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"""Module for simple AGGRESCAN3D method."""
from __future__ import annotations
import pathlib
from aggrescan import analysis
from aggrescan.aggrescan_3d import Residue
def run_aggrescan3d(
structure_path: str,
distance: float = 10,
) -> list[Residue]:
"""Run AGGRESCAN3D on the input structure.
Args:
structure_path: Path to pdb structure.
distance: Radius around the central atom within which atoms are included in the
aggrescan3d score calculation.
Returns:
List of aggrescan3D `Residue` objects.
`Residue` objects have the following attributes:
- chain: Chain ID.
- rsa: Relative surface area. Value in range [0, 100].
- score: Aggrescan3D score.
- resi: Residue index.
- resn: One letter residue type.
- coords: Tuple of (x, y, z) coordinates.
"""
struct_path = pathlib.Path(structure_path)
# Check if structure exists. If it doesn't, it only gets caught by freeSASA and it
# throws a confusing error message.
if not struct_path.exists():
raise RuntimeError(f"Structure '{structure_path}' does not exist.")
config = {
"distance": distance,
"naccess": False,
"ph": False,
}
analysis._run_free_sasa(target=structure_path, agg=".")
residues: list[Residue] = analysis._run_aggrescan(
target=structure_path, working_dir=".", config=config,
)
return residues
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