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)

Referenced by add_rosetta_options_4(), and numeric::EulerAngles< typename >.angular_distance_between().

tuple demo.D100_Docking.translation = float(options.translation)

Referenced by add_rosetta_options_4(), and numeric::VoxelGrid< typename >.Translate().