Hello OpenBabel users,
I've been having issues with OpenBabel and thought I might use some help from
more experienced users.
My main problem is that I have (apparently) installed OpenBabel succesfully,
but other softwares cannot access it. For example, when I try to run a programm
that uses OpenBabel ('mk_prepare_ligand.py -i 1iep_ligand.sdf -o
1iep_ligand.pdbqt --pH 7.4'), I get the following error:
'Traceback (most recent call last):
File "/home/artur/.local/bin/mk_prepare_ligand.py", line 11, in <module>
from openbabel import openbabel as ob
ModuleNotFoundError: No module named 'openbabel''
Furthermore, if I try to remove openbabel from my system, I receive a message
(in Portuguese, so I won't copy it here) saying that "openbabel isn't
installed, so it won't be removed". However, I can easily execute the comand
obabel through my Ubuntu 20.04 terminal.
Additionally, if I try the command pip install -U openbabel, I get the
following error message:
Collecting openbabel
Using cached openbabel-3.1.1.1.tar.gz (82 kB)
Building wheels for collected packages: openbabel
Building wheel for openbabel (setup.py) ... error
ERROR: Command errored out with exit status 1:
command: /usr/bin/python3 -u -c 'import sys, setuptools, tokenize;
sys.argv[0] = '"'"'/tmp/pip-install-ctx5tcrx/openbabel/setup.py'"'"';
__file__='"'"'/tmp/pip-install-ctx5tcrx/openbabel/setup.py'"'"';f=getattr(tokenize,
'"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"',
'"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))'
bdist_wheel -d /tmp/pip-wheel-xzrzd_1p
cwd: /tmp/pip-install-ctx5tcrx/openbabel/
Complete output (66 lines):
running bdist_wheel
running build
running build_ext
Warning: invalid version number '3.1.1.1'.
Guessing Open Babel location:
- include_dirs: ['/usr/include/python3.8', '/usr/local/include/openbabel3']
- library_dirs: ['/usr/local/lib']
building 'openbabel._openbabel' extension
swigging openbabel/openbabel-python.i to openbabel/openbabel-python_wrap.cpp
swig -python -c++ -small -O -templatereduce -naturalvar
-I/usr/include/python3.8 -I/usr/local/include/openbabel3 -o
openbabel/openbabel-python_wrap.cpp openbabel/openbabel-python.i
then several errors similar to these: openbabel/openbabel-python.i:246: Error:
Unable to find 'openbabel/babelconfig.h'
openbabel/openbabel-python.i:248: Error: Unable to find 'openbabel/data.h'
openbabel/openbabel-python.i:249: Error: Unable to find 'openbabel/obutil.h'
And then finally: Error: SWIG failed. Is Open Babel installed?
You may need to manually specify the location of Open Babel include and
library directories. For example:
python setup.py build_ext -I/usr/local/include/openbabel3 -L/usr/local/lib
python setup.py install
----------------------------------------
ERROR: Command errored out with exit status 1: /usr/bin/python3 -u -c 'import
sys, setuptools, tokenize; sys.argv[0] =
'"'"'/tmp/pip-install-ctx5tcrx/openbabel/setup.py'"'"';
__file__='"'"'/tmp/pip-install-ctx5tcrx/openbabel/setup.py'"'"';f=getattr(tokenize,
'"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"',
'"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install
--record /tmp/pip-record-ik_t9mkr/install-record.txt
--single-version-externally-managed --user --prefix= --compile
--install-headers /home/artur/.local/include/python3.8/openbabel Check the logs
for full command output.
I have no clue as of why Swig is failing, since I have installed it perfectly.
I don't quite understand how to execute the suggestion given after this error,
so I don't know what to do. I tried following the instructions at
https://open-babel.readthedocs.io/en/latest/Installation/install.html#compile-bindings,
but maybe I did something wrong.
Would anyone be able to help me out? Any help is more than appreciated.
Thank you so much in advance!
--
Artur
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