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Add code for AlphaFold-Multimer.  
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# Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#      http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
"""Shared utils for tests."""

import dataclasses

from alphafold.model.geometry import rigid_matrix_vector
from alphafold.model.geometry import rotation_matrix
from alphafold.model.geometry import vector
import jax.numpy as jnp
import numpy as np


def assert_rotation_matrix_equal(matrix1: rotation_matrix.Rot3Array,
                                 matrix2: rotation_matrix.Rot3Array):
  for field in dataclasses.fields(rotation_matrix.Rot3Array):
    field = field.name
    np.testing.assert_array_equal(
        getattr(matrix1, field), getattr(matrix2, field))


def assert_rotation_matrix_close(mat1: rotation_matrix.Rot3Array,
                                 mat2: rotation_matrix.Rot3Array):
  np.testing.assert_array_almost_equal(mat1.to_array(), mat2.to_array(), 6)


def assert_array_equal_to_rotation_matrix(array: jnp.ndarray,
                                          matrix: rotation_matrix.Rot3Array):
  """Check that array and Matrix match."""
  np.testing.assert_array_equal(matrix.xx, array[..., 0, 0])
  np.testing.assert_array_equal(matrix.xy, array[..., 0, 1])
  np.testing.assert_array_equal(matrix.xz, array[..., 0, 2])
  np.testing.assert_array_equal(matrix.yx, array[..., 1, 0])
  np.testing.assert_array_equal(matrix.yy, array[..., 1, 1])
  np.testing.assert_array_equal(matrix.yz, array[..., 1, 2])
  np.testing.assert_array_equal(matrix.zx, array[..., 2, 0])
  np.testing.assert_array_equal(matrix.zy, array[..., 2, 1])
  np.testing.assert_array_equal(matrix.zz, array[..., 2, 2])


def assert_array_close_to_rotation_matrix(array: jnp.ndarray,
                                          matrix: rotation_matrix.Rot3Array):
  np.testing.assert_array_almost_equal(matrix.to_array(), array, 6)


def assert_vectors_equal(vec1: vector.Vec3Array, vec2: vector.Vec3Array):
  np.testing.assert_array_equal(vec1.x, vec2.x)
  np.testing.assert_array_equal(vec1.y, vec2.y)
  np.testing.assert_array_equal(vec1.z, vec2.z)


def assert_vectors_close(vec1: vector.Vec3Array, vec2: vector.Vec3Array):
  np.testing.assert_allclose(vec1.x, vec2.x, atol=1e-6, rtol=0.)
  np.testing.assert_allclose(vec1.y, vec2.y, atol=1e-6, rtol=0.)
  np.testing.assert_allclose(vec1.z, vec2.z, atol=1e-6, rtol=0.)


def assert_array_close_to_vector(array: jnp.ndarray, vec: vector.Vec3Array):
  np.testing.assert_allclose(vec.to_array(), array, atol=1e-6, rtol=0.)


def assert_array_equal_to_vector(array: jnp.ndarray, vec: vector.Vec3Array):
  np.testing.assert_array_equal(vec.to_array(), array)


def assert_rigid_equal_to_rigid(rigid1: rigid_matrix_vector.Rigid3Array,
                                rigid2: rigid_matrix_vector.Rigid3Array):
  assert_rot_trans_equal_to_rigid(rigid1.rotation, rigid1.translation, rigid2)


def assert_rigid_close_to_rigid(rigid1: rigid_matrix_vector.Rigid3Array,
                                rigid2: rigid_matrix_vector.Rigid3Array):
  assert_rot_trans_close_to_rigid(rigid1.rotation, rigid1.translation, rigid2)


def assert_rot_trans_equal_to_rigid(rot: rotation_matrix.Rot3Array,
                                    trans: vector.Vec3Array,
                                    rigid: rigid_matrix_vector.Rigid3Array):
  assert_rotation_matrix_equal(rot, rigid.rotation)
  assert_vectors_equal(trans, rigid.translation)


def assert_rot_trans_close_to_rigid(rot: rotation_matrix.Rot3Array,
                                    trans: vector.Vec3Array,
                                    rigid: rigid_matrix_vector.Rigid3Array):
  assert_rotation_matrix_close(rot, rigid.rotation)
  assert_vectors_close(trans, rigid.translation)