CalculatorPlugin (JChem API documentation (c)1998-2008 ChemAxon Ltd.)

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chemaxon.marvin.plugin
Class CalculatorPlugin

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

All Implemented Interfaces:: chemaxon.license.Licensable

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

public abstract class CalculatorPlugin
extends java.lang.Object
implements chemaxon.license.Licensable
extends java.lang.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
Version:: 5.1 04/25/2008
Author:: Nora Mate, Zsolt Mohacsi

Field Summary
`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 java.lang.String`	`COVALENT_HYDRATION_ERROR_REMARK` Covalent hydration error remark.
`protected static java.lang.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 static java.lang.String`	`INCORRECT_AROMATIC_NITROGEN_REMARK` Incorrect aromatic nitrogen remark.
`protected static java.lang.String`	`INSTABLE_TAUTOMERIC_FORM_REMARK` Instable tautomeric form remark.
`protected java.lang.String`	`licenseEnvironment` Member storing license environment.
`static int`	`MOLECULE` Calculation domain type: calculation refers to the molecule.
`protected static java.lang.Double`	`NAN` Double constant for `Double.NaN`.
`static java.lang.String`	`PLUGIN_CLASS_KEY` Plugin class key in manifest.
`static java.lang.String`	`PLUGIN_DIR` The plugin directory (relative to CLASSPATH).
`static int`	`RED` Constant storing the red rgb value (the acidic pKa result color).

Constructor Summary
`CalculatorPlugin()` Constructor.

Method Summary
`void`	`checkMolecule(Molecule mol)` Checks the input molecule.
`protected void`	`checkType(java.lang.String type, java.lang.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(java.lang.String clname, java.lang.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. microspecies, major tautomeric form).
`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)` Makes all explicit H-s implicit.
`java.lang.String`	`format(double x)` Converts a double into String, applying the maximum number of fractional digits specified.
`java.lang.String`	`format(double[][] t, int intlen)` Converts a `double[][]` `2xN` table to a 2-column tab-separated string representation of the table.
`java.lang.String`	`format(double x, int intlen)` Converts a double into String, applying the maximum number of fractional digits specified.
`java.lang.StringBuffer`	`format(double x, java.lang.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.
`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.
`java.lang.String`	`getErrorMessage()` Returns the calculation error information message if `run()` returned `false` (calculation error).
`int`	`getInputMolDim()` Returns the input molecule dimension.
`protected Molecule`	`getMainMolecule(Molecule mol)` Deprecated. Use `createModifiedInputMolecule(Molecule)` instead
`double`	`getpH()` Returns the pH where the major microspecies should be taken.
`static java.net.URL`	`getPluginResource(java.lang.String path)` Returns the plugin JAR as resource URL, given the JAR file path relatively to the "plugins" directory.
`java.lang.String`	`getProductName()` Returns the product identifier of the plugin as given by `LicenseManager`.
`java.lang.String`	`getRemark()` Returns the calculation remark.
`java.lang.Object`	`getResult(int index)` Returns the result item for the specified type and index.
`java.lang.Object`	`getResult(java.lang.Object type, int index)` Returns the result item for the specified type and index.
`java.lang.Object`	`getResult(java.lang.Object type, java.lang.String arg)` Returns the result item for the specified argument string.
`java.lang.Object`	`getResult(java.lang.String arg)` Returns the result item for the specified argument string.
`int`	`getResultAsRGB(int index, java.lang.Object result)` Returns the specified result color as int format (alpha<<24 + red<<16 + green<<8 + blue).
`int`	`getResultAsRGB(java.lang.Object type, int index, java.lang.Object result)` Returns the specified result color as int format (alpha<<24 + red<<16 + green<<8 + blue).
`java.lang.String`	`getResultAsString(int index, java.lang.Object result)` Returns the specified result in String format for the first result type.
`java.lang.String`	`getResultAsString(java.lang.Object type, int index, java.lang.Object result)` Returns the specified result in String format.
`int`	`getResultCount()` Returns the number of result items for the first result type.
`int`	`getResultCount(java.lang.Object type)` Returns the number of result items for the given result key.
`int`	`getResultDomain()` Returns the calculation domain `ATOM` or `MOLECULE`.
`int`	`getResultDomain(java.lang.Object type)` Returns the calculation domain `ATOM` or `MOLECULE`.
`java.lang.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, java.lang.Object result)` Returns the specified result color(s) as int format (alpha<<24 + red<<16 + green<<8 + blue).
`long`	`getResultsAsRGB(java.lang.Object type, int index, java.lang.Object result)` Returns the specified result color(s) as int format (alpha<<24 + red<<16 + green<<8 + blue).
`java.lang.String`	`getResultsAsString(int index, java.lang.Object result)` Returns the specified result with possible subresults.
`java.lang.String`	`getResultsAsString(java.lang.Object type, int index, java.lang.Object result)` Returns the specified result with possible subresults.
`chemaxon.marvin.plugin.PluginMDocSource`	`getResultSource()` Returns the result as a document source object.
`java.lang.Object[]`	`getResultTypes()` Returns the result types.
`java.lang.String`	`getTypeString(java.lang.Object type)` Returns a string representation of the given type.
`java.lang.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(java.lang.Object type, int index, java.lang.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.
`java.lang.Class`	`loadClass(java.lang.String clname)` Loads a class, first tries from original CALSSPATH, then from the class loader used to load this plugin class.
`static java.lang.String`	`readAttribute(java.lang.String attribute, java.lang.String jar)` Reads an attribute from JAR manifest.
`protected static java.lang.String`	`removeWhitespace(java.lang.String str)` Removes whitespace characters from the given string.
`abstract boolean`	`run()` Runs the tool.
`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(java.lang.String pr)` Sets the precision in the decimal format.
`protected abstract void`	`setInputMolecule(Molecule mol)` Sets the input molecule.
`void`	`setLicenseEnvironment(java.lang.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.
`void`	`setParameters(java.util.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

PLUGIN_DIR

public static final java.lang.String PLUGIN_DIR

The plugin directory (relative to CLASSPATH).

