TopologyAnalyserPlugin (Marvin API documentation (c) 1998-2021 ChemAxon Ltd.)

java.lang.Object
- chemaxon.marvin.plugin.CalculatorPlugin
- - chemaxon.marvin.calculations.TopologyAnalyserPlugin

All Implemented Interfaces:

chemaxon.license.Licensable
```
@PublicAPI
public class TopologyAnalyserPlugin
extends CalculatorPlugin
```
Calculates topological data. Data types:
- "aliphaticAtom" (API/cxcalc only, atomic boolean property)
- "aliphaticAtomCount"
- "aliphaticBondCount"
- "aliphaticRingCount"
- "aliphaticRingCountOfSize" (API/cxcalc only, number of aliphatic rings of given size)
- "aliphaticRings" (API/Chemical Terms only)
- "aliphaticRingsOfSize" (API/Chemical Terms only)
- "aromaticAtom" (API/cxcalc only, atomic boolean property)
- "aromaticAtomCount"
- "aromaticBondCount"
- "aromaticRingCount"
- "aromaticRingCountOfSize" (API/cxcalc only, number of aromatic rings of given size)
- "aromaticRings" (API/Chemical Terms only)
- "aromaticRingsOfSize" (API/Chemical Terms only)
- "asymmetricAtom" (API/cxcalc only, atomic boolean property)
- "asymmetricAtomCount"
- "asymmetricAtoms"
- "atomCount"
- "balabanIndex"
- "bondCount"
- "bondType" (API/cxcalc only, the bond type)
- "carboaliphaticRingCount"
- "carboaromaticRingCount"
- "carboRingCount"
- "carboRingCountOfSize" (API/Chemical Terms only)
- "carboRings" (API/Chemical Terms only)
- "carboRingsOfSize" (API/Chemical Terms only)
- "chainAtom" (API/cxcalc only, atomic boolean property)
- "chainAtomCount"
- "chainBond" (API/cxcalc only, bond boolean property)
- "chainBondCount"
- "chiralCenter" (API/cxcalc only, atomic boolean property)
- "chiralCenterCount"
- "chiralCenters"
- "connected" (API/cxcalc only, true if two atoms are connected)
- "connectedGraph" (API/cxcalc only, true if the molecule graph is connected)
- "cyclomaticNumber"
- "distanceCount" (API only, number of atoms at given distance from a given atom)
- "distanceDegree" (atomic)
- "eccentricity" (atomic)
- "fragmentCount",
- "fsp3",
- "fusedAliphaticRingCount"
- "fusedAliphaticRingCountOfSize" (API/Chemical Terms only)
- "fusedAliphaticRings" (API/Chemical Terms only)
- "fusedAliphaticRingsOfSize" (API/Chemical Terms only)
- "fusedAromaticRingCount"
- "fusedAromaticRingCountOfSize" (API/Chemical Terms only)
- "fusedAromaticRings" (API/Chemical Terms only)
- "fusedAromaticRingsOfSize" (API/Chemical Terms only)
- "fusedRingCount"
- "hararyIndex"
- "heteroaliphaticRingCount" (API/Chemical Terms only)
- "heteroaliphaticRingCountOfSize" (API/Chemical Terms only)
- "heteroaliphaticRings" (API/Chemical Terms only)
- "heteroaliphaticRingsOfSize" (API/Chemical Terms only)
- "heteroaromaticRingCount"
- "heteroaromaticRingCountOfSize" (API/Chemical Terms only)
- "heteroaromaticRings" (API/Chemical Terms only)
- "heteroaromaticRingsOfSize" (API/Chemical Terms only)
- "heteroRingCount"
- "heteroRingCountOfSize" (API/Chemical Terms only)
- "heteroRings" (API/Chemical Terms only)
- "heteroRingsOfSize" (API/Chemical Terms only)
- "hyperWienerIndex"
- "largestAtomRingSize" (API/cxcalc only, atomic, size of largest ring containing atom)
- "largestRing" (API/Chemical Terms only)
- "largestRingSize"
- "largestRingsystem" (API/Chemical Terms only)
- "largestRingSystemSize",
- "plattIndex"
- "randicIndex"
- "ringAtom" (API/cxcalc only, atomic boolean property)
- "ringAtomCount"
- "ringBond" (API/cxcalc only, bond boolean property)
- "ringBondCount"
- "ringCount"
- "ringCountOfAtom" (API/cxcalc only, number of rings of given atom)
- "ringCountOfSize" (API only, number of rings of given size)
- "rings"
- "ringsOfSize"
- "ringSystemCount",
- "ringSystemCountOfSize",(API/cxcalc only, number of rings system of given size)
- "ringSystems" (API/Chemical Terms only)
- "ringSystemsOfSize" (API/Chemical Terms only)
- "rotatableBond" (API/cxcalc only, bond boolean property)
- "rotatableBondCount"
- "shortestPath" (API/cxcalc only, size of shortest path between two atoms)
- "smallestAtomRingSize" (API/cxcalc only, atomic, size of smallest ring containing atom)
- "smallestRing" (API/Chemical Terms only)
- "smallestRingSize"
- "smallestRingSystem" (API/Chemical Terms only)
- "smallestRingsyStemSize"
- "stereoDoubleBondCount"
- "stericEffectIndex" (atomic)
- "szegedIndex"
- "wienerIndex"
- "wienerPolarity"
API usage example (as an alternative, you can also use the TopologyAnalyser class directly):
```
    // read input molecule
    MolImporter mi = new MolImporter("test.mol");
    Molecule mol = mi.read();
    mi.close();

    // create plugin
    TopologyAnalyserPlugin plugin = new TopologyAnalyserPlugin();

    // set target molecule
    plugin.setMolecule(mol);

    // run the calculation
    plugin.run();

    // get molecular results
    int ringCount = plugin.getRingCount();
    int rotatableBondCount = plugin.getRotatableBondCount();
    int smallestRingSize = plugin.getSmallestRingSize();

    // get atomic result
    int count = mol.getAtomCount();
    double[] stericEffectIndexes = new double[count];
    for (int i=0; i < count; ++i) {
        stericEffectIndexes[i] = plugin.getStericEffectIndex(i);
    }

    // get bond result
    int index = plugin.getBondIndex(0,3); // bond index connecting atom 0 and atom 3
    boolean isChainBond = plugin.isChainBond(index);

    // do something with the results ...
 
```
For concurrent plugin example applications using ChemAxon's concurrent framework, refer to the Concurrent plugin examples.
Since:

Marvin 3.5, 09/27/2004

Version:

Marvin 5.3, 10/26/2009

Author:

Nora Mate, Zsolt Mohacsi

Nested Class Summary
- Nested classes/interfaces inherited from class chemaxon.marvin.plugin.CalculatorPlugin
  CalculatorPlugin.HydrogenData

Field Summary
- Fields inherited from class chemaxon.marvin.plugin.CalculatorPlugin
  ATOM, BLUE, CALCRGB_OFF, COVALENT_HYDRATION_ERROR_REMARK, CRITICAL_ERROR_MSG, EPSILON, explicitHydrogens, INCORRECT_AROMATIC_NITROGEN_REMARK, INSTABLE_TAUTOMERIC_FORM_REMARK, KEEP_HYDROGENS, keepHydrogens, licenseEnvironment, MOLECULE, MOLECULES, NAN, PLUGIN_CLASS_KEY, PLUGIN_DIR, RED, TRUE

Constructor Summary

Constructors
Constructor and Description

TopologyAnalyserPlugin()
Constructor.

Constructors
Constructor and Description
`TopologyAnalyserPlugin()` Constructor.

