=\"false\" fixMode=\"fix\" fixerClassName=\"chemaxon.fixers.ValenceFixer\"/> "' ) checks the molecule for aromaticity and valence errors |
| largestAtomRingSize |
Structural Calculations |
calculates the size of the largest ring of the input molecule containing the given atom |
the ring size |
atom index or MolAtom object |
largestAtomRingSize(1) returns the size of the largest ring containing atom 1* |
| largestRing |
Structural Calculations |
identifies the atoms in the largest ring of the input molecule |
the list of atom indices of the largest ring (or null if the molecule is acyclic) |
- |
largestRing()* returns the list of atoms of the largest ring in the input molecule |
| largestRingSize |
Structural Calculations |
calculates the number of atoms in the largest ring of the input molecule |
the largest ring size |
- |
largestRingSize()* returns the size of the largest ring in the input molecule |
| largestRingSystem |
Structural Calculations |
identifies the atoms in the largest ring system of the input molecule |
the list of atom indices of the largest ring system (or null if the molecule is acyclic) |
- |
largestRingSystem() * returns the list of atoms of the largest ring system in the input molecule |
| largestRingSystemSize |
Structural Calculations |
calculates the number of atoms in the largest ring system of the input molecule |
the size of the largest ring system |
- |
largestRingSystemSize() * returns the size of the largest ring system in the input molecule |
| logD |
Partitioning |
calculates logD at specific pH value(s) |
the logD value(s) |
method (of logP calculation), can be consensus (default) chemaxon user (requires training ID) logptrainingid (logP training library ID) pkacorrectionlibrary (pKa correction library ID) pH value (runs the defined pH range with the defined step size if not specified) lower (lower pH limit, default is 0.0) upper (upper pH limit, default is 14.0) step (pH step size, default is 0.5) anion (Cl- ion concentration, default is 0.1, can be between 0.0 and 0.25) kation (Na+/K+ ion concentration, default is 0.1, can be between 0.0 and 0.25) considertautomerization (for taking tautomerization and resonance into account, default is false ) precision (default is 2) |
logD('7.4') calculates the logD of the input molecule using the default settings logD('method:chemaxon', '7.4') calculates the logD of the input molecule using the Chemaxon logP model at pH 7.4 logD('method:user', 'logptrainingid:mylogpdata', 'considertautomerization:true') * calculates the logD of the input molecule using the user's own logP data taking tautomerization/resonance effects into consideration |
| logDKLOP |
Partitioning |
calculates logD value(s) using the Klopman (logP) method |
the logD value(s) |
all options (except method) of the logD() function |
logDKLOP('7.4') * calculates the logD value of the input molecule at pH 7.4 using the Klopman method |
| logDPHYS |
Partitioning |
calculates the logD value(s) using the PhysProp database |
the logD value(s) |
all options (except method) of the logD() function |
logPHYS('7.4') * calculates the logD value of the input molecule at pH 7.4 using the PhysProp database |
| logDUser |
Partitioning |
calculates logD value(s) based on the user's training data |
the logD value(s) |
all options (except method) of the logD() function, logP training ID must be specified |
logDUser('logptrainingid:mylogP', 'lower:1.0', 'upper:8.0') * calculates the logD values of the input molecule for all pH values between 1.0 and 8.0 using the default stepsize and the user's training data |
| logDVG |
Partitioning |
calculates logD value(s) using the VG (logP) method |
the logD value(s) |
all options (except method) of the logD() function |
logDVG('7.4') * calculates the logD value of the input molecule at pH 7.4 using the VG method |
| logDWeighted |
Partitioning |
calculates logD value(s) using the weighted (logP) method |
the logD value(s) |
all options (except method) of the logD() function |
logDWeighted('7.4') * calculates the logD value of the input molecule at pH 7.4 using the weighted method |
| logP |
Partitioning |
calculates the logP of the molecule |
the logP value |
method, can be consensus (default) chemaxon user trainingid (training library ID) type, can be logPTrue (= logP of the uncharged form of the input molecule or logD at the pI if the input molecule is zwitterionic) (default) logPMicro (= logP of the input molecule) logPNonionic (= logP of the uncharged form of the input molecule) logDpI (= logD at pI) increments (for atomic increments, default is false ) pH value (calculates the logP of the major microspecies of the input molecule at this pH value if specified) anion (Cl- ion concentration, default is 0.1, can be between 0.0 and 0.25) kation (Na+/K+ ion concentration, default is 0.1, can be between 0.0 and 0.25) considertautomerization (for taking tautomerization and resonance into account, default is false ) precision (default is 2) |
logP() calculates the most "typical" logP value of the input molecule logP('method:chemaxon') calculates the logP of the input molecule using the Chemaxon method logP('logPNonionic')* calculates the non-ionic, uncharged form of the input molecule |
| logPincrement, logPi |
Partitioning |
calculates atomic logP increment(s) |
the logP increment(s) |
atom index or MolAtom object |
logPincrement(2) calculates the atomic logP increment of atom 2 logPi(3) calculates the atomic logP increment of atom 3 |
| logPKLOP |
Partitioning |
calculates the logP value of the molecule using the Klopman method |
