Simon Mathis

For the second limit (3rd sentence), it should presumably be instead of . 

[Unexpected behaviour] Unexpected behavoiur when parsing mmCIF files

5

Thank you for providing pdbfixer. I was using it to fix various protein structures and noticed the following unexpected behaviour (including the code to reproduce): - The PDBFixer reports a...

Staging

1

Creating a draft pull request from `staging` to `main` here, to include all the updates from the Hackathon

TODOS: - [ ] make examples from binder accessible for local installation via auto download

Performance-improvement: Combine boolean masks

1

If numpy does short-circuit evaluation on these things this it'd be slightly faster to combine boolean masks. Does anyone know how numpy handles these type of cases (below)? Case: Case...

Feature: Just noticed this now. It'd be useful to also allow identifying nodes with other (custom) classes where we determine the class-to-class mapping. I will add this as an extra...

I feel like there has to be a way to make this much more efficient, maybe through stuff like `numba` or Cython, but that's something to leave for later. _Originally...

Fixing does not appear to work for inferring valence & formal charge states from molecules from some PDB files

4

Thank you for this nice library! I'm have a question re fixing 'broken' Mols by inferring the correct valences and charges that I was hoping `datamol` could fix for me....