Method Summary

All Methods Instance Methods Concrete Methods Deprecated Methods
Modifier and Type	Method and Description
`void`	`checkMolecule(Molecule mol)` Checks the input molecule.
`int`	`getAliphaticAtomCount()` Returns the aliphatic atom count.
`int`	`getAliphaticBondCount()` Returns the aliphatic bond count.
`int`	`getAliphaticRingCount()` Returns the aliphatic ring count.
`int`	`getAliphaticRingCount(int size)` Returns the number of aliphatic rings (SSSR smallest set of smallest rings) of a given size in the molecule.
`int`	`getAliphaticRingCountOfSize(int size)` Deprecated. Use `getAliphaticRingCount(int)`
`int[][]`	`getAliphaticRings()` Identifies the aliphatic rings in the molecule.
`int[][]`	`getAliphaticRings(int size)` Indentifies aliphatic rings in the molecule having a given size (number of atoms).
`int`	`getAllAtomCount()` Returns the atom count.
`int`	`getAromaticAtomCount()` Returns the aromatic atom count.
`int`	`getAromaticBondCount()` Returns the aromatic bond count.
`int`	`getAromaticRingCount()` Returns the aromatic ring count.
`int`	`getAromaticRingCount(int size)` Returns the number of aromatic rings (SSSR smallest set of smallest rings) of a given size in the molecule.
`int`	`getAromaticRingCountOfSize(int size)` Deprecated. Use `getAromaticRingCount(int)`
`int[][]`	`getAromaticRings()` Identifies the aromatic rings in the molecule.
`int[][]`	`getAromaticRings(int size)` Indentifies aromatic rings in the molecule having a given size (number of rings).
`int`	`getAsymmetricAtomCount()` Returns the number of asymmetric atoms.
`int[]`	`getAsymmetricAtoms()` Determines the asymmetric atoms.
`double`	`getBalabanIndex()` Calculates the Balaban distance connectivity of the molecule, which is the average distance sum connectivity.
`int`	`getBondCount()` Returns the bond count.
`int`	`getBondIndex(int i1, int i2)` Returns the index of the bond connecting two atoms, `-1` if the two atoms are not connected by bond.
`int`	`getBondType(int index)` Determines the type of a bond (aromatic bonds are automatically recognized)
`int`	`getCarboaliphaticRingCount()` Calculates the number of carboaliphatic rings in the molecule (aliphatic rings containing carbon atoms only).
`int`	`getCarboaromaticRingCount()` Calculates the number of carboaromatic rings in the molecule (aromatic rings containing carbon atoms only).
`int`	`getCarboRingCount()` Returns the carbo ring count.
`int`	`getCarboRingCount(int size)` Calculates the number of carbocyclic rings in the molecule (rings containing at least a non-carbon atom).
`int[][]`	`getCarboRings()` Identifies carbocyclic rings in the molecule (rings containing carbon atoms only).
`int[][]`	`getCarboRings(int size)` Identifies carbocyclic rings in the molecule (rings containing carbon atoms only) having the given number of atoms.
`int`	`getChainAtomCount()` Returns the chain atom count.
`int`	`getChainBondCount()` Returns the chain bond count.
`int`	`getChiralCenterCount()` Calculates the number of tetrahedral stereogenic centers.
`int[]`	`getChiralCenters()` Determines the chiral center atoms.
`Molecule`	`getColoredLargestConjugatedSystem()` Returns a `Molecule` in which the atoms of largest conjugated system are colored.
`int`	`getCyclomaticNumber()` Calculates the smallest number of graph edges which must be removed such that no circuit remains.
`int`	`getDistanceCount(int index, int distance)` Counts the given value in a row of the distance matrix.
`int`	`getDistanceDegree(int index)` Calculates the distance degree of an atom, which is the sum of the corresponding row values in the distance matrix.
`int`	`getEccentricity(int index)` Calculates the eccentricity of an atom, which is the greatest value in the corresponding row of the distance matrix.
`int`	`getFragmentCount()` Returns the number of fragments (disconnected parts) of the molecule.
`double`	`getFsp3()` Calculates the Fsp3 value of the given molecule. Fsp3 = number of sp3 carbons / number of carbons
`int`	`getFusedAliphaticRingCount()` Calculates the number of fused aliphatic rings (SSSR smallest set of smallest aliphatic rings) in the molecule.
`int`	`getFusedAliphaticRingCount(int size)` Calculates the number of fused aliphatic rings in the molecule (rings s).
`int[][]`	`getFusedAliphaticRings()` Identifies fused aliphatic rings (SSSR smallest set of smallest aliphatic rings) in the molecule.
`int[][]`	`getFusedAliphaticRings(int size)` Identifies fused aliphatic rings (SSSR smallest set of smallest aliphatic rings) in the molecule having the given size (number of atoms).
`int`	`getFusedAromaticRingCount()` Calculates the number of fused aromatic rings (SSSR smallest set of smallest aromatic rings) in the molecule.
`int`	`getFusedAromaticRingCount(int size)` Calculates the number of fused aromatic rings in the molecule (rings s).
`int[][]`	`getFusedAromaticRings()` Identifies fused aromatic rings (SSSR smallest set of smallest aromatic rings) in the molecule.
`int[][]`	`getFusedAromaticRings(int size)` Identifies fused aromatic rings (SSSR smallest set of smallest aromatic rings) in the molecule having the given size (number of atoms).
`int`	`getFusedRingCount()` Calculates the number of fused rings (SSSR smallest set of smallest rings) in the molecule.
`double`	`getHararyIndex()` Calculates the Harary index which is the half-sum of the off-diagonal elements of the reciprocal molecular distance matrix of the molecule.
`int`	`getHeteroaliphaticRingCount()` Calculates the number of aliphatic heterocyclic rings in the molecule (aliphatic rings containing at least a non-carbon atom).
`int`	`getHeteroaliphaticRingCount(int size)` Calculates the number of aliphatic heterocyclic rings in the molecule (aliphatic rings containing at least a non-carbon atom) having a given size (number of atoms).
`int[][]`	`getHeteroaliphaticRings()` Identifies heteroaliphatic rings in the molecule (aliphatic rings containing at least a non-carbon atom).
`int[][]`	`getHeteroaliphaticRings(int size)` Identifies heteroaliphatic rings in the molecule (aliphatic rings containing at least a non-carbon atom) having a given size (number of atoms).
`int`	`getHeteroaromaticRingCount()` Returns the heteroaromatic ring count.
`int`	`getHeteroaromaticRingCount(int size)` Calculates the number of aromatic heterocyclic rings in the molecule (aromatic rings containing at least a non-carbon atom) having a given size (number of atoms).
`int[][]`	`getHeteroaromaticRings()` Identifies heteroaromatic rings in the molecule (aromatic rings containing at least a non-carbon atom).
`int[][]`	`getHeteroaromaticRings(int size)` Identifies heteroaromatic rings in the molecule (aromatic rings containing at least a non-carbon atom) having a given size (number of atoms).
`int`	`getHeteroRingCount()` Returns the hetero ring count.
`int`	`getHeteroRingCount(int size)` Calculates the number of heterocyclic rings in the molecule (rings containing at least a non-carbon atom).
`int[][]`	`getHeteroRings()` Identifies heterocyclic rings in the molecule (rings containing at least a non-carbon atom).
`int[][]`	`getHeteroRings(int size)` Indentifies hetero rings in the molecule having a given size (number of atoms).
`int`	`getHyperWienerIndex()` Calculates the hyper Wiener index of the molecule.
`int[]`	`getLargestConjugatedSystem()` Returns the largest conjugated system in the molecule.
`int`	`getLargestConjugatedSystemSize()` Returns the largest conjugated system size (number of pi electron pairs).
`int[]`	`getLargestRing()` Identifies the atoms of the largest ring (number of atoms) in the molecule.
`int`	`getLargestRingSize()` Returns the largest ring size.
`int`	`getLargestRingSizeOfAtom(int index)` Returns the size of largest ring containing the specified atom.
`int[]`	`getLargestRingSystem()` Identifies the atoms of the largest ring system (number of rings) in the molecule.
`int`	`getLargestRingSystemSize()` Returns the size of the largest ring system (number of rings) in the molecule.
`int`	`getPlattIndex()` Calculates the Platt index of the molecule which is equal to the total sum of the edge degrees of a molecular graph.
`java.lang.String`	`getProductName()` Returns the product identifier of the plugin as given by `LicenseManager`.
`double`	`getRandicIndex()` Calculates the Randic index or molecular connectivity index as the harmonic sum of the geometric means of the node degrees for each edge.
`java.lang.String`	`getRemark()` Returns the calculation remark: if no results (no result types) then returns remark, otherwise returns `null`.
`java.lang.Object`	`getResult(java.lang.Object type, int index)` Returns the result item for the specified key and index.
`java.lang.Object`	`getResult(java.lang.Object type, java.lang.String arg)` Returns the shortest path between two atoms if type is set ot "shortestPath", returns connectivity info if type is set to "connected".
`java.lang.String`	`getResultAsString(java.lang.Object type, int index, java.lang.Object result)` Returns the specified result in String format.
`int`	`getResultCount(java.lang.Object type)` Returns the number of result items for the given result key.
`int`	`getResultDomain(java.lang.Object type)` Returns the calculation domain `CalculatorPlugin.ATOM` or `CalculatorPlugin.MOLECULE`.
`Molecule`	`getResultMolecule()` Returns the result molecule for display.
`Molecule[]`	`getResultMolecules()` Returns the result molecules, molecular results are set in the first molecule, atomic results are set in subsequent molecules as atom labels.
`java.lang.Object[]`	`getResultTypes()` Returns the result types.
`int`	`getRingAtomCount()` Returns the ring atom count.
`int`	`getRingBondCount()` Returns the ring bond count.
`int`	`getRingCount()` Returns the ring count.
`int`	`getRingCount(int size)` Calculates the number of rings (SSSR smallest set of smallest rings) of a given size in the molecule.
`int`	`getRingCountOfAtom(int index)` Calculates the number of rings (SSSR smallest set of smallest rings) an atom is part of.
`int`	`getRingCountOfSize(int size)` Deprecated. Use `getRingCount(int)`
`int[][]`	`getRings()` Identifies the rings in the molecule.
`int[][]`	`getRings(int size)` Identifies rings in the molecule having a given size.
`int`	`getRingSystemCount()` Returns the number of ring systems.
`int`	`getRingSystemCount(int size)` Returns the number of ring systems having a given size (number of rings) in the molecule.
`int`	`getRingSystemCountOfSize(int size)` Deprecated. Use `getRingSystemCount(int)`
`int[][]`	`getRingSystems()` Identifies the ring systems in the molecule.
`int[][]`	`getRingSystems(int size)` Indentifies the ring systems in the molecule having a given size (number of rings).
`int`	`getRotatableBondCount()` Returns the rotatable bond count.
`int`	`getShortestPath(int index1, int index2)` Calculates the shortest topological path (number of bonds) between two atoms.
`int[]`	`getSmallestRing()` Identifies the smallest ring (number of stoms) in the molecule.
`int`	`getSmallestRingSize()` Returns the smallest ring size.
`int`	`getSmallestRingSizeOfAtom(int index)` Returns the size of smallest ring containing the specified atom.
`int[]`	`getSmallestRingSystem()` Identifies the smallest ring system (number of rings) in the molecule.
`int`	`getSmallestRingSystemSize()` Returns the size of the smallest ring system (number of rings) in the molecule.
`java.lang.String`	`getStereo(int a)` Calculates absolute stereo configuration of the given atom.
`java.lang.String`	`getStereo(int a1, int a2)` Calculates absolute stereo configuration of the given double bond.
`int`	`getStereoDoubleBondCount()` Calculates the number of stereo double bonds.
`double`	`getStericEffectIndex(int index)` Calculates topological steric effect index (TSEI) of an atom from covalent radii values and topological distances.
`int`	`getSzegedIndex()` Calculates the Szeged index of the molecule.
`java.lang.String`	`getTypeString(java.lang.Object type)` Returns a string representation of the given type.
`int`	`getWienerIndex()` Calculates the Wiener index of the molecule, which is the average topological atom distance (half of the sumof all atom distances) in the molecule.
`int`	`getWienerPolarity()` Calculates the Wiener polarity number of the molecule, which is the number of 3 bond length distances in the molecule.
`boolean`	`handlesMultiFragmentMolecules()` Returns `true` if the plugin handles multifragment molecules, `false` otherwise.
`boolean`	`isAliphaticAtom(int index)` Returns `true` if aliphatic atom.
`boolean`	`isAromaticAtom(int index)` Returns `true` if aromatic atom.
`boolean`	`isAsymmetricAtom(int index)` Returns `true` if asymmetric atom.
`boolean`	`isChainAtom(int index)` Returns `true` if chain atom.
`boolean`	`isChainBond(int index)` Determines if a bond is a ring bond or a chain bond.
`boolean`	`isChiralCenter(int index)` Determines if an atom can be a tetrahedral stereogenic center.
`boolean`	`isConnected(int index1, int index2)` Returns `true` if two atoms are in the same connected component, `false` for atoms of disconnected structures.
`boolean`	`isConnectedGraph()` Determines if the molecule is a connected graph or not.
`boolean`	`isRingAtom(int index)` Returns `true` if ring atom.
`boolean`	`isRingBond(int index)` Determines if a bond is a ring bond or a chain bond.
`boolean`	`isRotatableBond(int index)` Determines if a bond is a rotatable or not
`boolean`	`run()` Runs the tool.
`void`	`setAromatizationMethod(int aromatizationMethod)` Sets the aromatization method.
`protected void`	`setInputMolecule(Molecule mol)` Sets the input molecule.
`void`	`setLicenseEnvironment(java.lang.String env)` Sets license environment to be stored.
`void`	`setParameters(java.util.Properties params)` Sets the input parameters for the plugin.
`void`	`standardize(Molecule mol)` Expands sgroups.

