auxillary_heads.py

import torch.nn as nn
from typing import Dict
from unicore.modules import LayerNorm
from .common import Linear
from .confidence import predicted_lddt, predicted_tm_score, predicted_aligned_error


class AuxiliaryHeads(nn.Module):
    def __init__(self, config):
        super(AuxiliaryHeads, self).__init__()

        self.plddt = PredictedLDDTHead(
            **config["plddt"],
        )

        self.distogram = DistogramHead(
            **config["distogram"],
        )

        self.masked_msa = MaskedMSAHead(
            **config["masked_msa"],
        )

        if config.experimentally_resolved.enabled:
            self.experimentally_resolved = ExperimentallyResolvedHead(
                **config["experimentally_resolved"],
            )

        if config.pae.enabled:
            self.pae = PredictedAlignedErrorHead(
                **config.pae,
            )

        self.config = config

    def forward(self, outputs):
        aux_out = {}
        plddt_logits = self.plddt(outputs["sm"]["single"])
        aux_out["plddt_logits"] = plddt_logits

        aux_out["plddt"] = predicted_lddt(plddt_logits.detach())

        distogram_logits = self.distogram(outputs["pair"])
        aux_out["distogram_logits"] = distogram_logits

        masked_msa_logits = self.masked_msa(outputs["msa"])
        aux_out["masked_msa_logits"] = masked_msa_logits

        if self.config.experimentally_resolved.enabled:
            exp_res_logits = self.experimentally_resolved(outputs["single"])
            aux_out["experimentally_resolved_logits"] = exp_res_logits

        if self.config.pae.enabled:
            pae_logits = self.pae(outputs["pair"])
            aux_out["pae_logits"] = pae_logits
            pae_logits = pae_logits.detach()
            aux_out.update(
                predicted_aligned_error(
                    pae_logits,
                    **self.config.pae,
                )
            )
            aux_out["ptm"] = predicted_tm_score(
                pae_logits, interface=False, **self.config.pae
            )

            iptm_weight = self.config.pae.get("iptm_weight", 0.0)
            if iptm_weight > 0.0:
                aux_out["iptm"] = predicted_tm_score(
                    pae_logits,
                    interface=True,
                    asym_id=outputs["asym_id"],
                    **self.config.pae,
                )
                aux_out["iptm+ptm"] = (
                    iptm_weight * aux_out["iptm"] + (1.0 - iptm_weight) * aux_out["ptm"]
                )

        return aux_out


class PredictedLDDTHead(nn.Module):
    def __init__(self, num_bins, d_in, d_hid):
        super(PredictedLDDTHead, self).__init__()

        self.num_bins = num_bins
        self.d_in = d_in
        self.d_hid = d_hid

        self.layer_norm = LayerNorm(self.d_in)

        self.linear_1 = Linear(self.d_in, self.d_hid, init="relu")
        self.linear_2 = Linear(self.d_hid, self.d_hid, init="relu")
        self.act = nn.GELU()
        self.linear_3 = Linear(self.d_hid, self.num_bins, init="final")

    def forward(self, s):
        s = self.layer_norm(s)
        s = self.linear_1(s)
        s = self.act(s)
        s = self.linear_2(s)
        s = self.act(s)
        s = self.linear_3(s)
        return s


class EnhancedHeadBase(nn.Module):
    def __init__(self, d_in, d_out, disable_enhance_head):
        super(EnhancedHeadBase, self).__init__()
        if disable_enhance_head:
            self.layer_norm = None
            self.linear_in = None
        else:
            self.layer_norm = LayerNorm(d_in)
            self.linear_in = Linear(d_in, d_in, init="relu")
        self.act = nn.GELU()
        self.linear = Linear(d_in, d_out, init="final")

    def apply_alphafold_original_mode(self):
        self.layer_norm = None
        self.linear_in = None

    def forward(self, x):
        if self.layer_norm is not None:
            x = self.layer_norm(x)
            x = self.act(self.linear_in(x))
        logits = self.linear(x)
        return logits


class DistogramHead(EnhancedHeadBase):
    def __init__(self, d_pair, num_bins, disable_enhance_head, **kwargs):
        super(DistogramHead, self).__init__(
            d_in=d_pair,
            d_out=num_bins,
            disable_enhance_head=disable_enhance_head,
        )

    def forward(self, x):
        logits = super().forward(x)
        logits = logits + logits.transpose(-2, -3)
        return logits


class PredictedAlignedErrorHead(EnhancedHeadBase):
    def __init__(self, d_pair, num_bins, disable_enhance_head, **kwargs):
        super(PredictedAlignedErrorHead, self).__init__(
            d_in=d_pair,
            d_out=num_bins,
            disable_enhance_head=disable_enhance_head,
        )


class MaskedMSAHead(EnhancedHeadBase):
    def __init__(self, d_msa, d_out, disable_enhance_head, **kwargs):
        super(MaskedMSAHead, self).__init__(
            d_in=d_msa,
            d_out=d_out,
            disable_enhance_head=disable_enhance_head,
        )


class ExperimentallyResolvedHead(EnhancedHeadBase):
    def __init__(self, d_single, d_out, disable_enhance_head, **kwargs):
        super(ExperimentallyResolvedHead, self).__init__(
            d_in=d_single,
            d_out=d_out,
            disable_enhance_head=disable_enhance_head,
        )