pyg-nightly 2.7.0.dev20241009__py3-none-any.whl → 2.8.0.dev20251207__py3-none-any.whl

torch_geometric/datasets/molecule_gpt_dataset.py

@@ -0,0 +1,492 @@
+import gzip
+import json
+import multiprocessing
+import os
+import sys
+from collections import defaultdict
+from multiprocessing import Pool
+from typing import Callable, List, Optional, Tuple
+
+import numpy as np
+import requests
+import torch
+from tqdm import tqdm
+
+from torch_geometric.data import Data, InMemoryDataset, download_url
+from torch_geometric.io import fs
+from torch_geometric.llm.models import LLM
+from torch_geometric.utils import one_hot
+
+
+def clean_up_description(description: str) -> str:
+    description = description + " "
+
+    # extra adj Pure
+    if description.startswith("Pure "):
+        description = description.replace("Pure ", "")
+    # fix typo
+    if description.startswith("Mercurycombines"):
+        description = description.replace("Mercurycombines",
+                                          "Mercury combines")
+
+    # a special case
+    description = description.replace(
+        "17-Hydroxy-6-methylpregna-3,6-diene-3,20-dione. ",
+        "17-Hydroxy-6-methylpregna-3,6-diene-3,20-dione is ")
+
+    # a special case
+    description = description.replace("5-Thymidylic acid. ",
+                                      "5-Thymidylic acid. is ")
+
+    # a special case
+    description = description.replace(
+        "5'-S-(3-Amino-3-carboxypropyl)-5'-thioadenosine. ",
+        "5'-S-(3-Amino-3-carboxypropyl)-5'-thioadenosine. is ")
+
+    # a special case
+    description = description.replace(
+        ("Guanosine 5'-(trihydrogen diphosphate), monoanhydride"
+         " with phosphorothioic acid. "),
+        ("Guanosine 5'-(trihydrogen diphosphate), monoanhydride"
+         " with phosphorothioic acid is "))
+
+    # a special case
+    description = description.replace("5'-Uridylic acid. ",
+                                      "5'-Uridylic acid is ")
+
+    # a special case
+    description = description.replace("5'-Adenylic acid, ",
+                                      "5'-Adenylic acid is ")
+
+    # a special case
+    description = description.replace(
+        "Uridine 5'-(tetrahydrogen triphosphate). ",
+        "Uridine 5'-(tetrahydrogen triphosphate). is ")
+
+    # a special case
+    description = description.replace("Inosine 5'-Monophosphate. ",
+                                      "Inosine 5'-Monophosphate. is ")
+
+    # a special case
+    description = description.replace("Pivaloyloxymethyl butyrate (AN-9), ",
+                                      "Pivaloyloxymethyl butyrate (AN-9) is ")
+
+    # a special case
+    description = description.replace(
+        "4-Amino-5-cyano-7-(D-ribofuranosyl)-7H- pyrrolo(2,3-d)pyrimidine. ",
+        "4-Amino-5-cyano-7-(D-ribofuranosyl)-7H- pyrrolo(2,3-d)pyrimidine is ")
+
+    # a special case
+    description = description.replace(
+        "Cardamonin (also known as Dihydroxymethoxychalcone), ",
+        "Cardamonin (also known as Dihydroxymethoxychalcone) is ")
+
+    # a special case
+    description = description.replace("Lithium has been used to treat ",
+                                      "Lithium is ")
+
+    # a special case
+    description = description.replace("4,4'-Methylenebis ",
+                                      "4,4'-Methylenebis is ")
+
+    # a special case
+    description = description.replace(
+        "2,3,7,8-Tetrachlorodibenzo-p-dioxin",
+        "2,3,7,8-Tetrachlorodibenzo-p-dioxin is ")
+
+    # a special case
+    description = description.replace("Exposure to 2,4,5-trichlorophenol ",
+                                      "2,4,5-Trichlorophenol exposure ")
+
+    index = 0
+    L = len(description)
+    if description.startswith('C.I. '):
+        start_index = len('C.I. ')
+    elif description.startswith('Nectriapyrone. D '):
+        start_index = len('Nectriapyrone. D ')
+    elif description.startswith(
+            'Salmonella enterica sv. Minnesota LPS core oligosaccharide'):
+        start_index = len(
+            'Salmonella enterica sv. Minnesota LPS core oligosaccharide')
+    else:
+        start_index = 0
+    for index in range(start_index, L - 1):
+        if index < L - 2:
+            if description[index] == '.' and description[
+                    index + 1] == ' ' and 'A' <= description[index + 2] <= 'Z':
+                break
+        elif index == L - 2:
+            break
+
+    first_sentence = description[:index + 1]
+    return first_sentence
+
