java.lang.Object
- chemaxon.marvin.plugin.CalculatorPlugin

All Implemented Interfaces:: chemaxon.license.Licensable

Direct Known Subclasses:: AlignmentPlugin, ConformerPlugin, ElementalAnalyserPlugin, GeometryPlugin, IonChargePlugin, IsoelectricPointPlugin, IUPACNamingPlugin, logDPlugin, logPPlugin, MajorMicrospeciesAccessorPlugin, MajorMicrospeciesPlugin, MarkushEnumerationPlugin, MolecularDynamicsPlugin, pKaPlugin, RefractivityPlugin, ResonancePlugin, StereoisomerPlugin, StructuralFrameworksPlugin, TautomerizationPlugin, TopologyAnalyserPlugin

@PublicAPI
public abstract class CalculatorPlugin
extends Object
implements chemaxon.license.Licensable

Common base class for calculator plugins. Provides a uniform framework for plugin calculations and calculation result queries.

API usage examples:

Charge calculation for one input molecule. This example shows the general API usage. Plugin specific API usage examples can be found in the specific plugin class headers.

    // fill parameters
    Properties params = new Properties();
    params.put("precision", "3");
    params.put("type", "total,sigma");

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

    // set plugin parameters
    plugin.setParameters(params);

    // set target molecule
    Molecule mol = MolImporter.importMol("Clc1cc(Cl)c(Cl)cc1");
    plugin.setMolecule(mol);

    // run the calculation
    plugin.run();

    // get the calculation results
    Object[] types = plugin.getResultTypes(); // now this is {"total", "sigma"}
    for (int i=0; i < types.length; ++i) {
        Object type = types[i];
        System.out.println();
        System.out.println(type + " charge: ");
        System.out.println("atom\tcharge");
        int count = plugin.getResultCount(type); // now this is the atom count
        for (int j=0; j < count; ++j) {
            Object result = plugin.getResult(type, j); // now this is the charge value on atom j
            String rtext = plugin.getResultAsString(type, j, result); // string representation
            System.out.println((j+1)+"\t"+rtext);
        }
    }

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

Since:: Marvin 3.0

Nested Class Summary

Nested Classes
Modifier and Type Class Description

protected static class CalculatorPlugin.HydrogenData

Field Summary

Fields
Modifier and Type	Field	Description
`static int`	`ATOM`	Calculation domain type: calculation refers to atoms.
`static int`	`BLUE`	Constant storing the blue rgb value (the basic pKa result color).
`protected static int`	`CALCRGB_OFF`	Calculator rgb offset.
`protected static String`	`COVALENT_HYDRATION_ERROR_REMARK`	Covalent hydration error remark.
`protected static String`	`CRITICAL_ERROR_MSG`	Critical error message.
`static double`	`EPSILON`	The microspecies is ignored if its distribution is less than EPSILON for all pH values.
`protected List<CalculatorPlugin.HydrogenData>`	`explicitHydrogens`	explicit hydrogens of the input molecule stored here key: index of the "parent" atom on the input molecule value: the hydrogen atom
`protected static String`	`INCORRECT_AROMATIC_NITROGEN_REMARK`	Incorrect aromatic nitrogen remark.
`protected static String`	`INSTABLE_TAUTOMERIC_FORM_REMARK`	Instable tautomeric form remark.
`protected static String`	`KEEP_HYDROGENS`
`protected boolean`	`keepHydrogens`
`protected String`	`licenseEnvironment`	Member storing license environment.
`static int`	`MOLECULE`	Calculation domain type: calculation refers to the molecule.
`static int`	`MOLECULES`	Calculation domain type: calculation refers to multiple molecule output.
`protected static Double`	`NAN`	Double constant for `Double.NaN`.
`static String`	`PLUGIN_CLASS_KEY`	Plugin class key in manifest.
`static String`	`PLUGIN_DIR`	The plugin directory (relative to CLASSPATH).
`static int`	`RED`	Constant storing the red rgb value (the acidic pKa result color).
`protected static String`	`TRUE`

Constructor Summary

Constructors
Constructor	Description
`CalculatorPlugin()`	Constructor.
`CalculatorPlugin(com.google.common.base.Function<Molecule,Boolean> sgExpander)`	Constructor.
`CalculatorPlugin(com.google.common.base.Function<Molecule,Boolean> sgExpander, com.google.common.base.Function<Molecule,Boolean> sgContractor)`	Constructor.

