Package chemaxon.marvin.calculations

Class MajorMicrospeciesAccessorPlugin

java.lang.Object

chemaxon.marvin.plugin.CalculatorPlugin

chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin

All Implemented Interfaces:

chemaxon.license.Licensable

Direct Known Subclasses:

ChargePlugin, HBDAPlugin, HuckelAnalysisPlugin, MSAPlugin, OrbitalElectronegativityPlugin, PolarizabilityPlugin, TPSAPlugin

@PublicAPI
public abstract class MajorMicrospeciesAccessorPlugin
extends CalculatorPlugin

Common base class for all plugins with possible major microspecies input.

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

Since:

Marvin 4.0.2

Nested Class Summary

Nested classes/interfaces inherited from class chemaxon.marvin.plugin.CalculatorPlugin

CalculatorPlugin.HydrogenData

Field Summary

Fields

Modifier and Type	Field	Description
protected chemaxon.calculations.pka.Ionizer	ionizer

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	Description
MajorMicrospeciesAccessorPlugin()	Constructor.

Method Summary

Modifier and Type	Method	Description
void	checkMolecule(Molecule mol)	Checks the input molecule.
protected Molecule	createModifiedInputMolecule(Molecule mol)	Returns the molecule form with largest distribution.
String	getErrorMessage()	Returns the calculation error information message or the empty string if there is no error.
String	getIonizerErrorMessage()	Returns the calculation error information message or the empty string if there is no error.
double	getpH()	Returns the pH where the major microspecies should be taken.
boolean	isLicensed()	Returns true if the plugin is licensed.
void	setParameters(Properties params)	Sets the input parameters for the plugin.
void	setpH(double pH)	Sets the pH: major microspecies on given pH is taken as input molecule if set to Double.NaN then the input molecule is taken as it is.
void	standardize(Molecule mol)	Standardizes the molecule.

Methods inherited from class chemaxon.marvin.plugin.CalculatorPlugin

arrangeHydrogenIncerments, canRepeat, checkLicense, checkType, containsCoordinateBond, containsMulticenterSgroup, containsPseudoAtom, containsSRUSgroup, create, createStandardizedMolecule, createStandardizedMolecule, dehydrogenize, format, format, format, format, getAtomCount, getAtomIndex, getAtomIndexMap, getCalcMolecule, getDisplayMolecule, getDocument, getDoublePrecision, getExplicitHydrogenData, getInputMolDim, getMainMolecule, getOriginalMolecule, getPluginResource, getProductName, getQueryMoleculeErrorMessage, getRemark, getResult, getResult, getResult, getResult, getResultAsRGB, getResultAsRGB, getResultAsString, getResultAsString, getResultCount, getResultCount, getResultDomain, getResultDomain, getResultMessage, getResultMolecule, getResultMolecules, getResultsAsRGB, getResultsAsRGB, getResultsAsString, getResultsAsString, getResultSource, getResultTypes, getTypeString, getWarningMessage, handlesMultiFragmentMolecules, isInputMoleculeAromatized, isMsCalc, isMultiThreadedRunEnabled, isNegligibleResult, isOK, isRgrouped, loadClass, readAttribute, removeWhitespace, restoreExplicitHydrogens, run, setAtomIndexMap, setDoublePrecision, setDoublePrecision, setDoublePrecision, setInputMolecule, 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

Field Detail

ionizer

protected chemaxon.calculations.pka.Ionizer ionizer

Constructor Detail

MajorMicrospeciesAccessorPlugin

public MajorMicrospeciesAccessorPlugin()

Constructor. Creates the ionizer object.

Method Detail

isLicensed

public boolean isLicensed()

Description copied from class: CalculatorPlugin

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

Specified by:

isLicensed in interface chemaxon.license.Licensable

Overrides:

isLicensed in class CalculatorPlugin

Returns:

true if the plugin is licensed

setParameters

public void setParameters(Properties params)
                   throws PluginException

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

• pH: major microspecies on given pH is taken as input molecule if omitted then the input molecule is taken as it is
• microspecies: "true" if major microspecies should be taken as input molecule (corresponds to 'take major microspecies' GUI checkbox)
• msdistr: "true" if microspecies distributions should be calculated (default: "false")

Overrides:

setParameters in class CalculatorPlugin

Parameters:

params - is the parameter table

Throws:

PluginException - on error

setpH

public void setpH(double pH)

Sets the pH: major microspecies on given pH is taken as input molecule if set to Double.NaN then the input molecule is taken as it is.

Parameters:

pH - is the pH value

getpH

public double getpH()

Returns the pH where the major microspecies should be taken. Returns Double.NaN if no microspecies calculation required.

Overrides:

getpH in class CalculatorPlugin

Returns:

the pH where the major microspecies should be taken or Double.NaN if no microspecies calculation

createModifiedInputMolecule

protected final Molecule createModifiedInputMolecule(Molecule mol)

Returns the molecule form with largest distribution. Returns a microspecies with largest distribution on a given pH if getpH() returns a value different from Double.NaN, otherwise returns the input molecule itself.

Overrides:

createModifiedInputMolecule in class CalculatorPlugin

Parameters:

mol - is the input molecule

Returns:

the molecule form with largest distribution

Throws:

PluginException - on access error

getErrorMessage

public String getErrorMessage()

Returns the calculation error information message or the empty string if there is no error.

Overrides:

getErrorMessage in class CalculatorPlugin

Returns:

the calculation error information message

getIonizerErrorMessage

public String getIonizerErrorMessage()

Returns the calculation error information message or the empty string if there is no error.

Returns:

the calculation error information message

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

standardize

public void standardize(Molecule mol)

Standardizes the molecule. Adds dehydrogenization to default standardization in case when major microsepcies calculation required.

Overrides:

standardize in class CalculatorPlugin

Parameters:

mol - is the molecule to be standardized