chemaxon.marvin.calculations
Class TopologyAnalyserPlugin

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

All Implemented Interfaces:

chemaxon.license.Licensable

public class TopologyAnalyserPlugin
extends CalculatorPlugin

Calculates topological data. Data types:

• "atomCount"
• "aliphaticAtomCount"
• "aromaticAtomCount"
• "bondCount"
• "aliphaticBondCount"
• "aromaticBondCount"
• "fragmentCount",
• "ringCount"
• "ringAtomCount"
• "chainAtomCount"
• "ringBondCount"
• "chainBondCount"
• "aliphaticRingCount"
• "aliphaticRingCountOfSize" (API/cxcalc only, number of aliphatic rings of given size)
• "aromaticRingCount"
• "aromaticRingCountOfSize" (API/cxcalc only, number of aromatic rings of given size)
• "heteroRingCount"
• "heteroaromaticRingCount"
• "carboRingCount"
• "carboaromaticRingCount"
• "smallestRingSize"
• "largestRingSize"
• "rotatableBondCount"
• "fusedRingCount"
• "fusedAliphaticRingCount"
• "fusedAromaticRingCount"
• "ringSystemCount",
• "ringSystemCountOfSize",(API/cxcalc only, number of rings system of given size)
• "largestRingSystemSize",
• "smallestRingsyStemSize",
• "asymmetricAtomCount"
• "chiralCenterCount"
• "cyclomaticNumber"
• "plattIndex"
• "randicIndex"
• "balabanIndex"
• "distanceDegree" (atomic)
• "eccentricity" (atomic)
• "hararyIndex"
• "hyperWienerIndex"
• "szegedIndex"
• "wienerIndex"
• "wienerPolarity"
• "stericEffectIndex" (atomic)
• "aromaticAtom" (API/cxcalc only, atomic boolean property)
• "aliphaticAtom" (API/cxcalc only, atomic boolean property)
• "chainAtom" (API/cxcalc only, atomic boolean property)
• "ringAtom" (API/cxcalc only, atomic boolean property)
• "asymmetricAtom" (API/cxcalc only, atomic boolean property)
• "chiralCenter" (API/cxcalc only, atomic boolean property)
• "largestAtomRingSize" (API/cxcalc only, atomic, size of largest ring containing atom)
• "smallestAtomRingSize" (API/cxcalc only, atomic, size of smallest ring containing atom)
• "shortestPath" (API/cxcalc only, size of shortest path between two atoms)
• "connected" (API/cxcalc only, true if two atoms are connected)
• "connectedGraph" (API/cxcalc only, true if the molecule graph is connected)
• "bondType" (API/cxcalc only, the bond type)
• "distanceCount" (API only, number of atoms at given distance from a given atom)
• "chainBond" (API/cxcalc only, bond boolean property)
• "ringBond" (API/cxcalc only, bond boolean property)
• "rotatableBond" (API/cxcalc only, bond boolean property)
• "ringCountOfSize" (API only, number of rings of given size)
• "ringCountOfAtom" (API/cxcalc only, number of rings of given atom)

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 5.1, 06/02/2008

Author:

Nora Mate, Zsolt Mohacsi

Field Summary

Fields inherited from class chemaxon.marvin.plugin.CalculatorPlugin

ATOM, BLUE, CALCRGB_OFF, COVALENT_HYDRATION_ERROR_REMARK, CRITICAL_ERROR_MSG, EPSILON, INCORRECT_AROMATIC_NITROGEN_REMARK, INSTABLE_TAUTOMERIC_FORM_REMARK, licenseEnvironment, MOLECULE, NAN, PLUGIN_CLASS_KEY, PLUGIN_DIR, RED

Constructor Summary

TopologyAnalyserPlugin()
Constructor.

