CalculatorPlugin (Marvin API documentation (c) 1998-2005 ChemAxon Ltd.)

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chemaxon.marvin.plugin
Class CalculatorPlugin

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

Direct Known Subclasses:: ElementalAnalyserPlugin, IonChargePlugin, logDPlugin, logPPlugin, MajorMicrospeciesPlugin, pKaPlugin, RefractivityPlugin, TopologyAnalyserPlugin

public abstract class CalculatorPlugin
extends java.lang.Object

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();
    plugin.validate(<charge license>);

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

    // set target molecule
    MolInputStream mis = new MolInputStream(new ByteArrayInputStream("Clc1cc(Cl)c(Cl)cc1".getBytes()));
    MolImporter mi = new MolImporter(mis);
    plugin.setMolecule(mi.read());

    // 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);
        }
    }

Since:: Marvin 3.0
Author:: Nora Mate

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.
`static int`	`CHART` Calculation domain type: calculation can be represented in a chart.
`protected static java.lang.String`	`HYDROGEN_VALENCE_ERROR_MSG`
`static int`	`MOLECULE` Calculation domain type: calculation refers to the molecule.
`protected static java.lang.Double`	`NAN` Double constant for `Double.NaN`.
`static int`	`RED` Constant storing the red rgb value (the acidic pKa result color).
`static int`	`SUBRESULT` Calculation domain type: subresult to be displayed in a separate text area.

Constructor Summary
`CalculatorPlugin()`

Method Summary
`protected boolean`	`check()` Protects plugin license.
`protected void`	`checkLicense()` Increases the call counter if no valid license exists for this plugin class.
`boolean`	`checkLicenseKey()` Checks the license key.
`void`	`checkMolecule(Molecule mol)` Checks the input molecule.
`protected void`	`checkType(java.lang.String type, java.lang.String[] typerange)` Checks result types.
`static CalculatorPlugin`	`create(java.lang.String name)` Creates a CalculatorPlugin object.
`protected Molecule`	`createImageMolecule()` Transforms molecule 'origmol' for molecule image purpose.
`protected Molecule`	`createStandardizedMolecule(Molecule mol, boolean om)` Creates standardized molecule, the original input molecule is cloned.
`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.
`protected 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 java.awt.Color`	`getChartColor(java.lang.Object type)` Returns the chart colors to be displayed in msketch/mview GUI.
`int`	`getDoublePrecision()` Returns the precision.
`java.lang.String`	`getErrorMessage()` Returns the calculation error information message if `run()` returned false (calculation error).
`protected java.lang.Object[]`	`getGUIResultTypes()` Returns the result types to be displayed in msketch/mview GUI.
`protected java.lang.String`	`getLicenseKey()` Returns the built-in license key for the given plugin class.
`protected Molecule`	`getMainMolecule(Molecule mol)` Returns the molecule form with largest distribution.
`protected java.lang.String`	`getMolText()` Returns the plugin molecule text to be displayed in the viewer.
`java.lang.String`	`getOutputClassName()` Returns the output provider class name for the command line interface.
`Molecule`	`getReferenceMolecule(java.lang.Object type, int index)` Returns the molecule to be used as reference image for the given result type and index.
`java.lang.Object`	`getResult(int index)` Returns the result item for the specified type and index.
`abstract 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.
`abstract 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.
`abstract 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`.
`abstract int`	`getResultDomain(java.lang.Object type)` Returns the calculation domain `ATOM` or `MOLECULE`.
`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.
`abstract java.lang.Object[]`	`getResultTypes()` Returns the result types.
`protected java.lang.String`	`getSuffix()` Returns the plugin text suffix.
`java.lang.String`	`getTypeString(java.lang.Object type)` Returns a string representation of the given type.
`java.lang.String`	`getXAxisLabel(java.lang.Object type)` Returns the X axis label to be displayed.
`java.lang.String[]`	`getXLabels()` Returns the X labels, X values formatted as strings.
`java.lang.String`	`getYAxisLabel(java.lang.Object type)` Returns the Y axis label to be displayed.
`boolean`	`handlesMultiFragmentMolecules()` Returns `true` if the plugin handles multifragment molecules, `false` otherwise.
`boolean`	`isLicensed()` Returns true if the plugin is licensed (has a license key).
`protected boolean`	`isMajorityMsCalculation()` Returns `true` if majority microspecies calculation takes place, ie, if pH is different form`Double.NaN`.
`protected boolean`	`isMajorMs()` Returns `true` if major microspecies required, `false` otherwise.
`protected boolean`	`isMsCalc()` Returns `true` if microspecies calculation.
`boolean`	`isNegligibleResult(java.lang.Object type, int index, java.lang.Object result)` Returns whether the result can be ignored.
`protected static boolean`	`isRgrouped(Molecule mol)` Returns `true` if molecule with R-groups.
`protected static java.lang.String`	`removeWhitespace(java.lang.String str)` Removes whitespace characters from the given string.
`abstract boolean`	`run()` Runs the tool.
`void`	`saveLicense()` Saves licenses in license file.
`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.
`boolean`	`setLicense(java.lang.String license)` Sets the license key in the license manager if the given license key matches the plugin's license key.
`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.
`abstract void`	`setParameters(java.util.Properties params)` Sets the input parameters for the plugin.
`protected 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`	`standardizeGroups(Molecule mol)` Default standardization: nitro groups: `[O-]-[N+] >> O=N` sulphynil groups: `[#6][S+:1]([#6])[#8-:2]>>[#6][S:1]([#6])=[O:2]`
`void`	`validate(java.lang.String license)` Validates the plugin.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