See Also:: Constant Field Values

PLUGIN_CLASS_KEY

public static final java.lang.String PLUGIN_CLASS_KEY

Plugin class key in manifest.

See Also:: Constant Field Values

CRITICAL_ERROR_MSG

protected static final java.lang.String CRITICAL_ERROR_MSG

Critical error message.

See Also:: Constant Field Values

INCORRECT_AROMATIC_NITROGEN_REMARK

protected static final java.lang.String INCORRECT_AROMATIC_NITROGEN_REMARK

Incorrect aromatic nitrogen remark.

See Also:: Constant Field Values

INSTABLE_TAUTOMERIC_FORM_REMARK

protected static final java.lang.String INSTABLE_TAUTOMERIC_FORM_REMARK

Instable tautomeric form remark.

See Also:: Constant Field Values

COVALENT_HYDRATION_ERROR_REMARK

protected static final java.lang.String COVALENT_HYDRATION_ERROR_REMARK

Covalent hydration error remark.

See Also:: Constant Field Values

licenseEnvironment

protected java.lang.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

NAN

protected static final java.lang.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

Constructor Detail

CalculatorPlugin

public CalculatorPlugin()

Constructor. Initializes decimal format.

Method Detail

getPluginResource

public static java.net.URL getPluginResource(java.lang.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 java.lang.String readAttribute(java.lang.String attribute,
                                             java.lang.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(java.lang.String clname,
                                      java.lang.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 java.lang.Class loadClass(java.lang.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

protected static void dehydrogenize(Molecule mol)

Makes all explicit H-s implicit.

Parameters:: mol - is the molecule

removeWhitespace

protected static java.lang.String removeWhitespace(java.lang.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(java.lang.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

getProductName

public java.lang.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(java.lang.String type,
                         java.lang.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(java.lang.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 java.lang.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 java.lang.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 java.lang.StringBuffer format(double x,
                                           java.lang.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 java.lang.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)

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

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

Parameters:: mol - is the input molecule
Returns:: the standardized molecule
Throws:: PluginException - on error
Since:: Marvin 5.0

getMainMolecule

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(java.util.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

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 java.lang.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 java.lang.String getWarningMessage()

Returns the calculation warning information message. The default implementation returns the empty string.

Returns:: the calculation warning information message

getResultMessage

public final java.lang.String getResultMessage()

Returns the plugin calculation error message, error or warning.

Returns:: the plugin calculation error message

getRemark

public java.lang.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 java.lang.Object[] getResultTypes()

Returns the result types. The default implementation returns null.

Returns:: the result types

getTypeString

public java.lang.String getTypeString(java.lang.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(java.lang.Object type)

Returns the calculation domain ATOM or MOLECULE. The default implementation returns MOLECULE.

Parameters:: type - is the result type
Returns:: the calculation domain
See Also:: getResultTypes()

getResultCount

public int getResultCount(java.lang.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 java.lang.Object getResult(java.lang.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 java.lang.String getResultAsString(java.lang.Object type,
                                          int index,
                                          java.lang.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 java.lang.String getResultsAsString(java.lang.Object type,
                                           int index,
                                           java.lang.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(java.lang.Object type,
                          int index,
                          java.lang.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(java.lang.Object type,
                            int index,
                            java.lang.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(java.lang.Object type,
                                  int index,
                                  java.lang.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 java.lang.Object getResult(java.lang.Object type,
                                  java.lang.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 or MOLECULE. 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 java.lang.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 java.lang.Object getResult(java.lang.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 java.lang.String getResultAsString(int index,
                                          java.lang.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 java.lang.String getResultsAsString(int index,
                                           java.lang.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,
                          java.lang.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,
                            java.lang.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.reaction.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

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chemaxon.marvin.plugin Class CalculatorPlugin

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

NAN

EPSILON

CalculatorPlugin

getPluginResource

readAttribute

create

loadClass

isRgrouped

containsPseudoAtom

containsMulticenterSgroup

containsSRUSgroup

containsCoordinateBond

dehydrogenize

removeWhitespace

getDocument

isLicensed

setLicenseEnvironment

getProductName

checkType

getDoublePrecision

setDoublePrecision

setDoublePrecision

setDoublePrecision

format

format

format

format

setProgressMonitor

setMolecule

setMolecule

setMolecule

createModifiedInputMolecule

getInputMolDim

getCalcMolecule

createStandardizedMolecule

createStandardizedMolecule

getMainMolecule

getDisplayMolecule

handlesMultiFragmentMolecules

isMsCalc

setParameters

getpH

checkMolecule

setInputMolecule

run

isOK

getErrorMessage

getWarningMessage

getResultMessage

getRemark

getResultTypes

getTypeString

getResultDomain

getResultCount

getResult

getResultAsString

getResultsAsString

getResultAsRGB

getResultsAsRGB

isNegligibleResult

getResult

getResultMolecule

getResultMolecules

getResultSource

getResultDomain

getResultCount

getResult

chemaxon.marvin.plugin
Class CalculatorPlugin