@Deprecated @SubjectToRemoval(date=APR_01_2015) public class EnumerationPlugin extends MarkushEnumerationPlugin
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 ...
}
}
// 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.
CalculatorPlugin.HydrogenDataCOLORING_ALL, COLORING_NONE, COLORING_RGROUPS, COLORING_SCAFFOLD, FILTER_VALENCEATOM, 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 and Description |
|---|
EnumerationPlugin()
Deprecated.
|
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, standardizearrangeHydrogenIncerments, 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, setMolecule, setProgressMonitor, standardizeIonicGroups, standardizeNeutralGroups