chemaxon.marvin.calculations
Class ResonancePlugin

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

All Implemented Interfaces:

chemaxon.license.Licensable

public class ResonancePlugin
extends CalculatorPlugin

Plugin class for finding resonant structures.

API usage example:

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

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

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

    // run the calculation
    plugin.run();

    // get the resonant structures
    System.out.println("Resonant structures");
    int count = plugin.getStructureCount();
    for (int i=0; i < count; ++i) {
        Molecule structure = plugin.getStructure(i);
        System.out.println(structure.toFormat("smiles"));
    }
 

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

Since:

Marvin 4.0

Version:

5.2 01/15/2009

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

ResonancePlugin()
Constructor.

Method Summary

void	checkMolecule(Molecule mol) Checks the input molecule.
protected Molecule	createStandardizedMolecule(Molecule mol) Creates standardized molecule, the original input molecule is cloned only if the original molecule should not be modified.
protected Molecule	createStandardizedMolecule(Molecule mol, boolean om) Deprecated. Use createStandardizedMolecule(Molecule) instead
java.lang.String	getErrorMessage() Returns the calculation error information message or the empty string if there is no error.
java.lang.String	getProductName() Returns the product identifier of the plugin as given by LicenseManager.
java.lang.String	getRemark() Returns a warning message if there are no resonants, null otherwise.
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.
chemaxon.marvin.plugin.PluginMDocSource	getResultSource() Returns the result as a document source object.
java.lang.Object[]	getResultTypes() Returns the result types.
Molecule	getStructure(int index) Returns a resonant structure.
int	getStructureCount() Returns the number of different resonant structures.
Molecule[]	getStructures() Returns resonant structures in Molecule[] array.
boolean	handlesMultiFragmentMolecules() Returns true if the plugin handles multifragment molecules, false otherwise.
boolean	isMultiThreadedRunEnabled() For internal use only.
boolean	run() Calculates the resonant structures.
void	setCleanResultStructures(boolean clean) Sets 2D cleaning of the result structures: if true then resonants returned by getStructure(int) and getStructures() methods are cleaned in 2D.
protected void	setInputMolecule(Molecule mol) Sets the input molecule.
void	setInputMoleculeModified(boolean inputMoleculeModified) Deprecated. Not used.
void	setMaxStructureCount(int max) Sets the maximum number of structures to be generated.
void	setParameters(java.util.Properties params) Sets the input parameters for the plugin.
void	setpH(double pH) Deprecated. As of Marvin 5.0 pH effect is not considered
void	setProgressMonitor(chemaxon.common.util.MProgressMonitor pmon) Sets a progress observer to be used in run() to display progress status.
void	setSymmetryFiltering(boolean filtering) Sets symmetry fitlering: if true then symmetrical structures are filtered out, otherwise symmetrical structures are returned as duplicates.
void	setTakeCanonicalForm(boolean canonical) Sets whether canonical form should be taken.
void	setTakeMajorContributors(boolean mcontrib) Sets whether major contributors should be taken.
void	standardize(Molecule mol) Standardizes the molecule.

Methods inherited from class chemaxon.marvin.plugin.CalculatorPlugin

arrangeHydrogenIncerments, canRepeat, checkLicense, checkType, containsCoordinateBond, containsMulticenterSgroup, containsPseudoAtom, containsSRUSgroup, create, createModifiedInputMolecule, dehydrogenize, format, format, format, format, getAtomCount, getAtomIndex, getCalcMolecule, getDisplayMolecule, getDocument, getDoublePrecision, getExplicitHydrogenData, getInputMolDim, getMainMolecule, getpH, getPluginResource, getQueryMoleculeErrorMessage, getResult, getResult, getResult, getResultAsRGB, getResultAsRGB, getResultAsString, getResultCount, getResultDomain, getResultMessage, getResultMolecule, getResultMolecules, getResultsAsRGB, getResultsAsRGB, getResultsAsString, getResultsAsString, getTypeString, getWarningMessage, isInputMoleculeAromatized, isLicensed, isMsCalc, isNegligibleResult, isOK, isRgrouped, loadClass, readAttribute, removeWhitespace, restoreExplicitHydrogens, setDoublePrecision, setDoublePrecision, setDoublePrecision, setKeepHydrogens, setLicenseEnvironment, setMolecule, setMolecule, setMolecule, setMolecule, standardizeIonicGroups, standardizeNeutralGroups

Methods inherited from class java.lang.Object

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

Constructor Detail

ResonancePlugin

public ResonancePlugin()

Constructor.

Method Detail

getProductName

public java.lang.String getProductName()

Description copied from class: CalculatorPlugin

Returns the product identifier of the plugin as given by LicenseManager. The name is used by the CalculatorPlugin.isLicensed() method.

Specified by:

getProductName in class CalculatorPlugin

Returns:

product identifier or a default string

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

setProgressMonitor

public void setProgressMonitor(chemaxon.common.util.MProgressMonitor pmon)

Sets a progress observer to be used in run() to display progress status. Short calculations may ignore the observer object. The default implementation does nothing.

Overrides:

setProgressMonitor in class CalculatorPlugin

Parameters:

pmon - is the progress monitor, may be null

setParameters

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

Sets the input parameters for the plugin. Parameters and value ranges:

• single: "true" if single fragment mode (calculation is performed separately for each fragment) (default: "false")
• type: structure,structures,count
• max: max structure count
• pH: consider pH effect at this pH (default: Double.NaN - do not consider pH effect)
• symfilter: true if filter symmetrical structures, false if allow duplicates (default: true)
• canonical: "true" if canonical form should be taken (default: "false")
• mcontrib: "true" if take major contributors (default: "true")

Overrides:

setParameters in class CalculatorPlugin

Parameters:

params - is the parameter table

Throws:

PluginException - on error

setCleanResultStructures

public void setCleanResultStructures(boolean clean)

Sets 2D cleaning of the result structures: if true then resonants returned by getStructure(int) and getStructures() methods are cleaned in 2D. Default: false.

Parameters:

clean - if true then result structures are cleaned in 2D

Since:

Marvin 5.2

setSymmetryFiltering

public void setSymmetryFiltering(boolean filtering)

Sets symmetry fitlering: if true then symmetrical structures are filtered out, otherwise symmetrical structures are returned as duplicates. Default: true.

Parameters:

filtering - is true if symmetrical structures should be filtered out

setMaxStructureCount

public void setMaxStructureCount(int max)

Sets the maximum number of structures to be generated. Default: 1000.

Parameters:

max - is the maximum number of structures to be generated

Since:

Marvin 4.1

setpH

public void setpH(double pH)

Deprecated. As of Marvin 5.0 pH effect is not considered

Sets the pH to be considered in calculation. By default, no pH effect considered (Double.NaN).

Parameters:

pH - is the pH value

setInputMoleculeModified

public void setInputMoleculeModified(boolean inputMoleculeModified)

Deprecated. Not used.

Sets whether the input molecule should be modified and returned as calculation result. Default: false.

Parameters:

inputMoleculeModified - is true if input molecule should be modified, false if it should be preserved

Since:

Marvin 4.1

checkMolecule

public void checkMolecule(Molecule mol)
                   throws PluginException

Checks the input molecule. Throws exception 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

createStandardizedMolecule

protected Molecule createStandardizedMolecule(Molecule mol,
                                              boolean om)
                                       throws PluginException

Deprecated. Use createStandardizedMolecule(Molecule) instead

Creates standardized molecule, the original input molecule is cloned only if the original molecule should not be modified.

Overrides:

createStandardizedMolecule in class CalculatorPlugin

Parameters:

mol - is the input molecule

om - is true if original input molecule is to be used for atom indexing false if modified molecule is to be used for atom indexing

Returns:

the standardized molecule

Throws:

PluginException - on error

See Also:

#see #is InputMoleculeModified()

createStandardizedMolecule

protected Molecule createStandardizedMolecule(Molecule mol)
                                       throws PluginException

Creates standardized molecule, the original input molecule is cloned only if the original molecule should not be modified.

Overrides:

createStandardizedMolecule in class CalculatorPlugin

Parameters:

mol - is the input molecule

Returns:

the standardized molecule

Throws:

PluginException - on error

See Also:

#see #is InputMoleculeModified()

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

setTakeCanonicalForm

public void setTakeCanonicalForm(boolean canonical)

Sets whether canonical form should be taken. Default: false.

Parameters:

canonical - is true if canonical form should be taken

Since:

Marvin 4.1

See Also:

getStructure(int), getStructures(), getStructureCount()

setTakeMajorContributors

public void setTakeMajorContributors(boolean mcontrib)

Sets whether major contributors should be taken. Default: true.

Parameters:

mcontrib - is true if major contributors should be taken

See Also:

getStructure(int), getStructures(), getStructureCount()

run

public boolean run()
            throws PluginException

Calculates the resonant structures.

Specified by:

run in class CalculatorPlugin

Returns:

true if the calculation was successful, false if the number of ionizable atoms exceeds the specified limit

Throws:

PluginException - on error

See Also:

CalculatorPlugin.getErrorMessage()

getResultSource

public chemaxon.marvin.plugin.PluginMDocSource getResultSource()
                                                        throws PluginException

Returns the result as a document source object. This is useful for displaying the molecules in a viewer dynamically as they become available instead of collecting all results before display.

Overrides:

getResultSource in class CalculatorPlugin

Returns:

the document source interface

Throws:

PluginException - on error

Since:

Marvin 5.0

getStructureCount

public int getStructureCount()

Returns the number of different resonant structures.

Returns:

the number of different resonant structures

See Also:

setTakeCanonicalForm(boolean), setTakeMajorContributors(boolean)

getStructure

public Molecule getStructure(int index)

Returns a resonant structure.

Parameters:

index - is the structure index

Returns:

the resonant structure

See Also:

setTakeCanonicalForm(boolean), setTakeMajorContributors(boolean)

getStructures

public Molecule[] getStructures()

Returns resonant structures in Molecule[] array.

Returns:

resonant structures

See Also:

setTakeCanonicalForm(boolean), setTakeMajorContributors(boolean)

getResultTypes

public java.lang.Object[] getResultTypes()

Returns the result types.

Overrides:

getResultTypes in class CalculatorPlugin

Returns:

the result types

getResultDomain

public int getResultDomain(java.lang.Object type)

Returns the calculation domain.

Overrides:

getResultDomain in class CalculatorPlugin

Parameters:

type - is the result type

Returns:

the calculation domain

See Also:

getResultTypes()

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()

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

getRemark

public java.lang.String getRemark()

Returns a warning message if there are no resonants, null otherwise.

Overrides:

getRemark in class CalculatorPlugin

Returns:

a warning message if there are no resonants

getErrorMessage

public java.lang.String getErrorMessage()

Returns the calculation error information message or the empty string if there is no error.

Overrides:

getErrorMessage in class CalculatorPlugin

Returns:

the calculation error information message

standardize

public void standardize(Molecule mol)

Standardizes the molecule. This is the same as the default standardization, but performs daylight aromatization.

Overrides:

standardize in class CalculatorPlugin

Parameters:

mol - is the molecule to be standardized

isMultiThreadedRunEnabled

public boolean isMultiThreadedRunEnabled()

For internal use only.

Overrides:

isMultiThreadedRunEnabled in class CalculatorPlugin

Returns:

true if multi-threaded run is enabled