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https://github.com/rdkit/rdkit.git
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24f1737839
* remove all of the "from __future__" imports * remove the first batch of rdkit.six imports/uses * next step of rdkit.six removal * removing xrange, range, and some maps * next round of removals * next round of cleanups * fix inchi test * last bits of "from rdkit.six" are gone * and the last of the six stuff is gone * strange importlib problem
53 lines
1.2 KiB
Python
53 lines
1.2 KiB
Python
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from rdkit import Chem
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from rdkit import RDConfig
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import time, sys, gzip
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import pickle
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from rdkit.RDLogger import logger
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logger = logger()
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logger.info('reading smarts')
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qs = []
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smas = []
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for line in file(RDConfig.RDDataDir + '/SmartsLib/RLewis_smarts.txt', 'r').readlines():
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if line[0] == '#':
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continue
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line = line.split(' ')
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p = Chem.MolFromSmarts(line[0])
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if not p:
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print(line[0], file=sys.stderr)
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continue
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smas.append(line[0])
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qs.append(p)
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logger.info('reading target counts')
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refFps = pickle.loads(gzip.open('fps.1000.counts.pkl.gz', 'rb').read())
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fps = []
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logger.info('reading mols:')
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ms = pickle.loads(gzip.open('mols.1000.pkl.gz', 'rb').read())
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t1 = time.time()
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nFail = 0
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for i, m in enumerate(ms):
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fp = [0] * len(qs)
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for j, q in enumerate(qs):
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o = m.GetSubstructMatches(q)
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if len(o) != refFps[i][j]:
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print(' >', i, j, o, refFps[i][j], Chem.MolToSmiles(m), smas[j])
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nFail += 1
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if nFail == 10:
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raise ValueError
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fp[j] = len(o)
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fps.append(fp)
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if not i % 50:
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logger.info('Done %d' % i)
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t2 = time.time()
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print('%.2f' % (t2 - t1))
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#pickle.dump(fps,file('fps.1000.counts.pkl','wb+'))
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nFail = 0
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for i, fp in enumerate(fps):
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if fp != refFps[i]:
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nFail += 1
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print('%d mismatches' % nFail)
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