chemaxon.marvin.calculations
Class TopologyAnalyserPlugin

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

public class TopologyAnalyserPlugin

extends CalculatorPlugin

Calculates topological data. Data types:

• "atomCount"
• "aliphaticAtomCount"
• "aromaticAtomCount"
• "bondCount"
• "aliphaticBondCount"
• "aromaticBondCount"
• "ringCount"
• "ringAtomCount"
• "chainAtomCount"
• "ringBondCount"
• "chainBondCount"
• "aliphaticRingCount"
• "aromaticRingCount"
• "heteroRingCount"
• "aromaticHeteroRingCount"
• "smallestRingSize"
• "largestRingSize"
• "rotatableBondCount"
• "fusedRingCount"
• "fusedAliphaticRingCount"
• "fusedAromaticRingCount"
• "aromaticAtom" (API/cxcalc only, atomic boolean property)
• "chainAtom" (API/cxcalc only, atomic boolean property)
• "ringAtom" (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)

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

    // do something with the results ...
 

Since:

Marvin 3.5, 27/09/2004

Author:

Nora Mate

Field Summary

Fields inherited from class chemaxon.marvin.plugin.CalculatorPlugin

ATOM, BLUE, CALCRGB_OFF, CHART, HYDROGEN_VALENCE_ERROR_MSG, MOLECULE, NAN, RED, SUBRESULT

Constructor Summary

TopologyAnalyserPlugin()

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	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	getBondCount() Returns the bond count.
int	getChainAtomCount() Returns the chain atom count.
int	getChainBondCount() Returns the chain bond count.
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.
int	getHeteroaromaticRingCount() Returns the heteroaromatic ring count.
int	getHeteroRingCount() Returns the hetero ring count.
int	getLargestRingSize() Returns the largest ring size.
int	getLargestRingSizeOfAtom(int index) Returns the size of largest ring containing the specified atom.
java.lang.Object	getResult(java.lang.Object type, int index) Returns the result item for the specified key and index.
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.
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	getRotatableBondCount() Returns the rotatable bond count.
int	getSmallestRingSize() Returns the smallest ring size.
int	getSmallestRingSizeOfAtom(int index) Returns the size of smallest ring containing the specified atom.
java.lang.String	getTypeString(java.lang.Object type) Returns a string representation of the given type.
boolean	handlesMultiFragmentMolecules() Returns true if the plugin handles multifragment molecules, false otherwise.
boolean	isAromaticAtom(int index) Returns true if aromatic atom.
boolean	isChainAtom(int index) Returns true if chain atom.
boolean	isRingAtom(int index) Returns true if ring atom.
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.
protected void	standardize(Molecule mol) Prevents default standardization: does nothing.

Methods inherited from class chemaxon.marvin.plugin.CalculatorPlugin

check, checkLicense, checkLicenseKey, checkType, create, createImageMolecule, createStandardizedMolecule, dehydrogenize, format, format, format, format, getAtomCount, getAtomIndex, getChartColor, getDoublePrecision, getErrorMessage, getGUIResultTypes, getLicenseKey, getMainMolecule, getMolText, getOutputClassName, getReferenceMolecule, getResult, getResult, getResult, getResultAsRGB, getResultAsRGB, getResultAsString, getResultCount, getResultDomain, getResultsAsRGB, getResultsAsRGB, getResultsAsString, getResultsAsString, getSuffix, getXAxisLabel, getXLabels, getYAxisLabel, isLicensed, isMajorityMsCalculation, isMajorMs, isMsCalc, isNegligibleResult, isRgrouped, removeWhitespace, saveLicense, setDoublePrecision, setDoublePrecision, setDoublePrecision, setLicense, setMolecule, setMolecule, setMolecule, standardizeGroups, validate

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

TopologyAnalyserPlugin

public TopologyAnalyserPlugin()

Method Detail

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"
  • "ringCount"
  • "aliphaticRingCount"
  • "aromaticRingCount"
  • "heteroRingCount"
  • "heteroaromaticRingCount"
  • "ringAtomCount"
  • "ringBondCount"
  • "chainAtomCount"
  • "chainBondCount"
  • "smallestRingSize"
  • "largestRingSize"
  • "fusedRingCount"
  • "fusedAliphaticRingCount"
  • "fusedAromaticRingCount"
  • "aromaticAtom" (API/cxcalc only, atomic boolean property)
  • "chainAtom" (API/cxcalc only, atomic boolean property)
  • "ringAtom" (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)
  (default: all molecular types)

Specified by:

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

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

getAromaticRingCount

public int getAromaticRingCount()

Returns the aromatic ring count.

Returns:

the aromatic ring count

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

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

isAromaticAtom

public boolean isAromaticAtom(int index)

Returns true if aromatic atom.

Parameters:

index - is the atom index

Returns:

true if aromatic 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

getResult

public java.lang.Object getResult(java.lang.Object type,
                                  int index)
                           throws PluginException

Returns the result item for the specified key and index.

Specified by:

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()

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.

Specified by:

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.

Specified by:

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.

Specified by:

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"
• "ringCount"
• "aliphaticRingCount"
• "aromaticRingCount"
• "heteroRingCount"
• "heteroaromaticRingCount"
• "ringAtomCount"
• "ringBondCount"
• "chainAtomCount"
• "chainBondCount"
• "smallestRingSize"
• "largestRingSize"
• "fusedRingCount"
• "fusedAliphaticRingCount"
• "fusedAromaticRingCount"
• "aromaticAtom" (API/cxcalc only, atomic boolean property)
• "chainAtom" (API/cxcalc only, atomic boolean property)
• "ringAtom" (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)

Specified by:

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()

standardize

protected 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