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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
demo.D120_Ligand_interface.pdb_filename = options.pdb_filename