the logP value |
all options (except method) of the logP() function |
logPKLOP() * calculates the logP of the molecule using the Klopman method |
| logPPHYS |
Partitioning |
calculates the logP value of the molecule using the PhysProp database |
the logP value |
all options (except method) of the logP() function |
logPPHYS() * calculates the logP of the molecule using the Physprop database |
| logPUser |
Partitioning |
calculates the logP value of the molecule based on the user's training data |
the logP value |
all options (except method) of the logP() function, logP training ID must be specified |
logPUser('logptrainingid:mylogP') * calculates the logP of the molecule based on the user's training data |
| logPVG |
Partitioning |
calculates the logP value of the molecule using the VG method |
the logP value |
all options (except method) of the logP() function |
logPVG() * calculates the logP of the molecule using the VG method |
| logPWeighted |
Partitioning |
calculates the logP value of the molecule using the weighted method |
the logP value |
all options (except method) of the logP() function |
logPWeighted() * calculates the logP of the molecule using the weighted method |
| logS |
Solubility |
calculates the (intrinsic or pH-dependent) solubility of the molecule in water |
the solubility value(s) |
unit (measurement unit), can be logS (default) mol/l mg/ml category (calculates qualitative solubility category, can be low, moderate or high) pH value (calculates intrinsic solubility if not specified) |
logS() calculates intrinsic solubility in logS unit logS('7.4', 'mol/l') calculates solubility at pH 7.4 in mol/l unit |
| lowestEnergyConformer, leconformer |
Structural Calculations |
generates the lowest energy conformer of the molecule |
the lowest energy conformer |
- |
* lowestEnergyConformer() generates the lowest energy conformer of the molecule |
| majormicrospecies, majorms |
Protonation |
generates the major microspecies of the molecule at a certain pH value |
the major microspecies |
pH value (must be specified) majortautomer (takes the major tautomer form of the molecule, default is false keephydrogens (keeps the explicit H atoms on the molecule, default is false* ) |
majormicrospecies('6.5') generates the major microspecies of the molecule at pH 6.5 majorms('7.4 majortautomer:true') generates the major microspecies at pH 7.4 taking tautomerization into consideration |
| majortautomer |
Isomers |
generates the major tautomer of the molecule |
the major tautomer |
* pH value (set if pH effect should be considered) |
majortautomer('7.4') * generates the major tautomer form of the molecule at pH 7.4 |
| map |
- |
returns the map number of an atom |
the map number |
atom index or MolAtom object |
map(2) * returns the map number of atom 2 |
| markushEnumerationCount, enumerationCount |
Markush Enumeration Plugin |
calculates the number of Markush enumerations |
the number of Markush enumerations |
(1-based) query atom indexes to be enumerated (default is all) |
markushEnumerationCount() returns the number of Markush enumerated structures of the input molecule markushEnumerationCount('4,5') returns the number of Markush enumerated structures of the input molecule, enumerating atoms 4 and 5 |
| markushEnumeration, enumeration markushEnumerations, enumerations |
Markush Enumeration Plugin |
generates Markush enumerated structures sequentially |
the enumerated structures |
(1-based) query atom indexes to be enumerated (default is all) the number of structures to be enumerated (default is all) |
markushEnumerations() returns all enumerated Markush structures of the input molecule markushEnumerations(1, '2, 3') returns one Markush structure enumerated on atoms 2 and 3 |
| markushEnumerationsDisplay |
Markush Enumeration Plugin |
generates Markush enumerated structures sequentially with scaffold alignment and scaffold/R group colouring and enumeration ID |
the enumerated structures with alignment, colouring data and enumation ID |
(1-based) query atom indexes to be enumerated (default is all) the number of structures to be enumerated (default is all) |
markushEnumerationsDisplay()* returns all enumerated Markush structures of the input molecule with scaffold alignment and colouring data |
| markushLibraryMagnitude |
Markush Enumeration Plugin |
calculates the Markush Library magnitude but performs no enumeration |
the Markush library magnitude |
(1-based) query atom indexes to be enumerated (default is all) |
markushLibraryMagnitude() returns the magnitude of the Markush library using all atoms for enumeration markushLibraryMagnitude('4, 5') returns the magnitude of the Markush library using only atoms 4 and 5 for enumeration |
| markushLibrarySize |
Markush Enumeration Plugin |
calculates the Markush library size but performs no enumeration |
the Markush library size |
(1-based) query atom indexes to be enumerated (default is all) |
markushLibrarySize('4, 5') * returns the size of the Markush library using only atoms 4 and 5 for enumeration |
| markushLibrarySizeAsString |
Markush Enumeration Plugin |
calculates the Markush library size and returns it as a string but performs no enumeration |
the Markush library size as a string |
(1-based) query atom indexes to be enumerated (default is all) |
markushLibrarySizeAsString('4, 5') * returns the size of the Markush library as a string using only atoms 4 and 5 for enumeration |
| mass |
- |
calculates the molecular mass |
the molecular mass |
