demo.D070_Refinement Namespace Reference

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

Variables
	extra_options
	parser = optparse.OptionParser()
	INTERPRETING RESULTS. More...
	dest
	default
	help
	options
	args
	pdb_filename = options.pdb_filename
	kT = float(options.kT)
	smallmoves = int(options.smallmoves)
	shearmoves = int(options.shearmoves)
	backbone_angle_max = int(options.backbone_angle_max)
	cycles = int(options.cycles)
	jobs = int(options.jobs)
	job_output = options.job_output

Function Documentation

sample_refinement()

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(), pyrosetta.distributed.io.pose_from_file, print(), basic::options::OptionKeys::run::PyMOLMover.PyMOLMover, range, oop_conformations.scorefxn, pyrosetta.standard_packer_task(), and str().

Variable Documentation

args

demo.D070_Refinement.args

backbone_angle_max

demo.D070_Refinement.backbone_angle_max = int(options.backbone_angle_max)

cycles

demo.D070_Refinement.cycles = int(options.cycles)

default

demo.D070_Refinement.default

dest

demo.D070_Refinement.dest

extra_options

demo.D070_Refinement.extra_options

help

demo.D070_Refinement.help

job_output

demo.D070_Refinement.job_output = options.job_output

jobs

demo.D070_Refinement.jobs = int(options.jobs)

kT

demo.D070_Refinement.kT = float(options.kT)

options

demo.D070_Refinement.options

parser

demo.D070_Refinement.parser = optparse.OptionParser()

INTERPRETING RESULTS.

COMMANDLINE COMPATIBILITY

pdb_filename

demo.D070_Refinement.pdb_filename = options.pdb_filename

shearmoves

demo.D070_Refinement.shearmoves = int(options.shearmoves)

smallmoves

demo.D070_Refinement.smallmoves = int(options.smallmoves)