Thanks, you were right! It fixed the issue and I can convert without any issue
Thanks Mo On Sun, May 8, 2022 at 9:19 PM Richard <roversts...@gmail.com> wrote: > Mo, > > I think the only thing you are missing is --gen3D. For example > converting two smiles string in test.smi > > $ cat test.smi > C(CC(C(=O)O)N)CN=C(N)N > C1=CC=C(C=C1)CC(C(=O)O)N > > obabel -i smi test.smi -o mol --gen3d -m > > Note the --gen3D command can be slow with a lot of chiral centers. > > -Richard > > On 5/8/22 18:36, Francois Berenger wrote: > > 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 > >> _______________________________________________ > >> OpenBabel-discuss mailing list > >> OpenBabel-discuss@lists.sourceforge.net > >> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > > > > > _______________________________________________ > > OpenBabel-discuss mailing list > > OpenBabel-discuss@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >
_______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
