logPPlugin (JChem Base API documentation (c) 1998-2020 ChemAxon Ltd.)

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

All Implemented Interfaces:: chemaxon.license.Licensable

@PublicAPI
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:

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

API usage example:

    // fill parameters
    Properties params = new Properties();
    params.put("type", "logP");

    // create plugin
    logPPlugin plugin = new logPPlugin();
    
    // set logP calculation method
    plugin.setlogPMethod(logPPlugin.METHOD_WEIGHTED);
    
    // set method weights
    plugin.setWeightOfMethods(1, 2, 1, 0);

    // set parameters
    plugin.setCloridIonConcentration(0.2);
    plugin.setNaKIonConcentration(0.2);

    // set result types
    plugin.setUserTypes("logPTrue,logPMicro");

    // for each input molecule run the calculation and display the results
    System.out.println("molecule\tlogP");
    MolImporter mi = new MolImporter("targets.sdf")));
    Molecule target = null;
    while ((target = mi.read()) != null) {

        // set the input molecule
        plugin.setMolecule(target);

        // run the calculation
        plugin.run();

        // get the overal logP value
        double logp = plugin.getlogPTrue(); 
        double logpm = plugin.getlogPMicro();

        System.out.println("True logP : "+logp);
        System.out.println("Micro logP: "+logpm);
        System.out.println();
    }  
    mi.close();

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

Version:: 5.4 09/28/2010
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 int`	`METHOD_KLOP` Deprecated. This field will not be available from May 2016. Use `LogPMethod` instead.
`static int`	`METHOD_PHYS` Deprecated. This field will not be available from May 2016. Use `LogPMethod` instead.
`static int`	`METHOD_USER_DEFINED` Deprecated. Use `LogPMethod.USER_DEFINED` instead.
`static int`	`METHOD_VG` Deprecated. Use `LogPMethod.CHEMAXON` instead.
`static int`	`METHOD_WEIGHTED` Deprecated. Use `LogPMethod.CONSENSUS` instead.

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

logPPlugin()
Constructor.

Constructors
Constructor and Description
`logPPlugin()` Constructor.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods Deprecated Methods
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`	`getAtomlogPHIncrement(int index)` Deprecated. Increments of implicit H-s are not calculated. Returns the same value as `getAtomlogPIncrement(int)`
`double`	`getAtomlogPIncrement(int index)` Returns the logP increment for the specified atom.
`java.lang.String`	`getErrorMessage()` Returns the calculation error information message if `run()` returned false (calculation error): hydrogen valence error.
`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`	`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.ATOM` or `CalculatorPlugin.MOLECULE`.
`Molecule`	`getResultMolecule()` Returns the result molecule for display.
`java.lang.Object[]`	`getResultTypes()` Returns the result types.
`double`	`getStandardError(java.lang.Object type, int index)`
`double`	`getStructurallogPIncrement()` Returns the structural logP increment.
`static java.lang.String[]`	`getTrainingIds()` Returns the id's of available logP trainings.
`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.
`java.lang.String`	`getWarningMessage()` Returns the calculation warning message.
`boolean`	`needError()`
`boolean`	`run()` Runs the logP calculation.
`void`	`setCloridIonConcentration(double c)` Sets the `Cl-` concentration (default: `0.1`).
`void`	`setConsiderTautomerization(boolean considerTautomerization)` Sets to consider tautomerization.
`protected void`	`setInputMolecule(Molecule mol)` Sets the input molecule.
`void`	`setlogPMethod(int method)` Deprecated. Use `setlogPMethod(LogPMethod)` instead.
`void`	`setlogPMethod(chemaxon.marvin.calculations.LogPMethod method)` Sets the logP calculation method.
`void`	`setNaKIonConcentration(double c)` Sets the `Na+, K+` concentration (default: `0.1`).
`void`	`setParameters(java.util.Properties params)` Sets the input parameters for the plugin.
`void`	`setTakeMajorTatomericForm(boolean takeMajorTautomericForm)` Deprecated. Use `setConsiderTautomerization(boolean)`
`void`	`setTraining(java.lang.String trainingId)` Sets the user defined training.
`void`	`setTrainingResults(java.io.InputStream trainingResultStream)` Sets the user defined training from a stream.
`void`	`setUserTypes(java.lang.String chtypes)` Sets user types.
`void`	`setWeightOfMethods(double wVG, double wKLOP, double wPHYS, double wUSER)` Deprecated. This function will not be available from May 2016. Use `setlogPMethod(LogPMethod)` instead.
`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, 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, setProgressMonitor, standardizeIonicGroups, standardizeNeutralGroups

