Augustin Žídek

mmCIF output - `_atom_site.label_entity_id` not written

1

Currently, OpenMM writes `?` in the `_atom_site.label_entity_id` mmCIF field: This happens in [pdbxfile.py#L453](https://github.com/openmm/openmm/blob/6da98153b5ebb2a887aa7c4ec34d26b189eb4e1a/wrappers/python/openmm/app/pdbxfile.py#L453): ```python line = "%s %5d %-3s %-4s . %-4s %s ? %5s %s %10.4f %10.4f %10.4f 0.0...

Fix RMSD externs to be compatible with Cython 3.0.

4

* We needed this fix internally to make mdtraj work with Cython 3.0. * This fixed it, however, we build rdkit ourselves using Blaze (Bazel), so this fix might not...

cif::pdb::reconstruct_pdbx is very slow

3

Hello, many thanks for the development and maintenance of libcifpp! I've noticed that `cif::pdb::reconstruct_pdbx` is very slow. E.g. on `7soy` mmCIF file from the PDB it takes < 0.2 seconds...