def create_top(o, struct, posres): print("attempting to auto-generate a topology...") top = md.topology(struct=struct, protein="protein", posres=posres, dirname=o) # topology returns: # {'top': '/home/andy/tmp/Au/top/system.top', # 'dirname': 'top', # 'posres': 'protein_posres.itp', # 'struct': '/home/andy/tmp/Au/top/protein.pdb'} print("succesfully auto-generated topology") print('pwd', os.getcwd()) print('top', top) """
# try to create an integrator attr(INTEGRATOR, str, integrator) attr(INTEGRATOR_ARGS, list, integrator_args) try: integrator_type = util.get_class(conf[INTEGRATOR]) integrator_type(None, *conf[INTEGRATOR_ARGS]) print("succesfully created integrator {}".format(integrator)) except Exception, e: print("error creating integrator {}".format(integrator)) raise e # make a top if we don't have one if top is None: print("attempting to auto-generate a topology...") with md.topology(struct=struct, protein="protein") as top: # topology returns: # {'top': '/home/andy/tmp/Au/top/system.top', # 'dirname': 'top', # 'struct': '/home/andy/tmp/Au/top/protein.pdb'} print("succesfully auto-generated topology") print('pwd', os.getcwd()) print('top', top) filedata_fromfile(TOPOL_TOP, top["top"]) filedata_fromfile(STRUCT_PDB, top["struct"]) include_dirs = [os.path.abspath(top.dirname)] read_includes(top["top"])