chemaxon.marvin.calculations
Class IUPACNamingPlugin

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

All Implemented Interfaces:

chemaxon.license.Licensable

public class IUPACNamingPlugin
extends CalculatorPlugin

IUPAC name generator plugin.

API usage example:

    // read input molecule
    MolImporter mi = new MolImporter("test.mol");
    Molecule mol = mi.read();
    mi.close();

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

    // set the input molecule
    plugin.setMolecule(mol);

    // run the calculation
    plugin.run();

    // get results
    String preferredIUPACName  = plugin.getPreferredIUPACName();
    String traditionalName  = plugin.getTraditionalName();

    // do something with the result ...
 

For concurrent plugin example applications using ChemAxon's concurrent framework, refer to the Concurrent plugin examples.

Since:

Marvin 4.1.7, 03/12/2007

Version:

Marvin 5.3.2, 03/12/2009

Author:

Zsolt Mohacsi

See Also:

Molecule.toFormat(String)

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

IUPACNamingPlugin()

Method Summary

boolean	canRepeat() Returns true if repeatedly running the same plugin object while getting the results on the GUI is allowed, false otherwise.
void	checkMolecule(Molecule mol) Checks the input molecule.
java.lang.String	getPreferredIUPACName() Returns the preferred IUPAC name.
java.lang.String	getProductName() Returns the product identifier of the plugin as given by LicenseManager.
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.
Molecule	getResultMolecule() Returns the result molecule for display.
java.lang.Object[]	getResultTypes() Returns the result types.
java.lang.String	getTraditionalName() Returns the traditional IUPAC name.
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	run() Runs the tool.
void	setGeneratePreferredIUPACName(boolean g) Sets preferred IUPAC name generation.
void	setGenerateTraditionalIUPACName(boolean g) Sets traditional IUPAC name generation.
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) Standardizes the molecule.

Methods inherited from class chemaxon.marvin.plugin.CalculatorPlugin

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

IUPACNamingPlugin

public IUPACNamingPlugin()

Method Detail

setParameters

public void setParameters(java.util.Properties params)
                   throws PluginException

Sets the input parameters for the plugin.

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)

Description copied from class: CalculatorPlugin

Checks the input molecule. Throws exception if the molecule is not accepted as input molecule, otherwise does nothing (simply returns). The default implementation refuses query molecules, molecules with SRU S-groups, molecules with multicenter S-groups and molecules with coordinate bonds.

Overrides:

checkMolecule in class CalculatorPlugin

Parameters:

mol - is the input molecule

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

setGeneratePreferredIUPACName

public void setGeneratePreferredIUPACName(boolean g)

Sets preferred IUPAC name generation.

Parameters:

g - if true then preferred IUPAC name is generated

Since:

Marvin 5.0

See Also:

getPreferredIUPACName()

setGenerateTraditionalIUPACName

public void setGenerateTraditionalIUPACName(boolean g)

Sets traditional IUPAC name generation.

Parameters:

g - if true then traditional IUPAC name is generated

Since:

Marvin 5.0

See Also:

getTraditionalName()

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()

getPreferredIUPACName

public java.lang.String getPreferredIUPACName()
                                       throws PluginException

Returns the preferred IUPAC name.

Returns:

the preferred IUPAC name

Throws:

PluginException - if name generation fail

See Also:

setGeneratePreferredIUPACName(boolean)

getTraditionalName

public java.lang.String getTraditionalName()
                                    throws PluginException

Returns the traditional IUPAC name.

Returns:

the traditional IUPAC name

Throws:

PluginException - if name generation fail

See Also:

setGenerateTraditionalIUPACName(boolean)

getResultTypes

public java.lang.Object[] getResultTypes()

Returns the result 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

canRepeat

public boolean canRepeat()

Description copied from class: CalculatorPlugin

Returns true if repeatedly running the same plugin object while getting the results on the GUI is allowed, false otherwise. For internal use.

Overrides:

canRepeat in class CalculatorPlugin

Returns:

true if allowed, false otherwise

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()

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

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

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.STRUCTURE_TO_NAME

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

standardize

public void standardize(Molecule mol)

Standardizes the molecule. Overrides the default standardization.

Overrides:

standardize in class CalculatorPlugin

Parameters:

mol - is the molecule to be standardized