chemaxon.marvin.calculations
Class PolarizabilityPlugin

java.lang.Object
  chemaxon.marvin.plugin.CalculatorPlugin
      chemaxon.marvin.calculations.MajorMicrospeciesPlugin
          chemaxon.marvin.calculations.PolarizabilityPlugin

public class PolarizabilityPlugin

extends MajorMicrospeciesPlugin

Plugin class for atom polarizability calculation.

API usage example:

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

    // create plugin
    PolarizabilityPlugin plugin = new PolarizabilityPlugin();
    plugin.validate(<polarizability license>);

    // optional: take major microspecies at pH=7.4
    // skip this if you want to calculate polarizability for the input molecule as it is
    plugin.setpH(7.4);

    // set target molecule
    plugin.setMolecule(mol);
	
    // run the calculation
    plugin.run();

    // get molecular polarizability
    double molpol = plugin.getMolPolarizability();
    System.out.println("molecular polarizability: "+molpol);

    // get polarizability values for each atom
    int count = mol.getAtomCount();
    for (int i=0; i < count; ++i) {
 	  double pol = plugin.getPolarizability(i);
 	  if (!Double.isNaN(pol)) {
 	      System.out.println("polarizability for atom "+(i+1)+": "+pol);
 	  }
    }
 

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

PolarizabilityPlugin()
Constructor.

Method Summary

void	checkMolecule(Molecule mol) Checks the input molecule.
double	getAveragePolarizabilityComponent() Returns the average polarizability component (for geom3D=true, see setGeom3D(boolean)).
java.lang.String	getErrorMessage() Returns the calculation error information message if run() returned false (calculation error): hydrogen valence error.
protected java.lang.String	getLicenseKey() Returns the built-in license key for the given plugin class.
double	getMolPolarizability() Returns the molecular polarizability value.
java.lang.String	getOutputClassName() Returns the output provider class name for the command line interface.
double	getPolarizability(int index) Returns the atom polarizability value.
double[]	getPrincipalPolarizabilityComponents() Returns the principal components a(xx), a(yy), a(zz) of polarizability tensor (for geom3D=true, see setGeom3D(boolean)).
Molecule	getReferenceMolecule(java.lang.Object type, int index) Returns the molecule to be used as reference image for the given result type and index.
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.
void	setGeom3D(boolean geom3D) Sets 3D geometry consideration.
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.calculations.MajorMicrospeciesPlugin

getMainMolecule, getMajorMicrospecies, getMolText, getpH, getSuffix, isMajorMs, setpH, standardize

Methods inherited from class chemaxon.marvin.plugin.CalculatorPlugin

check, checkLicense, checkLicenseKey, checkType, create, createImageMolecule, createStandardizedMolecule, dehydrogenize, format, format, format, format, getAtomCount, getAtomIndex, getChartColor, getDoublePrecision, getGUIResultTypes, getResult, getResult, getResult, getResultAsRGB, getResultAsRGB, getResultAsString, getResultCount, getResultDomain, getResultsAsRGB, getResultsAsRGB, getResultsAsString, getResultsAsString, getTypeString, getXAxisLabel, getXLabels, getYAxisLabel, handlesMultiFragmentMolecules, isLicensed, isMajorityMsCalculation, 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

PolarizabilityPlugin

public PolarizabilityPlugin()

Constructor.

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)
• type:
  • molecular
  • atomic
  (default: all)
• geom3D: "true" if 3D geometry should be considered (computes molecular polarizability and principal components of polarizability tensor) (default: "false")

Overrides:

setParameters in class MajorMicrospeciesPlugin

Parameters:

params - is the parameter table

Throws:

PluginException - on error

setGeom3D

public void setGeom3D(boolean geom3D)

Sets 3D geometry consideration. Call this before setting the input molecule in CalculatorPlugin.setMolecule(Molecule).

Parameters:

geom3D - if true, molecular polarizability and principal components of polarizability tensor are computed (default: false)

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 MajorMicrospeciesPlugin

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.

Overrides:

setInputMolecule in class MajorMicrospeciesPlugin

Parameters:

mol - is the input molecule

Throws:

PluginException - on error

run

public boolean run()
            throws PluginException

Runs the charge calculation.

Overrides:

run in class MajorMicrospeciesPlugin

Returns:

true if the calculation was successful, false on calculation error

Throws:

PluginException - on error

getErrorMessage

public java.lang.String getErrorMessage()

Returns the calculation error information message if run() returned false (calculation error): hydrogen valence error.

Overrides:

getErrorMessage in class MajorMicrospeciesPlugin

Returns:

the calculation error information message

getPolarizability

public double getPolarizability(int index)

Returns the atom polarizability value.

Parameters:

index - is the atom index

Returns:

the atom polarizability value, Double.NaN for H atoms

Since:

Marvin 3.4.1

getMolPolarizability

public double getMolPolarizability()

Returns the molecular polarizability value.

Returns:

the molecular polarizability value

getAveragePolarizabilityComponent

public double getAveragePolarizabilityComponent()

Returns the average polarizability component (for geom3D=true, see setGeom3D(boolean)).

Returns:

the average polarizability component

getPrincipalPolarizabilityComponents

public double[] getPrincipalPolarizabilityComponents()

Returns the principal components a(xx), a(yy), a(zz) of polarizability tensor (for geom3D=true, see setGeom3D(boolean)).

Returns:

the principal polarizability component array

getResultTypes

public java.lang.Object[] getResultTypes()

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

Overrides:

getResultTypes in class MajorMicrospeciesPlugin

Returns:

the result types

getResultDomain

public int getResultDomain(java.lang.Object type)

Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.

Overrides:

getResultDomain in class MajorMicrospeciesPlugin

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. Polarizability returns the atom count for type "atomic", 1 for type "molecular".

Overrides:

getResultCount in class MajorMicrospeciesPlugin

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. Polarizability returns the atom polarizability value as a Double object.

Overrides:

getResult in class MajorMicrospeciesPlugin

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

Overrides:

getResultAsString in class MajorMicrospeciesPlugin

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

getOutputClassName

public java.lang.String getOutputClassName()

Returns the output provider class name for the command line interface.

Overrides:

getOutputClassName in class MajorMicrospeciesPlugin

Returns:

the output provider class name

getReferenceMolecule

public Molecule getReferenceMolecule(java.lang.Object type,
                                     int index)

Returns the molecule to be used as reference image for the given result type and index. The default implementation returns the original molecule clone.

Overrides:

getReferenceMolecule in class MajorMicrospeciesPlugin

Parameters:

type - is the result type

index - is the result index

Returns:

the original molecule clone