single (takes the largest connected fragment of a multi-fragment input molecule if true, otherwise the whole molecule, default is false ) precision (default is 2) |
mass()* calculates the molecular mass of the input molecule |
| massspectrum |
- |
calculates the mass distribution of the molecule considering the relative abundance of the isotopes (mass spectrum) |
the mass spectrum as a series of discrete values |
single (takes the largest connected fragment of a multi-fragment input molecule if true, otherwise the whole molecule, default is false ) precision (default is 2) |
massspectrum()* calculates the mass spectrum of the molecule |
| match |
Structure Search |
performs substructure search and checks atom matching |
true if the query (sub)structure is found in the target molecule, false otherwisethe hit is required to include the target atom if specified |
target atom index or MolAtom object query molecule object/SMARTS string * query atom map(s): if specified, the mapped atoms should match the target atom (optional) |
match("[#8]C=O") performs substructure search without atom maps, the target being the input molecule, the query being the carboxylic molecule given as a SMARTS string match(6, "[#8][C:1]=O", 1) performs substructure search, checking if target atom 6 matches the C atom (with map 1) of the carboxylic group match(6, "[#8:1]C=[O:2]", 1, 2) * performs substructure search, checking if target atom 6 of the input molecule is a carboxylic O |
| matchCount |
Structure Search |
performs substructure search, checks atom matching and counts search hits |
the number of search hits |
target atom index or MolAtom object query molecule object/SMARTS string * query atom map(s): if specified, the mapped atoms should match the target atom (optional) |
matchCount("[#8]C=O") counts substructure search hits without atom maps, the target being the input molecule, the query being the carboxylic molecule given as a SMARTS string matchCount(6, "[#8]C=O") counts substructure search hits in which the target atom 6 matches any atom of the carboxylic group matchCount(6, "[#8:1]C=[O:2]", 1, 2) * counts search hits with target atom 6 being a carboxylic O |
| matchFirst |
Structure Search |
|
|
|
|
| max |
- |
takes the maximum value of a numerical array of elements |
the maximum value |
integer/real number array |
max(2, 4, 6) returns 6 max(1.1, 2.3, 4.5) returns 4.5 max(charge(0), charge(1), charge(2), charge(3)) returns the maximal partial charge of atoms 0, 1, 2 and 3 max(charge()) returns the maximal atomic partial charge of the input molecule |
| maxAtom |
- |
evaluates a function on the atoms of the molecule and finds the atoms with the largest value(s) |
atom indices corresponding to the largest values |
target atom indices/MolAtom objects or arrays of them (optional, default is all) the function given as a string * the number of largest values to be returned (optional, default is 1) |
maxAtom(1, 2, 3, 4, 'charge("7.4")', 2) returns the indices of the two largest partial charge values of atoms 1, 2, 3 and 4 of the major microspecies at pH 7.4 maxAtom('acceptor()', 3) returns the indices of the atoms with the three largest H-bond acceptor multiplicity |
| maximalProjectionArea |
Structural Calculations |
calculates the maximal projection area of the molecule |
the maximal projection area |
optimization (sets optimization level), can be 0 (very loose) 1 (normal, default) 2 (strict) 3 (very strict) optimizeprojection (sets projection optimization, default is false) calcforleconformer (set lowest energy conformer calculation), can be if2D (default) never always |
maximalprojectionarea('optimization:2')* calculates the maximal projection area of the conformer of the molecule with strict geometry optimization |
| maximalProjectionRadius |
Structural Calculations |
calculates the maximal projection radius of the molecule |
the maximal projection radius |
all options of the maximalprojectionarea() function |
maximalProjectionRadius('optimization:2') * calculates the maximal projection radius of the conformer of the molecule with strict geometry optimization |
| maximalProjectionSize |
Structural Calculations |
calculates the maximal distance in the molecule perpendicular to the maximal projection surface |
the maximal distance |
all options of the maximalprojectionarea() function |
maximalProjectionSize() * calculates the maximal distance in the conformer of the molecule perpendicular to its maximal projection surface |
| maxValue |
- |
evaluates a function on the atoms of the molecule and returns some of the largest value(s) |
the largest value(s) |
all options of the maxAtom() function |
maxValue(1, 2, 3, 4, 'charge("7.4")', 2) returns the two largest partial charge values of atoms 1, 2, 3 and 4 of the major microspecies at pH 7.4 maxValue('acceptor()', 3) returns the three largest H-bond acceptor multiplicities |
| microspecies, ms |
Protonation |
generates a microspecies at a specific pH value |
the microspecies |
pH value (as a string) microspecies index (integer starting from 0) by descending order of distribution (optional, default is 0) |
microspecies('7.4', 0) * generates the most dominant microspecies of the molecule at pH 7.4 |
| microspeciescount, mscount |
Protonation |
calculates the number of microspecies of the molecule at a given pH value |
the microspecies count |
* pH value (as a string) |
microspeciesCount('7.4') * calculates the number of microspecies of the molecule at pH 7.4 |
| microspeciesdistribution, msdistr |
Protonation |
calculates the microspecies distribution of the molecule at a given pH value |
the microspecies distribution |
