AF3 Rigid类的from_3_points方法解读
AlphaFold3 rigid_utils 模块Rigid类的 from_3_points 方法主要用来从三个点构建刚体变换 (Rigid transformation)，焦点头脑是 Gram-Schmidt 正交化来生成一个局部坐标系。输入为氨基酸残基的主链原子(N, CA, C）的坐标，返回的 Rigid 实例可以把该氨基酸残基原子的全局坐标转换为局部坐标。源代码：
@staticmethod
def from_3_points(
p_neg_x_axis: torch.Tensor,
origin: torch.Tensor,
p_xy_plane: torch.Tensor,
eps: float = 1e-8
) -> Rigid:
"""
Implements algorithm 21. Constructs transformations from sets of 3
points using the Gram-Schmidt algorithm.
Args:
p_neg_x_axis: [*, 3] coordinates
origin: [*, 3] coordinates used as frame origins
p_xy_plane: [*, 3] coordinates
eps: Small epsilon value
Returns:
A transformation object of shape [*]
"""
p_neg_x_axis = torch.unbind(p_neg_x_axis, dim=-1)
origin = torch.unbind(origin, dim=-1)
p_xy_plane = torch.unbind(p_xy_plane, dim=-1)
e0 =
e1 =
denom = torch.sqrt(sum((c * c for c in e0)) + eps)
e0 =
dot = sum((c1 * c2 for c1, c2 in zip(e0, e1)))
e1 =
denom = t
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