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Added a default setting of batch_size parameter in find() function #6

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Nov 15, 2020
Merged

Added a default setting of batch_size parameter in find() function #6

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12 changes: 7 additions & 5 deletions mongordkit/Search/similarity.py
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Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,8 @@
DEFAULT_PERM_LEN = 2048
DEFAULT_PERM_N = 100

# PyMongo configurations
DEFAULT_BATCH_SIZE = 100

def SimSearchNaive(mol, mol_collection, threshold=DEFAULT_THRESHOLD):
"""
Expand Down Expand Up @@ -52,15 +54,15 @@ def AddMorganFingerprints(mol_collection, count_collection):
:param radius: Radius of the desired Morgan fingerprints. Defaults to 2.
:param length: NBits in desired Morgan fingerprints. Defaults to 2048.
"""
for m in mol_collection.find():
for m in mol_collection.find(batch_size=DEFAULT_BATCH_SIZE):
bit_vector = list((AllChem.GetMorganFingerprintAsBitVect(Chem.Mol(m['rdmol']),
DEFAULT_MORGAN_RADIUS,
nBits=DEFAULT_MORGAN_LEN).GetOnBits()))
count = len(bit_vector)
mol_collection.update_one({'_id': m['_id']}, {'$set': {'fingerprints.morgan_fp': {'bits': bit_vector,
'count': count}}})
counts = {}
for m in mol_collection.find():
for m in mol_collection.find(batch_size=DEFAULT_BATCH_SIZE):
for bit in m['fingerprints']['morgan_fp']['bits']:
counts[bit] = counts.get(bit, 0) + 1
for k, v in counts.items():
Expand Down Expand Up @@ -184,12 +186,12 @@ def AddLocalityHashes(mol_collection, perm_collection, nBuckets=DEFAULT_BUCKET_N
"""
length = len(perm_collection.find_one()['permutation'])
permutations = []
for doc in perm_collection.find():
for doc in perm_collection.find(batch_size=DEFAULT_BATCH_SIZE):
if len(doc['permutation']) != length:
Exception('Permutations must split evenly into buckets')
return
permutations.append(doc['permutation'])
for moldoc in mol_collection.find():
for moldoc in mol_collection.find(batch_size=DEFAULT_BATCH_SIZE):
mol = Chem.Mol(moldoc['rdmol'])
min_hash = get_min_hash(mol, permutations)
hash_groups = hash_to_buckets(min_hash, nBuckets, length)
Expand All @@ -203,7 +205,7 @@ def AddHashCollections(db, mol_collection):
:param mol_collection: a MongoDB collection.
:return: None
"""
for moldoc in mol_collection.find():
for moldoc in mol_collection.find(batch_size=DEFAULT_BATCH_SIZE):
hash_groups = moldoc['LSH']
for number, hash in enumerate(hash_groups):
db['LSHash_' + str(number)].update_one({'_id': hash},
Expand Down