I have a mol file that causes MolFromMolBlock to get stuck.
I reproduced this problem with this simple python script (below).
I've attached the problem input molfile. I got the file
from the chembl08 download. Another large molfile finishes
in seconds, but I stopped this one after about 1 minute.
Can you see what might be the problem?
I'm afraid I am not using the most recent version, but
one I built last July.
From subversion:
URL: https://rdkit.svn.sourceforge.net/svnroot/rdkit/trunk
Repository Root: https://rdkit.svn.sourceforge.net/svnroot/rdkit
Repository UUID: 19320e9b-7711-0410-929e-f4fff3a11e9f
Revision: 1450
Node Kind: directory
Schedule: normal
Last Changed Author: glandrum
Last Changed Rev: 1450
Last Changed Date: 2010-07-08 21:15:09 -0700 (Thu, 08 Jul 2010)
Thanks,
TJ O'Donnell, Ph.D.
President, gNova, Inc.
from rdkit import Chem
import sys
mb = sys.stdin.read()
mol = Chem.MolFromMolBlock(mb)
if mol:
print len(mb),mol
print Chem.MolToSmiles(mol, isomericSmiles=False)
CDK 3/26/10,13:38
469504 0 0 0 0 0 0 0 0999 V2000
10.8216 -24.6695 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
10.8142 -30.3892 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
11.2281 -29.6728 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
12.0536 -29.6741 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
12.4664 -30.3915 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
12.0474 -31.1086 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
11.2233 -31.1037 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
10.8074 -31.8163 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
9.9824 -31.8123 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
9.5730 -31.0955 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.7480 -31.0916 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
9.9889 -30.3830 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
8.3321 -31.8041 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.3389 -30.3752 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
7.5139 -30.3713 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.1048 -29.6548 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.0980 -31.0838 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
8.7415 -32.5209 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
9.7280 -33.4167 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
9.0115 -33.8258 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.4011 -33.2708 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
9.5665 -32.5249 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
10.4016 -32.5121 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
11.2308 -32.5058 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
13.2914 -30.3942 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
13.7019 -29.6740 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
14.1221 -30.3792 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
13.7017 -28.8557 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
13.7238 -31.1064 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
11.6317 -31.7848 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
12.8988 -31.1177 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
12.4962 -31.8378 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
12.8916 -32.5619 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
13.7164 -32.5815 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
12.4622 -33.2663 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
14.1457 -31.8770 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
14.1117 -33.3056 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
14.9705 -31.8967 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
15.3999 -31.1922 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
15.3659 -32.6207 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
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13.9991 -34.7712 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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12.6686 -34.8791 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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14.4140 -28.4395 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
