MarkushEnumerationPlugin (Marvin API documentation (c) 1998-2015 ChemAxon Ltd.)

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

All Implemented Interfaces:: chemaxon.license.Licensable

public class MarkushEnumerationPlugin
extends CalculatorPlugin

Plugin class for enumerating Markush molecules.
Input: a Markush structure.
Output: the number of possible enumerations and the enumerated molecules.

Note: Enumeration does not consider R-Logic conditions.

API usage examples:

Sequential enumeration:

 // Create plugin
 MarkushEnumerationPlugin plugin = new MarkushEnumerationPlugin();
 
 // Set target molecule
 plugin.setMolecule(mol);
 
 // Run the calculation
 plugin.run();
 
 // 1. Get results one by one
 Molecule m = plugin.getNextStructure();
 while (m != null) {
     System.out.println(m.toFormat("smiles"));
     // ...
     // Getting next enumerated molecule
     m = plugin.getNextStructure();
 }
 
 // OR
 // 2. Get results in an array
 long size = plugin.getStructureCount();
 if (size != -1 && size <= Integer.MAX_VALUE) {
     Molecule[] enumerated = plugin.getStructures();
     for (int i = 0; i < enumerated.length; i++) {
         System.out.println(enumerated[i].toFormat("smiles"));
         // ...
     }
 }

Random enumeration:

 // Create plugin
 MarkushEnumerationPlugin plugin = new MarkushEnumerationPlugin();
 
 // Set random enumeration
 plugin.setRandomEnumeration();
 
 // Set the number of random structures to generate
 plugin.setMaxStructureCount(10);
 
 // Set target molecule
 plugin.setMolecule(mol);
 
 // Run the calculation
 plugin.run();
 
 for (int i = 0; i < 10; i++) {
     Molecule m = plugin.getNextStructure();
     System.out.println(m.toFormat("smiles"));
     // ...
 }

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

Since:: Marvin 5.0.3
Author:: Nora Mate, Peter Kovacs (pkovacs84)

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

Field Summary

Fields
Modifier and Type	Field and Description
`static int`	`COLORING_ALL` Constant for setting all coloring options, currently scaffold and R-groups.
`static int`	`COLORING_NONE` Constant for no hit coloring.
`static int`	`COLORING_RGROUPS` Constant for R-group coloring.
`static int`	`COLORING_SCAFFOLD` Constant for scaffold coloring.
`static MolFilter`	`FILTER_VALENCE` Filter constant: valence filter.

Fields inherited from class chemaxon.marvin.plugin.CalculatorPlugin
ATOM, BLUE, CALCRGB_OFF, COVALENT_HYDRATION_ERROR_REMARK, CRITICAL_ERROR_MSG, EPSILON, explicitHydrogens, INCORRECT_AROMATIC_NITROGEN_REMARK, INSTABLE_TAUTOMERIC_FORM_REMARK, KEEP_HYDROGENS, keepHydrogens, licenseEnvironment, MOLECULE, MOLECULES, NAN, PLUGIN_CLASS_KEY, PLUGIN_DIR, RED, TRUE

Constructor Summary

Constructors
Constructor and Description

MarkushEnumerationPlugin()
Constructor.

Constructors
Constructor and Description
`MarkushEnumerationPlugin()` Constructor.

