#!/bin/bash

# Example
# tRNA-mimicking RNA from TYM Virus
# Details:
# - Protein Data Bank (PDB) Entry: 4P5J
# - Reference: https://www.rcsb.org/structure/4P5J

# Define constants
FILENAME="example_FASTA_reader_cli.json"
JOB_NAME="example_FASTA_reader_cli_job"

# Absolute filepath to FASTA file
filepath_fasta="$(realpath "$(dirname "${BASH_SOURCE[0]}")/..")/data/rcsb_pdb_4P5J.fasta"

# Run the CLI command
af3cli config --filename "${FILENAME}" --jobname "${JOB_NAME}" \
  - rna add --fasta=True --sequence "${filepath_fasta}" \
  - debug --show  # Exclude this line to enable .json file creation