+
+def extract_name(
+    name_raw: str,
+    description: str,
+) -> Tuple[Optional[str], str, str]:
+    first_sentence = clean_up_description(description)
+
+    splitter = '  --  --  '
+    if ' are ' in first_sentence or ' were ' in first_sentence:
+        replaced_words = 'These molecules'
+    else:
+        replaced_words = 'This molecule'
+
+    first_sentence = first_sentence.replace(' is ', splitter)
+    first_sentence = first_sentence.replace(' are ', splitter)
+    first_sentence = first_sentence.replace(' was ', splitter)
+    first_sentence = first_sentence.replace(' were ', splitter)
+    first_sentence = first_sentence.replace(' appears ', splitter)
+    first_sentence = first_sentence.replace(' occurs ', splitter)
+    first_sentence = first_sentence.replace(' stands for ', splitter)
+    first_sentence = first_sentence.replace(' belongs to ', splitter)
+    first_sentence = first_sentence.replace(' exists ',
+                                            splitter)  # only for CID=11443
+    first_sentence = first_sentence.replace(' has been used in trials ',
+                                            splitter)
+    first_sentence = first_sentence.replace(' has been investigated ',
+                                            splitter)
+    first_sentence = first_sentence.replace(' has many uses ', splitter)
+
+    if splitter in first_sentence:
+        extracted_name = first_sentence.split(splitter, 1)[0]
+    elif first_sentence.startswith(name_raw):
+        extracted_name = name_raw
+    elif name_raw in first_sentence:
+        extracted_name = name_raw
+        extracted_name = None
+        print("=====", name_raw)
+        print("first sentence: ", first_sentence)
+    else:
+        extracted_name = None
+
+    if extracted_name is not None:
+        extracted_description = description.replace(extracted_name,
+                                                    replaced_words)
+    else:
+        extracted_description = description
+
+    return extracted_name, extracted_description, first_sentence
+
+
+class MoleculeGPTDataset(InMemoryDataset):
+    r"""The dataset from the `"MoleculeGPT: Instruction Following Large
+    Language Models for Molecular Property Prediction"
+    <https://ai4d3.github.io/2023/papers/34.pdf>`_ 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`)
+        total_page_num (int, optional): The number of pages from PubChem.
+            (default: :obj:`10`)
+        total_block_num (int, optional): The blocks of SDF files from PubChem.
+            (default: :obj:`1`)
+        num_units (int, optional): Number of units of the sample.
+            (default: :obj:`-1`, which means all units will be used)
+    """
+    description_url = (
+        'https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/annotations/'
+        'heading/json?heading_type=Compound&heading=Record+Description&page={}'
+    )
+    compound_url = ('https://ftp.ncbi.nlm.nih.gov/pubchem/Compound/'
+                    'CURRENT-Full/SDF')
+
+    def __init__(
+        self,
+        root: str,
+        transform: Optional[Callable] = None,
+        pre_transform: Optional[Callable] = None,
+        pre_filter: Optional[Callable] = None,
+        force_reload: bool = False,
+        total_page_num: int = 10,
+        total_block_num: int = 1,
+        num_units: int = -1,
+    ):
+        self.total_page_num = total_page_num
+        self.total_block_num = total_block_num
+        self.num_units = num_units
+
+        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 ['pubchem.csv']
+
+    @property
+    def processed_file_names(self) -> List[str]:
+        return ['data.pt']
+
+    def download(self) -> None:
+        # Step 01. Extract description
+        step1_folder = f"{self.raw_dir}/step_01_PubChemSTM_description"
+        if not os.path.exists(step1_folder):
+            os.makedirs(step1_folder)
+            valid_CID_set = set()
+            CID2name_raw, CID2name_extracted = defaultdict(list), defaultdict(
+                list)
+            CID2text_raw, CID2text_extracted = defaultdict(list), defaultdict(
+                list)
+
+            for page_index in tqdm(range(self.total_page_num)):
+                page_num = page_index + 1
+                f_out = open(
+                    f"{step1_folder}/Compound_description_{page_num}.txt", "w")
+
+                description_data = requests.get(
+                    self.description_url.format(page_num)).json()
+
+                description_data = description_data["Annotations"]
