Name | License | Description | Return value | Parameters | Examples |
atomicPolarizability | Structural Calculations License | calculates atomic polarizability | the polarizability values |
| Molecule Context 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 Reaction Context atomicPolarizability(ratom(1)) returns the polarizability of reactant atom matching map 1 in the reaction equation atomicPolarizability(patom(2), "7.4") returns the polarizability of the product atom matching map 2 of the major microspecies taken at pH 7.4 |
averagePolarizability | Structural Calculations License | calculates average molecular polarizability component considering 3D geometry | the polarizability value |
| Molecule Context 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 Reaction Context averagePolarizability(reactant(1)) returns the average polarizability component of the second reactant in the reaction equation averagePolarizability(product(0), "7.4") returns the average polarizability component of the first product major microspecies taken at pH 7.4 |
axxPol | Structural Calculations License | calculates principal component of polarizability tensor (a(xx), a(yy), a(zz)) | the principal component of polarizability tensor |
| Molecule Context 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 Reaction Context axxPol(reactant(1)) returns the principal component a(xx) of polarizability tensor of the second reactant in the reaction equation axxPol(product(0), "7.4") returns the principal component a(xx) of polarizability tensor of the first product major microspecies taken at pH 7.4 |
ayyPol | Structural Calculations License | calculates principal component of polarizability tensor (a(xx), a(yy), a(zz)) | the principal component of polarizability tensor |
| Molecule Context 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 Reaction Context ayyPol(reactant(1)) returns the principal component a(yy) of polarizability tensor of the second reactant in the reaction equation ayyPol(product(0), "7.4") returns the principal component a(yy) of polarizability tensor of the first product major microspecies taken at pH 7.4 |
azzPol | Structural Calculations License | calculates principal component of polarizability tensor (a(xx), a(yy), a(zz)) | the principal component of polarizability tensor |
| Molecule Context 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 Reaction Context azzPol(reactant(1)) returns the principal component a(zz) of polarizability tensor of the second reactant in the reaction equation azzPol(product(0), "7.4") returns the principal component a(zz) of polarizability tensor of the first product major microspecies taken at pH 7.4 |
charge | Structural Calculations License | calculates partial charges on atoms | the charge values |
| Molecule Context 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 Reaction Context charge(ratom(1), "aromaticsystem") returns the sum of partial pi charges in the aromatic system containing the reactant atom matching map 1 in the reaction equation charge(patom(2), "aromaticring", "7.4") returns the sum of partial charges in the smallest aromatic ring containing the product atom matching map 2 in the major microspecies taken at pH 7.4 |
molecularPolarizability | Structural Calculations License | calculates molecular polarizability | the polarizability value |
| Molecule Context 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 Reaction Context molecularPolarizability(reactant(1)) returns the molecular polarizability of the second reactant in the reaction equation molecularPolarizability(product(0), "7.4") returns the molecular polarizability of the first product major microspecies taken at pH 7.4 |
piOrbitalElectronegativity | Structural Calculations License | calculates atomic pi orbital electronegativity | the pi orbital electronegativity values |
| Molecule Context 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 Reaction Context pOEN(ratom(1)) returns the pi orbital electronegativity of reactant atom matching map 1 in the reaction equation pOEN(patom(2), "7.4") returns the pi orbital electronegativity of the product atom matching map 2 of the major microspecies taken at pH 7.4 |
resonantCharge | Structural Calculations License | calculates partial charges on atoms considering resonance effect | the charge values |
| Molecule Context 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 Reaction Context resonantCharge(ratom(1), "aromaticsystem") returns the sum of partial pi charges in the aromatic system containing the reactant atom matching map 1 in the reaction equation considering resonance effectresonantCharge(patom(2), "aromaticring", "7.4") returns the sum of partial charges in the smallest aromatic ring containing the product atom matching map 2 in the major microspecies taken at pH 7.4 considering resonance effect |
sigmaOrbitalElectronegativity | Structural Calculations License | calculates atomic sigma orbital electronegativity | the sigma orbital electronegativity values |
| Molecule Context 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 Reaction Context sOEN(ratom(1)) returns the sigma orbital electronegativity of reactant atom matching map 1 in the reaction equation sOEN(patom(2), "7.4") returns the sigma orbital electronegativity of the product atom matching map 2 of the major microspecies taken at pH 7.4 |
Name | License | Description | Return value | Parameters | Examples |
conformer | Structural Calculations License | calculates a conformer of the molecule | the conformer |
| Molecule Context (All) conformer(0) returns the first conformer of the input molecule Reaction Context (All) conformer(reactant(0), 1) returns the second conformer of the first reactant |
conformerCount | Structural Calculations License | 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 Reaction Context (All) conformerCount(reactant(0)) returns the number of calculated conformers of the first reactant |
