chemaxon.marvin.calculations

Class TPSAPlugin

java.lang.Object

chemaxon.marvin.plugin.CalculatorPlugin

chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin

chemaxon.marvin.calculations.TPSAPlugin

All Implemented Interfaces:

chemaxon.license.Licensable

@PublicAPI
public class TPSAPlugin
extends MajorMicrospeciesAccessorPlugin

Plugin class for TPSA (topological polar surface area) calculation.

Reference:

1. Ertl, P., Rohde, B., Selzer, P., J. Med. Chem., 2000, 43, pp. 3714-3717

API usage example:

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

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

    // optional: take major microspecies at pH=7.4
    plugin.setpH(7.4);

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

    // get result
    double area = plugin.getSurfaceArea();

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

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

Version:

Marvin 5.3.3

Author:

Nora Mate, Zsolt Mohacsi

Nested Class Summary

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

CalculatorPlugin.HydrogenData

Field Summary

Fields inherited from class chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin

ionizer

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
TPSAPlugin() Constructor.

Method Summary

Modifier and Type	Method and Description
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.
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.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.
Molecule	getResultMolecule() Returns the result molecule for display.
java.lang.Object[]	getResultTypes() Returns the result types.
double	getSurfaceArea() Returns the surface area.
double	getTPSA() Deprecated. as of Marvin 4.1, replaced by getSurfaceArea()
java.lang.String	getTypeString(java.lang.Object type) Returns a string representation of the given type.
boolean	run() Runs the surface area calculation.
void	setExcludePhosphorus(boolean p) Sets to exclude phosphorus from PSA calculation. Default: true, phosphorus i excluded.
void	setExcludeSulfur(boolean s) Sets to exclude sulfur from PSA calculation. Default: true, sulfur i excluded.
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.MajorMicrospeciesAccessorPlugin

createModifiedInputMolecule, getIonizerErrorMessage, getpH, isLicensed, setpH, standardize

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, getPluginResource, getQueryMoleculeErrorMessage, getRemark, getResult, getResult, getResult, getResultAsRGB, getResultAsRGB, getResultAsString, getResultCount, getResultDomain, getResultMessage, getResultMolecules, getResultsAsRGB, getResultsAsRGB, getResultsAsString, getResultsAsString, getResultSource, getWarningMessage, handlesMultiFragmentMolecules, isInputMoleculeAromatized, isMsCalc, isMultiThreadedRunEnabled, isNegligibleResult, isOK, isRgrouped, loadClass, readAttribute, removeWhitespace, restoreExplicitHydrogens, setAtomIndexMap, setDoublePrecision, setDoublePrecision, setDoublePrecision, setKeepHydrogens, setLicenseEnvironment, setMolecule, 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

TPSAPlugin

public TPSAPlugin()

Constructor. Creates the TPSA calculator object.

Method Detail

getProductName

public java.lang.String getProductName()

Description copied from class: CalculatorPlugin

Returns the product identifier of the plugin as given by LicenseManager. The name is used by the CalculatorPlugin.isLicensed() method.

Specified by:

getProductName in class CalculatorPlugin

Returns:

product identifier or a default string

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)
• pH: major microspecies on given pH is taken as input molecule if omitted then the input molecule is taken as it is

Overrides:

setParameters in class MajorMicrospeciesAccessorPlugin

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 MajorMicrospeciesAccessorPlugin

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 (standardized) input molecule

Throws:

PluginException - on error

setExcludeSulfur

public void setExcludeSulfur(boolean s)

Sets to exclude sulfur from PSA calculation.
Default: true, sulfur i excluded.

Parameters:

s - if true sulfur is excluded from PSA calculation

Since:

Marvin 5.3.3

setExcludePhosphorus

public void setExcludePhosphorus(boolean p)

Sets to exclude phosphorus from PSA calculation.
Default: true, phosphorus i excluded.

Parameters:

p - if true phosphorus is excluded from PSA calculation

Since:

Marvin 5.3.3

run

public boolean run()
            throws PluginException

Runs the surface area calculation.

Specified by:

run in class CalculatorPlugin

Returns:

true if the calculation was successful, false on calculation problems

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 MajorMicrospeciesAccessorPlugin

Returns:

the calculation error information message

getResultTypes

public java.lang.Object[] getResultTypes()

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

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 for the given result key. TPSA returns 1.

Overrides:

getResultCount in class CalculatorPlugin

Parameters:

type - is the result type

Returns:

the number of result items

See Also:

getResultTypes()

getTPSA

@Deprecated
public double getTPSA()

Deprecated. as of Marvin 4.1, replaced by getSurfaceArea()

Returns the TPSA value.

Returns:

the TPSA value

getSurfaceArea

public double getSurfaceArea()

Returns the surface area.

Returns:

the surface area

Since:

Marvin 4.1

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 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:

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.

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

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