import torch import torch.nn as nn import dgl from dgllife.model import GCN, GAT, MPNNGNN class MPNNWrapper(nn.Module): """ Wraps MPNNGNN to expose a GCN-compatible 2-argument call signature: forward(g, node_feats) → forward(g, node_feats, g.edata['e']) This satisfies contrastive.py line 66 which calls .GNN(g, ndata) as dead code. """ def __init__(self, mpnn: MPNNGNN): super().__init__() self._mpnn = mpnn def forward(self, g, node_feats, edge_feats=None): if edge_feats is None: edge_feats = g.edata.get('e') if edge_feats is None: raise ValueError("MPNN requires g.edata['e'] (bond features)") return self._mpnn(g, node_feats, edge_feats) # Forward attribute access to the wrapped MPNN (e.g. .parameters()) def __getattr__(self, name): try: return super().__getattr__(name) except AttributeError: return getattr(self._mpnn, name) class MolEnc(nn.Module): def __init__(self, args, in_dim,): super().__init__() self.return_emb = False self.gnn_type = getattr(args, 'gnn_type', 'gcn') if args.model in ('filipContrastive', 'crossAttenContrastive', 'filipGlobalContrastive'): self.return_emb = True dropout = [args.gnn_dropout for _ in range(len(args.gnn_channels))] batchnorm = [True for _ in range(len(args.gnn_channels))] out_dim = args.gnn_channels[len(args.gnn_channels) - 1] if self.gnn_type == 'mpnn': # MPNNGNN uses edge features (bond type, ring, stereo: 13-dim for 'full' bond_feature) edge_in_dim = getattr(args, 'edge_in_dim', 13) mpnn_edge_hidden = getattr(args, 'mpnn_edge_hidden', 128) mpnn_steps = getattr(args, 'mpnn_steps', 4) self.GNN = MPNNWrapper(MPNNGNN( node_in_feats=in_dim, edge_in_feats=edge_in_dim, node_out_feats=out_dim, edge_hidden_feats=mpnn_edge_hidden, num_step_message_passing=mpnn_steps, )) else: gnn_map = { "gcn": GCN(in_dim, args.gnn_channels, batchnorm=batchnorm, dropout=dropout), } self.GNN = gnn_map[self.gnn_type] self.pool = dgl.nn.pytorch.glob.MaxPooling() if not self.return_emb: self.fc1_graph = nn.Linear(out_dim, args.gnn_hidden_dim * 2) self.fc2_graph = nn.Linear(args.gnn_hidden_dim * 2, args.final_embedding_dim) self.dropout = nn.Dropout(args.fc_dropout) self.relu = nn.ReLU() def forward(self, g, fp=None) -> torch.Tensor: g1 = g f1 = g.ndata['h'] if self.gnn_type == 'mpnn': e1 = g.edata.get('e', None) if e1 is None: raise ValueError("MPNN requires edge features in g.edata['e'] — ensure bond_feature != 'none'") f = self.GNN(g1, f1, e1) else: f = self.GNN(g1, f1) if self.return_emb: return f h = self.pool(g1, f) if fp is not None: h = torch.concat((h, fp), dim=-1) h1 = self.relu(self.fc1_graph(h)) h1 = self.dropout(h1) h1 = self.fc2_graph(h1) h1 = self.dropout(h1) return h1