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - METHOD_VG
```
@Deprecated
public static final int METHOD_VG
```
    Deprecated. Use LogPMethod.CHEMAXON instead.
    
    logP calculation method "VG"
    
    See Also:
    
    setlogPMethod(LogPMethod), Constant Field Values
  - METHOD_KLOP
```
@Deprecated
public static final int METHOD_KLOP
```
    Deprecated. This field will not be available from May 2016. Use LogPMethod instead.
    
    logP calculation method "KLOP"
    
    See Also:
    
    setlogPMethod(LogPMethod), Constant Field Values
  - METHOD_PHYS
```
@Deprecated
public static final int METHOD_PHYS
```
    Deprecated. This field will not be available from May 2016. Use LogPMethod instead.
    
    logP calculation method "PHYS"
    
    See Also:
    
    setlogPMethod(LogPMethod), Constant Field Values
  - METHOD_USER_DEFINED
```
@Deprecated
public static final int METHOD_USER_DEFINED
```
    Deprecated. Use LogPMethod.USER_DEFINED instead.
    
    User defined logP calculation method.
    
    See Also:
    
    setlogPMethod(LogPMethod), Constant Field Values
  - METHOD_WEIGHTED
```
@Deprecated
public static final int METHOD_WEIGHTED
```
    Deprecated. Use LogPMethod.CONSENSUS instead.
    
    Weighted logP calculation method.
    
    See Also:
    
    setlogPMethod(LogPMethod), Constant Field Values
- Constructor Detail
  - logPPlugin
```
public logPPlugin()
```
    Constructor. Creates the logP 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.PARTITIONING_PLUGIN_GROUP
  - 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)
    - h: true or false (display increments on implicit H atoms)
    - majortautomer: true or false (take major tautomeric form)
    - method: vg, klop, phys, user, weighted
    Overrides:
    
    setParameters in class CalculatorPlugin
    
    Parameters:
    
    params - is the parameter table
    
    Throws:
    
    PluginException - on error
  - setCloridIonConcentration
```
public void setCloridIonConcentration(double c)
```
    Sets the Cl- concentration (default: 0.1).
    
    Parameters:
    
    c - is the concentration
  - setNaKIonConcentration
```
public void setNaKIonConcentration(double c)
```
    Sets the Na+, K+ concentration (default: 0.1).
    
    Parameters:
    
    c - is the concentration
  - setConsiderTautomerization
```
public void setConsiderTautomerization(boolean considerTautomerization)
```
    Sets to consider tautomerization. Default: false.
    
    Parameters:
    
    considerTautomerization - the calculation will consider tautomerization and resonance if set (true)
    
    Since:
    
    Marvin 5.4
  - setTakeMajorTatomericForm
```
@Deprecated
public void setTakeMajorTatomericForm(boolean takeMajorTautomericForm)
```
    Deprecated. Use setConsiderTautomerization(boolean)
    
    Sets to use major tautomeric form in calculation. Default: false.
    
    Parameters:
    
    takeMajorTautomericForm - the calculation will be performed on the major tutomeric form of the input molecule if set (true)
    
    Since:
    
    Marvin 5.0
  - 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
    
    Since:
    
    Marvin 5.0
  - setUserTypes
```
public void setUserTypes(java.lang.String chtypes)
                  throws PluginException
```
    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
    
    Throws:
    
    PluginException - for invalid type
  - 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
  - setlogPMethod
```
public void setlogPMethod(chemaxon.marvin.calculations.LogPMethod method)
```
    Sets the logP calculation method. The available methods are:
    - LogPMethod.CONSENSUS
    - LogPMethod.CHEMAXON
    - LogPMethod.USER_DEFINED
    The default is LogPMethod.CONSENSUS.
    Parameters:
    
    method - is the logP calculation method
    
    Since:
    
    Marvin 15.4.13
  - setlogPMethod
```
@Deprecated
public void setlogPMethod(int method)
```
    Deprecated. Use setlogPMethod(LogPMethod) instead.
    Sets the logP calculation method. The available methods are:
    The default is METHOD_WEIGHTED.
    Parameters:
    
    method - is the logP calculation method
    
    Since:
    
    Marvin 5.1.3
    
    See Also:
    
    setWeightOfMethods(double, double, double, double)
  - setWeightOfMethods
```
@Deprecated
public void setWeightOfMethods(double wVG,
                                           double wKLOP,
                                           double wPHYS,
                                           double wUSER)
```
    Deprecated. This function will not be available from May 2016. Use setlogPMethod(LogPMethod) instead.
    Sets the weight of logP calculation methods. Default:
    - weight of METHOD_VG method = 1
    - weight of METHOD_KLOP method = 1
    - weight of METHOD_PHYS method = 1
    - weight of METHOD_USER_DEFINED method = 0
    Has only effect in case of METHOD_WEIGHTED method.
    Parameters:
    
    wVG - weight of METHOD_VG method
    
    wKLOP - weight of METHOD_KLOP method
    
    wPHYS - weight of METHOD_PHYS method
    
    wUSER - weight of METHOD_USER_DEFINED method
    
    Since:
    
    Marvin 5.1.3
    
    See Also:
    
    setlogPMethod(int)
  - getTrainingIds
```
public static java.lang.String[] getTrainingIds()
```
    Returns the id's of available logP trainings.
    
    Returns:
    
    the id's of available logP trainings
    
    Since:
    
    Marvin 5.4
  - setTraining
```
public void setTraining(java.lang.String trainingId)
                 throws PluginException
```
    Sets the user defined training.
    
    Parameters:
    
    trainingId - the training id
    
    Throws:
    
    PluginException - if training id is invalid, or parameter file for training cannot be loaded
    
    Since:
    
    Marvin 5.4
  - setTrainingResults
```
public void setTrainingResults(java.io.InputStream trainingResultStream)
                        throws PluginException
```
    Sets the user defined training from a stream.
    
    Throws:
    
    PluginException - for I/O problems.
  - 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()
  - 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
  - getWarningMessage
```
public java.lang.String getWarningMessage()
```
    Returns the calculation warning message.
    
    Overrides:
    
    getWarningMessage in class CalculatorPlugin
    
    Returns:
    
    the calculation warning information message
    
    See Also:
    
    CalculatorPlugin.getWarningMessage()
  - 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
  - getAtomlogPIncrement
```
public double getAtomlogPIncrement(int index)
```
    Returns the logP increment for the specified atom.
    
    Parameters:
    
    index - is the atom index
    
    Returns:
    
    the logP increment
  - getAtomlogPHIncrement
```
@Deprecated
public double getAtomlogPHIncrement(int index)
```
    Deprecated. Increments of implicit H-s are not calculated. Returns the same value as getAtomlogPIncrement(int)
    
    Returns the sum of the implicit H logP increments for the specified atom.
    
    Parameters:
    
    index - is the atom index
    
    Returns:
    
    the logP increment sum
  - getStructurallogPIncrement
```
public double getStructurallogPIncrement()
```
    Returns the structural logP increment. The sum of atomic increments and structural increment is the predicted logP.
    
    Returns:
    
    the structural logP increment
    
    Since:
    
    Marvin 5.4
  - getResultTypes
```
public java.lang.Object[] getResultTypes()
```
    Returns the result types. Possible result types: "logPTrue" (most typical logP) "logPMicro", "logPNonionic", "logDpI", "increments".
    
    Overrides:
    
    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".
    
    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" and CalculatorPlugin.MOLECULE otherwise.
    
    Overrides:
    
    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" 1 otherwise.
    
    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. logP returns the required logP 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()
  - getStandardError
```
public double getStandardError(java.lang.Object type,
                               int index)
```
  - 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 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
  - 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. Does AROM_BASIC aromatization.
    
    Overrides:
    
    standardize in class CalculatorPlugin
    
    Parameters:
    
    mol - is the molecule to be standardized
  - needError
```
public boolean needError()
```

Class logPPlugin

Nested Class Summary

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

Field Summary

Fields inherited from class chemaxon.marvin.plugin.CalculatorPlugin

Constructor Summary

Method Summary

Methods inherited from class chemaxon.marvin.plugin.CalculatorPlugin

Methods inherited from class java.lang.Object

Field Detail

METHOD_VG

METHOD_KLOP

METHOD_PHYS

METHOD_USER_DEFINED

METHOD_WEIGHTED

Constructor Detail

logPPlugin

Method Detail

getProductName

setParameters

setCloridIonConcentration

setNaKIonConcentration

setConsiderTautomerization

setTakeMajorTatomericForm

createModifiedInputMolecule

setUserTypes

checkMolecule

setInputMolecule

setlogPMethod

setlogPMethod

setWeightOfMethods

getTrainingIds

setTraining

setTrainingResults

run

getErrorMessage

getWarningMessage

getlogPMicro

getlogPNonionic

getlogDpI

getlogPTrue

getAtomlogPIncrement

getAtomlogPHIncrement

getStructurallogPIncrement

getResultTypes

getUserTypes

getTypeString

getResultDomain

getResultCount

getResult

getStandardError

getResultAsString

getResultMolecule

standardize

needError