Script to plan RBFE alchemical networks

[hannahbaumann]

Input submission checklist

• created a directory for each system based on the template directory
• named and placed the directory with the following pattern: input_structures/prepared_structures/<set_name>/<system_name>

For each submitted directory:

• filled in system preparation details in the PREPARATION_DETAILS.md file
• added a PDB file with the protein named protein.pdb
• removed any cofactors from the PDB file and placed them in cofactors.sdf
• kept cystallographic waters and metals in the PDB file
• tested the PDB and, if available, cofactors.sdf file using the input validation script
• copied over the ligands SDF file to a file named ligands.sdf
• copied over the edges CSV file to a file named edges.csv

Summary of changes

Licensing agreement

• I agree to release these inputs under the combined MIT and CCBY SA 4.0 licenses of this repository

[pep8speaks]

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

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

Line 10:80: E501 line too long (88 > 79 characters)
Line 27:80: E501 line too long (82 > 79 characters)
Line 70:80: E501 line too long (88 > 79 characters)
Line 75:80: E501 line too long (85 > 79 characters)
Line 208:80: E501 line too long (85 > 79 characters)
Line 219:80: E501 line too long (80 > 79 characters)
Line 220:80: E501 line too long (80 > 79 characters)
Line 251:80: E501 line too long (81 > 79 characters)

• In the file industry_benchmarks/utils/tests/test_plan_rbfe_network.py:

Line 50:80: E501 line too long (83 > 79 characters)
Line 56:80: E501 line too long (84 > 79 characters)
Line 56:85: W291 trailing whitespace
Line 61:80: E501 line too long (82 > 79 characters)
Line 62:80: E501 line too long (82 > 79 characters)
Line 75:80: E501 line too long (97 > 79 characters)
Line 76:80: E501 line too long (82 > 79 characters)
Line 78:80: E501 line too long (85 > 79 characters)

Comment last updated at 2024-06-11 08:59:25 UTC

[IAlibay]

Needed tests:

• Serialize LigandNetwork; check it's there and that the network has the files we need it to have
  • Check the score annotations for at least one edge
  • Check the smcs have partial charges for at least one edge
• Check the type of files being created (so is there a json and how many)
• Check the settings in the JSON files (i.e. we should know that there are N json files with charge changes and N without)

[IAlibay]

Just reminding myself that I still have to look at the residue name stuff!

[IAlibay]

This is purely a "comment on python programming style" not something you need to take any action on.

Just wanted to say that folks generally expect "if not X" rather than "if X is False".

[IAlibay]

here we should be enforcing the input conformer when assigning partial charges

[hannahbaumann]

Changed this!

[IAlibay]

from today's call - should we pin the defaults?

[hannahbaumann]

Added this!

[RiesBen]

Looks Good to me!

I think for the future, we should make more use of the alchemical network planners, or develop them further, sucht they are more useful. But this is not an issue for this time. Still would like to get feedback on those. @IAlibay @hannahbaumann

[IAlibay]

Looks Good to me!

I think for the future, we should make more use of the alchemical network planners, or develop them further, sucht they are more useful. But this is not an issue for this time. Still would like to get feedback on those. @IAlibay @hannahbaumann

Yeah - this is definitely at the top of my mind as we plan out our next pieces of work.