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import torch.nn as nn
import torch.nn.functional as F
from torch_geometric.nn import knn_graph
class GaussianSmearing(nn.Module):
def __init__(self, start=0.0, stop=5.0, num_gaussians=50, fixed_offset=True):
super(GaussianSmearing, self).__init__()
self.start = start
self.stop = stop
self.num_gaussians = num_gaussians
if fixed_offset:
# customized offset
offset = torch.tensor([0, 1, 1.25, 1.5, 1.75, 2, 2.25, 2.5, 2.75, 3, 3.5, 4, 4.5, 5, 5.5, 6, 7, 8, 9, 10])
else:
offset = torch.linspace(start, stop, num_gaussians)
self.coeff = -0.5 / (offset[1] - offset[0]).item() ** 2
self.register_buffer('offset', offset)
def __repr__(self):
return f'GaussianSmearing(start={self.start}, stop={self.stop}, num_gaussians={self.num_gaussians})'
def forward(self, dist):
dist = dist.view(-1, 1) - self.offset.view(1, -1)
return torch.exp(self.coeff * torch.pow(dist, 2))
class AngleExpansion(nn.Module):
def __init__(self, start=1.0, stop=5.0, half_expansion=10):
super(AngleExpansion, self).__init__()
l_mul = 1. / torch.linspace(stop, start, half_expansion)
r_mul = torch.linspace(start, stop, half_expansion)
coeff = torch.cat([l_mul, r_mul], dim=-1)
self.register_buffer('coeff', coeff)
def forward(self, angle):
return torch.cos(angle.view(-1, 1) * self.coeff.view(1, -1))
class Swish(nn.Module):
def __init__(self):
super(Swish, self).__init__()
self.beta = nn.Parameter(torch.tensor(1.0))
def forward(self, x):
return x * torch.sigmoid(self.beta * x)
NONLINEARITIES = {
"tanh": nn.Tanh(),
"relu": nn.ReLU(),
"softplus": nn.Softplus(),
"elu": nn.ELU(),
"swish": Swish(),
'silu': nn.SiLU()
}
class MLP(nn.Module):
"""MLP with the same hidden dim across all layers."""
def __init__(self, in_dim, out_dim, hidden_dim, num_layer=2, norm=True, act_fn='relu', act_last=False):
super().__init__()
layers = []
for layer_idx in range(num_layer):
if layer_idx == 0:
layers.append(nn.Linear(in_dim, hidden_dim))
elif layer_idx == num_layer - 1:
layers.append(nn.Linear(hidden_dim, out_dim))
else:
layers.append(nn.Linear(hidden_dim, hidden_dim))
if layer_idx < num_layer - 1 or act_last:
if norm:
layers.append(nn.LayerNorm(hidden_dim))
layers.append(NONLINEARITIES[act_fn])
self.net = nn.Sequential(*layers)
def forward(self, x):
return self.net(x)
def outer_product(*vectors):
for index, vector in enumerate(vectors):
if index == 0:
out = vector.unsqueeze(-1)
else:
out = out * vector.unsqueeze(1)
out = out.view(out.shape[0], -1).unsqueeze(-1)
return out.squeeze()
def get_h_dist(dist_metric, hi, hj):
if dist_metric == 'euclidean':
h_dist = torch.sum((hi - hj) ** 2, -1, keepdim=True)
return h_dist
elif dist_metric == 'cos_sim':
hi_norm = torch.norm(hi, p=2, dim=-1, keepdim=True)
hj_norm = torch.norm(hj, p=2, dim=-1, keepdim=True)
h_dist = torch.sum(hi * hj, -1, keepdim=True) / (hi_norm * hj_norm)
return h_dist, hj_norm
def get_r_feat(r, r_exp_func, node_type=None, edge_index=None, mode='basic'):
if mode == 'origin':
r_feat = r
elif mode == 'basic':
r_feat = r_exp_func(r)
elif mode == 'sparse':
src, dst = edge_index
nt_src = node_type[src] # [n_edges, 8]
nt_dst = node_type[dst]
r_exp = r_exp_func(r)
r_feat = outer_product(nt_src, nt_dst, r_exp)
else:
raise ValueError(mode)
return r_feat
def compose_context(h_protein, h_ligand, pos_protein, pos_ligand, batch_protein, batch_ligand, mask_protein_side):
# previous version has problems when ligand atom types are fixed
# (due to sorting randomly in case of same element)
batch_ctx = torch.cat([batch_protein, batch_ligand], dim=0)
# sort_idx = batch_ctx.argsort()
sort_idx = torch.sort(batch_ctx, stable=True).indices