Method Summary

Methods
Modifier and Type	Method and Description
`void`	`checkMolecule(Molecule mol)` Checks the input molecule.
`BigInteger`	`countEnumerations()` Returns the number of all enumerated structures, no arithmetic overflow because counts in `BigInteger`.
`int`	`countEnumerationsMagnitude()` Returns the magnitude (the number of decimal "digits") of the number of all enumerated structures.
`boolean`	`getAlignScaffold()` Gets the scaffold aligning mode
`Molecule[]`	`getAromatizedStructures()` Returns the enumerated structures in aromatized form.
`int`	`getColoring()` Returns the hit coloring options.
`boolean`	`getEnumCodeNeeded()` Tests whether unique Markush enumeration code should be generated
`String`	`getLibrarySizeString()` Returns the display string representation of the Markush library size (number of all enumerated structures).
`int`	`getLimitedStructureCount()` Returns the number of structures to be generated.
`Molecule`	`getNextAromatizedStructure()` Returns the next enumerated structure.
`Molecule`	`getNextStructure()` Returns the next enumerated structure, or `null` if no more structures.
`String`	`getProductName()` Returns the product identifier of the plugin as given by `LicenseManager`.
`String`	`getRemark()` Returns a warning message in case of arithmetical overflow (the number of enumerated structures exceeds `Long.MAX_VALUE`), `null` otherwise.
`Object`	`getResult(Object type, int index)` Returns the result item for the specified key and index.
`Object`	`getResult(Object type, String arg)` Returns the enumerated structures.
`String`	`getResultAsString(Object type, int index, Object result)` Returns the specified result in String format.
`int`	`getResultCount(Object type)` Returns the number of result items for the given result key.
`int`	`getResultDomain(Object type)` Returns the calculation domain.
`Molecule`	`getResultMolecule()` Returns the result molecule for display.
`chemaxon.marvin.plugin.PluginMDocSource`	`getResultSource()` Returns the result as a document source object.
`Object[]`	`getResultTypes()` Returns the result types.
`long`	`getStructureCount()` Returns the number of all enumerated structures, `-1` in case of arithmetical overflow (if the number would exceed `Long.MAX_VALUE`).
`String`	`getStructureID()` Returns the structure ID used in Markush code (enumeration ID) generation.
`Molecule[]`	`getStructures()` Returns the enumerated structures.
`String`	`getTypeString(Object type)` Returns a string representation of the given type.
`boolean`	`handlesMultiFragmentMolecules()` Returns `true` if the plugin handles multifragment molecules, `false` otherwise.
`boolean`	`hasMoreStructures()` Returns `true` if there are more structures.
`boolean`	`isApproximateCount()` Returns `true` if count is approximate due to multiple position bonds with multicenters of variable size, `false` otherwise.
`protected boolean`	`isCleanNeeded()` Returns `true` if clean is needed for GUI display.
`protected boolean`	`isFiltered()` Return `true` if molecule filter is set.
`boolean`	`isHomologyEnumerated()` Indicates if homology groups are enumerated or not.
`boolean`	`isLicensed()` Returns `true` if the plugin is licensed.
`boolean`	`isRandomEnumeration()` Returns `true` if random enumeration is requested.
`boolean`	`run()` Creates enumerated structures.
`void`	`setAlignScaffold(boolean value)` Sets the scaffold aligning mode.
`void`	`setColoring(int coloring)` Sets hit coloring options.
`void`	`setEnumCodeNeeded(boolean value)` Indicates whether unique Markush enumeration code should be generated.
`void`	`setEnumerateHomology(boolean enumerate)` Sets if homology groups should be enumerated or not.
`void`	`setFilter(MolFilter filter)` Sets the molecule filter.
`protected void`	`setInputMolecule(Molecule mol)` Sets the input molecule.
`void`	`setLicenseEnvironment(String env)` Sets license environment to be stored.
`void`	`setMaxStructureCount(long max)` Sets the maximum number of structures to be generated.
`protected Molecule`	`setMolecule(Molecule mol, boolean st, boolean om, boolean storeExplicitHydrogens)`
`void`	`setParameters(Properties params)` Sets the input parameters for the plugin.
`void`	`setRandomEnumeration()` Sets random enumeration.
`void`	`setStructureID(String id)` Sets structure ID to be used in Markush code generation.

