How to use the maggma.advanced_stores.MongograntStore function in maggma

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github hackingmaterials / robocrystallographer / dev_scripts / download_pubchem.py View on Github external
def process_sdf_file(filename):
    mp_pubchem = MongograntStore("rw:knowhere.lbl.gov/mp_pubchem", "mp_pubchem",
                                 key="pubchem_id")
    mp_pubchem.connect()
    coll = mp_pubchem.collection

    skipped = 0
    pubchem_molecules = []
    for i, mol in enumerate(pybel.readfile('sdf', filename)):
        try:
            pubchem_id = int(mol.data['PUBCHEM_COMPOUND_CID'])
            xyz = mol.write(format="xyz")

            data = {'pubchem_id': pubchem_id,
                    'xyz': xyz}
            for key in keys:
                if key in mol.data:
                    data[key_map[key]] = mol.data[key]
github hackingmaterials / robocrystallographer / dev_scripts / process_pubchem.py View on Github external
except KeyError:
            mols.append(False)

    return mols


def task_done(future):
    results.append(future.result())
    pbar.update()


max_atoms = 12
batch_size = 5000
name_keys = ['name_iupac', 'name_traditional']

mp_pubchem = MongograntStore("rw:knowhere.lbl.gov/mp_pubchem", "mp_pubchem",
                             key="pubchem_id")
mp_pubchem.connect()
coll = mp_pubchem.collection

total_mols = coll.count()
batches = coll.find_raw_batches(batch_size=batch_size)
pbar = tqdm(total=total_mols/batch_size, desc="process")

results = []

with pebble.ProcessPool() as pool:
    for batch in batches:
        f = pool.schedule(process_batch, args=(batch, ))
        f.add_done_callback(task_done)

pbar.close()

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Framework to develop datapipelines from files on disk to full dissemenation API

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