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Error in python -m rf2aa.run_inference --config-name protein_sm #36

Open xie-yun-ai opened 8 months ago

xie-yun-ai commented 8 months ago

Error executing job with overrides: [] Traceback (most recent call last): File "/Data/RoseTTAFold2NA/RoseTTAFold-All-Atom-2/RoseTTAFold-All-Atom/rf2aa/run_inference.py", line 206, in main runner.infer() File "/Data/RoseTTAFold2NA/RoseTTAFold-All-Atom-2/RoseTTAFold-All-Atom/rf2aa/run_inference.py", line 153, in infer self.parse_inference_config() File "/Data/RoseTTAFold2NA/RoseTTAFold-All-Atom-2/RoseTTAFold-All-Atom/rf2aa/run_inference.py", line 81, in parse_inference_config sm_input = load_small_molecule( File "/Data/RoseTTAFold2NA/RoseTTAFold-All-Atom-2/RoseTTAFold-All-Atom/rf2aa/data/small_molecule.py", line 16, in load_small_molecule obmol, msa, ins, xyz, mask = parse_mol( File "/Data/RoseTTAFold2NA/RoseTTAFold-All-Atom-2/RoseTTAFold-All-Atom/rf2aa/data/parsers.py", line 787, in parse_mol ff.FastRotorSearch() AttributeError: 'OBForceField' object has no attribute 'FastRotorSearch'

This error has occurred. May I ask if anyone has encountered such a problem and for what reason

knight-qs commented 8 months ago

I referred to your solution ideas every step. After the monomerent prediction test was completed, I also tried python -m rf2aa.run_inference --config-name protein_sm, but surprisingly, I did not report any error. The rmsd of the predicted structure and the crystal structure on the pdb database is 0.417

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RyanGarciaLI commented 6 months ago

I also have this problem. The OpenBabel compilation may have some problems with Python binding. After making sure eigen3 is installed correctly. I rebuild OpenBabel using cmake -DRUN_SWIG=ON -DPYTHON_BINDINGS=ON -DEIGEN3_INCLUDE_DIR=/usr/local/include/eigen3/ ... Then it works.

rjacak-invenra commented 5 months ago

I ran into this issue, as well. Unfortunately, on Ubuntu 20.04, recompiling OpenBabel did not work for me. Installing the openbabel Python module using apt instead of pip did work though. $ sudo apt-get install python3-openbabel

I think it might be related to this openbabel issue which stems from the use of an unusual version number (3.1.1.1). When installing through apt, you get version 3.1.1+dfsg-6ubuntu5.