On 05/05/2022 05:50, Mohammad Goodarzi wrote:
Hello guys,
It has been sometimes that I used obabel but now I cannot use it to
convert lots of molecules to mol format.
I have a MAC and I am trying to convert SMILE to Mol
I do this
obabel .smi -omol -m
This is one example that I save it into a file with format .smi
CC1=CC=C(C=C1)C(=O)N1N=C(CC1C1=CC=CO1)C1=CC=C(NS(C)(=O)=O)C=C1
but the answer is empty
Here is an example command-line session:
# obabel in.smi -O out.mol
==============================
*** Open Babel Warning in WriteMolecule
No 2D or 3D coordinates exist. Stereochemical information will be
stored using an Open Babel extension. To generate 2D or 3D coordinates
instead use --gen2D or --gen3D.
1 molecule converted
# cat in.smi
CC1=CC=C(C=C1)C(=O)N1N=C(CC1C1=CC=CO1)C1=CC=C(NS(C)(=O)=O)C=C1 mol1
# cat out.mol
mol1
OpenBabel05092210342D
30 33 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 7 1 0 0 0 0
2 3 2 0 0 0 0
3 4 1 0 0 0 0
4 5 2 0 0 0 0
5 6 1 0 0 0 0
5 8 1 0 0 0 0
6 7 2 0 0 0 0
8 9 2 0 0 0 0
8 10 1 0 0 0 0
10 14 1 0 0 0 0
10 11 1 0 0 0 0
11 12 2 0 0 0 0
12 13 1 0 0 0 0
12 20 1 0 0 0 0
13 14 1 0 0 0 0
14 15 1 0 0 0 0
15 19 1 0 0 0 0
15 16 2 0 0 0 0
16 17 1 0 0 0 0
17 18 2 0 0 0 0
18 19 1 0 0 0 0
20 30 1 0 0 0 0
20 21 2 0 0 0 0
21 22 1 0 0 0 0
22 23 2 0 0 0 0
23 24 1 0 0 0 0
23 29 1 0 0 0 0
24 25 1 0 0 0 0
25 26 1 0 0 0 0
25 27 2 0 0 0 0
25 28 2 0 0 0 0
29 30 2 0 0 0 0
M END
any idea?
Thanks
Mo
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