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pharmai / plip

Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Adasme et al. (2021), https://doi.org/10.1093/nar/gkab294
http://plip.biotec.tu-dresden.de
GNU General Public License v2.0
458 stars 106 forks source link

TypeError: unhashable type: 'OBAtom' #58

Closed navanchauhan closed 4 years ago

navanchauhan commented 4 years ago 
platform: macOS Catalina
python: 3.7.7

With reference to #46 I have commented out the three lines from supplemental.py

Error:

$ python3 plip/plipcmd.py -I 6lu7

/usr/local/lib/python3.7/site-packages/openbabel/__init__.py:14: UserWarning: "import openbabel" is deprecated, instead use "from openbabel import openbabel"
  warnings.warn('"import openbabel" is deprecated, instead use "from openbabel import openbabel"')
Traceback (most recent call last):
  File "plip/plipcmd.py", line 311, in <module>
    main_init()
  File "plip/plipcmd.py", line 307, in main_init
    main(expanded_path, arguments.pdbid)  # Start main script
  File "plip/plipcmd.py", line 171, in main
    process_pdb(pdbpath, config.OUTPATH, outputprefix=outputprefix)
  File "plip/plipcmd.py", line 63, in process_pdb
    mol.load_pdb(pdbfile, as_string=as_string)
  File "/Users/navanchauhan/Desktop/nCOV-19/scripts/plip/plip/modules/preparation.py", line 1354, in load_pdb
    ligandfinder = LigandFinder(self.protcomplex, self.altconf, self.modres, self.covalent, self.Mapper)
  File "/Users/navanchauhan/Desktop/nCOV-19/scripts/plip/plip/modules/preparation.py", line 229, in __init__
    self.ligands = self.getligs()
  File "/Users/navanchauhan/Desktop/nCOV-19/scripts/plip/plip/modules/preparation.py", line 274, in getligs
    ligands.append(self.extract_ligand(kmer))
  File "/Users/navanchauhan/Desktop/nCOV-19/scripts/plip/plip/modules/preparation.py", line 311, in extract_ligand
    hetatoms_res = set([(obatom.GetIdx(), obatom) for obatom in pybel.ob.OBResidueAtomIter(obresidue)
TypeError: unhashable type: 'OBAtom'
vjhaupt commented 4 years ago

which PLIP and openbabel version do you use and how did you install PLIP?

navanchauhan commented 4 years ago

I am using the stable branch, I tried using plip without installing from the root directory

I then tried installing via setup.py which has now narrowed the problem to missing header files. After copying the header files from the brew Cellar folder, there is still a missing header file openbabel/atomclass.h

I installed open-babel using home-brew ( version 3.0.0 ) and have also installed pybel using pip

python3 setup.py install error:

