chemaxon.marvin.calculations

Class MajorMicrospeciesPlugin

java.lang.Object

chemaxon.marvin.plugin.CalculatorPlugin

chemaxon.marvin.calculations.MajorMicrospeciesPlugin

All Implemented Interfaces:

chemaxon.license.Licensable

@PublicAPI
public class MajorMicrospeciesPlugin
extends CalculatorPlugin

Plugin class that calculates the major microspecies on a given pH.

API usage example:

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

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

    // set pH
    plugin.setpH(7.4);

    // set target molecule
    plugin.setMolecule(mol);
        
    // run the calculation
    plugin.run();

    // get result
    Molecule msmol = plugin.getMajorMicrospecies();

    // print result
    System.out.println("Major microspecies at pH=7.4: "+msmol.toFormat("smiles"));
 

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

Version:

5.2 11/19/2008

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
MajorMicrospeciesPlugin() Constructor.

Method Summary

Modifier and Type	Method and Description
void	checkMolecule(Molecule mol) Checks the input molecule.
protected Molecule	createModifiedInputMolecule(Molecule mol) Returns the major tautomeric form of the molecule.
protected Molecule	getDisplayMolecule() Returns the molecule object to be used for GUI display.
java.lang.String	getErrorMessage() Returns the calculation error information message or the empty string if there is no error.
java.lang.String	getIonizerErrorMessage() Returns the calculation error information message or the empty string if there is no error.
Molecule	getMajorMicrospecies() Returns the major microspecies at the pH set in setpH(double).
Molecule	getMicrospecies(int index) Returns the microspecies molecule.
int	getMicrospeciesCount() Returns the number of microspecies
double	getpH() Returns the pH where the major microspecies should be taken.
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 microsepcies if pH is different from Double.NaN, otherwise returns the input molecule itself.
java.lang.String	getResultAsString(java.lang.Object type, int index, java.lang.Object result) Returns the specified result molecule in SMILES format.
int	getResultCount(java.lang.Object type) Returns the number of result items: 1.
int	getResultDomain(java.lang.Object type) Returns the calculation domain CalculatorPlugin.MOLECULE.
Molecule	getResultMolecule() Returns the major microspecies for display.
java.lang.Object[]	getResultTypes() Returns the result types (possible types: "majority-ms").
Molecule	getSortedMicrospecies(int index) Returns the microspecies molecule, sorted by descreasing distribution at the given pH.
double	getSortedMsDistribution(int index) Returns the microspecies distribution, sorted by descreasing distribution at the given pH.
boolean	handlesMultiFragmentMolecules() Returns true if the plugin handles multifragment molecules, false otherwise.
boolean	run() Stores the input molecule with ungrouped sgroups.
void	setCorrectionLibrary(java.lang.String correctionLibraryId) Sets the correction library.
void	setCorrectionLibraryPath(java.lang.String correctionLibraryPath) Sets the correction library file directly.
protected void	setInputMolecule(Molecule mol) Sets the input molecule.
void	setKeepExplicitHydrogens(boolean keepExplicitHydrogens) Sets if result molecule keeps explicit hydrogens or not
Molecule	setMolecule(Molecule mol, boolean st, boolean om) Sets the input molecule after an optional standardization and/or modification.
void	setParameters(java.util.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	setTakeMajorTatomericForm(boolean takeMajorTautomericForm) Sets to use major tautomeric form in calculation.
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, getDocument, getDoublePrecision, getExplicitHydrogenData, getInputMolDim, getMainMolecule, getOriginalMolecule, getPluginResource, getQueryMoleculeErrorMessage, getRemark, getResult, getResult, getResult, getResultAsRGB, getResultAsRGB, getResultAsString, getResultCount, getResultDomain, getResultMessage, getResultMolecules, getResultsAsRGB, getResultsAsRGB, getResultsAsString, getResultsAsString, getResultSource, getTypeString, getWarningMessage, isInputMoleculeAromatized, isLicensed, isMsCalc, isMultiThreadedRunEnabled, isNegligibleResult, isOK, isRgrouped, loadClass, readAttribute, removeWhitespace, restoreExplicitHydrogens, setAtomIndexMap, setDoublePrecision, setDoublePrecision, setDoublePrecision, setKeepHydrogens, setLicenseEnvironment, 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

MajorMicrospeciesPlugin

public MajorMicrospeciesPlugin()

Constructor. Creates the ionizer object.

Method Detail

setMolecule

public Molecule setMolecule(Molecule mol,
                            boolean st,
                            boolean om)
                     throws PluginException

Description copied from class: CalculatorPlugin

Sets the input molecule after an optional standardization and/or modification. Standardization includes plugin specific standardization (e.g. dehydrogenize, aromatize) and sgroup expansion, modification usually means taking a microspecies form, or the major tautomeric form of the input molecule (usually optional). The input molecule is left unchanged (it is cloned before standardization/modification if required).

Overrides:

setMolecule in class CalculatorPlugin

Parameters:

mol - is the input molecule

st - is true if standardization is required

om - is true if original input molecule is to be used for atom indexing false if modified molecule is to be used for atom indexing

Returns:

the molecule to be used for atom indexing

Throws:

PluginException - on error

See Also:

CalculatorPlugin.setInputMolecule(Molecule), CalculatorPlugin.createStandardizedMolecule(Molecule), CalculatorPlugin.createModifiedInputMolecule(Molecule)

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.PROTONATION_PLUGIN_GROUP

setParameters

public void setParameters(java.util.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

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

setTakeMajorTatomericForm

public void setTakeMajorTatomericForm(boolean takeMajorTautomericForm)

Sets to use major tautomeric form in calculation. Default: false.

