lingyuzeng/analysis_pdb
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update error handle

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hotwa
2024-01-10 09:47:01 +08:00
parent fbb1fcf3f4
commit a937bd0334
1 changed files with 5 additions and 2 deletions
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7
gentop.py
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@@ -41,8 +41,11 @@ def generate_gmx_top_files(directory, num_cores, forcefield="amber99sb-ildn", wa
# Run the command and capture the standard error (stderr) to a log file # Run the command and capture the standard error (stderr) to a log file
log_file = parent.joinpath(f"{name}_topol.log") log_file = parent.joinpath(f"{name}_topol.log")
with open(log_file, "w") as log: try:
subprocess.run(cmd, check=True, cwd=directory, stderr=log) with open(log_file, "w") as log:
subprocess.run(cmd, check=True, cwd=directory, stderr=log)
except subprocess.CalledProcessError as e:
print(f"Error processing {pdb_file.name}: {e}")
# Example usage # Example usage
directory = "pdb_top" # Replace with your actual directory path directory = "pdb_top" # Replace with your actual directory path