Robert T. McGibbon comments

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Robert T. McGibbon

Python 3.10: Deprecation warnings in asyncio and ssl

It looks to me like we're still seeing these warnings, and one error, when testing trio 0.19.0 for python3.10 in nixpkgs. Subscribing myself to this issue.

doc build for out-of-core (iterload) can't find data/frame0.h5

I think this bug still exists.

load() removes first element from a list of filenames

I thought that was fixed. What version of mdtraj do you have? Is the fix in https://github.com/mdtraj/mdtraj/pull/1706 not working, or do you have a version that doesn't include that?

Reading Charges property PDB files

I am indifferent. If you added it I wouldn't object.

residue.is_nucleic and 'nucleic' in atom selection DSL

@dwhswenson: is this still relevant? I'm happy to hit "merge".

residue.is_nucleic and 'nucleic' in atom selection DSL

Honestly I don't really know anything about the conventions for nucleic acid names, so I'm not really in a position to review much.

MDTraj 1.9.7 on M1 chip fails with image_molecules()

Hi Alex and Sander, I just wanted to give you a heads up re: https://github.com/mdtraj/mdtraj/pull/1738/files. This is one of those issues where I'm probably not able to help, and I...

Possible MDtraj reading issue for a 1 atom molecule mol2 files

This is probably the relevant code: https://github.com/mdtraj/mdtraj/blob/c0d3c985a61698d5a97c7772c373aa0a1a0300ee/mdtraj/formats/mol2.py#L170-L227 Based on the docstrings and the fact that this file has seen minimal updates in the last 7 years, I'm not particularly surprised....

Possible MDtraj reading issue for a 1 atom molecule mol2 files

For clarification: do VMD-produced mol2 files that contain systems with more than 1 atoms get loaded correctly? Is the issue specific to system with only 1 atom?

Possible MDtraj reading issue for a 1 atom molecule mol2 files

Seems like this bug probably still exists.