code: public void init(String sourceMolFileName, String targetMolFileName, boolean removeHydrogen,
              boolean cleanAndConfigureMolecule) throws CDKException {
          this.removeHydrogen = removeHydrogen;
          init(new MolHandler(sourceMolFileName, cleanAndConfigureMolecule, removeHydrogen), new MolHandler(
                  targetMolFileName, cleanAndConfigureMolecule, removeHydrogen));
      }
docs: Initialize the query and targetAtomCount mol via mol files
  @param sourceMolFileName source mol file name
  @param targetMolFileName target mol file name
  @param removeHydrogen    set true to make hydrogens implicit before search
  @param cleanAndConfigureMolecule eg: percieveAtomTypesAndConfigureAtoms, detect aromaticity etc
  @throws CDKException