code: private IAtomContainerSet readAtomContainerSet(IAtomContainerSet molSet) throws IOException {
          SmilesParser parser = new SmilesParser(molSet.getBuilder());
          parser.kekulise(false);
          String line = input.readLine();
          line = input.readLine(); // skip the first line
          while (line != null) {
              String[] cols = line.split(",");
              try {
                  IAtomContainer mol = parser.parseSmiles(cols[1]);
                  mol.setProperty("focusSupport", cols[5]);
                  mol.setProperty("complementSupport", cols[7]);
                  mol.setProperty("atomCount", cols[2]);
                  mol.setProperty("bondCount", cols[3]);
                  molSet.addAtomContainer(mol);
              } catch (InvalidSmilesException exception) {
                  logger.error("Skipping invalid SMILES: " + cols[1]);
                  logger.debug(exception);
              }
              line = input.readLine();
          }
          return molSet;
      }
docs: Read the file content into a {@link IAtomContainerSet}.
  @param molSet an {@link IAtomContainerSet} to store the structures
  @return the {@link IAtomContainerSet} containing the molecules read in
  @throws java.io.IOException if there is an error during reading