lingyuzeng/analysis_pdb
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update to cwd

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hotwa
2024-01-09 10:11:43 +08:00
parent 117bbf19c5
commit 930acfe247
1 changed files with 5 additions and 9 deletions
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14
gentop.py
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@@ -5,8 +5,7 @@ import os
def generate_gmx_top_files(directory, num_cores, forcefield="amber99sb-ildn", water_model="tip3p"): 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 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 by running the 'gmx_mpi pdb2gmx' command in batch, with the working directory set to the specified directory.
are generated in the same directory as the PDB files.
Args: Args:
directory (str): Directory containing PDB files. 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: if gmxrc_path:
subprocess.run(f"source {gmxrc_path}", shell=True, executable='/bin/bash') 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 # 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 # Iterate over each PDB file and execute the GROMACS command
for pdb_file in pdb_files: 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" output_gro = f"{name}.gro"
topol_file = "topol.top" topol_file = "topol.top"
# Construct and run the command # Construct and run the command with the working directory set to 'directory'
cmd = [ cmd = [
"mpirun", "-np", str(num_cores), "mpirun", "-np", str(num_cores),
"gmx_mpi", "pdb2gmx", "gmx_mpi", "pdb2gmx",
@@ -42,9 +38,9 @@ def generate_gmx_top_files(directory, num_cores, forcefield="amber99sb-ildn", wa
"-ignh", "-ignh",
"-p", topol_file "-p", topol_file
] ]
subprocess.run(cmd, check=True, cwd=directory_path) subprocess.run(cmd, check=True, cwd=directory)
# Example usage # 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 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 generate_gmx_top_files(directory, num_cores) # Run the function