Methods inherited from class chemaxon.marvin.plugin.CalculatorPlugin
arrangeHydrogenIncerments, canRepeat, checkLicense, checkType, containsCoordinateBond, containsMulticenterSgroup, containsPseudoAtom, containsSRUSgroup, create, createModifiedInputMolecule, createStandardizedMolecule, createStandardizedMolecule, dehydrogenize, format, format, format, format, getAtomCount, getAtomIndex, getAtomIndexMap, getCalcMolecule, getDisplayMolecule, getDocument, getDoublePrecision, getErrorMessage, getExplicitHydrogenData, getInputMolDim, getMainMolecule, getOriginalMolecule, getpH, getPluginResource, getQueryMoleculeErrorMessage, getResult, getResult, getResultAsRGB, getResultAsRGB, getResultAsString, getResultCount, getResultDomain, getResultMessage, getResultMolecules, getResultsAsRGB, getResultsAsRGB, getResultsAsString, getResultsAsString, getWarningMessage, isInputMoleculeAromatized, isMsCalc, isMultiThreadedRunEnabled, isNegligibleResult, isOK, isRgrouped, loadClass, readAttribute, removeWhitespace, restoreExplicitHydrogens, setAtomIndexMap, setDoublePrecision, setDoublePrecision, setDoublePrecision, setKeepHydrogens, setMolecule, setMolecule, setMolecule, setProgressMonitor, standardize, standardizeIonicGroups, standardizeNeutralGroups

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

- Field Detail
  - FILTER_VALENCE
```
public static final MolFilter FILTER_VALENCE
```
    Filter constant: valence filter. Set this filter in setFilter(chemaxon.util.MolFilter) in order to reject molecules with valence errors.
    
    Since:
    
    Marvin 5.1
    
    See Also:
    setFilter(chemaxon.util.MolFilter)
  - COLORING_NONE
```
public static final int COLORING_NONE
```
    Constant for no hit coloring.
    
    Since:
    
    Marvin 5.1
    
    See Also:
    Constant Field Values
  - COLORING_SCAFFOLD
```
public static final int COLORING_SCAFFOLD
```
    Constant for scaffold coloring.
    
    Since:
    
    Marvin 5.1
    
    See Also:
    Constant Field Values
  - COLORING_RGROUPS
```
public static final int COLORING_RGROUPS
```
    Constant for R-group coloring.
    
    Since:
    
    Marvin 5.1
    
    See Also:
    Constant Field Values
  - COLORING_ALL
```
public static final int COLORING_ALL
```
    Constant for setting all coloring options, currently scaffold and R-groups.
    
    Since:
    
    Marvin 5.1
    
    See Also:
    Constant Field Values
- Constructor Detail
  - MarkushEnumerationPlugin
```
public MarkushEnumerationPlugin()
```
    Constructor.
- Method Detail
  - isLicensed
```
public boolean isLicensed()
```
    Description copied from class: CalculatorPlugin
    
    Returns true if the plugin is licensed. The license checking is based on the product name, returned by CalculatorPlugin.getProductName().
    
    Specified by:
    
    isLicensed in interface chemaxon.license.Licensable
    
    Overrides:
    
    isLicensed in class CalculatorPlugin
    
    Returns:
    true if the plugin is licensed
  - setLicenseEnvironment
```
public void setLicenseEnvironment(String env)
```
    Description copied from class: CalculatorPlugin
    
    Sets license environment to be stored.
    
    Specified by:
    
    setLicenseEnvironment in interface chemaxon.license.Licensable
    
    Overrides:
    
    setLicenseEnvironment in class CalculatorPlugin
    
    Parameters:
    env - environment String to be stored and passed to the LicenseHandler in the isLicensed method
  - getProductName
```
public String getProductName()
```
    Returns the product identifier of the plugin as given by LicenseManager.
    
    Specified by:
    
    getProductName in class CalculatorPlugin
    
    Returns:
    The identifier LicenseManager.MARKUSH_ENUM_PLUGIN
  - 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. Returns true if parameter "single" is set to "false", false otherwise (default: false).
    
    Overrides:
    
    handlesMultiFragmentMolecules in class CalculatorPlugin
    
    Returns:
    true if the plugin handles multifragment molecules, false otherwise
  - setParameters
```
public void setParameters(Properties params)
                   throws PluginException
```
    Sets the input parameters for the plugin. Enumeration parameters and value ranges:
    - type: structure,structures,count
    - calctype: enumerate,random
    - mode: count mode (small, large, magnitude or string, default: small)
    - max: max structure count
    - atoms: 1-based atom indexes to be enumerated (','-separated list)
    - code: true if Markush code should be generated (default: false)
    - valencecheck: true if valence filter is on (default: false)
    - alignscaffold: true if scaffold alignment is set (default: false)
    - coloring: "scaffold", "rgroups", "none" or "all" (default: "none")
    Overrides:
    
    setParameters in class CalculatorPlugin
    
    Parameters:
    params - is the parameter table
    
    Throws:
    
    PluginException - on error
  - setRandomEnumeration
```
public void setRandomEnumeration()
```
    Sets random enumeration. Must be called before setting the molecule in CalculatorPlugin.setMolecule(chemaxon.struc.Molecule). Set also the number of requested structures in setMaxStructureCount(long), otherwise only one randomly enumerated structure will be generated.
    
    Since:
    
    Marvin 5.1
  - isRandomEnumeration
```
public boolean isRandomEnumeration()
```
    Returns true if random enumeration is requested.
    
    Returns:
    true if random enumeration is requested
  - setEnumerateHomology
```
public void setEnumerateHomology(boolean enumerate)
```
    Sets if homology groups should be enumerated or not. Must be called before setting the molecule.
    
    Since:
    
    Marvin 5.2
  - isHomologyEnumerated
```
public boolean isHomologyEnumerated()
```
    Indicates if homology groups are enumerated or not.
    
    Since:
    
    Marvin 5.2
  - setEnumCodeNeeded
```
public void setEnumCodeNeeded(boolean value)
```
    Indicates whether unique Markush enumeration code should be generated. Must be called before setting the molecule.
    
    Parameters:
    value - true, if code generation is needed
    Since:
    
    Marvin 5.1.2
  - getEnumCodeNeeded
```
public boolean getEnumCodeNeeded()
```
    Tests whether unique Markush enumeration code should be generated
    
    Returns:
    true, if code generation is needed
    Since:
    
    Marvin 5.1.2
  - setStructureID
```
public void setStructureID(String id)
```
    Sets structure ID to be used in Markush code generation. The name of the SDF / MRV tag storing the ID in the Markush structure or else the ID itself. Must be called before setting the molecule. Set null for no structure ID (default). Calling this method with non-null argument will automatically switch on Markush code generation.
    
    Parameters:
    id - the tag name or the ID
    Since:
    
    Marvin 5.1.3
    
    See Also:
    setEnumCodeNeeded(boolean)
  - getStructureID
```
public String getStructureID()
```
    Returns the structure ID used in Markush code (enumeration ID) generation.
    
    Returns:
    the structure ID storing tag name or the ID itself
    Since:
    
    Marvin 5.1.3
    
    See Also:
    setStructureID(java.lang.String)
  - setFilter
```
public void setFilter(MolFilter filter)
```
    Sets the molecule filter. Must be called before setting the molecule. Default: null (get all enumerated structures).
    
    Parameters:
    filter - the molecule filter or null for no filtering
    Since:
    
    Marvin 5.0
    
    See Also:
    MolFilter, FILTER_VALENCE
  - isFiltered
```
protected boolean isFiltered()
```
    Return true if molecule filter is set.
    
    Returns:
    true if molecule filter is set
  - isApproximateCount
```
public boolean isApproximateCount()
                           throws PluginException
```
    Returns true if count is approximate due to multiple position bonds with multicenters of variable size, false otherwise.
    
