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import gzip
import pickle
import sys
import time
from rdkit import Chem, RDConfig
from rdkit.RDLogger import logger
logger = logger()
logger.info('reading smarts')
qs = []
smas = []
for line in file(RDConfig.RDDataDir + '/SmartsLib/RLewis_smarts.txt', 'r').readlines():
if line[0] == '#':
continue
line = line.split(' ')
p = Chem.MolFromSmarts(line[0])
if not p:
print(line[0], file=sys.stderr)
continue
smas.append(line[0])
qs.append(p)
logger.info('reading target counts')
refFps = pickle.loads(gzip.open('fps.1000.counts.pkl.gz', 'rb').read())
fps = []
logger.info('reading mols:')
ms = pickle.loads(gzip.open('mols.1000.pkl.gz', 'rb').read())
t1 = time.time()
nFail = 0
for i, m in enumerate(ms):
fp = [0] * len(qs)
for j, q in enumerate(qs):
o = m.GetSubstructMatches(q)
if len(o) != refFps[i][j]:
print(' >', i, j, o, refFps[i][j], Chem.MolToSmiles(m), smas[j])
nFail += 1
if nFail == 10:
raise ValueError
fp[j] = len(o)
fps.append(fp)
if not i % 50:
logger.info('Done %d' % i)
t2 = time.time()
print('%.2f' % (t2 - t1))
#pickle.dump(fps,file('fps.1000.counts.pkl','wb+'))
nFail = 0
for i, fp in enumerate(fps):
if fp != refFps[i]:
nFail += 1
print('%d mismatches' % nFail)
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