demo.D120_Ligand_interface Namespace Reference

Functions
def	sample_ligand_interface
	Methods. More...

Variables
int	counter = 0
	AddPyMOLObserver(test_pose, True) More...
tuple	parser = optparse.OptionParser()
	INTERPRETING RESULTS. More...
string	default = '../demos/data/test_lig.pdb'
string	help = 'the PDB file containing the ligand and protein to dock'
	pdb_filename = options.pdb_filename
	partners = options.partners
tuple	ligand_params = options.ligand_params.split(',')
tuple	jobs = int(options.jobs)
	job_output = options.job_output

Function Documentation

def demo.D120_Ligand_interface.sample_ligand_interface	(		pdb_filename,
			partners,
			ligand_params = [''],
			jobs = 1,
			job_output = 'ligand_output'
	)

Methods.

Performs ligand-protein docking using Rosetta fullatom docking
    (DockingHighRes) on the ligand-protein complex in  <pdb_filename>
    using the relative chain  <partners>  .
    If the ligand parameters (a .params file, see below) are not defaultly
    loaded into PyRosetta,  <ligand_params>  must supply the list of files
    including the ligand parameters.
    <jobs>  trajectories are performed with output structures named
    <job_output>_(job#).pdb.

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

Variable Documentation

int demo.D120_Ligand_interface.counter = 0

AddPyMOLObserver(test_pose, True)

string demo.D120_Ligand_interface.default = '../demos/data/test_lig.pdb'

string demo.D120_Ligand_interface.help = 'the PDB file containing the ligand and protein to dock'

demo.D120_Ligand_interface.job_output = options.job_output

tuple demo.D120_Ligand_interface.jobs = int(options.jobs)

tuple demo.D120_Ligand_interface.ligand_params = options.ligand_params.split(',')

tuple demo.D120_Ligand_interface.parser = optparse.OptionParser()

INTERPRETING RESULTS.

COMMANDLINE COMPATIBILITY

demo.D120_Ligand_interface.partners = options.partners

Referenced by add_rosetta_options_7(), and DockGlycansProtocol.apply().

demo.D120_Ligand_interface.pdb_filename = options.pdb_filename