# 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 config import * from alphafold.model.model import * from alphafold.utils.utils import my_tree_map from tests.alphafold.utils.utils import ( random_template_feats, random_extra_msa_feats, ) class TestModel(unittest.TestCase): def test_dry_run(self): batch_size = 2 n_seq = 5 n_templ = 7 n_res = 11 n_extra_seq = 13 c = model_config("model_1").model c.no_cycles = 2 c.evoformer_stack.no_blocks = 4 # no need to go overboard here c.evoformer_stack.blocks_per_ckpt = None # don't want to set up # deepspeed for this test model = AlphaFold(c) batch = {} tf = torch.randint( c.input_embedder.tf_dim - 1, size=(batch_size, n_res) ) batch["target_feat"] = nn.functional.one_hot( tf, c.input_embedder.tf_dim).float() batch["aatype"] = torch.argmax(batch["target_feat"], dim=-1) batch["residue_index"] = torch.arange(n_res) batch["msa_feat"] = torch.rand( (batch_size, n_seq, n_res, c.input_embedder.msa_dim) ) t_feats = random_template_feats(n_templ, n_res, batch_size=batch_size) batch.update({k:torch.tensor(v) for k, v in t_feats.items()}) extra_feats = random_extra_msa_feats( n_extra_seq, n_res, batch_size=batch_size ) batch.update({k:torch.tensor(v) for k, v in extra_feats.items()}) batch["msa_mask"] = torch.randint( low=0, high=2, size=(batch_size, n_seq, n_res) ) batch["seq_mask"] = torch.randint( low=0, high=2, size=(batch_size, n_res) ) add_recycling_dims = lambda t: ( t.unsqueeze(-1).expand(*t.shape, c.no_cycles) ) batch = my_tree_map(add_recycling_dims, batch, torch.Tensor) with torch.no_grad(): out = model(batch) if __name__ == "__main__": unittest.main()