Hello,
I just downloaded the NCI Natural Products Set II sdf file and I cannot get
OpenBabel to convert it to any format.
I get this error:
==============================
*** Open Babel Warning in OpenBabel::MDLFormat::ReadMolecule
WARNING: Problems reading a MDL file
Cannot read atom and bond count
Expected standard 6 character atom and bond count
This is what the first entry in the sdf looks like:
757
CML DOM 02221007322D
30 32 0 0 0 0 0 0 0 0999 V2000
-1.7627 -1.5440 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-0.7617 -1.2290 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
0.8432 2.0199 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.4812 1.6519 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.2052 1.6519 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.4812 0.9149 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.2052 0.9149 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.8432 0.5459 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.4327 0.5459 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.0577 0.9079 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.6867 0.5449 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.8432 -0.1900 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.4327 -0.1900 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.6867 -0.1900 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.5832 -0.8800 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.6857 -0.9100 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.1567 -0.8800 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.3967 -0.9100 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.2957 -0.5420 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-2.9367 -0.1723 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.3847 1.9919 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-1.0252 1.6214 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.1567 -1.6400 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
0.4841 -2.0099 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.1249 -1.6399 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
0.4841 -2.7499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.8432 2.7099 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1.4841 3.0799 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.1062 2.0119 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
2.7467 1.6413 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 18 2 0 0 0 0
17 2 1 1 0 0 0
3 5 2 0 0 0 0
3 4 1 0 0 0 0
3 27 1 0 0 0 0
4 6 2 0 0 0 0
4 29 1 0 0 0 0
5 7 1 0 0 0 0
5 21 1 0 0 0 0
6 8 1 0 0 0 0
7 8 2 0 0 0 0
7 9 1 0 0 0 0
8 12 1 0 0 0 0
9 10 2 0 0 0 0
9 13 1 0 0 0 0
10 11 1 0 0 0 0
11 14 2 0 0 0 0
12 15 1 0 0 0 0
13 16 2 0 0 0 0
13 17 1 0 0 0 0
14 18 1 0 0 0 0
14 19 1 0 0 0 0
15 17 1 0 0 0 0
16 18 1 0 0 0 0
17 23 1 6 0 0 0
19 20 1 0 0 0 0
21 22 1 0 0 0 0
23 24 1 0 0 0 0
24 25 2 0 0 0 0
24 26 1 0 0 0 0
27 28 1 0 0 0 0
29 30 1 0 0 0 0
M END
I've tried copying in different, known-to-work, count lines but to no avail.
http://forums.openbabel.org/file/n3734151/npset_ii.sdf npset_ii.sdf
Thanks for any help.
Cheers,
David
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