# Copyright 2021 AlQuraishi Laboratory # # 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. import torch import numpy as np import unittest from openfold.model.triangular_attention import TriangleAttention from openfold.utils.tensor_utils import tree_map import tests.compare_utils as compare_utils from tests.config import consts if compare_utils.alphafold_is_installed(): alphafold = compare_utils.import_alphafold() import jax import haiku as hk class TestTriangularAttention(unittest.TestCase): def test_shape(self): c_z = consts.c_z c = 12 no_heads = 4 starting = True tan = TriangleAttention(c_z, c, no_heads, starting) batch_size = consts.batch_size n_res = consts.n_res x = torch.rand((batch_size, n_res, n_res, c_z)) shape_before = x.shape x = tan(x) shape_after = x.shape self.assertTrue(shape_before == shape_after) def _tri_att_compare(self, starting=False): name = ( "triangle_attention_" + ("starting" if starting else "ending") + "_node" ) def run_tri_att(pair_act, pair_mask): config = compare_utils.get_alphafold_config() c_e = config.model.embeddings_and_evoformer.evoformer tri_att = alphafold.model.modules.TriangleAttention( c_e.triangle_attention_starting_node if starting else c_e.triangle_attention_ending_node, config.model.global_config, name=name, ) act = tri_att(pair_act=pair_act, pair_mask=pair_mask) return act f = hk.transform(run_tri_att) n_res = consts.n_res pair_act = np.random.rand(n_res, n_res, consts.c_z) pair_mask = np.random.randint(low=0, high=2, size=(n_res, n_res)) # Fetch pretrained parameters (but only from one block)] params = compare_utils.fetch_alphafold_module_weights( "alphafold/alphafold_iteration/evoformer/evoformer_iteration/" + name ) params = tree_map(lambda n: n[0], params, jax.numpy.DeviceArray) out_gt = f.apply(params, None, pair_act, pair_mask).block_until_ready() out_gt = torch.as_tensor(np.array(out_gt)) model = compare_utils.get_global_pretrained_openfold() module = ( model.evoformer.blocks[0].tri_att_start if starting else model.evoformer.blocks[0].tri_att_end ) out_repro = module( torch.as_tensor(pair_act, dtype=torch.float32).cuda(), mask=torch.as_tensor(pair_mask, dtype=torch.float32).cuda(), ).cpu() self.assertTrue(torch.max(torch.abs(out_gt - out_repro) < consts.eps)) @compare_utils.skip_unless_alphafold_installed() def test_tri_att_end_compare(self): self._tri_att_compare() @compare_utils.skip_unless_alphafold_installed() def test_tri_att_start_compare(self): self._tri_att_compare(starting=True) if __name__ == "__main__": unittest.main()