import torch import torch.nn as nn from src.utils.license_register import register_license from src.model.modules.primitives import Linear from src.utils.data.constants import BOND_TYPE from src.api.model_interface import ( PairFormerOutput, PairwiseOutput, ) @register_license('bytedance2024') class DistogramHead(nn.Module): """Implements Algorithm 1 [Line17] in AF3 Computes a distogram probability distribution. For use in computation of distogram loss, subsection 1.9.8 (AF2) """ def __init__(self, c_z: int = 128, no_bins: int = 64) -> None: """ Args: c_z (int, optional): hidden dim [for pair embedding]. Defaults to 128. no_bins (int, optional): Number of distogram bins. Defaults to 64. """ super(DistogramHead, self).__init__() self.c_z = c_z self.no_bins = no_bins self.linear = Linear( in_features=self.c_z, out_features=self.no_bins, initializer="zeros" ) def forward(self, z: torch.Tensor) -> torch.Tensor: # [*, N, N, C_z] """ Args: z (torch.Tensor): pairformer output [*, N_token, N_token, C_z] Returns: torch.Tensor: distogram probability distribution [*, N_token, N_token, no_bins] """ # [*, N, N, no_bins] logits = self.linear(z) logits = logits + logits.transpose(-2, -3) return logits @register_license('odesign2025') class BondTypeHead(nn.Module): """Implements a bond type classifier head. Computes bond type probability distribution. """ def __init__(self, c_z: int = 1, c_hidden: int = 128, no_bond_types: int = len(BOND_TYPE)) -> None: """ Args: c_in (int, optional): hidden dim [for pair embedding]. Defaults to 1. c_hidden (int, optional): hidden dim. Defaults to 128. no_bond_types (int, optional): Number of bond types. Defaults to len(BOND_TYPE). """ super(BondTypeHead, self).__init__() self.c_in = c_z self.c_hidden = c_hidden self.no_bond_types = no_bond_types self.classifier = nn.Sequential( Linear(self.c_in, self.c_hidden), Linear(self.c_hidden, no_bond_types), ) def forward(self, z: torch.Tensor) -> torch.Tensor: """ Args: z (torch.Tensor): pairformer output [*, N_token, N_token, c_z] Returns: torch.Tensor: bond type probability distribution [*, N_token, N_token, no_bond_types] """ # [*, N_token, N_token, no_bond_types] logits = self.classifier(z.unsqueeze(0)) return logits @register_license('odesign2025') class PairwiseHead(nn.Module): """Implements a pairwise head. Computes pairwise probability distribution. """ def __init__( self, c_z: int = 128, no_bond_types: int = len(BOND_TYPE), no_bins: int = 64, bond_reconstruction = True ) -> PairwiseOutput: """ Args: c_in (int, optional): hidden dim [for pair embedding]. Defaults to 1. c_hidden (int, optional): hidden dim. Defaults to 128. no_bond_types (int, optional): Number of bond types. Defaults to len(BOND_TYPE). """ super(PairwiseHead, self).__init__() self.distogram_head = DistogramHead(c_z=c_z, no_bins=no_bins) self.bond_reconstruction = bond_reconstruction if bond_reconstruction: self.bond_type_head = BondTypeHead(c_z=c_z, no_bond_types=no_bond_types) def forward(self, input_embedding: PairFormerOutput) -> PairwiseOutput: """ Args: input (PairFormerOutput): pairformer output [*, N_token, N_token, c_z] Returns: PairwiseOutput: bond type probability distribution [*, N_token, N_token, no_bond_types] """ # [*, N_token, N_token, no_bond_types] distogram = self.distogram_head(input_embedding.z) if self.bond_reconstruction: token_bond_type_logits = self.bond_type_head(input_embedding.z) else: token_bond_type_logits = None return PairwiseOutput(distogram, token_bond_type_logits)