model/AuxiliaryPredictor.py

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, p_drop=0.1):
        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)