Irfan Alibay

Ok MDA wheel build fine, but the presence of h5py in the azp script is messing with us. I'll switch to a new PR at this point to keep the...

Closing as superseded by #3862

> I think something I've got wrong historically is the difference between segments and chainIDs. Currently chainID is an atom attribute, but really it should alias to segid (unless I'm...

@richardjgowers I'm pretty sure there's an issue about this somewhere already. Because they are technically different fields on read you can't just equate them. honestly I'd just remove any reliance...

Yeah it's not really bad, but there are some times the bot gets a bit annoying. I think we agreed this was a starting point, so any improvements would be...

I know that at least Maestro (maybe also pymol) will let you add two connect entries if you have a double bond in a PDB file, raising an exception would...

Honestly I'd probably be ok with this being pre-3.0, it feels more like a bug / undefined behaviour thing than an API break (unless there's some specific reason for its...

From a packaging standpoint we absolutely can't ship the library with a 300 MB+ database. Unfortunately relying on external downloads isn't likely to go very well on clusters or some...

In the first instance though, I would push for an initial solution that does not rely on the CCD. The standard residues are well defined (except from bond orders and...

Reading HELIX, etc.. and dumping them into a residue-wide attribute isn't too bad imho, to speed this discussion up, can we come up with quick solutions for what we do...