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)

Referenced by add_rosetta_options_10(), add_rosetta_options_12(), add_rosetta_options_13(), add_rosetta_options_14(), APDBCMover.apply(), and main().

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)