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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).
The text was updated successfully, but these errors were encountered:
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).
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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).
The text was updated successfully, but these errors were encountered: