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Support EdgeIndex in sdf and tu dataset #10141

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0dac4fe
update
XinweiHe Mar 26, 2025
99763bb
fix
XinweiHe Mar 28, 2025
1d772c4
fix
XinweiHe Mar 28, 2025
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13 changes: 11 additions & 2 deletions torch_geometric/io/sdf.py
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
import torch

from torch_geometric import EdgeIndex
from torch_geometric.data import Data
from torch_geometric.io import parse_txt_array
from torch_geometric.utils import coalesce, one_hot
Expand All @@ -19,10 +20,18 @@ def parse_sdf(src: str) -> Data:
bond_block = lines[1 + num_atoms:1 + num_atoms + num_bonds]
row, col = parse_txt_array(bond_block, end=2, dtype=torch.long).t() - 1
row, col = torch.cat([row, col], dim=0), torch.cat([col, row], dim=0)
edge_index = torch.stack([row, col], dim=0)
edge_index = EdgeIndex(
torch.stack([row, col], dim=0),
is_undirected=True,
sparse_size=(num_atoms, num_atoms),
)
edge_attr = parse_txt_array(bond_block, start=2, end=3) - 1
edge_attr = torch.cat([edge_attr, edge_attr], dim=0)
edge_index, edge_attr = coalesce(edge_index, edge_attr, num_atoms)
edge_index, edge_attr = coalesce( # type: ignore
edge_index,
edge_attr,
num_atoms,
)

return Data(x=x, edge_index=edge_index, edge_attr=edge_attr, pos=pos)

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7 changes: 6 additions & 1 deletion torch_geometric/io/tu.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@
import torch
from torch import Tensor

from torch_geometric import EdgeIndex
from torch_geometric.data import Data
from torch_geometric.io import fs, read_txt_array
from torch_geometric.utils import coalesce, cumsum, one_hot, remove_self_loops
Expand Down Expand Up @@ -75,7 +76,11 @@ def read_tu_data(
num_nodes = int(edge_index.max()) + 1 if x is None else x.size(0)
edge_index, edge_attr = remove_self_loops(edge_index, edge_attr)
edge_index, edge_attr = coalesce(edge_index, edge_attr, num_nodes)

edge_index = EdgeIndex(
edge_index,
is_undirected=True,
sparse_size=(num_nodes, num_nodes),
)
data = Data(x=x, edge_index=edge_index, edge_attr=edge_attr, y=y)
data, slices = split(data, batch)

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