conformers | Structural Calculations License | 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 Reaction Context (All) conformers(reactant(0)) returns conformers of the first reactant in an array |
hasValidConformer | Structural Calculations License | 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) Reaction Context (All) hasValidConformer(reactant(0)) returns true the if the first reactant exists in 3D space hasValidConformer(product(1)) returns true the if the second product exist in 3D space |
lowestEnergyConformer | Structural Calculations License | 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 Reaction Context (All) lowestEnergyConformer(reactant(0)) returns the lowest energy conformer of the first reactant lowestEnergyConformer(product(1)) returns the lowest energy conformer of the second product |
mmff94OptimizedStructure | Structural Calculations License | 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 Reaction Context (All) mmff94OptimizedStructure(reactant(0)) returns the MMFF94 optimized lowest energy conformer of the first reactant mmff94OptimizedStructure(product(1)) returns the MMFF94 optimized lowest energy conformer of the second product |
Name | License | Description | Return value | Parameters | Examples |
conformer | Structural Calculations License | calculates a conformer of the molecule | the conformer |
| Molecule Context |
conformerCount | Structural Calculations License | returns the number of calculated conformers | the number of calculated conformers | - | Molecule Context |
conformers | Structural Calculations License | calculates conformers of the molecule (maximum number of conformers to be calculated can be set, default: 100) | the conformer array | - | Molecule Context |
hasValidConformer | Structural Calculations License | 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 |
lowestEnergyConformer leconformer | Structural Calculations License | calculates the lowest energy conformer of the molecule | the lowest energy conformer | - | Molecule Context |
mmff94OptimizedStructure | Structural Calculations License | calculates the MMFF94 optimized lowest energy conformer | the MMFF94 optimized lowest energy conformer | - | Molecule Context |
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 |
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 |
composition | - | returns the composition | the composition | - | Molecule Context |
dotDisconnectedFormula | - | returns the dot-disconnected formula | the dot-disconnected formula | - | Molecule Context |
dotDisconnectedIsotopeFormula | - | returns the dot-disconnected isotope formula | the dot-disconnected isotope formula | - | Molecule Context |
dotDisconnectedFormulaWithGrouping | - | returns the grouped dot-disconnected formula | the grouped dot-disconnected formula | - | Molecule Context |
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elementalAnalysis | - | performs elemental analysis on molecule represented by formula | the value calculated by the invoked function (e.g., mass) |
| Molecule Context |
exactMass | - | calculates the exact mass of the molecule | the exact mass | - | Molecule Context |
formula | - | returns the formula | the formula | - | Molecule Context |
isotopeComposition | - | returns the isotope composition | the isotope composition | - | Molecule Context |
isotopeFormula | - | returns the isotope formula | the isotope formula | - | Molecule Context |
mass | - | calculates the molecule mass | the mass | - | Molecule Context |
massspectrum | - | calculates the mass spectrum, the m/z:relative abundance plot | the mass spectrum as a series of discrete values | - | Molecule Context |
sortableFormula | - | returns the fixed digit sortable formula | fixed digit sortable molecular formula | - | Molecule Context |
Name | License | Description | Return value | Parameters | Examples | |
abs | - | returns the absolute value of a number | the absolute value | integer or real number | General (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 | |
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 | |
array | - | constructs an integer array from its arguments | the integer array | integers or MolAtom objects | General (All) | |
atno atomicNumber | - | returns the atomic number | the atomic number | atom index or MolAtom object | Molecule Context | |
atomProp | - |
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atoms | - |
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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) | |
connections | - | returns the bond plus implicit H count of an atom | the bond plus implicit H count | atom index or MolAtom object | Molecule Context | |
count | - | determines the number of elements in an array | the number of array elements | integer array or real number array | General (All) | ]]></ac:plain-text-body></ac:structured-macro> |
elemanal | - |
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eval | - |
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field property | - | returns a molecule property (SDF field value) | the molecule property | the property key (SDF field name) | Molecule Context | |
fieldAsString propertyAsString | - | returns a molecule property (SDF field value) as string | the molecule property as string | the property key (SDF field name) | Molecule Context | |
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 | ]]></ac:plain-text-body></ac:structured-macro> |
formalCharge totalCharge | - | calculates formal charge of molecule | the formal charge value | atom index or MolAtom object (optional) | Molecule Context | |
fragments | - | converts the molecule to its disconnected fragments | the disconnected fragments of the molecule | - | Molecule Context | |
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 | |
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 | |
hasRadical | - | determines if any atom in the molecule has radical | true if any atom in the molecule has radical, false otherwise | - | Molecule Context | |
