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CGNN-3D: add filtering by node type #5

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CGNN-3D: add filtering by node type #5

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13 changes: 8 additions & 5 deletions kinodata/model/complex_transformer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -99,17 +99,19 @@ def __init__(
interaction_radius: float = 8.0,
max_num_neighbors: int = 16,
rbf_size: int = None,
interacting_node_type = NodeType.Complex: NodeType,
) -> None:
super().__init__(hidden_channels, act, bias)
self.interaction_radius = interaction_radius
self.max_num_neighbors = max_num_neighbors
self.rbf_size = rbf_size if rbf_size else hidden_channels
self.distance_embedding = GaussianDistEmbedding(rbf_size, interaction_radius)
self.lin = Linear(rbf_size, hidden_channels, bias=False)
self.interacting_node_type = interacting_node_type

def interactions(self, data: HeteroData) -> Tuple[Tensor, OptTensor, OptTensor]:
pos = data[NodeType.Complex].pos
batch = data[NodeType.Complex].batch
pos = data[self.interacting_node_type].pos
batch = data[self.interacting_node_type].batch
edge_index = knn_graph(pos, self.max_num_neighbors + 1, batch, loop=True)
distances = (pos[edge_index[0]] - pos[edge_index[1]]).pow(2).sum(dim=1).sqrt()
mask = distances <= self.interaction_radius
Expand Down Expand Up @@ -161,7 +163,7 @@ def __init__(
) -> None:
super().__init__(config)
assert len(config["node_types"]) == 1
assert config["node_types"][0] == NodeType.Complex
self.node_type = config["node_types"]
self.act = resolve_act(act)
self.d_cut = interaction_radius
self.max_num_neighbors = max_num_neighbors
Expand All @@ -170,7 +172,7 @@ def __init__(
for mode in interaction_modes:
if mode == "covalent":
module = CovalentInteractions(
hidden_channels, act, intr_bias, config["node_types"][0]
hidden_channels, act, intr_bias, self.node_type,
)
elif mode == "structural":
module = StructuralInteractions(
Expand All @@ -180,6 +182,7 @@ def __init__(
interaction_radius,
max_num_neighbors,
hidden_channels,
interacting_node_type = self.node_type,
)
else:
raise ValueError(mode)
Expand Down Expand Up @@ -216,7 +219,7 @@ def __init__(
)

def forward(self, data: HeteroData) -> NodeEmbedding:
node_store = data[NodeType.Complex]
node_store = data[self.node_type]
node_repr = self.act(
self.atomic_num_embedding(node_store.z)
+ self.lin_atom_features(node_store.x)
Expand Down