running install
running bdist_egg
running egg_info
writing plip.egg-info/PKG-INFO
writing dependency_links to plip.egg-info/dependency_links.txt
writing requirements to plip.egg-info/requires.txt
writing top-level names to plip.egg-info/top_level.txt
reading manifest file 'plip.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'plip.egg-info/SOURCES.txt'
installing library code to build/bdist.macosx-10.15-x86_64/egg
running install_lib
running build_py
creating build/bdist.macosx-10.15-x86_64/egg
creating build/bdist.macosx-10.15-x86_64/egg/plip
copying build/lib/plip/__init__.py -> build/bdist.macosx-10.15-x86_64/egg/plip
copying build/lib/plip/plipcmd.py -> build/bdist.macosx-10.15-x86_64/egg/plip
creating build/bdist.macosx-10.15-x86_64/egg/plip/modules
copying build/lib/plip/modules/webservices.py -> build/bdist.macosx-10.15-x86_64/egg/plip/modules
copying build/lib/plip/modules/pymolplip.py -> build/bdist.macosx-10.15-x86_64/egg/plip/modules
copying build/lib/plip/modules/detection.py -> build/bdist.macosx-10.15-x86_64/egg/plip/modules
copying build/lib/plip/modules/config.py -> build/bdist.macosx-10.15-x86_64/egg/plip/modules
copying build/lib/plip/modules/chimeraplip.py -> build/bdist.macosx-10.15-x86_64/egg/plip/modules
copying build/lib/plip/modules/__init__.py -> build/bdist.macosx-10.15-x86_64/egg/plip/modules
copying build/lib/plip/modules/visualize.py -> build/bdist.macosx-10.15-x86_64/egg/plip/modules
copying build/lib/plip/modules/mp.py -> build/bdist.macosx-10.15-x86_64/egg/plip/modules
copying build/lib/plip/modules/plipxml.py -> build/bdist.macosx-10.15-x86_64/egg/plip/modules
copying build/lib/plip/modules/plipremote.py -> build/bdist.macosx-10.15-x86_64/egg/plip/modules
copying build/lib/plip/modules/report.py -> build/bdist.macosx-10.15-x86_64/egg/plip/modules
copying build/lib/plip/modules/preparation.py -> build/bdist.macosx-10.15-x86_64/egg/plip/modules
copying build/lib/plip/modules/supplemental.py -> build/bdist.macosx-10.15-x86_64/egg/plip/modules
byte-compiling build/bdist.macosx-10.15-x86_64/egg/plip/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.macosx-10.15-x86_64/egg/plip/plipcmd.py to plipcmd.cpython-37.pyc
byte-compiling build/bdist.macosx-10.15-x86_64/egg/plip/modules/webservices.py to webservices.cpython-37.pyc
byte-compiling build/bdist.macosx-10.15-x86_64/egg/plip/modules/pymolplip.py to pymolplip.cpython-37.pyc
byte-compiling build/bdist.macosx-10.15-x86_64/egg/plip/modules/detection.py to detection.cpython-37.pyc
byte-compiling build/bdist.macosx-10.15-x86_64/egg/plip/modules/config.py to config.cpython-37.pyc
byte-compiling build/bdist.macosx-10.15-x86_64/egg/plip/modules/chimeraplip.py to chimeraplip.cpython-37.pyc
byte-compiling build/bdist.macosx-10.15-x86_64/egg/plip/modules/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.macosx-10.15-x86_64/egg/plip/modules/visualize.py to visualize.cpython-37.pyc
byte-compiling build/bdist.macosx-10.15-x86_64/egg/plip/modules/mp.py to mp.cpython-37.pyc
byte-compiling build/bdist.macosx-10.15-x86_64/egg/plip/modules/plipxml.py to plipxml.cpython-37.pyc
byte-compiling build/bdist.macosx-10.15-x86_64/egg/plip/modules/plipremote.py to plipremote.cpython-37.pyc
byte-compiling build/bdist.macosx-10.15-x86_64/egg/plip/modules/report.py to report.cpython-37.pyc
byte-compiling build/bdist.macosx-10.15-x86_64/egg/plip/modules/preparation.py to preparation.cpython-37.pyc
byte-compiling build/bdist.macosx-10.15-x86_64/egg/plip/modules/supplemental.py to supplemental.cpython-37.pyc
creating build/bdist.macosx-10.15-x86_64/egg/EGG-INFO
installing scripts to build/bdist.macosx-10.15-x86_64/egg/EGG-INFO/scripts
running install_scripts
running build_scripts
creating build/bdist.macosx-10.15-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.7/plipcmd.py -> build/bdist.macosx-10.15-x86_64/egg/EGG-INFO/scripts
changing mode of build/bdist.macosx-10.15-x86_64/egg/EGG-INFO/scripts/plipcmd.py to 755
copying plip.egg-info/PKG-INFO -> build/bdist.macosx-10.15-x86_64/egg/EGG-INFO
copying plip.egg-info/SOURCES.txt -> build/bdist.macosx-10.15-x86_64/egg/EGG-INFO
copying plip.egg-info/dependency_links.txt -> build/bdist.macosx-10.15-x86_64/egg/EGG-INFO
copying plip.egg-info/not-zip-safe -> build/bdist.macosx-10.15-x86_64/egg/EGG-INFO
copying plip.egg-info/requires.txt -> build/bdist.macosx-10.15-x86_64/egg/EGG-INFO
copying plip.egg-info/top_level.txt -> build/bdist.macosx-10.15-x86_64/egg/EGG-INFO
creating 'dist/plip-1.4.5-py3.7.egg' and adding 'build/bdist.macosx-10.15-x86_64/egg' to it
removing 'build/bdist.macosx-10.15-x86_64/egg' (and everything under it)
Processing plip-1.4.5-py3.7.egg
removing '/usr/local/lib/python3.7/site-packages/plip-1.4.5-py3.7.egg' (and everything under it)
creating /usr/local/lib/python3.7/site-packages/plip-1.4.5-py3.7.egg
Extracting plip-1.4.5-py3.7.egg to /usr/local/lib/python3.7/site-packages
plip 1.4.5 is already the active version in easy-install.pth
Installing plipcmd.py script to /usr/local/bin

Installed /usr/local/lib/python3.7/site-packages/plip-1.4.5-py3.7.egg
Processing dependencies for plip==1.4.5
Searching for openbabel
Reading https://pypi.org/simple/openbabel/
Downloading https://files.pythonhosted.org/packages/9c/30/eb9c3d3d3b86981f6c6a7b8eceb6f4a13b9a12673efbc842b7cebe0ce39a/openbabel-2.4.1.tar.gz#sha256=bc536b292fece9763a65b04fe637af9d393ae17f656321305fe2569a0d8de43f
Best match: openbabel 2.4.1
Processing openbabel-2.4.1.tar.gz
Writing /var/folders/p7/nz2vlh1n4zd5q7pwrp81_l_00000gn/T/easy_install-s2o_qbya/openbabel-2.4.1/setup.cfg
Running openbabel-2.4.1/setup.py -q bdist_egg --dist-dir /var/folders/p7/nz2vlh1n4zd5q7pwrp81_l_00000gn/T/easy_install-s2o_qbya/openbabel-2.4.1/egg-dist-tmp-id5s9bb4
file openbabel.py (for module openbabel) not found
Warning: package openbabel-2.0 could not be found by pkg-config.
Guessing Open Babel location:
- include_dirs: ['/usr/local/include', '/usr/local/opt/openssl@1.1/include', '/usr/local/opt/sqlite/include', '/usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/include/python3.7m', '/usr/local/include/openbabel-2.0']
- library_dirs: ['/usr/local/lib', '/usr/local/opt/openssl@1.1/lib', '/usr/local/opt/sqlite/lib', '/usr/local/lib']
file openbabel.py (for module openbabel) not found
file openbabel.py (for module openbabel) not found
openbabel-python.i:292: Error: Unable to find 'openbabel/atomclass.h'

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/openbabel-2.0 -L/usr/local/lib
  python setup.py install
error: Setup script exited with 1
vjhaupt commented 4 years ago

The issue is apparently the failed openbabel installation. First make sure that openbabel is functional and then try with PLIP again. You should use the feature/docker for now if you want to use openbabel 3 with python 3 (this will soon be merged in the stable branch).

BTW: We will publish a docker container with a complete setup soon. You could consider waiting for that.

I am closing the issue since it is related to the broken openbabel installation.