chemaxon.marvin.calculations
Class HBDAPlugin

java.lang.Object
  chemaxon.marvin.plugin.CalculatorPlugin
      chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin
          chemaxon.marvin.calculations.HBDAPlugin

All Implemented Interfaces:

chemaxon.license.Licensable

public class HBDAPlugin
extends MajorMicrospeciesAccessorPlugin

Plugin class for H bond acceptor/donor calculation.

API usage example:

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

    // set plugin parameters
    plugin.setDoublePrecision(2);
    plugin.setpHLower(2.0);
    plugin.setpHUpper(12.0);
    plugin.setpHStep(2.0);

    // optional: take major microspecies at pH=7.4
    // skip this if you want to calculate HBDA for the input molecule as it is
    plugin.setpH(7.4);

    // read target molecule
    MolImporter mi = new MolImporter("target.mol");
    Molecule mol = mi.read();
    mi.close();

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

    // run the calculation
    plugin.run();

    // get results

    // average acceptor/donor counts by microspecies distributions at given pH-s
    double[] pHs = plugin.getpHs();
    double[] msacc = plugin.getMsAcceptorCounts();
    double[] msdon = plugin.getMsDonorCounts();

    System.out.println("pH\tmsacc\tmsdon");
    for (int i=0; i 

 

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




Version:
  
5.3.2 03/16/2010
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
ACCEPTOR_SIGN



          Acceptor sign displayed in GUI.



static java.lang.String
DONOR_SIGN



          Donor sign displayed in GUI.



static double
EPSILON



           


 
Fields inherited from class chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin
ionizer
 
Fields inherited from class chemaxon.marvin.plugin.CalculatorPlugin
ATOM, BLUE, CALCRGB_OFF, COVALENT_HYDRATION_ERROR_REMARK, CRITICAL_ERROR_MSG, 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
HBDAPlugin()



          Constructor.
 



Method Summary




 void
checkMolecule(Molecule mol)



          Checks the input molecule.



 int
getAcceptorAtomCount()



          Returns the overall acceptor atom count (without multiplicity) in the molecule.



 int
getAcceptorCount()



          Returns the overall acceptor count (with multiplicity) in the molecule.



 int
getAcceptorCount(int index)



          Returns the atomic acceptor count corresponding to the specified atom index.



 int
getDonorAtomCount()



          Returns the overall donor atom count (without multiplicity) in the molecule.



 int
getDonorCount()



          Returns the overall donor count (with multiplicity) in the molecule.



 int
getDonorCount(int index)



          Returns the atomic donor count corresponding to the specified atom index.



 java.lang.String
getErrorMessage()



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



 double[]
getMsAcceptorCounts()



          Returns the average acceptor counts over the microspecies distribution
 for different pH-s.



 double[]
getMsDonorCounts()



          Returns the average donor counts over the microspecies distribution
 for different pH-s.



 double[]
getpHs()



          Returns the pH array.



 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 type and index.



 int
getResultAsRGB(java.lang.Object type,
               int index,
               java.lang.Object result)



          Returns the specified result color(s) as int format
 (alpha<<24 + red<<16 + green<<8 + blue).



 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 type.



 int
getResultDomain(java.lang.Object type)



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



 Molecule
getResultMolecule()



          Returns the result molecule for display.



 long
getResultsAsRGB(java.lang.Object type,
                int index,
                java.lang.Object result)



          Returns the specified result color(s) as int format
 (alpha<<24 + red<<16 + green<<8 + blue).



 java.lang.String
getResultsAsString(java.lang.Object type,
                   int index,
                   java.lang.Object result)



          Returns the specified result in GUI-specific String format:
 A for acceptor, D for donor.



 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 H-bond donor/acceptor atoms found, returns
 the empty string otherwise.



 boolean
isLicensed()



          Returns true if the plugin is licensed.



protected  boolean
isMsCalc()



          Returns true if microspecies calculation.



 boolean
isNegligibleResult(java.lang.Object type,
                   int index,
                   java.lang.Object result)



          Returns whether the result can be ignored.



 boolean
run()



          Runs the charge calculation.



 void
setExcludeHalogens(boolean e)



          Sets if halogens should be excluded from hydrogen bond acceptors.



 void
setExcludeSulfur(boolean e)



          Sets if sulfur atom should be excluded from hydrogen bond acceptors.



protected  void
setGUIMode(boolean guimode)



          Sets GUI mode.



protected  void
setInputMolecule(Molecule mol)



          Sets the input molecule.



 void
setMsCalc(boolean mscalc)



          Sets microspecies calculation.



 void
setParameters(java.util.Properties params)



          Sets the input parameters for the plugin.



 void
setpHLower(double lower)



          Sets pH lower limit for the calculation of microspecies distributions.



 void
setpHStep(double step)



          Sets pH step for the calculation of microspecies distributions.



 void
setpHUpper(double upper)



          Sets pH upper limit for the calculation of microspecies distributions.


