/** * Creates from a PDB File a BioPolymer. */ private void readBioPolymer(String biopolymerFile) { try { // Read PDB file FileReader fileReader = new FileReader(biopolymerFile); ISimpleChemObjectReader reader = new ReaderFactory().createReader(fileReader); IChemFile chemFile = (IChemFile) reader.read((IChemObject) new ChemFile()); // Get molecule from ChemFile IChemSequence chemSequence = chemFile.getChemSequence(0); IChemModel chemModel = chemSequence.getChemModel(0); IAtomContainerSet setOfMolecules = chemModel.getMoleculeSet(); protein = (IBioPolymer) setOfMolecules.getAtomContainer(0); } catch (IOException | CDKException exc) { logger.error("Could not read BioPolymer from file>" + biopolymerFile + " due to: " + exc.getMessage()); logger.debug(exc); } }
ReaderFactory readerFactory = new ReaderFactory(); readerFactory.registerFormat((IChemFormatMatcher) MDLFormat .getInstance());
boolean deducebonds = false; ReaderFactory readerFactory = new ReaderFactory(); IChemFile emptyChemFile; IChemFile chemFile;
try { content = (String) transfer.getTransferData(DataFlavor.stringFlavor); reader = new ReaderFactory().createReader(new StringReader(content));