chemaxon.marvin.calculations
Class ChargePlugin

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

All Implemented Interfaces:

chemaxon.license.Licensable

public class ChargePlugin
extends MajorMicrospeciesAccessorPlugin

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();

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

    // 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);
          }
    }
 

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

Version:

4.1, 07/25/2006

Author:

Nora Mate

Field Summary

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, EPSILON, INCORRECT_AROMATIC_NITROGEN_REMARK, INSTABLE_TAUTOMERIC_FORM_REMARK, licenseEnvironment, MOLECULE, NAN, PLUGIN_CLASS_KEY, PLUGIN_DIR, RED

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	getAromaticRingCharge(int index, int chgtype) Returns the 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.
double	getAromaticSystemCharge(int index, int chgtype) Returns the 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.
double	getPiCharge(int index) Returns the pi charge of a specified atom.
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.
double	getResultantImplicitHCharge(int index) Returns the 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.
Molecule	getResultMolecule() Returns the result molecule for display.
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.
java.lang.String	getTypeString(java.lang.Object type) Returns a string representation of the given type.
boolean	isLicensed() Returns true if the plugin is licensed.
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.
void	setTakeResonantStructures(boolean resonance) Sets calculation with resonant structures.

Methods inherited from class chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin

checkMolecule, createModifiedInputMolecule, getIonizerErrorMessage, getpH, setpH, standardize

Methods inherited from class chemaxon.marvin.plugin.CalculatorPlugin

checkType, containsCoordinateBond, containsMulticenterSgroup, containsPseudoAtom, containsSRUSgroup, create, createStandardizedMolecule, createStandardizedMolecule, dehydrogenize, format, format, format, format, getAtomCount, getAtomIndex, getCalcMolecule, getDisplayMolecule, getDocument, getDoublePrecision, getInputMolDim, getMainMolecule, getPluginResource, getRemark, getResult, getResult, getResult, getResultAsRGB, getResultAsRGB, getResultAsString, getResultCount, getResultDomain, getResultMessage, getResultMolecules, getResultsAsRGB, getResultsAsRGB, getResultsAsString, getResultsAsString, getResultSource, getWarningMessage, handlesMultiFragmentMolecules, isInputMoleculeAromatized, isMsCalc, isMultiThreadedRunEnabled, isNegligibleResult, isOK, isRgrouped, loadClass, readAttribute, removeWhitespace, setDoublePrecision, setDoublePrecision, setDoublePrecision, setLicenseEnvironment, setMolecule, setMolecule, setMolecule, setProgressMonitor, standardizeIonicGroups, standardizeNeutralGroups

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

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.

Overrides:

getProductName in class CalculatorPlugin

Returns:

The identifier LicenseManager.CHARGE_PLUGIN_GROUP

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, aromaticsystemsigma,aromaticsystempi, aromaticring, aromaticringsigma, aromaticringpi
• 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
• resonance: true or false - true if calculate with resonant structures (default: false)
• pH: major microspecies on given pH is taken as input molecule if omitted then the input molecule is taken as it is

Overrides:

setParameters in class MajorMicrospeciesAccessorPlugin

Parameters:

params - is the parameter table

Throws:

PluginException - on error

setTakeResonantStructures

public void setTakeResonantStructures(boolean resonance)

Sets calculation with resonant structures. Default: false.

Parameters:

resonance - is true if charge should be calculated with resonant structures

Since:

Marvin 4.1

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 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

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 the implicit H charge around a central atom

Parameters:

index - is the central atom index

Returns:

the 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

getAromaticSystemCharge

public double getAromaticSystemCharge(int index,
                                      int chgtype)

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

Parameters:

index - is the atom index

chgtype - is the charge type: 0 - total, 1 - sigma, 2 - pi

Returns:

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

Since:

Marvin 4.1

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

getAromaticRingCharge

public double getAromaticRingCharge(int index,
                                    int chgtype)

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

Parameters:

index - is the atom index

chgtype - is the charge type: 0 - total, 1 - sigma, 2 - pi

Returns:

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

Since:

Marvin 4.1

getResultTypes

public java.lang.Object[] getResultTypes()

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

Overrides:

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.

Overrides:

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 type. Charge returns the atom count.

Overrides:

getResultCount in class CalculatorPlugin

Parameters:

type - is the result type

Returns:

the number of result items

See Also:

getResultTypes()

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

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 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.

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

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