Method Summary

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	getAliphaticRingCountOfSize(int size) Returns the number of aliphatic rings (SSSR smallest set of smallest rings) of a given size in the molecule.
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	getAromaticRingCountOfSize(int size) Returns the number of aromatic rings (SSSR smallest set of smallest rings) of a given size in the molecule.
int	getAsymmetricAtomCount() Returns the number of 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	getCarboaromaticRingCount() Returns the carboaromatic ring count.
int	getCarboRingCount() Returns the carbo ring count.
int	getChainAtomCount() Returns the chain atom count.
int	getChainBondCount() Returns the chain bond count.
int	getChiralCenterCount() Calculates the number of tetrahedral stereogenic centers.
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.
int	getFusedAliphaticRingCount() Calculates the number of fused aliphatic rings (SSSR smallest set of smallest aliphatic rings) in the molecule.
int	getFusedAromaticRingCount() Calculates the number of fused aromatic rings (SSSR smallest set of smallest aromatic rings) in the molecule.
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	getHeteroaromaticRingCount() Returns the heteroaromatic ring count.
int	getHeteroRingCount() Returns the hetero ring count.
int	getHyperWienerIndex() Calculates the hyper Wiener index of the molecule.
int	getLargestRingSize() Returns the largest ring size.
int	getLargestRingSizeOfAtom(int index) Returns the size of largest ring containing the specified atom.
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.
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	getRingCountOfAtom(int index) Calculates the number of rings (SSSR smallest set of smallest rings) an atom is part of.
int	getRingCountOfSize(int size) Calculates the number of rings (SSSR smallest set of smallest rings) of a given size in the molecule.
int	getRingSystemCount() Returns the number of ring systems.
int	getRingSystemCountOfSize(int size) Returns the number of ring systems having a given size (number of rings) in the molecule.
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	getSmallestRingSize() Returns the smallest ring size.
int	getSmallestRingSizeOfAtom(int index) Returns the size of smallest ring containing the specified atom.
int	getSmallestRingSystemSize() Returns the size of the smallest ring system (number of rings) in the molecule.
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	isLicensed() Returns true if the plugin is licensed.
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.
protected void	setInputMolecule(Molecule mol) Sets the input molecule.
void	setParameters(java.util.Properties params) Sets the input parameters for the plugin.
void	standardize(Molecule mol) Prevents default standardization: does nothing.

Methods inherited from class chemaxon.marvin.plugin.CalculatorPlugin

checkType, containsCoordinateBond, containsMulticenterSgroup, containsPseudoAtom, containsSRUSgroup, create, createModifiedInputMolecule, createStandardizedMolecule, createStandardizedMolecule, dehydrogenize, format, format, format, format, getAtomCount, getAtomIndex, getCalcMolecule, getDisplayMolecule, getDocument, getDoublePrecision, getErrorMessage, getInputMolDim, getMainMolecule, getpH, getPluginResource, getResult, getResult, getResultAsRGB, getResultAsRGB, getResultAsString, getResultCount, getResultDomain, getResultMessage, getResultsAsRGB, getResultsAsRGB, getResultsAsString, getResultsAsString, getResultSource, getWarningMessage, isInputMoleculeAromatized, isMsCalc, isMultiThreadedRunEnabled, isNegligibleResult, isOK, isRgrouped, loadClass, readAttribute, removeWhitespace, setDoublePrecision, setDoublePrecision, setDoublePrecision, setLicenseEnvironment, 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

isLicensed

public boolean isLicensed()

Description copied from class: CalculatorPlugin

Returns true if the plugin is licensed. Implement this only if you want to sell your plugin and protect it with a license key. The default implementation always returns true which means that the plugin is free: no license key is required. This method returns only information about the licensing, license checking has to be implemented separately.

Specified by:

isLicensed in interface chemaxon.license.Licensable

Overrides:

isLicensed in class CalculatorPlugin

Returns:

true if the plugin is licensed

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:
  • "atomCount"
  • "aliphaticAtomCount"
  • "aromaticAtomCount"
  • "bondCount"
  • "aliphaticBondCount"
  • "aromaticBondCount"
  • "rotatableBondCount"
  • "fragmentCount",
  • "ringCount"
  • "aliphaticRingCount"
  • "aliphaticRingCountOfSize" (number of aliphatic rings of given size)
  • "aromaticRingCount"
  • "aromaticRingCountOfSize" (number of aromatic rings of given size)
  • "heteroRingCount"
  • "heteroaromaticRingCount"
  • "carboRingCount"
  • "carboaromaticRingCount"
  • "ringAtomCount"
  • "ringBondCount"
  • "chainAtomCount"
  • "chainBondCount"
  • "smallestRingSize"
  • "largestRingSize"
  • "fusedRingCount"
  • "fusedAliphaticRingCount"
  • "fusedAromaticRingCount"
  • "ringSystemCount",
  • "ringSystemCountOfSize",(number of rings system of given size)
  • "largestRingSystemSize",
  • "smallestRingsyStemSize",
  • "asymmetricAtomCount"
  • "chiralCenterCount"
  • "cyclomaticNumber"
  • "plattIndex"
  • "randicIndex"
  • "balabanIndex"
  • "distanceDegree" (atomic)
  • "eccentricity" (atomic)
  • "hararyIndex"
  • "hyperWienerIndex"
  • "szegedIndex"
  • "wienerIndex"
  • "wienerPolarity"
  • "stericEffectIndex" (atomic)
  • "aromaticAtom" (API/cxcalc only, atomic boolean property)
  • "aliphaticAtom" (API/cxcalc only, atomic boolean property)
  • "chainAtom" (API/cxcalc only, atomic boolean property)
  • "ringAtom" (API/cxcalc only, atomic boolean property)
  • "asymmetricAtom" (API/cxcalc only, atomic boolean property)
  • "chiralCenter" (API/cxcalc only, atomic boolean property)
  • "largestAtomRingSize" (API/cxcalc only, atomic, size of largest ring containing atom)
  • "smallestAtomRingSize" (API/cxcalc only, atomic, size of smallest ring containing atom)
  • "shortestPath" (API/cxcalc only, size of shortest path between two atoms)
  • "connected" (API/cxcalc only, true if two atoms are connected)
  • "connectedGraph" (API/cxcalc only, true if the molecule graph is connected)
  • "bondType" (API/cxcalc only, the bond type)
  • "distanceCount" (API only, number of atoms at given distance from a given atom)
  • "chainBond" (API/cxcalc only, bond boolean property)
  • "ringBond" (API/cxcalc only, bond boolean property)
  • "rotatableBond" (API/cxcalc only, bond boolean property)
  • "ringCountOfSize" (number of rings of given size)
  • "ringCountOfAtom" (API/cxcalc only, number of rings of given atom)
  (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

