Protein check script

[IAlibay]

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
• [ ] did not re-protonate the residues, but left protonation state of the protein unchanged
• [ ] 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/maint/__init__.py:

Line 1:1: W391 blank line at end of file

• In the file industry_benchmarks/utils/maint/check_protein_prep.py:

Line 69:80: E501 line too long (109 > 79 characters) Line 71:80: E501 line too long (113 > 79 characters) Line 73:80: E501 line too long (95 > 79 characters)

Comment last updated at 2024-07-12 14:05:28 UTC