Examples of molecules()

Examples of org.openscience.cdk.MoleculeSet.molecules()

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            theInputMoleculeSet = MoleculeSetFilter.getMoleculesByStringMatch(thePropertyCalculator.getMoleculeSet(), SPECIES_PROPERTY_NAME, "Panax ginseng");
            theFrame.setLogTextArea().append(Integer.toString(theInputMoleculeSet.getAtomContainerCount()));
        } catch (CDKException e) {
            JOptionPane.showMessageDialog(null, "CDKException in MolecularPropertyCaluculator!!", "Error", JOptionPane.ERROR_MESSAGE);
        }
        for (IAtomContainer theMolecule : theInputMoleculeSet.molecules()) {
            theFrame.setLogTextArea().append(theMolecule.getProperty(MolecularPropertyCalculator.MOLECULAR_FORMULA_PROPERTY_NAME).toString());
        }
    }

    private static IMoleculeSet __readFolderWithTag(File theDir, String tagPropertyName, String theTag) {
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Examples of org.openscience.cdk.interfaces.IMoleculeSet.molecules()

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            theInputMoleculeSet = MoleculeSetFilter.getMoleculesByStringMatch(thePropertyCalculator.getMoleculeSet(), SPECIES_PROPERTY_NAME, "Panax ginseng");
            theFrame.setLogTextArea().append(Integer.toString(theInputMoleculeSet.getAtomContainerCount()));
        } catch (CDKException e) {
            JOptionPane.showMessageDialog(null, "CDKException in MolecularPropertyCaluculator!!", "Error", JOptionPane.ERROR_MESSAGE);
        }
        for (IAtomContainer theMolecule : theInputMoleculeSet.molecules()) {
            theFrame.setLogTextArea().append(theMolecule.getProperty(MolecularPropertyCalculator.MOLECULAR_FORMULA_PROPERTY_NAME).toString());
        }
    }

    private static IMoleculeSet __readFolderWithTag(File theDir, String tagPropertyName, String theTag) {
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Examples of org.openscience.cdk.interfaces.IMoleculeSet.molecules()

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        new File(theOutputDir).mkdir();
        for (File theInputMoleculeFile : theInputFolder) {
            File theOutputMoleculeFile = new File(theOutputDir + theInputMoleculeFile.getName());
            IMoleculeSet inputMolSet = SDFReader.openMoleculeFile(theInputMoleculeFile);

            for (IAtomContainer eachMol : inputMolSet.molecules()) {
                List<String> cidList = theUrlParser.getCIDList("\"" + (String) eachMol.getProperty(inchiPropertyName) + "\"[INCHI]");
                for (String cid : cidList) {
                    StringBuilder propertyString = new StringBuilder();
                    for (String activityString : theUrlParser.getPubchemCSV(cid, new ArrayList<String>(Arrays.asList("active", activityName)))) {
                        if (!activityString.contains("Nohitsfor:")) {
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