Thomas Holder

Quote from https://github.com/deepmind/alphafold/issues/788#issuecomment-1612902410 > the `_struct_asym` table is corrupt as it contains author chain IDs instead of internal chain IDs. As far as I can tell, the bug should be...

Opening a file with `as_handle` does not really become an iterator. It becomes a context manager via the [contextlib.contextmanager](https://docs.python.org/3/library/contextlib.html#contextlib.contextmanager) decorator. `as_handle_and_flag` is used 4 times.

Seems reasonable. The docstring of `MMCIFParser` actually says: > auth_residues [...] If false, use the mmCIF "label" residue numbering, which **has no insertion codes**, and strictly increments residue numbers. So...

That's correct, `ruff check` doesn't produce any output on success. If you want to see it fail, I can make a branch with the ruff check enabled but without the...

I would also suggest to add a [ruff pre-commit hook](https://beta.ruff.rs/docs/usage/#pre-commit).

The intended CI failure with W605 violoations can now be seen in https://github.com/mdtraj/mdtraj/actions/runs/5715704737/job/15486056503 I noticed that this makes all matrix jobs fail, which is a bit unfortunate. The alternative is...

> I'm toying with a mega-linter PR in [a branch](https://github.com/mdtraj/mdtraj/tree/lint-add-pre-commit) that might sweep away all of these changes. Nice, go for it! [Biopython also runs pre-commit in CI](https://github.com/biopython/biopython/blob/master/.github/workflows/ci.yml), which I...

There are actual errors in the TeX strings which would get fixed by raw strings. Example: Docstring of [mdtraj.asphericity](https://www.mdtraj.org/1.9.8.dev0/api/generated/mdtraj.asphericity.html?highlight=asphericity#mdtraj.asphericity), current:  After raw string fix: 

Thanks for your comment. How would you define "the structure of the document"? For the real-world examples that I've seen so far, it would make sense to simply merge the...

How to use it in Word: First create two paragraphs. Then put the cursor on the first paragraph and hit Ctrl+Alt+Enter to join them. I know one use case for...