chemaxon.marvin.calculations
Class logDPlugin

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

public class logDPlugin

extends CalculatorPlugin

Plugin class for logD calculation.

Field Summary

Fields inherited from class chemaxon.marvin.plugin.CalculatorPlugin

ATOM, CHART, MOLECULE, NAN, SUBRESULT

Constructor Summary

logDPlugin()
Constructor.

Method Summary

double	calclogD(double pH) Returns the logD value at fixed pH.
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[]	getlogDs() Returns the logD array.
java.lang.String	getOutputClassName() Returns the output provider class name for the command line interface.
double[]	getpHs() Returns the pH array.
double[]	getReflogDs() Returns the reference logD array.
double[]	getRefpHs() Returns the reference pH array.
java.lang.Object	getResult(java.lang.Object type, int index) Returns the result item for the specified type 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 CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.
java.lang.Object[]	getResultTypes() Returns the result types.
java.lang.String	getXAxisLabel(java.lang.Object type) Returns the X axis label to be displayed in case of chart data.
java.lang.String[]	getXLabels() Returns the X label array (pH array as String[]).
java.lang.String	getYAxisLabel(java.lang.Object type) Returns the Y axis label to be displayed.
boolean	run() Runs the logD calculation.
protected void	setInputMolecule(Molecule mol) Sets the input molecule.
void	setParameters(java.util.Properties params) Sets the input parameters for the plugin.
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, getResultAsRGB, getResultAsRGB, getResultAsString, getResultCount, getResultDomain, getResultsAsRGB, getResultsAsRGB, getResultsAsString, getResultsAsString, getTypeString, 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

logDPlugin

public logDPlugin()

Constructor. Creates the charge 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. Charge 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)
• lower: pH lower limit (default: 0.0)
• upper: pH upper limit (default: 14.0)
• count: pH step count between lower and upper limits (default: 0.5)
• ref1-ref4: reference pH values

Specified by:

setParameters in class CalculatorPlugin

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 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 logD 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()

calclogD

public double calclogD(double pH)
                throws PluginException

Returns the logD value at fixed pH.

Parameters:

pH - is the pH value

Returns:

the logD value at the given pH

Throws:

PluginException - on error

getResultTypes

public java.lang.Object[] getResultTypes()

Returns the result types. Possible result types: "logD", "reflogD".

Specified by:

getResultTypes in class CalculatorPlugin

Returns:

the result types

getRefpHs

public double[] getRefpHs()

Returns the reference pH array.

Returns:

the reference pH array

getReflogDs

public double[] getReflogDs()

Returns the reference logD array.

Returns:

the reference logD array

getpHs

public double[] getpHs()

Returns the pH array.

Returns:

the pH array

getlogDs

public double[] getlogDs()

Returns the logD array.

Returns:

the logD array

getXAxisLabel

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

Returns the X axis label to be displayed in case of chart data.

Overrides:

getXAxisLabel in class CalculatorPlugin

Parameters:

type - is the result type

getYAxisLabel

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

Returns the Y axis label to be displayed.

Overrides:

getYAxisLabel in class CalculatorPlugin

Parameters:

type - is the result type

getResultDomain

public int getResultDomain(java.lang.Object type)

Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE. Can be combined with CalculatorPlugin.CHART to denote chart-type data. logD returns CalculatorPlugin.MOLECULE combined with CalculatorPlugin.CHART for type "logD", CalculatorPlugin.MOLECULE combined with CalculatorPlugin.SUBRESULT for type "reflogD".

Specified by:

getResultDomain in class CalculatorPlugin

Parameters:

type - is the result type

Returns:

CalculatorPlugin.MOLECULE

See Also:

CalculatorPlugin.getResultTypes()

getResultCount

public int getResultCount(java.lang.Object type)

Returns the number of result items for the given result key. logD returns 1.

Specified by:

getResultCount in class CalculatorPlugin

Parameters:

type - is the result type

Returns:

the number of result items

See Also:

CalculatorPlugin.getResultTypes()

getResult

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

Returns the result item for the specified type and index. logD returns the main or reference (pH, logD) arrays as a double[2][] with the 0-th element the pH array and the 1-st element the logD array.

Specified by:

getResult in class CalculatorPlugin

Parameters:

type - is the result type: "logD" or "reflogD"

index - is the result index

Returns:

the result item for the specified type 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. logD returns the rounded (pH, logD) value pairs in string format: the values are rounded using the 'precision' input parameter that determines the number of fractional digits displayed, pH and logD are separated by a tab character.

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

getXLabels

public java.lang.String[] getXLabels()

Returns the X label array (pH array as String[]).

Overrides:

getXLabels in class CalculatorPlugin

Returns:

the X label array

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. 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