Update MOF processing script

[Andrew-S-Rosen]

Hey @vxfung, could you update the process.py script for the QMOF Database? I'm changing how the data is structured going forward to better accommodate multiple levels of theory. This script below should work for the future versions while also being backwards compatible with several prior versions of the database.

import os
import csv
import json
import pandas as pd
from pymatgen.core import Structure
from pymatgen.io.ase import AseAtomsAdaptor
from ase.io import write

# Read in QMOF data
with open("qmof.json") as f:
    qmof = json.load(f)
qmof_df = pd.json_normalize(qmof).set_index("qmof_id")

with open("qmof_structure_data.json") as f:
    qmof_struct_data = json.load(f)

# Make MOF_data folder
if not os.path.exists("MOF_data"):
    os.mkdir("MOF_data")

# Write out data
targets = []
for entry in qmof_struct_data:
    qmof_id = entry["qmof_id"]
    print(f"Writing {qmof_id}")
    mof = AseAtomsAdaptor().get_atoms(Structure.from_dict(entry["structure"]))
    write(os.path.join("MOF_data", f"{qmof_id}.json"), mof)
    targets.append([qmof_id, qmof_df.loc[qmof_id]["outputs.pbe.bandgap"]])

with open(os.path.join("MOF_data", "targets.csv"), "w", newline="") as f:
    wr = csv.writer(f)
    wr.writerows(targets)

print(len(targets))

Closes #1 and #7.

[vxfung]

Thanks, updated!