Method Summary

All Methods Static Methods Instance Methods Abstract Methods Concrete Methods Deprecated Methods
Modifier and Type	Method	Description
`protected void`	`arrangeHydrogenIncerments(Molecule mol, int atomIndex, String label, double hydrogenIncrement)`
`boolean`	`canRepeat()`	Returns `true` if repeatedly running the same plugin object while getting the results on the GUI is allowed, `false` otherwise.
`protected void`	`checkLicense()`
`void`	`checkMolecule(Molecule mol)`	Checks the input molecule.
`protected void`	`checkType(String type, String[] typerange)`	Checks result types.
`protected static boolean`	`containsCoordinateBond(MoleculeGraph mol)`	Decides whether a molecule graph contains coordinate bonds.
`protected static boolean`	`containsMulticenterSgroup(Molecule mol)`	Decides whether a molecule contains Multicenter S-groups.
`protected static boolean`	`containsPseudoAtom(Molecule mol)`	Returns `true` if molecule contains pseudo atom.
`protected static boolean`	`containsSRUSgroup(Molecule mol)`	Decides whether a molecule contains SRU S-groups.
`static CalculatorPlugin`	`create(String clname, String jar)`	Loads a plugin, first tries to load it from CLASSPATH, then from JAR.
`protected Molecule`	`createModifiedInputMolecule(Molecule mol)`	Returns the modified input molecule (e.g.
`protected Molecule`	`createStandardizedMolecule(Molecule mol)`	Creates standardized molecule, the original input molecule is cloned.
`protected Molecule`	`createStandardizedMolecule(Molecule mol, boolean om)`	Deprecated. Use `createStandardizedMolecule(Molecule)` instead
`protected static void`	`dehydrogenize(Molecule mol)`	Deprecated. `MoleculeGraph.implicitizeHydrogens(int)` with parameter `MolAtom.ALL_H` does the same.
`String`	`format(double x)`	Converts a double into String, applying the maximum number of fractional digits specified.
`String`	`format(double[][] t, int intlen)`	Converts a `double[][]` `2xN` table to a 2-column tab-separated string representation of the table.
`String`	`format(double x, int intlen)`	Converts a double into String, applying the maximum number of fractional digits specified.
`StringBuffer`	`format(double x, StringBuffer s)`	Converts a double into String, applying the maximum number of fractional digits specified.
`int`	`getAtomCount()`	Returns the number of atoms in the input molecule.
`int`	`getAtomIndex(int index)`	Returns the atom index in the standardized molecule, or the atom index itself if the input molecule has not been standardized.
`protected int[]`	`getAtomIndexMap()`
`Molecule`	`getCalcMolecule()`	Returns the molecule used in the calculation.
`protected Molecule`	`getDisplayMolecule()`	Returns the molecule object to be used for GUI display.
`static MDocument`	`getDocument(Molecule structure)`	Returns encapsulating document, creates it if needed.
`int`	`getDoublePrecision()`	Returns the precision.
`String`	`getErrorMessage()`	Returns the calculation error information message if `run()` returned `false` (calculation error).
`protected List<CalculatorPlugin.HydrogenData>`	`getExplicitHydrogenData(Molecule cmol, int n)`
`int`	`getInputMolDim()`	Returns the input molecule dimension.
`protected Molecule`	`getMainMolecule(Molecule mol)`	Deprecated. Use `createModifiedInputMolecule(Molecule)` instead
`protected Molecule`	`getOriginalMolecule()`
`double`	`getpH()`	Returns the pH where the major microspecies should be taken.
`static URL`	`getPluginResource(String path)`	Returns the plugin JAR as resource URL, given the JAR file path relatively to the "plugins" directory.
`abstract String`	`getProductName()`	Returns the product identifier of the plugin as given by `LicenseManager`.
`protected static String`	`getQueryMoleculeErrorMessage(Molecule mol)`
`String`	`getRemark()`	Returns the calculation remark.
`Object`	`getResult(int index)`	Returns the result item for the specified type and index.
`Object`	`getResult(Object type, int index)`	Returns the result item for the specified type and index.
`Object`	`getResult(Object type, String arg)`	Returns the result item for the specified argument string.
`Object`	`getResult(String arg)`	Returns the result item for the specified argument string.
`int`	`getResultAsRGB(int index, Object result)`	Returns the specified result color as int format (alpha<<24 + red<<16 + green<<8 + blue).
`int`	`getResultAsRGB(Object type, int index, Object result)`	Returns the specified result color as int format (alpha<<24 + red<<16 + green<<8 + blue).
`String`	`getResultAsString(int index, Object result)`	Returns the specified result in String format for the first result type.
`String`	`getResultAsString(Object type, int index, Object result)`	Returns the specified result in String format.
`int`	`getResultCount()`	Returns the number of result items for the first result type.
`int`	`getResultCount(Object type)`	Returns the number of result items for the given result key.
`int`	`getResultDomain()`	Returns the calculation domain `ATOM`, `MOLECULE` or `MOLECULES`.
`int`	`getResultDomain(Object type)`	Returns the calculation domain `ATOM`, `MOLECULE` or `MOLECULES`.
`String`	`getResultMessage()`	Returns the plugin calculation error message, error or warning.
`Molecule`	`getResultMolecule()`	Returns the result molecule for display.
`Molecule[]`	`getResultMolecules()`	Returns the result molecule array for display.
`long`	`getResultsAsRGB(int index, Object result)`	Returns the specified result color(s) as int format (alpha<<24 + red<<16 + green<<8 + blue).
`long`	`getResultsAsRGB(Object type, int index, Object result)`	Returns the specified result color(s) as int format (alpha<<24 + red<<16 + green<<8 + blue).
`String`	`getResultsAsString(int index, Object result)`	Returns the specified result with possible subresults.
`String`	`getResultsAsString(Object type, int index, Object result)`	Returns the specified result with possible subresults.
`chemaxon.marvin.plugin.PluginMDocSource`	`getResultSource()`	Returns the result as a document source object.
`Object[]`	`getResultTypes()`	Returns the result types.
`String`	`getTypeString(Object type)`	Returns a string representation of the given type.
`String`	`getWarningMessage()`	Returns the calculation warning information message.
`boolean`	`handlesMultiFragmentMolecules()`	Returns `true` if the plugin handles multifragment molecules, `false` otherwise.
`boolean`	`isInputMoleculeAromatized()`	Returns `true` if the input molecule has aromatic bond.
`boolean`	`isLicensed()`	Returns `true` if the plugin is licensed.
`protected boolean`	`isMsCalc()`	Returns `true` if microspecies calculation.
`boolean`	`isMultiThreadedRunEnabled()`	For internal use only.
`boolean`	`isNegligibleResult(Object type, int index, Object result)`	Returns whether the result can be ignored.
`boolean`	`isOK()`	Returns `true` if no calculation error, `false` on error.
`protected static boolean`	`isRgrouped(Molecule mol)`	Returns `true` if molecule with R-groups.
`Class`	`loadClass(String clname)`	Loads a class, first tries from original CALSSPATH, then from the class loader used to load this plugin class.
`static String`	`readAttribute(String attribute, String jar)`	Reads an attribute from JAR manifest.
`protected static String`	`removeWhitespace(String str)`	Removes whitespace characters from the given string.
`protected boolean`	`restoreExplicitHydrogens(Molecule molecule)`	When the input molecule is set, the explicit H-s may be stored `setMolecule(Molecule, boolean, boolean, boolean)` The parameter should be topologically equal to the input molecule for a successfull restore.
`abstract boolean`	`run()`	Runs the tool.
`protected boolean`	`setAtomIndexMap(int[] map)`
`void`	`setDoublePrecision(int precision)`	Sets the double -> string conversion precision (maximal number of fraction digits) with zero-padding (12.56 -> 12.5600 if precision=4).
`void`	`setDoublePrecision(int precision, boolean pad)`	Sets the double -> string conversion precision (maximal number of fraction digits).
`protected void`	`setDoublePrecision(String pr)`	Sets the precision in the decimal format.
`protected abstract void`	`setInputMolecule(Molecule mol)`	Sets the input molecule.
`protected void`	`setKeepHydrogens(Properties properties)`
`void`	`setLicenseEnvironment(String env)`	Sets license environment to be stored.
`Molecule`	`setMolecule(Molecule mol)`	Sets the input molecule after standardization.
`Molecule`	`setMolecule(Molecule mol, boolean st)`	Sets the input molecule after an optional standardization.
`Molecule`	`setMolecule(Molecule mol, boolean st, boolean om)`	Sets the input molecule after an optional standardization and/or modification.
`protected Molecule`	`setMolecule(Molecule mol, boolean st, boolean om, boolean storeExplicitHydrogens)`
`void`	`setParameters(Properties params)`	Sets the input parameters for the plugin.
`void`	`setProgressMonitor(MProgressMonitor pmon)`	Sets a progress observer to be used in `run()` to display progress status.
`void`	`standardize(Molecule mol)`	Standardizes the molecule by performing the transformations necessary to run the plugin (aromatize, dehydrogenize, bring nitro groups to common form, ...).
`protected static void`	`standardizeIonicGroups(Molecule mol)`	Default standardization: nitro groups: `[O-:1][N+:2] >> [O:1]=[N:2]`, `[NH1+:1][O-:2] >> [H:3][O:2][N:1]` sulphynil groups: `[#6][S+:1]([#6])[#8-:2]>>[#6][S:1]([#6])=[O:2]`
`protected static void`	`standardizeNeutralGroups(Molecule mol)`	Neutral -> ionic standardization: `[O:1]=[N:2] >> [O-:1][N+:2]`, `[H:3][O:2][N:1] >> [NH1+:1][O-:2]` sulphynil group transformation: `[#6][S:1]([#6])=[O:2] >> [#6][S+:1]([#6])[#8-:2]`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - KEEP_HYDROGENS
```
protected static final String KEEP_HYDROGENS
```
    See Also:
    
