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demo.D070_Refinement Namespace Reference

Functions

def sample_refinement
 Methods. More...
 

Variables

tuple parser = optparse.OptionParser()
 INTERPRETING RESULTS. More...
 
string default = '../test/data/test_in.pdb'
 
string help = 'the PDB file containing the protein to refine'
 
 pdb_filename = options.pdb_filename
 
tuple kT = float(options.kT)
 
tuple smallmoves = int(options.smallmoves)
 
tuple shearmoves = int(options.shearmoves)
 
tuple backbone_angle_max = int(options.backbone_angle_max)
 
tuple cycles = int(options.cycles)
 
tuple jobs = int(options.jobs)
 
 job_output = options.job_output
 

Function Documentation

def demo.D070_Refinement.sample_refinement (   pdb_filename,
  kT = 1.0,
  smallmoves = 3,
  shearmoves = 5,
  backbone_angle_max = 7,
  cycles = 9,
  jobs = 1,
  job_output = 'refine_output' 
)

Methods.

Performs fullatom structural refinement on the input  <pdb_filename>  by
    perturbing backbone torsion angles with a maximum perturbation of
    <backbone_angle_max>  for  <cycles>  trials of
    <smallmoves>  perturbations of a random residue's phi or psi and
    <shearmoves>  perturbations of a random residue's phi and the preceding
    residue's psi followed by gradient based backbone torsion angle
    minimization and sidechain packing with an acceptance criteria scaled
    by  <kT>.  <jobs>  trajectories are performed, continually exporting
    structures to a PyMOL instance.
    Output structures are named  <job_output>_(job#).pdb.

References ObjexxFCL.len(), name, pyrosetta.distributed.io.pose_from_file, fmt.print(), basic::options::OptionKeys::run::PyMOLMover.PyMOLMover, basic::options::OptionKeys::relax::range.range, basic::options::OptionKeys::DisulfideInsertion.scorefxn, and pyrosetta.standard_packer_task().

Variable Documentation

tuple demo.D070_Refinement.backbone_angle_max = int(options.backbone_angle_max)
tuple demo.D070_Refinement.cycles = int(options.cycles)
string demo.D070_Refinement.default = '../test/data/test_in.pdb'
string demo.D070_Refinement.help = 'the PDB file containing the protein to refine'
demo.D070_Refinement.job_output = options.job_output
tuple demo.D070_Refinement.jobs = int(options.jobs)
tuple demo.D070_Refinement.kT = float(options.kT)
tuple demo.D070_Refinement.parser = optparse.OptionParser()

INTERPRETING RESULTS.

COMMANDLINE COMPATIBILITY

demo.D070_Refinement.pdb_filename = options.pdb_filename
tuple demo.D070_Refinement.shearmoves = int(options.shearmoves)
tuple demo.D070_Refinement.smallmoves = int(options.smallmoves)