hasValenceError | - | determines if any atom in the molecule has valence error | true in case of valence error, false otherwise | - | Molecule Context | |
HBDA | Structural Calculations License |
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hCount | - | returns the hydrogen count of an atom | the hydrogen count | atom index or array of atom indeces (separated by , or | Molecule Context | |
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 | |
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) | |
ionCharge | Structural Calculations License |
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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 | |
isQuery | - | decides whether the given molecule contains any query features | true if the molecule contains any query features, false otherwise | - | Molecule Context | |
map | - | returns the atom map number | the atom map number | atom index or MolAtom object | Molecule Context | |
max | - | takes maximum of its array and/or numerical parameters | the maximum value | integers, real numbers, integer arrays, real number arrays | General (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 | |
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 | |
min | - | takes minimum of its array and/or numerical parameters | the minimum value | integers, real numbers, integer arrays, real number arrays | General (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 | |
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 | |
molAtom | - | creates a MolAtom | the MolAtom object | atomic number | Molecule Context | |
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 | |
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 | |
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) | |
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 | |
radicalCount | - | returns the radical count of an atom | the radical count | atom index or MolAtom object | Molecule Context | |
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 | |
sortAsc | - | sorts an array in ascending order | the sorted array | integer array or real number array | General (All) | |
sortDesc | - | sorts an array in descending order | the sorted array | integer array or real number array | General (All) | |
sum | - | computes the sum of array elements | the sum | integer array or real number array | General (All) | |
topanal | Structural Calculations License |
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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 | |
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 |
Name | License | Description | Return value | Parameters | Examples |
aliphaticAtom | Structural Calculations License | checks if the specified atom is aliphatic | true for aliphatic atoms, false for non-aliphatic atoms |
| Molecule Context |
aliphaticAtomCount | Structural Calculations License | calculates the aliphatic atom count | the aliphatic atom count | - | Molecule Context |
aliphaticBondCount | Structural Calculations License | calculates the aliphatic bond count | the aliphatic bond count | - | Molecule Context |
aliphaticRingCount | Structural Calculations License | calculates the aliphatic ring count | the aliphatic ring count | - | Molecule Context |
aliphaticRingCountOfSize | Structural Calculations License | calculates the number of aliphatic rings of given size | the number of aliphatic rings of given size | the ring size | Molecule Context |
aliphaticRings | Structural Calculations License | 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 |
aliphaticRingsOfSize | Structural Calculations License | 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 |
angle | Structural Calculations License | calculates the angle between three atoms | the angle between three atoms |
| Molecule Context |
aromaticAtom | Structural Calculations License | checks if the specified atom is aromatic | true for aromatic atoms, false for non-aromatic atoms |
| Molecule Context |
aromaticAtomCount | Structural Calculations License | calculates the aromatic atom count | the aromatic atom count | - | Molecule Context |
aromaticBondCount | Structural Calculations License | calculates the aromatic bond count | the aromatic bond count | - | Molecule Context |
aromaticRingCount | Structural Calculations License | calculates the aromatic ring count | the aromatic ring count | - | Molecule Context |
aromaticRingCountOfSize | Structural Calculations License | calculates the number of aromatic rings of given size | the number of aromatic rings of given size | the ring size | Molecule Context |
aromaticRings | Structural Calculations License | 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 |
aromaticRingsOfSize | Structural Calculations License | 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 |
ASAHydrophobic | Structural Calculations License | calculates the water accessible molecular surface area of all hydrophobic atoms | the molecular surface area |
| Molecule Context |
ASANegative | Structural Calculations License | calculates the water accessible molecular surface area of all atoms with negative partial charge | the molecular surface area |
| Molecule Context |
ASAPlus | Structural Calculations License | calculates the water accessible molecular surface area of all atoms with positive partial charge | the molecular surface area |
| Molecule Context |
ASAPolar | Structural Calculations License | calculates the water accessible molecular surface area of all polar atoms | the molecular surface area |
| Molecule Context |
asymmetricAtom | Structural Calculations License | checks if the specified atom is an asymmetric atom | true for asymmetric atoms, false for symmetric atoms |
| Molecule Context |
asymmetricAtomCount | Structural Calculations License | calculates the number of asymmetric atoms | the asymmetric atom count | - | Molecule Context |
asymmetricAtoms | Structural Calculations License | determines the asymmetric atoms | indexes of asymmetric atoms | - | Molecule Context |
