src/bce/model/dihedral.py

import torch
import torch.nn as nn
import torch.nn.functional as F


class DihedralFeatures(nn.Module):
    def __init__(self, node_embed_dim):
        """ Embed dihedral angle features. """
        super(DihedralFeatures, self).__init__()
        # 3 dihedral angles; sin and cos of each angle
        node_in = 6
        # Normalization and embedding
        self.node_embedding = nn.Linear(node_in,  node_embed_dim, bias=True)
        self.norm_nodes = Normalize(node_embed_dim)

    def forward(self, X):
        """ Featurize coordinates as an attributed graph """
        with torch.no_grad():
            V = self._dihedrals(X)
        V = V.squeeze(1)
        V = self.node_embedding(V)
        V = self.norm_nodes(V)
        return V

    @staticmethod
    def _dihedrals(X, eps=1e-7,):
        # First 3 coordinates are [N, CA, C] / [C4', C1', N1/N9]
        if len(X.shape) == 4:
            X = X[..., :3, :].reshape(X.shape[0], 3*X.shape[1], 3)
        else:
            X = X[:, :3, :]

        # Shifted slices of unit vectors
        dX = X[:,1:,:] - X[:,:-1,:]
        U = F.normalize(dX, dim=-1)
        u_2 = U[:,:-2,:]
        u_1 = U[:,1:-1,:]
        u_0 = U[:,2:,:]
        # Backbone normals
        n_2 = F.normalize(torch.cross(u_2, u_1, dim=-1), dim=-1)
        n_1 = F.normalize(torch.cross(u_1, u_0, dim=-1), dim=-1)

        # Angle between normals
        cosD = (n_2 * n_1).sum(-1)
        cosD = torch.clamp(cosD, -1+eps, 1-eps)
        D = torch.sign((u_2 * n_1).sum(-1)) * torch.acos(cosD)

        # This scheme will remove phi[0], psi[-1], omega[-1]
        D = F.pad(D, (1,2), 'constant', 0)
        D = D.view((D.size(0), int(D.size(1)/3), 3))

        # Lift angle representations to the circle
        D_features = torch.cat((torch.cos(D), torch.sin(D)), 2)
        return D_features


class Normalize(nn.Module):
    def __init__(self, features, epsilon=1e-6):
        super(Normalize, self).__init__()
        self.gain = nn.Parameter(torch.ones(features))
        self.bias = nn.Parameter(torch.zeros(features))
        self.epsilon = epsilon

    def forward(self, x, dim=-1):
        mu = x.mean(dim, keepdim=True)
        sigma = torch.sqrt(x.var(dim, keepdim=True) + self.epsilon)
        gain = self.gain
        bias = self.bias
        # Reshape
        if dim != -1:
            shape = [1] * len(mu.size())
            shape[dim] = self.gain.size()[0]
            gain = gain.view(shape)
            bias = bias.view(shape)
        return gain * (x - mu) / (sigma + self.epsilon) + bias