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:

    // 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 ...
       }
    }

    // OR
    // 3. Print out some random enumerated structures
    for (int i = 0; i < 10; i++) {
      Molecule m = plugin.getRandomStructure();
      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

Field Summary

Fields inherited from class chemaxon.marvin.plugin.CalculatorPlugin

ATOM, BLUE, CALCRGB_OFF, COVALENT_HYDRATION_ERROR_REMARK, CRITICAL_ERROR_MSG, EPSILON, INCORRECT_AROMATIC_NITROGEN_REMARK, INSTABLE_TAUTOMERIC_FORM_REMARK, licenseEnvironment, MOLECULE, NAN, PLUGIN_CLASS_KEY, PLUGIN_DIR, RED

Constructor Summary

EnumerationPlugin()
Deprecated.

Methods inherited from class chemaxon.marvin.calculations.MarkushEnumerationPlugin

checkMolecule, countEnumerations, countEnumerationsMagnitude, getAromatizedStructures, getLibrarySizeString, getLimitedStructureCount, getNextAromatizedStructure, getNextStructure, getRandomStructure, getRandomStructures, getRemark, getResult, getResult, getResultAsString, getResultCount, getResultDomain, getResultMolecule, getResultSource, getResultTypes, getStructureCount, getStructures, getTypeString, handlesMultiFragmentMolecules, hasMoreStructures, isFiltered, isLicensed, isRandomEnumeration, run, setFilter, setInputMolecule, setLicenseEnvironment, setMaxStructureCount, setParameters, standardize

Methods inherited from class chemaxon.marvin.plugin.CalculatorPlugin

checkType, containsCoordinateBond, containsMulticenterSgroup, containsPseudoAtom, containsSRUSgroup, create, createModifiedInputMolecule, createStandardizedMolecule, createStandardizedMolecule, dehydrogenize, format, format, format, format, getAtomCount, getAtomIndex, getCalcMolecule, getDisplayMolecule, getDocument, getDoublePrecision, getErrorMessage, getInputMolDim, getMainMolecule, getpH, getPluginResource, getResult, getResult, getResultAsRGB, getResultAsRGB, getResultAsString, getResultCount, getResultDomain, getResultMessage, getResultMolecules, getResultsAsRGB, getResultsAsRGB, getResultsAsString, getResultsAsString, getWarningMessage, isInputMoleculeAromatized, isMsCalc, isMultiThreadedRunEnabled, isNegligibleResult, isOK, isRgrouped, loadClass, readAttribute, removeWhitespace, setDoublePrecision, setDoublePrecision, setDoublePrecision, 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.