pH value (as a string) the microspecies index by descending order of distribution (optional, uses the major microspecies if not specified) |
microspeciesdistribution('7.4') returns the distribution of the major microspecies (with the largest distribution) at pH 7.4 msdistr('8.0', 2) returns the distribution of the 2nd most dominant microspecies of the input molecule at pH 8.0 |
| min |
- |
takes the minimum value of a numerical array of elements |
the minimum value |
integer/real number array |
min(2, 4, 6) returns 2 min(1.1, 2.3, 4.5) returns 1.1 min(charge(0), charge(1), charge(2), charge(3)) returns the minimal partial charge of atoms 0, 1, 2 and 3 min(charge()) returns the minimal atomic partial charge of the input molecule |
| minAtom |
- |
evaluates a function on the atoms of the molecule and finds the atoms with the minimal value(s) |
atom indices corresponding to the smallest values |
target atom indices/MolAtom objects or arrays of them (optional, default is all atoms) the function given as a string * the number of smallest values to be returned (optional, default is 1) |
minAtom(1, 2, 3, 4, 'charge("7.4")', 2) returns the indices of the two smallest partial charge values of atoms 1, 2, 3 and 4 of the major microspecies at pH 7.4 minAtom('acceptor()', 3) returns the indices of the atoms with the three smallest H-bond acceptor multiplicity |
| minimalProjectionArea |
Structural Calculations |
calculates the minimal projection area of the molecule |
the minimal projection area |
optimization (sets optimization level), can be 0 (very loose) 1 (normal, default) 2 (strict) 3 (very strict) optimizeprojection (sets projection optimization, default is false) calcforleconformer (set lowest energy conformer generation), can be if2D (default) never always |
minimalprojectionarea('optimization:2')* calculates the minimal projection area of the conformer of the molecule with strict geometry optimization |
| minimalProjectionRadius |
Structural Calculations |
calculates the minimal projection radius of the molecule |
the minimal projection radius |
all options of the minimalProjectionArea() function |
minimalProjectionRadius('optimization:2') * calculates the minimal projection radius of the conformer of the molecule with strict geometry optimization |
| minimalProjectionSize |
Structural Calculations |
calculates the maximal distance in the molecule perpendicular to the minimal projection surface |
the maximal distance |
all options of the minimalProjectionArea() function |
minimalProjectionSize() * calculates the maximal distance in the conformer of the molecule perpendicular to its minimal projection surface |
| minValue |
- |
evaluates a function on the atoms of the molecule and returns some of the smallest value(s) |
the smallest value(s) |
all options of the minAtom() function |
minValue(1, 2, 3, 4, 'charge("7.4")', 2) returns the two smallest partial charge values of atoms 1, 2, 3 and 4 of the major microspecies at pH 7.4 minValue('acceptor()', 3) returns the three smallest H-bond acceptor multiplicities |
| mmff94Energy |
Structural Calculations |
calculates the MMFF94 energy of the input molecule |
the MMFF94 energy |
calcforleconformer (sets lowest energy conformer generation option), can be if2D (default) never always mmff94optimization (sets MMFF94 forcefield optimization, default is false* ) |
mmff94Energy() * calculates the MMFF94 energy of the (conformer) of the input molecule |
| mmff94OptimizedStructure |
Structural Calculations |
calculates the MMFF94- optimized lowest energy conformer |
the MMFF94-optimized lowest energy conformer |
- |
mmff94OptimizedStructure() * returns the MMFF94 optimized lowest energy conformer of input molecule |
| molAtom |
- |
creates a MolAtom object of a given atomic number |
the MolAtom object |
the atomic number |
MolAtom(6) * returns a C atom |
| molBinFormat, molImage |
- |
returns the binary representation (image, PDF, GZIP compressed molecule file) of the molecule in a specified format |
the binary representation of the molecule in the given format |
the binary format with its options (e.g. 'jpeg', 'pdf', 'gzip:sdf', 'png:w150,h150') |
molImage('jpeg:w100,Q95, #ffff00') * returns the 100x100 image of the molecule in JPEG format with yellow background and 95% quality |
| molecularPolarizability, molPol |
Structural Calculations |
calculates the molecular polarisability of the molecule |
the molecular polarizability |
type, can be molecular (default) atomic pH value (used for calculating the major microspecies if specified) |
molecularPolarizability('7.4') calculates the molecular polarizability of the major microspecies of the input molecule at pH 7.4 molPol('type:atomic') calculates the atomic molecular polarizability of the input molecule |
| molString, molFormat, molConvert |
- |
returns the string representation of a molecule/an array of molecules in a given format |
the string representation of the molecule(s) |
the array of molecules (optional, the context is used as an input if not specified) the molecule format as a string (e.g. "sdf", "smiles", "mrv") * the clean dimension |
molFormat('mrv') returns the MRV representation of the input molecule molString(tautomers(), 'sdf', 2) returns the 2D-cleaned tautomers of the input molecule in SDF format |
| mostStableTautomer |
Isomers |
generates the most stable tautomer form of the molecule |
the most stable tautomer |
- |
mostStableTautomer()* returns the most stable tautomer form of the input molecule |
| mpo |
Protonation, Partitioning, Structural Calculations |