    Returns:
    true if count is approximate
    
    Throws:
    
    PluginException
  - setMaxStructureCount
```
public void setMaxStructureCount(long max)
```
    Sets the maximum number of structures to be generated. Set -1 for unlimited. Default: unlimited for the sequential case, 1 for the random case. Must be called before setting the molecule in CalculatorPlugin.setMolecule(chemaxon.struc.Molecule).
    
    Parameters:
    max - is the maximum number of structures to be generated
    See Also:
    setRandomEnumeration()
  - setAlignScaffold
```
public void setAlignScaffold(boolean value)
```
    Sets the scaffold aligning mode. Must be called before setting the molecule in CalculatorPlugin.setMolecule(chemaxon.struc.Molecule).
    
    Parameters:
    value - if true, tries to align scaffold in enumerated structures as it was in the original Markush structure
    Since:
    
    Marvin 5.1
  - getAlignScaffold
```
public boolean getAlignScaffold()
```
    Gets the scaffold aligning mode
    
    Returns:
    true, if enumerated structures should be aligned to the scaffold
    Since:
    
    Marvin 5.1
  - setColoring
```
public void setColoring(int coloring)
```
    Sets hit coloring options. Must be called before setting the molecule in CalculatorPlugin.setMolecule(chemaxon.struc.Molecule).
    
    Parameters:
    coloring - COLORING_SCAFFOLD, COLORING_RGROUPS, COLORING_NONE, or COLORING_ALL
    Since:
    
    Marvin 5.1
  - getColoring
```
public int getColoring()
```
    Returns the hit coloring options.
    
    Returns:
    the hit coloring options
    Since:
    
    Marvin 5.1
    
    See Also:
    COLORING_NONE, COLORING_SCAFFOLD, COLORING_RGROUPS, COLORING_ALL
  - isCleanNeeded
```
protected boolean isCleanNeeded()
```
    Returns true if clean is needed for GUI display.
    
    Returns:
    true if clean is needed for GUI display
  - checkMolecule
```
public void checkMolecule(Molecule mol)
                   throws PluginException
```
    Checks the input molecule.
    
    Overrides:
    
    checkMolecule in class CalculatorPlugin
    
    Parameters:
    mol - is the input molecule
    
    Throws:
    
    PluginException - with error message for the user if the molecule is refused
  - setMolecule
```
protected Molecule setMolecule(Molecule mol,
                   boolean st,
                   boolean om,
                   boolean storeExplicitHydrogens)
                        throws PluginException
```
    Overrides:
    
    setMolecule in class CalculatorPlugin
    
    Throws:
    
    PluginException
  - setInputMolecule
```
protected void setInputMolecule(Molecule mol)
                         throws PluginException
```
    Sets the input molecule.
    
    Specified by:
    
    setInputMolecule in class CalculatorPlugin
    
    Parameters:
    mol - is the input molecule
    
    Throws:
    
    PluginException - on error
  - run
```
public boolean run()
            throws PluginException
```
    Creates enumerated structures.
    
    Specified by:
    
    run in class CalculatorPlugin
    
    Returns:
    true
    
    Throws:
    
    PluginException - on error
    See Also:
    CalculatorPlugin.getErrorMessage()
  - countEnumerations
```
public BigInteger countEnumerations()
                             throws PluginException
```
    Returns the number of all enumerated structures, no arithmetic overflow because counts in BigInteger.
    In case when the result does not exceed Long.MAX_VALUE, the number of enumerates is also returned by getStructureCount() (after run() is called).
    Note: run() need not be called before using this function.
    
    Returns:
    the number of enumerated structures
    
    Throws:
    
    PluginException - on expansion error
    See Also:
    getLimitedStructureCount(), getStructureCount(), countEnumerationsMagnitude()
  - countEnumerationsMagnitude
```
public int countEnumerationsMagnitude()
                               throws PluginException
```
    Returns the magnitude (the number of decimal "digits") of the number of all enumerated structures. No arithmetic overflow because counts in BigInteger.
    Note: run() need not be called before using this function.
    
