chemaxon.marvin.calculations
Class TPSAPlugin

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

public class TPSAPlugin

extends MajorMicrospeciesPlugin

Plugin class for TPSA (topological polar surface area) calculation. Both the incremental TPSA values for atoms and the overal TPSA value for the molecule can be calculated by this plugin.

Reference:

1. J.Med.Chem. 2000, 43, 3714-3717

API usage example:

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

    // create plugin
    TPSAPlugin plugin = new TPSAPlugin();
    plugin.validate(<TPSA license>);

    // optional: take major microspecies at pH=7.4
    // skip this if you want to calculate PSA for the input molecule as it is
    plugin.setpH(7.4);

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

    // get result
    double psa = plugin.getTPSA();

    // print result
    System.out.println("topological polar surface area (pH=7.4): "+psa);
 

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

TPSAPlugin()
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 java.lang.String	getLicenseKey() Returns the built-in license key for the given plugin class.
java.lang.String	getOutputClassName() Returns the output provider class name for the command line interface.
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 result item for the specified key 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.MOLECULE.
java.lang.Object[]	getResultTypes() Returns the result types.
double	getTPSA() Returns the TPSA value.
boolean	run() Runs the logP calculation.
protected void	setInputMolecule(Molecule mol) Sets the input molecule.
void	setParameters(java.util.Properties params) Sets the input parameters for the plugin.

Methods inherited from class chemaxon.marvin.calculations.MajorMicrospeciesPlugin

getMainMolecule, getMajorMicrospecies, getMolText, getpH, getSuffix, isMajorMs, setpH, standardize

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, 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

TPSAPlugin

public TPSAPlugin()

Constructor. Creates the logP calculator object.

Method Detail

getLicenseKey

protected final java.lang.String getLicenseKey()

Returns the built-in license key for the given plugin class. This license key has to be checked against the license key read from the property file.

Overrides:

getLicenseKey in class CalculatorPlugin

Returns:

the built-in license key for the given plugin class

See Also:

CalculatorPlugin.checkLicense()

setParameters

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

Sets the input parameters for the plugin. TPSA parameters and value ranges:

• precision: 0-8 or inf (number of displayed fractional digits, inf for unrounded value)

Overrides:

setParameters in class MajorMicrospeciesPlugin

Parameters:

params - is the parameter table

Throws:

PluginException - on error

checkMolecule

public void checkMolecule(Molecule mol)
                   throws PluginException

Checks the input molecule. Throws exception if the molecule is RxnMolecule, if the molecule contains R-groups or if the molecule consists of more than one fragments.

Overrides:

checkMolecule in class MajorMicrospeciesPlugin

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.

Overrides:

setInputMolecule in class MajorMicrospeciesPlugin

Parameters:

mol - is the (standardized) input molecule

Throws:

PluginException - on error

run

public boolean run()
            throws PluginException

Runs the logP calculation.

Overrides:

run in class MajorMicrospeciesPlugin

Returns:

true if the calculation was successful, false on calculation problems

Throws:

PluginException - on error

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 MajorMicrospeciesPlugin

Returns:

the calculation error information message

getResultTypes

public java.lang.Object[] getResultTypes()

Returns the result types. Possible result types: "PSA".

Overrides:

getResultTypes in class MajorMicrospeciesPlugin

Returns:

the result types

getResultDomain

public int getResultDomain(java.lang.Object type)

Returns the calculation domain CalculatorPlugin.MOLECULE.

Overrides:

getResultDomain in class MajorMicrospeciesPlugin

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 for the given result key. TPSA returns 1.

Overrides:

getResultCount in class MajorMicrospeciesPlugin

Parameters:

type - is the result type

Returns:

the number of result items

See Also:

getResultTypes()

getTPSA

public double getTPSA()

Returns the TPSA value.

Returns:

the TPSA value

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. The default implementation returns the original molecule clone.

Overrides:

getReferenceMolecule in class MajorMicrospeciesPlugin

Parameters:

type - is the result type

index - is the result index

Returns:

the original molecule clone

getResult

public java.lang.Object getResult(java.lang.Object type,
                                  int index)
                           throws PluginException

Returns the result item for the specified key and index. TPSA returns the required TPSA value as a Double object.

Overrides:

getResult in class MajorMicrospeciesPlugin

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:

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. logP returns the rounded logP value in string format: the value is rounded using the 'precision' input parameter that determines the number of fractional digits displayed.

Overrides:

getResultAsString in class MajorMicrospeciesPlugin

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

getOutputClassName

public java.lang.String getOutputClassName()

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

Overrides:

getOutputClassName in class MajorMicrospeciesPlugin

Returns:

the output provider class name