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[attract] module #1034

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AnnaKravchenko
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@AnnaKravchenko AnnaKravchenko commented Sep 18, 2024 •
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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

For now:

  • created modules/sampling/attract/ with default.yaml

  • started to work on init.py

  • fixed minor typos in unrelated files

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

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

__init__.py of [attract] can 1/ get input pdbs 2/ convert them to att…
2d6164b 
…ract CG 3/ add required by attract files to working directory
@AnnaKravchenko AnnaKravchenko self-assigned this Sep 18, 2024
@AnnaKravchenko AnnaKravchenko linked an issue Sep 18, 2024 that may be closed by this pull request
[attract] as a sampling module #1027
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@AnnaKravchenko AnnaKravchenko added enhancement Enhancing an existing feature of adding a new one feature New feature request labels Sep 18, 2024
@rvhonorato rvhonorato added m|attract and removed enhancement Enhancing an existing feature of adding a new one labels Sep 18, 2024
@AnnaKravchenko
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AnnaKravchenko commented Sep 18, 2024 •
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  • 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’)

@rvhonorato rvhonorato changed the base branch from main to attract-module September 20, 2024 12:26
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feature New feature request m|attract
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attract
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[attract] as a sampling module
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@AnnaKravchenko @rvhonorato