"""Protein structure analysis tools using BioPython."""
from typing import Any
from Bio.PDB import PDBList, PDBParser
def fetch_pdb_structure(pdb_id: str, file_format: str = "pdb") -> dict[str, Any]:
"""
Fetch a protein structure from the PDB database.
Args:
pdb_id: PDB identifier (e.g., '1ABC')
file_format: File format - 'pdb' or 'cif' (default: 'pdb')
Returns:
Dictionary containing structure information and file location
"""
try:
pdb_id = pdb_id.upper()
pdbl = PDBList()
file_path = pdbl.retrieve_pdb_file(
pdb_id, pdir=".", file_format=file_format, overwrite=True
)
return {
"success": True,
"pdb_id": pdb_id,
"format": file_format,
"file_path": file_path,
"message": f"Structure {pdb_id} downloaded successfully",
}
except Exception as e:
return {"success": False, "error": str(e), "pdb_id": pdb_id}
def calculate_structure_stats(pdb_file: str) -> dict[str, Any]:
"""
Calculate statistics for a PDB structure file.
Args:
pdb_file: Path to PDB file
Returns:
Dictionary containing structure statistics
"""
try:
parser = PDBParser(QUIET=True)
structure = parser.get_structure("structure", pdb_file)
num_models = len(structure)
num_chains = sum(len(model) for model in structure)
num_residues = sum(len(chain) for model in structure for chain in model)
num_atoms = sum(len(residue) for model in structure for chain in model for residue in chain)
chain_info = []
for model in structure:
for chain in model:
chain_id = chain.get_id()
chain_length = len(chain)
chain_info.append({"chain_id": chain_id, "num_residues": chain_length})
return {
"success": True,
"file": pdb_file,
"num_models": num_models,
"num_chains": num_chains,
"num_residues": num_residues,
"num_atoms": num_atoms,
"chains": chain_info,
}
except Exception as e:
return {"success": False, "error": str(e), "file": pdb_file}
def find_active_site(
pdb_file: str, residue_numbers: list[int], chain_id: str = "A"
) -> dict[str, Any]:
"""
Extract information about specific residues (e.g., active site).
Args:
pdb_file: Path to PDB file
residue_numbers: List of residue numbers to analyze
chain_id: Chain identifier (default: 'A')
Returns:
Dictionary containing active site residue information
"""
try:
parser = PDBParser(QUIET=True)
structure = parser.get_structure("structure", pdb_file)
model = structure[0]
chain = model[chain_id]
active_site_info = []
for res_num in residue_numbers:
try:
residue = chain[res_num]
res_name = residue.get_resname()
atoms = [atom.get_name() for atom in residue]
active_site_info.append(
{
"residue_number": res_num,
"residue_name": res_name,
"num_atoms": len(atoms),
"atoms": atoms,
}
)
except KeyError:
active_site_info.append(
{
"residue_number": res_num,
"error": f"Residue {res_num} not found in chain {chain_id}",
}
)
return {
"success": True,
"file": pdb_file,
"chain_id": chain_id,
"num_residues_analyzed": len(residue_numbers),
"active_site": active_site_info,
}
except Exception as e:
return {"success": False, "error": str(e), "file": pdb_file, "chain_id": chain_id}
