OpenBabel 3 compatibility?

[alanwilter]

OpenBabel 3 compatibility?

[lkagami]

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

[alanwilter]

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

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On Thu, 7 Nov 2019 at 18:00, Simon Bray ***@***.***> 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. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#10?email_source=notifications&email_token=AA5YDSUHYN253UFD4D5YVCTQSRCT7A5CNFSM4JKKCVMKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4HXVKI5A>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AA5YDSRQNAOBJ7G45I3VTQ3QSRCT7ANCNFSM4JKKCVMA> .

-- Wanna help a great cause? Please: https://www.raymondnicolettrust.com/events/2020/parismarathon And many thanks! Alan Silva 🚲🏊‍♂🏃‍♂🇧🇷🇫🇷🇬🇧

[simonbray]

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]

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

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On Thu, 7 Nov 2019 at 21:25, Simon Bray ***@***.***> 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. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#10?email_source=notifications&email_token=AA5YDSQ6QDWTSKEDYIXHH33QSR2TLA5CNFSM4JKKCVMKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEDNWGSI#issuecomment-551248713>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AA5YDSQMQLYYIHWIVTZJCIDQSR2TLANCNFSM4JKKCVMA> .

-- Wanna help a great cause? Please: https://www.raymondnicolettrust.com/events/2020/parismarathon And many thanks! Alan Silva 🚲🏊‍♂🏃‍♂🇧🇷🇫🇷🇬🇧

[simonbray]

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]

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 ***@***.***> wrote: Closed #10 <#10>. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#10?email_source=notifications&email_token=AA5YDSTXHHYGHZ5KOA3APJLQSUTKNA5CNFSM4JKKCVMKYY3PNVWWK3TUL52HS4DFWZEXG43VMVCXMZLOORHG65DJMZUWGYLUNFXW5KTDN5WW2ZLOORPWSZGOUXKJ5KQ#event-2782174890>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AA5YDSQPUHWWZRARHOQBY4DQSUTKNANCNFSM4JKKCVMA> .

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