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$plip -i 1vsn -yv
...
Checking status of PDB ID 1vsn ... entry is up to date.
Downloading file from PDB ... file downloaded as ./1vsn.pdb
...
PDB structure successfully read.
Analyzing one ligand...
...
Contains 2 aromatic ring(s).
Traceback (most recent call last):
File "/home/user/bin/source/pliptool/plip/plipcmd", line 306, in
main(expanded_path, arguments.pdbid) # Start main script
File "/home/user/bin/source/pliptool/plip/plipcmd", line 172, in main
process_pdb(pdbpath, config.OUTPATH, outputprefix=outputprefix)
File "/home/user/bin/source/pliptool/plip/plipcmd", line 68, in process_pdb
mol.characterize_complex(ligand)
File "/home/user/bin/source/pliptool/plip/modules/preparation.py", line 1390, in characterize_complex
lig_obj = Ligand(self, ligand)
File "/home/user/bin/source/pliptool/plip/modules/preparation.py", line 1001, in init
descvalues = self.molecule.calcdesc()
File "/usr/lib/python2.7/dist-packages/pybel.py", line 361, in calcdesc
raise ValueError("%s is not a recognised Open Babel descriptor type" % descname)
ValueError: @w7� is not a recognised Open Babel descriptor type
Please check your OpenBabel installation. It might be that your Python bindings don't match the installed OpenBabel version.
See here for installation instructions.
Question was also added to the new FAQ in the README.md .
$plip -i 1vsn -yv
...
Checking status of PDB ID 1vsn ... entry is up to date.
Downloading file from PDB ... file downloaded as ./1vsn.pdb
...
PDB structure successfully read.
Analyzing one ligand...
...
Contains 2 aromatic ring(s).
Traceback (most recent call last):
File "/home/user/bin/source/pliptool/plip/plipcmd", line 306, in
main(expanded_path, arguments.pdbid) # Start main script
File "/home/user/bin/source/pliptool/plip/plipcmd", line 172, in main
process_pdb(pdbpath, config.OUTPATH, outputprefix=outputprefix)
File "/home/user/bin/source/pliptool/plip/plipcmd", line 68, in process_pdb
mol.characterize_complex(ligand)
File "/home/user/bin/source/pliptool/plip/modules/preparation.py", line 1390, in characterize_complex
lig_obj = Ligand(self, ligand)
File "/home/user/bin/source/pliptool/plip/modules/preparation.py", line 1001, in init
descvalues = self.molecule.calcdesc()
File "/usr/lib/python2.7/dist-packages/pybel.py", line 361, in calcdesc
raise ValueError("%s is not a recognised Open Babel descriptor type" % descname)
ValueError: @w7� is not a recognised Open Babel descriptor type
#System set-up:
Python 2.7.2
Open Babel version: 2.3.2
Ubuntu 16.04 LTS
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