balabanIndex | Structural Calculations License | calculates the Balaban index | the Balaban index | - | Molecule Context |
bondCount | - | calculates the bond count | the bond count | - | Molecule Context |
bondType | Structural Calculations License | 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 |
carboaliphaticRingCount | Structural Calculations License | calculates the number of carboaliphatic rings in the molecule (aliphatic rings containing carbon atoms only) | number of carboaliphatic rings | - | Molecule Context |
carboaromaticRingCount | Structural Calculations License | calculates the number of carboaromatic rings in the molecule (aromatic rings containing carbon atoms only) | number of carboaromatic rings | - | Molecule Context |
carboRingCount | Structural Calculations License | calculates the number of carbocyclic rings in the molecule (rings containing carbon atoms only) | number of carbocyclic rings | - | Molecule Context |
carboRingCountOfSize | Structural Calculations License | 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 |
carboRings | Structural Calculations License | 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 |
carboRingsOfSize | Structural Calculations License | 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 |
chainAtom | Structural Calculations License | checks if the specified atom is a chain atom | true for chain atoms, false for non-chain atoms |
| Molecule Context |
chainAtomCount | Structural Calculations License | calculates the chain atom count | the chain atom count | - | Molecule Context |
chainBond | Structural Calculations License | 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 |
chainBondCount | Structural Calculations License | calculates the chain bond count | the chain bond count | - | Molecule Context |
chiralCenter | Structural Calculations License | checks if the specified atom is a tetrahedral stereogenic center | true for tetrahedral stereogenic center atoms |
| Molecule Context |
chiralCenterCount | Structural Calculations License | calculates the number of tetrahedral stereogenic center atoms | the tetrahedral stereogenic center count | - | Molecule Context |
chiralCenters | Structural Calculations License | determines the chiral center atoms | indexes of chiral center atoms | - | Molecule Context |
connected | Structural Calculations License | checks if two atoms are connected | true if the two atoms belong to the same connected component, false otherwise |
| Molecule Context |
connectedGraph | Structural Calculations License | checks whether the molecule graph is connected | true if the molecule graph is connected, false otherwise | - | Molecule Context |
cyclomaticNumber | Structural Calculations License | calculates the cyclomatic number | the cyclomatic number | - | Molecule Context |
dihedral | Structural Calculations License | calculates the dihedral of four atoms | the dihedral of four atoms |
| Molecule Context |
distance | Structural Calculations License | calculates the distance between two atoms | the distance between two atoms |
| Molecule Context |
distanceDegree | Structural Calculations License | calculates the distance degree of an atom | the distance degree |
| Molecule Context |
dreidingEnergy | Structural Calculations License | returns the Dreiding energy of the input molecule (conformer) | the dreiding energy | - | Molecule Context |
eccentricity | Structural Calculations License | calculates the eccentricity of an atom | the eccentricity of an atom |
| Molecule Context |
fragmentCount | Structural Calculations License | returns the number of fragments (disconnected parts) | the fragment count | - | Molecule Context |
fsp3 | Structural Calculations License | returns the fsp3 of the molecule | the fsp3 value | - | Molecule Context |
fusedAliphaticRingCount | Structural Calculations License | calculates the number of fused aliphatic rings (SSSR smallest set of smallest aliphatic rings) | the fused aliphatic ring count | - | Molecule Context |
fusedAliphaticRingCountOfSize | Structural Calculations License | calculates the number of fused aliphatic rings of given size | the number of fused aliphatic rings of given size | the ring size | Molecule Context |
fusedAliphaticRings | Structural Calculations License | 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 |
fusedAliphaticRingsOfSize | Structural Calculations License | 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 |
fusedAromaticRingCount | Structural Calculations License | calculates the number of fused aromatic rings (SSSR smallest set of smallest aromatic rings) | the fused aromatic ring count | - | Molecule Context |
fusedAromaticRingCountOfSize | Structural Calculations License | calculates the number of fused aromatic rings of given size | the number of fused aromatic rings of given size | the ring size | Molecule Context |
fusedAromaticRings | Structural Calculations License | 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 |
fusedAromaticRingsOfSize | Structural Calculations License | 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 |
fusedRingCount | Structural Calculations License | calculates the number of fused rings (SSSR smallest set of smallest rings) | the fused ring count | - | Molecule Context |
hararyIndex | Structural Calculations License | calculates the Harary index | the Harary index | - | Molecule Context |
heteroaliphaticRingCount | Structural Calculations License | calculates the number of aliphatic heterocyclic rings (SSSR smallest set of smallest aliphatic rings) | the aliphatic heterocyclic ring count | - | Molecule Context |
heteroaliphaticRingCountOfSize | Structural Calculations License | calculates the number of aliphatic heterocyclic rings of given size | the number of aliphatic heterocyclic rings of given size | the ring size | Molecule Context |
heteroaliphaticRings | Structural Calculations License | 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 |
