input params in topoaa/defaults.cfg now with proper behaviour

[joaomcteixeira]

• input params from topoaa are now distributed over molecules.
• input params are written to the CNS file, both defaults and the user injected, without the mol suffix.
• In the case of docking two molecules (A and B), where B is an ensemble, each model of the ensemble will get the same parameters corresponding to the molecule number: A gets mol1 and all models of B get mol2.
• For the particular case of input, new parameters can be added even if they are not defined in the defaults.cfg. This allows for more flexibility, though it adds responsibility to the user as typos won't be spotted.
• Adds correct sorting for integer suffixed files: for example, file_1, file_2, file_10, are now sorted properly according to their numeration (useful for ensembles).

To use this function, the user config should go as follows:

[topoaa]
# general topoaa params go here
[topoaa.input.mol1]
# mol1 specific parameters
other_parameter_needed_but_not_defined_in_defaults = true
[topoaa.input.mol2]
# mol2 specific parameters

Special features:

Despite topoaa/defaults.cfg defining only 20 molecules (mol20) we can add more in the user config file for special cases without the need to modify the defaults. However, in these extreme cases, you would need to define all parameters in the user config.

[codecov-commenter]

Codecov Report

Merging #169 (59db085) into main (d5f4715) will increase coverage by 0.71%.
The diff coverage is 81.08%.

@@            Coverage Diff             @@
##             main     #169      +/-   ##
==========================================
+ Coverage   40.45%   41.16%   +0.71%     
==========================================
  Files          41       41              
  Lines        2257     2276      +19     
==========================================
+ Hits          913      937      +24     
+ Misses       1344     1339       -5     

Impacted Files	Coverage Δ
src/haddock/modules/topology/topoaa/__init__.py	20.22% <14.28%> (-0.23%)	⬇️
src/haddock/libs/libpdb.py	27.45% <50.00%> (ø)
src/haddock/libs/libcns.py	29.54% <100.00%> (+0.19%)	⬆️
src/haddock/libs/libutil.py	54.43% <100.00%> (+9.81%)	⬆️
tests/test_libutil.py	100.00% <100.00%> (ø)

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