Hi there @OpenBabel,
A Friday evening tedious problem.
Can anyone tell me why the following mol file
LACMAD
ChemPy 3D 0
31 32 0 0 1 0 0 0 0 0999 V2000
0.5638 11.8582 6.3019 N 0 0 0 0 0 0 0 0 0 0 0 0
1.4523 10.9079 6.2742 C 0 0 0 0 0 0 0 0 0 0 0 0
2.6393 8.6490 6.0005 C 0 0 0 0 0 0 0 0 0 0 0 0
3.6157 9.5336 6.1990 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.8701 11.5600 6.0553 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.5976 11.2436 7.3580 C 0 0 0 0 0 0 0 0 0 0 0 0
0.9538 13.2682 6.4783 C 0 0 0 0 0 0 0 0 0 0 0 0
1.0954 13.6836 7.9125 C 0 0 0 0 0 0 0 0 0 0 0 0
5.0709 9.2990 6.3918 C 0 0 0 0 0 0 0 0 0 0 0 0
5.7068 8.1628 5.7098 C 0 0 0 0 0 0 0 0 0 0 0 0
7.3942 6.5562 4.9445 C 0 0 0 0 0 0 0 0 0 0 0 0
6.2378 6.4077 4.2764 C 0 0 0 0 0 0 0 0 0 0 0 0
5.2488 7.3334 4.6938 C 0 0 0 0 0 0 0 0 0 0 0 0
5.7027 10.0757 7.0933 O 0 0 0 0 0 0 0 0 0 0 0 0
3.1336 11.1912 6.5004 S 0 0 0 0 0 0 0 0 0 0 0 0
1.0084 9.2415 5.9760 S 0 0 0 0 0 0 0 0 0 0 0 0
7.3632 7.8323 6.0953 S 0 0 0 0 0 0 0 0 0 0 0 0
2.7779 7.4849 6.3379 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.2737 12.2580 5.5375 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.9305 10.8631 5.0883 H 0 0 0 0 0 0 0 0 0 0 0 0
1.8847 13.3015 6.0357 H 0 0 0 0 0 0 0 0 0 0 0 0
0.3371 13.9095 6.2317 H 0 0 0 0 0 0 0 0 0 0 0 0
8.0340 6.0205 4.7697 H 0 0 0 0 0 0 0 0 0 0 0 0
5.9807 5.9511 3.1934 H 0 0 0 0 0 0 0 0 0 0 0 0
4.3071 7.5363 4.0020 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.0459 10.4681 7.9060 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.5958 10.8817 7.1791 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.6488 12.1229 7.9958 H 0 0 0 0 0 0 0 0 0 0 0 0
0.4883 13.3910 8.3634 H 0 0 0 0 0 0 0 0 0 0 0 0
1.3053 14.6861 7.8243 H 0 0 0 0 0 0 0 0 0 0 0 0
1.8010 12.8139 8.2817 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 0 0 0 0 0
2 16 1 0 0 0 0
3 4 2 0 0 0 0
4 15 1 0 0 0 0
5 1 1 0 0 0 0
6 5 1 0 0 0 0
7 1 1 0 0 0 0
8 7 1 0 0 0 0
9 4 1 0 0 0 0
10 9 1 0 0 0 0
11 17 1 0 0 0 0
12 11 2 0 0 0 0
12 13 1 0 0 0 0
13 10 2 0 0 0 0
14 9 2 0 0 0 0
15 2 0 0 0 0 0
16 3 1 0 0 0 0
17 10 1 0 0 0 0
18 3 1 0 0 0 0
19 5 1 0 0 0 0
20 5 1 0 0 0 0
21 7 1 0 0 0 0
22 7 1 0 0 0 0
23 11 1 0 0 0 0
24 12 1 0 0 0 0
25 13 1 0 0 0 0
26 6 1 0 0 0 0
27 6 1 0 0 0 0
28 6 1 0 0 0 0
29 8 1 0 0 0 0
30 8 1 0 0 0 0
31 8 1 0 0 0 0
M END
Fails when trying to babel ligand.mol ligand.smi:
x...@yyy$ babel ligand_LACMAD.mol ligand_LACMAD.smi
==============================
*** Open Babel Warning in ReadMolecule
WARNING: Problems reading a MDL file
Invalid bond specification, atom numbers or bond order are wrong.
0 molecules converted
1 warnings 2 audit log messages
I can see no problems with it... (atom numbers and bonds look OK too)
Many Thanks
JP
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