ChargePlugin (JChem Base API documentation (c) 1998-2019 ChemAxon Ltd.)

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

All Implemented Interfaces:

chemaxon.license.Licensable
```
@PublicAPI
public class ChargePlugin
extends MajorMicrospeciesAccessorPlugin
```
Plugin class for partial charge calculation. Sigma, pi and total charge values can be calculated by this plugin. For formal charge calculation use the following methods: MoleculeGraph.getFormalCharge(), MolAtom.getCharge().
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();

    // 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:

5.3.1, 01/26/2010

Author:

Nora Mate

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

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, 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

Constructors
Constructor and Description

ChargePlugin()
Constructor.

Constructors
Constructor and Description
`ChargePlugin()` Constructor.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`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.
`int`	`getFormalCharge()` Returns the formal charge of the molecule.
`int`	`getFormalCharge(int index)` Returns the formal charge of a specified atom.
`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`	`handlesMultiFragmentMolecules()` Returns `true` if the plugin handles multifragment molecules, `false` otherwise.
`boolean`	`isLicensed()` Returns `true` if the plugin is licensed.
`boolean`	`run()` Runs the charge calculation.
`protected void`	`setInputMolecule(Molecule mol)` Sets the input molecule.
`Molecule`	`setMolecule(Molecule mol, boolean st, boolean om)` Sets the input molecule after an optional standardization and/or modification.
`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
arrangeHydrogenIncerments, canRepeat, checkLicense, checkType, containsCoordinateBond, containsMulticenterSgroup, containsPseudoAtom, containsSRUSgroup, create, createStandardizedMolecule, createStandardizedMolecule, dehydrogenize, format, format, format, format, getAtomCount, getAtomIndex, getAtomIndexMap, getCalcMolecule, getDisplayMolecule, getDocument, getDoublePrecision, getExplicitHydrogenData, getInputMolDim, getMainMolecule, getOriginalMolecule, getPluginResource, getQueryMoleculeErrorMessage, getRemark, getResult, getResult, getResult, getResultAsRGB, getResultAsRGB, getResultAsString, getResultCount, getResultDomain, getResultMessage, getResultMolecules, getResultsAsRGB, getResultsAsRGB, getResultsAsString, getResultsAsString, getResultSource, getWarningMessage, isInputMoleculeAromatized, isMsCalc, isMultiThreadedRunEnabled, isNegligibleResult, isOK, isRgrouped, loadClass, readAttribute, removeWhitespace, restoreExplicitHydrogens, setAtomIndexMap, setDoublePrecision, setDoublePrecision, setDoublePrecision, setKeepHydrogens, 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.
    
    Specified by:
    
    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, formalcharge, "atomicformalcharge", 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
  - setMolecule
```
public Molecule setMolecule(Molecule mol,
                            boolean st,
                            boolean om)
                     throws PluginException
```
    Description copied from class: CalculatorPlugin
    
    Sets the input molecule after an optional standardization and/or modification. Standardization includes plugin specific standardization (e.g. dehydrogenize, aromatize) and sgroup expansion, modification usually means taking a microspecies form, or the major tautomeric form of the input molecule (usually optional). The input molecule is left unchanged (it is cloned before standardization/modification if required).
    
    Overrides:
    
    setMolecule in class CalculatorPlugin
    
    Parameters:
    
    mol - is the input molecule
    
    st - is true if standardization is required
    
    om - is true if original input molecule is to be used for atom indexing false if modified molecule is to be used for atom indexing
    
    Returns:
    
    the molecule to be used for atom indexing
    
    Throws:
    
    PluginException - on error
    
    See Also:
    
    CalculatorPlugin.setInputMolecule(Molecule), CalculatorPlugin.createStandardizedMolecule(Molecule), CalculatorPlugin.createModifiedInputMolecule(Molecule)
  - handlesMultiFragmentMolecules
```
public boolean handlesMultiFragmentMolecules()
```
    Description copied from class: CalculatorPlugin
    
    Returns true if the plugin handles multifragment molecules, false otherwise. In the latter case the plugin takes the fragment with more atoms if a multifragment molecule is given as input. The default implementation returns false.
    
    Overrides:
    
    handlesMultiFragmentMolecules in class CalculatorPlugin
    
    Returns:
    
    true if the plugin handles multifragment molecules, false otherwise
  - 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
  - getFormalCharge
```
public int getFormalCharge()
```
    Returns the formal charge of the molecule.
    
    Returns:
    
    the formal charge of the molecule
    
    Since:
    
    Marvin 5.2
    
    See Also:
    
    MoleculeGraph.getFormalCharge()
  - getFormalCharge
```
public int getFormalCharge(int index)
```
    Returns the formal charge of a specified atom.
    
    Parameters:
    
    index - is the atom index
    
    Returns:
    
    the formal charge of a specified atom
    
    Since:
    
    Marvin 5.2
    
    See Also:
    
    MolAtom.getCharge()
  - getTotalCharge
```
public double getTotalCharge(int index)
```
    Returns the total charge of a specified atom. Total charge is the sum of partial charges on the 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
    
    See Also:
    
    MolAtom.getCharge(), MoleculeGraph.getFormalCharge()
  - 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.
    
    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", "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

Class ChargePlugin

Nested Class Summary

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

Field Summary

Fields inherited from class chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin

Fields inherited from class chemaxon.marvin.plugin.CalculatorPlugin

Constructor Summary

Method Summary

Methods inherited from class chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin

Methods inherited from class chemaxon.marvin.plugin.CalculatorPlugin

Methods inherited from class java.lang.Object

Constructor Detail

ChargePlugin

Method Detail

isLicensed

getProductName

setParameters

setTakeResonantStructures

setInputMolecule

setMolecule

handlesMultiFragmentMolecules

run

getErrorMessage

getFormalCharge

getFormalCharge

getTotalCharge

getSigmaCharge

getPiCharge

getResultantImplicitHCharge

getAromaticSystemCharge

getAromaticSystemCharge

getAromaticRingCharge

getAromaticRingCharge

getResultTypes

getResultDomain

getResultCount

getTypeString

getResult

getResultAsString

getResultMolecule