import torch import torch.nn as nn from rf2aa.chemical import ChemicalData as ChemData class DistanceNetwork(nn.Module): def __init__(self, n_feat, p_drop=0.0): super(DistanceNetwork, self).__init__() #HACK: dimensions are hard coded here self.proj_symm = nn.Linear(n_feat, 61+37) # must match bin counts defined in kinematics.py 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[:,:,:,:61].permute(0,3,1,2) logits_omega = logits_symm[:,:,:,61:].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=0.0): super(MaskedTokenNetwork, self).__init__() #fd note this predicts probability for the mask token (which is never in ground truth) # it should be ok though(?) self.proj = nn.Linear(n_feat, ChemData().NAATOKENS) 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 PAENetwork(nn.Module): def __init__(self, n_feat, n_bin_pae=64): super(PAENetwork, self).__init__() self.proj = nn.Linear(n_feat, n_bin_pae) 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, L, 64) return logits.permute(0,3,1,2) class BinderNetwork(nn.Module): def __init__(self, n_bin_pae=64): super(BinderNetwork, self).__init__() self.classify = torch.nn.Linear(n_bin_pae, 1) self.reset_parameter() def reset_parameter(self): nn.init.zeros_(self.classify.weight) nn.init.zeros_(self.classify.bias) def forward(self, pae, same_chain): logits = pae.permute(0,2,3,1) logits_inter = torch.mean( logits[same_chain==0], dim=0 ).nan_to_num() # all zeros if single chain prob = torch.sigmoid( self.classify( logits_inter ) ) return prob aux_predictor_factory = { "c6d": DistanceNetwork, "mlm": MaskedTokenNetwork, "plddt": LDDTNetwork, "pae": PAENetwork, "binder": BinderNetwork }