heteroaliphaticRingsOfSize | Structural Calculations License | 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 |
heteroaromaticRingCount | Structural Calculations License | calculates the number of aromatic heterocyclic rings (SSSR smallest set of smallest aromatic rings) | the aromatic heterocyclic ring count | - | Molecule Context |
heteroaromaticRingCountOfSize | Structural Calculations License | calculates the number of aromatic heterocyclic rings of given size | the number of aromatic heterocyclic rings of given size | the ring size | Molecule Context |
heteroaromaticRings | Structural Calculations License | 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 |
heteroaromaticRingsOfSize | Structural Calculations License | 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 |
heteroRingCount | Structural Calculations License | calculates the number of heterocyclic rings (SSSR smallest set of smallest rings) | the heterocyclic ring count | - | Molecule Context |
heteroRingCountOfSize | Structural Calculations License | calculates the number of heterocyclic rings of given size | the number of heterocyclic rings of given size | the ring size | Molecule Context |
heteroRings | Structural Calculations License | 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 |
heteroRingsOfSize | Structural Calculations License | 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 |
hyperWienerIndex | Structural Calculations License | calculates the Hyper Wiener index | the Hyper Wiener index | - | Molecule Context |
largestAtomRingSize | Structural Calculations License | calculates the size of the largest ring containing the specified atom | the size of the largest ring containing the specified atom |
| Molecule Context |
largestConjugatedSystem | Structural Calculations License | returns the atom list of the largest conjugated system in the molecule | - |
| Molecule Context |
largestConjugatedSystemSize | Structural Calculations License | returns the number of pi electron pairs in the largest conjugated system | - |
| Molecule Context |
largestConjugatedSystemMol | Structural Calculations License | returns the input molecule with the largest conjugated system coloured in green | This function should be used with the output option -f mrv to export colour in the output |
| Molecule Context |
largestRing | Structural Calculations License | 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 |
largestRingSize | Structural Calculations License | calculates the largest ring size | the largest ring size | - | Molecule Context |
largestRingSystem | Structural Calculations License | 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 |
largestRingSystemSize | Structural Calculations License | calculates the size of the largest ring system (number of rings) | the size of the largest ring system | - | Molecule Context |
maximalProjectionArea | Structural Calculations License | returns the maximal projection area | the maximal projection area | - | Molecule Context |
maximalProjectionRadius | Structural Calculations License | returns the maximal projection radius | the maximal projection radius | - | Molecule Context |
maximalProjectionSize | Structural Calculations License | returns the maximal distance in the molecule perpendicular to the maximal projection area | the maximal distance in the molecule (the actual conformer) perpendicular to its maximal projection area | - | Molecule Context |
minimalProjectionArea | Structural Calculations License | returns the minimal projection area | the minimal projection area | - | Molecule Context |
minimalProjectionRadius | Structural Calculations License | returns the minimal projection radius | the minimal projection radius | - | Molecule Context |
minimalProjectionSize | Structural Calculations License | returns the maximal distance in the molecule perpendicular to the minimal projection area | the maximal distance of the molecule (the actual conformer) perpendicular to its minimal projection area | - | Molecule Context |
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mmff94Energy | Structural Calculations License | returns the MMFF94 energy of the input molecule (conformer) | the MMFF94 energy | - | Molecule Context |
plattIndex | Structural Calculations License | calculates the Platt index | the Platt index | - | Molecule Context |
randicIndex | Structural Calculations License | calculates the Randic index | the Randic index | - | Molecule Context |
ringAtom | Structural Calculations License | checks if the specified atom is a ring atom | true for ring atoms, false for non-ring atoms |
| Molecule Context |
ringAtomCount | Structural Calculations License | calculates the ring atom count | the ring atom count | - | Molecule Context |
ringBond | Structural Calculations License | 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 |
ringBondCount | Structural Calculations License | calculates the ring bond count | the ring bond count | - | Molecule Context |
ringCount | Structural Calculations License | calculates the ring count | the ring count | - | Molecule Context |
ringCountOfAtom | Structural Calculations License | calculates the number of rings passing through an atom | the number of rings passing through an atom |
| Molecule Context |
ringCountOfSize | Structural Calculations License | calculates the number of rings of given size | the number of rings of given size | the ring size | Molecule Context |
rings | Structural Calculations License | identifies the rings in the molecule | atom indexes of the rings in the molecule (null if the molecule is acyclic) | - | Molecule Context |
ringsOfSize | Structural Calculations License | 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 |
ringSystemCount | Structural Calculations License | calculates the number of rings systems | the number of rings systems | - | Molecule Context |
ringSystemCountOfSize | Structural Calculations License | calculates the number of rings systems of given size | the number of rings systems of given size | the ring system size | Molecule Context |
