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