chemaxon.marvin.calculations
Class logDPlugin

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

All Implemented Interfaces:

chemaxon.license.Licensable

public class logDPlugin
extends CalculatorPlugin

Plugin class for logD calculation.

API usage example:

        // instantiate plugin
        logDPlugin plugin = new logDPlugin();

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

        // set parameters
        plugin.setCloridIonConcentration(0.2);
        plugin.setNaKIonConcentration(0.2);
      plugin.setpHLower(3.0);
      plugin.setpHUpper(6.0);
      plugin.setpHStep(1.0);

        MolImporter importer = new MolImporter("targets.sdf");
        Molecule mol = null;
        while ((mol = importer.read()) != null) {
            // set molecule and run calculation
            plugin.setMolecule(mol);
            plugin.run();
            
            double[] pHs = plugin.getpHs();
            double[] logDs = plugin.getlogDs();

            // get and print logD values
            for (int i=0; i < pHs.length; ++i) {

                double pH = pHs[i];
                double logD = logDs[i];

                System.out.println(pH+", "+logD);
            }
        }
        importer.close();
 

Another example showing logD calculation at a single pH value:

        // instantiate plugin
        logDPlugin plugin = new logDPlugin();

      // set pH
      plugin.setpH(3.0);

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

        // run the calculation
        plugin.run();

        // get result
        double logD = plugin.getlogD();

        // print result
        System.out.println("logD at pH 3.0: "+logD);
 

 

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




Version:
  
5.4 09/29/2010
Author:
  
Nora Mate, Zsolt Mohacsi







Nested Class Summary

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



Field Summary




static int
METHOD_KLOP



          logP calculation method "KLOP"



static int
METHOD_PHYS



          logP calculation method: "PHYS"



static int
METHOD_USER_DEFINED



          User defined  logP calculation method



static int
METHOD_VG



          logP calculation method "VG"



static int
METHOD_WEIGHTED



          Weighted logP calculation method


 
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
logDPlugin()



          Constructor.
 



Method Summary




 double
calclogD(double pH)



          Returns the logD value at fixed pH.



 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  Molecule
getImageMolecule()



          Returns the molecule to be used for legend image.



 double
getlogD()



          Returns the logD value for the pH specified in setpH(double).



 double[]
getlogDs()



          Returns the logD array.



static java.lang.String[]
getLogPTrainingIds()



          Returns the id's of available logP trainings.



 double[]
getpHs()



          Returns the pH array.



 java.lang.String
getProductName()



          Returns the product identifier of the plugin as given by LicenseManager.



 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.



 boolean
run()



          Runs the logD calculation.



 void
setCloridIonConcentration(double c)



          Sets the Cl- concentration (default: 0.1).



 void
setConsiderTautomerization(boolean considerTautomerization)



          Sets to consider tautomerization in calculation.



protected  void
setInputMolecule(Molecule mol)



          Sets the input molecule.



 void
setlogPMethod(int method)



          Sets the logP calculation method.



 void
setLogPTrainingId(java.lang.String trainingId)



          Sets the user defined logP training.



 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
setpH(double pH)



          Sets a single pH value for the logD calculation.



 void
setpHLower(double lower)



          Sets pH lower limit (default: 0.0).



 void
setpHStep(double step)



          Sets pH step to be taken between the pH lower and upper limits
 (default: 1.0).



 void
setpHUpper(double upper)



          Sets pH upper limit (default: 14.0).



 void
setpKaCorrectionLibrary(java.lang.String correctionLibraryId)



          Sets the pKa correction library.



 void
setWeightOfMethods(double wVG,
                   double wKLOP,
                   double wPHYS,
                   double wUSER)



          Sets the weight of logP calculation methods.



 void
standardize(Molecule mol)



          Standardizes the molecule.


 
Methods inherited from class chemaxon.marvin.plugin.CalculatorPlugin
arrangeHydrogenIncerments, canRepeat, checkLicense, checkType, containsCoordinateBond, containsMulticenterSgroup, containsPseudoAtom, containsSRUSgroup, create, createModifiedInputMolecule, createStandardizedMolecule, createStandardizedMolecule, dehydrogenize, format, format, format, format, getAtomCount, getAtomIndex, getCalcMolecule, getDisplayMolecule, getDocument, getDoublePrecision, getExplicitHydrogenData, getInputMolDim, getMainMolecule, getpH, getPluginResource, getQueryMoleculeErrorMessage, getRemark, getResult, getResult, getResultAsRGB, getResultAsRGB, getResultAsString, getResultCount, getResultDomain, getResultMessage, getResultMolecule, getResultMolecules, getResultsAsRGB, getResultsAsRGB, getResultsAsString, getResultsAsString, getResultSource, getTypeString, getWarningMessage, handlesMultiFragmentMolecules, isInputMoleculeAromatized, isLicensed, isMsCalc, isMultiThreadedRunEnabled, isNegligibleResult, isOK, isRgrouped, loadClass, readAttribute, removeWhitespace, restoreExplicitHydrogens, 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
public static final int METHOD_VG

logP calculation method "VG"


