#!/bin/bash

# Example
# Human SIRT2 Histone Deacetylase
# Details:
# - Protein Data Bank (PDB) Entry: 1J8F
# - Reference: https://www.rcsb.org/structure/1J8F
# - Simplified demonstration uses one monomer with one associated zinc ion for clarity.

# Define constants
FILENAME="example_protein_ccd_cli.json"
JOB_NAME="example_protein_ccd_cli_job"

# Protein sequence for SIRT2 monomer fetched from the FASTA file
PROTEIN_SEQUENCE="\
GEADMDFLRNLFSQTLSLGSQKERLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRSPSTGLYDNLEKYH\
LPYPEAIFEISYFKKHPEPFFALAKELYPGQFKPTICHYFMRLLKDKGLLLRCYTQNIDTLERIAGLEQEDLVEAHGT\
FYTSHCVSASCRHEYPLSWMKEKIFSEVTPKCEDCQSLVKPDIVFFGESLPARFFSCMQSDFLKVDLLLVMGTSLQVQ\
PFASLISKAPLSTPRLLINKEKAGQSDPFLGMIMGLGGGMDFDSKKAYRDVAWLGECDQGCLALAELLGWKKELEDLV\
RREHASIDAQS\
"

# Zinc ion CCD representation
ZINC_ION_CCD="ZN"

# Run the CLI command
af3cli config --filename "${FILENAME}" --jobname "${JOB_NAME}" \
  - protein add --sequence "${PROTEIN_SEQUENCE}" \
  - ligand add --ccd "${ZINC_ION_CCD}" \
  - debug --show  # Exclude this line to enable .json file creation
