| Name | License | Description | Return value | Parameters | Examples |
|---|---|---|---|---|---|
| atomicPolarizability atomPol pol polarizability |
Charge Plugin Group | calculates atomic polarizability | the polarizability values |
|
Molecule Context
(All)atomicPolarizability(0) returns the polarizability of atom 0 of the input molecule atomicPolarizability(2, "7.4")
returns the polarizability of atom 2 of the major microspecies taken at pH 7.4
|
| averagePolarizability averagePol avgPol |
Charge Plugin Group | calculates average molecular polarizability component considering 3D geometry | the polarizability value |
|
Molecule Context
(All)averagePolarizability() returns the average polarizability component of the input molecule averagePolarizability("7.4")
returns the average polarizability component of the major microspecies taken at pH 7.4
|
| axxPol | Charge Plugin Group | calculates principal component of polarizability tensor (a(xx), a(yy), a(zz)) | the principal component of polarizability tensor |
|
Molecule Context
(All)axxPol() returns the principal component a(xx) of polarizability tensor of the input molecule
axxPol("7.4") returns the principal component a(xx) of polarizability tensor of the major microspecies taken
at pH 7.4
|
| ayyPol | Charge Plugin Group | calculates principal component of polarizability tensor (a(xx), a(yy), a(zz)) | the principal component of polarizability tensor |
|
Molecule Context
(All)ayyPol() returns the principal component a(yy) of polarizability tensor of the input molecule
ayyPol("7.4") returns the principal component a(yy) of polarizability tensor of the major microspecies taken
at pH 7.4
|
| azzPol | Charge Plugin Group | calculates principal component of polarizability tensor (a(xx), a(yy), a(zz)) | the principal component of polarizability tensor |
|
Molecule Context
(All)azzPol() returns the principal component a(zz) of polarizability tensor of the input molecule
azzPol("7.4") returns the principal component a(zz) of polarizability tensor of the major microspecies taken
at pH 7.4
|
| charge | Charge Plugin Group | calculates partial charges on atoms for result types "aromaticsystem" / "aromaticring", calculates the sum of partial charges of the atoms in the aromatic system / smallest aromatic ring containing the atom |
the charge values |
|
Molecule Context
(All)charge(0) returns the partial charge on atom 0 of the input molecule charge(2, "pi", "7.4")
returns the partial "pi" charge on atom 2 of the major microspecies taken at pH 7.4
|
| molecularPolarizability molPol |
Charge Plugin Group | calculates molecular polarizability | the polarizability value |
|
Molecule Context
(All)molecularPolarizability() returns the molecular polarizability of the input molecule molecularPolarizability("7.4")
returns the molecular polarizability of the major microspecies taken at pH 7.4
|
| piOrbitalElectronegativity pOEN |
Charge Plugin Group | calculates atomic pi orbital electronegativity | the pi orbital electronegativity values |
|
Molecule Context
(All)piOrbitalElectronegativity(0) returns the pi orbital electronegativity of atom 0 of
the input molecule piOrbitalElectronegativity(2, "7.4") returns the pi orbital electronegativity of atom 2
of the major microspecies taken at pH 7.4
|
| resonantCharge | Charge Plugin Group | calculates partial charges on atoms considering resonance effect for result types "aromaticsystem" / "aromaticring", calculates the sum of partial charges of the atoms in the aromatic system / smallest aromatic ring containing the atom |
the charge values |
|
Molecule Context
(All)resonantCharge(0) returns the partial charge on atom 0 of the input molecule considering resonance effectresonantCharge(2, "pi", "7.4")
returns the partial "pi" charge on atom 2 of the major microspecies taken at pH 7.4 considering resonance effect
|
| sigmaOrbitalElectronegativity sOEN |
Charge Plugin Group | calculates atomic sigma orbital electronegativity | the sigma orbital electronegativity values |
|
Molecule Context
(All)sigmaOrbitalElectronegativity(0) returns the sigma orbital electronegativity of atom 0
of the input molecule sigmaOrbitalElectronegativity(2, "7.4") returns the sigma orbital electronegativity
of atom 2 of the major microspecies taken at pH 7.4
|
| Name | License | Description | Return value | Parameters | Examples |
|---|---|---|---|---|---|
| conformer | Conformation Plugin Group | calculates a conformer of the molecule | the conformer |
|
Molecule Context
(All)conformer(0) returns the first conformer of the input molecule
|
| conformerCount | Conformation Plugin Group | returns the number of calculated conformers | the number of calculated conformers | - |
Molecule Context
(All)conformerCount() returns the number of calculated conformers of the input molecule
|
| conformers | Conformation Plugin Group | calculates conformers of the molecule (maximum number of conformers to be calculated can be set, default: 100) | the conformer array | - |
Molecule Context
(All)conformers() returns conformers of the input molecule in an array
|
| hasValidConformer | Conformation Plugin Group | returns true if the input molecule exist in 3D space (has a valid conformer) | true if the input molecule exist in 3D space | - |
Molecule Context
(All)hasValidConformer() returns true if the input molecule exists in 3D space (has a valid conformer)
|
| lowestEnergyConformer leconformer |
Conformation Plugin Group | calculates the lowest energy conformer of the molecule | the lowest energy conformer | - |
Molecule Context
(All)lowestEnergyConformer() returns the lowest energy conformer of the input molecule
|
| mmff94OptimizedStructure | Conformation Plugin Group | calculates the MMFF94 optimized lowest energy conformer | the MMFF94 optimized lowest energy conformer | - |
Molecule Context
(All)mmff94OptimizedStructure() returns the MMFF94 optimized lowest energy conformer of the input molecule
|
| Name | License | Description | Return value | Parameters | Examples |
|---|---|---|---|---|---|
| dissimilarity | - | computes the dissimilarity value between two molecules
Note 1: Dissimilarity function requires JChem. Note 2: The dissimilarity values returned by dissimilarity function and similarity search in JChem database may differ because of the applied fingerprints. Dissimilarity function uses the default options of the chemical fingerprints (length=1024, bonds=7, bits=2) optimized for similarity search. Database similarity search uses fingerprints specified during the generation of the given table, optimized for substructure (and related) search types. |
the dissimilarity value | descriptor:metric or descriptor (with default metric) (optional, chemical fingerprint with Tanimoto metric is taken by default), one or two molecules (if only one is specified then the other one is taken from the context) |
Molecule Context
(All)dissimilarity("PF", "c1ccccc1", "C1CCCCC1") returns the dissimilarity value between the benzene
ring and cyclohexane, computed with pharmacophore fingerprint and its default metric (Tanimoto) dissimilarity("c1ccccc1", "C1CCCCC1")
returns the dissimilarity value between the benzene ring and cyclohexane, computed with default fingerprint and its
default metric (chemical fingerprint with Tanimoto)
dissimilarity("PF:Euclidean", "c1ccccc1") returns the dissimilarity value between the benzene ring
and the input molecule, computed with pharmacophore fingerprint and Euclidean metric dissimilarity("LogD", "c1ccccc1")
returns the dissimilarity value between the benzene ring and the input molecule, computed with the LogD descriptor and
its default AbsDiff metric
|
| Descriptor | Metric |
|---|---|
| ChemicalFingerprint (or CF) | Tanimoto (default) Euclidean |
| PharmacophoreFingerprint (or PF) | Tanimoto (default) Euclidean |
| ECFP | Tanimoto (default) Euclidean |
| Burden eigenvalue descriptor (or BCUT) (BCUT is a trademark of Tripos, Inc., used with permission) | Euclidean |
| HDon | Euclidean |
| HAcc | AbsDiff |
| Heavy | AbsDiff |
| LogD | AbsDiff |
| LogP | AbsDiff |
| Mass | AbsDiff |
| TPSA | AbsDiff |
| Name | License | Description | Return value | Parameters | Examples |
|---|---|---|---|---|---|
| atomCount | - | calculates the number of atoms (all atoms or specific atoms) | the atom count |
|
Molecule Context
(All)atomCount() returns the number of atoms in the input molecule atomCount("6") returns
the number of carbon atoms in the input molecule
|
| composition | - | returns the composition | the composition | - |
Molecule Context
(All)composition() returns the composition of the input molecule
|
| dotDisconnectedFormula | - | returns the dot-disconnected formula | the dot-disconnected formula | - |
Molecule Context
(All)dotDisconnectedFormula() returns the dot-disconnected formula of the input molecule
|
| dotDisconnectedIsotopeFormula | - | returns the dot-disconnected isotope formula | the dot-disconnected isotope formula | - |
Molecule Context
(All)dotDisconnectedIsotopeFormula() returns the dot-disconnected isotope formula of the input molecule
|
| elementalAnalysis | - | performs elemental analysis on molecule represented by formula | the value calculated by the invoked function (e.g., mass) |
|
Molecule Context
(All)elementalAnalysis('C12H25O', 'mass') returns the mass of molecule represented by formula
|
| exactMass | - | calculates the exact mass of the molecule | the exact mass | - |
Molecule Context
(All)exactMass() returns the exact mass of the input molecule
|
| formula | - | returns the formula | the formula | - |
Molecule Context
(All)formula() returns the formula of the input molecule
|
| groupedDotDisconnectedFormula | - | returns the grouped dot-disconnected formula | the grouped dot-disconnected formula | - |
Molecule Context
(All)groupedDotDisconnectedFormula() returns the grouped dot-disconnected formula of the input molecule
|
| isotopeComposition | - | returns the isotope composition | the isotope composition | - |
Molecule Context
(All)isotopeComposition() returns the isotope composition of the input molecule
|
| isotopeFormula | - | returns the isotope formula | the isotope formula | - |
Molecule Context
(All)isotopeFormula() returns the isotope formula of the input molecule
|
| mass | - | calculates the molecule mass | the mass | - |
Molecule Context
(All)mass() returns the mass of the input molecule
|
| massSpectrum | - | returns the mass spectrum | the mass spectrum | - |
Molecule Context
(All)massSpectrum() returns the mass spectrum of the input molecule
|
| sortableFormula | - | returns the fixed digit sortable formula | fixed digit sortable molecular formula | - |
Molecule Context
(All)sortableFormula() returns the sortable formula of the input molecule; sortableFormula('digits:4')
returns the 4 digit sortable formula of the input molecule
|
| Name | License | Description | Return value | Parameters | Examples |
|---|---|---|---|---|---|
| abs | - | returns the absolute value of a number | the absolute value | integer or real number |
General
(All)abs(7)returns 7abs(-4.9)returns 4.9
Reaction Context (All) |
| agentCount | - | counts the agents in the reaction | the number of agents in the reaction, or -1 if the the input (molecule) is not a reaction |
- |
Molecule Context
(All)agentCount() returns n if the given molecule is a reaction and contains n agents.
agentCount() returns -1 if the given molecule is not a reaction.
|
| arom | - | returns if the atom has an aromatic bond | true if the atom has an aromatic bond, false otherwise |
atom index or MolAtom object |
Molecule Context
(All)arom(0) returns if the atom 0 has an aromatic bond
|
| array | - | constructs an integer array from its arguments | the integer array | integers or MolAtom objects |
General
(All)array(2, 5, 6, 8)
Reaction Context (All) |
| atno atomicNumber |
- | returns the atomic number | the atomic number | atom index or MolAtom object |
Molecule Context
(All)atno(0) returns the atomic number of atom 0
|
| atomProp | - | ||||
| atoms | - | ||||
| booleanToNumber | - | returns the number representation of a boolean value (true = 1, false = 0),
or the number itself, if the input is a number |
the number representation of a boolean value | boolean or number |
General
(All)booleanToNumber(1<2)returns 1booleanToNumber(2+2==5)returns 0booleanToNumber(5*5)returns 25
Reaction Context (All) |
| connections | - | returns the bond plus implicit H count of an atom | the bond plus implicit H count | atom index or MolAtom object |
Molecule Context
(All)connections(2) returns the number of connections of atom 2
|
| count | - | determines the number of elements in an array | the number of array elements | integer array or real number array |
General
(All)count(array(3.4, 5.6, 1.2)) returns 3
Reaction Context (All) |
| elemanal | - | ||||
| eval | - | ||||
| field property |
- | returns a molecule property (SDF field value) | the molecule property | the property key (SDF field name) |
Molecule Context
(All)field('ACTIVITY') returns the value of the ACTIVITY property (SDF field) field('ACTIVITY') > 2
returns 1 if the ACTIVITY value is bigger than 2, returns 0 otherwise
|
| fieldAsString propertyAsString |
- | returns a molecule property (SDF field value) as string | the molecule property as string | the property key (SDF field name) |
Molecule Context
(All)fieldAsString('ID') returns the value of the ID property (SDF field)
|
| filter | - | filters target atoms by filtering condition | target atom indices satisfying the filtering condition | target atom indices / objects or index / atom object array (optional, all atoms taken if omitted), filtering condition (boolean expression) |
Molecule Context
(All)filter("charge() > 0") returns the indices of atoms with positive partial charge in the input
molecule filter(6, 7, 8, 9, "match('[#8][C:1]=O', 1)") returns the carboxylic carbons out of atoms 6,
7, 8, 9 in the input molecule
|
| formalCharge totalCharge |
- | calculates formal charge of molecule | the formal charge value | atom index or MolAtom object (optional) |
Molecule Context
(All)formalCharge() returns the formal charge of the input molecule
formalCharge(0) returns the formal charge of atom 0
|
| fragments | - | converts the molecule to its disconnected fragments | the disconnected fragments of the molecule | - |
Molecule Context
(All)fragments() returns the disconnected fragments of the molecule
|
| hasAromatizationError | - | determines if there is error in the aromatization of the molecule | true if there is an error in the aromatization of the molecule, false otherwise |
- |
Molecule Context
(All)hasAromatizationError() returns true if there is an error in the aromatization of the molecule,
false otherwise
|
| hasIsotope | - | determines if any atom in the molecule is a specific isotope of the element | true if any atom in the molecule is a specific isotope of the element, false otherwise |
- |
Molecule Context
(All)hasIsotope() returns true if any atom in the molecule is a specific isotope of the element, false otherwise
|
| hasRadical | - | determines if any atom in the molecule has radical | true if any atom in the molecule has radical, false otherwise |
- |
Molecule Context
(All)hasRadical() returns true if any atom in the molecule has radical, false otherwise
|
| hasValenceError | - | determines if any atom in the molecule has valence error | true in case of valence error, false otherwise |
- |
Molecule Context
(All)hasValenceError() returns true if any atom in the molecule has valence error, false otherwise
|
| HBDA | HBDA Plugin | ||||
| hCount | - | returns the hydrogen count of an atom | the hydrogen count | atom index or MolAtom object |
Molecule Context
(All)hCount(0) returns the hydrogen count of atom 0
|
| importMol | - | imports and returns the molecule from its string representation | the string representation of the molecule | the molecule in string representation (e.g. "c1ccccc1") |
Molecule Context
(All)importMol("c1ccccc1") returns benzene molecule
|
| in | - | determines whether an integer / atom index is contained in a given integer array | true if the array contains the specified integer, false otherwise |
an integer or MolAtom object and an integer array |
General
(All)in(5, array(3, 5, 1)) returns true in(2, array(3, 5, 1)) returns false
Reaction Context (All) |
| ionCharge | Charge Plugin Group | ||||
| isEmpty | - | decides whether the given molecule is empty (does not contain any atoms, bonds, or non-empty S-groups) | true if the molecule does not contain any atoms, bonds, or non-empty S-groups, false otherwise |
- |
Molecule Context
(All)isQuery() returns true if the given molecule does not contain any atoms, bonds, or non-empty S-groups, false otherwise
|
| isQuery | - | decides whether the given molecule contains any query features | true if the molecule contains any query features, false otherwise |
- |
Molecule Context
(All)isQuery() returns true if the given molecule contains any query features, false otherwise
|
| map | - | returns the atom map number | the atom map number | atom index or MolAtom object |
Molecule Context
(All)map(3) returns the atom map number of atom 3
|
| max | - | takes maximum of its array and/or numerical parameters | the maximum value | integers, real numbers, integer arrays, real number arrays |
General
(All)min(2, 8, 6) returns 2 max(3.4, 5.6, 1.2) returns 5.6
Reaction Context (All) |
| maxAtom | - | evaluates objective function for each atom, finds largest value(s) | the atom index / indices corresponding to the largest evaluation result(s) | target atom indices / objects or index / atom object array (optional, all atoms taken if omitted), the objective function (as inner expression string), the number of largest values to be taken (optional, takes only one if omitted) |
Molecule Context
(All)maxAtom(6, 7, 8, 9, "charge('7.4')", 2)
selects the two largest partial charges on atoms 6, 7, 8, 9 in the major microspecies at pH 7.4
of the input molecule and returns the corresponding indices
|
| maxValue | - | evaluates objective function for each atom, finds largest value(s) | the largest evaluation result(s) | target atom indices / objects or index / atom object array (optional, all atoms taken if omitted), the objective function (as inner expression string), the number of largest values to be taken (optional, takes only one if omitted) |
Molecule Context
(All)maxValue(6, 7, 8, 9, "charge('7.4')", 2) returns the two largest partial charges on
atoms 6, 7, 8, 9 in the major microspecies at pH 7.4 of the input molecule
|
| min | - | takes minimum of its array and/or numerical parameters | the minimum value | integers, real numbers, integer arrays, real number arrays |
General
(All)min(2, 8, 6) returns 2 max(3.4, 5.6, 1.2) returns 5.6
Reaction Context (All) |
| minAtom | - | evaluates objective function for each atom, finds smallest value(s) | the atom index / indices corresponding to the smallest evaluation result(s) | target atom indices / objects or index / atom object array (optional, all atoms taken if omitted), the objective function (as inner expression string), the number of smallest values to be taken (optional, takes only one if omitted) |
Molecule Context
(All)minAtom("charge('7.4')") returns the atom index corresponding to minimum partial charge in the
major microspecies at pH 7.4 of the input molecule
|
| minValue | - | evaluates objective function for each atom, finds smallest value(s) | the smallest evaluation result(s) | target atom indices / objects or index / atom object array (optional, all atoms taken if omitted), the objective function (as inner expression string), the number of smallest values to be taken (optional, takes only one if omitted) |
Molecule Context
(All)minValue("charge('7.4')") returns the minimum partial charge in the major microspecies at pH 7.4
of the input molecule
|
| molAtom | - | creates a MolAtom | the MolAtom object | atomic number |
Molecule Context
(All)molAtom(6) returns a carbon atom
|
| molBinFormat molImage |
- | returns the binary representation (image, pdf, GZIP compressed molecule file) of the molecule in specified format | the binary representation (image, pdf, GZIP compressed molecule file) of the molecule | the binary format with options (e.g. "jpeg", "png:w150,h150", "pdf", "gzip:sdf") |
Molecule Context
(All)molImage("jpeg:w100,Q95,#ffff00") returns the 100x100 JPEG image of the input molecule with yellow background, 95% quality
|
| molString molConvert molFormat |
- | returns the string representation of a molecule, or an array of molecules, in specified molecule format | the string representation of the molecule(s) |
|
Molecule Context
(All)molFormat("mrv") returns the ChemAxon Marvin Document format representation of the input molecule
molFormat(tautomers(), "sdf", 2) returns the SDF format representation of the tautomers of the input molecule
|
| pair bond |
- | converts two atoms or 0-based atom indexes into an "index1-index2" 1-based atom index setter string (used for pairing atoms in shortestPath) |
the generated string | two atom indexes or two MolAtom objects |
General
(All)pair(2, 5) returns "3-6"
|
| productCount | - | counts the products in the reaction | the number of products in the reaction, or -1 if the the input (molecule) is not a reaction |
- |
Molecule Context
(All)productCount() returns n if the given molecule is a reaction and contains n products.
productCount() returns -1 if the given molecule is not a reaction.
|
| radicalCount | - | returns the radical count of an atom | the radical count | atom index or MolAtom object |
Molecule Context
(All)radicalCount(0) returns the radical count of atom 0
|
| reactantCount | - | counts the reactants in the reaction | the number of reactants in the reaction, or -1 if the the input (molecule) is not a reaction |
- |
Molecule Context
(All)reactantCount() returns n if the given molecule is a reaction and contains n reactants.
reactantCount() returns -1 if the given molecule is not a reaction.
