# 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 functools import partialmethod from typing import Optional from abc import ABC, abstractmethod import torch import torch.nn as nn from dockformer.model.primitives import Linear, LayerNorm from dockformer.utils.precision_utils import is_fp16_enabled from dockformer.utils.tensor_utils import permute_final_dims class BaseTriangleMultiplicativeUpdate(nn.Module, ABC): """ Implements Algorithms 11 and 12. """ @abstractmethod def __init__(self, c_z, c_hidden, _outgoing): """ Args: c_z: Input channel dimension c: Hidden channel dimension """ super(BaseTriangleMultiplicativeUpdate, self).__init__() self.c_z = c_z self.c_hidden = c_hidden self._outgoing = _outgoing self.linear_g = Linear(self.c_z, self.c_z, init="gating") self.linear_z = Linear(self.c_hidden, self.c_z, init="final") self.layer_norm_in = LayerNorm(self.c_z) self.layer_norm_out = LayerNorm(self.c_hidden) self.sigmoid = nn.Sigmoid() def _combine_projections(self, a: torch.Tensor, b: torch.Tensor, ) -> torch.Tensor: if(self._outgoing): a = permute_final_dims(a, (2, 0, 1)) b = permute_final_dims(b, (2, 1, 0)) else: a = permute_final_dims(a, (2, 1, 0)) b = permute_final_dims(b, (2, 0, 1)) p = torch.matmul(a, b) return permute_final_dims(p, (1, 2, 0)) @abstractmethod def forward(self, z: torch.Tensor, mask: Optional[torch.Tensor] = None, inplace_safe: bool = False, _add_with_inplace: bool = False ) -> torch.Tensor: """ Args: x: [*, N_res, N_res, C_z] input tensor mask: [*, N_res, N_res] input mask Returns: [*, N_res, N_res, C_z] output tensor """ pass class TriangleMultiplicativeUpdate(BaseTriangleMultiplicativeUpdate): """ Implements Algorithms 11 and 12. """ def __init__(self, c_z, c_hidden, _outgoing=True): """ Args: c_z: Input channel dimension c: Hidden channel dimension """ super(TriangleMultiplicativeUpdate, self).__init__(c_z=c_z, c_hidden=c_hidden, _outgoing=_outgoing) self.linear_a_p = Linear(self.c_z, self.c_hidden) self.linear_a_g = Linear(self.c_z, self.c_hidden, init="gating") self.linear_b_p = Linear(self.c_z, self.c_hidden) self.linear_b_g = Linear(self.c_z, self.c_hidden, init="gating") def forward(self, z: torch.Tensor, mask: Optional[torch.Tensor] = None, inplace_safe: bool = False, _add_with_inplace: bool = False, ) -> torch.Tensor: """ Args: x: [*, N_res, N_res, C_z] input tensor mask: [*, N_res, N_res] input mask Returns: [*, N_res, N_res, C_z] output tensor """ if mask is None: mask = z.new_ones(z.shape[:-1]) mask = mask.unsqueeze(-1) z = self.layer_norm_in(z) a = mask a = a * self.sigmoid(self.linear_a_g(z)) a = a * self.linear_a_p(z) b = mask b = b * self.sigmoid(self.linear_b_g(z)) b = b * self.linear_b_p(z) # Prevents overflow of torch.matmul in combine projections in # reduced-precision modes a_std = a.std() b_std = b.std() if(is_fp16_enabled() and a_std != 0. and b_std != 0.): a = a / a.std() b = b / b.std() if(is_fp16_enabled()): with torch.cuda.amp.autocast(enabled=False): x = self._combine_projections(a.float(), b.float()) else: x = self._combine_projections(a, b) del a, b x = self.layer_norm_out(x) x = self.linear_z(x) g = self.sigmoid(self.linear_g(z)) x = x * g return x class TriangleMultiplicationOutgoing(TriangleMultiplicativeUpdate): """ Implements Algorithm 11. """ __init__ = partialmethod(TriangleMultiplicativeUpdate.__init__, _outgoing=True) class TriangleMultiplicationIncoming(TriangleMultiplicativeUpdate): """ Implements Algorithm 12. """ __init__ = partialmethod(TriangleMultiplicativeUpdate.__init__, _outgoing=False)