@PublicAPI public class IonChargePlugin extends CalculatorPlugin
For concurrent plugin example applications using ChemAxon's concurrent framework, refer to the Concurrent plugin examples.
CalculatorPlugin.HydrogenData
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 and Description |
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IonChargePlugin()
Constructor.
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Modifier and Type | Method and Description |
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void |
checkMolecule(Molecule mol)
Checks the input molecule.
|
java.lang.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. |
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 . |
java.lang.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.
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protected void |
setInputMolecule(Molecule mol)
Sets the input molecule.
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void |
setParameters(java.util.Properties params)
Sets the input parameters for the plugin.
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void |
standardize(Molecule mol)
Standardizes the molecule.
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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, getResultMolecule, getResultMolecules, getResultsAsRGB, getResultsAsRGB, getResultsAsString, getResultsAsString, getResultSource, getTypeString, 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
public IonChargePlugin()
public java.lang.String getProductName()
LicenseManager
.getProductName
in class CalculatorPlugin
LicenseManager.CHARGE_PLUGIN_GROUP
public void setParameters(java.util.Properties params) throws PluginException
setParameters
in class CalculatorPlugin
params
- is the parameter tablePluginException
- on errorpublic void checkMolecule(Molecule mol) throws PluginException
checkMolecule
in class CalculatorPlugin
mol
- is the input moleculePluginException
- with error message for the user if the molecule is refusedprotected void setInputMolecule(Molecule mol) throws PluginException
setInputMolecule
in class CalculatorPlugin
mol
- is the input moleculePluginException
- on errorpublic boolean run() throws PluginException
run
in class CalculatorPlugin
PluginException
- on errorCalculatorPlugin.getErrorMessage()
public java.lang.String getErrorMessage()
run()
returned false (calculation error): the number of ionizable atoms
exceeds the specified limit (given in the "ions" parameter) or
hydrogen valence error.getErrorMessage
in class CalculatorPlugin
public java.lang.Object[] getResultTypes()
getResultTypes
in class CalculatorPlugin
public int getResultDomain(java.lang.Object type)
CalculatorPlugin.ATOM
or
CalculatorPlugin.MOLECULE
.
pKa always returns CalculatorPlugin.ATOM
.getResultDomain
in class CalculatorPlugin
type
- is the result typeCalculatorPlugin.ATOM
getResultTypes()
public int getResultCount(java.lang.Object type)
getResultCount
in class CalculatorPlugin
type
- is the result typegetResultTypes()
public java.lang.Object getResult(java.lang.Object type, int index) throws PluginException
getResult
in class CalculatorPlugin
type
- is the result typeindex
- is the result indexPluginException
- if the result cannot be returnedCalculatorPlugin.getResultTypes()
public java.lang.String getResultAsString(java.lang.Object type, int index, java.lang.Object result) throws PluginException
getResultAsString
in class CalculatorPlugin
type
- is the result typeindex
- is the result indexresult
- is the result itemPluginException
- if an invalid result item is givenpublic void standardize(Molecule mol)
standardize
in class CalculatorPlugin
mol
- is the molecule to be standardized