ringSystems | Structural Calculations License | 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 |
ringSystemsOfSize | Structural Calculations License | 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 |
rotatableBond | Structural Calculations License | 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 |
rotatableBondCount | Structural Calculations License | calculates the rotatable bond count | the rotatable bond count | - | Molecule Context |
| Structural Calculations License | 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 |
smallestAtomRingSize | Structural Calculations License | calculates the size of the smallest ring containing the specified atom | the size of the smallest ring containing the specified atom |
| Molecule Context |
smallestRing | Structural Calculations License | 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 |
smallestRingSize | Structural Calculations License | calculates the smallest ring size | the smallest ring size | - | Molecule Context |
smallestRingSystem | Structural Calculations License | 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 |
smallestRingSystemSize | Structural Calculations License | calculates the size of the smallest ring system (number of rings) | the size of the smallest ring system | - | Molecule Context |
stereoDoubleBondCount | Structural Calculations License | calculates the number of stereo double bonds | the stereo double bond count | - | Molecule Context |
stericEffectIndex | Structural Calculations License | calculates the steric effect index of an atom | the steric effect index of an atom |
| Molecule Context |
stericHindrance | Structural Calculations License | calculates the steric hindrance of an atom | the steric hindrance of an atom |
| Molecule Context |
szegedIndex | Structural Calculations License | calculates the Szeged index | the Szeged index | - | Molecule Context |
topologicalPolarSurfaceArea PSA | - | calculates the topological polar surface area (2D) | the polar surface area (2D) |
| Molecule Context |
vanDerWaalsSurfaceArea | Structural Calculations License | calculates the van der Waals surface area | the molecular surface area |
| Molecule Context |
waterAccessibleSurfaceArea ASA solventAccessibleSurfaceArea | Structural Calculations License | calculates the solvent accessible / water accessible molecular surface area | the molecular surface area |
| Molecule Context |
wienerIndex | Structural Calculations License | calculates the Wiener index | the Wiener index | - | Molecule Context |
wienerPolarity | Structural Calculations License | calculates the Wiener polarity | the Wiener polarity | - | Molecule Context |
Name | License | Description | Return value | Parameters | Examples |
acceptor acc | Structural Calculations License | calculates atomic hydrogen bond acceptor multiplicity | the atomic hydrogen bond acceptor multiplicity |
| Molecule Context |
acceptorCount | Structural Calculations License | calculates molecular hydrogen bond acceptor count (the number of acceptor atoms) | the molecular hydrogen bond acceptor count |
| Molecule Context |
acceptorSiteCount accSiteCount | Structural Calculations License | calculates molecular hydrogen bond acceptor multiplicity (the sum of atomic multiplicities) | the molecular hydrogen bond acceptor multiplicity |
| Molecule Context |
donor don | Structural Calculations License | calculates atomic hydrogen bond donor multiplicity | the atomic hydrogen bond donor multiplicity |
| Molecule Context |
donorCount | Structural Calculations License | calculates molecular hydrogen bond donor count (the number of donor atoms) | the molecular hydrogen bond donor count |
| Molecule Context |
donorSiteCount donSiteCount | Structural Calculations License | calculates molecular hydrogen bond acceptor / donor multiplicity (the sum of atomic multiplicities) | the molecular hydrogen bond acceptor / donor multiplicity |
| Molecule Context |
Name | License | Description | Return value | Parameters | Examples |
chargeDensity totalChargeDensity | Structural Calculations License | calculates the charge density of atoms | the charge density of the atom, NaN for non-existing values |
| Molecule Context |
electronDensity piChargeDensity | Structural Calculations License | calculates the electron density of atoms | the electron density of the atom, NaN for non-existing values |
| Molecule Context |
electrophilicity energyNu nucleophilicLocalizationEnergy | Structural Calculations License | calculates electrophilicity of atoms | the electrophilicity of the atom, NaN for non-aromatic atoms |
| Molecule Context |
electrophilicityOrder aromaticElectrophilicityOrder orderE | Structural Calculations License | calculates E | the E |
| Molecule Context |
hmoChargeDensity | Structural Calculations License | calculates the HMO charge density of atoms | the charge density of the atom, NaN for non-existing values |
| Molecule Context |
hmoElectronDensity | Structural Calculations License | calculates the HMO electron density of atoms | the electron density of the atom, NaN for non-existing values |
| Molecule Context |
hmoElectrophilicityOrder hmoOrderE | Structural Calculations License | calculates HMO E | the E |
| Molecule Context |
hmoElectrophilicLocalizationEnergy | Structural Calculations License | calculates HMO localization energy L | the localization energy L |
| Molecule Context |
hmoNucleophilicityOrder hmoOrderNu | Structural Calculations License | calculates HMO Nu | the Nu |
| Molecule Context |
hmoNucleophilicLocalizationEnergy | Structural Calculations License | calculates HMO localization energy L | the localization energy L |
| Molecule Context |
hmoPiEnergy | Structural Calculations License | calculates the HMO pi energy of the molecule | the pi energy of the molecule |
| Molecule Context |
