chemaxon.marvin.calculations

Class RefractivityPlugin

java.lang.Object

chemaxon.marvin.plugin.CalculatorPlugin

chemaxon.marvin.calculations.RefractivityPlugin

All Implemented Interfaces:

chemaxon.license.Licensable

@PublicAPI
public class RefractivityPlugin
extends CalculatorPlugin

Plugin class for refractivity calculation. Both the incremental values for atoms and the overal refractivity value for the molecule can be calculated by this plugin.

API usage example:

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

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

    // set double precision for string conversion (optional)
    plugin.setDoublePrecision(3);

    // set target molecule
    plugin.setMolecule(mol);
        
    // run the calculation
    plugin.run();
        
    // get molecular refractivity
    double refractivity = plugin.getRefractivity();
    System.out.println("molecular refractivity: "+plugin.format(refractivity));

    // get refractivity increments values for each atom
    String str = "";
    int count = mol.getAtomCount();
    for (int i=0; i < count; ++i) {
          double increment = plugin.getRefractivityIncrement(i);
          str += plugin.format(increment);
          str += ";";
    }
    System.out.println("refractivity increments for atoms: "+str);
 

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

Author:

Nora Mate

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

Constructors

Constructor and Description
RefractivityPlugin() Constructor.

Method Summary

Modifier and Type	Method and Description
void	checkMolecule(Molecule mol) Checks the input molecule.
java.lang.String	getErrorMessage() Returns the calculation error information message if run() returned false (calculation error): hydrogen valence error.
java.lang.String	getProductName() Returns the product identifier of the plugin as given by LicenseManager.
double	getRefractivity() Returns the refractivity value.
double	getRefractivityHIncrement(int index) Returns the refractivity increment on the H atoms attached to a given atom.
double	getRefractivityIncrement(int index) Returns the refractivity increment for a given atom.
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 CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.
Molecule	getResultMolecule() Returns the result molecule for display.
java.lang.Object[]	getResultTypes() Returns the result types.
java.lang.String	getTypeString(java.lang.Object type) Returns a string representation of the given type.
boolean	run() Runs the refractivity calculation.
protected void	setInputMolecule(Molecule mol) Sets the input molecule.
void	setParameters(java.util.Properties params) Sets the input parameters for the plugin.
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, createStandardizedMolecule, createStandardizedMolecule, dehydrogenize, format, format, format, format, getAtomCount, getAtomIndex, getAtomIndexMap, getCalcMolecule, getDisplayMolecule, getDocument, getDoublePrecision, getExplicitHydrogenData, getInputMolDim, getMainMolecule, getOriginalMolecule, getpH, getPluginResource, getQueryMoleculeErrorMessage, getRemark, getResult, getResult, getResult, getResultAsRGB, getResultAsRGB, getResultAsString, getResultCount, getResultDomain, getResultMessage, getResultMolecules, getResultsAsRGB, getResultsAsRGB, getResultsAsString, getResultsAsString, getResultSource, getWarningMessage, handlesMultiFragmentMolecules, isInputMoleculeAromatized, isLicensed, isMsCalc, isMultiThreadedRunEnabled, isNegligibleResult, isOK, isRgrouped, loadClass, readAttribute, removeWhitespace, restoreExplicitHydrogens, setAtomIndexMap, setDoublePrecision, setDoublePrecision, setDoublePrecision, setKeepHydrogens, setLicenseEnvironment, setMolecule, 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

RefractivityPlugin

public RefractivityPlugin()

Constructor. Creates the refractivity calculator object.

Method Detail

getProductName

public java.lang.String getProductName()

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

Specified by:

getProductName in class CalculatorPlugin

Returns:

The identifier LicenseManager.REFRACTIVITY_PLUGIN

setParameters

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

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

• precision: 0-8 or inf (number of displayed fractional digits, inf for unrounded value)
• type: increments,refractivity
• h: true or false (display increments on H atoms)

Overrides:

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 is RxnMolecule, if the molecule contains R-groups or if the molecule consists of more than one fragments.

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 (standardized) input molecule

Throws:

PluginException - on error

run

public boolean run()
            throws PluginException

Runs the refractivity calculation.

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()

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 CalculatorPlugin

Returns:

the calculation error information message

getRefractivity

public double getRefractivity()

Returns the refractivity value. The refractivity calculation should be run beforehand by run().

Returns:

the refractivity value

getRefractivityIncrement

public double getRefractivityIncrement(int index)

Returns the refractivity increment for a given atom. The refractivity calculation should be run beforehand by run().

Parameters:

index - is the atom index

Returns:

the refractivity increment for a given atom

getRefractivityHIncrement

public double getRefractivityHIncrement(int index)

Returns the refractivity increment on the H atoms attached to a given atom. The refractivity calculation should be run beforehand by run().

Parameters:

index - is the atom index

Returns:

the refractivity increment on the H atoms attached to a given atom

getResultTypes

public java.lang.Object[] getResultTypes()

Returns the result types. Possible result types: refractivity,increments,inch

Overrides:

getResultTypes in class CalculatorPlugin

Returns:

the result types

getTypeString

public java.lang.String getTypeString(java.lang.Object type)

Returns a string representation of the given type.

Overrides:

getTypeString in class CalculatorPlugin

Parameters:

type - is the type object

Returns:

the type string

getResultDomain

public int getResultDomain(java.lang.Object type)

Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE. Returns CalculatorPlugin.ATOM for type "increments" or "inch" and CalculatorPlugin.MOLECULE otherwise.

Overrides:

getResultDomain in class CalculatorPlugin

Parameters:

type - is the result type

Returns:

CalculatorPlugin.MOLECULE or CalculatorPlugin.ATOM

See Also:

getResultTypes()

getResultCount

public int getResultCount(java.lang.Object type)

Returns the number of result items for the given result key. Refractivity returns the atom count for types "increments" and "inch" 1 otherwise.

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. Refractivity returns the required refractivity value or atomic increment as a Double object.

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:

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. Refractivity returns the rounded refractivity 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

standardize

public void standardize(Molecule mol)

Standardizes the molecule. This is done by performing the transformations necessary to run the plugin (e.g. aromatize, dehydrogenize, bring nitro groups to common form). Apart from the default standardization (aromatize and nitro) removes explicit hydrogens. TODO: replace by call to chemaxon.standardizer.Standardizer

Overrides:

standardize in class CalculatorPlugin

Parameters:

mol - is the molecule to be standardized