mindsponge.common.make_transform_from_reference
- mindsponge.common.make_transform_from_reference(point_a, point_b, point_c)[source]
Using GramSchmidt process to construct rotation and translation from given points.
Calculate the rotation matrix and translation meets
point_b is the original point.
point_c is on the x_axis.
the plane a-b-c is on the x-y plane.
\[\begin{split}\begin{split} &\vec v_1 = \vec x_3 - \vec x_2 \\ &\vec v_2 = \vec x_1 - \vec x_2 \\ &\vec e_1 = \vec v_1 / ||\vec v_1|| \\ &\vec u_2 = \vec v_2 - \vec e_1(\vec e_1^T\vec v_2) \\ &\vec e_2 = \vec u_2 / ||\vec u_2|| \\ &\vec e_3 = \vec e_1 \times \vec e_2 \\ &rotation = (\vec e_1, \vec e_2, \vec e_3) \\ &translation = (\vec x_2) \\ \end{split}\end{split}\]- Parameters
point_a (float, tensor) -> (tensor) – Spatial location information of atom ‘N’, shape is \([..., N_{res}, 3]\) .
point_b (float, tensor) -> (tensor) – Spatial location information of atom ‘CA’, shape is \([..., N_{res}, 3]\) .
point_c (float, tensor) -> (tensor) – Spatial location information of atom ‘C’, shape is \([..., N_{res}, 3]\) .
- Returns
Tuple, rots \((xx, xy, xz, yx, yy, yz, zx, zy, zz)\) , the shape of every element is \((..., N_{res})\) .
Tuple, trans \((x, y, z)\) , the shape of every element is \((..., N_{res})\) .
- Supported Platforms:
Ascend
GPU
Examples
>>> import numpy as np >>> import mindspore as ms >>> from mindspore import Tensor >>> from mindsponge.common.geometry import make_transform_from_reference >>> input_0 = Tensor(np.ones((4, 256, 3)), ms.float32) >>> input_1 = Tensor(np.ones((4, 256, 3)), ms.float32) >>> input_2 = Tensor(np.ones((4, 256, 3)), ms.float32) >>> rots, trans = make_transform_from_reference(input_0, input_1, input_2) >>> print(len(rots), rots[0].shape, len(trans), trans[0].shape) 9, (4, 256), 3, (4, 256)