Methods inherited from class chemaxon.marvin.plugin.CalculatorPlugin
arrangeHydrogenIncerments, canRepeat, checkLicense, checkType, containsCoordinateBond, containsMulticenterSgroup, containsPseudoAtom, containsSRUSgroup, create, createModifiedInputMolecule, createStandardizedMolecule, createStandardizedMolecule, dehydrogenize, format, format, format, format, getAtomCount, getAtomIndex, getAtomIndexMap, getCalcMolecule, getDisplayMolecule, getDocument, getDoublePrecision, getErrorMessage, getExplicitHydrogenData, getInputMolDim, getMainMolecule, getOriginalMolecule, getpH, getPluginResource, getQueryMoleculeErrorMessage, getResult, getResult, getResultAsRGB, getResultAsRGB, getResultAsString, getResultCount, getResultDomain, getResultMessage, getResultsAsRGB, getResultsAsRGB, getResultsAsString, getResultsAsString, getResultSource, getWarningMessage, isInputMoleculeAromatized, isLicensed, isMsCalc, isMultiThreadedRunEnabled, isNegligibleResult, isOK, isRgrouped, loadClass, readAttribute, removeWhitespace, restoreExplicitHydrogens, setAtomIndexMap, setDoublePrecision, setDoublePrecision, setDoublePrecision, setKeepHydrogens, setMolecule, setMolecule, setMolecule, setMolecule, setProgressMonitor, standardizeIonicGroups, standardizeNeutralGroups

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - TopologyAnalyserPlugin
```
public TopologyAnalyserPlugin()
```
    Constructor. Creates the topology analyser object.
- Method Detail
  - setLicenseEnvironment
```
public void setLicenseEnvironment(java.lang.String env)
```
    Description copied from class: CalculatorPlugin
    
    Sets license environment to be stored.
    
