As soon as docker image is on external docker registry, the documentation
for the singularity container must be updated

This Dockerfile is a bit optimistic but will hopefully work next week.
- It requires Openstructure 1.9.0 tag to be around
- It requires ProMod3 repository to be public
- It requires ProMod3 1.3.0 tag to be around

For optimal usage of the Penultimate library, one needs to consider the secondary
structure, as there are specific rotamer probabilities for helices, sheets, coils.
We're currently not doing that and would need to adapt some code in the sidechain
reconstruction algorithms. Lets remove the Penultimate Lib for now and use a custom
backbone independent lib instead.

The user provided profiles are mapped on the gapless target sequences
by exact sequence match. The mapping works with an all or nothing principle.
Either all target sequences must be covered by a profile or none. An error
is thrown otherwise.
To avoid ambiguities, the sequences of all provided profiles must be unique
=> in case of a homo-oligomer, one profile must be provided.
If an additional profile is provided that does not match any target sequence,
an error is thrown.

This immediately improves functionality as we can also load
gzipped stuff or cif files.

There is no guarantee, that we have a stereochemically valid template. If no
feasible peptide bond can be built, a gap is added in order to properly deal
with the problem at the loop modelling stage.

thanks Gerardo for pointing that out

Advantage:
Makes it possible to provide sampler/closer/scorer/cooler objects implemented
in both, Python and C++
Disadvantage:
Code duplication as we also need that functionality directly in C++

It was neither documented nor used anywhere...

Use Python's own JSON module for more robust unit testing. Alternative JSON modules may be faster but may also deliver slightly different output concerning whitespaces.

The documentation looks cleaner that way...

Reason for that is that we don't want to create a fancy website
but rather host the static doc somewhere.