chemaxon.marvin.calculations
Class IsoelectricPointPlugin

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

All Implemented Interfaces:

chemaxon.license.Licensable

public class IsoelectricPointPlugin
extends CalculatorPlugin

Plugin class for isoelectric point and pH - charge distribution calculation.

API usage example:

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

    // set plugin parameters
    plugin.setpHStep(0.4);

    // set target molecule
    plugin.setMolecule(mol);

    // run the calculation
    plugin.run();

    // get results

    // isoelectric point
    double pI = plugin.getpI();

    // charge distribution
    double[] pHs = plugin.getpHs();
    double[] charges = plugin.getChargeDistribution();

    // print results
    if (Double.isNaN(pI)) {
         System.out.println("No isoelectric point.");
    } else {
       System.out.println("pI = "+plugin.format(pI));
    }   
    System.out.println("\npH\tcharge");
    for (int i=0; i 

 

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




Since:
  
Marvin 3.6
Version:
  
5.2.2 05/07/2009
Author:
  
Nora Mate, Zsolt Mohacsi







Nested Class Summary

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



Field Summary




static java.lang.String
TYPE_DISTR



          Type constant for microspecies distribution.


 
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
IsoelectricPointPlugin()



          Constructor.
 



Method Summary




 void
checkMolecule(Molecule mol)



          Checks the input molecule.



 double[]
getChargeDistribution()



          Returns the charge distribution array over pH values.



 java.lang.String
getErrorMessage()



          Returns the calculation error information message if run()
 returned false (calculation error): hydrogen valence error.



 double[]
getpHs()



          Returns the pH array.



 double
getpI()



          Returns the isoelectric point.



 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.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.



 Molecule
getResultMolecule()



          Returns the result molecule for display.



 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.String
getWarningMessage()



          Returns the calculation warning information message
 if no isoelectric point exists, returns the empty string otherwise.



protected  boolean
isChargeCalc()



          Returns true if pH-Charge calculation.



 boolean
run()



          Runs the isoelectric point and charge distribution calculations.



protected  void
setInputMolecule(Molecule mol)



          Sets the input molecule.



 void
setKeepExplicitHydrogens(boolean keepExplicitHydrogens)



          Sets if result molecule keeps explicit hydrogens or not



 void
setParameters(java.util.Properties params)



          Sets the input parameters for the plugin.



 void
setpH(double pH)



          Sets a single pH value for the calculation of charge distribution.



 void
setpHLower(double lower)



          Sets pH lower limit for the calculation of charge distribution
 (default: 0.0).



 void
setpHStep(double step)



          Sets pH step for the calculation of charge distribution.



 void
setpHUpper(double upper)



          Sets pH upper limit for the calculation of charge distribution
 (default: 14.0).



 void
setProgressMonitor(chemaxon.common.util.MProgressMonitor pmon)



          Sets a progress observer to be used in run() to display progress status.



 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, getResultMolecules, getResultsAsRGB, getResultsAsRGB, getResultsAsString, getResultsAsString, getResultSource, handlesMultiFragmentMolecules, isInputMoleculeAromatized, isLicensed, isMsCalc, isMultiThreadedRunEnabled, isNegligibleResult, isOK, isRgrouped, loadClass, readAttribute, removeWhitespace, restoreExplicitHydrogens, setDoublePrecision, setDoublePrecision, setDoublePrecision, setKeepHydrogens, setLicenseEnvironment, setMolecule, setMolecule, setMolecule, setMolecule, standardizeIonicGroups, standardizeNeutralGroups
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 





Field Detail



TYPE_DISTR
public static final java.lang.String TYPE_DISTR

Type constant for microspecies distribution.


See Also:
Constant Field Values





Constructor Detail



IsoelectricPointPlugin
public IsoelectricPointPlugin()

Constructor.
 Creates the isoelectric point 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.PROTONATION_PLUGIN_GROUP





setProgressMonitor
public void setProgressMonitor(chemaxon.common.util.MProgressMonitor pmon)

Sets a progress observer to be used in run() to display progress status.
 Short calculations may ignore the observer object.
 The default implementation does nothing.