    Constant Field Values
  - TRUE
```
protected static final String TRUE
```
    See Also:
    
    Constant Field Values
  - keepHydrogens
```
protected boolean keepHydrogens
```
  - PLUGIN_DIR
```
public static final String PLUGIN_DIR
```
    The plugin directory (relative to CLASSPATH).
    
    See Also:
    
    Constant Field Values
  - PLUGIN_CLASS_KEY
```
public static final String PLUGIN_CLASS_KEY
```
    Plugin class key in manifest.
    
    See Also:
    
    Constant Field Values
  - CRITICAL_ERROR_MSG
```
protected static final String CRITICAL_ERROR_MSG
```
    Critical error message.
    
    See Also:
    
    Constant Field Values
  - INCORRECT_AROMATIC_NITROGEN_REMARK
```
protected static final String INCORRECT_AROMATIC_NITROGEN_REMARK
```
    Incorrect aromatic nitrogen remark.
    
    See Also:
    
    Constant Field Values
  - INSTABLE_TAUTOMERIC_FORM_REMARK
```
protected static final String INSTABLE_TAUTOMERIC_FORM_REMARK
```
    Instable tautomeric form remark.
    
    See Also:
    
    Constant Field Values
  - COVALENT_HYDRATION_ERROR_REMARK
```
protected static final String COVALENT_HYDRATION_ERROR_REMARK
```
    Covalent hydration error remark.
    
    See Also:
    
    Constant Field Values
  - licenseEnvironment
```
protected String licenseEnvironment
```
    Member storing license environment.
  - RED
```
public static final int RED
```
    Constant storing the red rgb value (the acidic pKa result color).
    
    See Also:
    
    Constant Field Values
  - BLUE
```
public static final int BLUE
```
    Constant storing the blue rgb value (the basic pKa result color).
    
    See Also:
    
    Constant Field Values
  - CALCRGB_OFF
```
protected static final int CALCRGB_OFF
```
    Calculator rgb offset.
    
    See Also:
    
    Constant Field Values
  - ATOM
```
public static final int ATOM
```
    Calculation domain type: calculation refers to atoms.
    
    See Also:
    
    Constant Field Values
  - MOLECULE
```
public static final int MOLECULE
```
    Calculation domain type: calculation refers to the molecule.
    
    See Also:
    
    Constant Field Values
  - MOLECULES
```
public static final int MOLECULES
```
    Calculation domain type: calculation refers to multiple molecule output.
    
    Since:
    
    Marvin 5.2
    
    See Also:
    
    Constant Field Values
  - NAN
```
protected static final Double NAN
```
    Double constant for Double.NaN.
  - EPSILON
```
public static final double EPSILON
```
    The microspecies is ignored if its distribution is less than EPSILON for all pH values.
    