    Specified by:
    
    setLicenseEnvironment in interface chemaxon.license.Licensable
    
    Overrides:
    
    setLicenseEnvironment in class CalculatorPlugin
    
    Parameters:
    
    env - environment String to be stored and passed to the LicenseHandler in the isLicensed method
  - getProductName
```
public java.lang.String getProductName()
```
    Returns the product identifier of the plugin as given by LicenseManager.
    
    Specified by:
    
    getProductName in class CalculatorPlugin
    
    Returns:
    
    The identifier LicenseManager.GEOMETRY_PLUGIN_GROUP
  - setParameters
```
public void setParameters(java.util.Properties params)
                   throws PluginException
```
    Sets the input parameters for the plugin. Parameters:
    - single: "true" if single fragment mode (calculation is performed separately for each fragment) (default: "false")
    - type: result types, separated by ',', possible values:
      See TopologyAnalyserPlugin class header (data types). (default: all molecular types)
    - atoms: <atom1-atom2> valid for type="shortestPath" and bond-type calculations only, sets the atom pair, used by cxcalc, for internal use only; API usage: call getShortestPath(int,int) instead.
    Overrides:
    
    setParameters in class CalculatorPlugin
    
    Parameters:
    
    params - is the parameter table
    
    Throws:
    
    PluginException - on error
    
    See Also:
    
    class header
  - handlesMultiFragmentMolecules
```
public boolean handlesMultiFragmentMolecules()
```
    Returns true if the plugin handles multifragment molecules, false otherwise. In the latter case the plugin takes the fragment with more atoms if a multifragment molecule is given as input. Returns true if parameter "single" is set to "false", false otherwise (default: false).
    
    Overrides:
    
    handlesMultiFragmentMolecules in class CalculatorPlugin
    
    Returns:
    
    true if the plugin handles multifragment molecules, false otherwise
  - checkMolecule
```
public void checkMolecule(Molecule mol)
                   throws PluginException
```
    Checks the input molecule. Throws exception if the molecule is RxnMolecule or if the molecule contains R-groups.
    
    Overrides:
    
    checkMolecule in class CalculatorPlugin
    
    Parameters:
    
    mol - is the input molecule
    
    Throws:
    
    PluginException - with error message for the user if the molecule is refused
  - setInputMolecule
```
protected void setInputMolecule(Molecule mol)
                         throws PluginException
```
    Sets the input molecule.
    
    Specified by:
    
    setInputMolecule in class CalculatorPlugin
    
    Parameters:
    
    mol - is the input molecule
    
    Throws:
    
    PluginException - on error
  - getLargestConjugatedSystem
```
public int[] getLargestConjugatedSystem()
```
    Returns the largest conjugated system in the molecule.
    
    Returns:
    
    atom indexes of the largest conjugated system in the molecule
    
    Since:
    
    version 17.1.9
  - getLargestConjugatedSystemSize
```
public int getLargestConjugatedSystemSize()
```
    Returns the largest conjugated system size (number of pi electron pairs).
    
    Returns:
    
    the largest conjugated system size
    
    Since:
    
    version 17.1.9
  - getColoredLargestConjugatedSystem
```
public Molecule getColoredLargestConjugatedSystem()
```
    Returns a Molecule in which the atoms of largest conjugated system are colored.
    
    Returns:
    
    a molecule with colored atoms
    
    Since:
    
    version 17.1.23
  - getAllAtomCount
```
public int getAllAtomCount()
```
    Returns the atom count.
    
    Returns:
    
    the atom count
  - getAliphaticAtomCount
```
public int getAliphaticAtomCount()
```
    Returns the aliphatic atom count.
    
    Returns:
    
    the aliphatic atom count
  - getAromaticAtomCount
```
public int getAromaticAtomCount()
```
    Returns the aromatic atom count.
    
    Returns:
    
    the aromatic atom count
  - getBondCount
```
public int getBondCount()
```
    Returns the bond count.
    
    Returns:
    
    the bond count
  - getAliphaticBondCount
```
public int getAliphaticBondCount()
```
    Returns the aliphatic bond count.
    
    Returns:
    
    the aliphatic bond count
  - getAromaticBondCount
```
public int getAromaticBondCount()
```
    Returns the aromatic bond count.
    
    Returns:
    
    the aromatic bond count
  - getFragmentCount
```
public int getFragmentCount()
```
    Returns the number of fragments (disconnected parts) of the molecule.
    
    Returns:
    
    number of fragments in the molecule
    
    Since:
    
    Marvin 5.1
  - getFsp3
```
public double getFsp3()
```
    Calculates the Fsp3 value of the given molecule.
    Fsp3 = number of sp3 carbons / number of carbons
    
    Returns:
    
    the fsp3 value of the given molecule or Double.NaN if there is no carbon in the structure.
  - getRingCount
```
public int getRingCount()
```
    Returns the ring count.
    
    Returns:
    
    the ring count
  - getAliphaticRingCount
```
public int getAliphaticRingCount()
```
    Returns the aliphatic ring count.
    
    Returns:
    
    the aliphatic ring count
  - getAliphaticRingCount
```
public int getAliphaticRingCount(int size)
```
    Returns the number of aliphatic rings (SSSR smallest set of smallest rings) of a given size in the molecule.
    
    Parameters:
    
    size - size of the ring to count
    
    Returns:
    
    number of aliphatic rings with the specified size in the molecule
    
    Since:
    
    Marvin 5.2
  - getAliphaticRingCountOfSize
```
@Deprecated
public int getAliphaticRingCountOfSize(int size)
```
    Deprecated. Use getAliphaticRingCount(int)
    
    Returns the number of aliphatic rings (SSSR smallest set of smallest rings) of a given size in the molecule.
    
    Parameters:
    
    size - size of the ring to count
    
    Returns:
    
    number of aliphatic rings with the specified size in the molecule
    
    Since:
    
    Marvin 5.1
  - getAliphaticRings
```
public int[][] getAliphaticRings()
```
    Identifies the aliphatic rings in the molecule.
    
    Returns:
    
    aliphatic rings of the molecule (null if the molecule does not contain aliphatic rings)
    
    Since:
    
    version 5.2
  - getAliphaticRings
```
public int[][] getAliphaticRings(int size)
```
    Indentifies aliphatic rings in the molecule having a given size (number of atoms).
    
    Parameters:
    
    size - size of the aliphatic rings to return
    
    Returns:
    
    aliphatic rings in the molecule having the given size (null if the molecule does not contain aliphatic rings)
    
    Since:
    
    version 5.2
  - getAromaticRingCount
```
public int getAromaticRingCount()
```
    Returns the aromatic ring count.
    
    Returns:
    
    the aromatic ring count
  - getAromaticRingCount
```
public int getAromaticRingCount(int size)
```
    Returns the number of aromatic rings (SSSR smallest set of smallest rings) of a given size in the molecule.
    
    Parameters:
    
    size - size of the ring to count
    
    Returns:
    
    number of aromatic rings with the specified size in the molecule
    
    Since:
    
    Marvin 5.2
  - getAromaticRingCountOfSize
```
@Deprecated
public int getAromaticRingCountOfSize(int size)
```
    Deprecated. Use getAromaticRingCount(int)
    
    Returns the number of aromatic rings (SSSR smallest set of smallest rings) of a given size in the molecule.
    
    Parameters:
    
    size - size of the ring to count
    
    Returns:
    
    number of aromatic rings with the specified size in the molecule
    
    Since:
    
    Marvin 5.1
  - getAromaticRings
```
public int[][] getAromaticRings()
```
    Identifies the aromatic rings in the molecule.
    
    Returns:
    
    aromatic rings of the molecule (null if the molecule is aliphatic)
    
    Since:
    
    version 5.2
  - getAromaticRings
```
public int[][] getAromaticRings(int size)
```
    Indentifies aromatic rings in the molecule having a given size (number of rings).
    
