code: 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);
          }
      }
docs: Creates from a PDB File a BioPolymer.