download QM9 dataset

[Powerd0g]

🐛 Describe the bug

code: from torch_geometric.datasets import QM9 path = './dataset/QM9' dataset = QM9(path)

bug: Downloading https://deepchemdata.s3-us-west-1.amazonaws.com/datasets/molnet_publish/qm9.zip Extracting dataset\QM9\raw\qm9.zip Downloading https://ndownloader.figshare.com/files/3195404 Traceback (most recent call last): File "D:\anaconda\envs\py37\lib\urllib\request.py", line 1350, in do_open encode_chunked=req.has_header('Transfer-encoding')) File "D:\anaconda\envs\py37\lib\http\client.py", line 1281, in request self._send_request(method, url, body, headers, encode_chunked) File "D:\anaconda\envs\py37\lib\http\client.py", line 1327, in _send_request self.endheaders(body, encode_chunked=encode_chunked) File "D:\anaconda\envs\py37\lib\http\client.py", line 1276, in endheaders self._send_output(message_body, encode_chunked=encode_chunked) File "D:\anaconda\envs\py37\lib\http\client.py", line 1036, in _send_output self.send(msg) File "D:\anaconda\envs\py37\lib\http\client.py", line 976, in send self.connect() File "D:\anaconda\envs\py37\lib\http\client.py", line 1443, in connect super().connect() File "D:\anaconda\envs\py37\lib\http\client.py", line 948, in connect (self.host,self.port), self.timeout, self.source_address) File "D:\anaconda\envs\py37\lib\socket.py", line 707, in create_connection for res in getaddrinfo(host, port, 0, SOCK_STREAM): File "D:\anaconda\envs\py37\lib\socket.py", line 752, in getaddrinfo for res in _socket.getaddrinfo(host, port, family, type, proto, flags): socket.gaierror: [Errno 11001] getaddrinfo failed

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "D:/Remtan/Desktop/postgraduated/GNN/test.py", line 6, in dataset = QM9(path) File "D:\anaconda\envs\py37\lib\site-packages\torch_geometric\datasets\qm9.py", line 135, in init super().init(root, transform, pre_transform, pre_filter) File "D:\anaconda\envs\py37\lib\site-packages\torch_geometric\data\in_memory_dataset.py", line 56, in init super().init(root, transform, pre_transform, pre_filter) File "D:\anaconda\envs\py37\lib\site-packages\torch_geometric\data\dataset.py", line 84, in init self._download() File "D:\anaconda\envs\py37\lib\site-packages\torch_geometric\data\dataset.py", line 145, in _download self.download() File "D:\anaconda\envs\py37\lib\site-packages\torch_geometric\datasets\qm9.py", line 172, in download file_path = download_url(self.raw_url2, self.raw_dir) File "D:\anaconda\envs\py37\lib\site-packages\torch_geometric\data\download.py", line 34, in download_url data = urllib.request.urlopen(url, context=context) File "D:\anaconda\envs\py37\lib\urllib\request.py", line 222, in urlopen return opener.open(url, data, timeout) File "D:\anaconda\envs\py37\lib\urllib\request.py", line 525, in open response = self._open(req, data) File "D:\anaconda\envs\py37\lib\urllib\request.py", line 543, in _open '_open', req) File "D:\anaconda\envs\py37\lib\urllib\request.py", line 503, in _call_chain result = func(*args) File "D:\anaconda\envs\py37\lib\urllib\request.py", line 1393, in https_open context=self._context, check_hostname=self._check_hostname) File "D:\anaconda\envs\py37\lib\urllib\request.py", line 1352, in do_open raise URLError(err) urllib.error.URLError: <urlopen error [Errno 11001] getaddrinfo failed>

Process finished with exit code 1

maybe i cannot get in https://ndownloader.figshare.com/files/3195404 I really want to solve this bug, and i also want to know what rdkit do in QM9 dataset. Thanks！

Environment

• PyG version: 2.0.4
• PyTorch version: 1.11.0
• OS: Win11
• Python version: 3.7.13
• CUDA/cuDNN version: cu11.3 cuDNN8.0
• How you installed PyTorch and PyG (conda, pip, source): conda
• Any other relevant information (e.g., version of torch-scatter):
• rdkit: 2020.09.1.0

[rusty1s]

This is weird, downloading works for me. Does manually downloading https://ndownloader.figshare.com/files/3195404 work? You could then just move this file to ./dataset/QM9/raw/uncharacterized.txt.

[Powerd0g]

thanks for replying so fast. i can't get in https://ndownloader.figshare.com/files/3195404. and i also want to know what rdkit do to QM9 dataset.

------------------ Original message ------------------ From: "Matthias Fey"; Sendtime: Monday, Jun 6, 2022 4:01 PM To: "pyg-team/pytorch_geometric"; Cc: @.***>; "Author"; Subject: Re: [pyg-team/pytorch_geometric] download QM9 dataset (Issue #4770)

This is weird, downloading works for me. Does manually downloading https://ndownloader.figshare.com/files/3195404 works? You could then just move this file to ./dataset/QM9/raw/uncharacterized.txt.

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>

[rusty1s]

If rdkit is installed, we use it to process the raw data. Otherwise, we will load the pre-processed data directly. If you cannot access/download the raw files, you can consider to temporarily disable rdkit such that the pre-processed data is used.

[Powerd0g]

i check the raw data of QM9 from the file named gdb9.sdf, find that each node feature has three coordinates. So how to adds them to each node feature. Thanks!

[rusty1s]

The coordinates are already present in data.pos. You can add them to the node features via

x = torch.cat([data.x, data.pos], dim=-1)