Fix disulfide bond detection for split cysteines with altlocs - #94

torchref/base/coordinates/local_frame.py:17:1: UP035 `typing.Tuple` is deprecated, use `tuple` instead

torchref/base/coordinates/__init__.py:39:11: RUF022 `__all__` is not sorted help: Apply an isort-style sorting to `__all__`

torchref/base/coordinates/__init__.py:15:1: I001 Import block is un-sorted or un-formatted help: Organize imports

torchref/base/alignment/__init__.py:9:11: RUF022 `__all__` is not sorted help: Apply an isort-style sorting to `__all__`

torchref/base/alignment/__init__.py:4:1: I001 Import block is un-sorted or un-formatted help: Organize imports

torchref/base/__init__.py:140:11: RUF022 `__all__` is not sorted help: Apply an isort-style sorting to `__all__`

torchref/base/__init__.py:111:5: F401 `.alignment.rotation_matrix_euler_zyz` imported but unused; consider removing, adding to `__all__`, or using a redundant alias help: Add unused import `rotation_matrix_euler_zyz` to __all__

torchref/base/__init__.py:46:1: I001 Import block is un-sorted or un-formatted help: Organize imports

torchref/_bootstrap.py:36:38: RUF013 PEP 484 prohibits implicit `Optional` help: Convert to `T | None`

torchref/__init__.py:124:11: RUF022 `__all__` is not sorted help: Apply an isort-style sorting to `__all__`