    Parameters:
    
    size - size of the aromatic rings to return
    
    Returns:
    
    aromatic rings in the molecule having the given size (null if the molecule is aliphatic or contains different sized aromatic rings only)
    
    Since:
    
    version 5.2
  - getHeteroRingCount
```
public int getHeteroRingCount()
```
    Returns the hetero ring count.
    
    Returns:
    
    the hetero ring count
  - getHeteroRingCount
```
public int getHeteroRingCount(int size)
```
    Calculates the number of heterocyclic rings in the molecule (rings containing at least a non-carbon atom).
    
    Parameters:
    
    size - size of the rings to count
    
    Returns:
    
    number of heterocyclic rings
    
    Since:
    
    version 5.2
  - getHeteroRings
```
public int[][] getHeteroRings()
```
    Identifies heterocyclic rings in the molecule (rings containing at least a non-carbon atom).
    
    Returns:
    
    heterocyclic rings (null of no heterocyclic ring found in the molecule.
    
    Since:
    
    version 5.2
  - getHeteroRings
```
public int[][] getHeteroRings(int size)
```
    Indentifies hetero rings in the molecule having a given size (number of atoms).
    
    Parameters:
    
    size - size of the aliphatic rings to return
    
    Returns:
    
    aliphatic rings in the molecule having the given size (null if the molecule does not contain aliphatic rings)
    
    Since:
    
    version 5.2
  - getHeteroaliphaticRingCount
```
public int getHeteroaliphaticRingCount()
```
    Calculates the number of aliphatic heterocyclic rings in the molecule (aliphatic rings containing at least a non-carbon atom).
    
    Returns:
    
    number of heteroaliphatic rings
    
    Since:
    
    version 5.2
  - getHeteroaliphaticRingCount
```
public int getHeteroaliphaticRingCount(int size)
```
    Calculates the number of aliphatic heterocyclic rings in the molecule (aliphatic rings containing at least a non-carbon atom) having a given size (number of atoms).
    
    Parameters:
    
    size - size of the heteroaliphatc rings to count
    
    Returns:
    
    number of heteroaliphatic rings having the given size
    
    Since:
    
    version 5.2
  - getHeteroaliphaticRings
```
public int[][] getHeteroaliphaticRings()
```
    Identifies heteroaliphatic rings in the molecule (aliphatic rings containing at least a non-carbon atom).
    
    Returns:
    
    atom indexes of heteroaliphatic rings
    
    Since:
    
    version 5.2
  - getHeteroaliphaticRings
```
public int[][] getHeteroaliphaticRings(int size)
```
    Identifies heteroaliphatic rings in the molecule (aliphatic rings containing at least a non-carbon atom) having a given size (number of atoms).
    
    Parameters:
    
    size - size of the heteroaliphatic rings to count
    
    Returns:
    
    heteroaliphatic rings having the given size
    
    Since:
    
    version 5.2
  - getHeteroaromaticRingCount
```
public int getHeteroaromaticRingCount()
```
    Returns the heteroaromatic ring count.
    
    Returns:
    
    the heteroaromatic ring count
  - getHeteroaromaticRingCount
```
public int getHeteroaromaticRingCount(int size)
```
    Calculates the number of aromatic heterocyclic rings in the molecule (aromatic rings containing at least a non-carbon atom) having a given size (number of atoms).
    
    Parameters:
    
    size - size of the heteroaromatic rings to count
    
    Returns:
    
    number of heteroaromatic rings having the given size
    
    Since:
    
    version 5.2
  - getHeteroaromaticRings
```
public int[][] getHeteroaromaticRings()
```
    Identifies heteroaromatic rings in the molecule (aromatic rings containing at least a non-carbon atom).
    
    Returns:
    
    heteroaromatic rings
    
    Since:
    
    version 5.2
  - getHeteroaromaticRings
```
public int[][] getHeteroaromaticRings(int size)
```
    Identifies heteroaromatic rings in the molecule (aromatic rings containing at least a non-carbon atom) having a given size (number of atoms).
    
    Parameters:
    
    size - size of the heteroaromatic rings to count
    
    Returns:
    
    heteroaromatic rings having the given size
    
    Since:
    
    version 5.2
  - getCarboRingCount
```
public int getCarboRingCount()
```
    Returns the carbo ring count.
    
    Returns:
    
    the carbo ring count
  - getCarboRingCount
```
public int getCarboRingCount(int size)
```
    Calculates the number of carbocyclic rings in the molecule (rings containing at least a non-carbon atom).
    
    Parameters:
    
    size - size of the rings to count
    
    Returns:
    
    number of carbocyclic rings with the given size
    
    Since:
    
    version 5.2
  - getCarboRings
```
public int[][] getCarboRings()
```
    Identifies carbocyclic rings in the molecule (rings containing carbon atoms only).
    
    Returns:
    
    carbocyclic rings (null if no carbocyclic ring found in the molecule.
    
    Since:
    
    version 5.2
  - getCarboRings
```
public int[][] getCarboRings(int size)
```
    Identifies carbocyclic rings in the molecule (rings containing carbon atoms only) having the given number of atoms.
    
    Parameters:
    
    size - size of the rings to count
    
    Returns:
    
    carbocyclic rings with the given size (null if no carbocyclic ring found in the molecule.
    
    Since:
    
    version 5.2
  - getCarboaliphaticRingCount
```
public int getCarboaliphaticRingCount()
```
    Calculates the number of carboaliphatic rings in the molecule (aliphatic rings containing carbon atoms only).
    
    Returns:
    
    number of carboaliphatic rings
  - getCarboaromaticRingCount
```
public int getCarboaromaticRingCount()
```
    Calculates the number of carboaromatic rings in the molecule (aromatic rings containing carbon atoms only).
    
    Returns:
    
    number of carboaromatic rings
  - getRingAtomCount
```
public int getRingAtomCount()
```
    Returns the ring atom count.
    
    Returns:
    
    the ring atom count
  - getRingBondCount
```
public int getRingBondCount()
```
    Returns the ring bond count.
    
    Returns:
    
    the ring bond count
  - getChainAtomCount
```
public int getChainAtomCount()
```
    Returns the chain atom count.
    
    Returns:
    
    the chain atom count
  - getChainBondCount
```
public int getChainBondCount()
```
    Returns the chain bond count.
    
    Returns:
    
    the chain bond count
  - getRotatableBondCount
```
public int getRotatableBondCount()
```
    Returns the rotatable bond count.
    
    Returns:
    
    the rotatable bond count
  - getSmallestRingSize
```
public int getSmallestRingSize()
```
    Returns the smallest ring size.
    
    Returns:
    
    the smallest ring size
  - getLargestRingSize
```
public int getLargestRingSize()
```
    Returns the largest ring size.
    
    Returns:
    
    the largest ring size
  - getFusedRingCount
```
public int getFusedRingCount()
```
    Calculates the number of fused rings (SSSR smallest set of smallest rings) in the molecule.
    
    Returns:
    
    number of fused rings in the molecule
  - getFusedAliphaticRingCount
```
public int getFusedAliphaticRingCount()
```
    Calculates the number of fused aliphatic rings (SSSR smallest set of smallest aliphatic rings) in the molecule.
    
    Returns:
    
    number of fused aliphatic rings in the molecule
  - getFusedAliphaticRingCount
```
public int getFusedAliphaticRingCount(int size)
```
    Calculates the number of fused aliphatic rings in the molecule (rings s).
    
    Parameters:
    
    size - size of the fused aliphatic rings to count
    
    Returns:
    
    number of fused aliphatic rings having the given size
    
    Since:
    
    version 5.2
  - getFusedAliphaticRings
```
public int[][] getFusedAliphaticRings()
```
    Identifies fused aliphatic rings (SSSR smallest set of smallest aliphatic rings) in the molecule.
    
