code: public String convertMolFileSMILESWithAtomMapping(String molfile, List<Attachment> attachments) throws CTKException, ChemistryException{
  		return SMILES.convertMolToSMILESWithAtomMapping(molfile, attachments);
  	}
docs: method to generate a smiles with atom mapping for a given molfile with the given attachments
  @param molfile given molfile
  @param attachments given attachments
  @return smiles with atom mapping
  @throws CTKException general ChemToolKit exception passed to HELMToolKit
  @throws ChemistryException if the chemistry engine can not be initialized