demo.D080_Loop_modeling Namespace Reference

Functions
def	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. More...

Variables
	extra_options
	parser = optparse.OptionParser()
	INTERPRETING RESULTS. More...
	dest
	default
	help
	options
	args
	pdb_filename = options.pdb_filename
	loop_begin = int(options.loop_begin)
	loop_end = int(options.loop_end)
	loop_cutpoint = int(options.loop_cutpoint)
	frag_filename = options.frag_filename
	frag_length = int(options.frag_length)
	outer_cycles_low = int(options.outer_cycles_low)
	inner_cycles_low = int(options.inner_cycles_low)
	init_temp_low = float(options.init_temp_low)
	final_temp_low = float(options.final_temp_low)
	outer_cycles_high = int(options.outer_cycles_high)
	inner_cycles_high = int(options.inner_cycles_high)
	init_temp_high = float(options.init_temp_high)
	final_temp_high = float(options.final_temp_high)
	jobs = int(options.jobs)
	job_output = options.job_output

Function Documentation

sample_single_loop_modeling()

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

Variable Documentation

args

demo.D080_Loop_modeling.args

default

demo.D080_Loop_modeling.default

dest

demo.D080_Loop_modeling.dest

extra_options

demo.D080_Loop_modeling.extra_options

final_temp_high

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

final_temp_low

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

frag_filename

demo.D080_Loop_modeling.frag_filename = options.frag_filename

frag_length

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

Referenced by get_min_frag_rmsd(), homolog_finder(), main(), SwapElementsMover1.pick_fragments(), SwapElementsMover2.pick_fragments(), pick_fragments(), VarLengthBuildKristin.public_pick_fragments(), register_options(), and run().

help

demo.D080_Loop_modeling.help

init_temp_high

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

init_temp_low

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

inner_cycles_high

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

inner_cycles_low

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

job_output

demo.D080_Loop_modeling.job_output = options.job_output

jobs

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

loop_begin

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

Referenced by ccd_close_zf_chainbreak(), diversify_sam_loop_test(), dna_dr_loop_test(), do_KIC(), loop_modeling_test(), main(), not1_loop_test(), setup_loops_fragment_libraries_with_ss(), setup_loops_from_mapping(), and NativeEnsemble.write_schema_to_db().

loop_cutpoint

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

loop_end

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

options

demo.D080_Loop_modeling.options

outer_cycles_high

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

outer_cycles_low

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

parser

demo.D080_Loop_modeling.parser = optparse.OptionParser()

INTERPRETING RESULTS.

COMMANDLINE COMPATIBILITY

pdb_filename

demo.D080_Loop_modeling.pdb_filename = options.pdb_filename