|
| sortAsc | - | sorts an array in ascending order | the sorted array | integer array or real number array |
General
(All)sortAsc(array(3.4, 5.6, 1.2)) returns array(1.2, 3.4, 5.6)
Reaction Context (All) |
| sortDesc | - | sorts an array in descending order | the sorted array | integer array or real number array |
General
(All)sortDesc(array(3.4, 5.6, 1.2)) returns array(5.6, 3.4, 1.2)
Reaction Context (All) |
| sum | - | computes the sum of array elements | the sum | integer array or real number array |
General
(All)sum(array(3.4, 5.6, 1.2)) returns 10.2
Reaction Context (All) |
| topanal | Geometry Plugin Group | ||||
| valence | - | returns the sum of bond orders and query H atoms of an atom | the sum of bond orders and query H atoms | atom index or MolAtom object |
Molecule Context
(All)valence(0) returns the valence of atom 0
|
| whereIsValenceError | - | returns the index of the first atom with valence error, or -1 if there is no valence error |
the index of the first atom with valence error, or -1 if there is no valence error |
- |
Molecule Context
(All)whereIsValenceError() returns the index of the first atom with valence error, or -1
if there is no valence error in the molecule
|
| Name | License | Description | Return value | Parameters | Examples |
|---|---|---|---|---|---|
| aliphaticAtom | Geometry Plugin Group | checks if the specified atom is aliphatic | true for aliphatic atoms,false for non-aliphatic atoms |
|
Molecule Context
(All)aliphaticAtom(2) returns true if atom 2 of the input molecule is
aliphatic, false otherwise
|
| aliphaticAtomCount | Geometry Plugin Group | calculates the aliphatic atom count | the aliphatic atom count | - |
Molecule Context
(All)aliphaticAtomCount() returns the number of aliphatic atoms in the input molecule
|
| aliphaticBondCount | Geometry Plugin Group | calculates the aliphatic bond count | the aliphatic bond count | - |
Molecule Context
(All)aliphaticBondCount() returns the number of bonds in the input molecule
|
| aliphaticRingCount | Geometry Plugin Group | calculates the aliphatic ring count | the aliphatic ring count | - |
Molecule Context
(All)aliphaticRingCount() returns the number of aliphatic rings in the input molecule
|
| aliphaticRingCountOfSize | Geometry Plugin Group | calculates the number of aliphatic rings of given size | the number of aliphatic rings of given size | the ring size |
Molecule Context
(All)aliphaticRingCountOfSize(6) returns the number of aliphatic rings of size 6 in the input molecule
|
| aliphaticRings | Geometry Plugin Group | identifies the aliphatic rings in the molecule | atom indexes of the aliphatic rings in the molecule (null if the molecule does not contain aliphatic rings) | - |
Molecule Context
(All)aliphaticRings() returns the atom indexes of the aliphatic rings in the input molecule
|
| aliphaticRingsOfSize | Geometry Plugin Group | identifies the aliphatic rings in the molecule having a given size (number of atoms) | atom indexes of the aliphatic rings in the molecule having the given size (null if the molecule does not contain aliphatic rings) | the ring size |
Molecule Context
(All)aliphaticRings() returns the atom indexes of the aliphatic rings in the input molecule having the given size
|
| angle | Geometry Plugin Group | calculates the angle between three atoms | the angle between three atoms |
|
Molecule Context
(All)angle('1-2-3') and angle(atoms(0, 1, 2)) both return the angle between atoms 1,
2 and 3 in the input molecule
|
| aromaticAtom | Geometry Plugin Group | checks if the specified atom is aromatic | true for aromatic atoms,false for non-aromatic atoms |
|
Molecule Context
(All)aromaticAtom(2) returns true if atom 2 of the input molecule is
aromatic, false otherwise
|
| aromaticAtomCount | Geometry Plugin Group | calculates the aromatic atom count | the aromatic atom count | - |
Molecule Context
(All)aromaticAtomCount() returns the number of aromatic atoms in the input molecule
|
| aromaticBondCount | Geometry Plugin Group | calculates the aromatic bond count | the aromatic bond count | - |
Molecule Context
(All)aromaticBondCount() returns the number of aromatic bonds in the input molecule
|
| aromaticRingCount | Geometry Plugin Group | calculates the aromatic ring count | the aromatic ring count | - |
Molecule Context
(All)aromaticRingCount() returns the number of aromatic rings in the input molecule
|
| aromaticRingCountOfSize | Geometry Plugin Group | calculates the number of aromatic rings of given size | the number of aromatic rings of given size | the ring size |
Molecule Context
(All)aromaticRingCountOfSize(6) returns the number of aromatic rings of size 6 in the input molecule
|
| aromaticRings | Geometry Plugin Group | identifies the aromatic rings in the molecule | atom indexes of the aromatic rings in the molecule (null if the molecule does not contain aromatic rings) | - |
Molecule Context
(All)aromaticRings() returns the atom indexes of the aromatic rings in the input molecule
|
| aromaticRingsOfSize | Geometry Plugin Group | identifies the aromatic rings in the molecule having a given size (number of atoms) | atom indexes of the aromatic rings in the molecule having the given size (null if the molecule does not contain aromatic rings) | the ring size |
Molecule Context
(All)aromaticRings() returns the atom indexes of the aromatic rings in the input molecule having the given size
|
| ASAHydrophobic | Geometry Plugin Group | calculates the water accessible molecular surface area of all hydrophobic atoms | the molecular surface area |
|
Molecule Context
(All)ASAHydrophobic() returns the water accessible surface area of all atoms of the input molecule with hydrophobic partial charge
ASAHydrophobic('7.4')returns the water accessible surface area of all atoms with hydrophobic partial charge of the major microspecies taken at
pH 7.4
|
| ASANegative | Geometry Plugin Group | calculates the water accessible molecular surface area of all atoms with negative partial charge | the molecular surface area |
|
Molecule Context
(All)ASANegative() returns the water accessible surface area of all atoms of the input molecule with negative partial charge
ASANegative('7.4')returns the water accessible surface area of all atoms with negative partial charge of the major microspecies taken at
pH 7.4
|
| ASAPlus | Geometry Plugin Group | calculates the water accessible molecular surface area of all atoms with positive partial charge | the molecular surface area |
|
Molecule Context
(All)ASAPlus() returns the water accessible surface area of all atoms of the input molecule with positive partial charge
ASAPlus('7.4')returns the water accessible surface area of all atoms with positive partial charge of the major microspecies taken at
pH 7.4
|
| ASAPolar | Geometry Plugin Group | calculates the water accessible molecular surface area of all polar atoms | the molecular surface area |
|
Molecule Context
(All)ASAPolar() returns the water accessible surface area of all atoms of the input molecule with polar partial charge
ASAPolar('7.4')returns the water accessible surface area of all atoms with polar partial charge of the major microspecies taken at
pH 7.4
|
| asymmetricAtom | Geometry Plugin Group | checks if the specified atom is an asymmetric atom | true for asymmetric atoms,false for symmetric atoms |
|
Molecule Context
(All)asymmetricAtom(2) returns true if atom 2 of the input molecule is an
asymmetric atom, false otherwise
|
| asymmetricAtomCount | Geometry Plugin Group | calculates the number of asymmetric atoms | the asymmetric atom count | - |
Molecule Context
(All)asymmetricAtomCount() returns the number of asymmetric atoms in the input molecule
|
| asymmetricAtoms | Geometry Plugin Group | determines the asymmetric atoms | indexes of asymmetric atoms | - |
Molecule Context
(All)asymmetricAtoms() returns the indexes of asymmetric atoms in the input molecule
|
| balabanIndex | Geometry Plugin Group | calculates the Balaban index | the Balaban index | - |
Molecule Context
(All)
calculates the Balaban index
Reaction Context
(All) |
| bondCount | - | calculates the bond count | the bond count | - |
Molecule Context
(All)bondCount() returns the number of bonds in the input molecule
|
| bondType | Geometry Plugin Group | returns the bond type between two atoms | the bond type between two atoms, -1 if there is no bond between the two atoms |
|
Molecule Context
(All)bondType('2-3') and bondType(bond(1, 2)) both return the bond type between atoms 1
and 2 in the input molecule
|
| carboaliphaticRingCount | Geometry Plugin Group | calculates the number of carboaliphatic rings in the molecule (aliphatic rings containing carbon atoms only) | number of carboaliphatic rings | - |
Molecule Context
(All)carboaliphaticRingCount() returns the number of carboaliphatic rings in the input molecule
|
| carboaromaticRingCount | Geometry Plugin Group | calculates the number of carboaromatic rings in the molecule (aromatic rings containing carbon atoms only) | number of carboaromatic rings | - |
Molecule Context
(All)carboaromaticRingCount() returns the number of carboaromatic rings in the input molecule
|
| carboRingCount | Geometry Plugin Group | calculates the number of carbocyclic rings in the molecule (rings containing carbon atoms only) | number of carbocyclic rings | - |
Molecule Context
(All)carboRingCount() returns the number of carbocyclic rings in the input molecule
|
| carboRingCountOfSize | Geometry Plugin Group | calculates the number of carbocyclic rings of given size (rings containing carbon atoms only) | the number of carbocyclic rings of given size | the ring size |
Molecule Context
(All)carboRingCountOfSize(6) returns the number of carbocyclic rings of size 6 in the input molecule
|
| carboRings | Geometry Plugin Group | identifies the carbocyclic rings in the molecule (rings containing carbon atoms only) | atom indexes of the carbocyclic rings in the molecule (null if the molecule does not contain carbocyclic rings) | - |
Molecule Context
(All)carboRings() returns the atom indexes of the carbocyclic rings in the input molecule
|
| carboRingsOfSize | Geometry Plugin Group | identifies the carbocyclic rings in the molecule having a given size (number of atoms) | atom indexes of the carbocyclic rings in the molecule having the given size (null if the molecule does not carbocyclic carbo rings) | the ring size |
Molecule Context
(All)carboRings() returns the atom indexes of the carbocyclic rings in the input molecule having the given size
|
| chainAtom | Geometry Plugin Group | checks if the specified atom is a chain atom | true for chain atoms,false for non-chain atoms |
|
Molecule Context
(All)chainAtom(2) returns true if atom 2 of the input molecule is a chain
atom, false otherwise
|
| chainAtomCount | Geometry Plugin Group | calculates the chain atom count | the chain atom count | - |
Molecule Context
