update to cwd

gentop.py

@@ -5,8 +5,7 @@ import os
 def generate_gmx_top_files(directory, num_cores, forcefield="amber99sb-ildn", water_model="tip3p"):
     """
     Generate GROMACS topology (.top) files for each PDB file in the specified directory
-    by running the 'gmx_mpi pdb2gmx' command in batch. All intermediate and output files
-    are generated in the same directory as the PDB files.
+    by running the 'gmx_mpi pdb2gmx' command in batch, with the working directory set to the specified directory.
 
     Args:
     directory (str): Directory containing PDB files.
@@ -19,11 +18,8 @@ def generate_gmx_top_files(directory, num_cores, forcefield="amber99sb-ildn", wa
     if gmxrc_path:
         subprocess.run(f"source {gmxrc_path}", shell=True, executable='/bin/bash')
 
-    # Convert directory to Path object for ease of use
-    directory_path = Path(directory)
-
     # Find all PDB files in the specified directory
-    pdb_files = directory_path.glob("*.pdb")
+    pdb_files = Path(directory).glob("*.pdb")
 
     # Iterate over each PDB file and execute the GROMACS command
     for pdb_file in pdb_files:
@@ -31,7 +27,7 @@ def generate_gmx_top_files(directory, num_cores, forcefield="amber99sb-ildn", wa
         output_gro = f"{name}.gro"
         topol_file = "topol.top"
 
-        # Construct and run the command
+        # Construct and run the command with the working directory set to 'directory'
         cmd = [
             "mpirun", "-np", str(num_cores),
             "gmx_mpi", "pdb2gmx", 
@@ -42,9 +38,9 @@ def generate_gmx_top_files(directory, num_cores, forcefield="amber99sb-ildn", wa
             "-ignh", 
             "-p", topol_file
         ]
-        subprocess.run(cmd, check=True, cwd=directory_path)
+        subprocess.run(cmd, check=True, cwd=directory)
 
 # Example usage
-directory = "./pdb_top"  # Replace with your actual directory path
+directory = "pdb_top"  # Replace with your actual directory path
 num_cores = max(os.cpu_count() - 2, 1)  # Determine the number of cores to use
 generate_gmx_top_files(directory, num_cores)  # Run the function