calculates the CNS Multiparameter Optimisation (MPO) Score |
the MPO score |
- |
mpo() returns the MPO score of the input molecule |
| nucleophilicity, electrophilicLocalizationEnergy, energyE |
Structural Calculations |
calculates the nucleophilicity of aromatic centers (by calculating localization energies for electrophilic attack) |
the nucleophilicity of the atom, NaN for non-aromatic atoms |
atom index or MolAtom object pH value (used for calculating the major microspecies if specified) |
nucleophilicity(2)* returns the nucleophilicity of atom 2 of the input molecule |
| nucleophilicityOrder, aromaticNucleophilicityOrder, orderNu |
Structural Calculations |
calculates the nucleophilic order (Nu(-) order) of atoms |
the nucleophilic order (index 0, 1, 2...) |
atom index or MolAtom object pH value (used for calculating the major microspecies if specified) |
nucleophilicityOrder(2, '7.4') * returns the nucleophil order of atom 2 of the major microspecies of the input molecule at pH 7.4 |
| pair |
- |
converts two atoms or 0-based atom indexes into an "index1-index2" 1-based atom index setter string (used for pairing atoms) |
the atom index setter string |
two atom indexes or MolAtom objects |
pair(2, 5)* returns "6-3" |
| piEnergy |
Structural Calculations |
calculates the π energy of the molecule |
the π energy of the molecule |
* pH value (used for calculating the major microspecies if specified) |
piEnergy() returns the π energy of the molecule piEnergy('7.4') returns the π energy of the microspecies |
| piOrbitalElectronegativity, pOEN |
Structural Calculations |
calculates atomic π orbital electronegativity |
the atomic electronegativity |
atom index or MolAtom object pH value (used for calculating the major microspecies if specified) |
piOrbitalElectronegativity(2) returns the π orbital electronegativity of atom 2 of the input molecule pOEN(1, '7.4') returns the π orbital electronegativity of the major microspecies of the input molecule at pH 7.4 |
| pKa |
Protonation |
calculates pKa values |
the pKa values |
atom index or MolAtom object strength index as a string (e.g. '1' for strongest, '2' for the 2nd strongest pKa) the pKa type to be calculated as a string, can be acidic basic pKa (default) mode, can be macro (default) micro prefix, can be static (default) dynamic model, can be small (default) large considertautomerization (default is false ) min (minimal pKa value to be calculated) max (maximal pKa value to be calculated) na (number of acidic pKa values to be calculated, default is 2 nb (number of basic pKa values to be calculated, default is 2) temperature (sets the temperature in K, default is 298K) correctionlibrary (sets the correction library ID) correctionlibrarypath (sets the correction library path)Notes: 1. When strength index is used, only 'acidic' or 'basic' type can be used. 1. If the 'pKa' type is used, the returned pKa values are of mixed type, depending on the atom's acidic or basic features. 1. To get a specific type of pKa, either 'acidic' or 'basic' type should be specified. You can use acidicpKa() or basicpKa() functions as an alternative, too. 1. Acidic pKa is returned for an atom if acidicpKa() ≤ 14.8-basicpKa()* , otherwise basicpKa() is returned |
pKa(0) returns the pKa value of atom 0 of the input molecule pKa(4, 'basic') returns the basic pKa value of atom 4 pKa('acidic', '1') returns the strongest acidic pKa value of the molecule pKa('basic', 'prefix:dynamic') returns the basic pKa values of the input molecule using the dynamic prefix pKa('acidic', 'considertautomerization:true', 'mode:micro') * returns the acidic pKa values of the input molecule using the micro mode and tautomerization |
| pKaUseCorrection |
Protonation |
|
|
|
|
| plattIndex |
Structural Calculations |
calculates the Platt index of the molecule |
the Platt index |
- |
plattIndex() * calculates the Platt index of the input molecule |
| productCount |
- |
counts the products in a chemical reaction |
the number of products in the reaction or -1 if the input molecule is not a reaction |
- |
productCount()* returns -1 for a molecule that is not a reaction |
| radicalCount |
- |
returns the radical count of an atom |
the radical count |
atom index or MolAtom object |
radicalCount(1)* returns the radical count of atom 1 of the input molecule |
| randicIndex |
Structural Calculations |
calculates the Randic index |
the Randic index |
- |
randicIndex() * calculates the Randic index of the input molecule |
| randomMarkushEnumeration, randomMarkushEnumerations, randomEnumeration, randomEnumerations |
Markush Enumeration Plugin |
generates Markush enumerated structures of the molecule randomly |
the enumerated Markush structures |
the number of structures to be returned (default is 1) the (1-based) atom indexes of the query atoms to be enumerated, given as a string list (default is all) |
randomMarkushEnumerations() returns a randomly enumerated Markush structure of the input molecule randomMarkushEnumerations(4, '2,3') returns 4 randomly enumerated Markush structures of the input molecule, enumerating only atoms 2 and 3 |
| randomMarkushEnumerationDisplay |
Markush Enumeration Plugin |
generates Markush enumerated structures of the molecule randomly with scaffold alignment, 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 indexes of the query atoms to be enumerated, given as a string list (default is all) |
randomMarkushEnumerationDisplay() returns a randomly enumerated Markush structure of the input molecule with scaffold aligment and scaffold/R-group colouring data randomMarkushEnumerations(4, '2,3') returns 4 randomly enumerated Markush structures of the input molecule, enumerating only atoms 2 and 3, with scaffold alignment and scaffold/R-group colouring data |