(All)chainAtomCount() returns the number of chain atoms in the input molecule
|
| chainBond | Geometry Plugin Group | checks if two atoms are connected by a chain bond | true if the two atoms are connected by a chain bond, false otherwise |
|
Molecule Context
(All)chainBond('2-3') and chainBond(bond(1, 2)) both return true if atoms 1
and 2 are connected by a chain bond the input molecule
|
| chainBondCount | Geometry Plugin Group | calculates the chain bond count | the chain bond count | - |
Molecule Context
(All)chainBondCount() returns the number of chain bonds in the input molecule
|
| chiralCenter | Geometry Plugin Group | checks if the specified atom is a tetrahedral stereogenic center | true for tetrahedral stereogenic center atoms |
|
Molecule Context
(All)chiralCenter(2) returns true if atom 2 of the input molecule is a
tetrahedral stereogenic center, false otherwise
|
| chiralCenterCount | Geometry Plugin Group | calculates the number of tetrahedral stereogenic center atoms | the tetrahedral stereogenic center count | - |
Molecule Context
(All)chiralCenterCount() returns the number of tetrahedral stereogenic centers in the input molecule
|
| chiralCenters | Geometry Plugin Group | determines the chiral center atoms | indexes of chiral center atoms | - |
Molecule Context
(All)chiralCenters() returns the indexes of chiral center atoms in the input molecule
|
| connected | Geometry Plugin Group | checks if two atoms are connected | true if the two atoms belong to the same connected component, false otherwise |
|
Molecule Context
(All)connected('2-3') and connected(pair(1, 2)) both return true if atoms 1
and 2 are in the same connected component of the input molecule
|
| connectedGraph | Geometry Plugin Group | checks whether the molecule graph is connected | true if the molecule graph is connected, false otherwise |
- |
Molecule Context
(All)connectedGraph() returns true if the input molecule graph is connected
|
| cyclomaticNumber | Geometry Plugin Group | calculates the cyclomatic number | the cyclomatic number | - |
Molecule Context
(All)cyclomaticNumber() returns the cyclomatic number of the input molecule
|
| dihedral | Geometry Plugin Group | calculates the dihedral of four atoms | the dihedral of four atoms |
|
Molecule Context
(All)dihedral('1-2-3-4') and dihedral(atoms(0, 1, 2, 3)) both return the dihedral of atoms 1,
2, 3 and 4 in the input molecule
|
| distance | Geometry Plugin Group | calculates the distance between two atoms | the distance between two atoms |
|
Molecule Context
(All)distance('1-2') and distance(pair(0, 1)) both return the distance between atoms 1
and 2 in the input molecule
|
| distanceDegree | Geometry Plugin Group | calculates the distance degree of an atom | the distance degree |
|
Molecule Context
(All)distanceDegree(2) returns the distance degree of atom 2 of the input molecule
|
| dreidingEnergy | Geometry Plugin Group | returns the Dreiding energy of the input molecule (conformer) | the dreiding energy | - |
Molecule Context
(All)dreidingEnergy() returns the dreiding energy of the input molecule (conformer)
|
| eccentricity | Geometry Plugin Group | calculates the eccentricity of an atom | the eccentricity of an atom |
|
Molecule Context
(All)eccentricity(2) returns the eccentricity of atom 2 of the input molecule
|
| fragmentCount | Geometry Plugin Group | returns the number of fragments (disconnected parts) | the fragment count | - |
Molecule Context
(All)fragmentCount() returns the number of fragments in the input molecule
|
| fsp3 | Geometry Plugin Group | returns the fsp3 of the molecule | the fsp3 value | - |
Molecule Context
(All)fsp3() returns the fsp3 value of the input molecule
|
| fusedAliphaticRingCount | Geometry Plugin Group | calculates the number of fused aliphatic rings (SSSR smallest set of smallest aliphatic rings) |
the fused aliphatic ring count | - |
Molecule Context
(All)fusedAliphaticRingCount() returns the number of fused aliphatic rings in the input molecule
|
| fusedAliphaticRingCountOfSize | Geometry Plugin Group | calculates the number of fused aliphatic rings of given size | the number of fused aliphatic rings of given size | the ring size |
Molecule Context
(All)fusedAliphaticRingCountOfSize(6) returns the number of fused aliphatic rings of size 6 in the input molecule
|
| fusedAliphaticRings | Geometry Plugin Group | identifies the fused aliphatic rings in the molecule | atom indexes of the fused aliphatic rings in the molecule (null if the molecule does not contain fused aliphatic rings) | - |
Molecule Context
(All)fusedAliphaticRings() returns the atom indexes of the fused aliphatic rings in the input molecule
|
| fusedAliphaticRingsOfSize | Geometry Plugin Group | identifies the fused aliphatic rings in the molecule having a given size (number of atoms) | atom indexes of the fused aliphatic rings in the molecule having the given size (null if the molecule does not contain fused aliphatic rings) | the ring size |
Molecule Context
(All)fusedAliphaticRings() returns the atom indexes of the fused aliphatic rings in the input molecule having the given size
|
| fusedAromaticRingCount | Geometry Plugin Group | calculates the number of fused aromatic rings (SSSR smallest set of smallest aromatic rings) |
the fused aromatic ring count | - |
Molecule Context
(All)fusedAromaticRingCount() returns the number of fused aromatic rings in the input molecule
|
| fusedAromaticRingCountOfSize | Geometry Plugin Group | calculates the number of fused aromatic rings of given size | the number of fused aromatic rings of given size | the ring size |
Molecule Context
(All)fusedAromaticRingCountOfSize(6) returns the number of fused aromatic rings of size 6 in the input molecule
|
| fusedAromaticRings | Geometry Plugin Group | identifies the fused aromatic rings in the molecule | atom indexes of the fused aromatic rings in the molecule (null if the molecule does not contain fused aromatic rings) | - |
Molecule Context
(All)fusedAromaticRings() returns the atom indexes of the fused aromatic rings in the input molecule
|
| fusedAromaticRingsOfSize | Geometry Plugin Group | identifies the fused aromatic rings in the molecule having a given size (number of atoms) | atom indexes of the fused aromatic rings in the molecule having the given size (null if the molecule does not contain fused aromatic rings) | the ring size |
Molecule Context
(All)fusedAromaticRings() returns the atom indexes of the fused aromatic rings in the input molecule having the given size
|
| fusedRingCount | Geometry Plugin Group | calculates the number of fused rings (SSSR smallest set of smallest rings) |
the fused ring count | - |
Molecule Context
(All)fusedRingCount() returns the number of fused rings in the input molecule
|
| hararyIndex | Geometry Plugin Group | calculates the Harary index | the Harary index | - |
Molecule Context
(All)
calculates the Harary index
Reaction Context
(All) |
| heteroaliphaticRingCount | Geometry Plugin Group | calculates the number of aliphatic heterocyclic rings (SSSR smallest set of smallest aliphatic rings) |
the aliphatic heterocyclic ring count | - |
Molecule Context
(All)heteroaliphaticRingCount() returns the number of aliphatic heterocyclic rings in the input molecule
|
| heteroaliphaticRingCountOfSize | Geometry Plugin Group | calculates the number of aliphatic heterocyclic rings of given size | the number of aliphatic heterocyclic rings of given size | the ring size |
Molecule Context
(All)heteroaliphaticRingCountOfSize(6) returns the number of aliphatic heterocyclic rings of size 6 in the input molecule
|
| heteroaliphaticRings | Geometry Plugin Group | identifies the aliphatic heterocyclic rings in the molecule | atom indexes of the aliphatic heterocyclic rings in the molecule (null if the molecule does not contain aliphatic heterocyclic rings) | - |
Molecule Context
(All)heteroaliphaticRings() returns the atom indexes of the aliphatic heterocyclic rings in the input molecule
|
| heteroaliphaticRingsOfSize | Geometry Plugin Group | identifies the aliphatic heterocyclic rings in the molecule having a given size (number of atoms) | atom indexes of the aliphatic heterocyclic rings in the molecule having the given size (null if the molecule does not contain aliphatic heterocyclic rings) | the ring size |
Molecule Context
(All)heteroaliphaticRings() returns the atom indexes of the aliphatic heterocyclic rings in the input molecule having the given size
|
| heteroaromaticRingCount | Geometry Plugin Group | calculates the number of aromatic heterocyclic rings (SSSR smallest set of smallest aromatic rings) |
the aromatic heterocyclic ring count | - |
Molecule Context
(All)heteroaromaticRingCount() returns the number of aromatic heterocyclic rings in the input molecule
|
| heteroaromaticRingCountOfSize | Geometry Plugin Group | calculates the number of aromatic heterocyclic rings of given size | the number of aromatic heterocyclic rings of given size | the ring size |
Molecule Context
(All)heteroaromaticRingCountOfSize(6) returns the number of aromatic heterocyclic rings of size 6 in the input molecule
|
| heteroaromaticRings | Geometry Plugin Group | identifies the aromatic heterocyclic rings in the molecule | atom indexes of the aromatic heterocyclic rings in the molecule (null if the molecule does not contain aromatic heterocyclic rings) | - |
Molecule Context
(All)heteroaromaticRings() returns the atom indexes of the aromatic heterocyclic rings in the input molecule
|
| heteroaromaticRingsOfSize | Geometry Plugin Group | identifies the aromatic heterocyclic rings in the molecule having a given size (number of atoms) | atom indexes of the aromatic heterocyclic rings in the molecule having the given size (null if the molecule does not contain aromatic heterocyclic rings) | the ring size |
Molecule Context
(All)heteroaromaticRings() returns the atom indexes of the aromatic heterocyclic rings in the input molecule having the given size
|
| heteroRingCount | Geometry Plugin Group | calculates the number of heterocyclic rings (SSSR smallest set of smallest rings) |
the heterocyclic ring count | - |
Molecule Context
(All)heteroRingCount() returns the number of heterocyclic rings in the input molecule
|
| heteroRingCountOfSize | Geometry Plugin Group | calculates the number of heterocyclic rings of given size | the number of heterocyclic rings of given size | the ring size |
Molecule Context
(All)heteroRingCountOfSize(6) returns the number of heterocyclic rings of size 6 in the input molecule
|
| heteroRings | Geometry Plugin Group | identifies the heterocyclic rings in the molecule | atom indexes of the heterocyclic rings in the molecule (null if the molecule does not contain heterocyclic rings) | - |
Molecule Context
(All)heteroRings() returns the atom indexes of the heterocyclic rings in the input molecule
|
