DockingProtocol().set_autofoldtree Question

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    • June 3, 2011 at 3:07 pm #933
      Anonymous

        I’m at a loss of how to switch DockingProtocol().setup_foldtree to DockingProtocol().set_autofoldtree in the DDG script. A simple substitution clearly doesn’t work; stating that it does not match the C++ signature.
        Can someone post how to overcome this?
        Many thanks,
        Brett

      • June 3, 2011 at 5:24 pm #5711
        Anonymous

          Try this:

          dock = DockingProtocol()
          dock.set_autofoldtree( True )

          More generally, to get a better idea of how to use a particular function, you can use the ? operator in ipython. For example:
          dock.set_autofoldtree?
          Type: instancemethod
          Base Class:
          String Form: >
          Namespace: Interactive
          Docstring:
          set_autofoldtree( (DockingProtocol)arg1, (bool)autofoldtree) -> None :
          protocols/docking/DockingProtocol.hh:140

          C++ signature :
          void set_autofoldtree(protocols::docking::DockingProtocol {lvalue},bool)

          This shows that the set_autofoldtree method requires a DockingProtocol instance (python takes care of this) and a boolean.

        • June 3, 2011 at 6:34 pm #5713
          Anonymous

            You can also try a very similar method in PyRosetta from rosetta.protocols.docking.setup_foldtree which requires a Vector1 argument containing the movable jumps. For example, using test_dock.pdb:

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

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