Duck tape broken networks

[RiesBen]

This adds a script for taping disconnected networks together.

Functionality:

1. The script will read in the input alchemical network that was created to run all simulations (default: './alchemicalNetwork/alchemical_network.json') and the resulting result .json files (default: './results*/*json'). From this information the script will detect missing nodes and network disconnectivities steming from edge simulation failure. (It will expect at least one solvent and one complex edge being finished in order to accept an edge as successful.)

2. Next the script will use Konnektor to tape the disconnected network parts and missing nodes together to a fixed network. for each compartment, three edges will be used by default to connect the network. The approach here works in a greedy fashion and starts with the largest compartment and adds the next largest with 3 edges to it. in the next iteration the next largest compartment is added to the already merged network with 3 edges and so on.

3. Afterwards a new alchemicalNetwork containing only the connnecting edges will be written out (default: './tapesForAlchemicalNetwork'). This can be used to add misisng network connections to your already precalculated result folders. After simulating the additional edges, from the new alchemical network folder, you will be able to simply use the same analysis approach to retrieve the now hopefully connected network information.

ToDos:

• Read Input and construct:
  • read result jsons
    • check if both transformations run, otherwise no edge
  • read in input alchemical network
  • get the single disconnected networks
• Taping
  • tape disconnected networks together
  • filter only new network edges
• Write out
  • generate new transformations
  • write out new alchemical network
• Write CLI
• Test script

[pep8speaks]

Hello @RiesBen! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

• In the file industry_benchmarks/utils/tape_networks.py:

Line 16:80: E501 line too long (88 > 79 characters)
Line 114:1: W293 blank line contains whitespace
Line 232:5: E731 do not assign a lambda expression, use a def
Line 244:9: E722 do not use bare 'except'
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Line 284:46: W291 trailing whitespace
Line 300:80: E501 line too long (81 > 79 characters)
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Line 368:80: E501 line too long (82 > 79 characters)
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Line 469:1: W293 blank line contains whitespace
Line 472:80: E501 line too long (91 > 79 characters)
Line 473:80: E501 line too long (85 > 79 characters)
Line 474:1: W293 blank line contains whitespace
Line 476:80: E501 line too long (85 > 79 characters)
Line 477:1: W293 blank line contains whitespace
Line 481:80: E501 line too long (95 > 79 characters)
Line 482:1: W293 blank line contains whitespace
Line 484:80: E501 line too long (87 > 79 characters)
Line 488:1: W293 blank line contains whitespace
Line 492:78: W291 trailing whitespace
Line 496:1: W293 blank line contains whitespace
Line 500:80: E501 line too long (92 > 79 characters)
Line 501:1: W293 blank line contains whitespace
Line 503:80: E501 line too long (87 > 79 characters)
Line 506:1: W293 blank line contains whitespace
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Line 514:80: E501 line too long (84 > 79 characters)
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Line 531:80: E501 line too long (87 > 79 characters)
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Line 561:80: E501 line too long (80 > 79 characters)

Comment last updated at 2024-09-17 13:26:30 UTC

[IAlibay]

Closing as supplemented.