    Returns:
    the magnitude of the number of enumerated structures
    
    Throws:
    
    PluginException - on expansion error
    See Also:
    getLimitedStructureCount(), getStructureCount(), countEnumerations()
  - getStructureCount
```
public long getStructureCount()
```
    Returns the number of all enumerated structures, -1 in case of arithmetical overflow (if the number would exceed Long.MAX_VALUE). To handle the case of arithmetical overflow, call countEnumerations() or countEnumerationsMagnitude(). Returns the number of structures to be returned in case of random enumeration.
    Warning: run() must be called before using this function.
    
    Returns:
    the number of enumerated structures
    See Also:
    setRandomEnumeration(), setMaxStructureCount(long), getLimitedStructureCount(), countEnumerations(), countEnumerationsMagnitude()
  - getLimitedStructureCount
```
public int getLimitedStructureCount()
```
    Returns the number of structures to be generated. This is the minimum of the actual structure count returned by getStructureCount() and the specified maximum (see setMaxStructureCount(long)). Returns the number of structures to be returned in case of random enumeration.
    
    Returns:
    the number of structures to be generated
    See Also:
    setRandomEnumeration(), setMaxStructureCount(long), getStructureCount()
  - hasMoreStructures
```
public boolean hasMoreStructures()
```
    Returns true if there are more structures.
    
    Returns:
    true if there are more structures
  - getNextStructure
```
public Molecule getNextStructure()
```
    Returns the next enumerated structure, or null if no more structures.
    
    Returns:
    the sructure
  - getNextAromatizedStructure
```
public Molecule getNextAromatizedStructure()
```
    Returns the next enumerated structure. The structure is returned in aromatized form.
    
    Returns:
    the structure
  - getStructures
```
public Molecule[] getStructures()
                         throws PluginException
```
    Returns the enumerated structures.
    
    Returns:
    the enumerated structures
    
    Throws:
    
    PluginException - if too many structures
  - getAromatizedStructures
```
public Molecule[] getAromatizedStructures()
                                   throws PluginException
```
    Returns the enumerated structures in aromatized form.
    
    Returns:
    the enumerated structures in aromatized form
    
    Throws:
    
    PluginException - if too many structures
  - 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.
    
    Overrides:
    
    getResultSource in class CalculatorPlugin
    
    Returns:
    the document source interface
    
    Throws:
    
    PluginException - on error
    Since:
    
    Marvin 5.0
  - getResultTypes
```
public Object[] getResultTypes()
```
    Returns the result types.
    
    Overrides:
    
    getResultTypes in class CalculatorPlugin
    
    Returns:
    the result types
  - getResultDomain
```
public int getResultDomain(Object type)
```
    Returns the calculation domain.
    
    Overrides:
    
    getResultDomain in class CalculatorPlugin
    
    Parameters:
    type - is the result type
    
    Returns:
    the calculation domain
    See Also:
    getResultTypes()
  - getResultCount
```
public int getResultCount(Object type)
```
    Returns the number of result items for the given result key.
    
    Overrides:
    
    getResultCount in class CalculatorPlugin
    
    Parameters:
    type - is the result type
    
    Returns:
    the number of result items
    See Also:
    getResultTypes()
  - getTypeString
```
public String getTypeString(Object type)
```
    Returns a string representation of the given type.
    
    Overrides:
    
    getTypeString in class CalculatorPlugin
    
    Parameters:
    type - is the type object
    
    Returns:
    the type string
  - getResult
```
public Object getResult(Object type,
               int index)
                 throws PluginException
```
    Returns the result item for the specified key and index.
    
