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DockingProtocol

Runs the full (post refactoring) docking protocol with the defaults currently in trunk. This mover is not currently sensitive to symmetry.

<DockingProtocol name="&string" docking_score_low="(interchain_cen &string)" docking_score_high="(docking &string)" low_res_protocol_only="(0 &bool)" docking_local_refine(0 &bool) dock_min="(0 &bool)" ignore_default_docking_task="(0 &bool)" task_operations="('' comma-separated list)" partners="(&string)"/>
  • docking_score_low: score function used in centroid mode of the docking steps
  • docking_score_high: score function used in full atom mode of docking
  • low_res_protocol_only: if true, only do centroid level docking
  • docking_local_refine: if true skip the centroid level and only do full atom docking
  • dock_min: if true minimize the final full atom structure
  • partners: allows fold tree modifications to dock across multiple chains (example: docking chains L+H with A is partners="LH_A")
  • ignore_default_docking_task: allows you to ignore the default DockingTaskFactory set by docking and give it your own definition of an interface. Not suggested.
  • task_operations: comma separated list of TaskOperations, these will be appended onto that defined by DockingTaskFactory, unless ignore_default_docking_task is turned on.
  • partners: _ separated list of chains to dock.

See Also