Parameters:

takeMajorTautomericForm - the calculation will be performed on the major tutomeric form of the input molecule if set (true)

Since:

Marvin 5.2

setCorrectionLibrary

public void setCorrectionLibrary(java.lang.String correctionLibraryId)

Sets the correction library.

Parameters:

correctionLibraryId - is the correction library identifier

Since:

Marvin 21.16

setCorrectionLibraryPath

public void setCorrectionLibraryPath(java.lang.String correctionLibraryPath)

Sets the correction library file directly.

Parameters:

correctionLibraryPath -

Since:

Marvin 21.16

createModifiedInputMolecule

protected final Molecule createModifiedInputMolecule(Molecule mol)
                                              throws PluginException

Returns the major tautomeric form of the molecule.

Overrides:

createModifiedInputMolecule in class CalculatorPlugin

Parameters:

mol - is the input molecule

Returns:

the major tautomeric form of the molecule

Throws:

PluginException - on error

Since:

Marvin 5.2

run

public boolean run()
            throws PluginException

Stores the input molecule with ungrouped sgroups.

Specified by:

run in class CalculatorPlugin

Returns:

true if the calculation was successful, false on calculation error

Throws:

PluginException - on error

See Also:

CalculatorPlugin.getErrorMessage()

getMajorMicrospecies

public Molecule getMajorMicrospecies()
                              throws PluginException

Returns the major microspecies at the pH set in setpH(double).

Returns:

the major microspecies

Throws:

PluginException - if run() has not been called beforehand

getMicrospeciesCount

public int getMicrospeciesCount()
                         throws PluginException

Returns the number of microspecies

Returns:

the number of microspecies

Throws:

PluginException - on error

getMicrospecies

public Molecule getMicrospecies(int index)
                         throws PluginException

Returns the microspecies molecule.

Parameters:

index - is the microspecies index

Returns:

the microspecies molecule

Throws:

PluginException - on error

getSortedMicrospecies

public Molecule getSortedMicrospecies(int index)
                               throws PluginException

Returns the microspecies molecule, sorted by descreasing distribution at the given pH.

Parameters:

index - is the microspecies index

Returns:

the microspecies molecule

Throws:

PluginException - on error

getSortedMsDistribution

public double getSortedMsDistribution(int index)
                               throws PluginException

Returns the microspecies distribution, sorted by descreasing distribution at the given pH.

Parameters:

index - is the microspecies index

Returns:

the microspecies distribution

Throws:

PluginException - on error

getResultTypes

public java.lang.Object[] getResultTypes()

Returns the result types (possible types: "majority-ms").

Overrides:

getResultTypes in class CalculatorPlugin

Returns:

the result types

getResultDomain

public int getResultDomain(java.lang.Object type)

Returns the calculation domain CalculatorPlugin.MOLECULE.

Overrides:

getResultDomain in class CalculatorPlugin

Parameters:

type - is the result type

Returns:

CalculatorPlugin.MOLECULE

See Also:

getResultTypes()

getResultCount

public int getResultCount(java.lang.Object type)

Returns the number of result items: 1.

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 microsepcies if pH is different from Double.NaN, otherwise returns the input molecule itself.

Overrides:

getResult in class CalculatorPlugin

Parameters:

type - is the result type ("major-ms", "ms", "ms-count" or "ms-distr")

index - is the microspecies index

Returns:

the result item for the specified type 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 molecule in SMILES format.

Overrides:

getResultAsString in class CalculatorPlugin

Parameters:

type - is the result type

index - is the result index

result - is the result item (molecule)

Returns:

the specified result in String format

Throws:

PluginException - if an invalid result item is given

getDisplayMolecule

protected Molecule getDisplayMolecule()
                               throws PluginException

Returns the molecule object to be used for GUI display. This is the major microspecies returned by getMajorMicrospecies().

Overrides:

getDisplayMolecule in class CalculatorPlugin

Returns:

the molecule object to be used for GUI display

Throws:

PluginException - on error

getResultMolecule

public Molecule getResultMolecule()
                           throws PluginException

Returns the major microspecies for display.

Overrides:

getResultMolecule in class CalculatorPlugin

Returns:

the major microspecies

Throws:

PluginException - on error

Since:

Marvin 4.0

getErrorMessage

public java.lang.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 java.lang.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

setKeepExplicitHydrogens

public void setKeepExplicitHydrogens(boolean keepExplicitHydrogens)

Sets if result molecule keeps explicit hydrogens or not

Parameters:

keepExplicitHydrogens - if the result should keep explicit hydrogens or not

handlesMultiFragmentMolecules

public boolean handlesMultiFragmentMolecules()

Returns true if the plugin handles multifragment molecules, false otherwise. This plugin handles multifragment molecules, so it returns true.

Overrides:

handlesMultiFragmentMolecules in class CalculatorPlugin

Returns:

true because this plugin handles multifragment molecules in case of salt type strutures.e.g.[Na+].CC([O-])=O