Talktorial 11b: Problems connecting to OPAL web services

[simsurp]

Hi.
Thank you very much for putting together these talktorials. It's aweTsome !
I'm having issues connecting to the OPAL web services. The line client = Client("http://nbcr-222.ucsd.edu/opal2/services/vina_1.1.2?wsdl") in the fonction opal_run_docking(protein, ligand, center, size, stream_output=True) is giving me an ExpatError and SAXParseException.
Any idea on how I could fix that?
Thanks again.

ExpatError Traceback (most recent call last)
~/anaconda3/envs/teachopencadd/lib/python3.6/xml/sax/expatreader.py in feed(self, data, isFinal)
216 # except when invoked from close.
--> 217 self._parser.Parse(data, isFinal)
218 except expat.error as e:

ExpatError: syntax error: line 1, column 0

During handling of the above exception, another exception occurred:

SAXParseException Traceback (most recent call last)
in
1 from suds.client import Client
----> 2 client = Client("http://nbcr-222.ucsd.edu/opal2/services/vina_1.1.2?wsdl")

[simsurp]

I just found this from the NBCR website:
Please Note: NBCR and its associated websites/services have been retired as of April 30, 2020.
Could that explain my problem?

[jaimergp]

Ooooh! Definitely!

Well, that means this notebook has only historic value for now :) We'll try to find a webservice alternative to run Vina. If you find something, please let us know! Thanks for the report!

[simsurp]

That’s sad. Do you think that it could now work with SwissDock ?

[jaimergp]

Last time I tried it wasn't working, but I didn't investigate more since we had OPAL anyway. Might be worth the try now, but I am a bit short of time lately... You can try asking them if the SOAP access is back online. If they reply affirmatively, I could help!

[jaimergp]

Possible alternatives:

• PLIDFlow: https://pistacho.ac.uma.es/galaxy-bitlab/
• Webina: https://durrantlab.pitt.edu/webina/ - this one is super cool, runs entirely on the client because it's a JS/WebAssembly port of AutoDock Vina. That means the user has to do it manually on a different tab, though.
• Blaster: https://blaster.docking.org/start.shtml
• Mti: https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::MTiAutoDock

[dominiquesydow]

As a heads-up: This issue will be closed automatically with the merge of #74. The docking part of the former 11b talkorial was moved to talktorial T015, which uses smina for docking.