Further cleaning of the topoaa, rigidbody and flexref modules

[amjjbonvin]

The topoaa module is still giving some errors (even if working) because the python machinery ois not writing to the CNS input file the molecule-specific parameters defined in the default config.

E.g.:

[input.mol1]
prot_segid = 'A'
fix_origin = false
dna = false
shape = false
cg = false
cyclicpept = false

This should be corrected (open issue #125)

This pull request should also address issue #126

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closes #125 and closes #126

[amjjbonvin]

flexref part is working, but required further cleaning

[codecov-commenter]

Codecov Report

Merging #127 (bd209f7) into main (c3651f6) will decrease coverage by 0.09%.
The diff coverage is 0.00%.

@@            Coverage Diff             @@
##             main     #127      +/-   ##
==========================================
- Coverage   43.41%   43.32%   -0.10%     
==========================================
  Files          38       38              
  Lines        1875     1879       +4     
==========================================
  Hits          814      814              
- Misses       1061     1065       +4     

Impacted Files	Coverage Δ
src/haddock/libs/libcns.py	14.20% <0.00%> (-0.26%)	⬇️
src/haddock/modules/refinement/flexref/__init__.py	22.66% <0.00%> (-0.31%)	⬇️
src/haddock/modules/sampling/rigidbody/__init__.py	22.07% <ø> (ø)

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[rvhonorato]

This PR has multiple changes over multiple modules with 119 file changes. I cannot check everything, will trust @amjjbonvin on it 🧙🏽

[rvhonorato]

Identifier here starts at 0

[amjjbonvin]

Yes - this is still how models are numbered currently, starting at 0 instead of 1 (which might be more logical from a user perspective)

[joaomcteixeira]

Rodrigo was updating the examples PDB to 2OOB. You might wish to use them here also. Otherwise, we can change that in the future in another PR. It is not clear to me if you made all changes you wanted in this PR. If so, go ahead 😉

I will correct the model_0 issue a new PR, now

[joaomcteixeira]

If you have added already everything you needed go forward merging it.

[amjjbonvin]

Will keep working on the other modules - by merging this one already

[joaomcteixeira]

👏 🚀 🎸