process_residue_db.py Command Help

Command: $SCHRODINGER/run process_residue_db.py

usage: process_residue_db.py [-h] [--skip-minimization] [--allow-non-alpha-aa]
                             [--iupac-chirality]
                             residue_db

This script processes a residue database to extract only amino acids compatible
with mmshare workflows. This includes:

    - creating and assigning unique residue names to each residue
    - validating that the residue is an alpha amino acid
    - standardizing the structure
    - generating 3D coordinates
    - applying natural analog properties
    - validating that the residue is usable in mutation

Output includes a processed residue database file containing only successfully
processed residues, as well as CSV files logging the outcomes of processing for
both successful and failed residues, including failure reasons for any failed
residues.

positional arguments:
  residue_db            Path to residue database

options:
  -h, --help            show this help message and exit
  --skip-minimization   Debug option to skip minimization step. Not recommended for database generation
  --allow-non-alpha-aa  Allow non-alpha amino acids to be processed.
  --iupac-chirality     Use IUPAC names to determine chirality when the chirality is otherwise undefined. This is a last resort option mainly intended for the enamine database.