pyg-nightly 2.7.0.dev20250124__tar.gz → 2.7.0.dev20250126__tar.gz

{pyg_nightly-2.7.0.dev20250124 → pyg_nightly-2.7.0.dev20250126}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: pyg-nightly
-Version: 2.7.0.dev20250124
+Version: 2.7.0.dev20250126
 Summary: Graph Neural Network Library for PyTorch
 Keywords: deep-learning,pytorch,geometric-deep-learning,graph-neural-networks,graph-convolutional-networks
 Author-email: Matthias Fey <matthias@pyg.org>

{pyg_nightly-2.7.0.dev20250124 → pyg_nightly-2.7.0.dev20250126}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend="flit_core.buildapi"
 
 [project]
 name="pyg-nightly"
-version="2.7.0.dev20250124"
+version="2.7.0.dev20250126"
 authors=[
     {name="Matthias Fey", email="matthias@pyg.org"},
 ]

{pyg_nightly-2.7.0.dev20250124 → pyg_nightly-2.7.0.dev20250126}/torch_geometric/__init__.py

@@ -30,7 +30,7 @@ from .lazy_loader import LazyLoader
 contrib = LazyLoader('contrib', globals(), 'torch_geometric.contrib')
 graphgym = LazyLoader('graphgym', globals(), 'torch_geometric.graphgym')
 
-__version__ = '2.7.0.dev20250124'
+__version__ = '2.7.0.dev20250126'
 
 __all__ = [
     'Index',

{pyg_nightly-2.7.0.dev20250124 → pyg_nightly-2.7.0.dev20250126}/torch_geometric/datasets/__init__.py

@@ -79,6 +79,7 @@ from .neurograph import NeuroGraphDataset
 from .web_qsp_dataset import WebQSPDataset, CWQDataset
 from .git_mol_dataset import GitMolDataset
 from .molecule_gpt_dataset import MoleculeGPTDataset
+from .instruct_mol_dataset import InstructMolDataset
 from .tag_dataset import TAGDataset
 
 from .dbp15k import DBP15K
@@ -196,6 +197,7 @@ homo_datasets = [
     'CWQDataset',
     'GitMolDataset',
     'MoleculeGPTDataset',
+    'InstructMolDataset',
     'TAGDataset',
 ]
 

pyg_nightly-2.7.0.dev20250126/torch_geometric/datasets/instruct_mol_dataset.py

@@ -0,0 +1,134 @@
+import json
+import sys
+from typing import Callable, List, Optional
+
+import torch
+from tqdm import tqdm
+
+from torch_geometric.data import Data, InMemoryDataset
+from torch_geometric.io import fs
+from torch_geometric.utils import one_hot
+
+
+class InstructMolDataset(InMemoryDataset):
+    r"""The dataset from the `"InstructMol: Multi-Modal Integration for
+    Building a Versatile and Reliable Molecular Assistant in Drug Discovery"
+    <https://arxiv.org/pdf/2311.16208>`_ paper.
+
+    Args:
+        root (str): Root directory where the dataset should be saved.
+        transform (callable, optional): A function/transform that takes in an
+            :obj:`torch_geometric.data.Data` object and returns a transformed
+            version. The data object will be transformed before every access.
+            (default: :obj:`None`)
+        pre_transform (callable, optional): A function/transform that takes in
+            an :obj:`torch_geometric.data.Data` object and returns a
+            transformed version. The data object will be transformed before
+            being saved to disk. (default: :obj:`None`)
+        pre_filter (callable, optional): A function that takes in an
+            :obj:`torch_geometric.data.Data` object and returns a boolean
+            value, indicating whether the data object should be included in the
+            final dataset. (default: :obj:`None`)
+        force_reload (bool, optional): Whether to re-process the dataset.
+            (default: :obj:`False`)
+    """
+    raw_url = 'https://huggingface.co/datasets/OpenMol/PubChemSFT/blob/main'
+
+    def __init__(
+        self,
+        root: str,
+        transform: Optional[Callable] = None,
+        pre_transform: Optional[Callable] = None,
+        pre_filter: Optional[Callable] = None,
+        force_reload: bool = False,
+    ):
+        super().__init__(root, transform, pre_transform, pre_filter,
+                         force_reload=force_reload)
+        self.load(self.processed_paths[0])
+
+    @property
+    def raw_file_names(self) -> List[str]:
+        return ['all_clean.json']
+
+    @property
+    def processed_file_names(self) -> List[str]:
+        return ['data.pt']
+
+    def download(self) -> None:
+        print('downloading dataset...')
+        fs.cp(f'{self.raw_url}/all_clean.json', self.raw_dir)
+
+    def process(self) -> None:
+        try:
+            from rdkit import Chem
+            from rdkit.Chem.rdchem import BondType as BT
+            WITH_RDKIT = True
+
+        except ImportError:
+            WITH_RDKIT = False
+
+        if not WITH_RDKIT:
+            print(("Using a pre-processed version of the dataset. Please "
+                   "install 'rdkit' to alternatively process the raw data."),
+                  file=sys.stderr)
+
+            data_list = fs.torch_load(self.raw_paths[0])
+            data_list = [Data(**data_dict) for data_dict in data_list]
+
+            if self.pre_filter is not None:
+                data_list = [d for d in data_list if self.pre_filter(d)]
+
+            if self.pre_transform is not None:
+                data_list = [self.pre_transform(d) for d in data_list]
+
+            self.save(data_list, self.processed_paths[0])
+            return
+
+        # types of atom and bond
+        types = {'H': 0, 'C': 1, 'N': 2, 'O': 3, 'F': 4, 'Unknow': 5}
+        bonds = {BT.SINGLE: 0, BT.DOUBLE: 1, BT.TRIPLE: 2, BT.AROMATIC: 3}
+
+        # load data
+        mols = json.load(open(f'{self.raw_dir}/all_clean.json'))
+
+        data_list = []
+        for smiles, qa_pairs in tqdm(mols.items(), total=len(mols)):
+            mol = Chem.MolFromSmiles(smiles)
+            if mol is None:
+                continue
+
+            x: torch.Tensor = torch.tensor([
+                types[atom.GetSymbol()] if atom.GetSymbol() in types else 5
+                for atom in mol.GetAtoms()
+            ])
+            x = one_hot(x, num_classes=len(types), dtype=torch.float)
+
+            rows, cols, edge_types = [], [], []
+            for bond in mol.GetBonds():
+                i, j = bond.GetBeginAtomIdx(), bond.GetEndAtomIdx()
+                edge_types += [bonds[bond.GetBondType()]] * 2
+                rows += [i, j]
+                cols += [j, i]
+
+            edge_index = torch.tensor([rows, cols], dtype=torch.long)
+            edge_type = torch.tensor(edge_types, dtype=torch.long)
+            edge_attr = one_hot(edge_type, num_classes=len(bonds))
+
+            for question, answer in qa_pairs:
+                data = Data(
+                    x=x,
+                    edge_index=edge_index,
+                    edge_attr=edge_attr,
+                    smiles=smiles,
+                    instruction=question,
+                    y=answer,
+                )
+
+                if self.pre_filter is not None and not self.pre_filter(data):
+                    continue
+                if self.pre_transform is not None:
+                    data = self.pre_transform(data)
+
+                data_list.append(data)
+
+        self.save(data_list, self.processed_paths[0])