1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
|
import re
splitExpr = re.compile('[\t ]')
from Chem import rdmol
def runit(fName):
inLines = open(fName, 'r').readlines()
nFailed = 0
nPassed = 0
nTried = 0
for line in inLines:
if len(line):
smi = splitExpr.split(line)[1]
if smi[-1] == '\n':
smi = smi[:-1]
if smi[-1] == '\r':
smi = smi[:-1]
nTried += 1
print('trying: "%s"' % smi)
m = rdmol.MolFromSmiles(smi)
nPassed += 1
print('frags')
nFrags = max(rdmol.FindMolFrags(m)) + 1
print('sssr')
rings = rdmol.FindSSSR(m)
cyclomat = m.getNumBonds() - m.getNumAtoms() + nFrags
assert cyclomat == len(rings), 'bad num rings for %s\n\t%s!=%s' % (smi, cyclomat, len(rings))
print('span')
nChords = m.getNumBonds() - len(rdmol.FindSpanningTree(m))
assert len(rings) == nChords, 'bad num chords for %s\n\t%s!=%s' % (smi, nChords, len(rings))
m = None
print('%d of %d passed' % (nPassed, nTried))
if __name__ == '__main__':
import sys
fName = 'ntp_smiles.txt'
if len(sys.argv) > 1:
fName = sys.argv[1]
runit(fName)
|