Overrides:
setProgressMonitor in class CalculatorPlugin


Parameters:
pmon - is the progress monitor, may be null





setParameters
public void setParameters(java.util.Properties params)
                   throws PluginException

Sets the input parameters for the plugin.
 Isoelectric point parameters and value ranges:
 

 
type: pI,chargedistr
 
precision: 0-8 or inf (default: 2)
 
pH: pH value - calculate charge distribution at a single pH
 
lower: pH lower limit (default: 0.0)
 
upper: pH upper limit (default: 14.0)
 
step: pH step to be taken between lower and upper limits (default: 0.5)
 


Overrides:
setParameters in class CalculatorPlugin


Parameters:
params - is the parameter table
Throws:
PluginException - on error





isChargeCalc
protected boolean isChargeCalc()

Returns true if pH-Charge calculation.



Returns:
true if pH-Charge calculation





setpHLower
public void setpHLower(double lower)

Sets pH lower limit for the calculation of charge distribution
 (default: 0.0).


Parameters:
lower - is the pH lower limit
Since:
  
Marvin 5.2






setpHUpper
public void setpHUpper(double upper)

Sets pH upper limit for the calculation of charge distribution
 (default: 14.0).


Parameters:
upper - is the pH upper limit
Since:
  
Marvin 5.2






setpHStep
public void setpHStep(double step)

Sets pH step for the calculation of charge distribution.
 Range: between 0.0 and 0.5.
 The default value is 0.5.


Parameters:
step - is the pH step





setpH
public void setpH(double pH)

Sets a single pH value for the calculation of charge distribution.


Parameters:
pH - is the pH value
Since:
  
Marvin 5.2






checkMolecule
public void checkMolecule(Molecule mol)
                   throws PluginException

Checks the input molecule.
 Throws exception if the molecule molecule contains R-groups.


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 input molecule
Throws:
PluginException - on error





run
public boolean run()
            throws PluginException

Runs the isoelectric point and charge distribution calculations.


Specified by:
run in class CalculatorPlugin



Returns:
true if the calculation was successful, 
         false if the number of ionizable atoms exceeds the specified limit
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





getpI
public double getpI()

Returns the isoelectric point.



Returns:
the isoelectric point





getpHs
public double[] getpHs()

Returns the pH array.



Returns:
the pH array





getChargeDistribution
public double[] getChargeDistribution()

Returns the charge distribution array over pH values.



Returns:
the charge distribution array
See Also:
getpHs()





getResultTypes
public java.lang.Object[] getResultTypes()

Returns the result types.


Overrides:
getResultTypes in class CalculatorPlugin



Returns:
the result types





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

Returns the calculation domain.


Overrides:
getResultDomain in class CalculatorPlugin


Parameters:
type - is the result type
Returns:
the calculation domain
See Also:
getResultTypes()





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

Returns the number of result items for the given result key.
 pKa returns the atom count.


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.


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:
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.
 If the type is TYPE_DISTR then returns the pH - distribution
 table as a 2-column tab-separated table with the 0-th element 
 the pH array and the 1-st element the distribution array 
 corresponding to the microspecies with the specified index (result index).
 Otherwise returns the rounded pI value with one fractional digit precision.


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





getWarningMessage
public java.lang.String getWarningMessage()

Returns the calculation warning information message
 if no isoelectric point exists, returns the empty string otherwise.


Overrides:
getWarningMessage in class CalculatorPlugin



Returns:
the calculation warning information message





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 and stores the index-map between atom indices
 in the original and the new molecule. This map is used when the macropKa
 values and types are queried and the new atom indices should be mapped to
 the original ones.
 TODO: replace by call to chemaxon.reaction.Standardizer


Overrides:
standardize in class CalculatorPlugin


Parameters:
mol - is the molecule to be standardized





setKeepExplicitHydrogens
public void setKeepExplicitHydrogens(boolean keepExplicitHydrogens)

Sets if result molecule keeps explicit hydrogens or not


Parameters:
keepExplicitHydrogens - if the result should keep explicit hydrogens or not