Adding ligand prep 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

[hannahbaumann]

Missing currently: Instructions on how to visualize and inspect mappings.

[hannahbaumann]

Since we decided to remove alternate binding modes/protonation states, it may not be useful any more to copy over the edges.csv file containing the Schrodinger edges. Should we remove this step from the instructions and PR template?

[IAlibay]

Since we decided to remove alternate binding modes/protonation states, it may not be useful any more to copy over the edges.csv file containing the Schrodinger edges. Should we remove this step from the instructions and PR template?

Yes please!