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update models #3

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update models #3

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11 changes: 6 additions & 5 deletions src/protein_ligand_embedder/model_wrapper.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@
from torch_geometric.loader import DataLoader
from DockingModels import EquivariantElucidatedDiffusion
from datasets import Dataset
from torch_scatter import scatter, scatter_mean


class ProteinLigandWrapper(nn.Module):
Expand Down Expand Up @@ -37,11 +38,11 @@ def get_emnbeddings(
tqdm_dataloader = tqdm(dataloader)
for batch in tqdm_dataloader:
batch = batch.to(self.diffusion_model.device)
_, x_t = self.diffusion_model.sample(batch, num_steps, dtype)
lig_seq_len = torch.bincount(batch['ligand'].batch).tolist()
lig_coords = torch.split(x_t, lig_seq_len)

col_emb.append(lig_coords)
x_t, rec_node_attr, lig_node_attr = self.diffusion_model.sample(batch, num_steps, dtype)
rec_node_attr = scatter_mean(rec_node_attr, batch['receptor'].batch, dim=0)
lig_node_attr = scatter_mean(lig_node_attr, batch['ligand'].batch, dim=0)
embedding = torch.cat([lig_node_attr, rec_node_attr], dim=1)
col_emb.append(embedding)
emb_dict['embedding'] = col_emb

return Dataset.from_dict(emb_dict)