| reactantCount |
- |
counts the reactants in a reaction |
the reactant count or -1 if the input is not a reaction |
- |
reactantCount() * returns the number of reactants in the molecule or -1 |
| refractivity, refrac |
Structural Calculations |
calculates the molar refractivity of the molecule |
the molar refractivity |
type, can be refractivity (default) increments (sum of the increments of non-H atoms) inch (sum of the increments of H atoms) * precision (default is 2) |
refractivity() calculates the molar refractivity of the input molecule refrac('type:increments, precision:3') calculates the sum of non-H atomic refractivity increments of the input molecule with 3-digit precision |
| refractivityIncrements, refraci |
Structural Calculations |
calculates atomic refractivity increment(s) of the molecule |
the atomic refractivity increment(s) |
atom index or MolAtom object |
refractivityIncrements(2) * calculates the refractivity increment of atom 2 of the input molecule |
| resonants |
Structural Calculations |
generates resonant structures of the molecule |
the resonant structures |
type, can be structures (returns all resonant structures, default) structure (returns only 1 structure) count (returns the resonant structure count) max (the maximal number of resonant structures, default is 200) pH (considers pH effect, default is no pH effect) symfilter (filters symmetrical structures if true , allows duplicates otherwise, default is true ) canonical (generates canonical resonant structure if true ) mcontrib (takes major resonant contribution if true, default is true ) single (single fragment mode, generates resonant structures for each fragment if true , default is false ) |
resonants('max:20, pH:7.4') generates at most 20 resonant structures for the input molecule considering pH effect at 7.4 resonants('canonical:true', 'pH:7.4') generates the canonical resonant form of the input molecule at pH 7.4 |
| resonant |
Structural Calculations |
generates a resonant structure of the molecule |
the resonant structure |
the resonant structure index (0-based) |
resonant(1) * returns the 2nd resonant structure of the input molecule |
| resonantCharge |
Structural Calculations |
calculates atomic partial charges considering effect of resonance |
the atomic partial charges |
atom index or MolAtom object pH value (used for calculating the major microspecies if specified) result type, can be total (default) pi sigma aromaticsystem aromaticsystemsigma aromaticsystempi aromaticring aromaticringsigma aromaticringpi |
resonantCharge(1, 'type:sigma') calculates the sigma partial charge of the 2nd atom of the input molecule resonantCharge(0, 'pH:7.4') calculates the total partial charge of the 1st atom of the major microspecies of the input molecule at pH 7.4 |
| resonantCount |
Structural Calculations |
calculates the number of resonant structures |
the number of resonant structures |
all options of the resonants() function |
resonantCount('pH:7.4') * returns the number of resonant structures generated at pH 7.4 |
| ringAtom |
Structural Calculations |
checks if an atom is a ring atom |
true for ring atoms, false for non-ring atoms |
atom index or MolAtom object |
ringAtom(2)* returns if atom 2 of the input molecule is a ring atom |
| ringAtomCount |
Structural Calculations |
calculates the number of ring atoms in the molecule |
the ring atom count |
- |
ringAtomCount() * returns the number of ring atoms of the input molecule |
| ringBond |
Structural Calculations |
checks if two atoms in the molecule are connected by a ring bond |
true if the two atoms are connected by a ring bond, false otherwise |
the (1-based) atom indexes of the two atoms in a string "index1-index2" (e.g. '2-3') |
ringBond('1-2') checks if atom 1 and 2 of the input molecule are connected by a ring bond ringBond(bond(2, 3)) checks if atom 2 and 3 of the input molecule are connected by a ring bond |
| ringBondCount |
Structural Calculations |
calculates the number of ring bonds in the molecule |
the ring bond count |
- |
ringBondCount() * returns the number of ring bonds in the input molecule |
| ringCount |
Structural Calculations |
calculates the number of rings in the molecule |
the ring count |
- |
ringCount() * returns the number of rings in the input molecule |
| ringCountOfAtom |
Structural Calculations |
calculates the number of rings in the molecule passing through an atom |
the number of rings passing through the atom |
atom index or MolAtom object |
ringCountOfAtom(2) * returns the number of rings passing through atom 2 |
| ringCountOfSize |
Structural Calculations |
calculates the number of rings of a given size in the molecule |
the number of rings of the given size |
the ring size |
ringCountOfSize(5)* returns the number of 5-membered rings of the input molecule |
| rings |
Structural Calculations |
identifies the rings in the molecule |
the list of atom indexes of the rings (or null if the molecule is acyclic) |
- |
rings()* returns the list of atom indexes of the rings in the input molecule |
| ringsOfSize |
Structural Calculations |
identifies the rings of a given size in the molecule |
the list of atom indexes of the rings having that size (or null if the molecule is acyclic or only contains rings of different size) |
the ring size |
ringsOfSize(6)* returns the 6-membered rings of the input molecule as a list of atom indexes |
| ringSystemCount |
