Hi all, I made a pull request to Pymol-script-repo where oldnumeric is replaced with numpy in the bundled ADT copy. Anyone willing to review and test this?
https://github.com/Pymol-Scripts/Pymol-script-repo/pull/98 Cheers, Thomas > On Jun 13, 2018, at 11:24 AM, J.R. W <jwillis0...@gmail.com> wrote: > > Enrique, > > I don’t know a lot about AutoDock, but I do know a lot about python. That > error comes from using a new versions of numpy (1.14) that does not have old > numeric with it anymore (deprecated in 1.9). > > You can do a few things. Run the script within pymol which uses a earlier > release of numpy. rOr you could downgrade your numpy to 1.8 by using > > Pip install ‘numpy==1.8’ —force-reinstall > > > But I’d recommend you do that in an environment. This is the perfect time for > virtual environments > > https://realpython.com/python-virtual-environments-a-primer/ > > > >> On Jun 12, 2018, at 2:36 PM, Enrique Ordaz <en.ordaz...@gmail.com> wrote: >> >> Dear everyone, >> I have recently installed the open-source Pymol 1.7.x on Ubuntu 16.04 >> sudo-apt-get install pymol >> >> I then added the Pymol-script-repo which includes the Autodock/Vina plugin >> and ADT. This has worked well for me in the past. However on this new >> installation I keep getting the following error: >> >> Batch: >> /home/enrique/Pymol-script-repo/modules/ADT/AutoDockTools/Utilities24/prepare_receptor4.py >> -r /home/enrique/pymol/receptor.1crl.pdb -o >> /home/enrique/pymol/receptor.1crl.pdbqt -A checkhydrogens >> Traceback (most recent call last): >> File >> "/home/enrique/Pymol-script-repo/modules/ADT/AutoDockTools/Utilities24/prepare_receptor4.py", >> line 10, in <module> >> import MolKit.molecule >> File "/home/enrique/Pymol-script-repo/modules/ADT/MolKit/molecule.py", >> line 25, in <module> >> from mglutil.util import misc >> File "/home/enrique/Pymol-script-repo/modules/ADT/mglutil/util/misc.py", >> line 19, in <module> >> import numpy.oldnumeric as Numeric >> ImportError: No module named oldnumeric >> >> Hope someone can help me or point me in the right direction. >> >> Best regards, >> Enrique Ordaz -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
