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Goodman-lab / DP5

Python workflow for DP5 and DP4 analysis of organic molecules
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AttributeError: 'str' object has no attribute 'decode'. Did you mean: 'encode'? #71

Open vas2201 opened 1 year ago

vas2201 commented 1 year ago

Dear All,

I am trying to run PyDP4 on nmrbox, but i am getting following error. Could you please advise, I dont have to submit slurm script , I can run on cpus by default as such. I am using tinker and nwchem.

Could you please advise on regarding this error?.

(DP5) @scandium:~/projects/LigandNMR/test1$ ../DP5-master/PyDP4.py -w gmnos ogc CandidateNMR

PyDP4 script, integrating Tinker/MacroModel, Gaussian/NWChem and DP4 v1.0

Copyright (c) 2015-2019 Kristaps Ermanis, Alexander Howarth, Jonathan M. Goodman Distributed under MIT license

Settings read from settings.cfg: TinkerPath: /home/nmrbox/spenumutchu/projects/LigandNMR/tinker/ NWChemPath: /home/nmrbox/spenumutchu/anaconda3/envs/DP5/bin/nwchem ['ogc'] CandidateNMR NMR_path /home/nmrbox/spenumutchu/projects/LigandNMR/test1/CandidateNMR Current working directory: /home/nmrbox/spenumutchu/projects/LigandNMR/test1 Initial input files: ['ogc'] NMR file: [PosixPath('/home/nmrbox/spenumutchu/projects/LigandNMR/test1/CandidateNMR')] Workflow: gmnos

Generating diastereomers... Generated input files: ['ogc0']

Assuming all computations are done? ... False Using preexisting DFT data? ... False No conformational search was requested. Skipping...

Setting up geometry optimization calculations...

Running geometry optimization calculations...

Running NWChem DFT geometry optimizations locally... [] There were no jobs to run.

Reading DFT optimized geometries... NWChem.py, ReadGeometries: No geometry optimisation output

vas2201 commented 1 year ago

Hi there, I made some progress, Looks like i did not define sterocenters. Once i used the following command, I am still getting the follwing error.

So could you please advise to fix this error ?

(DP5) spenumutchu@scandium:~/projects/LigandNMR/test1$ ../DP5-master/PyDP4.py -w gmoenas ogc NMRdata -t t -d n --nProc 4 -f mmff -c 4

PyDP4 script, integrating Tinker/MacroModel, Gaussian/NWChem and DP4 v1.0

Copyright (c) 2015-2019 Kristaps Ermanis, Alexander Howarth, Jonathan M. Goodman Distributed under MIT license

Settings read from settings.cfg: TinkerPath: /home/nmrbox/spenumutchu/projects/LigandNMR/tinker/ NWChemPath: /home/nmrbox/spenumutchu/anaconda3/envs/DP5/bin/nwchem ['ogc'] NMRdata NMR_path /home/nmrbox/spenumutchu/projects/LigandNMR/test1/NMRdata Current working directory: /home/nmrbox/spenumutchu/projects/LigandNMR/test1 Initial input files: ['ogc'] NMR file: [PosixPath('/home/nmrbox/spenumutchu/projects/LigandNMR/test1/NMRdata')] Workflow: gmoenas

Generating diastereomers... Getting inchi from file ogc.sdf Traceback (most recent call last): File "/home/nmrbox/spenumutchu/projects/LigandNMR/test1/../DP5-master/PyDP4.py", line 843, in main(settings) File "/home/nmrbox/spenumutchu/projects/LigandNMR/test1/../DP5-master/PyDP4.py", line 241, in main InchiGen.GenDiastereomers(settings.InputFiles[0], nStereo[0], settings.SelectedStereocentres)) File "/home/nmrbox/spenumutchu/projects/LigandNMR/DP5-master/InchiGen.py", line 304, in GenDiastereomers return GenSelectDiastereomers(structf, atoms) File "/home/nmrbox/spenumutchu/projects/LigandNMR/DP5-master/InchiGen.py", line 239, in GenSelectDiastereomers ds_inchis = GenSelectDSInchis(inchi, translated_atoms) File "/home/nmrbox/spenumutchu/projects/LigandNMR/DP5-master/InchiGen.py", line 255, in GenSelectDSInchis layers = inchi.decode().split('/') AttributeError: 'str' object has no attribute 'decode'. Did you mean: 'encode'?