fix up run script to match quickrun better

[IAlibay]

Fixes #72

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 and removed any duplicate binding modes or protonation states, keeping the more favorable state

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 @IAlibay! 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 30:80: E501 line too long (156 > 79 characters) Line 39:80: E501 line too long (88 > 79 characters) Line 190:80: E501 line too long (84 > 79 characters) Line 192:1: W293 blank line contains whitespace Line 216:80: E501 line too long (84 > 79 characters)

Comment last updated at 2024-06-13 19:52:42 UTC

[mikemhenry]

Oh and one more thing, we need to have some " around a few of those variables if there is a chance that spaces could end up in the file names, but if that can't happen we should be good!