[Open Babel] Why this happening? using ob.py from html

I call python file by using ajax (html file) with sending a data. And in that python file, when I typed "import openbabel" then it didn't work. However when I typed "import openbabel" in python command line or run a python file with openbabel, it didn't call error. It works very well. Only callin

Re: [Open Babel] InChi notation of a small molecule

> but problem is coming in identifying the real number of the atoms in the pdb > files as Inchi notation is gives its own identifying number. I'm not sure I understand your question. I think you're trying to match atoms from the PDB to the InChI. This will be difficult, since InChI intentionally

Re: [Open Babel] obabel crash while removing salt (removing counter-ions)

Hi Chris, Thank you so much for your fast reply and solution. Indeed the problematic molecule can be bypassed as you suggested! -- View this message in context: http://forums.openbabel.org/obabel-crash-while-removing-salt-removing-counter-ions-tp4561055p4561399.html Sent from the General disc

Re: [Open Babel] Disabled aromaticity conversion in SMILES

(Please cc to list) I think it would be quite a bit of work to implement this feature. Could you explain why it might be useful? - Noel On 12 April 2012 17:21, Camille Gardet wrote: > Oh.. > > ** ** > > Will it be in featured change or not at all ? > > ** ** > > Regards, > > Camill

Re: [Open Babel] obabel crash while removing salt (removing counter-ions)

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

[Open Babel] obabel crash while removing salt (removing counter-ions)

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

Re: [Open Babel] The Python binding of FindAutomorphisms?

I understand the problem. However, I don't think it can be done from Python. After some googling, I can't see any evidence that SWIG supports functors in Python. You could double-check this on the SWIG user mailing list. - Noel On 16 April 2012 07:58, Klniu wrote: > Hi there > > I have used Fin