chemaxon.marvin.calculations
Class PredictorPlugin

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

All Implemented Interfaces:

chemaxon.license.Licensable

public class PredictorPlugin
extends CalculatorPlugin

Plugin class for running previously trained predictions on molecules.

API usage example:

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

    // set the prediction
    try {
        plugin.setPrediction("pampa");
    } catch (PluginException e) {
        System.err.println("Invalid prediction id, or parameter file for prediction cannot be loaded.");
        // ...
    }

    // for each input molecule run the calculation and display the results
    MolImporter importer = new MolImporter("mols.sdf");
    Molecule mol = null;
    int count = 0;
    while ((mol = importer.read()) != null) {

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

        // run the calculation
        plugin.run();

        // get the result
        double predictedValue = plugin.getPredictedValue(); 

        // print '[mol number]: predicted value'
        System.out.println("["+(++count)+"]: "+predictedValue);
    }  
    importer.close();
 /* 

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

Since:

Marvin 5.4

Author:

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, MOLECULES, NAN, PLUGIN_CLASS_KEY, PLUGIN_DIR, RED

Constructor Summary

PredictorPlugin()

Method Summary

java.lang.String	getErrorMessage() Returns the calculation error information message if CalculatorPlugin.run() returned false (calculation error).
double	getPredictedValue() Returns the predicted value.
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 type and index.
java.lang.Object	getResult(java.lang.Object type, java.lang.String arg) Returns the result item for the specified argument string.
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.
double	getStandardError()
static java.lang.String[]	getTrainingIds() Returns the id's of available predictions.
boolean	needError()
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	setTraining(java.lang.String trainingId) Sets the prediction.
void	standardize(Molecule mol) Standardizes the molecule by performing the transformations necessary to run the plugin (aromatize, dehydrogenize, bring nitro groups to common form, ...).

Methods inherited from class chemaxon.marvin.plugin.CalculatorPlugin

canRepeat, checkLicense, checkMolecule, checkType, containsCoordinateBond, containsMulticenterSgroup, containsPseudoAtom, containsSRUSgroup, create, createModifiedInputMolecule, createStandardizedMolecule, createStandardizedMolecule, dehydrogenize, format, format, format, format, getAtomCount, getAtomIndex, getCalcMolecule, getDisplayMolecule, getDocument, getDoublePrecision, getInputMolDim, getMainMolecule, getpH, getPluginResource, getQueryMoleculeErrorMessage, getRemark, getResult, getResult, getResultAsRGB, getResultAsRGB, getResultAsString, getResultCount, getResultCount, getResultDomain, getResultDomain, getResultMessage, getResultMolecules, getResultsAsRGB, getResultsAsRGB, getResultsAsString, getResultsAsString, getResultSource, getTypeString, getWarningMessage, handlesMultiFragmentMolecules, isInputMoleculeAromatized, isLicensed, 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

PredictorPlugin

public PredictorPlugin()

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

setInputMolecule

protected void setInputMolecule(Molecule mol)
                         throws PluginException

Description copied from class: CalculatorPlugin

Sets the input molecule.

Specified by:

setInputMolecule in class CalculatorPlugin

Parameters:

mol - is the input molecule

Throws:

PluginException - on error

setParameters

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

Description copied from class: CalculatorPlugin

Sets the input parameters for the plugin.

Overrides:

setParameters in class CalculatorPlugin

Parameters:

params - is the parameter table

Throws:

PluginException - on error

getTrainingIds

public static java.lang.String[] getTrainingIds()

Returns the id's of available predictions.

Returns:

the id's of available predictions

setTraining

public void setTraining(java.lang.String trainingId)
                 throws PluginException

Sets the prediction.

Parameters:

trainingId - the training id

Throws:

PluginException - if training id is invalid, or parameter file for training cannot be loaded

run

public boolean run()
            throws PluginException

Description copied from class: CalculatorPlugin

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()

getPredictedValue

public double getPredictedValue()

Returns the predicted value.

Returns:

the predicted value

getStandardError

public double getStandardError()

getResultTypes

public java.lang.Object[] getResultTypes()

Description copied from class: CalculatorPlugin

Returns the result types. The default implementation returns null.

Overrides:

getResultTypes in class CalculatorPlugin

Returns:

the result types

getResult

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

Description copied from class: CalculatorPlugin

Returns the result item for the specified type and index. The default implementation returns null.

Overrides:

getResult in class CalculatorPlugin

Parameters:

type - is the result type

index - is the result index

Returns:

the result item for the specified type 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

Description copied from class: CalculatorPlugin

Returns the result item for the specified argument string. The default implementation calls CalculatorPlugin.getResult(Object, int) with the argument string converted to an integer (result index).

Overrides:

getResult in class CalculatorPlugin

Parameters:

type - is the result type

arg - is the argument string

Returns:

the result item for the specified type and argument string

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

Description copied from class: CalculatorPlugin

Returns the specified result in String format. The default implementation returns null.

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()

Description copied from class: CalculatorPlugin

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

getErrorMessage

public java.lang.String getErrorMessage()

Description copied from class: CalculatorPlugin

Returns the calculation error information message if CalculatorPlugin.run() returned false (calculation error). The default implementation returns the empty string.

Overrides:

getErrorMessage in class CalculatorPlugin

Returns:

the calculation error information message

standardize

public void standardize(Molecule mol)

Description copied from class: CalculatorPlugin

Standardizes the molecule by performing the transformations necessary to run the plugin (aromatize, dehydrogenize, bring nitro groups to common form, ...). This implementation performs the following transformations:

• aromatization
• nitro group transformation: [O-:1][N+:2] >> [O:1]=[N:2], [NH1+:1][O-:2] >> [H:3][O:2][N:1]
• sulphynil group transformation: [#6][S+:1]([#6])[#8-:2] >> [#6][S:1]([#6])=[O:2]

To be overridden by subclasses that require other standardization (or none at all). TODO: replace by call to chemaxon.reaction.Standardizer

Overrides:

standardize in class CalculatorPlugin

Parameters:

mol - is the molecule to be standardized

needError

public boolean needError()