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alanwilter / acpype

OFFICIAL: AnteChamber PYthon Parser interfacE
https://alanwilter.github.io/acpype/
GNU General Public License v3.0
201 stars 46 forks source link

OpenBabel 3 compatibility? #10

Closed simonbray closed 4 years ago

simonbray commented 4 years ago

Hi, it seems acpype is not compatible with the newest version of OpenBabel. When I try and create a topology from a PDB file the initial conversion to mol2 fails with ERROR: no 'babel' executable; you need it if input is PDB. I am installing with conda and it works fine if I pin openbabel==2.4.1.

Thanks a lot for your work on this very useful tool.

lkagami commented 4 years ago

Hi Simon, Thank you for your rating. We will be evaluating compatibility. Thanks also for using Acpype. Bests, Luciano

alanwilter commented 4 years ago

Hi Simon,

Many thanks for spotting that. I've updated the code to handle this 'obabel' scenario, though openbabel 3 is still alpha, not even bet AFAIK. I found weird that Conda is already doing a release with that.

Anyway, it should work now.

Best wishes,

Alan

On Thu, 7 Nov 2019 at 18:00, Simon Bray notifications@github.com wrote:

Hi, it seems acpype is not compatible with the newest version of OpenBabel. When I try and create a topology from a PDB file the initial conversion to mol2 fails with ERROR: no 'babel' executable; you need it if input is PDB. I am installing with conda and it works fine if I pin openbabel==2.4.1.

Thanks a lot for your work on this very useful tool.

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simonbray commented 4 years ago

You're welcome!

However, the obabel interface is not quite the same as babel, so unfortunately your latest commit won't be enough to get it working. See here: https://openbabel.org/docs/dev/Command-line_tools/babel.html#babel-vs-obabel

I would suggest replacing babel with obabel completely. This will still work fine in OpenBabel 2 as babel was already deprecated in favour of obabel.

alanwilter commented 4 years ago

Sorry, I forgot that point, fixing it ...

On Thu, 7 Nov 2019 at 21:25, Simon Bray notifications@github.com wrote:

You're welcome!

However, the obabel interface is not quite the same as babel, so unfortunately your latest commit won't be enough to get it working. See here: https://openbabel.org/docs/dev/Command-line_tools/babel.html#babel-vs-obabel

I would suggest replacing babel with obabel completely. This will still work fine in OpenBabel 2 as babel was already deprecated in favour of obabel.

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simonbray commented 4 years ago

Hi Alan, I just tested the new version and it seems to work (and produce the same results) for both versions 2 and 3. Thanks for the quick fix! :)

alanwilter commented 4 years ago

Thanks Simon. I didn’t replied earlier because I found something else that requires my attention, but yes this should be fixed and we keep compatible with Babel v 2.

On Fri 8 Nov 2019 at 10:02, Simon Bray notifications@github.com wrote:

Closed #10 https://github.com/alanwilter/acpype/issues/10.

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