Structural Calculations |
calculates the number of ring systems in the molecule |
the ring system count |
- |
ringSystemCount() * returns the number of ring systems of the input molecule |
| ringSystemCountOfSize |
Structural Calculations |
calculates the number of ring systems of a given size in the molecule |
the number of ring systems of the given size |
the ring system size |
ringSystemCountOfSize(8) * returns the number of 8-membered ring systems of the input molecule |
| ringSystems |
Structural Calculations |
identifies the ring systems of the molecule |
the list of atom indexes of the ring systems (or null if the molecule is acyclic) |
- |
ringSystems() * returns the list of atom indexes of the ring systems in the input molecule |
| ringSystemsOfSize |
Structural Calculations |
identifies the ring systems of a given size in the molecule |
the list of atom indexes of the ring systems of the given size (or null if the molecule is acyclic or only contains ring systems of different size) |
the ring system size |
ringSystemsOfSize(8) * returns the list of atom indexes of the 8-membered ring systems in the input molecule |
| rotatableBond |
Structural Calculations |
checks if two atoms of the molecule are connected by a rotatable bond |
true if the two atoms are connected by a rotatable bond, false otherwise |
the (1-based) atom indexes of the two atoms in a string "index1-index2" (e.g. '2-3') |
rotatableBond('2-3') returns true if atoms 2 and 3 of input molecule are connected by a rotatable bond rotatableBond(bond(1,2)) returns true if atoms 1 and 2 of the input molecule are connected by a rotatable bond |
| rotatableBondCount |
Structural Calculations |
calculates the number of rotatable bonds in the molecule |
the rotatable bond count |
- |
rotatableBondCount() * returns the number of rotatable bonds of the input molecule |
| shortestPath |
Structural Calculations |
calculates the length of the shortest path between two atoms in the molecule |
the length of the shortest path or Integer.MAXVALUE if the two atoms are disconnected |
the (1-based) atom indexes of the two atoms in a string "index1-index2" (e.g. '2-3') |
shortestPath('2-3') returns the length of the shortest path between atoms 2 and 3 of the input molecule shortestPath(pair(1, 3)) returns the length of the shortest path between atoms 1 and 3 of the input molecule |
| sigmaOrbitalElectronegativity, sOEN |
Structural Calculations |
calculates atomic sigma orbital electronegativity |
the atomic sigma OE value(s) |
atom index or MolAtom object pH value (used for calculating the major microspecies if specified) |
sigmaOrbitalElectronegativity(2) returns the sigma orbital electronegativity of atom 2 of the input molecule sOEN(3, '7.4') returns the sigma orbital electronegativity of atom 3 of the major microspecies of the input molecule at pH 7.4 |
| smallestAtomRingSize |
Structural Calculations |
calculates the size of the smallest ring that contains a specified atom |
the size of the smallest ring that contains the specified atom (0 is returned is the specified atom is acyclic) |
atom index or MolAtom object |
smallestAtomRingSize(2)* returns the size of the smallest ring that contains atom 2 of the input molecule |
| smallestRing |
Structural Calculations |
identifies the atoms of the smallest ring of the molecule |
the atom indexes of the smallest ring (or null if the molecule is acyclic) |
- |
smallestRing() * returns the atom indexes of the smallest ring of the input molecule |
| smallestRingSize |
Structural Calculations |
calculates the size of the smallest ring |
the smallest ring size (0 is returned if the molecule is acyclic) |
- |
smallestRingSize() * returns the size of the smallest ring of the input molecule |
| smallestRingSystem |
Structural Calculations |
identifies the atoms of the smallest ring system of the molecule |
the atom indexes of the smallest ring system (or null if the molecule is acyclic) |
- |
smallestRingSystem() * returns the atom indexes of the smallest ring system of the input molecule |
| smallestRingSystemSize |
Structural Calculations |
calculates the size of the smallest ring system |
the smallest ring system size (the number of rings, 0 is returned if the molecule is acyclic) |
- |
smallestRingSystemSize() * returns the size of the smallest ring system (the number of rings) of the input molecule |
| sortableFormula |
- |
returns a fixed digit sortable formula of the molecule |
the fixed digit sortable formula |
digits (the number of digits) |
sortableFormula(digits:3) * returns the 3-digit sortable formula of the input molecule |
| sortAsc |
- |
sorts a numerical array in ascending order |
the sorted array |
the numerical (integer or real) array |
sortAsc(array(4.2, 2.4, 3.5)) returns the array(2.4, 3.5, 4.2) sortAsc(charge()) returns the atomic partial charges of the input molecule in ascending order |
| sortDesc |
- |
sorts a numerical array in descending order |
the sorted array |
the numerical (integer or real) array |
sortDesc(array(4.2, 2.4, 3.5)) returns array(4.2, 3.5, 2.4) sortDesc(pKa('basic')) returns the basic pKa values of the input molecule in descending order |
| stereoAnalysis |
Isomers |
calculates stereo descriptors of the molecule |
a list of stereo descriptors |
the stereo descriptor type (optional, all types of stereo descriptors are calculated if not specified) |
stereoAnalysis() calculates all stereo descriptors of the input molecule stereoAnalysis('tetrahedralStereoCenters') identifies all tetrahedral stereocenters of the input molecule stereoAnalysis('transDoubleBonds')* identifies all trans double bonds of the input molecule |
