Public bug reported:
When running Autodock Tools scripts, one commonly gets the error
"ImportError: No module named oldnumeric"
Example:
/usr/lib/python2.7/dist-packages/AutoDockTools/Utilities24/prepare_ligand4.py
-l tmp.pdb -o ligand.pdbqt -A checkhydrogens
…
Traceback (most recent call last):
File
"/usr/lib/python2.7/dist-packages/AutoDockTools/Utilities24/prepare_ligand4.py",
line 11, in <module>
from AutoDockTools.MoleculePreparation import AD4LigandPreparation
File "/usr/lib/python2.7/dist-packages/AutoDockTools/MoleculePreparation.py",
line 12, in <module>
from MolKit.torTree import TorTree
File "/usr/lib/python2.7/dist-packages/MolKit/torTree.py", line 12, in
<module>
from molecule import AtomSet, BondSet
File "/usr/lib/python2.7/dist-packages/MolKit/molecule.py", line 26, in
<module>
from numpy.oldnumeric import sum, array, less_equal, take, nonzero, argsort
ImportError: No module named oldnumeric
The suggested workaround to downgrade numpy used to work in 16.04.
(https://www.researchgate.net/post/Can_anyone_solve_prepare_Ligandpy_error_importerror_no_module_named_oldnumeric)
sudo pip install numpy==1.8
But it fails in 16.10 with "RuntimeError: module compiled against API
version 0xa but this version of numpy is 0x9"
If the autodocktools package is put into Ubuntu 16.10 repositories, it
should be compiled against a compatible numpy version, and the
repositories should also provide the appropriate numpy version.
ProblemType: Bug
DistroRelease: Ubuntu 16.10
Package: autodocktools 1.5.7-1
ProcVersionSignature: Ubuntu 4.8.0-26.28-generic 4.8.0
Uname: Linux 4.8.0-26-generic x86_64
ApportVersion: 2.20.3-0ubuntu8
Architecture: amd64
CurrentDesktop: Unity
Date: Wed Nov 9 20:21:40 2016
EcryptfsInUse: Yes
InstallationDate: Installed on 2016-11-05 (4 days ago)
InstallationMedia: Ubuntu 16.10 "Yakkety Yak" - Release amd64 (20161012.2)
PackageArchitecture: all
SourcePackage: autodocktools
UpgradeStatus: No upgrade log present (probably fresh install)
** Affects: autodocktools (Ubuntu)
Importance: Undecided
Status: New
** Tags: amd64 apport-bug yakkety
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https://bugs.launchpad.net/bugs/1640586
Title:
No module named oldnumeric
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