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CSP_Rank/af2_min.py
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# 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}") |