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demo.D100_Docking Namespace Reference

Functions

def sample_docking
 Methods. More...
 

Variables

int counter = 0
 AddPyMOLObserver(test_pose, True) More...
 
tuple parser = optparse.OptionParser()
 alternate application of the DockingProtocol pieces docking_low.apply(test_pose) docking_high.apply(test_pose) More...
 
string default = '../test/data/test_dock.pdb'
 
string help = 'the PDB file containing the proteins to dock'
 
 pdb_filename = options.pdb_filename
 
 partners = options.partners
 
tuple translation = float(options.translation)
 
tuple rotation = float(options.rotation)
 
tuple jobs = int(options.jobs)
 
 job_output = options.job_output
 

Function Documentation

def demo.D100_Docking.sample_docking (   pdb_filename,
  partners,
  translation = 3.0,
  rotation = 8.0,
  jobs = 1,
  job_output = 'dock_output' 
)

Methods.

Performs protein-protein docking using the Rosetta standard DockingProtocol
    on the proteins in  <pdb_filename>  using the relative chain
    <partners>  with an initial perturbation using  <translation>
    Angstroms and  <rotation>  degrees.  <jobs>  trajectories are performed
    with output structures named  <job_output>_(job#).pdb.
    structures are exported to a PyMOL instance.

References pyrosetta.create_score_function, pyrosetta.distributed.io.pose_from_file, and pyrosetta.Vector1().

Variable Documentation

int demo.D100_Docking.counter = 0

AddPyMOLObserver(test_pose, True)

string demo.D100_Docking.default = '../test/data/test_dock.pdb'
string demo.D100_Docking.help = 'the PDB file containing the proteins to dock'
demo.D100_Docking.job_output = options.job_output
tuple demo.D100_Docking.jobs = int(options.jobs)
tuple demo.D100_Docking.parser = optparse.OptionParser()

alternate application of the DockingProtocol pieces docking_low.apply(test_pose) docking_high.apply(test_pose)

INTERPRETING RESULTS.

INTERPRETING RESULTS COMMANDLINE COMPATIBILITY

demo.D100_Docking.partners = options.partners
demo.D100_Docking.pdb_filename = options.pdb_filename
tuple demo.D100_Docking.rotation = float(options.rotation)
tuple demo.D100_Docking.translation = float(options.translation)