Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

NameError: name 'dock_molecule' is not defined #141

Open
HannibaltheArrow opened this issue Feb 26, 2024 · 1 comment
Open

NameError: name 'dock_molecule' is not defined #141

HannibaltheArrow opened this issue Feb 26, 2024 · 1 comment

Comments

@HannibaltheArrow
Copy link

Using Toolkit version 2023.1 and presumably OEDocking TK 4.2.1.
In the notebook OEDocking.ipynb, section 3.4: I get the following error.

NameError Traceback (most recent call last)
Cell In[13], line 37
32 #Loop over 3D molecules from the input filestream
33 for mcmol in ifs.GetOEMols():
34 #for mcmol in oemols:
35 #Call our docking function
36 # Print score
---> 37 dockedMol, score = dock_molecule( dock, sdtag, num_poses, mcmol )
38 print("{} {} score = {:.4f}".format(sdtag, dockedMol.GetTitle(), score))
40 #Write docked molecules to output filestreamot defined

NameError: name 'dock_molecule' is not defined

This could possibly relate to the dock_molecule method being depreciated in a previous update as I cannot find any documentation relating to this method. In fact under the documentation for the OEDock class, it specifically states "Dock molecules using the "OEDock.DockMultiConformerMolecule"method (https://docs.eyesopen.com/toolkits/python/dockingtk/OEDockingClasses/OEDock.html#OEDocking::OEDock::DockMultiConformerMolecule).

@HannibaltheArrow
Copy link
Author

Also in the same vein, the functions oedocking.OEWriteReceptorFile() and oedocking.OEReadReceptorFile() appear to be depreciated; having been replaced with the functions oechem.OEWriteDesignUnit() oechem.OEReadDesignUnit() respectively (https://docs.eyesopen.com/toolkits/python/dockingtk/releasenotes/version4_0_0.html).

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant