chemaxon.marvin.calculations
Class PolarizationPlugin

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

public class PolarizationPlugin

extends CalculatorPlugin

Plugin class for atom polarization calculation.

Field Summary

Fields inherited from class chemaxon.marvin.plugin.CalculatorPlugin

ATOM, CHART, MOLECULE, NAN, SUBRESULT

Constructor Summary

PolarizationPlugin()
Constructor.

Method Summary

void	checkMolecule(Molecule mol) Checks the input molecule.
protected java.lang.String	getLicenseKey() Returns the built-in license key for the given plugin class.
java.lang.Object	getResult(java.lang.Object type, int index) Returns the result item for the specified type 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 (possible types: sigma, pi, total).
boolean	run() Runs the charge calculation.
protected void	setInputMolecule(Molecule mol) Sets the input molecule.
void	setParameters(java.util.Properties params) Sets the input parameters for the plugin.

Methods inherited from class chemaxon.marvin.plugin.CalculatorPlugin

check, checkLicense, checkLicenseKey, create, createStandardizedMolecule, dehydrogenize, format, format, format, format, getAtomCount, getAtomIndex, getDoublePrecision, getErrorMessage, getOutputClassName, getReferenceMolecule, getResult, getResult, getResult, getResultAsRGB, getResultAsRGB, getResultAsString, getResultCount, getResultDomain, getResultsAsRGB, getResultsAsRGB, getResultsAsString, getResultsAsString, getTypeString, getXAxisLabel, getXLabels, getYAxisLabel, handlesMultiFragmentMolecules, isLicensed, isNegligibleResult, isRgrouped, setDoublePrecision, setDoublePrecision, setLicense, setMolecule, setMolecule, standardize, standardizeNitro, validate

Methods inherited from class java.lang.Object

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

Constructor Detail

PolarizationPlugin

public PolarizationPlugin()

Constructor. Creates the charge / atom polarization calculator object.

Method Detail

getLicenseKey

protected final java.lang.String getLicenseKey()

Returns the built-in license key for the given plugin class. This license key has to be checked against the license key read from the property file.

Overrides:

getLicenseKey in class CalculatorPlugin

Returns:

the built-in license key for the given plugin class

See Also:

CalculatorPlugin.checkLicense()

setParameters

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

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

• precision: 0-8 or inf (number of displayed fractional digits, inf for unrounded value)

Specified by:

setParameters in class CalculatorPlugin

Parameters:

params - is the parameter table

Throws:

PluginException - on error

checkMolecule

public void checkMolecule(Molecule mol)
                   throws PluginException

Checks the input molecule. Throws exception if the molecule 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

run

public boolean run()
            throws PluginException

Runs the charge calculation.

Specified by:

run in class CalculatorPlugin

Returns:

true if the calculation was successful, false on calculation error

Throws:

PluginException - on error

See Also:

CalculatorPlugin.getErrorMessage()

getResultTypes

public java.lang.Object[] getResultTypes()

Returns the result types (possible types: sigma, pi, total).

Specified by:

getResultTypes in class CalculatorPlugin

Returns:

the result types

getResultDomain

public int getResultDomain(java.lang.Object type)

Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE. Polarization always returns CalculatorPlugin.ATOM.

Specified by:

getResultDomain in class CalculatorPlugin

Parameters:

type - is the result type

Returns:

CalculatorPlugin.ATOM

See Also:

getResultTypes()

getResultCount

public int getResultCount(java.lang.Object type)

Returns the number of result items for the given result key. Polarization returns the atom count.

Specified by:

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 type and index. Polarization returns the atom polarization value as a Double object.

Specified by:

getResult in class CalculatorPlugin

Parameters:

type - is the result type (not used)

index - is the atom index

Returns:

the result item for the specified type and index

Throws:

PluginException - if the result cannot be returned

See Also:

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. Polarization returns the rounded atom polarization value in string format: the value is rounded using the 'precision' input parameter that determines the number of fractional digits displayed.

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