Initial commit: RoseTTAFold-All-Atom configured for Wes with Harbor images and s3:// paths

rf2aa/SE3Transformer/tests/test_equivariance.py

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+# Copyright (c) 2021, NVIDIA CORPORATION & AFFILIATES. All rights reserved.
+#
+# Permission is hereby granted, free of charge, to any person obtaining a
+# copy of this software and associated documentation files (the "Software"),
+# to deal in the Software without restriction, including without limitation
+# the rights to use, copy, modify, merge, publish, distribute, sublicense,
+# and/or sell copies of the Software, and to permit persons to whom the
+# Software is furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+# DEALINGS IN THE SOFTWARE.
+#
+# SPDX-FileCopyrightText: Copyright (c) 2021 NVIDIA CORPORATION & AFFILIATES
+# SPDX-License-Identifier: MIT
+
+import torch
+import pytest
+
+from rf2aa.SE3Transformer.se3_transformer.model import SE3Transformer
+from rf2aa.SE3Transformer.se3_transformer.model.fiber import Fiber
+from tests.utils import get_random_graph, assign_relative_pos, get_max_diff, rot
+
+# Tolerances for equivariance error abs( f(x) @ R  -  f(x @ R) )
+TOL = 1e-3
+CHANNELS, NODES = 32, 512
+
+
+def _get_outputs(model, R):
+    feats0 = torch.randn(NODES, CHANNELS, 1)
+    feats1 = torch.randn(NODES, CHANNELS, 3)
+
+    coords = torch.randn(NODES, 3)
+    graph = get_random_graph(NODES)
+    if torch.cuda.is_available():
+        feats0 = feats0.cuda()
+        feats1 = feats1.cuda()
+        R = R.cuda()
+        coords = coords.cuda()
+        graph = graph.to('cuda')
+        model.cuda()
+
+    graph1 = assign_relative_pos(graph, coords)
+    out1 = model(graph1, {'0': feats0, '1': feats1}, {})
+    graph2 = assign_relative_pos(graph, coords @ R)
+    out2 = model(graph2, {'0': feats0, '1': feats1 @ R}, {})
+
+    return out1, out2
+
+
+def _get_model(**kwargs):
+    return SE3Transformer(
+        num_layers=4,
+        fiber_in=Fiber.create(2, CHANNELS),
+        fiber_hidden=Fiber.create(3, CHANNELS),
+        fiber_out=Fiber.create(2, CHANNELS),
+        fiber_edge=Fiber({}),
+        num_heads=8,
+        channels_div=2,
+        **kwargs
+    )
+
+@pytest.mark.skip
+def test_equivariance():
+    model = _get_model()
+    R = rot(*torch.rand(3))
+    if torch.cuda.is_available():
+        R = R.cuda()
+    out1, out2 = _get_outputs(model, R)
+
+    assert torch.allclose(out2['0'], out1['0'], atol=TOL), \
+        f'type-0 features should be invariant {get_max_diff(out1["0"], out2["0"])}'
+    assert torch.allclose(out2['1'], (out1['1'] @ R), atol=TOL), \
+        f'type-1 features should be equivariant {get_max_diff(out1["1"] @ R, out2["1"])}'
+
+@pytest.mark.skip
+def test_equivariance_pooled():
+    model = _get_model(pooling='avg', return_type=1)
+    R = rot(*torch.rand(3))
+    if torch.cuda.is_available():
+        R = R.cuda()
+    out1, out2 = _get_outputs(model, R)
+
+    assert torch.allclose(out2, (out1 @ R), atol=TOL), \
+        f'type-1 features should be equivariant {get_max_diff(out1 @ R, out2)}'
+
+@pytest.mark.skip
+def test_invariance_pooled():
+    model = _get_model(pooling='avg', return_type=0)
+    R = rot(*torch.rand(3))
+    if torch.cuda.is_available():
+        R = R.cuda()
+    out1, out2 = _get_outputs(model, R)
+
+    assert torch.allclose(out2, out1, atol=TOL), \
+        f'type-0 features should be invariant {get_max_diff(out1, out2)}'

rf2aa/SE3Transformer/tests/utils.py

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+# Copyright (c) 2021, NVIDIA CORPORATION & AFFILIATES. All rights reserved.
+#
+# Permission is hereby granted, free of charge, to any person obtaining a
+# copy of this software and associated documentation files (the "Software"),
+# to deal in the Software without restriction, including without limitation
+# the rights to use, copy, modify, merge, publish, distribute, sublicense,
+# and/or sell copies of the Software, and to permit persons to whom the
+# Software is furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+# DEALINGS IN THE SOFTWARE.
+#
+# SPDX-FileCopyrightText: Copyright (c) 2021 NVIDIA CORPORATION & AFFILIATES
+# SPDX-License-Identifier: MIT
+
+import dgl
+import torch
+
+
+def get_random_graph(N, num_edges_factor=18):
+    graph = dgl.transforms.remove_self_loop(dgl.rand_graph(N, N * num_edges_factor))
+    return graph
+
+
+def assign_relative_pos(graph, coords):
+    src, dst = graph.edges()
+    graph.edata['rel_pos'] = coords[src] - coords[dst]
+    return graph
+
+
+def get_max_diff(a, b):
+    return (a - b).abs().max().item()
+
+
+def rot_z(gamma):
+    return torch.tensor([
+        [torch.cos(gamma), -torch.sin(gamma), 0],
+        [torch.sin(gamma), torch.cos(gamma), 0],
+        [0, 0, 1]
+    ], dtype=gamma.dtype)
+
+
+def rot_y(beta):
+    return torch.tensor([
+        [torch.cos(beta), 0, torch.sin(beta)],
+        [0, 1, 0],
+        [-torch.sin(beta), 0, torch.cos(beta)]
+    ], dtype=beta.dtype)
+
+
+def rot(alpha, beta, gamma):
+    return rot_z(alpha) @ rot_y(beta) @ rot_z(gamma)