Add timeout feature during conformer generation

wujinkui commented 5 years ago

Dear professors: When I used the function fprints_from_smiles in e3fp, it cost much time to find the conformers if there were none. For example, I wanted to get the fingerprint of A, it cost 10 minutes to find the conforms, and it returned error at last. So, I suggest that you could add a function named Timeout in the function to avoid the situation

sethaxen commented 5 years ago

We tried to add a timeout feature when e3fp was first released, but at the time, there wasn't a good way to do this in Python. It's worth revisiting to see if the language or a package has provided this feature since then.

In the meantime, if you could provide the molecule that you're having difficulty with, we could check to see if the issue is some trivial bug.

wujinkui commented 5 years ago

2019-07-22 12:32:48,316|INFO|Generating conformers for c1cc2c3cscc3c3c(c4c[nH]cc4c4ccc5nsnc5c34)c2c2cscc12. 2019-07-22 12:39:53,661|WARNING|Problem generating conformers for c1cc2c3cscc3c3c(c4c[nH]cc4c4ccc5nsnc5c34)c2c2cscc12.

This is the molecule that I'm having difficulty with. c1cc2c3cscc3c3c(c4c[nH]cc4c4ccc5nsnc5c34)c2c2cscc12 It was a valid smiles for that I had tried it in Rdkit. Actually, I also tried some other package to solve the problem.

I tried eventlet, it seemed I got right result. But the program was broken down after running the code in JupyterNotebook

I also tried timeout_decorator. As you can see, the parameter of timeout is 5 second, however I waited for a much longer time to get a Type Error

Thanks a lot! I will try to solve the problem later

------------------ 原始邮件 ------------------ 发件人: "Seth Axen"notifications@github.com; 发送时间: 2019年7月22日(星期一) 中午12:37 收件人: "keiserlab/e3fp"e3fp@noreply.github.com; 抄送: "四川大学工艺专业吴金奎"565225589@qq.com; "State change"state_change@noreply.github.com; 主题: Re: [keiserlab/e3fp] Add timeout feature during conformer generation(#34)

We tried to add a timeout feature when e3fp was first released, but at the time, there wasn't a good way to do this in Python. It's worth revisiting to see if the language or a package has provided this feature since then.

In the meantime, if you could provide the molecule that you're having difficulty with, we could check to see if the issue is some trivial bug.

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keiserlab / e3fp

Add timeout feature during conformer generation #34