James Krieger

Pages for mutations S.Q613, S.A222, S.Y145, S.T572 don't open

2

When clicking on these mutations, there is an empty pages saying "An unexpected error has occurred." Given the current importance of A222V and Y145H in AY.4.2, it would be great...

feature request: converter from molpro to nmd

1

https://github.com/prody/NMWiz/pull/1 could potentially be a useful feature for prody

modehunter interpolateModel

2

This function for thin plate spline interpolation has been copied and modified from the Python 2 code in SITUS ModeHunter in accordance with its legal notice. It should be a...

fix mode ens for empty labels in addModeSets

1

Labels are needed for various downstream functions including getEigvecs and getArray so they need to be set no matter what. The if conditions we had inside the main if condition...

Extend ClustENM kwargs for more functionality

4

Here are some suggested improvement for ClustENM that are helpful for Scipion. - Add more kwargs for ANM options to include sparse and kdtree for buildHessian and turbo for calcModes...

It would be good to have this feature, which we used in https://pubmed.ncbi.nlm.nih.gov/35187088/, available within ProDy as part of showProjection. It would mean adding Seaborn as another dependency, but it...

I just realised there is one because ChimeraX uses it. It would be good for us to have too.

added gromos rmsd clustering

3

This method is the same as the one used in https://manual.gromacs.org/documentation/current/onlinehelp/gmx-cluster.html

deprecation prep

1

I have introduced some try/except blocks to account for things becoming deprecated. The relevant warnings came from pytest from Python 3.8 on Ubuntu 20.04 (Windows Subsystem for Linux 2): ```...

added trajectory wrap method

30

Previously there was only a function to wrapAtoms for individual frames. This extends that to the whole trajectory.