    See Also:
    
    Constant Field Values
  - explicitHydrogens
```
protected List<CalculatorPlugin.HydrogenData> explicitHydrogens
```
    explicit hydrogens of the input molecule stored here key: index of the "parent" atom on the input molecule value: the hydrogen atom
- Constructor Detail
  - CalculatorPlugin
```
public CalculatorPlugin()
```
    Constructor. Initializes decimal format.
  - CalculatorPlugin
```
@Beta
public CalculatorPlugin(com.google.common.base.Function<Molecule,Boolean> sgExpander)
```
    Constructor. This constructor is intended to be used only internally. Please note that this constuctor is annotated with the Beta annotation, so it can be subject to incompatible changes or complete removal in any of the upcoming releases without further notification.
    
    Parameters:
    
    sgExpander - Method to use to expand sgroups.
  - CalculatorPlugin
```
@Beta
public CalculatorPlugin(com.google.common.base.Function<Molecule,Boolean> sgExpander,
                        com.google.common.base.Function<Molecule,Boolean> sgContractor)
```
    Constructor. This constructor is intended to be used only internally. Please note that this constuctor is annotated with the Beta annotation, so it can be subject to incompatible changes or complete removal in any of the upcoming releases without further notification.
    
    Parameters:
    
    sgExpander - Method to use to expand sgroups.
    
    sgContractor - Method to use to contract sgroups.
- Method Detail
  - getPluginResource
```
public static URL getPluginResource(String path)
```
    Returns the plugin JAR as resource URL, given the JAR file path relatively to the "plugins" directory.
    
    Parameters:
    
    path - is the relative jar file path
    
    Returns:
    
    the corresponding resource URL
  - readAttribute
```
public static String readAttribute(String attribute,
                                   String jar)
                            throws PluginException
```
    Reads an attribute from JAR manifest.
    
    Parameters:
    
    attribute - is the attribute name
    
    jar - is the JAR file name
    
    Returns:
    
    the attribute value, or null if not exists
    
    Throws:
    
    PluginException
    
    Since:
    
    Marvin 4.0
  - create
```
public static CalculatorPlugin create(String clname,
                                      String jar)
                               throws PluginException
```
    Loads a plugin, first tries to load it from CLASSPATH, then from JAR. If the plugin class name is null then it is read from the manifest attribute PLUGIN_CLASS_KEY.
    
    Parameters:
    
    clname - is the plugin class name
    
    jar - is the plugin JAR file name
    
    Returns:
    
    the created plugin
    
    Throws:
    
    PluginException
    
    Since:
    
    Marvin 4.0
  - loadClass
```
public final Class loadClass(String clname)
                      throws PluginException
```
    Loads a class, first tries from original CALSSPATH, then from the class loader used to load this plugin class.
    
    Parameters:
    
    clname - is the class name
    
    Returns:
    
    the Class object, or null if could not be loaded
    
    Throws:
    
    PluginException
    
    Since:
    
    Marvin 4.0
  - isRgrouped
```
protected static boolean isRgrouped(Molecule mol)
```
    Returns true if molecule with R-groups.
    
    Parameters:
    
    mol - is the molecule
    
    Returns:
    
    true if molecule with R-groups
  - containsPseudoAtom
```
protected static boolean containsPseudoAtom(Molecule mol)
```
    Returns true if molecule contains pseudo atom.
    
    Parameters:
    
    mol - the molecule to examine
    
    Returns:
    
    true if the molecule contains pseudo atom, false otherwise
  - containsMulticenterSgroup
```
protected static boolean containsMulticenterSgroup(Molecule mol)
```
    Decides whether a molecule contains Multicenter S-groups.
    
    Parameters:
    
    mol - the molecule to examine
    
    Returns:
    
    true if the molecule contains at least one MulticenterSgroup false otherwise.
  - containsSRUSgroup
```
protected static boolean containsSRUSgroup(Molecule mol)
```
    Decides whether a molecule contains SRU S-groups.
    
    Parameters:
    
    mol - the molecule to examine
    
    Returns:
    
    true if the molecule contains at least one SRU S-group false otherwise.
  - containsCoordinateBond
```
protected static boolean containsCoordinateBond(MoleculeGraph mol)
```
    Decides whether a molecule graph contains coordinate bonds.
    
    Parameters:
    
    mol - the molecule to examine
    
    Returns:
    
    true if the molecule contains at least one coordinate bond false otherwise.
  - dehydrogenize
```
@Deprecated
protected static void dehydrogenize(Molecule mol)
```
    Deprecated.
    MoleculeGraph.implicitizeHydrogens(int) with parameter MolAtom.ALL_H does the same.
    
    Makes all explicit H-s implicit.
    
    Parameters:
    
    mol - is the molecule
  - removeWhitespace
```
protected static String removeWhitespace(String str)
```
    Removes whitespace characters from the given string.
    
    Parameters:
    
    str - is the string
    
    Returns:
    
    the string without whitespace characters
  - getDocument
```
public static MDocument getDocument(Molecule structure)
```
    Returns encapsulating document, creates it if needed.
    
    Parameters:
    
    structure - the molecule
    
    Returns:
    
    the encapsulating document
    
    Since:
    
    Marvin 5.0
  - 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
    
    Returns:
    
    true if the plugin is licensed
  - setLicenseEnvironment
```
public void setLicenseEnvironment(String env)
```
    Sets license environment to be stored.
    
    Specified by:
    
    setLicenseEnvironment in interface chemaxon.license.Licensable
    
    Parameters:
    
    env - environment String to be stored and passed to the LicenseHandler in the isLicensed method
  - checkLicense
```
protected final void checkLicense()
```
  - getProductName
```
public abstract String getProductName()
```
    Returns the product identifier of the plugin as given by LicenseManager. The name is used by the isLicensed() method.
    
    Returns:
    
    product identifier or a default string
  - checkType
```
protected void checkType(String type,
                         String[] typerange)
                  throws PluginException
```
    Checks result types.
    
