def get_dict_element(): c.execute('''SELECT id,name,charge,multiplicity, num_atoms,num_elec,symmetry FROM ele_tab''') d = defaultdict(dict) for i in c.fetchall(): d[str(i[1])] = { "id": str(i[0]), "charge": int(i[2]), "multiplicity": int(i[3]), "num_atoms": int(i[4]), "symmetry": str(i[6]) } for ele in d: f = get_formula(ele) d[ele]["formula"] = f for geo in list_geo(): l = [get_coord(ele, a, geo) for a in f] d[ele][geo] = l return d
def get_dict_element(): c.execute('''SELECT id,name,charge,multiplicity, num_atoms,num_elec,symmetry FROM ele_tab''') d = defaultdict(dict) for i in c.fetchall(): d[str(i[1])] = {"id": str(i[0]), "charge": int(i[2]), "multiplicity": int(i[3]), "num_atoms": int(i[4]), "symmetry": str(i[6])} for ele in d: f = get_formula(ele) d[ele]["formula"] = f for geo in list_geo(): l = [get_coord(ele, a, geo) for a in f] d[ele][geo] = l return d
print "File in misc is corupted. Git reset may cure the disease." sys.exit(1) if __name__ == '__main__': arguments = docopt(__doc__, version='G2 Api ' + version) if arguments["list_geometries"]: if arguments["--ele"]: str_ = cond_sql_or("id_tab.name", arguments["--ele"]) str_ = "AND".join(str_) else: str_ = '(1)' print ", ".join(list_geo(str_)) elif arguments["list_elements"]: str_ = cond_sql_or("geo_tab.name", arguments["--geo"]) str_ = "AND".join(str_) l = [x for x in list_ele(str_) if "-" not in x and "+" not in x] print ", ".join(l) elif arguments["get_g09"] or arguments["get_xyz"]: from collections import namedtuple get_general = namedtuple('get_general', ['get', 'ext'])
return "\n".join(map(str, g09_file_format)) if __name__ == '__main__': arguments = docopt(__doc__, version='G2 Api ' + version) if arguments["list_geometries"]: if arguments["--ele"]: cond = cond_sql_or("ele_tab.name", arguments["--ele"]) where = "AND".join(cond) else: where = '(1)' r = list_geo(where_cond=where) assert r, "No geometries for {0} elements".format(arguments["--ele"]) print ", ".join(r) elif arguments["list_elements"]: if arguments['--geo']: cond = cond_sql_or("geo_tab.name", arguments["--geo"]) where = "AND".join(str_) r = list_ele(where_cond=where) assert r, "No element for {0} geometries".format( arguments["--geo"]) print ", ".join(r)
return "\n".join(map(str, g09_file_format)) if __name__ == '__main__': arguments = docopt(__doc__, version='G2 Api ' + version) if arguments["list_geometries"]: if arguments["--ele"]: cond = cond_sql_or("ele_tab.name", arguments["--ele"]) where = "AND".join(cond) else: where = '(1)' r = list_geo(where_cond=where) assert r, "No geometries for {0} elements".format(arguments["--ele"]) print ", ".join(r) elif arguments["list_elements"]: if arguments['--geo']: cond = cond_sql_or("geo_tab.name", arguments["--geo"]) where = "AND".join(str_) r = list_ele(where_cond=where) assert r, "No element for {0} geometries".format(arguments["--geo"]) print ", ".join(r) elif arguments['--run']: