does not import from PQR

[drew-parsons]

Avogadro version: (please complete the following information from the About box):

• Avogadrolibs: 1.98.1
• Qt: 5.15.10

Desktop version: (please complete the following information):

• OS: Linux (debian unstable)
• Version 6.5.13
• Compiler g++ 13.2.0

Describe the bug
I am trying to load the a molecule from PQR. The PQR search engine does find them, for instance searching "benzene" by name, there is only one entry, the PQR search box finds it and displays the preview image for the molecule. But when I click on Download, the screen remains blank. The molecule is not imported.

Molecules do import successfully via the "Download by Name" search box. Actually there's something weird going on there. It was working, but after testing a few different molecules while writing this bug report, it stopped importing too. But with no error message written to console (the PQR error is consistent, see below) so it's probably a different issue.

I couldn't import anything from PDB but that I think that's a separate issue (I might not be using the right search term for pdb).

To Reproduce
Steps to reproduce the behavior:

1. Go to 'File' menu
2. Click on 'Import'-'Search PQR...'
3. Search by "benzene" (name).
4. Click 'Search'
5. Click on the found molecule, wait for the preview image to appear
6. Click 'Download'
7. See error

Expected behavior
Molecule should import successfully from PQR without an obabel error.

Screenshots
An error is printed to console

Reading to format:  "cjson" cjson
OBProcess::executeObabel: Running "obabel" "-imol2 -ocjson"
"obabel"  stderr:
 "obabel: cannot write output format!\n"

Additional context
Openbabel version is 3.1.1

[ghutchis]

Sounds like there might be an OpenSSL issue? Does the "Download Plugins" work show anything?

There's definitely an issue in some cases in which the OpenSSL version for Qt doesn't match the installed version of OpenSSL.

[drew-parsons]

I don't think OpenSSL is the problem. Certainly "Download Plugins" shows all the plugins (20 or so of them). I could, for instance, download nanocar-avogadro and Glycans_to_SMILES_script. Not sure what they do exactly or how to use them (I couldn't see any change to the UI), but I can see that they were downloaded into ~/.local/share/OpenChemistry/Avogadro/other/

Given the message "cannot write output format", I thought maybe the PQR problem was a permissions error, e.g. trying to download the file to /usr/bin or some such (I haven't checked where the downloaded data would be written)

[ghutchis]

Oh, okay. I'm trying to switch to using obabel support for CJSON by default. In principle, the Avogadro code should detect that your obabel doesn't support CJSON and use CML instead.

That's definitely a bug.

[ghutchis]

And I'll look at downloading into "other" .. that's also a bug. Sigh.

[drew-parsons]

True, cjson is not in the list

$ obabel -L formats | grep -i cml
cml -- Chemical Markup Language
cmlr -- CML Reaction format
$ obabel -L formats | grep -i json
cdjson -- ChemDoodle JSON
pcjson -- PubChem JSON

[ghutchis]

Yes. It's in obabel HEAD but not a released version. I will release a 3.2 fairly soon.

[ghutchis]

Wait - you said you can't use PDB download either? That should directly read through native Avogadro code (MMTF) not Open Babel.

[drew-parsons]

I'm not certain that I'm using the right search term with PDB. If I enter lysozyme, for instance, it tells me "Could not read the PDB molecule: lysozyme"

[ghutchis]

Yeah, at the moment, I'm not aware of a generic search API for PDB -- would be nice.

Try 1CRN or 6vxx as PDB codes.

[drew-parsons]

Alas, 1CRN and 6vxx aren't found by the PDB search either.

[avo-bot]

This issue has been mentioned on Avogadro Discussion. There might be relevant details there:

https://discuss.avogadro.cc/t/timing-a-1-99-release-urgent-fixes-features-etc/5256/3

[drew-parsons]

PQR import is now working in v1.99 (imports benzene), but PDB import is still not working.

[ghutchis]

I'm going to close this. Please open a new issue for PDB import and we can debug that.