[attract] module

[AnnaKravchenko]

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Checklist

• Tests added for the new code
• Documentation added for the code changes
• Does not break licensing
• Does not add any dependencies, if it does please add a thorough explanation

Summary of the Pull Request

So far [attract] module can:

• Make sure ATTRACT is installed
• Coarse-grain protein and RNA
• Fragment RNA and prepare required for ATTRACT files.

It requires strictly 1 protein and 1 RNA molecules as an input.

Installation guidlines are inhaddock3/src/haddock/modules/sampling/attract/install.md

Related Issue

#1027

Additional Info

Currently required environment variables:

$ATTRACTDIR=/trinity/login/arha/tools/attract/bin
$ATTRACTTOOLD=/trinity/login/arha/tools/attract/tools
$LIBRARY=/trinity/login/arha/tools/nalib 
$RANDSEARCH=/trinity/login/arha/data/ssRNA/randsearch

If you import these variables - [attract] may run* on tintin.
*now only create required by ATTRACT folder structure and pass two models to the next module

[AnnaKravchenko]

• Add instructions on how to install ATTRACT
• Move small functions in separate .py
• Move 'nalib check' to ‘general installation check’ with corresponding message
• Try to do all I need to do with pdb within 1 function (to not open/close file multiple time)
• Use sys.executable rather than subprocess.run
• Be more consistent with the style (particularly replace open(file,'r’) with with open(file,w) as)
• Think if it can/should be a class?
• ! Check if python3 (‘def') in attract is compatible with python3 of haddock3 (‘hdd3’)