Oliver Beckstein
Oliver Beckstein
# Bug: no search results after adding new sitemaps ### If it is a DocSearch index issue, what is the related `index_name` ? * `index_name`= mdanalysis * index file [mdanalysis.json](https://github.com/algolia/docsearch-configs/blob/master/configs/mdanalysis.json)...
## Is your feature request related to a problem? ## The testing code uses pytest and relies on numpy.testing. It contains some deprecated testing constructs such as [`assert_almost_equal()`](https://numpy.org/doc/stable/reference/generated/numpy.testing.assert_almost_equal.html), [`assert_array_almost_equal()`](https://numpy.org/doc/stable/reference/generated/numpy.testing.assert_array_almost_equal.html) and...
## Is your feature request related to a problem? ## The new experimental `nucleicacids` analysis module contains the https://github.com/MDAnalysis/mdanalysis/blob/c01d82bb86b480c8b2ae87f36497e7fc0a726c84/package/MDAnalysis/analysis/nucleicacids.py#L61 class as its base class. It presents results in a `Results`...
## Is your feature request related to a problem? ## MDAnalysis does not have a transformation to create “unwrapped” no-jump trajectories where particles are never put back in the primary...
# Background MDAnalysis has existed for a while and so there’s a bit of history built into our development process. One of these pieces of history is that we follow...
## Expected behavior ## Our tests do not use deprecated constructs that will be removed. ## Actual behavior ## Tests trigger `DeprecationWarning` for uses of using the `rmsf` attribute instead...
Fixes #2988 Changes made in this Pull Request: - Do not any longer use deprecated NumPy API. - requires Cython >= 3.0 (tested locally with 3.0a6) - fixed direct ndarray.base...
## Is your feature request related to a problem? ## Can we have `mda.fetch_alphafold()` to get a model from https://www.alphafold.ebi.ac.uk/ ? ## Describe the solution you'd like ## ```python u...
## Is your feature request related to a problem? ## We have many analysis tools for complicated problems, all using the consistent AnalysisBase approach. However, there's no functionality for fairly...
https://gitlab.com/KomBioMol/gromologist is a Python package for handling top and itp files.