| stereoDoubleBondCount |
Structural Calculations |
calculates the number of stereogenic double bonds of the molecule |
the number of stereogenic double bonds |
- |
stereoDoubleBondCount()* returns the number of stereo double bonds of the input molecule |
| stereoisomer |
Isomers |
generates a stereoisomer of the molecule |
the stereoisomer |
the stereoisomer index (0-based) |
stereoisomer(1) * returns the 2nd stereoisomer of the input molecule |
| stereoisomers |
Isomers |
generates stereoisomers of the molecule |
the array of stereoisomers |
maxstereoisomers (sets the maximal number of stereoisomers to be generated, default is all) |
stereoisomers('maxstereoisomers:10') * returns at most 10 stereoisomers of the input molecule |
| stereoisomerCount |
Isomers |
returns the number of generated stereoisomers of the molecule |
the number of generated stereoisomers |
- |
stereoIsomerCount()* returns the number of generated stereoisomers of the input molecule |
| stericEffectIndex |
Structural Calculations |
calculates the steric effect index of an atom |
the steric effect index of the atom |
atom index or MolAtom object |
stericEffectIndex(1) * returns the steric effect index of atom 1 (with index 1) of the input molecule |
| stericHindrance |
Structural Calculations |
calculates the steric hindrance of an atom |
the steric hindrance of the atom |
atom index or MolAtom object |
stericHindrance(2) * returns the steric hindrance of atom 2 (with index 2) of the input molecule |
| sum |
- |
calculates the sum of an array of numbers |
the sum |
the numerical (integer or real) array |
sum(array(1.0, 2.0, 3.0)) returns 6.0 sum(charge()) returns the sum of atomic partial charges of the input molecule |
| szegedIndex |
Structural Calculations |
calculates the Szeged index of the molecule |
the Szeged index |
- |
szegedIndex() * returns the Szeged index of the input molecule |
| tautomerCount |
Isomers |
calculates the number of (all) tautomers |
the number of tautomers |
- |
tautomerCount() * returns the number of (all) tautomers of the input molecule |
| tetrahedralStereoisomer |
Isomers |
generates a tetrahedral stereoisomer of the molecule |
a tetrahedral stereoisomer |
the stereoisomer index (0-based) |
tetrahedralStereoisomer(1)* returns the 2nd tetrahedral stereoisomer of the input molecule |
| tetrahedralStereoisomerCount |
Isomers |
calculates the number of tetrahedral stereoisomers of the molecule |
the number of tetrahedral stereoisomers |
- |
tetrahedralStereoisomerCount()* returns the number of tetrahedral stereoisomers of the input molecule |
| tetrahedralStereoisomers |
Isomers |
generates tetrahedral stereoisomers of the molecule |
the array of tetrahedral stereoisomers |
maxstereoisomers (sets the maximal number of stereoisomers to be generated, default is all) |
tetrahedralStereoisomers('maxstereoisomers:10') * returns at most 10 tetrahedral stereoisomers of the input molecule |
| topologicalPolarSurfaceArea, PSA |
- |
calculates the (2D) topological polar surface area |
the polar surface area |
pH value (used for calculating the major microspecies if specified) |
topologicalPolarSurfaceArea() * returns the topological polar surface area of the input molecule |
| traditionalName |
Structure To Name |
generates the traditional name of the molecule |
the traditional name |
- |
traditionalName()* returns the traditional name of the input molecule |
| valence |
- |
returns the sum of bond orders and the query H atoms (valence) of an atom of the molecule |
the valence of the atom |
atom index or MolAtom object |
valence(1) * returns the valence of atom 1 |
| vanDerWaalsSurfaceArea |
Structural Calculations |
calculates the van der Waals (vdW) surface area of the molecule |
the vdW surface area |
pH value (used for calculating the major microspecies if specified) |
* vanDerWaalsSurfaceArea('7.4') returns the van der Waals surface area of the major microspecies of the input molecule at pH 7.4 |
| volume |
Structural Calculations |
calculates the van der Waals (vdW) volume of the molecule |
the vdW volume |
optimization (sets optimization level), can be 0 (very loose) 1 (normal, default) 2 (strict) 3 (very strict) calcforleconformer (sets lowest energy conformer generation option), can be if2D (default) never * always |
volume()* calculates the vdW volume of the input molecule |
| waterAccessibleSurfaceArea, solventAccessibleSurfaceArea, ASA |
Structural Calculations |
calculates the solvent/water accessible surface area of the molecule |
the molecular surface area |
pH value (used for calculating the major microspecies if specified) |
solventAccessibleSurfaceArea('7.4') * calculates the solvent accessible surface area of the major microspecies of the input molecule at pH 7.4 |
| whereIsValenceError |
- |
returns the index of the first atom of the molecule with a valence error |
the index of the first atom with the valence error or -1 if there is no valence error in the molecule |
- |
whereIsValenceError() * returns the index of the first atom of the input molecule with a valence error or -1 if there is no valence error in the input molecule |
| wienerIndex |
Structural Calculations |
calculates the Wiener index of the molecule |
the Wiener index |
- |
wienerIndex()* returns the Wiener index of the input molecule |
| wienerPolarity |
Structural Calculations |
calculates the Wiener polarity of the molecule |
the Wiener polarity |
- |
wienerPolarity()* returns the Wiener polarity of the input molecule |