chemaxon.marvin.calculations
Class PolarizabilityPlugin

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

All Implemented Interfaces:

chemaxon.license.Licensable

public class PolarizabilityPlugin
extends MajorMicrospeciesAccessorPlugin

Plugin class for atom polarizability calculation.

API usage example:

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

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

    // 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);
          }
    }
 

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

Author:

Nora Mate

Field Summary

Fields inherited from class chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin

ionizer

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, NAN, PLUGIN_CLASS_KEY, PLUGIN_DIR, RED

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.
double	getHPolarizability(int index) Returns the sum of the implicit H atom polarizability values around the given heavy atom.
double	getMolPolarizability() Returns the molecular polarizability value.
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)).
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.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.
Molecule	getResultMolecule() Returns the result molecule for display.
java.lang.Object[]	getResultTypes() Returns the result types (possible types: sigma, pi, total).
boolean	isLicensed() Returns true if the plugin is licensed.
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.MajorMicrospeciesAccessorPlugin

createModifiedInputMolecule, getIonizerErrorMessage, getpH, setpH, standardize

Methods inherited from class chemaxon.marvin.plugin.CalculatorPlugin

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

PolarizabilityPlugin

public PolarizabilityPlugin()

Constructor.

Method Detail

isLicensed

public boolean isLicensed()

Returns true if the plugin is licensed. The license checking is based on the product name, returned by getProductName().

Specified by:

isLicensed in interface chemaxon.license.Licensable

Overrides:

isLicensed in class MajorMicrospeciesAccessorPlugin

Returns:

true if the plugin is licensed

getProductName

public java.lang.String getProductName()

Returns the product identifier of the plugin as given by LicenseManager.

Overrides:

getProductName in class CalculatorPlugin

Returns:

The identifier LicenseManager.CHARGE_PLUGIN_GROUP

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 MajorMicrospeciesAccessorPlugin

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 MajorMicrospeciesAccessorPlugin

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()

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 MajorMicrospeciesAccessorPlugin

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

Since:

Marvin 3.4.1

getHPolarizability

public double getHPolarizability(int index)

Returns the sum of the implicit H atom polarizability values around the given heavy atom.

Parameters:

index - is the heavy atom index

Returns:

the sum of the implicit H atom polarizability values

Since:

Marvin 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 CalculatorPlugin

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

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 type and index. Polarizability returns the atom polarizability value as a Double object.

Overrides:

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. 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 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

Since:

Marvin 4.0