Hello, I'm trying to learn these pipelines and so I'm repeating them. But I got to an error that I couldn't figure out.
This happened when I was calculating the fingerprints/substructures using padelpy in this cell[[
from padelpy import padeldescriptor
fingerprint = 'Substructure'
fingerprint_output_file = ''.join([fingerprint,'.csv']) #Substructure.csv
fingerprint_descriptortypes = fp[fingerprint]
padeldescriptor(mol_dir='molecule.smi',
d_file=fingerprint_output_file, #'Substructure.csv'
#descriptortypes='SubstructureFingerprint.xml',
descriptortypes= fingerprint_descriptortypes,
detectaromaticity=True,
standardizenitro=True,
standardizetautomers=True,
threads=2,
removesalt=True,
log=True,
fingerprints=True)
]]
The error
[[
RuntimeError Traceback (most recent call last)
~\AppData\Local\Temp\ipykernel_12200\3496867877.py in
16 removesalt=True,
17 log=True,
---> 18 fingerprints=True)
~\anaconda3\envs\my-rdkit-env\lib\site-packages\padelpy\wrapper.py in padeldescriptor(maxruntime, waitingjobs, threads, d_2d, d_3d, config, convert3d, descriptortypes, detectaromaticity, mol_dir, d_file, fingerprints, log, maxcpdperfile, removesalt, retain3d, retainorder, standardizenitro, standardizetautomers, tautomerlist, usefilenameasmolname, sp_timeout, headless)
156 if err != b'':
157 raise RuntimeError('PaDEL-Descriptor encountered an error: {}'.format(
--> 158 err.decode('utf-8')
159 ))
160 return
RuntimeError: PaDEL-Descriptor encountered an error: ago 31, 2022 1:03:02 AM padeldescriptor.PaDELDescriptorApp StartCmd
GRAVE: Cannot read in descriptor types file
java.lang.NullPointerException
at libpadeldescriptor.libPaDELDescriptorType.SetDescriptorTypes(Unknown Source)
at libpadeldescriptor.libPaDELDescriptorMaster.SetDescriptorTypes(Unknown Source)
at padeldescriptor.PaDELDescriptorApp.StartCmd(Unknown Source)
at padeldescriptor.PaDELDescriptorApp.launchCommandLine(Unknown Source)
at padeldescriptor.PaDELDescriptorApp.main(Unknown Source)
]]
Could you help me with this?
Thank you these videos and github access are very useful