    Returns:
    
    atom indexes of the fused aliphatic rings in the molecule
    
    Since:
    
    version 5.2
  - getFusedAliphaticRings
```
public int[][] getFusedAliphaticRings(int size)
```
    Identifies fused aliphatic rings (SSSR smallest set of smallest aliphatic rings) in the molecule having the given size (number of atoms).
    
    Parameters:
    
    size - size of the fused aliphatic rings to count
    
    Returns:
    
    atom indexes of the fused aliphatic rings in the molecule having the given number of atoms
    
    Since:
    
    version 5.2
  - getFusedAromaticRingCount
```
public int getFusedAromaticRingCount()
```
    Calculates the number of fused aromatic rings (SSSR smallest set of smallest aromatic rings) in the molecule.
    
    Returns:
    
    number of fused aromatic rings in the molecule
  - getFusedAromaticRingCount
```
public int getFusedAromaticRingCount(int size)
```
    Calculates the number of fused aromatic rings in the molecule (rings s).
    
    Parameters:
    
    size - size of the fused aromatic rings to count
    
    Returns:
    
    number of fused aromatic rings having the given size
    
    Since:
    
    version 5.2
  - getFusedAromaticRings
```
public int[][] getFusedAromaticRings()
```
    Identifies fused aromatic rings (SSSR smallest set of smallest aromatic rings) in the molecule.
    
    Returns:
    
    atom indexes of the fused aromatic rings in the molecule
    
    Since:
    
    version 5.2
  - getFusedAromaticRings
```
public int[][] getFusedAromaticRings(int size)
```
    Identifies fused aromatic rings (SSSR smallest set of smallest aromatic rings) in the molecule having the given size (number of atoms).
    
    Parameters:
    
    size - size of the fused aromatic rings to count
    
    Returns:
    
    atom indexes of the fused aromatic rings in the molecule
    
    Since:
    
    version 5.2
  - getRingSystemCount
```
public int getRingSystemCount()
```
    Returns the number of ring systems. Fused and spiro rings belong to to one ring system.
    
    Returns:
    
    number of ring systems in the molecule
    
    Since:
    
    Marvin 5.1
  - getRingSystemCount
```
public int getRingSystemCount(int size)
```
    Returns the number of ring systems having a given size (number of rings) in the molecule.
    
    Parameters:
    
    size - size of the ring to count
    
    Returns:
    
    number of ring systems with the specified size in the molecule
    
    Since:
    
    Marvin 5.2
  - getRingSystemCountOfSize
```
@Deprecated
public int getRingSystemCountOfSize(int size)
```
    Deprecated. Use getRingSystemCount(int)
    
    Returns the number of ring systems having a given size (number of rings) in the molecule.
    
    Parameters:
    
    size - size of the ring to count
    
    Returns:
    
    number of ring systems with the specified size in the molecule
    
    Since:
    
    Marvin 5.1
  - getLargestRing
```
public int[] getLargestRing()
```
    Identifies the atoms of the largest ring (number of atoms) in the molecule.
    
    Returns:
    
    atom indexes of the largest ring in the molecule (null when acyclic)
    
    Since:
    
    version 5.2
  - getLargestRingSystem
```
public int[] getLargestRingSystem()
```
    Identifies the atoms of the largest ring system (number of rings) in the molecule.
    
    Returns:
    
    atom indexes of the largest ring system in the molecule (null when acyclic)
    
    Since:
    
    version 5.2
  - getLargestRingSystemSize
```
public int getLargestRingSystemSize()
```
    Returns the size of the largest ring system (number of rings) in the molecule.
    
    Returns:
    
    size of the largest ring system in the molecule (0 when acylcic)
    
    Since:
    
    Marvin 5.1
  - getSmallestRingSystemSize
```
public int getSmallestRingSystemSize()
```
    Returns the size of the smallest ring system (number of rings) in the molecule.
    
    Returns:
    
    size of the smallest ring system in the molecule (0 when acylcic)
    
    Since:
    
    Marvin 5.1
  - isAromaticAtom
```
public boolean isAromaticAtom(int index)
```
    Returns true if aromatic atom.
    
    Parameters:
    
    index - is the atom index
    
    Returns:
    
    true if aromatic atom
  - isAliphaticAtom
```
public boolean isAliphaticAtom(int index)
```
    Returns true if aliphatic atom.
    
    Parameters:
    
    index - is the atom index
    
    Returns:
    
    true if aliphatic atom
  - isChainAtom
```
public boolean isChainAtom(int index)
```
    Returns true if chain atom.
    
    Parameters:
    
    index - is the atom index
    
    Returns:
    
    true if chain atom
  - isRingAtom
```
public boolean isRingAtom(int index)
```
    Returns true if ring atom.
    
    Parameters:
    
    index - is the atom index
    
    Returns:
    
    true if ring atom
  - getSmallestRingSizeOfAtom
```
public int getSmallestRingSizeOfAtom(int index)
```
    Returns the size of smallest ring containing the specified atom.
    
    Parameters:
    
    index - is the atom index
    
    Returns:
    
    the size of smallest ring containing the specified atom
  - getLargestRingSizeOfAtom
```
public int getLargestRingSizeOfAtom(int index)
```
    Returns the size of largest ring containing the specified atom.
    
    Parameters:
    
    index - is the atom index
    
    Returns:
    
    the size of largest ring containing the specified atom
  - getCyclomaticNumber
```
public int getCyclomaticNumber()
```
    Calculates the smallest number of graph edges which must be removed such that no circuit remains. Also known as circuit rank.
    
    Returns:
    
    cyclomatic number of the molecule
  - getAsymmetricAtomCount
```
public int getAsymmetricAtomCount()
```
    Returns the number of asymmetric atoms.
    
    Returns:
    
    the number of asymmetric atoms
  - getAsymmetricAtoms
```
public int[] getAsymmetricAtoms()
```
    Determines the asymmetric atoms.
    
    Returns:
    
    indexes of asymmetric atoms
    
    Since:
    
    Marvin 5.3
  - isAsymmetricAtom
```
public boolean isAsymmetricAtom(int index)
```
    Returns true if asymmetric atom.
    
    Parameters:
    
    index - is the atom index
    
    Returns:
    
    true if asymmetric atom
  - getChiralCenterCount
```
public int getChiralCenterCount()
```
    Calculates the number of tetrahedral stereogenic centers. This function identifies two chiral centers in 1,4-dimethylcyclohexane, which does not contain asymmetric atoms.
    
    Returns:
    
    number of tetrahedral stereogenic center atoms
  - getChiralCenters
```
public int[] getChiralCenters()
```
    Determines the chiral center atoms.
    
    Returns:
    
    indexes of chiral center atoms
    
    Since:
    
    Marvin 5.3
  - isChiralCenter
```
public boolean isChiralCenter(int index)
```
    Determines if an atom can be a tetrahedral stereogenic center.
    
    Parameters:
    
    index - is the atom index
    
    Returns:
    
    true if the atom is stereogenic.
  - getStereo
```
public java.lang.String getStereo(int a)
```
    Calculates absolute stereo configuration of the given atom. Returns "R" or "S" correspondingly, if the atom is stereo, otherwise it returns an empty string,
    
    Parameters:
    
    a - index of the atom
    
    Returns:
    
    the absolute stereo configuration of the atom
    
    Since:
    
    Marvin 5.2.1
  - getStereo
```
public java.lang.String getStereo(int a1,
                                  int a2)
```
    Calculates absolute stereo configuration of the given double bond. Returns "E" or "Z" correspondingly, if the bond is a stereo double bond, otherwise it returns an empty string. Double bonds in small rings are not considered stereo bonds.
    