mask_ligand = torch.cat([
torch.zeros([batch_protein.size(0)], device=batch_protein.device).bool(),
torch.ones([batch_ligand.size(0)], device=batch_ligand.device).bool(),
], dim=0)[sort_idx]
mask_protein = torch.cat([
mask_protein_side,
torch.zeros([batch_ligand.size(0)], device=batch_ligand.device).bool(),
], dim=0)[sort_idx]
batch_ctx = batch_ctx[sort_idx]
h_ctx = torch.cat([h_protein, h_ligand], dim=0)[sort_idx] # (N_protein+N_ligand, H)
pos_ctx = torch.cat([pos_protein, pos_ligand], dim=0)[sort_idx] # (N_protein+N_ligand, 3)
return h_ctx, pos_ctx, batch_ctx, mask_ligand, mask_protein, sort_idx
def compose_context_prop(h_protein, h_ligand, pos_protein, pos_ligand, batch_protein, batch_ligand):
batch_ctx = torch.cat([batch_protein, batch_ligand], dim=0)
sort_idx = batch_ctx.argsort()
mask_protein = torch.cat([
torch.ones([batch_protein.size(0)], device=batch_protein.device).bool(),
torch.zeros([batch_ligand.size(0)], device=batch_ligand.device).bool(),
], dim=0)[sort_idx]
batch_ctx = batch_ctx[sort_idx]
h_ctx = torch.cat([h_protein, h_ligand], dim=0)[sort_idx] # (N_protein+N_ligand, H)
pos_ctx = torch.cat([pos_protein, pos_ligand], dim=0)[sort_idx] # (N_protein+N_ligand, 3)
return h_ctx, pos_ctx, batch_ctx
class ShiftedSoftplus(nn.Module):
def __init__(self):
super().__init__()
self.shift = torch.log(torch.tensor(2.0)).item()
def forward(self, x):
return F.softplus(x) - self.shift
def hybrid_edge_connection(ligand_pos, protein_pos, k, ligand_index, protein_index):
# fully-connected for ligand atoms
dst = torch.repeat_interleave(ligand_index, len(ligand_index))
src = ligand_index.repeat(len(ligand_index))
mask = dst != src
dst, src = dst[mask], src[mask]
ll_edge_index = torch.stack([src, dst])
# knn for ligand-protein edges
ligand_protein_pos_dist = torch.unsqueeze(ligand_pos, 1) - torch.unsqueeze(protein_pos, 0)
ligand_protein_pos_dist = torch.norm(ligand_protein_pos_dist, p=2, dim=-1)
knn_p_idx = torch.topk(ligand_protein_pos_dist, k=k, largest=False, dim=1).indices
knn_p_idx = protein_index[knn_p_idx]
knn_l_idx = torch.unsqueeze(ligand_index, 1)
knn_l_idx = knn_l_idx.repeat(1, k)
pl_edge_index = torch.stack([knn_p_idx, knn_l_idx], dim=0)
pl_edge_index = pl_edge_index.view(2, -1)
return ll_edge_index, pl_edge_index
def batch_hybrid_edge_connection(x, k, mask_ligand, batch, add_p_index=False):
batch_size = batch.max().item() + 1
batch_ll_edge_index, batch_pl_edge_index, batch_p_edge_index = [], [], []
with torch.no_grad():
for i in range(batch_size):
ligand_index = ((batch == i) & (mask_ligand == 1)).nonzero()[:, 0]
protein_index = ((batch == i) & (mask_ligand == 0)).nonzero()[:, 0]
ligand_pos, protein_pos = x[ligand_index], x[protein_index]
ll_edge_index, pl_edge_index = hybrid_edge_connection(
ligand_pos, protein_pos, k, ligand_index, protein_index)
batch_ll_edge_index.append(ll_edge_index)
batch_pl_edge_index.append(pl_edge_index)
if add_p_index:
all_pos = torch.cat([protein_pos, ligand_pos], 0)
p_edge_index = knn_graph(all_pos, k=k, flow='source_to_target')
p_edge_index = p_edge_index[:, p_edge_index[1] < len(protein_pos)]
p_src, p_dst = p_edge_index
all_index = torch.cat([protein_index, ligand_index], 0)
p_edge_index = torch.stack([all_index[p_src], all_index[p_dst]], 0)
batch_p_edge_index.append(p_edge_index)
if add_p_index:
edge_index = [torch.cat([ll, pl, p], -1) for ll, pl, p in zip(
batch_ll_edge_index, batch_pl_edge_index, batch_p_edge_index)]
else:
edge_index = [torch.cat([ll, pl], -1) for ll, pl in zip(batch_ll_edge_index, batch_pl_edge_index)]
edge_index = torch.cat(edge_index, -1)
return edge_index
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