enerzyme.tasks.extractor.extract_submol_with_center#
- enerzyme.tasks.extractor.extract_submol_with_center(mol: Mol, center_atom_indices: List[int], radius: float = 5, dual_topology: List[Tuple[int, int, int | None]] = [], must_include_indices: List[int] = [])[source]#
Extract a fragment from a molecule with center atoms.
Params:#
- mol: Mol
The molecule to be extracted.
- center_atom_indices: List[int]
The indices of the center atoms.
- radius: float
The radius of the fragmentation.
- dual_topology: List[Tuple[int, int, Optional[int]]]
The dual topology of the molecule.