 
Methods inherited from class chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin
createModifiedInputMolecule, getIonizerErrorMessage, getpH, setpH, standardize
 
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, getCalcMolecule, getDisplayMolecule, getDocument, getDoublePrecision, getExplicitHydrogenData, getInputMolDim, getMainMolecule, getPluginResource, getQueryMoleculeErrorMessage, getRemark, getResult, getResult, getResult, getResultAsRGB, getResultAsString, getResultCount, getResultDomain, getResultMessage, getResultMolecules, getResultsAsRGB, getResultsAsString, getResultSource, handlesMultiFragmentMolecules, isInputMoleculeAromatized, isMultiThreadedRunEnabled, 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



EPSILON
public static final double EPSILON


See Also:
Constant Field Values




ACCEPTOR_SIGN
public static final java.lang.String ACCEPTOR_SIGN

Acceptor sign displayed in GUI.


See Also:
Constant Field Values




DONOR_SIGN
public static final java.lang.String DONOR_SIGN

Donor sign displayed in GUI.


See Also:
Constant Field Values





Constructor Detail



HBDAPlugin
public HBDAPlugin()

Constructor.
 Creates the calculator object.






Method Detail



isLicensed
public boolean isLicensed()

Returns true if the plugin is licensed. The license checking
 is based on the product name, returned by getProductName().


Specified by:
isLicensed in interface chemaxon.license.Licensable
Overrides:
isLicensed in class MajorMicrospeciesAccessorPlugin



Returns:
true if the plugin is licensed





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.HBDA_PLUGIN





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

Sets the input parameters for the plugin.
 Charge parameters and value ranges:
 

 
type:
     

     
acc: atomic acceptors
     
don: atomic donors
     
accsitecount: molecular acceptor count with multiplicity
     
donsitecount: molecular donor count with multiplicity
     
acceptorcount: molecular acceptor atom count without multiplicity
     
donorcount: molecular donor atom count without multiplicity
     
msacc: average acceptor count over microspecies by pH
     
msdon: average donor count over microspecies by pH
     
excludesulfur: exclude sulfur atoms from acceptors
     
 
precision: 0-8 or inf
 (number of displayed fractional digits, inf for unrounded value)
 
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)
 


Overrides:
setParameters in class MajorMicrospeciesAccessorPlugin


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





setpHLower
public void setpHLower(double lower)

Sets pH lower limit for the calculation of microspecies distributions.
 Also activates the calculation of microspecies distributions.
 The default value is 0.0.


Parameters:
lower - is the pH lower limit
Since:
  
Marvin 3.5.1






setpHUpper
public void setpHUpper(double upper)

Sets pH upper limit for the calculation of microspecies distributions.
 Also activates the calculation of microspecies distributions.
 The default value is 14.0.


Parameters:
upper - is the pH upper limit
Since:
  
Marvin 3.5.1






setpHStep
public void setpHStep(double step)

Sets pH step for the calculation of microspecies distributions.
 Also activates the calculation of microspecies distributions.
 The default value is 0.5.


Parameters:
step - is the pH step
Since:
  
Marvin 3.5.1






setMsCalc
public void setMsCalc(boolean mscalc)

Sets microspecies calculation.


Parameters:
mscalc - is true if microspecies calculation required
Since:
  
Marvin 3.5.1
See Also:
setpHLower(double lower), 
setpHUpper(double upper), 
setpHStep(double step), 
MajorMicrospeciesAccessorPlugin.setpH(double pH)





isMsCalc
protected boolean isMsCalc()

Returns true if microspecies calculation.


Overrides:
isMsCalc in class CalculatorPlugin



Returns:
true if microspecies calculation





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 MajorMicrospeciesAccessorPlugin


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





setExcludeSulfur
public void setExcludeSulfur(boolean e)

Sets if sulfur atom should be excluded from hydrogen bond acceptors.
 Default: true


Parameters:
e - if true then sulfur atom is not considered to be hydrogen bond acceptor.
Since:
  
Marvin 5.3






setExcludeHalogens
public void setExcludeHalogens(boolean e)

Sets if halogens should be excluded from hydrogen bond acceptors.
 Default: true


Parameters:
e - if true then halogens are not considered to be hydrogen bond acceptor.
Since:
  
Marvin 5.3.2






run
public boolean run()
            throws PluginException

Runs the charge calculation.


Specified by:
run in class CalculatorPlugin



Returns:
true if the calculation was successful, false on calculation error
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 MajorMicrospeciesAccessorPlugin



Returns:
the calculation error information message





getWarningMessage
public java.lang.String getWarningMessage()

Returns the calculation warning information message
 if no H-bond donor/acceptor atoms found, returns
 the empty string otherwise.


Overrides:
getWarningMessage in class CalculatorPlugin



Returns:
the calculation warning information message





getpHs
public double[] getpHs()

Returns the pH array.



Returns:
the pH array





getMsAcceptorCounts
public double[] getMsAcceptorCounts()

Returns the average acceptor counts over the microspecies distribution
 for different pH-s. The pH array is returned by getpHs() and
 determined by the "lower", "upper" and "step" plugin parameters.



