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isayevlab / Auto3D_pkg

Auto3D generates low-energy conformers from SMILES/SDF
MIT License
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Error when running tutorial #37

Closed yrq3027 closed 1 year ago

yrq3027 commented 1 year ago

Hi! I cannot get result file when run the tutorial.ipynb with followed error. Can you help me, thank you! Isomer generation for job1 Enumerating cis/tran isomers for unspecified double bonds... Enumerating R/S isomers for unspecified atomic centers... Removing enantiomers... Enumerating conformers/rotamers, removing duplicates... 100%|███████████████████████████████████████████████████████████████████████████████████| 4/4 [00:00<00:00, 110.89it/s] Process Process-4: Traceback (most recent call last): File "C:\Users\yuanrong.fan\AppData\Local\miniconda3\envs\auto3D\lib\multiprocessing\process.py", line 315, in _bootstrap self.run() File "C:\Users\yuanrong.fan\AppData\Local\miniconda3\envs\auto3D\lib\multiprocessing\process.py", line 108, in run self._target(*self._args, **self._kwargs) File "C:\Users\yuanrong.fan\AppData\Local\miniconda3\envs\auto3D\lib\site-packages\Auto3D\auto3D.py", line 114, in isomer_wraper engine.run() File "C:\Users\yuanrong.fan\AppData\Local\miniconda3\envs\auto3D\lib\site-packages\Auto3D\isomer_engine.py", line 239, in run self.combine_SDF(self.rdk_tmp, self.enumerated_sdf) File "C:\Users\yuanrong.fan\AppData\Local\miniconda3\envs\auto3D\lib\site-packages\Auto3D\isomer_engine.py", line 192, in combine_SDF mols = pybel.readfile('sdf', file) File "C:\Users\yuanrong.fan\AppData\Local\miniconda3\envs\auto3D\lib\openbabel\pybel.py", line 159, in readfile raise ValueError("%s is not a recognised Open Babel format" % format) ValueError: sdf is not a recognised Open Babel format

LiuCMU commented 1 year ago

Hi, can you check your Open Babel version?

conda list openbabel

it should be at least 3.x

yrq3027 commented 1 year ago

Thank you. OPenbabel is 3.1.1. I use the windows system,should I change?

LiuCMU commented 1 year ago

Hi, this is interesting. SDF should be a readable format for pybel 🤔

Are you running the tutorial.ipynb as is?

Auto3D runs on different OS. I tested it on Windows a while ago. But if you have access to a linux/unix system, could you try to run tutorial.ipynb to see if the problem persists? thanks!

yrq3027 commented 1 year ago

Hi, it worked on ubuntu with docker. I cannot successful install openbabel on windows