Jonathan Barnoud
Jonathan Barnoud
I commented in https://github.com/MDAnalysis/mdanalysis/issues/3168#issuecomment-1755942135
This has been years in the making. Thank you for making this milestone happen!
I have been on record as one of those (if not the one) that dislike auto-formatting. I had issues with fixes that were suboptimal readability-wise, portions of the code where...
This is fixed, but we should make sure the number is respected when a protein is inserted.
I do not know how @Tsjerk's magic trick really works and how reliable it is. In my experience, it was fairly reliable, but I was only using it on very...
We need a way of adding arbitrary bonds anyway (I need it to bind the heme to the hemoglobin for instance), using such mechanics to let the user add the...
The problem you describe looks like a misformatted input file. I would suggest issuing a warning when a misformatted line is detected (with a tolerance for when the model index...
> I don't see how the modelidx can be ambiguous. If you give one that's the model you want, and no other. If you give no modelidx you don't really...
Works for me.
The -ss option takes a secondary structure sequence as a string. It seems I omitted that martinize 1 could take a file.