Sander Roet

don't allow non-sorted or non-unique indices in atom_slice

5

closes #1664 I could not think of a trivial to fix on the `topology` side. A couple things that needed to be taken into account: 1. What happens if atom...

Python 3.10 release?

4

Background: PyEmma is a testing dependency for a package I maintain. We are trying to enable tests on python 3.10. Currently when trying to run `conda install pyemma` in a...

**Describe your problem** We ran into an issue where running an 3D auto-refine job would always generate the following error: log running with GPU ``` RELION version: 4.0.0-commit-1569f0 Precision: BASE=double...

Modelangelo v1.0.1 failing if the fasta contains unknown residues "X"

4

Hey, I have a fasta file where certain residues are unknown and therefor represented with `X` such as (1 at the start and 1 at place 105): ``` >chain 'CM'...

Regenerate webhook for read the docs

2

@dwhswenson I assume you got the same emails as me, but I don't have the permissions to fix it. (don't have admin rights on this repo or on RtD) Our...

[WIP]: cythonisation

1

Here I am trying to see if we can get a speedup with cythonization of the `contactobject` via type hinting (as is done in for the scheduler in `dask/distributed`). To...

As mentioned in #101 , there are some limitations on the DaskContactFrequency, mainly: - The whole trajectory has to fit into memory as it is loaded once to figure out...

I was a bit surprised to see this dependency still in the build-system part as it also defines `numpy>2`. It is officially [deprecated](https://github.com/scipy/oldest-supported-numpy?tab=readme-ov-file#deprecation-notice-for-numpy-20) and the backwards compatibility issue has been...