nucleophilicity electrophilicLocalizationEnergy energyE | Structural Calculations License | calculates nucleophilicity of atoms | the nucleophilicity of the atom, NaN for non-aromatic atoms |
| Molecule Context |
nucleophilicityOrder aromaticNucleophilicityOrder orderNu | Structural Calculations License | calculates Nu | the Nu |
| Molecule Context |
piEnergy | Structural Calculations License | calculates the pi energy of the molecule. Deprecated. | the pi energy of the molecule |
| Molecule Context |
Name | License | Description | Return value | Parameters | Examples |
allTautomer | Isomers License | returns a tautomeric form from all tautomers | the tautomer |
| Molecule Context |
allTautomers | Isomers License | returns all tautomer forms in an array | the tautomer array | the normalization option (default is false) | Molecule Context |
canonicalResonant | - | constructs the canonical resonant structure | the canonical resonant structure | - | Molecule Context |
canonicalTautomer | Isomers License | generates the canonical tautomer structure | the canonical tautomer | option that switches on the normalization (defaults is false) | Molecule Context |
dominantTautomer tautomer | Isomers License | returns the i-th dominant tautomeric form | the i-th dominant tautomer |
| Molecule Context |
dominantTautomerCount | Isomers License | calculates the number of dominant tautomers | the number of dominant tautomers |
| Molecule Context |
dominantTautomers tautomers | Isomers License | constructs all dominant tautomeric forms (ordered by distribution) | the dominant tautomer array |
| Molecule Context |
doubleBondStereoisomer | Isomers License | generates a double bond stereoisomer of the molecule | the double bond stereoisomer |
| Molecule Context |
doubleBondStereoisomerCount | Isomers License | returns the number of generated double bond stereoisomers | the number of generated double bond stereoisomers | - | Molecule Context |
doubleBondStereoisomers | Isomers License | 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 |
genericTautomer | Isomers License | constructs the generic tautomer structure | the generic tautomer structure | - | Molecule Context |
majorTautomer | Isomers License | constructs the major tautomer structure | the major tautomer structure |
| Molecule Context |
mostStableTautomer | Isomers License | deprecated, use majorTautomer instead. constructs the most stable tautomer structure | the most stable tautomer structure | - | Molecule Context |
resonant | - | constructs a resonant structure | the resonant structure | - | Molecule Context |
resonantCount | - | calculates the number of resonant structures | the number of resonant structures | - | Molecule Context |
resonants | - | constructs all resonant structures | the resonant structure array | - | Molecule Context |
stereoAnalysis | - | calculates stereo descriptors of molecule | list of stereo descriptors |
| Molecule Context |
stereoisomer | Isomers License | generates a stereoisomer of the molecule | the stereoisomer |
| Molecule Context |
stereoisomerCount | Isomers License | returns the number of generated stereoisomers | the number of generated stereoisomers | - | Molecule Context |
stereoisomers | Isomers License | generates stereoisomers of the molecule (maximum number of stereoisomers to be generated can be set, default: all) | the stereoisomer array | - | Molecule Context |
tautomerCount | Isomers License | calculates the number of tautomers | the number of tautomers | - | Molecule Context |
tetrahedralStereoisomer | Isomers License | generates a tetrahedral stereoisomer of the molecule | the tetrahedral stereoisomer | - | Molecule Context |
tetrahedralStereoisomerCount | Isomers License | returns the number of generated tetrahedral stereoisomers | the number of generated tetrahedral stereoisomers | - | Molecule Context |
tetrahedralStereoisomers | Isomers License | 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 |
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 |
markushEnumerationCount enumerationCount | Markush Enumeration Plugin | calculates the number of Markush enumerations | the number of Markush enumerations |
| Molecule Context |
markushEnumerations enumeration enumerations markushEnumeration | Markush Enumeration Plugin | constructs Markush enumerated structures sequentially | the enumerated structures |
| Molecule Context |
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 |
markushLibraryMagnitude | Markush Enumeration Plugin | calculates the Markush library magnitude, no enumeration is done | the Markush library magnitude |
| Molecule Context |
markushLibrarySize | Markush Enumeration Plugin | calculates the Markush library size, no enumeration is done | the Markush library size |
| Molecule Context |
markushLibrarySizeAsString | Markush Enumeration Plugin | calculates the Markush library size and returns it as string, no enumeration is done | the Markush library size |
| Molecule Context |
randomMarkushEnumerations randomEnumeration randomEnumerations randomMarkushEnumeration | Markush Enumeration Plugin | constructs Markush enumerated structures randomly | the enumerated structures |
| Molecule Context |
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 |
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 |
| Molecule Context | ]]></ac:plain-text-body></ac:structured-macro> |
match | - | performs substructure search and optionally checks for atom matching | true if matching substructure found, false otherwise |
| Molecule Context | ]]></ac:plain-text-body></ac:structured-macro> |
matchCount | - | performs substructure search and optionally checks for atom matching, counts search hits | the number of search hits |
| Molecule Context | ]]></ac:plain-text-body></ac:structured-macro> |
matchFirst | - | performs substructure search and optionally checks for atom matching | index of the first matching substructure (1-based indexing) |
| Molecule Context | ]]></ac:plain-text-body></ac:structured-macro> |
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.