HYDROGEN_VALENCE_ERROR_MSG

protected static final java.lang.String HYDROGEN_VALENCE_ERROR_MSG

See Also:: Constant Field Values

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

CHART

public static final int CHART

Calculation domain type: calculation can be represented in a chart.

See Also:: Constant Field Values

SUBRESULT

public static final int SUBRESULT

Calculation domain type: subresult to be displayed in a separate text area.

See Also:: Constant Field Values

NAN

protected static final java.lang.Double NAN

Double constant for Double.NaN.

Constructor Detail

CalculatorPlugin

public CalculatorPlugin()

Method Detail

create

public static CalculatorPlugin create(java.lang.String name)
                               throws PluginException

Creates a CalculatorPlugin object. The plugin class is dynamically loaded. The plugin class is given by the 'name' parameter which is either the full class name of the plugin or the plugin class name in package chemaxon.marvin.calculations.

Parameters:: name - is the plugin class name in package chemaxon.marvin.calculations or the full plugin class name with package name
Returns:: the created plugin object
Throws:: PluginException - if the class cannot be loaded or not found or cannot be instantiated

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

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

check

protected final boolean check()

Protects plugin license. To be called from plugin.getLicenseKey().

Returns:: true if check is passed, false otherwise

validate

public final void validate(java.lang.String license)

Validates the plugin.

Parameters:: license - is the license key

isLicensed

public final boolean isLicensed()

Returns true if the plugin is licensed (has a license key).

Returns:: true if the plugin is licensed

checkLicenseKey

public final boolean checkLicenseKey()

Checks the license key.

Returns:: true if plugin has valid license in the license manager

setLicense

public final boolean setLicense(java.lang.String license)

Sets the license key in the license manager if the given license key matches the plugin's license key.

Parameters:: license - is the license key to be checked
Returns:: true if the license key is matched

saveLicense

public final void saveLicense()

Saves licenses in license file. For internal use.

checkLicense

protected final void checkLicense()
                           throws PluginException

Increases the call counter if no valid license exists for this plugin class. To be called from the run() method of the plugin.

Throws:: PluginException - if license check fails and the max number of calls without license has been reached

getLicenseKey

protected java.lang.String getLicenseKey()

Returns the built-in license key for the given plugin class. This license key has to be checked against the license key read from the property file. To be overridden by plugin classes having a license key.

Returns:: the built-in license key for the given plugin class
See Also:: checkLicense()

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

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

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

createStandardizedMolecule

protected final Molecule createStandardizedMolecule(Molecule mol,
                                                    boolean om)

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

isMajorityMsCalculation

protected boolean isMajorityMsCalculation()

Returns true if majority microspecies calculation takes place, ie, if pH is different formDouble.NaN. The default implementation returns false.

Returns:: true if majority microspecies calculation takes place

getSuffix

protected java.lang.String getSuffix()

Returns the plugin text suffix. The default implementation returns the empty string.

Returns:: the plugin text suffix

getMolText

protected java.lang.String getMolText()

Returns the plugin molecule text to be displayed in the viewer. The default implementation returns null.

Returns:: the plugin molecule text

getMainMolecule

protected Molecule getMainMolecule(Molecule mol)

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

getReferenceMolecule

public Molecule getReferenceMolecule(java.lang.Object type,
                                     int index)

Returns the molecule to be used as reference image for the given result type and index. The default implementation returns the original molecule clone.