    Parameters:
    
    type - is the type given by the user
    
    typerange - is the array containing the valid types
    
    Throws:
    
    PluginException - if the user-type is not contained in the type-range
  - getDoublePrecision
```
public final int getDoublePrecision()
```
    Returns the precision. This is the max. number of fractional digits.
    
    Returns:
    
    the precision
  - setDoublePrecision
```
protected final void setDoublePrecision(String pr)
```
    Sets the precision in the decimal format. This is done according to the user defined precision value: 0..8 means maximal number of fractional digits, ending padded with zeros (e.g. 12.56 -> 12.5600 for precision 4). 'inf' means maximal number of digits set to 10, no padding zeros (e.g. 12.56 -> 12.56)
    
    Parameters:
    
    pr - is the precision string ("0"..."8" or "inf")
  - setDoublePrecision
```
public final void setDoublePrecision(int precision)
```
    Sets the double -> string conversion precision (maximal number of fraction digits) with zero-padding (12.56 -> 12.5600 if precision=4).
    
    Parameters:
    
    precision - is the precision
  - setDoublePrecision
```
public final void setDoublePrecision(int precision,
                                     boolean pad)
```
    Sets the double -> string conversion precision (maximal number of fraction digits).
    
    Parameters:
    
    precision - is the precision
    
    pad - is true if fractional ending zeros should be printed e.g. 12.56 -> 12.56 if precision=4, pad=false 12.56 -> 12.5600 if precision=4, pad=true
  - format
```
public final String format(double x)
```
    Converts a double into String, applying the maximum number of fractional digits specified.
    
    Parameters:
    
    x - is the double value to be converted
    
    Returns:
    
    the result as String
    
    See Also:
    
    setDoublePrecision(int precision, boolean pad)
  - format
```
public final String format(double x,
                           int intlen)
```
    Converts a double into String, applying the maximum number of fractional digits specified. Adds leading spaces to ensure the given integral part length.
    
    Parameters:
    
    x - is the double value to be converted
    
    intlen - is the required integral part length
    
    Returns:
    
    the result as String
    
    See Also:
    
    setDoublePrecision(int precision, boolean pad)
  - format
```
public final StringBuffer format(double x,
                                 StringBuffer s)
```
    Converts a double into String, applying the maximum number of fractional digits specified. Appends the result to the specified StringBuffer.
    
    Parameters:
    
    x - is the double value to be converted
    
    s - is the StringBuffer to be used
    
    Returns:
    
    the StringBuffer with the current item appended
    
    See Also:
    
    setDoublePrecision(int precision, boolean pad)
  - format
```
public final String format(double[][] t,
                           int intlen)
```
    Converts a double[][] 2xN table to a 2-column tab-separated string representation of the table.
    
    Parameters:
    
    t - is the table
    
    intlen - is the required integral part length
    
    Returns:
    
    the string representation
  - setProgressMonitor
```
public void setProgressMonitor(MProgressMonitor pmon)
```
    Sets a progress observer to be used in run() to display progress status. Short calculations may ignore the observer object. The default implementation does nothing.
    
    Parameters:
    
    pmon - is the progress monitor, may be null
  - setMolecule
```
public final Molecule setMolecule(Molecule mol)
                           throws PluginException
```
    Sets the input molecule after standardization. Standardization includes plugin specific standardization (e.g. dehydrogenize, aromatize) and sgroup expansion. The input molecule is left unchanged (it is cloned for standardization).
    
    Parameters:
    
    mol - is the input molecule
    
    Returns:
    
    the molecule to be used for atom indexing
    
    Throws:
    
    PluginException - on error
  - setMolecule
```
public Molecule setMolecule(Molecule mol,
                            boolean st)
                     throws PluginException
```
    Sets the input molecule after an optional standardization. Standardization includes plugin specific standardization (e.g. dehydrogenize, aromatize) and sgroup expansion. The input molecule is left unchanged (it is cloned if standardization is required).
    
    Parameters:
    
    mol - is the input molecule
    
    st - is true if standardization is required
    
    Returns:
    
    the molecule to be used for atom indexing
    
    Throws:
    
    PluginException - on error
  - setMolecule
```
public Molecule setMolecule(Molecule mol,
                            boolean st,
                            boolean om)
                     throws PluginException
```
    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).
    
    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:
    
    setInputMolecule(Molecule), createStandardizedMolecule(Molecule), createModifiedInputMolecule(Molecule)
  - setMolecule
```
protected Molecule setMolecule(Molecule mol,
                               boolean st,
                               boolean om,
                               boolean storeExplicitHydrogens)
                        throws PluginException
```
    Throws:
    
    PluginException
  - setAtomIndexMap
```
protected boolean setAtomIndexMap(int[] map)
```
  - getAtomIndexMap
```
protected int[] getAtomIndexMap()
```
  - getExplicitHydrogenData
```
protected List<CalculatorPlugin.HydrogenData> getExplicitHydrogenData(Molecule cmol,
                                                                      int n)
```
  - createModifiedInputMolecule
```
protected Molecule createModifiedInputMolecule(Molecule mol)
                                        throws PluginException
```
    Returns the modified input molecule (e.g. microspecies, major tautomeric form). This method is used for modifying the input molecule set by setMolecule(Molecule) before passing the molecule to the calulation with setInputMolecule(Molecule) method. The default implementation returns the input molecule itself.
    
    Parameters:
    
    mol - is the input molecule
    
    Returns:
    
    the modified input molecule
    
    Throws:
    
    PluginException
  - getInputMolDim
```
public int getInputMolDim()
```
    Returns the input molecule dimension.
    
    Returns:
    
    the input molecule dimension
  - getCalcMolecule
```
public Molecule getCalcMolecule()
```
    Returns the molecule used in the calculation. This can be a standardized and/or modified version (e.g. microspecies, major tautomeric form) of the input molecule. Standardized if parameter 'st' is set to true in setMolecule(chemaxon.struc.Molecule, boolean) or setMolecule(chemaxon.struc.Molecule, boolean, boolean). Input molecule is modified, if the plugin overrides the createModifiedInputMolecule(Molecule) mehod.
    