    Overrides:
    
    getResult in class CalculatorPlugin
    
    Parameters:
    type - is the result type
    index - is the result index
    
    Returns:
    the result item for the specified key and index
    
    Throws:
    
    PluginException - if the result cannot be returned
    See Also:
    CalculatorPlugin.getResultTypes()
  - getResult
```
public Object getResult(Object type,
               String arg)
                 throws PluginException
```
    Returns the enumerated structures. For internal use only.
    
    Overrides:
    
    getResult in class CalculatorPlugin
    
    Parameters:
    type - is the result type ("structures")
    arg - is the atom string as a '-'-separated list
    
    Returns:
    the enumerated structures
    
    Throws:
    
    PluginException - on error
    See Also:
    CalculatorPlugin.getResultTypes()
  - getResultAsString
```
public String getResultAsString(Object type,
                       int index,
                       Object result)
                         throws PluginException
```
    Returns the specified result in String format.
    
    Overrides:
    
    getResultAsString in class CalculatorPlugin
    
    Parameters:
    type - is the result type
    index - is the result index
    result - is the result item
    
    Returns:
    the specified result in String format
    
    Throws:
    
    PluginException - if an invalid result item is given
  - getRemark
```
public String getRemark()
```
    Returns a warning message in case of arithmetical overflow (the number of enumerated structures exceeds Long.MAX_VALUE), null otherwise.
    
    Overrides:
    
    getRemark in class CalculatorPlugin
    
    Returns:
    a warning message if there are no tautomers
  - getLibrarySizeString
```
public String getLibrarySizeString()
                            throws PluginException
```
    Returns the display string representation of the Markush library size (number of all enumerated structures). It can be of three different forms: exact count (for relative small values); the exact count and " (~ 10^x)" for larger values; and only "~ 10^x" for the largest values. If the count is approximate, then the returned string always starts with "~".
    No arithmetic overflow can occur because counts in BigInteger.
    Note: run() need not be called before using this function.
    
    Returns:
    display string representation of the library size or null in case of random enumeration.
    
    Throws:
    
    PluginException - on expansion error
    See Also:
    countEnumerations(), countEnumerationsMagnitude()
  - getResultMolecule
```
public Molecule getResultMolecule()
                           throws PluginException
```
    Returns the result molecule for display. Atomic results are stored in atom extra labels (MolAtom.getExtraLabel()). Molecular results are stored in molecule properties with keys being the result types (Molecule.getProperty(String)).
    
    Overrides:
    
    getResultMolecule in class CalculatorPlugin
    
    Returns:
    the result molecule
    
    Throws:
    
    PluginException - on error
    Since:
    
    Marvin 4.0

Class MarkushEnumerationPlugin

Nested Class Summary

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

Field Summary

Fields inherited from class chemaxon.marvin.plugin.CalculatorPlugin

Constructor Summary

Method Summary

Methods inherited from class chemaxon.marvin.plugin.CalculatorPlugin

Methods inherited from class java.lang.Object

Field Detail

FILTER_VALENCE

COLORING_NONE

COLORING_SCAFFOLD

COLORING_RGROUPS

COLORING_ALL

Constructor Detail

MarkushEnumerationPlugin

Method Detail

isLicensed

setLicenseEnvironment

getProductName

handlesMultiFragmentMolecules

setParameters

setRandomEnumeration

isRandomEnumeration

setEnumerateHomology

isHomologyEnumerated

setEnumCodeNeeded

getEnumCodeNeeded

setStructureID

getStructureID

setFilter

isFiltered

isApproximateCount

setMaxStructureCount

setAlignScaffold

getAlignScaffold

setColoring

getColoring

isCleanNeeded

checkMolecule

setMolecule

setInputMolecule

run

countEnumerations

countEnumerationsMagnitude

getStructureCount

getLimitedStructureCount

hasMoreStructures

getNextStructure

getNextAromatizedStructure

getStructures

getAromatizedStructures

getResultSource

getResultTypes

getResultDomain

getResultCount

getTypeString

getResult

getResult

getResultAsString

getRemark

getLibrarySizeString

getResultMolecule