demo.D080_Loop_modeling Namespace Reference

Functions
def	sample_single_loop_modeling
	Methods. More...

Variables
tuple	parser = optparse.OptionParser()
	INTERPRETING RESULTS. More...
string	default = '../test/data/test_in.pdb'
string	help = 'the PDB file containing the loop to remodel'
	pdb_filename = options.pdb_filename
tuple	loop_begin = int(options.loop_begin)
tuple	loop_end = int(options.loop_end)
tuple	loop_cutpoint = int(options.loop_cutpoint)
	frag_filename = options.frag_filename
tuple	frag_length = int(options.frag_length)
tuple	outer_cycles_low = int(options.outer_cycles_low)
tuple	inner_cycles_low = int(options.inner_cycles_low)
tuple	init_temp_low = float(options.init_temp_low)
tuple	final_temp_low = float(options.final_temp_low)
tuple	outer_cycles_high = int(options.outer_cycles_high)
tuple	inner_cycles_high = int(options.inner_cycles_high)
tuple	init_temp_high = float(options.init_temp_high)
tuple	final_temp_high = float(options.final_temp_high)
tuple	jobs = int(options.jobs)
	job_output = options.job_output

Function Documentation

def demo.D080_Loop_modeling.sample_single_loop_modeling	(		pdb_filename,
			loop_begin,
			loop_end,
			loop_cutpoint,
			frag_filename,
			frag_length,
			outer_cycles_low = 2,
			inner_cycles_low = 5,
			init_temp_low = 2.0,
			final_temp_low = 0.8,
			outer_cycles_high = 5,
			inner_cycles_high = 10,
			init_temp_high = 2.2,
			final_temp_high = 0.6,
			jobs = 1,
			job_output = 'loop_output'
	)

Methods.

Performs simple single loop construction on the input  <pdb_filename>
    with loop from  <loop_begin>  to  <loop_end>  with a
    cutpoint at  <loop_cutpoint>  using fragments of length  <frag_length>
    in the file  <frag_filename>.  <jobs>  trajectories are performed,
    each using a low resolution (centroid) simulated annealing with
    <outer_cycles>  rounds and  <inner_cycles>  steps per round decrementing
    "temperature" from  <init_temp>  to  <final_temp>  geometrically.
    Output structures are named  <job_output>_(job#).pdb.

References pyrosetta.create_score_function, name, pyrosetta.distributed.io.pose_from_file, ObjexxFCL.pow(), basic::options::OptionKeys::run::PyMOLMover.PyMOLMover, basic::options::OptionKeys::relax::range.range, and demo.D060_Folding.scorefxn_high.

Variable Documentation

string demo.D080_Loop_modeling.default = '../test/data/test_in.pdb'

tuple demo.D080_Loop_modeling.final_temp_high = float(options.final_temp_high)

tuple demo.D080_Loop_modeling.final_temp_low = float(options.final_temp_low)

demo.D080_Loop_modeling.frag_filename = options.frag_filename

tuple demo.D080_Loop_modeling.frag_length = int(options.frag_length)

Referenced by main(), register_options(), and run().

string demo.D080_Loop_modeling.help = 'the PDB file containing the loop to remodel'

tuple demo.D080_Loop_modeling.init_temp_high = float(options.init_temp_high)

tuple demo.D080_Loop_modeling.init_temp_low = float(options.init_temp_low)

tuple demo.D080_Loop_modeling.inner_cycles_high = int(options.inner_cycles_high)

tuple demo.D080_Loop_modeling.inner_cycles_low = int(options.inner_cycles_low)

demo.D080_Loop_modeling.job_output = options.job_output

tuple demo.D080_Loop_modeling.jobs = int(options.jobs)

tuple demo.D080_Loop_modeling.loop_begin = int(options.loop_begin)

tuple demo.D080_Loop_modeling.loop_cutpoint = int(options.loop_cutpoint)

tuple demo.D080_Loop_modeling.loop_end = int(options.loop_end)

tuple demo.D080_Loop_modeling.outer_cycles_high = int(options.outer_cycles_high)

tuple demo.D080_Loop_modeling.outer_cycles_low = int(options.outer_cycles_low)

tuple demo.D080_Loop_modeling.parser = optparse.OptionParser()

INTERPRETING RESULTS.

COMMANDLINE COMPATIBILITY

demo.D080_Loop_modeling.pdb_filename = options.pdb_filename