Parameters:: type - is the result type; index - is the result index
Returns:: the original molecule clone

createImageMolecule

protected Molecule createImageMolecule()

Transforms molecule 'origmol' for molecule image purpose.

Returns:: the transformed molecule

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 abstract 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

isMajorMs

protected boolean isMajorMs()

Returns true if major microspecies required, false otherwise. The default implementation returns false.

Returns:: true if major microspecies required

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 accepts every molecule (does nothing).

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()

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

getResultTypes

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

Returns the result types.

Returns:: the result types

getGUIResultTypes

protected java.lang.Object[] getGUIResultTypes()

Returns the result types to be displayed in msketch/mview GUI. The default implementation returns getResultTypes().

Returns:: the result types

getChartColor

protected java.awt.Color getChartColor(java.lang.Object type)

Returns the chart colors to be displayed in msketch/mview GUI. The default implementation returns null which means that the default colors should be used in case of chart display.

Parameters:: type - is the result type
Returns:: the chart color for the given result type

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 abstract int getResultDomain(java.lang.Object type)

Returns the calculation domain ATOM or MOLECULE. Can be combined with CHART to denote chart-type data.

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

getResultCount

public abstract int getResultCount(java.lang.Object type)

Returns the number of result items for the given result key.

Parameters:: type - is the result type
Returns:: the number of result items
See Also:: getResultTypes()

getResult

public abstract java.lang.Object getResult(java.lang.Object type,
                                           int index)
                                    throws PluginException

Returns the result item for the specified type and index.

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 abstract java.lang.String getResultAsString(java.lang.Object type,
                                                   int index,
                                                   java.lang.Object result)
                                            throws PluginException

Returns the specified result 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

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()

getXAxisLabel

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

Returns the X axis label to be displayed. The default implementation returns the empty string.

Parameters:: type - is the result type

getYAxisLabel

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

Returns the Y axis label to be displayed. The default implementation returns getTypeString(Object).

Parameters:: type - is the result type

getXLabels

public java.lang.String[] getXLabels()

Returns the X labels, X values formatted as strings.

Returns:: the X labels

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

getOutputClassName

public java.lang.String getOutputClassName()

Returns the output provider class name for the command line interface. The default is CalculatorOutput, override this method if your plugin requires a subclass of CalculatorOutput.

Returns:: the output provider class name

getAtomCount

public final int getAtomCount()

Returns the number of atoms in the input molecule.

Returns:: the number of atoms in the input molecule

getAtomIndex

protected 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

standardize

protected 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-]-[N+]=O >> O=N=O
sulphynil group transformation: [#6][S+:1]([#6])[#8-:2]>>[#6][S:1]([#6])=[O:2]

To be overriden 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

standardizeGroups

protected static void standardizeGroups(Molecule mol)

Default standardization:

nitro groups: [O-]-[N+] >> O=N
sulphynil groups: [#6][S+:1]([#6])[#8-:2]>>[#6][S:1]([#6])=[O:2]

Parameters:: mol - is the molecule to be standardized

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chemaxon.marvin.plugin Class CalculatorPlugin

HYDROGEN_VALENCE_ERROR_MSG

RED

BLUE

CALCRGB_OFF

ATOM

MOLECULE

CHART

SUBRESULT

NAN

CalculatorPlugin

create

isRgrouped

dehydrogenize

removeWhitespace

check

validate

isLicensed

checkLicenseKey

setLicense

saveLicense

checkLicense

getLicenseKey

checkType

getDoublePrecision

setDoublePrecision

setDoublePrecision

setDoublePrecision

format

format

format

format

setMolecule

setMolecule

setMolecule

createStandardizedMolecule

isMajorityMsCalculation

getSuffix

getMolText

getMainMolecule

getReferenceMolecule

createImageMolecule

handlesMultiFragmentMolecules

isMsCalc

setParameters

isMajorMs

checkMolecule

setInputMolecule

run

getErrorMessage

getResultTypes

getGUIResultTypes

getChartColor

getTypeString

getResultDomain

getResultCount

getResult

getResultAsString

getResultsAsString

getResultAsRGB

getResultsAsRGB

isNegligibleResult

getResult

getXAxisLabel

getYAxisLabel

getXLabels

getResultDomain

getResultCount

getResult

getResult

getResultAsString

getResultsAsString

getResultAsRGB

getResultsAsRGB

getOutputClassName

getAtomCount

getAtomIndex

standardize

standardizeGroups

chemaxon.marvin.plugin
Class CalculatorPlugin