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

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

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

getAliphaticRingCountOfSize

public int getAliphaticRingCountOfSize(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 5.1

getAromaticRingCount

public int getAromaticRingCount()

Returns the aromatic ring count.

Returns:

the aromatic ring count

getAromaticRingCountOfSize

public int getAromaticRingCountOfSize(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 5.1

getHeteroRingCount

public int getHeteroRingCount()

Returns the hetero ring count.

Returns:

the hetero ring count

getHeteroaromaticRingCount

public int getHeteroaromaticRingCount()

Returns the heteroaromatic ring count.

Returns:

the heteroaromatic ring count

getCarboRingCount

public int getCarboRingCount()

Returns the carbo ring count.

Returns:

the carbo ring count

getCarboaromaticRingCount

public int getCarboaromaticRingCount()

Returns the carboaromatic ring count.

Returns:

the carboaromatic ring count

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

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

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

getRingSystemCountOfSize

public int getRingSystemCountOfSize(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 5.1

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

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

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.

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

getRingCountOfSize

public int getRingCountOfSize(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

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

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:

• "atomCount"
• "aliphaticAtomCount"
• "aromaticAtomCount"
• "bondCount"
• "aliphaticBondCount"
• "aromaticBondCount"
• "rotatableBondCount"
• "fragmentCount",
• "ringCount"
• "aliphaticRingCount"
• "aliphaticRingCountOfSize"
• "aromaticRingCount"
• "aromaticRingCountOfSize"
• "heteroRingCount"
• "heteroaromaticRingCount"
• "carboRingCount"
• "carboaromaticRingCount"
• "ringAtomCount"
• "ringBondCount"
• "chainAtomCount"
• "chainBondCount"
• "smallestRingSize"
• "largestRingSize"
• "fusedRingCount"
• "fusedAliphaticRingCount"
• "fusedAromaticRingCount"
• "ringSystemCount",
• "ringsyStemCountOfSize",
• "largestRingSystemSize",
• "smallestRingsyStemSize",
• "asymmetricAtomCount"
• "chiralCenterCount"
• "cyclomaticNumber"
• "plattIndex"
• "randicIndex"
• "balabanIndex"
• "distanceDegree" (atomic)
• "eccentricity" (atomic)
• "hararyIndex"
• "hyperWienerIndex"
• "szegedIndex"
• "wienerIndex"
• "wienerPolarity"
• "stericEffectIndex" (atomic)
• "aromaticAtom" (API/cxcalc only, atomic boolean property)
• "aliphaticAtom" (API/cxcalc only, atomic boolean property)
• "chainAtom" (API/cxcalc only, atomic boolean property)
• "ringAtom" (API/cxcalc only, atomic boolean property)
• "asymmetricAtom" (API/cxcalc only, atomic boolean property)
• "chiralCenter" (API/cxcalc only, atomic boolean property)
• "largestAtomRingSize" (API/cxcalc only, atomic, size of largest ring containing atom)
• "smallestAtomRingSize" (API/cxcalc only, atomic, size of smallest ring containing atom)
• "shortestPath" (API/cxcalc only, size of shortest path between two atoms)
• "connected" (API/cxcalc only, true if two atoms are connected)
• "connectedGraph" (API/cxcalc only, true if the molecule graph is connected)
• "bondType" (API/cxcalc only, the bond type)
• "distanceCount" (API only, number of atoms at given distance from a given atom)
• "chainBond" (API/cxcalc only, bond boolean property)
• "ringBond" (API/cxcalc only, bond boolean property)
• "rotatableBond" (API/cxcalc only, bond boolean property)
• "ringCountOfSize" (API only, number of rings of given size)
• "ringCountOfAtom" (API/cxcalc only, number of rings of given atom)

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)

Prevents default standardization: does nothing. TopologyAnalyser does not need standardization.

Overrides:

standardize in class CalculatorPlugin

Parameters:

mol - is the molecule to be standardized