+                assert description_data["Page"] == page_num
+
+                record_list = description_data["Annotation"]
+
+                for record in record_list:
+                    try:
+                        CID = record["LinkedRecords"]["CID"][0]
+                        if "Name" in record:
+                            name_raw = record["Name"]
+                            CID2name_raw[CID].append(name_raw)
+                        else:
+                            name_raw = None
+
+                        data_list = record["Data"]
+                        for data in data_list:
+                            description = data["Value"]["StringWithMarkup"][0][
+                                "String"].strip()
+
+                            extracted_name, extracted_description, _ = extract_name(  # noqa: E501
+                                name_raw, description)
+                            if extracted_name is not None:
+                                CID2name_extracted[CID].append(extracted_name)
+
+                            CID2text_raw[CID].append(description)
+                            CID2text_extracted[CID].append(
+                                extracted_description)
+
+                            valid_CID_set.add(CID)
+                            f_out.write(f"{CID}\n")
+                            f_out.write(f"{extracted_description}\n\n")
+                    except Exception:
+                        continue
+
+            valid_CID_list = sorted(list(valid_CID_set))
+            print(f"Total CID (with raw name) {len(CID2name_raw)}")
+            print(f"Total CID (with extracted name) {len(CID2name_extracted)}")
+            print(f"Total CID {len(valid_CID_list)}")
+
+            with open(f"{self.raw_dir}/CID2name_raw.json", "w") as f:
+                json.dump(CID2name_raw, f)
+
+            with open(f"{self.raw_dir}/CID2name.json", "w") as f:
+                json.dump(CID2name_extracted, f)
+
+            with open(f"{self.raw_dir}/CID2text_raw.json", "w") as f:
+                json.dump(CID2text_raw, f)
+
+            with open(f"{self.raw_dir}/CID2text.json", "w") as f:
+                json.dump(CID2text_extracted, f)
+
+        # Step 02. Download SDF Files
+        step2_folder = f"{self.raw_dir}/step_02_PubChemSTM_SDF"
+        if not os.path.exists(step2_folder):
+            for block_id in tqdm(range(self.total_block_num)):
+                block_size = 500000
+                l_id = block_id * block_size + 1
+                r_id = (block_id + 1) * block_size
+
+                compound_file_name = f"Compound_{l_id:09d}_{r_id:09d}.sdf.gz"
+                download_url(f"{self.compound_url}/{compound_file_name}",
+                             step2_folder)
+
+    def process(self, use_mp: bool = False) -> 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
+
+        # Step 03. Filter out SDF
+        step2_folder = f"{self.raw_dir}/step_02_PubChemSTM_SDF"
+        step3_folder = f"{self.raw_dir}/step_03_PubChemSTM_filtered"
+        if not os.path.exists(step3_folder):
+            os.makedirs(step3_folder)
+            with open(f"{self.raw_dir}/CID2text.json") as f:
+                CID2text = json.load(f)
+            target_CID_list = set(CID2text.keys())
+
+            block_size = 500000
+
+            def extract_one_SDF_file(block_id: int) -> None:
+                valid_mol_count = 0
+
+                writer = Chem.SDWriter(
+                    f'{step3_folder}/filtered_{block_id}.sdf')
+                l_id = block_id * block_size + 1
+                r_id = (block_id + 1) * block_size
+
+                compound_file_name = f"Compound_{l_id:09d}_{r_id:09d}.sdf.gz"
+                gzip_loader = gzip.open(f"{step2_folder}/{compound_file_name}")
+                suppl = Chem.ForwardSDMolSupplier(gzip_loader)
+
+                for mol in tqdm(suppl):
+                    if mol is None:
+                        continue
+                    cid = mol.GetProp("PUBCHEM_COMPOUND_CID")
+
+                    if cid not in target_CID_list:
+                        continue
+
+                    writer.write(mol)
+                    valid_mol_count += 1
+
+                writer.close()
+                print(f"block id: {block_id}\nfound {valid_mol_count}\n\n")
+                sys.stdout.flush()
+                return
+
+            if use_mp:
+                num_process = multiprocessing.cpu_count()
+                print(f"{num_process} CPUs")
+                num_process = 8
