chemaxon.marvin.calculations

Class IsoelectricPointPlugin

java.lang.Object

chemaxon.marvin.plugin.CalculatorPlugin

chemaxon.marvin.calculations.IsoelectricPointPlugin

All Implemented Interfaces:

chemaxon.license.Licensable

@PublicAPI
public class IsoelectricPointPlugin
extends CalculatorPlugin

Plugin class for isoelectric point and pH - charge distribution calculation.

API usage example:

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

    // set plugin parameters
    plugin.setpHStep(0.4);

    // set target molecule
    plugin.setMolecule(mol);

    // run the calculation
    plugin.run();

    // get results

    // isoelectric point
    double pI = plugin.getpI();

    // charge distribution
    double[] pHs = plugin.getpHs();
    double[] charges = plugin.getChargeDistribution();

    // print results
    if (Double.isNaN(pI)) {
         System.out.println("No isoelectric point.");
    } else {
       System.out.println("pI = "+plugin.format(pI));
    }   
    System.out.println("\npH\tcharge");
    for (int i=0; i < pHs.length; ++i) {
        System.out.println(plugin.format(pHs[i])+"\t"+
                             plugin.format(charges[i]));
    }
 

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

Since:

Marvin 3.6

Version:

5.2.2 05/07/2009

Author:

Nora Mate, Zsolt Mohacsi

Nested Class Summary

Nested classes/interfaces inherited from class chemaxon.marvin.plugin.CalculatorPlugin

CalculatorPlugin.HydrogenData

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	TYPE_DISTR Type constant for microspecies distribution.

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
IsoelectricPointPlugin() 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.
double[]	getChargeDistribution() Returns the charge distribution array over pH values.
double[][]	getChargePlusMinusDistribution() Returns the plus and the minus parts of the charge distribution array over pH values.
java.lang.String	getErrorMessage() Returns the calculation error information message if run() returned false (calculation error): hydrogen valence error.
double[]	getpHs() Returns the pH array.
double	getpI() Returns the isoelectric point.
double[][]	getpKaOfpI() Returns the pKa values of the calculated isoelectric point.
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 key and index.
java.lang.Object	getResult(java.lang.Object type, java.lang.String arg) Returns the result item for the specified pH.
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.
Molecule	getResultMolecule() Returns the result molecule for display.
java.lang.Object[]	getResultTypes() Returns the result types.
java.lang.String	getTypeString(java.lang.Object type) Returns a string representation of the given type.
java.lang.String	getWarningMessage() Returns the calculation warning information message if no isoelectric point exists, returns the empty string otherwise.
protected boolean	isChargeCalc() Returns true if pH-Charge calculation.
boolean	run() Runs the isoelectric point and charge distribution calculations.
void	setConsiderTautomerization(boolean considerTautomerization) Sets to consider tautomerization.
protected void	setInputMolecule(Molecule mol) Sets the input molecule.
void	setKeepExplicitHydrogens(boolean keepExplicitHydrogens) Sets if result molecule keeps explicit hydrogens or not
void	setParameters(java.util.Properties params) Sets the input parameters for the plugin.
void	setpH(double pH) Sets a single pH value for the calculation of charge distribution.
void	setpHLower(double lower) Sets pH lower limit for the calculation of charge distribution (default: 0.0).
void	setpHStep(double step) Sets pH step for the calculation of charge distribution.
void	setpHUpper(double upper) Sets pH upper limit for the calculation of charge distribution (default: 14.0).
void	setProgressMonitor(MProgressMonitor pmon) Sets a progress observer to be used in run() to display progress status.
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, getDisplayMolecule, getDocument, getDoublePrecision, getExplicitHydrogenData, getInputMolDim, getMainMolecule, getOriginalMolecule, getpH, getPluginResource, getQueryMoleculeErrorMessage, getRemark, getResult, getResult, getResultAsRGB, getResultAsRGB, getResultAsString, getResultCount, getResultDomain, getResultMessage, getResultMolecules, getResultsAsRGB, getResultsAsRGB, getResultsAsString, getResultsAsString, getResultSource, handlesMultiFragmentMolecules, isInputMoleculeAromatized, isLicensed, isMsCalc, isMultiThreadedRunEnabled, isNegligibleResult, isOK, isRgrouped, loadClass, readAttribute, removeWhitespace, restoreExplicitHydrogens, setAtomIndexMap, setDoublePrecision, setDoublePrecision, setDoublePrecision, setKeepHydrogens, setLicenseEnvironment, setMolecule, setMolecule, setMolecule, setMolecule, standardizeIonicGroups, standardizeNeutralGroups

Methods inherited from class java.lang.Object

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

Field Detail

TYPE_DISTR

public static final java.lang.String TYPE_DISTR

Type constant for microspecies distribution.

See Also:

Constant Field Values

Constructor Detail

IsoelectricPointPlugin

public IsoelectricPointPlugin()

Constructor. Creates the isoelectric point calculator object.

Method Detail

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

setProgressMonitor

public void setProgressMonitor(MProgressMonitor pmon)

Sets a progress observer to be used in run() to display progress status. Short calculations may ignore the observer object. The default implementation does nothing.

