import torch import torch.nn as nn class DistanceNetwork(nn.Module): def __init__(self, n_feat, p_drop=0.1): super(DistanceNetwork, self).__init__() # self.proj_symm = nn.Linear(n_feat, 37*2) self.proj_asymm = nn.Linear(n_feat, 37+19) self.reset_parameter() def reset_parameter(self): # initialize linear layer for final logit prediction nn.init.zeros_(self.proj_symm.weight) nn.init.zeros_(self.proj_asymm.weight) nn.init.zeros_(self.proj_symm.bias) nn.init.zeros_(self.proj_asymm.bias) def forward(self, x): # input: pair info (B, L, L, C) # predict theta, phi (non-symmetric) logits_asymm = self.proj_asymm(x) logits_theta = logits_asymm[:,:,:,:37].permute(0,3,1,2) logits_phi = logits_asymm[:,:,:,37:].permute(0,3,1,2) # predict dist, omega logits_symm = self.proj_symm(x) logits_symm = logits_symm + logits_symm.permute(0,2,1,3) logits_dist = logits_symm[:,:,:,:37].permute(0,3,1,2) logits_omega = logits_symm[:,:,:,37:].permute(0,3,1,2) return logits_dist, logits_omega, logits_theta, logits_phi class MaskedTokenNetwork(nn.Module): def __init__(self, n_feat): super(MaskedTokenNetwork, self).__init__() self.proj = nn.Linear(n_feat, 21) self.reset_parameter() def reset_parameter(self): nn.init.zeros_(self.proj.weight) nn.init.zeros_(self.proj.bias) def forward(self, x): B, N, L = x.shape[:3] logits = self.proj(x).permute(0,3,1,2).reshape(B, -1, N*L) return logits class LDDTNetwork(nn.Module): def __init__(self, n_feat, n_bin_lddt=50): super(LDDTNetwork, self).__init__() self.proj = nn.Linear(n_feat, n_bin_lddt) self.reset_parameter() def reset_parameter(self): nn.init.zeros_(self.proj.weight) nn.init.zeros_(self.proj.bias) def forward(self, x): logits = self.proj(x) # (B, L, 50) return logits.permute(0,2,1) class ExpResolvedNetwork(nn.Module): def __init__(self, d_msa, d_state, p_drop=0.1): super(ExpResolvedNetwork, self).__init__() self.norm_msa = nn.LayerNorm(d_msa) self.norm_state = nn.LayerNorm(d_state) self.proj = nn.Linear(d_msa+d_state, 1) self.reset_parameter() def reset_parameter(self): nn.init.zeros_(self.proj.weight) nn.init.zeros_(self.proj.bias) def forward(self, seq, state): B, L = seq.shape[:2] seq = self.norm_msa(seq) state = self.norm_state(state) feat = torch.cat((seq, state), dim=-1) logits = self.proj(feat) return logits.reshape(B, L)