chemaxon.marvin.calculations
Class logPPlugin

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

public class logPPlugin

extends CalculatorPlugin

Plugin class for logP calculation. Both the incremental logP values for atoms and the overal logP value for the molecule can be calculated by this plugin.

Reference:

1. J.Chem.Inf.Comput.Sci. 1989, 29, 163-172

Field Summary

Fields inherited from class chemaxon.marvin.plugin.CalculatorPlugin

ATOM, CHART, MOLECULE, NAN, SUBRESULT

Constructor Summary

logPPlugin()
Constructor.

Method Summary

void	checkMolecule(Molecule mol) Checks the input molecule.
protected java.lang.String	getLicenseKey() Returns the built-in license key for the given plugin class.
double	getlogDpI() Returns the logD value at pI.
double	getlogPMicro() Returns the micro logP value.
double	getlogPNonionic() Returns the logP value for the non-ionic form.
double	getlogPTrue() Returns the most typical logP among logD at pI, micro logP and nonionic logP.
java.lang.String	getOutputClassName() Returns the output provider class name for the command line interface.
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.ATOM or CalculatorPlugin.MOLECULE.
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.Object[]	getUserTypes() Returns the user defined result types.
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.
void	setUserTypes(java.lang.String chtypes) Sets user types.
protected void	standardize(Molecule mol) Standardizes the molecule.

Methods inherited from class chemaxon.marvin.plugin.CalculatorPlugin

check, checkLicense, checkLicenseKey, create, createStandardizedMolecule, dehydrogenize, format, format, format, format, getAtomCount, getAtomIndex, getDoublePrecision, getErrorMessage, getReferenceMolecule, getResult, getResult, getResult, getResultAsRGB, getResultAsRGB, getResultAsString, getResultCount, getResultDomain, getResultsAsRGB, getResultsAsRGB, getResultsAsString, getResultsAsString, getXAxisLabel, getXLabels, getYAxisLabel, handlesMultiFragmentMolecules, isLicensed, isNegligibleResult, isRgrouped, setDoublePrecision, setDoublePrecision, setLicense, setMolecule, setMolecule, standardizeNitro, validate

Methods inherited from class java.lang.Object

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

Constructor Detail

logPPlugin

public logPPlugin()

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. logP parameters and value ranges:

• precision: 0-8 or inf (number of displayed fractional digits, inf for unrounded value)
• anion: Cl- ion concentration (default: 0.1)
• kation: Na+ plus K+ ion concentration (default: 0.1)
• type: increments,logP,logPTrue,logPMicro,logPNonionic,logDpI (logP means all of, logPTrue means the most typical of logPMicro,logPNonionic,logDpI which exists for the input molecule)
• implh: true or false (display increments on implicit H atoms)

Specified by:

setParameters in class CalculatorPlugin

Parameters:

params - is the parameter table

Throws:

PluginException - on error

setUserTypes

public void setUserTypes(java.lang.String chtypes)

Sets user types. Possible types: logP,logPTrue,logPMicro,logPNonionic,logDpI (logP means all of, logPTrue means the most typical of logPMicro,logPNonionic,logDpI which exists for the input molecule) multiple values should be separated by "," (e.g.: "logPTrue,logPNonionic,logDpI").

Parameters:

chtypes - is the type string

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 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 (standardized) input molecule

Throws:

PluginException - on error

run

public boolean run()
            throws PluginException

Runs the logP 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()

getlogPMicro

public double getlogPMicro()

Returns the micro logP value. The logP calculation should be run beforehand by run().

Returns:

the micro logP value

getlogPNonionic

public double getlogPNonionic()

Returns the logP value for the non-ionic form. The logP calculation should be run beforehand by run().

Returns:

the nonionic logP value

getlogDpI

public double getlogDpI()

Returns the logD value at pI. The logP calculation should be run beforehand by run().

Returns:

the logDpI value

getlogPTrue

public double getlogPTrue()

Returns the most typical logP among logD at pI, micro logP and nonionic logP.

Returns:

the most typical logP value

getResultTypes

public java.lang.Object[] getResultTypes()

Returns the result types. Possible result types: "logPTrue" (most typical logP) "logPMicro", "logPNonionic", "logDpI", "increments", "implh".

Specified by:

getResultTypes in class CalculatorPlugin

Returns:

the result types

getUserTypes

public java.lang.Object[] getUserTypes()

Returns the user defined result types. Possible result types: "logP" (all of micro logP, nonionic logP and logD at pI), "logPTrue" (most typical logP), "logPMicro", "logPNonionic", "logDpI", "increments", "implh".

Returns:

the result types

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

getResultDomain

public int getResultDomain(java.lang.Object type)

Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE. Returns CalculatorPlugin.ATOM for type "increments" or "implh" and CalculatorPlugin.MOLECULE otherwise.

Specified by:

getResultDomain in class CalculatorPlugin

Parameters:

type - is the result type

Returns:

CalculatorPlugin.MOLECULE or CalculatorPlugin.ATOM

See Also:

getResultTypes()

getResultCount

public int getResultCount(java.lang.Object type)

Returns the number of result items for the given result key. logP returns the atom count for types "increments" and "implh" 1 otherwise.

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

Specified by:

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. 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.

Specified by:

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

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 "chemaxon.marvin.calculations.logPOutput"

standardize

protected 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. TODO: replace by call to chemaxon.reaction.Standardizer

Overrides:

standardize in class CalculatorPlugin

Parameters:

mol - is the molecule to be standardized