+                p = Pool(num_process)
+
+                block_id_list = np.arange(self.total_block_num)
+                with p:
+                    p.map(extract_one_SDF_file, block_id_list)
+            else:
+                for block_id in range(self.total_block_num):
+                    extract_one_SDF_file(block_id)
+
+        # Step 04. Merge SDF
+        with open(f"{self.raw_dir}/CID2text.json") as f:
+            CID2text = json.load(f)
+        target_CID_list = set(CID2text.keys())
+        print(f'The length of target_CID_list: {len(target_CID_list)}')
+
+        writer = Chem.SDWriter(f'{self.raw_dir}/molecules.sdf')
+
+        found_CID_set = set()
+        for block_id in range(self.total_block_num + 1):
+            compound_file_path = f"{step3_folder}/filtered_{block_id}.sdf"
+            try:
+                suppl = Chem.SDMolSupplier(compound_file_path)
+
+                for mol in tqdm(suppl):
+                    writer.write(mol)
+                    cid = mol.GetProp("PUBCHEM_COMPOUND_CID")
+                    found_CID_set.add(cid)
+            except Exception:
+                print(f"block id: {block_id} with 0 valid SDF file")
+                continue
+
+        writer.close()
+        print(f"In total: {len(found_CID_set)} molecules")
+
+        # Step 05. Convert to PyG data format
+        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}
+
+        data_list = []
+        # Real data
+        CID2text_file = f'{self.raw_dir}/CID2text.json'
+
+        with open(CID2text_file) as f:
+            CID2text_data = json.load(f)
+
+        suppl = Chem.SDMolSupplier(f'{self.raw_dir}/molecules.sdf')
+
+        llm = LLM(
+            # model_name='lmsys/vicuna-7b-v1.5',
+            model_name='TinyLlama/TinyLlama-1.1B-Chat-v0.1',
+            num_params=1,
+            dtype=torch.bfloat16,
+        )
+        prompt = ("Propose a question regarding the molecule '∼' "
+                  "whose answer is: {}:")
+        for mol in tqdm(suppl):
+            if mol.HasProp('PUBCHEM_COMPOUND_CID'):
+                CID = mol.GetProp("PUBCHEM_COMPOUND_CID")
+                CAN_SMILES = mol.GetProp("PUBCHEM_SMILES")
+
+                m: Chem.Mol = Chem.MolFromSmiles(CAN_SMILES)
+                if m is None:
+                    continue
+                RDKit_CAN_SMILES = Chem.MolToSmiles(m)
+
+                ground_truth = CID2text_data[CID][0]
+
+                instruction = llm.inference([prompt.format(ground_truth)])[0]
+
+                x: torch.Tensor = torch.tensor([
+                    types[atom.GetSymbol()] if atom.GetSymbol() in types else 5
+                    for atom in m.GetAtoms()
+                ])
+                x = one_hot(x, num_classes=len(types), dtype=torch.float)
+
+                rows, cols, edge_types = [], [], []
+                for bond in m.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))
+
+                data = Data(
+                    x=x,
+                    edge_index=edge_index,
+                    edge_attr=edge_attr,
+                    smiles=RDKit_CAN_SMILES,
+                    instruction=instruction,
+                    y=ground_truth,
+                )
+
+                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)
+
+                if self.num_units > 0 and len(data_list) >= self.num_units:
+                    break
+
+        self.save(data_list, self.processed_paths[0])

torch_geometric/datasets/molecule_net.py

@@ -210,8 +210,9 @@ class MoleculeNet(InMemoryDataset):
             data.y = y
 
             if data.num_nodes == 0:
-                warnings.warn(f"Skipping molecule '{smiles}' since it "
-                              f"resulted in zero atoms")
+                warnings.warn(
+                    f"Skipping molecule '{smiles}' since it "
+                    f"resulted in zero atoms", stacklevel=2)
                 continue
 
             if self.pre_filter is not None and not self.pre_filter(data):

torch_geometric/datasets/ppi.py

@@ -107,7 +107,8 @@ class PPI(InMemoryDataset):
         for s, split in enumerate(['train', 'valid', 'test']):
             path = osp.join(self.raw_dir, f'{split}_graph.json')
             with open(path) as f:
-                G = nx.DiGraph(json_graph.node_link_graph(json.load(f)))
+                G = nx.DiGraph(
+                    json_graph.node_link_graph(json.load(f), edges="links"))
 
             x = np.load(osp.join(self.raw_dir, f'{split}_feats.npy'))
             x = torch.from_numpy(x).to(torch.float)