Overrides:

setProgressMonitor in class CalculatorPlugin

Parameters:

pmon - is the progress monitor, may be null

setParameters

public void setParameters(java.util.Properties params)
                   throws PluginException

Sets the input parameters for the plugin. Isoelectric point parameters and value ranges:

• type: pI,chargedistr
• precision: 0-8 or inf (default: 2)
• pH: pH value - calculate charge distribution at a single pH
• lower: pH lower limit (default: 0.0)
• upper: pH upper limit (default: 14.0)
• step: pH step to be taken between lower and upper limits (default: 0.5)

Overrides:

setParameters in class CalculatorPlugin

Parameters:

params - is the parameter table

Throws:

PluginException - on error

isChargeCalc

protected boolean isChargeCalc()

Returns true if pH-Charge calculation.

Returns:

true if pH-Charge calculation

setpHLower

public void setpHLower(double lower)

Sets pH lower limit for the calculation of charge distribution (default: 0.0).

Parameters:

lower - is the pH lower limit

Since:

Marvin 5.2

setpHUpper

public void setpHUpper(double upper)

Sets pH upper limit for the calculation of charge distribution (default: 14.0).

Parameters:

upper - is the pH upper limit

Since:

Marvin 5.2

setpHStep

public void setpHStep(double step)

Sets pH step for the calculation of charge distribution. Range: between 0.0 and 0.5. The default value is 0.5.

Parameters:

step - is the pH step

setpH

public void setpH(double pH)

Sets a single pH value for the calculation of charge distribution.

Parameters:

pH - is the pH value

Since:

Marvin 5.2

setConsiderTautomerization

public void setConsiderTautomerization(boolean considerTautomerization)

Sets to consider tautomerization. Default: false.

Parameters:

considerTautomerization - the calculation will consider tautomerization and resonance if set (true)

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

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

run

public boolean run()
            throws PluginException

Runs the isoelectric point and charge distribution calculations.

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 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

getpI

public double getpI()

Returns the isoelectric point.

Returns:

the isoelectric point

getpKaOfpI

public double[][] getpKaOfpI()

Returns the pKa values of the calculated isoelectric point.

Returns:

array of the pKa values acidic pKa is returned in the zero column e.g [atomindex][0] basic pKa is returned in the first column e.g. [atomindex][1]

getpHs

public double[] getpHs()

Returns the pH array.

Returns:

the pH array

getChargeDistribution

public double[] getChargeDistribution()

Returns the charge distribution array over pH values.

Returns:

the charge distribution array

See Also:

getpHs()

getChargePlusMinusDistribution

public double[][] getChargePlusMinusDistribution()

Returns the plus and the minus parts of the charge distribution array over pH values.

Returns:

the distribution array of the negative and the positive charge count. negative charge count [0..size][0] positive charge count [0..size][1] size=(pHUpper-pHLower)/pHStepSize;

See Also:

getpHs()

getResultTypes

public java.lang.Object[] getResultTypes()

Returns the result types.

Overrides:

getResultTypes in class CalculatorPlugin

Returns:

the result types

getResultDomain

public int getResultDomain(java.lang.Object type)

Returns the calculation domain.

Overrides:

getResultDomain in class CalculatorPlugin

Parameters:

type - is the result type

Returns:

the calculation domain

See Also:

getResultTypes()

getResultCount

public int getResultCount(java.lang.Object type)

Returns the number of result items for the given result key. pKa 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 java.lang.Object getResult(java.lang.Object type,
                                  int index)
                           throws PluginException

Returns the result item for the specified key and index.

Overrides:

getResult in class CalculatorPlugin

Parameters:

type - is the result type

index - is the result index

Returns:

the result item for the specified key and index

Throws:

PluginException - if the result cannot be returned

See Also:

CalculatorPlugin.getResultTypes()

getResult

public java.lang.Object getResult(java.lang.Object type,
                                  java.lang.String arg)
                           throws PluginException

Returns the result item for the specified pH.

Overrides:

getResult in class CalculatorPlugin

Parameters:

type - is the result type (not used)

arg - is the pH as string

Returns:

the result item for the specified pH

Throws:

PluginException - if the result cannot be returned

See Also:

CalculatorPlugin.getResultTypes()

getResultAsString

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

Returns the specified result in String format. If the type is TYPE_DISTR then returns the pH - distribution table as a 2-column tab-separated table with the 0-th element the pH array and the 1-st element the distribution array corresponding to the microspecies with the specified index (result index). Otherwise returns the rounded pI value with one fractional digit precision.

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

getTypeString

public java.lang.String getTypeString(java.lang.Object type)

Returns a string representation of the given type.

Overrides:

getTypeString in class CalculatorPlugin

Parameters:

type - is the type object

Returns:

the type string

getWarningMessage

public java.lang.String getWarningMessage()

Returns the calculation warning information message if no isoelectric point exists, returns the empty string otherwise.

Overrides:

getWarningMessage in class CalculatorPlugin

Returns:

the calculation warning information message

getResultMolecule

public Molecule getResultMolecule()
                           throws PluginException

Returns the result molecule for display. Atomic results are stored in atom extra labels (MolAtom.getExtraLabel()). Molecular results are stored in molecule properties with keys being the result types (Molecule.getProperty(String)).

Overrides:

getResultMolecule in class CalculatorPlugin

Returns:

the result molecule

Throws:

PluginException - on error

Since:

Marvin 4.0

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

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