‘DockingProtocol’ object has no attribute ‘setup_foldtree’

[Anonymous]

Hi around, sorry for disturbing with my problem that I haven’t found posted or solved and if it has been solved I didn’t find it. I recently downloaded PyRosetta and would like to use it for docking. The easiest, I thought, is to take an example script that comes with PyRosetta – docking.py, taking the test_dock.pdb that also comes with PyRsoetta and run it to get an idea about computational time. But it doesn’t work by writing:
=========
docking.py in ()
15 print “setting up docking fold tree”
16 dock_prot = DockingProtocol() #DockingProtocol object contains many useful docking functions
—> 17 dock_prot.setup_foldtree(p)
18 # DockingProtocol().setup_foldtree(p, “E_I”)

19 dock_jump = 1

AttributeError: ‘DockingProtocol’ object has no attribute ‘setup_foldtree’
WARNING: Failure executing file:
Python 2.6.1 (r261:67515, Jun 24 2010, 21:47:49)
=========
I tired to execute the script by typing the commands line by line but it doesn’t work either. I also tried Linux and MacOs X versions of PyRosetta to assure that the problem is not caused by something that is not installed or distribution related. I’m sure there is some small stupid error that I do but not able at the state of being to find it out:-(.

Thanks for helping in advance!

Karel K

[Anonymous]

Sorry, the setup_foldtree method was moved. The default method (DockingProtocol().setup_foldtree(pose)) will no longer work although you can use set_autofold_tree to let the protocol take care of it. The method can now be accessed in PyRosetta from rosetta.protocols.docking.setup_foldtree and requires a Vector1 argument containing the movable jumps. For example, using test_dock.pdb:

rosetta.protocols.docking.setup_foldtree( pose , “E_I” , Vector1(1) )

I haven’t checked set_autofoldtee but you can try:

DockingProtocol().set_autofold_tree = True

We’ll fix the script soon, thanks for finding the bug. You weren’t doing anything wrong, its one of the many things that needs to be updated soon.

Thanks,
Evan

[Anonymous]

Thanks, I’ve used the
“dock_prot.set_autofold_tree=True”
and the script goes further, then it complains about
“recover_sidechains = ReturnSidechainMover(starting_p)”
since it is not defined, I made it to
“recover_sidechains = ReturnSidechainMover(p)”
and again the script goes further but as soon as it reaches
“docking_highres = DockingHighRes( scorefxn_high_min, dock_jump )”
it complains again and I was not able to find out what is the option to be set, I understood that he misses one option which I could figure out, so I commented that line and the script continues. Then it reaches
“jd.native_pose = starting_p”
and complains, with changing it to again to
“jd.native_pose = p”
it proceeds and needs ‘just’ to comment out “print
“high resolution stage docking””
and
“docking_highres.apply(p)”
and finally it writes
“docking complete!”.
So if you could help me to resolve the highres docking stuff, I’ll be happy user:-)

Thanks in advance!

KK

[Anonymous]

If you are using the newest version of PyRosetta, try this:


docking_highres = DockingHighResLegacy( dock_jump, scorefxn_high_min )


[Author]

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