chemaxon.marvin.calculations
Class MarkushEnumerationPlugin

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

All Implemented Interfaces:

chemaxon.license.Licensable

Direct Known Subclasses:

EnumerationPlugin

public class MarkushEnumerationPlugin
extends CalculatorPlugin

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

API usage examples:

• Sequential enumeration:

      // read input molecule
      MolImporter mi = new MolImporter("testMarkush.mrv");
      Molecule mol = mi.read();
      mi.close();
  
      // 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"));
          // using molecule ...
          // ...
          // 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"));
           // using molecules ...
         }
      }
   

• Random enumeration:

      // read input molecule
      MolImporter mi = new MolImporter("testMarkush.mrv");
      Molecule mol = mi.read();
      mi.close();
  
      // 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"));
        // using molecule ...
      }
  
   

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

Since:

Marvin 5.0.3

Version:

Marvin 5.0.3, 03/18/2008

Author:

Nora Mate

Nested Class Summary

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

CalculatorPlugin.HydrogenData

Field Summary

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

MarkushEnumerationPlugin()
Constructor.

Method Summary

void	checkMolecule(Molecule mol) Checks the input molecule.
java.math.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
java.lang.String	getLibrarySizeString() Returns the string representation of the Markush library size.
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.
java.lang.String	getProductName() Returns the product identifier of the plugin as given by LicenseManager.
java.lang.String	getRemark() Returns a warning message in case of arithmetical overflow (the number of enumerated structures exceeds Long.MAX_VALUE), null otherwise.
java.lang.Object	getResult(java.lang.Object type, int index) Returns the result item for the specified key and index.
java.lang.Object	getResult(java.lang.Object type, java.lang.String arg) Returns the enumerated structures.
java.lang.String	getResultAsString(java.lang.Object type, int index, java.lang.Object result) Returns the specified result in String format.
int	getResultCount(java.lang.Object type) Returns the number of result items for the given result key.
int	getResultDomain(java.lang.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.
java.lang.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).
java.lang.String	getStructureID() Returns the structure ID used in Markush code (enumeration ID) generation.
Molecule[]	getStructures() Returns the enumerated structures.
java.lang.String	getTypeString(java.lang.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(java.lang.String env) Sets license environment to be stored.
void	setMaxStructureCount(long max) Sets the maximum number of structures to be generated.
void	setParameters(java.util.Properties params) Sets the input parameters for the plugin.
void	setRandomEnumeration() Sets random enumeration.
void	setStructureID(java.lang.String id) Sets structure ID to be used in Markush code generation.
void	standardize(Molecule mol) Prevents default standardization: does nothing.

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, getCalcMolecule, getDisplayMolecule, getDocument, getDoublePrecision, getErrorMessage, getExplicitHydrogenData, getInputMolDim, getMainMolecule, 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, setDoublePrecision, setDoublePrecision, setDoublePrecision, setKeepHydrogens, setMolecule, setMolecule, setMolecule, setMolecule, setProgressMonitor, 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(java.lang.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 java.lang.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(java.util.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(java.lang.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 java.lang.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()

Returns true if count is approximate due to multiple position bonds with multicenters of variable size, false otherwise.

Returns:

true if count is approximate

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

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 java.math.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().

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.

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.

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 java.lang.Object[] getResultTypes()

Returns the result types.

Overrides:

getResultTypes in class CalculatorPlugin

Returns:

the result types

getResultDomain

public int getResultDomain(java.lang.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(java.lang.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 java.lang.String getTypeString(java.lang.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 java.lang.Object getResult(java.lang.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 java.lang.Object getResult(java.lang.Object type,
                                  java.lang.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 java.lang.String getResultAsString(java.lang.Object type,
                                          int index,
                                          java.lang.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 java.lang.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 java.lang.String getLibrarySizeString()
                                      throws PluginException

Returns the string representation of the Markush library size. If the library is too big then returns an approximate form (e.g. "~ 10^45"). Returns null in case of random enumeration.

Returns:

the library size string

Throws:

PluginException

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

standardize

public void standardize(Molecule mol)

Prevents default standardization: does nothing.

Overrides:

standardize in class CalculatorPlugin

Parameters:

mol - is the molecule to be standardized