Package chemaxon.marvin.calculations
Class MajorMicrospeciesAccessorPlugin
- java.lang.Object
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- chemaxon.marvin.plugin.CalculatorPlugin
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- chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin
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- 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
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Nested Class Summary
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Nested classes/interfaces inherited from class chemaxon.marvin.plugin.CalculatorPlugin
CalculatorPlugin.HydrogenData
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Field Summary
Fields Modifier and Type Field Description protected chemaxon.calculations.pka.Ionizer
ionizer
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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
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Constructor Summary
Constructors Constructor Description MajorMicrospeciesAccessorPlugin()
Constructor.
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Method Summary
All Methods Instance Methods Concrete Methods 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()
Returnstrue
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 toDouble.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
addHeavyAtomLimitChecker, addInputChecker, 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
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Method Detail
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isLicensed
public boolean isLicensed()
Description copied from class:CalculatorPlugin
Returnstrue
if the plugin is licensed. The license checking is based on the product name, returned byCalculatorPlugin.getProductName()
.- Specified by:
isLicensed
in interfacechemaxon.license.Licensable
- Overrides:
isLicensed
in classCalculatorPlugin
- Returns:
true
if the plugin is licensed
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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 classCalculatorPlugin
- Parameters:
params
- is the parameter table- Throws:
PluginException
- on error
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setpH
public void setpH(double pH)
Sets the pH: major microspecies on given pH is taken as input molecule if set toDouble.NaN
then the input molecule is taken as it is.- Parameters:
pH
- is the pH value
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getpH
public double getpH()
Returns the pH where the major microspecies should be taken. ReturnsDouble.NaN
if no microspecies calculation required.- Overrides:
getpH
in classCalculatorPlugin
- Returns:
- the pH where the major microspecies should be taken
or
Double.NaN
if no microspecies calculation
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createModifiedInputMolecule
protected final Molecule createModifiedInputMolecule(Molecule mol)
Returns the molecule form with largest distribution. Returns a microspecies with largest distribution on a given pH ifgetpH()
returns a value different fromDouble.NaN
, otherwise returns the input molecule itself.- Overrides:
createModifiedInputMolecule
in classCalculatorPlugin
- Parameters:
mol
- is the input molecule- Returns:
- the molecule form with largest distribution
- Throws:
PluginException
- on access error
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getErrorMessage
public String getErrorMessage()
Returns the calculation error information message or the empty string if there is no error.- Overrides:
getErrorMessage
in classCalculatorPlugin
- Returns:
- the calculation error information message
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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
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checkMolecule
public void checkMolecule(Molecule mol) throws PluginException
Checks the input molecule. Throws exception if the molecule molecule contains R-groups.- Overrides:
checkMolecule
in classCalculatorPlugin
- Parameters:
mol
- is the input molecule- Throws:
PluginException
- with error message for the user if the molecule is refused
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standardize
public void standardize(Molecule mol)
Standardizes the molecule. Adds dehydrogenization to default standardization in case when major microsepcies calculation required.- Overrides:
standardize
in classCalculatorPlugin
- Parameters:
mol
- is the molecule to be standardized
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