CalculatorPlugin (Marvin API documentation (c) 1998-2004 ChemAxon Ltd.)

Overview

Package

Class

Tree

Deprecated

Index

Help

PREV CLASS NEXT CLASS

FRAMES NO FRAMES

SUMMARY: NESTED | FIELD | CONSTR | METHOD

DETAIL: FIELD | CONSTR | METHOD

chemaxon.marvin.plugin
Class CalculatorPlugin

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

Direct Known Subclasses:: ChargePlugin, ElementalAnalyserPlugin, IonChargePlugin, logDPlugin, logPPlugin, pKaPlugin, PolarizationPlugin, TPSAPlugin

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.

Example usage:

Charge calculation for one input molecule. This example shows the general usage.

    // 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);
        }
    }

LogP calculation for multiple input molecules read from an SDF file. This example shows a looser API usage, applying some specific knowledge about logP calculation (e.g. one result for the "molecule" and an incremental value for each "atom") - these assumptions enable us to write slightly more specific and readable code.

    // fill parameters
    Properties params = new Properties();
    params.put("type", "logP,increments");

    // create plugin
    logPPlugin plugin = new logPPlugin();
    plugin.validate(<logP license>);

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

    // set MolImporter
    MolInputStream mis = new MolInputStream(new FileInputStream("target.sdf"));
    MolImporter mi = new MolImporter(mis);

    // for each input molecule run the calculation and display the results
    System.out.println("molecule\tlogP\tincrements");
    Molecule target = null;
    while ((target = mi.read()) != null) {

        // set the input molecule
        plugin.setMolecule(target);

        // run the calculation
        plugin.run();

        // get the overal logP value
        double logp = ((Double)plugin.getResult("logP", 0)).doubleValue(); 

        // get the incremental values
        int count = target.getAtomCount();
        String[] increments = new String[count];
        for (int i=0; i < count; ++i) {
	      Object result = plugin.getResult("increments", i);
            increments[i] = plugin.getResultAsString("increments", i, result); 
        }

        // display the results
        StringBuffer s = new StringBuffer();
        s.append(target.toFormat("smiles")+"\t"+logp+"\t");
        for (int i=0; i < count; ++i) {
            if (i > 0) {
               s.append(";");
            }
            s.append(increments[i]);
        }
        System.out.println(new String(s));
    }

Since:: 3.0
Author:: Nora Mate

Field Summary
`static int`	`ATOM` Calculation domain type: calculation refers to atoms.
`static int`	`CHART` Calculation domain type: calculation can be represented in a chart.
`static int`	`MOLECULE` Calculation domain type: calculation refers to the molecule.
`protected static java.lang.Double`	`NAN` Double constant for `Double.NaN`.
`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.
`static CalculatorPlugin`	`create(java.lang.String name)` Creates a CalculatorPlugin object.
`protected Molecule`	`createStandardizedMolecule(Molecule mol)` 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.
`protected 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.
`int`	`getDoublePrecision()` Returns the precision.
`java.lang.String`	`getErrorMessage()` Returns the calculation error information message if `run()` returned false (calculation error).
`protected java.lang.String`	`getLicenseKey()` Returns the built-in license key for the given plugin class.
`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.
`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).
`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.
`abstract boolean`	`run()` Runs the tool.
`protected 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.
`void`	`setMolecule(Molecule mol)` Sets the input molecule after standardization.
`void`	`setMolecule(Molecule mol, boolean st)` 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 void`	`standardizeNitro(Molecule mol)` Standardizes nitro groups: [O-]-[N+]=O >> O=N=O.
`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

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

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

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()

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

protected 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 precsion=4, pad=false 12.56 -> 12.5600 if precsion=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 void 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
Throws:: PluginException - on error

setMolecule

public void 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
Throws:: PluginException - on error

createStandardizedMolecule

protected final Molecule createStandardizedMolecule(Molecule mol)

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

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

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

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

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

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

protected 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 aromatization and the nitro group transformation: [O-]-[N+]=O >> O=N=O. 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

standardizeNitro

protected final void standardizeNitro(Molecule mol)

Standardizes nitro groups: [O-]-[N+]=O >> O=N=O.

Parameters:: mol - is the molecule to be standardized

Overview

Package

Class

Tree

Deprecated

Index

Help

PREV CLASS NEXT CLASS

FRAMES NO FRAMES

SUMMARY: NESTED | FIELD | CONSTR | METHOD

DETAIL: FIELD | CONSTR | METHOD

chemaxon.marvin.plugin Class CalculatorPlugin

ATOM

MOLECULE

CHART

SUBRESULT

NAN

CalculatorPlugin

create

isRgrouped

dehydrogenize

check

validate

isLicensed

checkLicenseKey

setLicense

checkLicense

getLicenseKey

getDoublePrecision

setDoublePrecision

setDoublePrecision

format

format

format

format

setMolecule

setMolecule

createStandardizedMolecule

getReferenceMolecule

handlesMultiFragmentMolecules

setParameters

checkMolecule

setInputMolecule

run

getErrorMessage

getResultTypes

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

standardizeNitro

chemaxon.marvin.plugin
Class CalculatorPlugin