Update run instructions

[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

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

[pep8speaks]

Hello @hannahbaumann! Thanks for opening 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)