The following issues were observed:
- warning about non-writable directory which was set as IPYTHONDIR env var
  Not very surprising, it's a directory that lives in container space...
- stale kernels
  I didn't investigate that one properly. It had something to do with bending
  around all Jupyter/IPython relevant directories to custom set directories
  in the image. Reason for doing that is potential Python modules that reside
  in user home of the host that get imported in the container. I removed the
  bending around with the full knowledge that the described problem may occur.
- version updates
  Some changes related to different Python versions between old base image
  (Ubuntu 20.04) and the new one (Ubuntu 22.04).

nglview requires ipywidgets < 8

adapt to changes in ost release-2.4.0 branch in conop processors

The Motif finder algorithm was designed to have a database of small motifs
and search them in one target structure. Needs some changes for the use case
of lots of larger structures in which we want to find 1 Motif.

'ling' instead of 'filling' also catches 'sampling' which is used in
CloseLargeDeletions desaster recovery.

Avoids triggering errors with more strict parameter checks introduced
in OpenMM 7.4

Add tolerance values that are passed to the according SD/LBFGS minimizers

Check for and report non-planar rings in the modelling result. This check is
also incorporated in energy minimization, potentially increasing the number
of minimization steps.