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forlilab / Meeko

Interface for AutoDock, molecule parameterization
https://meeko.readthedocs.io/
GNU Lesser General Public License v2.1
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Problem using mk_prepare_ligand.py with -v in version 0.5.1 #166

Closed xavgit closed 2 months ago

xavgit commented 2 months ago

Hi, I receive the following using the following:

$ mk_prepare_ligand.py -v -i DB00116.sdf --merge_these_atom_types --rigid_macrocycles /usr/lib/python3/dist-packages/apport/report.py:13: DeprecationWarning: the imp module is deprecated in favour of importlib; see the module's documentation for alternative uses import fnmatch, glob, traceback, errno, sys, atexit, imp, stat Traceback (most recent call last): File "/home/xxxx/.local/bin/mk_prepare_ligand.py", line 8, in sys.exit(main()) File "/home/xxxx/.local/lib/python3.8/site-packages/meeko/cli/mk_prepare_ligand.py", line 364, in main if args.verbose: preparator.show_setup() AttributeError: 'MoleculePreparation' object has no attribute 'show_setup'

Without the -v there is not problem in the execution of the previous call to mk_prepare_ligand.py?

Any suggestion?

Thanks.

Saverio

diogomart commented 2 months ago

It's a bug, will be fixed in v0.6.0. You can change line 364 from

            if args.verbose: preparator.show_setup()

to

            if args.verbose: preparator.setup.show()

to fix it locally. Won't fix it for reactive docking if the --reactive_smarts matches more than once.

diogomart commented 2 months ago

It had been mostly fixed in the develop branch. Just added a minor fix in 05526d925d1269a444e210ca2564cfc6ff83b9ce #167