    Parameters:
    
    a1 - index of the atom at one end of the double bond
    
    a2 - index of the atom at the other end of the double bond
    
    Returns:
    
    the absolute stereo configuration of the atom
    
    Since:
    
    Marvin 5.2.1
  - getStereoDoubleBondCount
```
public int getStereoDoubleBondCount()
```
    Calculates the number of stereo double bonds.
    
    Returns:
    
    number of stereo double bonds atoms
    
    Since:
    
    Marvin 5.2.1
  - getShortestPath
```
public int getShortestPath(int index1,
                           int index2)
```
    Calculates the shortest topological path (number of bonds) between two atoms. It returns Integer.MAX_VALUE for atoms of disconnected structures.
    
    Parameters:
    
    index1 - is the index of the first atom
    
    index2 - is the index of the second atom
    
    Returns:
    
    the shortest path between two atoms
  - isConnected
```
public boolean isConnected(int index1,
                           int index2)
```
    Returns true if two atoms are in the same connected component, false for atoms of disconnected structures.
  - getPlattIndex
```
public int getPlattIndex()
```
    Calculates the Platt index of the molecule which is equal to the total sum of the edge degrees of a molecular graph.
    
    Returns:
    
    the Platt index
  - getRandicIndex
```
public double getRandicIndex()
```
    Calculates the Randic index or molecular connectivity index as the harmonic sum of the geometric means of the node degrees for each edge.
    
    Returns:
    
    the Randic index
  - getBalabanIndex
```
public double getBalabanIndex()
```
    Calculates the Balaban distance connectivity of the molecule, which is the average distance sum connectivity.
    
    Returns:
    
    the Balaban index (Integer.MAX_VALUE for disconnected graphs)
  - getDistanceDegree
```
public int getDistanceDegree(int index)
```
    Calculates the distance degree of an atom, which is the sum of the corresponding row values in the distance matrix.
    
    Parameters:
    
    index - atom index
    
    Returns:
    
    the distance degree of the atom (Integer.MAX_VALUE for disconnected graphs)
  - getEccentricity
```
public int getEccentricity(int index)
```
    Calculates the eccentricity of an atom, which is the greatest value in the corresponding row of the distance matrix.
    
    Parameters:
    
    index - atom index
    
    Returns:
    
    the eccentricity value of the atom (Integer.MAX_VALUE for disconnected graphs)
  - getHararyIndex
```
public double getHararyIndex()
```
    Calculates the Harary index which is the half-sum of the off-diagonal elements of the reciprocal molecular distance matrix of the molecule.
    
    Returns:
    
    the Harary index (Integer.MAX_VALUE for disconnected graphs)
  - getHyperWienerIndex
```
public int getHyperWienerIndex()
```
    Calculates the hyper Wiener index of the molecule.
    
    Returns:
    
    the hyper Wiener index (Integer.MAX_VALUE for disconnected graphs)
  - getSzegedIndex
```
public int getSzegedIndex()
```
    Calculates the Szeged index of the molecule. The Szeged index is based on the Wiener number, which is calculated by simply counting the number of nodes on both sides of each edge (and sum these counts). The Szeged index extends the Wiener number for cyclic graphs by counting those nodes only which are nearer to the given side of the edge than to the other. Unreachable nodes (disconnected graphs) or those at equidistance position to both sides of the given edge are not taken into account.
    
    Returns:
    
    the Szeged index
  - getWienerIndex
```
public int getWienerIndex()
```
    Calculates the Wiener index of the molecule, which is the average topological atom distance (half of the sumof all atom distances) in the molecule.
    
    Returns:
    
    the Wiener index (Integer.MAX_VALUE for disconnected graphs)
  - getWienerPolarity
```
public int getWienerPolarity()
```
    Calculates the Wiener polarity number of the molecule, which is the number of 3 bond length distances in the molecule.
    
    Returns:
    
    the Wiener polarity number
  - getStericEffectIndex
```
public double getStericEffectIndex(int index)
```
    Calculates topological steric effect index (TSEI) of an atom from covalent radii values and topological distances. The stericEffectIndex is related to the steric hindrance of the given atom.
    
    Parameters:
    
    index - atom index
    
    Returns:
    
    the topological steric effect index of the atom
  - getBondType
```
public int getBondType(int index)
```
    Determines the type of a bond (aromatic bonds are automatically recognized)
    
    Parameters:
    
    index - bond index
    
    Returns:
    
    bond type
  - getDistanceCount
```
public int getDistanceCount(int index,
                            int distance)
```
    Counts the given value in a row of the distance matrix.
    
    Parameters:
    
    index - atom index
    
    distance - the distance value to count
    
    Returns:
    
    the distance count of a value for the atom
  - isRingBond
```
public boolean isRingBond(int index)
```
    Determines if a bond is a ring bond or a chain bond.
    
    Parameters:
    
    index - bond index
    
    Returns:
    
    true if the bond is a ring bond, false if chain bond
  - isChainBond
```
public boolean isChainBond(int index)
```
    Determines if a bond is a ring bond or a chain bond.
    
    Parameters:
    
    index - bond index
    
    Returns:
    
    true if the bond is a chain bond, false if chain bond
  - isConnectedGraph
```
public boolean isConnectedGraph()
```
    Determines if the molecule is a connected graph or not. There is a path from any node to any other node in the graph.
    
    Returns:
    
    true if the graph is connected, false if the graph is disconnected.
  - isRotatableBond
```
public boolean isRotatableBond(int index)
```
    Determines if a bond is a rotatable or not
    
    Parameters:
    
    index - bond index
    
    Returns:
    
    true if the bond is a rotatable bond, false otherwise
  - getRingCountOfAtom
```
public int getRingCountOfAtom(int index)
```
    Calculates the number of rings (SSSR smallest set of smallest rings) an atom is part of.
    
    Parameters:
    
    index - atom index
    
    Returns:
    
    number of rings the atom is a member of
  - getRingCount
```
public int getRingCount(int size)
```
    Calculates the number of rings (SSSR smallest set of smallest rings) of a given size in the molecule.
    
    Parameters:
    
    size - size of the ring to count
    
    Returns:
    
    number of rings in the molecule
    
    Since:
    
    Marvin 5.2
  - getRingCountOfSize
```
@Deprecated
public int getRingCountOfSize(int size)
```
    Deprecated. Use getRingCount(int)
    
    Calculates the number of rings (SSSR smallest set of smallest rings) of a given size in the molecule.
    
    Parameters:
    
    size - size of the ring to count
    
    Returns:
    
    number of rings in the molecule
  - getRings
```
public int[][] getRings()
```
    Identifies the rings in the molecule.
    
    Returns:
    
    rings of the molecule (null if the molecule is acyclic)
    
    Since:
    
    version 5.2
  - getRings
```
public int[][] getRings(int size)
```
    Identifies rings in the molecule having a given size.
    
    Parameters:
    
    size - size of the ring systems to return
    
    Returns:
    
    rings of the molecule having the given size (null if the molecule is acyclic or contains different rings only)
    
    Since:
    
    version 5.2
  - getRingSystems
```
public int[][] getRingSystems()
```
    Identifies the ring systems in the molecule. Fused and spiro rings belong to one ring system.
    
    Returns:
    
    ring systems in the molecule (null if the molecule is acyclic)
    
    Since:
    
    version 5.2
  - getRingSystems
```
public int[][] getRingSystems(int size)
```
    Indentifies the ring systems in the molecule having a given size (number of rings). Fused and spiro rings belong to one ring system.
    
    Parameters:
    
    size - size of the ring systems to return
    
    Returns:
    
    ring systems in the molecule having the given size (null if the molecule is acyclic or contains different rings only)
    
    Since:
    
    version 5.2
  - getSmallestRing
```
public int[] getSmallestRing()
```
    Identifies the smallest ring (number of stoms) in the molecule.
    