| heteroRingsOfSize | Geometry Plugin Group | identifies the heterocyclic rings in the molecule having a given size (number of atoms) | atom indexes of the heterocyclic rings in the molecule having the given size (null if the molecule does not contain heterocyclic rings) | the ring size |
Molecule Context
(All)heteroRings() returns the atom indexes of the heterocyclic rings in the input molecule having the given size
|
| hyperWienerIndex | Geometry Plugin Group | calculates the Hyper Wiener index | the Hyper Wiener index | - |
Molecule Context
(All)
calculates the Hyper Wiener index
Reaction Context
(All) |
| largestAtomRingSize | Geometry Plugin Group | calculates the size of the largest ring containing the specified atom | the size of the largest ring containing the specified atom |
|
Molecule Context
(All)largestAtomRingSize(1) returns the size of the largest ring containing atom 1
in the input molecule
|
| largestRing | Geometry Plugin Group | identifies the atoms of the largest ring (number of atoms) in the molecule. | atom indexes of the largest ring in the molecule (null when acyclic) | - |
Molecule Context
(All)largestRingSize() returns the atom indexes of the largest ring in the input molecule
|
| largestRingSize | Geometry Plugin Group | calculates the largest ring size | the largest ring size | - |
Molecule Context
(All)largestRingSize() returns the size of the largest ring in the input molecule
|
| largestRingSystem | Geometry Plugin Group | identifies the atoms of the largest ring system (number of rings) in the molecule. | atom indexes of the largest ring system in the molecule (null when acyclic) | - |
Molecule Context
(All)largestRingSize() returns the atom indexes of the largest ring system in the input molecule
|
| largestRingSystemSize | Geometry Plugin Group | calculates the size of the largest ring system (number of rings) | the size of the largest ring system | - |
Molecule Context
(All)largestRingSystemSize() returns the size of the largest ring system in the input molecule
|
| maximalProjectionArea | Geometry Plugin Group | returns the maximal projection area | the maximal projection area | - |
Molecule Context
(All)maximalProjectionArea() returns the maximal projection area
|
| maximalProjectionRadius | Geometry Plugin Group | returns the maximal projection radius | the maximal projection radius | - |
Molecule Context
(All)maximalProjectionRadius() returns the maximal projection radius
|
| minimalProjectionArea | Geometry Plugin Group | returns the minimal projection area | the minimal projection area | - |
Molecule Context
(All)minimalProjectionArea() returns the minimal projection area
|
| minimalProjectionRadius | Geometry Plugin Group | returns the minimal projection radius | the minimal projection radius | - |
Molecule Context
(All)minimalProjectionRadius() returns the minimal projection radius
|
| mmff94Energy | Geometry Plugin Group | returns the MMFF94 energy of the input molecule (conformer) | the MMFF94 energy | - |
Molecule Context
(All)mmff94Energy() returns the MMFF94 energy of the input molecule (conformer)
|
| plattIndex | Geometry Plugin Group | calculates the Platt index | the Platt index | - |
Molecule Context
(All)
calculates the Platt index
Reaction Context
(All) |
| randicIndex | Geometry Plugin Group | calculates the Randic index | the Randic index | - |
Molecule Context
(All)
calculates the Randic index
Reaction Context
(All) |
| ringAtom | Geometry Plugin Group | checks if the specified atom is a ring atom | true for ring atoms,false for non-ring atoms |
|
Molecule Context
(All)ringAtom(2) returns true if atom 2 of the input molecule is a ring atom,
false otherwise
|
| ringAtomCount | Geometry Plugin Group | calculates the ring atom count | the ring atom count | - |
Molecule Context
(All)ringAtomCount() returns the number of ring atoms in the input molecule
|
| ringBond | Geometry Plugin Group | checks if two atoms are connected by a ring bond | true if the two atoms are connected by a ring bond, false otherwise |
|
Molecule Context
(All)ringBond('2-3') and ringBond(bond(1, 2)) both return true if atoms 1
and 2 are connected by a ring bond the input molecule
|
| ringBondCount | Geometry Plugin Group | calculates the ring bond count | the ring bond count | - |
Molecule Context
(All)ringBondCount() returns the number of ring bonds in the input molecule
|
| ringCount | Geometry Plugin Group | calculates the ring count | the ring count | - |
Molecule Context
(All)ringCount() returns the number of rings in the input molecule
|
| ringCountOfAtom | Geometry Plugin Group | calculates the number of rings passing through an atom | the number of rings passing through an atom |
|
Molecule Context
(All)ringCountOfAtom(2) returns the number of rings passsing through atom 2 of the input
molecule
|
| ringCountOfSize | Geometry Plugin Group | calculates the number of rings of given size | the number of rings of given size | the ring size |
Molecule Context
(All)ringCountOfSize(6) returns the number of rings of size 6 in the input molecule
|
| rings | Geometry Plugin Group | identifies the rings in the molecule | atom indexes of the rings in the molecule (null if the molecule is acyclic) | - |
Molecule Context
(All)rings() returns the atom indexes of the rings in the input molecule
|
| ringsOfSize | Geometry Plugin Group | identifies the rings in the molecule having a given size (number of atoms) | atom indexes of the rings in the molecule having the given size (null if the molecule is acyclic or contains different rings only) | the ring size |
Molecule Context
(All)rings() returns the atom indexes of the rings in the input molecule having the given size
|
| ringSystemCount | Geometry Plugin Group | calculates the number of rings systems | the number of rings systems | - |
Molecule Context
(All)ringSystemCount() returns the number of ring systems in the input molecule
|
| ringSystemCountOfSize | Geometry Plugin Group | calculates the number of rings systems of given size | the number of rings systems of given size | the ring system size |
Molecule Context
(All)ringSystemCountOfSize(4) returns the number of four-membered ring systems in the input molecule
|
| ringSystems | Geometry Plugin Group | identifies the ring systems in the molecule (fused and spiro rings belong to one ring system) | atom indexes of the ring systems in the molecule (null if the molecule is acyclic) | - |
Molecule Context
(All)ringSystems() returns the atom indexes of the ring systems in the input molecule
|
| ringSystemsOfSize | Geometry Plugin Group | identifies the ring systems in the molecule having a given size (number of atoms, fused and spiro rings belong to one ring system) | atom indexes of the ring systems in the molecule having the given size (null if the molecule is acyclic or contains different ringSystems only) | the ring size |
Molecule Context
(All)ringSystems() returns the atom indexes of the ring systems in the input molecule having the given size
|
| rotatableBond | Geometry Plugin Group | checks if two atoms are connected by a rotatable bond | true if the two atoms are connected by a rotatable bond, false otherwise |
|
Molecule Context
(All)rotatableBond('2-3') and rotatableBond(bond(1, 2)) both return true if
atoms 1 and 2 are connected by a rotatable bond the input molecule
|
| rotatableBondCount | Geometry Plugin Group | calculates the rotatable bond count | the rotatable bond count | - |
Molecule Context
(All)rotatableBondCount() returns the number of rotatable bonds in the input molecule
|
| shortestPath | Geometry Plugin Group | calculates the length of the shortest path between two atoms | the length of the shortest path between two atoms, Integer.MAX_VALUE if disconnected |
|
Molecule Context
(All)shortestPath('2-3') and shortestPath(pair(1, 2)) both return the shortest path length
between atoms 1 and 2 in the input molecule
|
| smallestAtomRingSize | Geometry Plugin Group | calculates the size of the smallest ring containing the specified atom | the size of the smallest ring containing the specified atom |
|
Molecule Context
(All)smallestAtomRingSize(0) returns the size of the smallest ring containing atom 0 in
the input molecule
|
| smallestRing | Geometry Plugin Group | identifies the atoms of the smallest ring (number of atoms) in the molecule. | atom indexes of the smallest ring in the molecule (null when acyclic) | - |
Molecule Context
(All)smallestRingSize() returns the atom indexes of the smallest ring in the input molecule
|
| smallestRingSize | Geometry Plugin Group | calculates the smallest ring size | the smallest ring size | - |
Molecule Context
(All)smallestRingSize() returns the size of the smallest ring in the input molecule
|
| smallestRingSystem | Geometry Plugin Group | identifies the atoms of the smallest ring system (number of rings) in the molecule. | atom indexes of the smallest ring system in the molecule (null when acyclic) | - |
Molecule Context
(All)smallestRingSize() returns the atom indexes of the smallest ring system in the input molecule
|
| smallestRingSystemSize | Geometry Plugin Group | calculates the size of the smallest ring system (number of rings) | the size of the smallest ring system | - |
Molecule Context
(All)smallestRingSystemSize() returns the size of the smallest ring system in the input molecule
|
| stereoDoubleBondCount | Geometry Plugin Group | calculates the number of stereo double bonds | the stereo double bond count | - |
Molecule Context
(All)stereoDoubleBondCount() returns the number of stereo double bonds in the input molecule
|
| stericEffectIndex | Geometry Plugin Group | calculates the steric effect index of an atom | the steric effect index of an atom |
|
Molecule Context
(All)
calculates the steric effect index of an atom
Reaction Context
(All) |
| stericHindrance | Geometry Plugin Group | calculates the steric hindrance of an atom | the steric hindrance of an atom |
|
Molecule Context
(All)stericHindrance(2) returns the steric hindrance of atom 2 of the input molecule
|
| szegedIndex | Geometry Plugin Group | calculates the Szeged index | the Szeged index | - |
Molecule Context
(All)
calculates the Szeged index
Reaction Context
(All) |
| topologicalPolarSurfaceArea PSA |
- | calculates the topological polar surface area (2D) | the polar surface area (2D) |
|
Molecule Context
(All)topologicalPolarSurfaceArea() returns the polar surface area of the input molecule
topologicalPolarSurfaceArea('7.4') returns the polar surface area of the major microspecies taken at pH 7.4
|
| vanDerWaalsSurfaceArea | Geometry Plugin Group | calculates the van der Waals surface area | the molecular surface area |
|
Molecule Context
(All)vanDerWaalsSurfaceArea() returns the van der Waals surface area of the input molecule
vanDerWaalsSurfaceArea('7.4') returns the van der Waals accessible surface area of the major microspecies taken at
pH 7.4
|