Back to Contents
Name | License | Description | Return value | Parameters | Examples |
name | Structure To Name License | returns the name(s) of the molecule specified by the export option | the name(s) of the molecule | either empty (IUPAC export option) or the specified name export option | Molecule Context |
traditionalName | Structure To Name License | returns the traditional name of the molecule | the traditional name of the molecule | - | Molecule Context |
Name | License | Description | Return value | Parameters | Examples |
HLB number | Partitioning License | calculates the HLB number | the HLB number |
| Molecule Context |
logD | Partitioning License | calculates logD at specified pH | the logD value |
| Molecule Context |
logDKLOP | Partitioning License | calculates logD at specified pH using method "KLOP" | the logD value |
| Molecule Context |
logDPHYS | Partitioning License | calculates logD at specified pH using method "PHYS" | the logD value |
| Molecule Context |
logDUser | Partitioning License | calculates logD at specified pH using the user defined method | the logD value |
| Molecule Context |
logDVG | Partitioning License | calculates logD at specified pH using method "VG" | the logD value |
| Molecule Context |
logDWeighted | Partitioning License | calculates logD at specified pH using weighted method | the logD value |
| Molecule Context |
logP | Partitioning License | calculates logP | the logP value |
| Molecule Context |
logPincrement logPi | Partitioning License | calculates the atomic logP increment | the atomic logP increment |
| Molecule Context |
logPKLOP | Partitioning License | calculates logP using method "KLOP" | the logP value |
| Molecule Context |
logPPHYS | Partitioning License | calculates logP using method "PHYS" | the logP value |
| Molecule Context |
logPUser | Partitioning License | calculates logP using the user defined method | the logP value |
| Molecule Context |
logPVG | Partitioning License | calculates logP using method "VG" | the logP value |
| Molecule Context |
logPWeighted | Partitioning License | calculates logP using weighted method | the logP value |
| Molecule Context |
Name | License | Description | Return value | Parameters | Examples |
acidicpKa apKa | Protonation License | calculates acidic pK a values | the acidic pK a values |
| Molecule Context |
acidicpKaLargeModel | Protonation License | calculates acidic pK a values using large model (this model is optimized for a large number of ionizable atoms) | the acidic pK a values |
| Molecule Context |
acidicpKaUseCorrection | Protonation License | calculates acidic pK a values using the correction library | the acidic pK a values |
| Molecule Context |
averageMicrospeciesCharge | Protonation License | 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 |
basicpKa bpKa | Protonation License | calculates basic pK a values | the basic pK a values |
| Molecule Context |
basicpKaLargeModel | Protonation License | calculates basic pK a values using large model (this model is optimized for a large number of ionizable atoms) | the basic pK a values |
| Molecule Context |
basicpKaUseCorrection | Protonation License | calculates basic pK a values using the correction library | the basic pK a values |
| Molecule Context |
isoelectricPoint pI | Protonation License | calculates isoelectric point | the isoelectric point | - | Molecule Context |
majorMicrospecies majorMs | Protonation License | calculates major microspecies at specified pH | the major microspecies |
| Molecule Context |
microspecies ms | Protonation License | calculates microspecies at specified pH | the microspecies |
| Molecule Context |
microspeciesCount msCount | Protonation License | calculates the number of microspecies at specified pH | the number of microspecies | - | Molecule Context |
microspeciesDistribution msDistr | Protonation License | calculates microspecies distribution at specified pH | the microspecies distribution |
| Molecule Context |
pKa | Protonation License | calculates pK a values | the pK a values |
| Molecule Context |
pKaUseCorrection | Protonation License | calculates pK a values using the correction library | the pK a values |
| Molecule Context |
Name | License | Description | Return value | Parameters | Examples |
refractivity refrac | Structural Calculations License | calculates molar refractivity | the refractivity value | - | Molecule Context |
refractivityIncrements refraci | Structural Calculations License | calculates atomic refractivity increments | the atomic refractivity increment |
| Molecule Context |
Name | License | Description | Return value | Parameters | Examples |
logS | Solubility License | Calculates intrinsic solubility or solubility at a specified pH | the logS value |
| Molecule Context |
Name | License | Description | Return value | Parameters | Examples |
bmf | Structural Calculations License | Returns the Bemis-Murcko framework of the input structure | BMF of the input structure | - | Molecule Context |
bmfl bemisMurckoFrameworkLoose | Structural Calculations License | 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 |
bmflp bemisMurckoFrameworkLoosePruned | Structural Calculations License | 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 |
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)
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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 |
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)
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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)
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or MolAtom object
order of atoms
order of atoms