João Rodrigues
João Rodrigues
Following #1714, this PR adds support for selections based on chain identifiers (names). The selection keyword is a bit clunky because `chainid` is already used for the chain index, but...
Hi all, As suggested by @jchodera and @janash on Twitter, it would be nice to have some sort of linter added to the cookiecutter. There's already some configuration for `flake8`,...
Spun-off from #3999. `psea` should run in a temporary directory to avoid leaving unnecessary output files. For example: ``` def run_psea(...): curdir = os.path.abspath(os.curdir) with tempfile.TemporaryDirectory() as tmpdir: os.chdir(tmpdir) .......
Spun-off from #3980. With the move to Github Actions, we lost some of the manual installation of third-party tools we had on Travis. We should restore some of these, in...
This has been somewhat raised in #3853, but it would be potentially interesting to add a small interface to bulk (or not) download Alphafold models and build a structured database...
The command-line interface for the `PDBList.py` module is quite clunky, using a series of complicated ifs and sys.argv calls to parse input from the user. It would be super nicer...
The current code in `PDBList.py` to move obsolete files expects a `.ent` extension, which is reserved for PDB-formatted files. We should extend this to depend on the file_format of choice...
In several places in `PDBList.py`, we try to build links to the databases expecting a url path of the form `/pub/pdb/...` (e.g. [here](https://github.com/JoaoRodrigues/biopython/blob/4d7042ed1185505691c7275c50bb539ef871211a/Bio/PDB/PDBList.py#L160)). While this works for RCSB (American site),...
Hi all, I've been using OpenMM to run simulations for the past couple of years. Unlike other tools, OpenMM does not write a 'topology' file (e.g. `.gro`, `.prmtop`) but instead...
Running `addMissingAtoms()` gives different results because the `LocalEnergyMinimizer` does not allow setting a random seed from `pdbfixer`. The end result is that re-built sidechains are pointing in different directions at...