14.4097 -27.6145 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
15.1309 -28.8487 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
15.8432 -28.4325 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
15.9284 -27.6151 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
16.7345 -27.4394 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
17.1510 -28.1522 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
16.6021 -28.7680 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
13.6931 -27.2057 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
13.6888 -26.3807 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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11.2309 -26.8149 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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10.8190 -26.1001 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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10.0375 -21.5609 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
9.3639 -20.2537 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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0.7773 -29.4847 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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385386 1 0 0 0 0
187191 2 0 0 0 0
386387 2 0 0 0 0
387382 1 0 0 0 0
89 91 1 6 0 0 0
383388 1 0 0 0 0
44 45 2 0 0 0 0
89 92 1 0 0 0 0
390370 1 1 0 0 0
191188 1 0 0 0 0
390391 1 0 0 0 0
188189 1 0 0 0 0
390392 1 0 0 0 0
189190 2 0 0 0 0
392393 1 0 0 0 0
190187 1 0 0 0 0
393394 1 0 0 0 0
45 41 1 0 0 0 0
393395 2 0 0 0 0
386398 1 0 0 0 0
92 93 1 0 0 0 0
391396 2 0 0 0 0
178192 1 0 0 0 0
391397 1 0 0 0 0
3 4 1 0 0 0 0
398397 1 0 0 0 0
192193 1 0 0 0 0
398399 1 0 0 0 0
93 94 1 0 0 0 0
399400 1 0 0 0 0
174194 1 0 0 0 0
399401 2 0 0 0 0
28 46 2 0 0 0 0
402400 1 0 0 0 0
194195 1 0 0 0 0
402403 1 0 0 0 0
93 95 2 0 0 0 0
402404 1 0 0 0 0
195196 1 0 0 0 0
421405 1 0 0 0 0
9 23 1 0 0 0 0
405406 2 0 0 0 0
195197 1 0 0 0 0
406407 1 0 0 0 0
91 96 1 0 0 0 0
407408 2 0 0 0 0
408404 1 0 0 0 0
196198 1 0 0 0 0
406409 1 0 0 0 0
96100 2 0 0 0 0
405410 1 0 0 0 0
193199 1 0 0 0 0
410411 2 0 0 0 0
28 47 1 0 0 0 0
411412 1 0 0 0 0
198200 1 0 0 0 0
412413 2 0 0 0 0
199201 1 0 0 0 0
413414 1 0 0 0 0
10 12 2 0 0 0 0
414415 2 0 0 0 0
415410 1 0 0 0 0
200201 1 0 0 0 0
415416 1 0 0 0 0
47 48 1 0 0 0 0
413417 1 0 0 0 0
201202 1 0 0 0 0
100 97 1 0 0 0 0
418419 1 0 0 0 0
202203 1 0 0 0 0
419420 2 0 0 0 0
419423 1 0 0 0 0
97 98 1 0 0 0 0
404421 2 0 0 0 0
202204 2 0 0 0 0
403422 1 0 0 0 0
98 99 2 0 0 0 0
423422 1 0 0 0 0
203205 1 0 0 0 0
423424 1 0 0 0 0
99 96 1 0 0 0 0
424425 1 0 0 0 0
203206 1 1 0 0 0
424426 1 6 0 0 0
23 24 1 0 0 0 0
403427 2 0 0 0 0
205207 1 0 0 0 0
425428 2 0 0 0 0
47 49 1 6 0 0 0
428429 1 0 0 0 0
429433 2 0 0 0 0
207208 1 0 0 0 0
433430 1 0 0 0 0
87101 1 0 0 0 0
430431 2 0 0 0 0
431425 1 0 0 0 0
207209 2 0 0 0 0
384432 1 0 0 0 0
6 7 2 0 0 0 0
432433 1 0 0 0 0
206210 1 0 0 0 0
434388 1 6 0 0 0
434435 1 0 0 0 0
210211 2 0 0 0 0
101102 1 0 0 0 0
49 50 1 0 0 0 0
83103 1 0 0 0 0
50 51 1 0 0 0 0
434439 1 0 0 0 0
435436 1 0 0 0 0
436437 1 0 0 0 0
437438 1 0 0 0 0
438439 1 0 0 0 0
211212 1 0 0 0 0
438440 1 6 0 0 0
212213 1 0 0 0 0
440441 1 0 0 0 0
213214 2 0 0 0 0
437442 1 1 0 0 0
214210 1 0 0 0 0
436443 1 6 0 0 0
103104 1 0 0 0 0
435444 1 1 0 0 0
197215 2 0 0 0 0
445444 1 0 0 0 0
445446 1 0 0 0 0
5 25 1 0 0 0 0
197216 1 0 0 0 0
104105 1 0 0 0 0
216217 1 0 0 0 0
11 13 1 6 0 0 0
445450 1 0 0 0 0
446447 1 0 0 0 0
447448 1 0 0 0 0
448449 1 0 0 0 0
449450 1 0 0 0 0
216218 1 6 0 0 0
449451 1 1 0 0 0
104106 1 0 0 0 0
448452 1 1 0 0 0
218219 1 0 0 0 0
447453 1 0 0 0 0
219220 1 0 0 0 0
447454 1 6 0 0 0
25 26 1 0 0 0 0
445455 1 1 0 0 0
105107 1 0 0 0 0
429456 1 0 0 0 0
7 2 1 0 0 0 0
457418 1 0 0 0 0
457411 1 0 0 0 0
102108 1 0 0 0 0
457458 1 1 0 0 0
458358 1 0 0 0 0
220221 2 0 0 0 0
458459 2 0 0 0 0
221222 1 0 0 0 0
398460 1 6 0 0 0
222223 1 0 0 0 0
402461 1 1 0 0 0
223219 2 0 0 0 0
423462 1 1 0 0 0
463464 1 0 0 0 0
463467 1 0 0 0 0
463469 1 0 0 0 0
463468 1 0 0 0 0
464466 1 0 0 0 0
464465 1 0 0 0 0
M END
> <chembl_id>
CHEMBL574220
> <chebi_id>
663543
------------------------------------------------------------------------------
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