| waterAccessibleSurfaceArea ASA solventAccessibleSurfaceArea |
Geometry Plugin Group | calculates the solvent accessible / water accessible molecular surface area | the molecular surface area |
|
Molecule Context
(All)waterAccessibleSurfaceArea() returns the solvent accessible / water accessible surface area of the input molecule
solventAccessibleSurfaceArea('7.4')returns the solvent accessible / water accessible surface area of the major microspecies taken at
pH 7.4
|
| wienerIndex | Geometry Plugin Group | calculates the Wiener index | the Wiener index | - |
Molecule Context
(All)wienerIndex() returns the Wiener index of the input molecule
|
| wienerPolarity | Geometry Plugin Group | calculates the Wiener polarity | the Wiener polarity | - |
Molecule Context
(All)wienerPolarity() returns the Wiener polarity of the input molecule
|
| Name | License | Description | Return value | Parameters | Examples |
|---|---|---|---|---|---|
| acceptor acc |
HBDA Plugin | calculates atomic hydrogen bond acceptor multiplicity | the atomic hydrogen bond acceptor multiplicity |
|
Molecule Context
(All)acceptor(2) returns the hydrogen bond acceptor multiplicity on atom 2 of the input molecule
|
| acceptorCount | HBDA Plugin | calculates molecular hydrogen bond acceptor count (the number of acceptor atoms) | the molecular hydrogen bond acceptor count |
|
Molecule Context
(All)acceptorCount() returns the number of hydrogen bond acceptor atoms in the input molecule
|
| acceptorSiteCount accSiteCount |
HBDA Plugin | calculates molecular hydrogen bond acceptor multiplicity (the sum of atomic multiplicities) | the molecular hydrogen bond acceptor multiplicity |
|
Molecule Context
(All)acceptorSiteCount() returns the hydrogen bond acceptor multiplicity of the input molecule
|
| donor don |
HBDA Plugin | calculates atomic hydrogen bond donor multiplicity | the atomic hydrogen bond donor multiplicity |
|
Molecule Context
(All)donor(1, "7.4") returns the hydrogen bond donor multiplicity on atom 1 of the major microspecies
at pH 7.4
|
| donorCount | HBDA Plugin | calculates molecular hydrogen bond donor count (the number of donor atoms) | the molecular hydrogen bond donor count |
|
Molecule Context
(All)donorCount("7.4") returns the number of hydrogen bond donor atoms in the major microspecies
at pH 7.4
|
| donorSiteCount donSiteCount |
HBDA Plugin | calculates molecular hydrogen bond acceptor / donor multiplicity (the sum of atomic multiplicities) | the molecular hydrogen bond acceptor / donor multiplicity |
|
Molecule Context
(All)donorSiteCount("7.4") returns the hydrogen bond donor multiplicity of the major microspecies
at pH 7.4
|
| Name | License | Description | Return value | Parameters | Examples |
|---|---|---|---|---|---|
| chargeDensity totalChargeDensity |
Huckel Analysis Plugin | calculates the charge density of atoms | the charge density of the atom, NaN for non-existing values |
|
Molecule Context
(All)chargeDensity(2) returns the charge density of atom 2 of the input molecule, NaN
for non-existing value
|
| electronDensity piChargeDensity |
Huckel Analysis Plugin | calculates the electron density of atoms | the electron density of the atom, NaN for non-existing values |
|
Molecule Context
(All)electronDensity(2) returns the electron density of atom 2 of the input molecule, NaN
for non-existing value
|
| electrophilicity energyNu nucleophilicLocalizationEnergy |
Huckel Analysis Plugin | calculates electrophilicity of atoms | the electrophilicity of the atom,NaN for non-aromatic atoms |
|
Molecule Context
(All)electrophilicity(2) returns the electrophilicity of atom 2 of the input
molecule, NaN if atom 2 is non-aromatic
|
| electrophilicityOrder aromaticElectrophilicityOrder orderE |
Huckel Analysis Plugin | calculates E(+) order of atoms | the E(+) order index of the atom ( 0, 1, 2, ...), |
|
Molecule Context
(All)electrophilicityOrder(2) returns the E(+) order index of atom 2 of the input molecule, e.g. returns
0 if atom 2 is the most electrophilic atom, 1 if atom 2 is the
second strongest electrophilic atom, etc.,
|
| hmoChargeDensity | Huckel Analysis Plugin | calculates the HMO charge density of atoms | the charge density of the atom, NaN for non-existing values |
|
Molecule Context
(All)hmoChargeDensity(2) returns the charge density of atom 2 of the input molecule, NaN
for non-existing value
|
| hmoElectronDensity | Huckel Analysis Plugin | calculates the HMO electron density of atoms | the electron density of the atom, NaN for non-existing values |
|
Molecule Context
(All)hmoElectronDensity(2) returns the electron density of atom 2 of the input molecule, NaN
for non-existing value
|
| hmoElectrophilicityOrder hmoOrderE |
Huckel Analysis Plugin | calculates HMO E(+) order of atoms | the E(+) order index of the atom ( 0, 1, 2, ...), |
|
Molecule Context
(All)hmoElectrophilicityOrder(2) returns the E(+) order index of atom 2 of the input molecule, e.g. returns
0 if atom 2 is the most electrophilic atom, 1 if atom 2 is the
second strongest electrophilic atom, etc.,
|
| hmoElectrophilicLocalizationEnergy | Huckel Analysis Plugin | calculates HMO localization energy L(+) of atoms | the localization energy L(+) of the atom,NaN for non-aromatic atoms |
|
Molecule Context
(All)hmoElectrophilicLocalizationEnergy(2) returns the electrophilic L(+) localization energy of atom 2 of the input
molecule, NaN if atom 2 is non-aromatic
|
| hmoNucleophilicityOrder hmoOrderNu |
Huckel Analysis Plugin | calculates HMO Nu(-) order of atoms | the Nu(-) order index of the atom ( 0, 1, 2, ...), |
|
Molecule Context
(All)hmoNucleophilicityOrder(2) returns the Nu(-) order index of atom 2 of the input molecule, e.g.
returns 0 if atom 2 is the most nucleophilic atom, 1 if atom 2 is
the second strongest nucleophilic atom, etc.,
|
| hmoNucleophilicLocalizationEnergy | Huckel Analysis Plugin | calculates HMO localization energy L(-) of atoms | the localization energy L(-) of the atom,NaN for non-aromatic atoms |
|
Molecule Context
(All)hmoNucleophilicLocalizationEnergy(2) returns the nucleophilic L(-) localization energy of atom 2 of the input
molecule, NaN if atom 2 is non-aromatic
|
| hmoPiEnergy | Huckel Analysis Plugin | calculates the HMO pi energy of the molecule | the pi energy of the molecule |
|
Molecule Context
(All)hmoPiEnergy() returns the pi energy of the input molecule
|
| nucleophilicity electrophilicLocalizationEnergy energyE |
Huckel Analysis Plugin | calculates nucleophilicity of atoms | the nucleophilicity of the atom,NaN for non-aromatic atoms |
|
Molecule Context
(All)nucleophilicity(2) returns the nucleophilicity of atom 2 of the input
molecule, NaN if atom 2 is non-aromatic
|
| nucleophilicityOrder aromaticNucleophilicityOrder orderNu |
Huckel Analysis Plugin | calculates Nu(-) order of atoms | the Nu(-) order index of the atom ( 0, 1, 2, ...), |
|
Molecule Context
(All)nucleophilicityOrder(2) returns the Nu(-) order index of atom 2 of the input molecule, e.g.
returns 0 if atom 2 is the most nucleophilic atom, 1 if atom 2 is
the second strongest nucleophilic atom, etc.,
|
| piEnergy | Huckel Analysis Plugin | calculates the pi energy of the molecule. Deprecated. | the pi energy of the molecule |
|
Molecule Context
(All)piEnergy() returns the pi energy of the input molecule
|
| Name | License | Description | Return value | Parameters | Examples |
|---|---|---|---|---|---|
| allTautomer | Isomers Plugin Group | constructs a tautomeric form | the tautomer |
|
Molecule Context
(All)tautomer(0) returns the first tautomer of the input molecule
|
| allTautomers | Isomers Plugin Group | constructs all tautomeric forms | the tautomer array | - |
Molecule Context
(All)tautomers() returns all tautomers of the input molecule in an array
|
| canonicalResonant | - | constructs the canonical resonant structure | the canonical resonant structure | - |
Molecule Context
(All)canonicalResonant() returns the canonical resonant structure of the input molecule
|
| canonicalTautomer | Isomers Plugin Group | constructs the canonical tautomer structure | the canonical tautomer structure | - |
Molecule Context
(All)canonicalTautomer() returns the canonical tautomer structure of the input molecule
|
| dominantTautomer tautomer |
Isomers Plugin Group | returns the i-th dominant tautomeric form | the i-th dominant tautomer |
|
Molecule Context
(All)dominantTautomer(0) returns the first dominant tautomer of the input molecule dominantTautomer(1, "2.0") returns
the second dominant tautomer of the input molecule, considering pH effect at pH 2.0
|
| dominantTautomerCount | Isomers Plugin Group | calculates the number of dominant tautomers | the number of dominant tautomers |
|
Molecule Context
(All)dominantTautomerCount() returns the number of dominant tautomers of the input molecule dominantTautomerCount("7.4")
returns the number of dominant tautomers of the input molecule, considering pH effect at pH 7.4
|
| dominantTautomers tautomers |
Isomers Plugin Group | constructs all dominant tautomeric forms (ordered by distribution) | the dominant tautomer array |
|
Molecule Context
(All)dominantTautomers() returns all dominant tautomers of the input molecule in an array dominantTautomers("2.0")
returns all dominant tautomers of the input molecule in an array, considering pH effect at pH 2.0
|
| doubleBondStereoisomer | Isomers Plugin Group | generates a double bond stereoisomer of the molecule | the double bond stereoisomer |
|
Molecule Context
(All)doubleBondStereoisomer(0) returns the first double bond stereoisomer of the input molecule
|
| doubleBondStereoisomerCount | Isomers Plugin Group | returns the number of generated double bond stereoisomers | the number of generated double bond stereoisomers | - |
Molecule Context
(All)doubleBondStereoisomerCount() returns the number of generated double bond stereoisomers of the
input molecule
|
| doubleBondStereoisomers | Isomers Plugin Group | generates double bond stereoisomers of the molecule (maximum number of double bond stereoisomers to be generated can be set, default: all) | the double bond stereoisomer array | - |
Molecule Context
(All)doubleBondStereoisomers() returns double bond stereoisomers of the input molecule in an array
|
| genericTautomer | Isomers Plugin Group | constructs the generic tautomer structure | the generic tautomer structure | - |
Molecule Context
(All)genericTautomer() returns the generic tautomer structure of the input molecule
|
| majorTautomer | Isomers Plugin Group | constructs the major tautomer structure | the major tautomer structure |
|
Molecule Context
(All)majorTautomer() returns the major tautomer structure of the input molecule
|
| mostStableTautomer | Isomers Plugin Group | deprecated, use majorTautomer instead. constructs the most stable tautomer structure | the most stable tautomer structure | - |
Molecule Context