Returns:
the average acceptor counts over the microspecies distribution
         for pH-s returned by getpHs()





getMsDonorCounts
public double[] getMsDonorCounts()

Returns the average donor counts over the microspecies distribution
 for different pH-s. The pH array is returned by getpHs()
 and determined by the "lower", "upper" and "step" plugin parameters.



Returns:
the average donor counts over the microspecies distribution
         for pH-s returned by getpHs()





getAcceptorCount
public int getAcceptorCount(int index)

Returns the atomic acceptor count corresponding to the specified atom index.


Parameters:
index - is the atom index
Returns:
the atomic acceptor count, -1 for H atoms





getDonorCount
public int getDonorCount(int index)

Returns the atomic donor count corresponding to the specified atom index.


Parameters:
index - is the atom index
Returns:
the atomic donor count, -1 for H atoms





getAcceptorCount
public int getAcceptorCount()

Returns the overall acceptor count (with multiplicity) in the molecule.



Returns:
the overall acceptor count (with multiplicity) in the molecule





getDonorCount
public int getDonorCount()

Returns the overall donor count (with multiplicity) in the molecule.



Returns:
the overall donor count (with multiplicity) in the molecule





getAcceptorAtomCount
public int getAcceptorAtomCount()

Returns the overall acceptor atom count (without multiplicity) in the molecule.



Returns:
the overall acceptor atom count (without multiplicity) in the molecule





getDonorAtomCount
public int getDonorAtomCount()

Returns the overall donor atom count (without multiplicity) in the molecule.



Returns:
the overall donor atom count (without multiplicity) in the molecule





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

Returns the result types.
 The possible types are described in setParameters(Properties params).


Overrides:
getResultTypes in class CalculatorPlugin



Returns:
the result types





setGUIMode
protected void setGUIMode(boolean guimode)

Sets GUI mode.


Parameters:
guimode - is true if GUI mode





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

Returns the calculation domain CalculatorPlugin.ATOM or
 CalculatorPlugin.MOLECULE.
 HBDA returns CalculatorPlugin.ATOM for types "acc" and "don",
 CalculatorPlugin.MOLECULE for types "accsitecount", "donsitecount",
 "acceptorcount", "donorcount",
 and returns CalculatorPlugin.MOLECULE for type "msacc" and "msdon".


Overrides:
getResultDomain in class CalculatorPlugin


Parameters:
type - is the result type
Returns:
the domain as described above
See Also:
getResultTypes()





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

Returns the number of result items for the given result type.
 Returns the atom count for types "acc" and "don", 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 type and index.
 HBDA returns the (pH, acceptor/donor count) arrays for types "msacceptor"
 and "msdonor" as a double[2][] with the 0-th element being
 the pH array and the 1-st element being the
 acceptor/donor count array. For types "acc" and "don"
 HBDA returns the acceptor/donor count corresponding to the
 specified atom index. For types "accsitecount" and "donsitecount" HBDA returns
 the sum of the atomic values.
cc     * @see #getResultTypes()


Overrides:
getResult in class CalculatorPlugin


Parameters:
type - is the result type
 ("acc", "don", "msacc", "msdon", "accsitecount", "donsitecount", "acceptorcount", "donorcount")
index - is the atom index for types "acc", "don",
              N/A for "msacc", "msdon", "accsitecount", "donsitecount", "acceptorcount", "donorcount"
Returns:
the result item for the specified type and index
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.


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





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

Returns the specified result color(s) as int format
 (alpha<<24 + red<<16 + green<<8 + blue).
 Returns "red" for acceptor "blue" for donor.


Overrides:
getResultAsRGB in class CalculatorPlugin


Parameters:
type - is the result type
index - is the result index
result - is the result item
Returns:
the specified result in color as int
Throws:
PluginException - if an invalid result item is given





getResultsAsRGB
public long getResultsAsRGB(java.lang.Object type,
                            int index,
                            java.lang.Object result)
                     throws PluginException

Returns the specified result color(s) as int format
 (alpha<<24 + red<<16 + green<<8 + blue).
 Returns "red" for acceptor "blue" for donor.


Overrides:
getResultsAsRGB in class CalculatorPlugin


Parameters:
type - is the result type
index - is the result index
result - is the result item
Returns:
the specified result in color as int
Throws:
PluginException - if an invalid result item is given





getResultsAsString
public java.lang.String getResultsAsString(java.lang.Object type,
                                           int index,
                                           java.lang.Object result)
                                    throws PluginException

Returns the specified result in GUI-specific String format:
 A for acceptor, D for donor.


Overrides:
getResultsAsString 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





isNegligibleResult
public boolean isNegligibleResult(java.lang.Object type,
                                  int index,
                                  java.lang.Object result)
                           throws PluginException

Returns whether the result can be ignored.
 Returns true for microspecies acceptor/donor count below EPSILON.
 Returns false for all other results.


Overrides:
isNegligibleResult in class CalculatorPlugin


Parameters:
type - is the result type
index - is the result index
result - is the result object
Returns:
true for microspecies acceptor/donor count below EPSILON
Throws:
PluginException





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