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MDAnalysis
MDAnalysis is a Python library to analyze molecular dynamics simulations.
The case when no coordinates following the specified convention in the Timestep are found and a `ValueError` is raised, is not tested: https://github.com/MDAnalysis/mdanalysis/blob/19e675b35f207a7e3769700f1466ce0a6d1605c7/package/MDAnalysis/coordinates/LAMMPS.py#L833-L838 (The incorrect f-string use is fixed in...
The [IMDv3 protocol implementation](https://github.com/MDAnalysis/mdanalysis/pull/4923) in MDAnalysis through the `IMDReader` needs an appropriate citation under references (`package/doc/sphinx/source/documentation_pages/references.rst`), once the IMDv3 paper has been published.
Fixes #5141 and perhaps fixes #5089 Changes made in this Pull Request: Adds option to explicitly read pdb directly with gemmi, with `format='pdb_gemmi'` upon Universe creation: ```python import MDAnalysis as...
## Is your feature request related to a problem? ## I'd like to directly compare AlphaFold predicted structures, datasets of PDBs and trajectories. LDDT https://academic.oup.com/bioinformatics/article/29/21/2722/195896?login=true#92198107 seems like a good tool...
The current MDAnalysis atom guesser incorrectly assigns the element type for certain atoms. This misassignment leads to incorrect bond guessing, particularly in DSM lipids—which is how the issue was originally...
## Is your feature request related to a problem? ## It's more of a suggestion. ## Describe the solution you'd like ## Pull #4712 is about to introduce `gemmi`-based backend...
Expected Behavior When using guess_TopologyAttrs to generate bonds for DSM lipids, the bonds around atom C3S (or any C*S) should be guessed correctly. For example: ("C3S", "C4S"), ("C3S", "C2S"), ("C3S",...
## Is your feature request related to a problem? ## OpenMM generate a PDB file with hexadecimal resid if there are more than 9999 residues. However, in MDAnalysis, hexadecimal resids...
This is a very early stage/WIP PR that adds support for building MDAnalysis with the [`meson`](https://github.com/mesonbuild/meson) build system and the [`spin`](https://github.com/scientific-python/spin) developer tool, following much of the broader scientific Python...
Fixes #5136 Changes made in this Pull Request: * Added 5 missing contributors from v2.10.0 to the `CHANGELOG` file. * Added 1 missing contributor from v2.10.0 to the `! AUTHORS`...
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MDAnalysis is a Python library to analyze molecular dynamics simulations.