    Returns:
    
    the molecule used in the calculation
    
    Since:
    
    Marvin 4.1
  - createStandardizedMolecule
```
@Deprecated
protected Molecule createStandardizedMolecule(Molecule mol,
                                              boolean om)
                                       throws PluginException
```
    Deprecated.
    Use createStandardizedMolecule(Molecule) instead
    
    Creates standardized molecule, the original input molecule is cloned. If handlesMultiFragmentMolecules() returns false then takes the largest fragment (measured by atom count). The cloned molecule is standardized by standardize(Molecule). Sets the atomIndexMap: atomIndexMap[i] is the index in the standardized molecule of the i-th atom in the original molecule or -1 if this atom has been removed.
    
    Parameters:
    
    mol - is the input molecule
    
    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 standardized molecule
    
    Throws:
    
    PluginException - on error
  - createStandardizedMolecule
```
protected Molecule createStandardizedMolecule(Molecule mol)
                                       throws PluginException
```
    Creates standardized molecule, the original input molecule is cloned. If handlesMultiFragmentMolecules() returns false then takes the largest fragment (measured by atom count). The cloned molecule is standardized by standardize(Molecule). Sets the atomIndexMap: atomIndexMap[i] is the index in the standardized molecule of the i-th atom in the original molecule or -1 if this atom has been removed.
    
    Parameters:
    
    mol - is the input molecule
    
    Returns:
    
    the standardized molecule
    
    Throws:
    
    PluginException - on error
    
    Since:
    
    Marvin 5.0
  - getMainMolecule
```
@Deprecated
protected Molecule getMainMolecule(Molecule mol)
                            throws PluginException
```
    Deprecated.
    Use createModifiedInputMolecule(Molecule) instead
    
    Returns the molecule form with largest distribution. Returns a microspecies with largest distribution on a given pH if pH is different from Double.NaN, otherwise returns the input molecule itself. The default implementation returns the input molecule itself.
    
    Parameters:
    
    mol - is the input molecule
    
    Returns:
    
    the molecule form with largest distribution
    
    Throws:
    
    PluginException
  - getDisplayMolecule
```
protected Molecule getDisplayMolecule()
                               throws PluginException
```
    Returns the molecule object to be used for GUI display. Plugins will add atom labels and/or molecule properties to display plugin results in the molecule. The default implementation returns the original molecule.
    
    Returns:
    
    the molecule object to be used for GUI display
    
    Throws:
    
    PluginException - on error
  - handlesMultiFragmentMolecules
```
public boolean handlesMultiFragmentMolecules()
```
    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.
    
    Returns:
    
    true if the plugin handles multifragment molecules, false otherwise
  - isMsCalc
```
protected boolean isMsCalc()
```
    Returns true if microspecies calculation. The default implementation returns false.
    
    Returns:
    
    false
  - setParameters
```
public void setParameters(Properties params)
                   throws PluginException
```
    Sets the input parameters for the plugin.
    
    Parameters:
    
    params - is the parameter table
    
    Throws:
    
    PluginException - on error
  - getpH
```
public double getpH()
```
    Returns the pH where the major microspecies should be taken. Returns Double.NaN if no microspecies calculation required.
    
    Returns:
    
    the pH where the major microspecies should be taken or Double.NaN if no microspecies calculation
  - checkMolecule
```
public void checkMolecule(Molecule mol)
                   throws PluginException
```
    Checks the input molecule. Throws exception if the molecule is not accepted as input molecule, otherwise does nothing (simply returns). The default implementation refuses query molecules, molecules with SRU S-groups, molecules with multicenter S-groups and molecules with coordinate bonds.
    
    Parameters:
    
    mol - is the input molecule
    
    Throws:
    
    PluginException - with error message for the user if the molecule is refused
  - getQueryMoleculeErrorMessage
```
protected static String getQueryMoleculeErrorMessage(Molecule mol)
```
  - setInputMolecule
```
protected abstract void setInputMolecule(Molecule mol)
                                  throws PluginException
```
    Sets the input molecule.
    
    Parameters:
    
    mol - is the input molecule
    
    Throws:
    
    PluginException - on error
  - run
```
public abstract boolean run()
                     throws PluginException
```
    Runs the tool.
    
    Returns:
    
    true if the calculation was successful, false on calculation problems
    
    Throws:
    
    PluginException - on error
    
    See Also:
    
    getErrorMessage()
  - isOK
```
public boolean isOK()
```
    Returns true if no calculation error, false on error. This is the same as the return value of the last call to run(). The default implementation returns true if both getErrorMessage() and getWarningMessage() return the empty string.
    
    Returns:
    
    true if no calculation error or warning
    
    Since:
    
    Marvin 4.0
  - getErrorMessage
```
public String getErrorMessage()
```
    Returns the calculation error information message if run() returned false (calculation error). The default implementation returns the empty string.
    
    Returns:
    
    the calculation error information message
  - getWarningMessage
```
public String getWarningMessage()
```
    Returns the calculation warning information message. The default implementation returns the empty string.
    
    Returns:
    
    the calculation warning information message
  - getResultMessage
```
public final String getResultMessage()
```
    Returns the plugin calculation error message, error or warning.
    
    Returns:
    
    the plugin calculation error message
  - getRemark
```
public String getRemark()
```
    Returns the calculation remark. While in case of warning or error returned in getErrorMessage() or getWarningMessage() there is no calculation result, in case of a remark the calculation can be performed although the result may not be correct or precise - depending on the remark. The default implementation returns null.
    