    Returns:
    
    atom indexes of the smallest ring in the molecule (null when acyclic)
    
    Since:
    
    version 5.2
  - getSmallestRingSystem
```
public int[] getSmallestRingSystem()
```
    Identifies the smallest ring system (number of rings) in the molecule.
    
    Returns:
    
    atom indexes of the smallest ring system in the molecule (null when acyclic)
    
    Since:
    
    version 5.2
  - getBondIndex
```
public int getBondIndex(int i1,
                        int i2)
```
    Returns the index of the bond connecting two atoms, -1 if the two atoms are not connected by bond.
    
    Parameters:
    
    i1 - the first atom index
    
    i2 - the second atom index
    
    Returns:
    
    the connectiong bond index, -1 if there is no such bond
  - setAromatizationMethod
```
public void setAromatizationMethod(int aromatizationMethod)
```
    Sets the aromatization method.
    
    Parameters:
    
    aromatizationMethod -
    
    See Also:
    
    MoleculeGraph.AROM_GENERAL, MoleculeGraph.AROM_BASIC, MoleculeGraph.AROM_LOOSE
  - getResult
```
public java.lang.Object getResult(java.lang.Object type,
                                  int index)
                           throws PluginException
```
    Returns the result item for the specified key and index.
    
    Overrides:
    
    getResult in class CalculatorPlugin
    
    Parameters:
    
    type - is the result type
    
    index - is the result index
    
    Returns:
    
    the result item for the specified key and index
    
    Throws:
    
    PluginException - if the result cannot be returned
    
    See Also:
    
    CalculatorPlugin.getResultTypes()
  - getResult
```
public java.lang.Object getResult(java.lang.Object type,
                                  java.lang.String arg)
                           throws PluginException
```
    Returns the shortest path between two atoms if type is set ot "shortestPath", returns connectivity info if type is set to "connected". For internal use only.
    
    Overrides:
    
    getResult in class CalculatorPlugin
    
    Parameters:
    
    type - is the result type ("shortestPath" or "connected")
    
    arg - is the atom string as atom1-atom2 (e.g. "2-3")
    
    Returns:
    
    the shortest path
    
    Throws:
    
    PluginException - on error
    
    See Also:
    
    CalculatorPlugin.getResultTypes()
  - getResultAsString
```
public java.lang.String getResultAsString(java.lang.Object type,
                                          int index,
                                          java.lang.Object result)
                                   throws PluginException
```
    Returns the specified result in String format.
    
    Overrides:
    
    getResultAsString in class CalculatorPlugin
    
    Parameters:
    
    type - is the result type
    
    index - is the result index
    
    result - is the result item
    
    Returns:
    
    the specified result in String format
    
    Throws:
    
    PluginException - if an invalid result item is given
  - getResultCount
```
public int getResultCount(java.lang.Object type)
```
    Returns the number of result items for the given result key.
    
    Overrides:
    
    getResultCount in class CalculatorPlugin
    
    Parameters:
    
    type - is the result type
    
    Returns:
    
    the number of result items
    
    See Also:
    
    getResultTypes()
  - getResultDomain
```
public int getResultDomain(java.lang.Object type)
```
    Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.
    
    Overrides:
    
    getResultDomain in class CalculatorPlugin
    
    Parameters:
    
    type - is the result key
    
    Returns:
    
    the calculation domain
    
    See Also:
    
    getResultTypes()
  - getResultTypes
```
public java.lang.Object[] getResultTypes()
```
    Returns the result types. Possible result types: see TopologyAnalyserPlugin class header (data types).
    
    Overrides:
    
    getResultTypes in class CalculatorPlugin
    
    Returns:
    
    the result types
  - getTypeString
```
public java.lang.String getTypeString(java.lang.Object type)
```
    Returns a string representation of the given type.
    
    Overrides:
    
    getTypeString in class CalculatorPlugin
    
    Parameters:
    
    type - is the type object
    
    Returns:
    
    the type string
  - run
```
public boolean run()
            throws PluginException
```
    Runs the tool.
    
    Specified by:
    
    run in class CalculatorPlugin
    
    Returns:
    
    true if the calculation was successful, false on calculation problems
    
    Throws:
    
    PluginException - on error
    
    See Also:
    
    CalculatorPlugin.getErrorMessage()
  - getResultMolecule
```
public Molecule getResultMolecule()
                           throws PluginException
```
    Returns the result molecule for display. Atomic results are stored in atom extra labels (MolAtom.getExtraLabel()). Molecular results are stored in molecule properties with keys being the result types (Molecule.getProperty(String)).
    
    Overrides:
    
    getResultMolecule in class CalculatorPlugin
    
    Returns:
    
    the result molecule
    
    Throws:
    
    PluginException - on error
    
    Since:
    
    Marvin 4.0
  - getResultMolecules
```
public Molecule[] getResultMolecules()
                              throws PluginException
```
    Returns the result molecules, molecular results are set in the first molecule, atomic results are set in subsequent molecules as atom labels.
    
    Overrides:
    
    getResultMolecules in class CalculatorPlugin
    
    Returns:
    
    the result molecules
    
    Throws:
    
    PluginException - on error
  - getRemark
```
public java.lang.String getRemark()
```
    Returns the calculation remark: if no results (no result types) then returns remark, otherwise returns null.
    
    Overrides:
    
    getRemark in class CalculatorPlugin
    
    Returns:
    
    the calculation remark
  - standardize
```
public void standardize(Molecule mol)
```
    Expands sgroups.
    
    Overrides:
    
    standardize in class CalculatorPlugin
    
    Parameters:
    
    mol - is the molecule to be standardized

Class TopologyAnalyserPlugin

Nested Class Summary

Nested classes/interfaces inherited from class chemaxon.marvin.plugin.CalculatorPlugin

Field Summary

Fields inherited from class chemaxon.marvin.plugin.CalculatorPlugin

Constructor Summary

Method Summary

Methods inherited from class chemaxon.marvin.plugin.CalculatorPlugin

Methods inherited from class java.lang.Object

Constructor Detail

TopologyAnalyserPlugin

Method Detail

setLicenseEnvironment

getProductName

setParameters

handlesMultiFragmentMolecules

checkMolecule

setInputMolecule

getLargestConjugatedSystem

getLargestConjugatedSystemSize

getColoredLargestConjugatedSystem

getAllAtomCount

getAliphaticAtomCount

getAromaticAtomCount

getBondCount

getAliphaticBondCount

getAromaticBondCount

getFragmentCount

getFsp3

getRingCount

getAliphaticRingCount

getAliphaticRingCount

getAliphaticRingCountOfSize

getAliphaticRings

getAliphaticRings

getAromaticRingCount

getAromaticRingCount

getAromaticRingCountOfSize

getAromaticRings

getAromaticRings

getHeteroRingCount

getHeteroRingCount

getHeteroRings

getHeteroRings

getHeteroaliphaticRingCount

getHeteroaliphaticRingCount

getHeteroaliphaticRings

getHeteroaliphaticRings

getHeteroaromaticRingCount

getHeteroaromaticRingCount

getHeteroaromaticRings

getHeteroaromaticRings

getCarboRingCount

getCarboRingCount

getCarboRings

getCarboRings

getCarboaliphaticRingCount

getCarboaromaticRingCount

getRingAtomCount

getRingBondCount

getChainAtomCount

getChainBondCount

getRotatableBondCount

getSmallestRingSize

getLargestRingSize

getFusedRingCount

getFusedAliphaticRingCount

getFusedAliphaticRingCount

getFusedAliphaticRings

getFusedAliphaticRings

getFusedAromaticRingCount

getFusedAromaticRingCount

getFusedAromaticRings

getFusedAromaticRings

getRingSystemCount

getRingSystemCount

getRingSystemCountOfSize

getLargestRing

getLargestRingSystem

getLargestRingSystemSize