chemaxon.marvin.calculations
Class ChargePlugin

java.lang.Object
  chemaxon.marvin.plugin.CalculatorPlugin
      chemaxon.marvin.calculations.MajorMicrospeciesPlugin
          chemaxon.marvin.calculations.ChargePlugin

public class ChargePlugin

extends MajorMicrospeciesPlugin

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)

API usage example:

    // create plugin
    ChargePlugin plugin = new ChargePlugin();
    plugin.validate(<charge license>);

    // read target molecule
    MolImporter mi = new MolImporter(new ByteArrayInputStream("Clc1cc(Cl)c(Cl)cc1".getBytes()));
    Molecule mol = mi.read();

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

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

    // run the calculation
    plugin.run();

    // get charge values for each atom
    int count = mol.getAtomCount();
    for (int i=0; i < count; ++i) {
	  double charge = plugin.getTotalCharge(i);
	  if (!Double.isNaN(charge)) {
	      System.out.println("total charge for atom "+(i+1)+": "+charge);
	  }
    }
 

Author:

Nora Mate

Field Summary

Fields inherited from class chemaxon.marvin.plugin.CalculatorPlugin

ATOM, BLUE, CALCRGB_OFF, CHART, HYDROGEN_VALENCE_ERROR_MSG, MOLECULE, NAN, RED, SUBRESULT

Constructor Summary

ChargePlugin()
Constructor.

Method Summary

double	getAromaticRingCharge(int index) Returns the total partial charge of the smallest aromatic ring containing the specified atom.
double	getAromaticSystemCharge(int index) Returns the total partial charge of the aromatic system containing the specified atom.
java.lang.String	getErrorMessage() Returns the calculation error information message if run() returned false (calculation error): hydrogen valence error.
protected java.lang.String	getLicenseKey() Returns the built-in license key for the given plugin class.
java.lang.String	getOutputClassName() Returns the output provider class name for the command line interface.
double	getPiCharge(int index) Returns the pi charge of a specified atom.
java.lang.Object	getResult(java.lang.Object type, int index) Returns the result item for the specified type and index.
double	getResultantImplicitHCharge(int index) Returns sum of implicit H charge around a central atom
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.
java.lang.Object[]	getResultTypes() Returns the result types (possible types: "sigma", "pi", "total").
double	getSigmaCharge(int index) Returns the sigma charge of a specified atom.
double	getTotalCharge(int index) Returns the total charge of a specified atom.
boolean	run() Runs the charge calculation.
protected 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.calculations.MajorMicrospeciesPlugin

checkMolecule, getMainMolecule, getMajorMicrospecies, getMolText, getpH, getReferenceMolecule, getSuffix, isMajorMs, setpH, standardize

Methods inherited from class chemaxon.marvin.plugin.CalculatorPlugin

check, checkLicense, checkLicenseKey, checkType, create, createImageMolecule, createStandardizedMolecule, dehydrogenize, format, format, format, format, getAtomCount, getAtomIndex, getChartColor, getDoublePrecision, getGUIResultTypes, getResult, getResult, getResult, getResultAsRGB, getResultAsRGB, getResultAsString, getResultCount, getResultDomain, getResultsAsRGB, getResultsAsRGB, getResultsAsString, getResultsAsString, getTypeString, getXAxisLabel, getXLabels, getYAxisLabel, handlesMultiFragmentMolecules, isLicensed, isMajorityMsCalculation, isMsCalc, isNegligibleResult, isRgrouped, removeWhitespace, saveLicense, setDoublePrecision, setDoublePrecision, setDoublePrecision, setLicense, setMolecule, setMolecule, setMolecule, standardizeGroups, 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:

• type: sigma,pi,total,aromaticsystem,aromaticring
• precision: 0-8 or inf (number of displayed fractional digits, inf for unrounded value)
• implh: true or false - true if implicit H data should be shown
• pH: majority microspecies on given pH is taken as input molecule if omitted then the input molecule is taken as it is

Overrides:

setParameters in class MajorMicrospeciesPlugin

Parameters:

params - is the parameter table

Throws:

PluginException - on error

setInputMolecule

protected void setInputMolecule(Molecule mol)
                         throws PluginException

Sets the input molecule.

Overrides:

setInputMolecule in class MajorMicrospeciesPlugin

Parameters:

mol - is the input molecule

Throws:

PluginException - on error

run

public boolean run()
            throws PluginException

Runs the charge calculation.

Overrides:

run in class MajorMicrospeciesPlugin

Returns:

true if the calculation was successful, false on calculation error

Throws:

PluginException - on error

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 MajorMicrospeciesPlugin

Returns:

the calculation error information message

getTotalCharge

public double getTotalCharge(int index)

Returns the total charge of a specified atom.

Parameters:

index - is the atom index

Returns:

the total charge of a specified atom, Double.NaN for implicit H-s

Since:

Marvin 3.4.1

getSigmaCharge

public double getSigmaCharge(int index)

Returns the sigma charge of a specified atom.

Parameters:

index - is the atom index

Returns:

the sigma charge of a specified atom, Double.NaN for implicit H-s

Since:

Marvin 3.4.1

getPiCharge

public double getPiCharge(int index)

Returns the pi charge of a specified atom.

Parameters:

index - is the atom index

Returns:

the pi charge of a specified atom, Double.NaN for implicit H-s

Since:

Marvin 3.4.1

getResultantImplicitHCharge

public double getResultantImplicitHCharge(int index)

Returns sum of implicit H charge around a central atom

Parameters:

index - is the central atom index

Returns:

the sum of implicit H charge around the central atom

Since:

Marvin 3.5

getAromaticSystemCharge

public double getAromaticSystemCharge(int index)

Returns the total partial charge of the aromatic system containing the specified atom.

Parameters:

index - is the atom index

Returns:

the total partial charge of the aromatic system containing the specified atom

Since:

Marvin 3.5

getAromaticRingCharge

public double getAromaticRingCharge(int index)

Returns the total partial charge of the smallest aromatic ring containing the specified atom.

Parameters:

index - is the atom index

Returns:

the total partial charge of the smallest aromatic ring containing the specified atom

Since:

Marvin 3.5

getResultTypes

public java.lang.Object[] getResultTypes()

Returns the result types (possible types: "sigma", "pi", "total").

Overrides:

getResultTypes in class MajorMicrospeciesPlugin

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.

Overrides:

getResultDomain in class MajorMicrospeciesPlugin

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 type. Charge returns the atom count.

Overrides:

getResultCount in class MajorMicrospeciesPlugin

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.

Overrides:

getResult in class MajorMicrospeciesPlugin

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()

getOutputClassName

public java.lang.String getOutputClassName()

Returns the output provider class name for the command line interface.

Overrides:

getOutputClassName in class MajorMicrospeciesPlugin

Returns:

the output provider class name

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.

Overrides:

getResultAsString in class MajorMicrospeciesPlugin

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