Package org.openscience.cdk

Examples of org.openscience.cdk.AtomContainerSet.addAtomContainer()

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            // try to read a Molecule
                IAtomContainer mol = (AtomContainer) cor.read(new AtomContainer());
                if(mol!=null )
                    try{
                        IAtomContainerSet newSet = new AtomContainerSet();
                        newSet.addAtomContainer(mol);
                        chemModel = new ChemModel();
                        chemModel.setMoleculeSet(newSet);
                        if (chemModel == null) {
                            error = "The object chemModel was empty unexpectedly!";
                        }
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            BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream()));
            String line;
            while ((line = in.readLine()) != null) {
                if (line.toLowerCase().startsWith("inchi=")) {
                    moleculeSet.addAtomContainer(parseInChI(line));
                }
            }
            in.close();
        } catch (Exception e) {
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            String line;
            while ((line = in.readLine()) != null)
            {
                if (line.toLowerCase().startsWith("inchi=")) {
                    IAtomContainer atc = parser.parseInchi(line);
                    moleculeSet.addAtomContainer(atc);
                }
            }
            in.close();
           
           
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