Hi Chris,
Thank you so much for your fast reply and solution. Indeed the problematic
molecule can be bypassed as you suggested!
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Sent from the General disc
The example files did not make it through to the mailing list. With
SMILES it is probably safe to just copy them in to the text. (Don't do
this for SDF files!)
The -e option enables obabel to continue with the next molecule after
an error, so if the crash is not too severe you may be able to g
Hi all,
I'm using Open Babel 2.3.1 running on a GNU/Linux OS.
I used to work with molecules DB in SMILES format. Normally with obabel you
can remove counter-ions (with the flag '-r', which remove all but the
largest contiguous fragment) with the following command:
/obabel -ismi file.smi -r -osmi