See Also:
Constant Field Values




METHOD_KLOP
public static final int METHOD_KLOP

logP calculation method "KLOP"


See Also:
Constant Field Values




METHOD_PHYS
public static final int METHOD_PHYS

logP calculation method: "PHYS"


See Also:
Constant Field Values




METHOD_USER_DEFINED
public static final int METHOD_USER_DEFINED

User defined  logP calculation method


See Also:
Constant Field Values




METHOD_WEIGHTED
public static final int METHOD_WEIGHTED

Weighted logP calculation method


See Also:
Constant Field Values





Constructor Detail



logDPlugin
public logDPlugin()

Constructor.
 Creates the charge 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.
 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)
 
pH: pH value - calculate logD at a single pH
 
lower: pH lower limit (default: 0.0)
 
upper: pH upper limit (default: 14.0)
 
count: pH step size between lower and upper limits (default: 0.5)
 
ref1-ref4: reference pH values
 
considertautomerization: consider tautomerization
 
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





setpHLower
public void setpHLower(double lower)

Sets pH lower limit (default: 0.0).


Parameters:
lower - is the pH lower limit





setpHUpper
public void setpHUpper(double upper)

Sets pH upper limit (default: 14.0).


Parameters:
upper - is the pH upper limit





setpHStep
public void setpHStep(double step)

Sets pH step to be taken between the pH lower and upper limits
 (default: 1.0).


Parameters:
step - is the pH step





setpH
public void setpH(double pH)

Sets a single pH value for the logD calculation.


Parameters:
pH - is the pH value





setConsiderTautomerization
public void setConsiderTautomerization(boolean considerTautomerization)

Sets to consider tautomerization in calculation.
 Default: false.


Parameters:
considerTautomerization - if true the calculation will be performed 
        considering tautomerization and resonance
Since:
  
Marvin 5.0






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(int method)

Sets the logP calculation method.
 The available methods are:
 

   
METHOD_VG
   
METHOD_KLOP
   
METHOD_PHYS
   
METHOD_USER_DEFINED
   
METHOD_WEIGHTED
 
 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
public void setWeightOfMethods(double wVG,
                               double wKLOP,
                               double wPHYS,
                               double wUSER)

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)





getLogPTrainingIds
public static java.lang.String[] getLogPTrainingIds()

Returns the id's of available logP trainings.



Returns:
the id's of available logP trainings
Since:
  
Marvin 5.4






setLogPTrainingId
public void setLogPTrainingId(java.lang.String trainingId)
                       throws PluginException

Sets the user defined logP training.


Parameters:
trainingId - the logP training id
Throws:
PluginException - if training id is invalid, or parameter file for training cannot be loaded
Since:
  
Marvin 5.4






setpKaCorrectionLibrary
public void setpKaCorrectionLibrary(java.lang.String correctionLibraryId)

Sets the pKa correction library.


Parameters:
correctionLibraryId - is the pKa correction library identifier
Since:
  
Marvin 5.4






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()





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





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".


Overrides:
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





getlogD
public double getlogD()

Returns the logD value for the pH specified in setpH(double).



Returns:
the logD value





getpHs
public double[] getpHs()

Returns the pH array.



Returns:
the pH array





getlogDs
public double[] getlogDs()

Returns the logD array.



Returns:
the logD array





getResultDomain
public int getResultDomain(java.lang.Object type)

Returns the calculation domain CalculatorPlugin.ATOM or 
 CalculatorPlugin.MOLECULE.
 logD returns CalculatorPlugin.MOLECULE.


Overrides:
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.


Overrides:
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 being the pH 
 array and the 1-st element being the logD array.


Overrides:
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.


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





getImageMolecule
protected Molecule getImageMolecule()
                             throws PluginException

Returns the molecule to be used for legend image.



Returns:
the image molecule
Throws:
PluginException - on error





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