chemaxon.marvin.calculations
Class MajorMicrospeciesPlugin

java.lang.Object
  chemaxon.marvin.plugin.CalculatorPlugin
      chemaxon.marvin.calculations.MajorMicrospeciesPlugin

Direct Known Subclasses:

ChargePlugin, HBDAPlugin, HuckelAnalysisPlugin, PolarizabilityPlugin, TPSAPlugin

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();

    // 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"));
 

Field Summary

Fields inherited from class chemaxon.marvin.plugin.CalculatorPlugin

ATOM, BLUE, CALCRGB_OFF, CHART, HYDROGEN_VALENCE_ERROR_MSG, MOLECULE, NAN, RED, SUBRESULT

Constructor Summary

MajorMicrospeciesPlugin()
Constructor.

Method Summary

void	checkMolecule(Molecule mol) Checks the input molecule.
java.lang.String	getErrorMessage() Returns the calculation error information message if run() returned false (calculation error): hydrogen valence error.
protected Molecule	getMainMolecule(Molecule mol) Returns the molecule form with largest distribution.
Molecule	getMajorMicrospecies() Returns the major microspecies at the pH set in setpH(double).
protected java.lang.String	getMolText() Returns the plugin molecule text to be displayed in the viewer.
java.lang.String	getOutputClassName() Returns the output provider class name for the command line interface.
double	getpH() Returns the pH where the majority microspecies should be taken.
Molecule	getReferenceMolecule(java.lang.Object type, int index) Returns the molecule to be used as reference image for the given result type and index.
java.lang.Object	getResult(java.lang.Object type, int index) Returns the majority 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 rsule 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.
java.lang.Object[]	getResultTypes() Returns the result types (possible types: "majority-ms").
protected java.lang.String	getSuffix() Returns the plugin text suffix.
protected boolean	isMajorMs() Returns true if major microspecies required, ie, if pH is different from Double.NaN.
boolean	run() Does nothing, the input molecule is already standardized and set to the majority microsepcies.
protected void	setInputMolecule(Molecule mol) Sets the input molecule.
void	setParameters(java.util.Properties params) Sets the input parameters for the plugin.
void	setpH(double pH) Sets the pH: majority microspecies on given pH is taken as input molecule if set to Double.NaN then the input molecule is taken as it is.
protected void	standardize(Molecule mol) Standardizes the molecule.

Methods inherited from class chemaxon.marvin.plugin.CalculatorPlugin

check, checkLicense, checkLicenseKey, checkType, create, createImageMolecule, createStandardizedMolecule, dehydrogenize, format, format, format, format, getAtomCount, getAtomIndex, getChartColor, getDoublePrecision, getGUIResultTypes, getLicenseKey, getResult, getResult, getResult, getResultAsRGB, getResultAsRGB, getResultAsString, getResultCount, getResultDomain, getResultsAsRGB, getResultsAsRGB, getResultsAsString, getResultsAsString, getTypeString, getXAxisLabel, getXLabels, getYAxisLabel, handlesMultiFragmentMolecules, isLicensed, isMajorityMsCalculation, isMsCalc, isNegligibleResult, isRgrouped, removeWhitespace, saveLicense, setDoublePrecision, setDoublePrecision, setDoublePrecision, setLicense, setMolecule, setMolecule, setMolecule, standardizeGroups, validate

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

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

Specified by:

setParameters in class CalculatorPlugin

Parameters:

params - is the parameter table

Throws:

PluginException - on error

setpH

public void setpH(double pH)

Sets the pH: majority 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 majority microspecies should be taken. Returns Double.NaN if no microspecies calculation required.

Returns:

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

getMainMolecule

protected Molecule getMainMolecule(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:

getMainMolecule in class CalculatorPlugin

Parameters:

mol - is the input molecule

Returns:

the molecule form with largest distribution

isMajorMs

protected boolean isMajorMs()

Returns true if major microspecies required, ie, if pH is different from Double.NaN.

Overrides:

isMajorMs in class CalculatorPlugin

Returns:

true if major microspecies required

getSuffix

protected java.lang.String getSuffix()

Returns the plugin text suffix. Returns " at pH " if pH is different from Double.NaN, returns the empty string otherwise.

Overrides:

getSuffix in class CalculatorPlugin

Returns:

the plugin text suffix

getMolText

protected java.lang.String getMolText()

Returns the plugin molecule text to be displayed in the viewer. Returns "pH = " if pH is different from Double.NaN, returns null otherwise.

Overrides:

getMolText in class CalculatorPlugin

Returns:

the plugin molecule text

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

Does nothing, the input molecule is already standardized and set to the majority microsepcies.

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()

getErrorMessage

public java.lang.String getErrorMessage()

Returns the calculation error information message if run() returned false (calculation error): hydrogen valence error.

Overrides:

getErrorMessage in class CalculatorPlugin

Returns:

the calculation error information message

getMajorMicrospecies

public Molecule getMajorMicrospecies()

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

Returns:

the major microspecies

getReferenceMolecule

public Molecule getReferenceMolecule(java.lang.Object type,
                                     int index)

Returns the molecule to be used as reference image for the given result type and index. Returns null.

Overrides:

getReferenceMolecule in class CalculatorPlugin

Parameters:

type - is the result type

index - is the result index

Returns:

null

getResultTypes

public java.lang.Object[] getResultTypes()

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

Specified by:

getResultTypes in class CalculatorPlugin

Returns:

the result types

getResultDomain

public int getResultDomain(java.lang.Object type)

Returns the calculation domain CalculatorPlugin.MOLECULE.

Specified by:

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.

Specified by:

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

Specified by:

getResult in class CalculatorPlugin

Parameters:

type - is the result type ("major-ms")

index - is no used

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 rsule molecule in SMILES format.

Specified by:

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

getOutputClassName

public java.lang.String getOutputClassName()

Returns the output provider class name for the command line interface.

Overrides:

getOutputClassName in class CalculatorPlugin

Returns:

the output provider class name

standardize

protected 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