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# Copyright 2021 AlQuraishi Laboratory
# 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.
from typing import Optional
import torch
import torch.nn as nn
from dockformer.model.primitives import Linear, LayerNorm
class PairTransition(nn.Module):
"""
Implements Algorithm 15.
"""
def __init__(self, c_z, n):
"""
Args:
c_z:
Pair transition channel dimension
n:
Factor by which c_z is multiplied to obtain hidden channel
dimension
"""
super(PairTransition, self).__init__()
self.c_z = c_z
self.n = n
self.layer_norm = LayerNorm(self.c_z)
self.linear_1 = Linear(self.c_z, self.n * self.c_z, init="relu")
self.relu = nn.ReLU()
self.linear_2 = Linear(self.n * self.c_z, c_z, init="final")
def _transition(self, z, mask):
# [*, N_res, N_res, C_z]
z = self.layer_norm(z)
# [*, N_res, N_res, C_hidden]
z = self.linear_1(z)
z = self.relu(z)
# [*, N_res, N_res, C_z]
z = self.linear_2(z)
z = z * mask
return z
def forward(self,
z: torch.Tensor,
mask: Optional[torch.Tensor] = None,
) -> torch.Tensor:
"""
Args:
z:
[*, N_res, N_res, C_z] pair embedding
Returns:
[*, N_res, N_res, C_z] pair embedding update
"""
# DISCREPANCY: DeepMind forgets to apply the mask in this module.
if mask is None:
mask = z.new_ones(z.shape[:-1])
# [*, N_res, N_res, 1]
mask = mask.unsqueeze(-1)
z = self._transition(z=z, mask=mask)
return z
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