File size: 1,028 Bytes
c289d87 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 | from __future__ import annotations
from pathlib import Path
from typing import Any, Dict
from Bio.PDB import MMCIFParser, PDBParser
def load_structure(path: str | Path, structure_id: str = "target") -> Any:
"""Load PDB or mmCIF structure object using Biopython."""
source = Path(path)
suffix = source.suffix.lower()
if suffix in {".pdb", ".ent"}:
parser = PDBParser(QUIET=True)
return parser.get_structure(structure_id, str(source))
if suffix in {".cif", ".mmcif"}:
parser = MMCIFParser(QUIET=True)
return parser.get_structure(structure_id, str(source))
raise ValueError(f"Unsupported structure extension: {source}")
def summarize_structure(path: str | Path) -> Dict[str, int]:
structure = load_structure(path)
residues = [r for r in structure.get_residues() if r.id[0] == " "]
atoms = list(structure.get_atoms())
chains = list(structure.get_chains())
return {"residue_count": len(residues), "atom_count": len(atoms), "chain_count": len(chains)}
|