snippet.java

byte[] molbytes = su.getFile(new ObjectId(oid));
        ByteArrayInputStream bais = new ByteArrayInputStream(molbytes);
        try {
            MolImporter importer = new MolImporter(bais);
            List<Molecule> mols = new ArrayList<Molecule>();
            while (true) {
                Molecule m = importer.read();
                if (m == null) break;
                m.setProperty("uuid", sub.getUserUuid());
                m.setProperty("pi_name", sub.getPiName());
                m.setProperty("sample_name", sub.getSampleName());
                m.setProperty("oid_submission", sub.getOid());
                m.setProperty("oid_structurefile", sub.getSdfOid());
                mols.add(m);
            }
            importer.close();
            return mols;
        } catch (IOException e) {
            log.warn("Format not recognized for submission oid " + sub.getOid()
                    + " structure file oid " + sub.getSdfOid());
            return null;
        }