chemaxon.marvin.calculations
Class EnumerationPlugin

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

All Implemented Interfaces:

chemaxon.license.Licensable

Deprecated. Use MarkushEnumerationPlugin

public class EnumerationPlugin
extends MarkushEnumerationPlugin

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
      EnumerationPlugin plugin = new EnumerationPlugin();
  
      // 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
      EnumerationPlugin plugin = new EnumerationPlugin();
  
      // set random enumeration
      plugin.setRandomEnumeration();
  
      // 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

Author:

Nora Mate

Nested Class Summary

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

CalculatorPlugin.HydrogenData

Field Summary

Fields inherited from class chemaxon.marvin.calculations.MarkushEnumerationPlugin

COLORING_ALL, COLORING_NONE, COLORING_RGROUPS, COLORING_SCAFFOLD, FILTER_VALENCE

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

EnumerationPlugin()
Deprecated.

Method Summary

Methods inherited from class chemaxon.marvin.calculations.MarkushEnumerationPlugin

checkMolecule, countEnumerations, countEnumerationsMagnitude, getAlignScaffold, getAromatizedStructures, getColoring, getEnumCodeNeeded, getLibrarySizeString, getLimitedStructureCount, getNextAromatizedStructure, getNextStructure, getProductName, getRemark, getResult, getResult, getResultAsString, getResultCount, getResultDomain, getResultMolecule, getResultSource, getResultTypes, getStructureCount, getStructureID, getStructures, getTypeString, handlesMultiFragmentMolecules, hasMoreStructures, isApproximateCount, isCleanNeeded, isFiltered, isHomologyEnumerated, isLicensed, isRandomEnumeration, run, setAlignScaffold, setColoring, setEnumCodeNeeded, setEnumerateHomology, setFilter, setInputMolecule, setLicenseEnvironment, setMaxStructureCount, setParameters, setRandomEnumeration, setStructureID, standardize

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

Constructor Detail

EnumerationPlugin

public EnumerationPlugin()

Deprecated.