Using Canvas, can I run fingerprint generation from the command line, and import the resulting fingerprints into the user interface ?

Yes, but you need to import the structures first into the user interface, then export to a structure file and include the Canvas_uid, the Canvas ID which will serve as the import key. Here are the steps.

1. Import the structures (file.mae) into a Canvas Project.
2. Export the structures using the Export option "Export Canvas UIDs", for instance test_uid.mae.
3. Run canvasFPGen on this exported file.
   
   $SCHRODINGER/utilities/canvasFPGen -imae test_uid.mae -odata test_uid.fp
   
4. Import test_uid.fp into the project by selecting "Files of type: .fp" and selecting "Update using Canvas UID"

You should find a column with the fingerprints added from the imported file. This same process can be used to generate molecular descriptors from the command line with the utility canvasMolDescriptors:

$SCHRODINGER/utilities/canvasMolDescriptors -imae test_uid.mae -omae test_uid_mdesc.mae

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