    Returns:
    
    the calculation remark
  - getResultTypes
```
public Object[] getResultTypes()
```
    Returns the result types. The default implementation returns null.
    
    Returns:
    
    the result types
  - getTypeString
```
public String getTypeString(Object type)
```
    Returns a string representation of the given type. The default implementation returns type.toString().
    
    Parameters:
    
    type - is the type object
    
    Returns:
    
    the type string
  - getResultDomain
```
public int getResultDomain(Object type)
```
    Returns the calculation domain ATOM, MOLECULE or MOLECULES. The default implementation returns MOLECULE.
    
    Parameters:
    
    type - is the result type
    
    Returns:
    
    the calculation domain
    
    See Also:
    
    getResultTypes()
  - canRepeat
```
public boolean canRepeat()
```
    Returns true if repeatedly running the same plugin object while getting the results on the GUI is allowed, false otherwise. For internal use.
    
    Returns:
    
    true if allowed, false otherwise
    
    Since:
    
    Marvin 5.2
  - getResultCount
```
public int getResultCount(Object type)
```
    Returns the number of result items for the given result key. The default implementation returns 1.
    
    Parameters:
    
    type - is the result type
    
    Returns:
    
    the number of result items
    
    See Also:
    
    getResultTypes()
  - getResult
```
public Object getResult(Object type,
                        int index)
                 throws PluginException
```
    Returns the result item for the specified type and index. The default implementation returns null.
    
    Parameters:
    
    type - is the result type
    
    index - is the result index
    
    Returns:
    
    the result item for the specified type and index
    
    Throws:
    
    PluginException - if the result cannot be returned
    
    See Also:
    
    getResultTypes()
  - getResultAsString
```
public String getResultAsString(Object type,
                                int index,
                                Object result)
                         throws PluginException
```
    Returns the specified result in String format. The default implementation returns null.
    
    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
  - getResultsAsString
```
public String getResultsAsString(Object type,
                                 int index,
                                 Object result)
                          throws PluginException
```
    Returns the specified result with possible subresults. (items separated by "|" characters) (e.g. both pKa values instead of the most significant pKa) in String format.
    
    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(Object type,
                          int index,
                          Object result)
                   throws PluginException
```
    Returns the specified result color as int format (alpha<<24 + red<<16 + green<<8 + blue).
    
    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(Object type,
                            int index,
                            Object result)
                     throws PluginException
```
    Returns the specified result color(s) as int format (alpha<<24 + red<<16 + green<<8 + blue). (e.g. both pKa colors instead of the most significant pKa color) as long (lower and upper bits).
    
    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
  - isNegligibleResult
```
public boolean isNegligibleResult(Object type,
                                  int index,
                                  Object result)
                           throws PluginException
```
    Returns whether the result can be ignored. Can be used to filter out out-of range values. The default implementation returns false.
    
    Parameters:
    
    type - is the result type
    
    index - is the result index
    
    result - is the result object
    
    Returns:
    
    true if the result can be ignored
    
    Throws:
    
    PluginException
  - getResult
```
public Object getResult(Object type,
                        String arg)
                 throws PluginException
```
    Returns the result item for the specified argument string. The default implementation calls getResult(Object, int) with the argument string converted to an integer (result index).
    
    Parameters:
    
    type - is the result type
    
    arg - is the argument string
    
    Returns:
    
    the result item for the specified type and argument string
    
    Throws:
    
    PluginException - if the result cannot be returned
    
    See Also:
    
    getResultTypes()
  - 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)).
    
    Returns:
    
    the result molecule
    
    Throws:
    
    PluginException - on error
    
    Since:
    
    Marvin 4.0
  - getResultMolecules
```
public Molecule[] getResultMolecules()
                              throws PluginException
```
    Returns the result molecule array for display. The display of the molecules in array have to be implemented in a class derived from CalculatorPluginDispaly class (example: MultipleDataDisplay class). 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)).
    
    Returns:
    
    the result molecule array
    
    Throws:
    
    PluginException - on error
    
    Since:
    
    Marvin 4.1
  - getResultSource
```
public chemaxon.marvin.plugin.PluginMDocSource getResultSource()
                                                        throws PluginException
```
    Returns the result as a document source object. This is useful for displaying the molecules in a viewer dynamically as they become available instead of collecting all results before display. The default implementation returns null.
    
    Returns:
    
    the document source interface
    
    Throws:
    
    PluginException - on error
    
    Since:
    
    Marvin 5.0
  - getResultDomain
```
public int getResultDomain()
```
    Returns the calculation domain ATOM, MOLECULE or MOLECULES. for the first result type.
    
    Returns:
    
    the calculation domain
  - getResultCount
```
public int getResultCount()
```
    Returns the number of result items for the first result type.
    
    Returns:
    
    the number of result items
    
    See Also:
    
    getResultTypes()
  - getResult
```
public Object getResult(int index)
                 throws PluginException
```
    Returns the result item for the specified type and index. for the first result type.
    
    Parameters:
    
    index - is the result index
    
    Returns:
    
    the result item for the specified type and index
    
    Throws:
    
    PluginException - if the result cannot be returned
    
    See Also:
    
    getResultTypes()
  - getResult
```
public Object getResult(String arg)
                 throws PluginException
```
    Returns the result item for the specified argument string. The default implementation calls getResult(Object, int) with the argument string converted to an integer (result index) and with the first result type.
    
    Parameters:
    
    arg - is the argument string
    
    Returns:
    
    the result item for the first result type and the given argument string
    
    Throws:
    
    PluginException - if the result cannot be returned
    
    See Also:
    
    getResultTypes()
  - getResultAsString
```
public String getResultAsString(int index,
                                Object result)
                         throws PluginException
```
    Returns the specified result in String format for the first result type.
    
    Parameters:
    
    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
  - getResultsAsString
```
public String getResultsAsString(int index,
                                 Object result)
                          throws PluginException
```
    Returns the specified result with possible subresults. (items separated by "|" characters) (e.g. both pKa values instead of the most significant pKa) in String format.
    
    Parameters:
    
    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(int index,
                          Object result)
                   throws PluginException
```
    Returns the specified result color as int format (alpha<<24 + red<<16 + green<<8 + blue). for the first result type.
    
    Parameters:
    
    index - is the result index
    
    result - is the result item
    
    Returns:
    
    the specified result in color as int format
    
    Throws:
    
    PluginException - if an invalid result item is given
  - getResultsAsRGB
```
public long getResultsAsRGB(int index,
                            Object result)
                     throws PluginException
```
    Returns the specified result color(s) as int format (alpha<<24 + red<<16 + green<<8 + blue). (e.g. both pKa colors instead of the most significant pKa color) as long (lower and upper bits).
    
    Parameters:
    
    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
  - getAtomCount
```
public final int getAtomCount()
```
    Returns the number of atoms in the input molecule.
    
    Returns:
    
    the number of atoms in the input molecule
  - getAtomIndex
```
public final int getAtomIndex(int index)
```
    Returns the atom index in the standardized molecule, or the atom index itself if the input molecule has not been standardized.
    
    Parameters:
    
    index - is the atom index in the input molecule
    
    Returns:
    
    the corresponding atom index in the standardized molecule, -1 if the atom has been removed
  - isInputMoleculeAromatized
```
public final boolean isInputMoleculeAromatized()
```
    Returns true if the input molecule has aromatic bond.
    
    Returns:
    
    true if the input molecule has aromatic bond
  - standardize
```
public void standardize(Molecule mol)
```
    Standardizes the molecule by performing the transformations necessary to run the plugin (aromatize, dehydrogenize, bring nitro groups to common form, ...). This implementation performs the following transformations:
    
    aromatization
    nitro group transformation: [O-:1][N+:2] >> [O:1]=[N:2], [NH1+:1][O-:2] >> [H:3][O:2][N:1]
    sulphynil group transformation: [#6][S+:1]([#6])[#8-:2] >> [#6][S:1]([#6])=[O:2]
    To be overridden by subclasses that require other standardization (or none at all). TODO: replace by call to chemaxon.standardizer.Standardizer
    Parameters:
    
    mol - is the molecule to be standardized
  - standardizeIonicGroups
```
protected static void standardizeIonicGroups(Molecule mol)
```
    Default standardization:
    
    nitro groups: [O-:1][N+:2] >> [O:1]=[N:2], [NH1+:1][O-:2] >> [H:3][O:2][N:1]
    sulphynil groups: [#6][S+:1]([#6])[#8-:2]>>[#6][S:1]([#6])=[O:2]
    Parameters:
    
    mol - is the molecule to be standardized
  - standardizeNeutralGroups
```
protected static void standardizeNeutralGroups(Molecule mol)
```
    Neutral -> ionic standardization:
    [O:1]=[N:2] >> [O-:1][N+:2], [H:3][O:2][N:1] >> [NH1+:1][O-:2]
    sulphynil group transformation: [#6][S:1]([#6])=[O:2] >> [#6][S+:1]([#6])[#8-:2]
    Parameters:
    
    mol - is the molecule to be standardized
  - isMultiThreadedRunEnabled
```
public boolean isMultiThreadedRunEnabled()
```
    For internal use only.
    
    Returns:
    
    true if multi-threaded run is enabled
  - restoreExplicitHydrogens
```
protected boolean restoreExplicitHydrogens(Molecule molecule)
```
    When the input molecule is set, the explicit H-s may be stored setMolecule(Molecule, boolean, boolean, boolean) The parameter should be topologically equal to the input molecule for a successfull restore.
    
    Parameters:
    
    molecule - the molecule to put the H-s on
    
    Returns:
    
    true if the restore was successful, false otherwise
  - setKeepHydrogens
```
protected void setKeepHydrogens(Properties properties)
```
  - arrangeHydrogenIncerments
```
protected void arrangeHydrogenIncerments(Molecule mol,
                                         int atomIndex,
                                         String label,
                                         double hydrogenIncrement)
```
  - getOriginalMolecule
```
protected Molecule getOriginalMolecule()
```

Class CalculatorPlugin

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

KEEP_HYDROGENS

TRUE

keepHydrogens

PLUGIN_DIR

PLUGIN_CLASS_KEY

CRITICAL_ERROR_MSG

INCORRECT_AROMATIC_NITROGEN_REMARK

INSTABLE_TAUTOMERIC_FORM_REMARK

COVALENT_HYDRATION_ERROR_REMARK

licenseEnvironment

RED

BLUE

CALCRGB_OFF

ATOM

MOLECULE

MOLECULES

NAN

EPSILON

explicitHydrogens

Constructor Detail

CalculatorPlugin

CalculatorPlugin

CalculatorPlugin

Method Detail

getPluginResource

readAttribute

create

loadClass

isRgrouped

containsPseudoAtom

containsMulticenterSgroup

containsSRUSgroup

containsCoordinateBond

dehydrogenize

removeWhitespace

getDocument

isLicensed

setLicenseEnvironment

checkLicense

getProductName

checkType

getDoublePrecision

setDoublePrecision

setDoublePrecision

setDoublePrecision

format

format

format

format

setProgressMonitor

setMolecule

setMolecule

setMolecule

setMolecule

setAtomIndexMap

getAtomIndexMap

getExplicitHydrogenData

createModifiedInputMolecule

getInputMolDim

getCalcMolecule

createStandardizedMolecule

createStandardizedMolecule

getMainMolecule

getDisplayMolecule

handlesMultiFragmentMolecules

isMsCalc

setParameters

getpH

checkMolecule

getQueryMoleculeErrorMessage

setInputMolecule

run

isOK