Package chemaxon.marvin.calculations

Class IonChargePlugin

java.lang.Object

chemaxon.marvin.plugin.CalculatorPlugin

chemaxon.marvin.calculations.IonChargePlugin

All Implemented Interfaces:

TaggedCalculator, chemaxon.license.Licensable

@PublicApi
public class IonChargePlugin
extends CalculatorPlugin

Plugin class for charge calculation on ionized microspecies.

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

Since:

Marvin 3.0

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	Description
IonChargePlugin()	Constructor.

Method Summary

Modifier and Type	Method	Description
void	checkMolecule(Molecule mol)	Checks the input molecule.
String	getErrorMessage()	Returns the calculation error information message if run() returned false (calculation error): the number of ionizable atoms exceeds the specified limit (given in the "ions" parameter) or hydrogen valence error.
String	getProductName()	Returns the product identifier of the plugin as given by LicenseManager.
Object	getResult(Object type, int index)	Returns the result item for the specified type and index.
String	getResultAsString(Object type, int index, Object result)	Returns the specified result in String format.
int	getResultCount(Object type)	Returns the number of result items for the given result key.
int	getResultDomain(Object type)	Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.
Object[]	getResultTypes()	Returns the result types (possible type: "charge").
boolean	run()	Runs the charge calculation on the microspecies with sufficiently large distribution on the given pH.
protected void	setInputMolecule(Molecule mol)	Sets the input molecule.
void	setParameters(Properties params)	Sets the input parameters for the plugin.
void	standardize(Molecule mol)	Standardizes the molecule.

Methods inherited from class chemaxon.marvin.plugin.CalculatorPlugin

addHeavyAtomLimitChecker, addInputChecker, arrangeHydrogenIncerments, canRepeat, checkLicense, checkType, containsCoordinateBond, containsMulticenterSgroup, containsPseudoAtom, containsSRUSgroup, create, create, createModifiedInputMolecule, createStandardizedMolecule, createStandardizedMolecule, dehydrogenize, format, format, format, format, getAtomCount, getAtomIndex, getAtomIndexMap, getAtomIndexMapping, getCalcMolecule, getDisplayMolecule, getDocument, getDoublePrecision, getExplicitHydrogenData, getInputMolDim, getMainMolecule, getOriginalMolecule, getpH, getPluginResource, getQueryMoleculeErrorMessage, getRemark, getResult, getResult, getResult, getResultAsRGB, getResultAsRGB, getResultAsString, getResultCount, getResultDomain, getResultMessage, getResultMolecule, getResultMolecules, getResultsAsRGB, getResultsAsRGB, getResultsAsString, getResultsAsString, getResultSource, getTypeString, getWarningMessage, handlesMultiFragmentMolecules, isInputMoleculeAromatized, isLicensed, isMsCalc, isMultiThreadedRunEnabled, isNegligibleResult, isOK, isRgrouped, loadClass, loadPluginClass, loadPluginClass, readAttribute, removeWhitespace, restoreExplicitHydrogens, setAtomIndexMap, setChemicalTermsArgument, setChemicalTermsParameters, setDoublePrecision, setDoublePrecision, setDoublePrecision, setKeepHydrogens, setLicenseEnvironment, setMolecule, setMolecule, setMolecule, setMolecule, setProgressMonitor, standardizeIonicGroups

Methods inherited from class java.lang.Object

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

Methods inherited from interface chemaxon.calculator.TaggedCalculator

tags

Constructor Details

IonChargePlugin

public IonChargePlugin()

Constructor. Creates the Ionizer object.

Method Details

getProductName

public String getProductName()

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

Specified by:

getProductName in class CalculatorPlugin

Returns:

The identifier LicenseManager.CHARGE_PLUGIN_GROUP

setParameters

public void setParameters(Properties params)
                   throws PluginException

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

• pH: the pH value (default: 7.0)
• min-percent: minimal species distribution
• charge-type: accumulated or single (default: single)
• max-ions: max number of ionizable atoms to be taken into account (default: 8)
• precision: 0-8 or inf (default: 2) (number of displayed fractional digits, inf for unrounded value)

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 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 on the microspecies with sufficiently large distribution on the given pH.

Specified by:

run in class CalculatorPlugin

Returns:

true if the calculation was successful, false if the number of ionizable atoms exceeds the specified limit

Throws:

PluginException - on error

See Also:

• CalculatorPlugin.getErrorMessage()

getErrorMessage

public String getErrorMessage()

Returns the calculation error information message if run() returned false (calculation error): the number of ionizable atoms exceeds the specified limit (given in the "ions" parameter) or hydrogen valence error.

Overrides:

getErrorMessage in class CalculatorPlugin

Returns:

the calculation error information message

getResultTypes

public Object[] getResultTypes()

Returns the result types (possible type: "charge").

Overrides:

getResultTypes in class CalculatorPlugin

Returns:

the result types

getResultDomain

public int getResultDomain(Object type)

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

Overrides:

getResultDomain in class CalculatorPlugin

Parameters:

type - is the result type

Returns:

CalculatorPlugin.ATOM

See Also:

• getResultTypes()

getResultCount

public int getResultCount(Object type)

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

Overrides:

getResultCount in class CalculatorPlugin

Parameters:

type - is the result type

Returns:

the number of result items

See Also:

• getResultTypes()

getResult

public Object getResult(Object type,
 int index)
                 throws PluginException

Returns the result item for the specified type and index. IonCharge returns one or more charge values for the specified atom index depending on whether the 'min-percent' parameter has been specified:

• one charge value for each atom index as a Double object if type is "charge" (no 'min-percent' parameter is given),
• a double array of charge values corresponding to the microspecies with occurrence percentage at least the given 'min-percent' value if type is "charges" ('distribution' parameter is given) - in this case the charge values are arranged according to descending microspecies distribution order (the first element of the charge array corresponds to the microspecies with maximal occurrence percentage).

Overrides:

getResult in class CalculatorPlugin

Parameters:

type - is the result type

index - is the result index

Returns:

the result item for the specified type and index

Throws:

PluginException - if the result cannot be returned

See Also:

• CalculatorPlugin.getResultTypes()

getResultAsString

public String getResultAsString(Object type,
 int index,
 Object result)
                         throws PluginException

Returns the specified result in String format. IonCharge returns the rounded ion charge value(s) in string format: the value is rounded using the 'precision' input parameter that determines the number of fractional digits displayed. Multiple values ("charges" case, double array) are separated by commas.

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

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 and stores the index-map between atom indices in the original and the new molecule. This map is used when the macropKa values and types are queried and the new atom indices should be mapped to the original ones. TODO: replace by call to chemaxon.standardizer.Standardizer

Overrides:

standardize in class CalculatorPlugin

Parameters:

mol - is the molecule to be standardized