(All)mostStableTautomer() returns the most stable tautomer structure of the input molecule
|
| resonant | - | constructs a resonant structure | the resonant structure | - |
Molecule Context
(All)resonant(0) returns the first resonant structure of the input molecule
|
| resonantCount | - | calculates the number of resonant structures | the number of resonant structures | - |
Molecule Context
(All)resonantCount() returns the number of resonant structures of the input molecule
|
| resonants | - | constructs all resonant structures | the resonant structure array | - |
Molecule Context
(All)resonants() returns all resonants of the input molecule in an array
|
| stereoAnalysis | - | calculates stereo descriptors of molecule | list of stereo descriptors |
|
Molecule Context
(All)stereoAnalysis() returns the stereo descriptors of the input moleculestereoAnalysis('tetrahedral') returns the tetrahedral stereo descriptors of the input molecule
|
| stereoisomer | Isomers Plugin Group | generates a stereoisomer of the molecule | the stereoisomer |
|
Molecule Context
(All)stereoisomer(0) returns the first stereoisomer of the input molecule
|
| stereoisomerCount | Isomers Plugin Group | returns the number of generated stereoisomers | the number of generated stereoisomers | - |
Molecule Context
(All)stereoisomerCount() returns the number of generated stereoisomers of the input molecule
|
| stereoisomers | Isomers Plugin Group | generates stereoisomers of the molecule (maximum number of stereoisomers to be generated can be set, default: all) | the stereoisomer array | - |
Molecule Context
(All)stereoisomers() returns stereoisomers of the input molecule in an array
|
| tautomerCount | Isomers Plugin Group | calculates the number of tautomers | the number of tautomers | - |
Molecule Context
(All)tautomerCount() returns the number of tautomers of the input molecule
|
| tetrahedralStereoisomer | Isomers Plugin Group | generates a tetrahedral stereoisomer of the molecule | the tetrahedral stereoisomer | - |
Molecule Context
(All)tetrahedralStereoisomer(0) returns the first tetrahedral stereoisomer of the input molecule
|
| tetrahedralStereoisomerCount | Isomers Plugin Group | returns the number of generated tetrahedral stereoisomers | the number of generated tetrahedral stereoisomers | - |
Molecule Context
(All)tetrahedralStereoisomerCount() returns the number of generated tetrahedral stereoisomers of the
input molecule
|
| tetrahedralStereoisomers | Isomers Plugin Group | generates tetrahedral stereoisomers of the molecule (maximum number of tetrahedral stereoisomers to be generated can be set, default: all) | the tetrahedral stereoisomer array | - |
Molecule Context
(All)tetrahedralStereoisomers() returns tetrahedral stereoisomers of the input molecule in an array
|
| Name | License | Description | Return value | Parameters | Examples |
|---|---|---|---|---|---|
| isMarkush | - | decides whether the given molecule contains any Markush features | true if the molecule contains any Markush features, false otherwise |
- |
Molecule Context
(All)isMarkush() returns true if the given molecule contains any Markush features, false otherwise
|
| markushEnumerationCount enumerationCount |
Markush Enumeration Plugin | calculates the number of Markush enumerations | the number of Markush enumerations |
|
Molecule Context
(All)markushEnumerationCount() returns the number of Markush enumerated structures of the input molecule markushEnumerationCount('4,5')
returns the number of Markush enumerated structures of the input molecule, enumerating only atoms 4, 5 (1-based)
|
| markushEnumerations enumeration enumerations markushEnumeration |
Markush Enumeration Plugin | constructs Markush enumerated structures sequentially | the enumerated structures |
|
Molecule Context
(All)markushEnumerations() returns all Markush enumerated structures of the input molecule markushEnumerations(1, '2,3')
returns one Markush enumerated structure of the input molecule, enumerating atoms 2, 3 (1-based)
|
| markushEnumerationsDisplay | Markush Enumeration Plugin | constructs Markush enumerated structures sequentially with scaffold alignment and scaffold/R-group coloring and enumeration ID | the enumerated structures with alignment and coloring data and enumeration ID |
|
Molecule Context
(All)markushEnumerationsDisplay() returns all Markush enumerated structures of the input molecule, with scaffold alignment and coloring data markushEnumerationsDisplay(1, '2,3')
returns one Markush enumerated structure of the input molecule, enumerating atoms 2, 3 (1-based), with scaffold alignment and coloring data
|
| markushLibraryMagnitude | Markush Enumeration Plugin | calculates the Markush library magnitude, no enumeration is done | the Markush library magnitude |
|
Molecule Context
(All)markushLibraryMagnitude() returns the Markush library magnitude for the input molecule markushLibraryMagnitude('4,5')
returns the Markush library magnitude for the input molecule, presuming only atoms 4, 5 (1-based) are enumerated
|
| markushLibrarySize | Markush Enumeration Plugin | calculates the Markush library size, no enumeration is done | the Markush library size |
|
Molecule Context
(All)markushLibrarySize() returns the Markush library size for the input molecule markushLibrarySize('4,5')
returns the Markush library size for the input molecule, presuming only atoms 4, 5 (1-based) are enumerated
|
| markushLibrarySizeAsString | Markush Enumeration Plugin | calculates the Markush library size and returns it as string, no enumeration is done | the Markush library size |
|
Molecule Context
(All)markushLibrarySize() returns the Markush library size as string for the input molecule markushLibrarySize('4,5')
returns the Markush library size as string for the input molecule, presuming only atoms 4, 5 (1-based) are enumerated
|
| randomMarkushEnumerations randomEnumeration randomEnumerations randomMarkushEnumeration |
Markush Enumeration Plugin | constructs Markush enumerated structures randomly | the enumerated structures |
|
Molecule Context
(All)randomMarkushEnumerations()
returns a randomly constructed enumerated structure of the input molecule randomMarkushEnumerations(4, '2,3') returns 4 randomly constructed enumerated structures of the input molecule, enumerating only atoms 2, 3 (1-based)
|
| randomMarkushEnumerationsDisplay | Markush Enumeration Plugin | constructs Markush enumerated structures randomly with scaffold alignment and scaffold/R-group coloring and enumeration ID | the enumerated structures with alignment and coloring data and enumeration ID |
|
Molecule Context
(All)randomMarkushEnumerationsDisplay()
returns a randomly constructed enumerated structure of the input molecule, with scaffold alignment and scaffold/R-group coloring datarandomMarkushEnumerationsDisplay(4, '2,3') returns 4 randomly constructed enumerated structures of the input molecule, enumerating only atoms 2, 3 (1-based), with scaffold alignment and coloring data
|
| Name | License | Description | Return value | Parameters | Examples |
|---|---|---|---|---|---|
| disjointMatchCount | - | performs substructure search, returns the maximal number of pairwise disjoint search hits | the maximal number of pairwise disjoint search hits |
Warning: if the target atom index and optionally query atom maps are specified then the return value can only be 0 or 1, therefore the result is similar to the result of the
match function. |
Molecule Context
(All)disjointMatchCount("[#8]C=O") counts the maximal number of pairwise disjoint carboxylic groups in the input molecule
|
| match | - | performs substructure search and optionally checks for atom matching | true if matching substructure found, false otherwise |
true if the query structure is found in the target molecule, the hit is required
to include the target atom if specified, furthermore if query atom map(s) are specified then these mapped atoms should
match the target atom. |
Molecule Context
(All)match("[#8]C=O") performs substructure search without atom matching requirement, the target is the
input molecule, the query is the carboxylic group given in the string parameter match(6, "[#8][C:1]=O", 1)
performs substructure search, checks if target atom 6 matches the carbon (atom with map 1)
of the carboxylic group query match(6, "[#8:1]C=[O:2]", 1, 2) performs substructure search, checks if
target atom 6 of the input molecule is a carboxylic oxygen
|
| matchCount | - | performs substructure search and optionally checks for atom matching, counts search hits | the number of search hits |
|
Molecule Context
(All)matchCount("[#8]C=O") counts search hits without atom matching requirement, the target is the
input molecule, the query is the carboxylic group given in the string parameter matchCount(6, "[#8]C=O")
counts search hits with target atom 6 matching any atom in a carboxylic group matchCount(6, "[#8:1]C=[O:2]", 1, 2)
counts search hits with target atom 6 of the input molecule being a carboxylic oxygen
|
| matchFirst | - | performs substructure search and optionally checks for atom matching | index of the first matching substructure (1-based indexing) |
|
Molecule Context
(All)matchFirst({amine,amide,alcohol}) performs substructure search without atom matching requirement,
the target is the input molecule, the queries are the amine, amide, and alcohol groups given in the string parameter. Function
returns 1 if there is an amine group in the input molecule, 2 if there is no amine, but there is an amide
group in the input molecule, and returns 3 if there is no amine or amide group, but there is an alcohol group in the
input molecule. Returns 0 if none of the listed groups is found in input molecule.
matchFirst(6, {"[#8][C:1]=O","[NX3:2][CX3:1]=[OX1:3]"}, 1) performs substructure search, checks if target
atom 6 matches the carbon (atom with map 1) of the carboxylic or amide group in query. Returns the index
of the query if match found, 0 otherwise.
matchFirst(6, {"[#8:1]C=[O:2]","[#6][OX2:1][CX3](=[O:2])[#6]"}, 1, 2) performs substructure search, checks if
target atom 6 of the input molecule is a carboxylic oxygen or an oxigen in an ester group. Returns the index
of the query if match found, 0 otherwise.
|
It is sometimes easier to refer molecules by names rather than explicit SMARTS strings or molecule file paths. For example, you may want to write nitro or carboxyl as query in a match function. Frequently used queries are pre-defined in the built-in functional groups file (chemaxon/marvin/templates/functionalgroups.cxsmi within MarvinBeans-templates.jar).
You can also define your favourite query SMARTS in marvin/config/marvin/templates/functionalgroups.cxsmi file and in $HOME\chemaxon\marvin\templates\functionalgroups.cxsmi (Windows) or $HOME/.chemaxon/marvin/templates/functionalgroups.cxsmi (UNIX / Linux) file where marvin is the Marvin istallation directory, $HOME is your user home directory.
