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.

Path should be entered by whoever uses the script with an appropriate path to the SMTL.