Openfold addition

[hlasimpk]

Changes to include OpenFold3 into ABCFold
The main changes include:

• af3_to_openfold: converting AF3 JSON into the OpenFold format
• run_openfold: Code to run OpenFold3
• checkinstall: Code to check if OpenFold3 is installed and make micromamba env if it's missing. This has also required the addition of code to install kalign2 and to download the default checkpoint (weights).
• output/openfold: code to convert the OpenFold output into the right format, there is one bit of code here to convert the mmcif output as the formatting is weird and not recognised by Biopython.
• There there is just lots of general changes to include it into the output pages.

I've added tests and updated the documentation.

[hlasimpk]

I'm going to preemptively comment to say I don't think this is the best solution, but it does work. If you can think of a different way to fix it though, let me know!

[hllelli2]

Try writing as one big block i.e. """"
text
"""

[hllelli2]

Make a comment explaining what this does

[hllelli2]

Make a class method fro cif file handler called from_openfold which handles this logic

[hllelli2]

The check to see if singularity is found on the system sometimes returns true even if singularity is not none.