| Name | License | Description | Return value | Parameters | Examples |
|---|---|---|---|---|---|
| name | IUPAC Naming Plugin | returns the preferred IUPAC name of the molecule | the preferred IUPAC name of the molecule | - |
Molecule Context
(All)name() returns the preferred IUPAC name of the input molecule
|
| traditionalName | IUPAC Naming Plugin | returns the traditional name of the molecule | the traditional name of the molecule | - |
Molecule Context
(All)traditionalName() returns the traditional name of the input molecule
|
| Name | License | Description | Return value | Parameters | Examples |
|---|---|---|---|---|---|
| logD | Partitioning Plugin Group | calculates logD at specified pH | the logD value |
|
Molecule Context
(All)logD('7.4') returns the logD at pH 7.4 of the input molecule
|
| logDKLOP | Partitioning Plugin Group | calculates logD at specified pH using method "KLOP" | the logD value |
|
Molecule Context
(All)logDKLOP('7.4') returns the logD at pH 7.4 of the input molecule
|
| logDPHYS | Partitioning Plugin Group | calculates logD at specified pH using method "PHYS" | the logD value |
|
Molecule Context
(All)logDPHYS('7.4') returns the logD at pH 7.4 of the input molecule
|
| logDUser | Partitioning Plugin Group | calculates logD at specified pH using the user defined method | the logD value |
|
Molecule Context
(All)logDUser('7.4') returns the logD at pH 7.4 of the input molecule
|
| logDVG | Partitioning Plugin Group | calculates logD at specified pH using method "VG" | the logD value |
|
Molecule Context
(All)logDVG('7.4') returns the logD at pH 7.4 of the input molecule
|
| logDWeighted | Partitioning Plugin Group | calculates logD at specified pH using weighted method | the logD value |
|
Molecule Context
(All)logDWeighted('7.4') returns the logD at pH 7.4 of the input molecule
|
| logP | Partitioning Plugin Group | calculates logP | the logP value |
|
Molecule Context
(All)logP() returns the most typical logP out of the input molecule logP, the logP
of the nonionic species and logD at pI logP('logPMicro') returns the logP of the input
molecule itself
|
| logPincrement logPi |
Partitioning Plugin Group | calculates the atomic logP increment | the atomic logP increment |
|
Molecule Context
(All)logPincrement(2) returns the logP increment on atom 2 of the input molecule
|
| logPKLOP | Partitioning Plugin Group | calculates logP using method "KLOP" | the logP value |
|
Molecule Context
(All)logPKLOP() returns the most typical logP out of the input molecule logP, the logP
of the nonionic species and logD at pI logPKLOP('logPMicro') returns the logP of the input
molecule itself
|
| logPPHYS | Partitioning Plugin Group | calculates logP using method "PHYS" | the logP value |
|
Molecule Context
(All)logPPHYS() returns the most typical logP out of the input molecule logP, the logP
of the nonionic species and logD at pI logPPHYS('logPMicro') returns the logP of the input
molecule itself
|
| logPUser | Partitioning Plugin Group | calculates logP using the user defined method | the logP value |
|
Molecule Context
(All)logPUser() returns the most typical logP out of the input molecule logP, the logP
of the nonionic species and logD at pI logPUser('logPMicro') returns the logP of the input
molecule itself
|
| logPVG | Partitioning Plugin Group | calculates logP using method "VG" | the logP value |
|
Molecule Context
(All)logPVG() returns the most typical logP out of the input molecule logP, the logP
of the nonionic species and logD at pI logPVG('logPMicro') returns the logP of the input
molecule itself
|
| logPWeighted | Partitioning Plugin Group | calculates logP using weighted method | the logP value |
|
Molecule Context
(All)logPWeighted() returns the most typical logP out of the input molecule logP, the logP
of the nonionic species and logD at pI logPWeighted('logPMicro') returns the logP of the input
molecule itself
|
| Name | License | Description | Return value | Parameters | Examples |
|---|---|---|---|---|---|
| acidicpKa apKa |
Protonation Plugin Group | calculates acidic pKa values | the acidic pKa values |
|
Molecule Context
(All)acidicpKa(0) returns the acidic pKa of atom 0 of the input molecule acidicpKa("2")
returns the second strongest acidic pKa value
|
| acidicpKaLargeModel | Protonation Plugin Group | calculates acidic pKa values using large model (this model is optimized for a large number of ionizable atoms) | the acidic pKa values |
|
Molecule Context
(All)acidicpKaLargeModel(0) returns the acidic pKa of atom 0 of the input molecule
acidicpKaLargeModel("2") returns the second strongest acidic pKa value
|
| acidicpKaUseCorrection | Protonation Plugin Group | calculates acidic pKa values using the correction library | the acidic pKa values |
|
Molecule Context
(All)acidicpKaUseCorrection(0) returns the acidic pKa of atom 0 of the input molecule
"acidicpKaUseCorrection"("2") returns the second strongest acidic pKa value
|
| averageMicrospeciesCharge | Protonation Plugin Group | calculates the average microspecies charge (weighted sum of charges of all the microspecies of the molecule) at the given pH | the average charge |
|
Molecule Context
(All)averageMicrospeciesCharge() returns the average charge of the microspecies of the input molecule
|
| basicpKa bpKa |
Protonation Plugin Group | calculates basic pKa values | the basic pKa values |
|
Molecule Context
(All)basicpKa(0) returns the basic pKa of atom 0 of the input molecule
basicpKa("2") returns the second strongest basic pKa value
|
| basicpKaLargeModel | Protonation Plugin Group | calculates basic pKa values using large model (this model is optimized for a large number of ionizable atoms) | the basic pKa values |
|
Molecule Context
(All)basicpKaLargeModel(0) returns the basic pKa of atom 0 of the input molecule
basicpKaLargeModel("2") returns the second strongest basic pKa value
|
| basicpKaUseCorrection | Protonation Plugin Group | calculates basic pKa values using the correction library | the basic pKa values |
|
Molecule Context
(All)basicpKaUseCorrection(0) returns the basic pKa of atom 0 of the input molecule
basicpKaUseCorrection("2") returns the second strongest basic pKa value
|
| isoelectricPoint pI |
Protonation Plugin Group | calculates isoelectric point | the isoelectric point | - |
Molecule Context
(All)isoelectricPoint() returns the isoelectric point of the input molecule
|
| majorMicrospecies majorMs |
Protonation Plugin Group | calculates major microspecies at specified pH | the major microspecies |
|
Molecule Context
(All)majorMicrospecies("7.4") returns the major microspecies of the input molecule at pH 7.4
|
| microspecies ms |
Protonation Plugin Group | calculates microspecies at specified pH | the microspecies |
|
Molecule Context
(All)microspecies("7.4", 1) returns the microspecies of the input molecule with second largest distribution at pH
7.4
|
| microspeciesCount msCount |
Protonation Plugin Group | calculates the number of microspecies at specified pH | the number of microspecies | - |
Molecule Context
(All)microspeciesCount() returns the number of microspecies of the input molecule
|
| microspeciesDistribution msDistr |
Protonation Plugin Group | calculates microspecies distribution at specified pH | the microspecies distribution |
|
Molecule Context
(All)microspeciesDistribution("5.4", 0) returns the largest microspecies distribution of the input molecule at pH 5.4
|
| pKa | Protonation Plugin Group | calculates pKa values | the pKa values |
In case of strength index the result type can be specified as "acidic" or "basic". In case of "pka"result type the returned pKa values are acidic or basic (mixed!), depending on the acidic or basic character of the given atom. Acidic pKa is returned for an atom, if acidicpKa() ≤ 14.8-basicpKa(), otherwise basic pKa is returned. Specifying "acidic" or "basic" result type is required to get the acidic or basic pKa values only (also acidicpKa or basicpKa functions can be used alternatively). |
Molecule Context
(All)pKa(0) returns the pKa of atom 0 of the input molecule pKa("acidic", "2")
returns the second strongest acidic pKa value
|
| pKaUseCorrection | Protonation Plugin Group | calculates pKa values using the correction library | the pKa values |
In case of strength index the result type can be specified as "acidic" or "basic". In case of "pka"result type the returned pKa values are acidic or basic (mixed!), depending on the acidic or basic character of the given atom. Acidic pKa is returned for an atom, if acidicpKa() ≤ 14.8-basicpKa(), otherwise basic pKa is returned. Specifying "acidic" or "basic" result type is required to get the acidic or basic pKa values only (also acidicpKaUseCorrection() or basicpKaUseCorrection() functions can be used alternatively). |
Molecule Context
(All)pKaUseCorrection(0) returns the pKa of atom 0 of the input molecule
pKaUseCorrection("acidic", "2") returns the second strongest acidic pKa value
|
| Name | License | Description | Return value | Parameters | Examples |
|---|---|---|---|---|---|
| refractivity refrac |
Refractivity Plugin | calculates molar refractivity | the refractivity value | - |
Molecule Context
(All)refractivity() returns the molar refractivity of the input molecule
|
| refractivityIncrements refraci |
Refractivity Plugin | calculates atomic refractivity increments | the atomic refractivity increment |
|
Molecule Context
(All)refractivityIncrements(2) returns the refractivity increment on atom 2 of the input molecule
|
| Name | License | Description | Return value | Parameters | Examples |
|---|---|---|---|---|---|
| logS | Solubility Plugin | calculates solubility at specified pH | the logS value |
|
Molecule Context
(All)logS('7.4') returns the logS at pH 7.4 of the input molecule
|
| logS0 | Solubility Plugin | calculates intrinsic solubility | the logS0 value | - |
Molecule Context
(All)logS0() returns the logS0 of the input molecule
|
| logSCategory | Solubility Plugin | calculates solubility category | the solubility category | - |
Molecule Context
(All)logSCategory() returns the solubilty category of the input molecule
|
| Name | License | Description | Return value | Parameters | Examples |
|---|---|---|---|---|---|
| bmf | Structural Frameworks Plugin | Returns the Bemis-Murcko framework of the input structure | BMF of the input structure | - |
Molecule Context
(All)bmf() returns the Bemis-Murcko framework of the input molecule
|
| bmfl bemisMurckoFrameworkLoose |
Structural Frameworks Plugin | Returns the Bemis-Murcko loose framework of the input structure. Calculated by removing side chains. Exocyclic non single bonded atoms are kept. Remaining atom and bond types are not changed. | Loose BMF of the input structure | - |
Molecule Context
(All)bmfl() returns the loose Bemis-Murcko framework of the input molecule
|
| bmflp bemisMurckoFrameworkLoosePruned |
Structural Frameworks Plugin | Returns the Bemis-Murcko loose framework of the input structure. Calculated by removing side cains. Atom and bond types are generalized by replacing all atoms with carbons and setting all bond types to single. Exocyclic non single bonded atoms are kept as single bonded carbons. | Generalized loose BMF of the input structure | - |
Molecule Context
(All)bmflp() returns the generalized loose Bemis-Murcko framework of the input molecule
|
| Name | License | Description | Return value | Parameters | Examples |
|---|---|---|---|---|---|
| check | - | checks the structure for errors, according to the configuration | the error report | Structure checker/fixer configuration as action string or XML string |
Molecule Context
(All)
|
| checkErrorCount | - | checks the structure for errors, according to the configuration | the total error count | Structure checker/fixer configuration as XML or action string |
Molecule Context
(All)checkErrorCount('"<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"no\"?><checkers><AromaticityErrorChecker fixMode=\"fix\" fixerClassName=\"chemaxon.fixers.RearomatizeFixer\" type=\"general\"/><ValenceErrorChecker allowTraditionalNitrogen=\"false\" fixMode=\"fix\" fixerClassName=\"chemaxon.fixers.ValenceFixer\"/></checkers>
"') or checkErrorCount("aromaticity..valence") checks for aromaticity and valence errors, and returns the total error count
|
| fix | - | checks the structure for errors, according to the configuration, and then fixes the errors | the fixed molecule | Structure checker/fixer configuration as action string or XML string |
Molecule Context
(All)
|
| isValid | - | checks the structure for errors, according to the configuration | true, if the structure is valid (has no errors), false otherwise | Structure checker/fixer configuration as action string or XML string |
Molecule Context
(All)
|
shortestPath(reactant(0), pair(ratom(1), ratom(2)))) and must contain all the atoms referred by atom indexes.aromaticAtomCount() is equivalent to aromaticatomcount(), but AromaticAtomCount() and AROMATICATOMCOUNT() are not recognized by the parser.match, matchCount, disjointMatchCount and dissimilarity functions are not available in Marvin, they can be used only if JChem software package is installed.