test_dssp_parsing.py

from Bio import PDB
import subprocess
import os
from CSpred.spartap_features import PDB_SPARTAp_DataReader

def test_dssp_parsing():

    # Write test PDB file
    test_pdb = "test.pdb"

    try:
        # 2. Run DSSP
        print("Running DSSP...")
        subprocess.run(["mkdssp", test_pdb], capture_output=True, check=True)
        
        # 3. Use PDB_SPARTAp_DataReader to parse the file
        print("Parsing with CSpred...")
        reader = PDB_SPARTAp_DataReader()
        df = reader.df_from_file_3res(test_pdb)
        
        # 4. Print results
        print("\nResults:")
        print(f"DataFrame shape: {df.shape}")
        print("\nFirst few rows:")
        print(df.head())
        
    except Exception as e:
        print(f"Error: {str(e)}")
    
    finally:
        if os.path.exists(test_pdb + ".dssp"):
            os.remove(test_pdb + ".dssp")

if __name__ == "__main__":
    test_dssp_parsing()