af2_min.py

# af2_min.py

import os
import sys
import subprocess
from paths import PDB_FILES
from os.path import exists

def activate_conda_env(env_name):
    conda_init = "source /home/tiburon/anaconda3/etc/profile.d/conda.sh"
    activate_command = f"conda activate {env_name} && python -c \"print('Environment activated')\""
    full_command = f"{conda_init} && {activate_command}"
    
    try:
        result = subprocess.run(full_command, shell=True, check=True, executable="/bin/bash" if sys.platform != "win32" else None)
        print(f"Conda environment '{env_name}' activated successfully.")
    except subprocess.CalledProcessError as e:
        print(f"Failed to activate conda environment '{env_name}': {e}")

def deactivate_conda_env():
    conda_init = "source /home/tiburon/anaconda3/etc/profile.d/conda.sh"
    deactivate_command = "conda deactivate && python -c \"print('Environment deactivated')\""
    full_command = f"{conda_init} && {deactivate_command}"
    
    try:
        result = subprocess.run(full_command, shell=True, check=True, executable="/bin/bash" if sys.platform != "win32" else None)
        print("Conda environment deactivated successfully.")
    except subprocess.CalledProcessError as e:
        print(f"Failed to deactivate conda environment: {e}")

# This is the first step in post-processing.
if len(sys.argv) < 2:
    print("Usage: af2_min.py <pdb_id>")
    raise

pdb = sys.argv[1].strip().lower()

if exists(f"{PDB_FILES}{pdb}"):
    

    activate_conda_env('OpenMM')

    af2_min_command = f'python3 OpenMM_mini.py -af2 -outD {PDB_FILES}{pdb}_af2_min {PDB_FILES}{pdb}/*.pdb' 
    
    try:
        result = subprocess.run(af2_min_command, shell=True, check=True, executable="/bin/bash" if sys.platform != "win32" else None)
    except subprocess.CalledProcessError as e:
        print(f"Failed to run OpenMM_mini.py: {e}")

    deactivate_conda_env()
else:
    print(f"Need to download structures from source, put them in {PDB_FILES}{pdb}")