properties = dict(sorted(struct.site_properties.items())) # fetch site properties出现错误 struct = Structure.from_dict(entry["structure"]) # Pymatgen structure KeyError: 'structure'

[xiaowangfeng]

when i run the code of make_cifs.py ,it will have the error---- properties = dict(sorted(struct.site_properties.items())) # fetch site properties出现错误 struct = Structure.from_dict(entry["structure"]) # Pymatgen structure KeyError: 'structure'

i can't solve it can you tell me what happened?

import os import json import pymatgen from pymatgen.core import Structure

------Settings------

struct_json_path = "E:\GANN-main\qmof_database\qmof.json" # path to structure json cif_folder_path = "E:\GANN-main\qmof_database\qmof_cif" # path to folder where CIFs will be stored write_site_props = True # if site properties should be written to CIF only_ddec_charge = False # set to True if you only want _atom_site_charge flags

------Settings------

Make new folder to store CIFs

if not os.path.exists(cif_folder_path): os.mkdir(cif_folder_path)

Read in structure data

with open("E:\GANN-main\qmof_database\qmof.json") as f: qmof_struct_data = json.load(f)

Loop over structures and write each one out to a CIF

qmof_structs = {} for entry in qmof_struct_data:

qmof_id = entry["qmof_id"]  # name for CIF
print(f"Writing {qmof_id}")

struct = Structure.from_dict(entry["structure"])  # Pymatgen structure
cif_path = os.path.join(cif_folder_path, f"{qmof_id}.cif")  # path to write CIF
struct.to(filename=cif_path)  # write CIF
properties = dict(sorted(struct.site_properties.items()))  # fetch site properties

# Overwrite CIF with site properties
if write_site_props:
    new_cif = ""
    i = 0
    prop_lines = False

    with open(cif_path, "r") as f:
        for line in f:
            if "_atom_site_occupancy" in line:
                new_cif += line
                if only_ddec_charge:
                    new_cif += f" _atom_site_charge\n"
                else:
                    for key in properties.keys():
                        new_cif += f" _atom_site_{key}\n"
                prop_lines = True
                continue

            if i == len(struct):
                prop_lines = False

            if prop_lines:
                new_cif += line.strip()
                if only_ddec_charge:
                    new_cif += f"  {properties['pbe_ddec_charge'][i]}"
                else:
                    for value_sets in properties.values():
                        new_cif += f"  {value_sets[i]}"
                new_cif += "\n"
                i += 1
            else:
                new_cif += line

    # Write out new CIF
    with open(cif_path, "w") as f:
        f.write(new_cif)

[Andrew-S-Rosen]

I will respond to your email(s) when I am back at work.

[xiaowangfeng]

thanks, I'll be looking forward to hearing from you.