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Here, the package pybel is imported incorrectly as import pybel. This leads to errors for big molecules created out of SMILES, since AllChem.EmbedMolecule of RDKit struggles to guess the atom coordinates of a molecule.
File "/opt/conda/envs/ligpargen/bin/ligpargen", line 33, in <module>
sys.exit(load_entry_point('LigPargen', 'console_scripts', 'ligpargen')())
File "/ligpargen/ligpargen/ligpargen.py", line 504, in main
molname=args.molname, workdir= args.path, debug= args.debug)
File "<string>", line 17, in __init__
File "/ligpargen/ligpargen/ligpargen.py", line 174, in __post_init__
moleculeRDkit, newIndexToOriginalIndex, atomsNameOriginal, residueNameOriginal = utilities.generateRDkitMolecule(self.ifile, self.smile, self.workdir, molnameA, self.debug)
File "/ligpargen/ligpargen/tools/utilities.py", line 139, in generateRDkitMolecule
mymol = pybel.readstring('smi', smile)
AttributeError: module 'pybel' has no attribute 'readstring'
Importing pybel as from openbabel import pybel solves the issue. I have tried it separately with RDKit in the Linux prompt and succeeded.
Would you fix the pybel import, please? I suppose, import openbabel might be necessary as well, but I'm not 100% sure.
The text was updated successfully, but these errors were encountered:
Here, the package pybel is imported incorrectly as
import pybel
. This leads to errors for big molecules created out of SMILES, since AllChem.EmbedMolecule of RDKit struggles to guess the atom coordinates of a molecule.Namely, the following set of commands :
leads to the following error :
Importing pybel as
from openbabel import pybel
solves the issue. I have tried it separately with RDKit in the Linux prompt and succeeded.Would you fix the pybel import, please? I suppose,
import openbabel
might be necessary as well, but I'm not 100% sure.The text was updated successfully, but these errors were encountered: