chemaxon.marvin.calculations
Class ChargePlugin

java.lang.Object
  extended bychemaxon.marvin.plugin.CalculatorPlugin
      extended bychemaxon.marvin.calculations.ChargePlugin

public class ChargePlugin
extends CalculatorPlugin

Plugin class for charge calculation. Sigma, pi and total charge values can be calculated by this plugin.

References:

  1. J.Gasteiger and M.Marsili: Tetrahedron Vol. 36. , pp. 3219-3288 (1980)
  2. M.Marsili and J.Gasteiger: International Symposium on Aromaticity, Dubrovnik, Yugoslavia , Sept (1979), Croat.Chim.Acta. (1979)
  3. Steven L. Dixon and Peter C. Jurs: J.Comp.Chem., Vol.13. No.4, 492-504 (1992)
  4. W.J.Mortier, K.V.Genechten and J.Gasteiger: J.Am.Chem.Soc., Vol. 107,829-835 (1985)


Field Summary
 
Fields inherited from class chemaxon.marvin.plugin.CalculatorPlugin
ATOM, CHART, MOLECULE, NAN, SUBRESULT
 
Constructor Summary
ChargePlugin()
          Constructor.
 
Method Summary
 void checkMolecule(Molecule mol)
          Checks the input molecule.
protected  java.lang.String getLicenseKey()
          Returns the built-in license key for the given plugin class.
 java.lang.Object getResult(java.lang.Object type, int index)
          Returns the result item for the specified type 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.
 java.lang.Object[] getResultTypes()
          Returns the result types (possible types: "sigma", "pi", "total").
 boolean run()
          Runs the charge calculation.
 void setInputMolecule(Molecule mol)
          Sets the input molecule.
 void setParameters(java.util.Properties params)
          Sets the input parameters for the plugin.
 
Methods inherited from class chemaxon.marvin.plugin.CalculatorPlugin
check, checkLicense, checkLicenseKey, create, createStandardizedMolecule, dehydrogenize, format, format, format, format, getAtomCount, getAtomIndex, getDoublePrecision, getErrorMessage, getOutputClassName, getReferenceMolecule, getResult, getResult, getResult, getResultAsRGB, getResultAsRGB, getResultAsString, getResultCount, getResultDomain, getResultsAsRGB, getResultsAsRGB, getResultsAsString, getResultsAsString, getTypeString, getXAxisLabel, getXLabels, getYAxisLabel, handlesMultiFragmentMolecules, isLicensed, isNegligibleResult, isRgrouped, setDoublePrecision, setDoublePrecision, setLicense, setMolecule, setMolecule, standardize, standardizeNitro, validate
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

ChargePlugin

public ChargePlugin()
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:

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 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

public 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 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()

getResultTypes

public java.lang.Object[] getResultTypes()
Returns the result types (possible types: "sigma", "pi", "total").

Specified by:
getResultTypes in class CalculatorPlugin
Returns:
the result types

getResultDomain

public int getResultDomain(java.lang.Object type)
Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE. Charge always returns CalculatorPlugin.ATOM.

Specified by:
getResultDomain in class CalculatorPlugin
Parameters:
type - is the result type
Returns:
CalculatorPlugin.ATOM
See Also:
getResultTypes()

getResultCount

public int getResultCount(java.lang.Object type)
Returns the number of result items for the given result key. Charge returns the atom count.

Specified by:
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. Charge returns the required charge value as a Double object.

Specified by:
getResult in class CalculatorPlugin
Parameters:
type - is the result type ("total", "pi", "sigma" or "implh")
index - is the atom index
Returns:
the result item for the specified type and index
Throws:
PluginException - if the result cannot be returned
See Also:
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. Charge returns the rounded charge value in string format: the value is rounded using the 'precision' input parameter that determines the number of fractional digits displayed.

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