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Rosetta
2019.07
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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 | |
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 , |
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inner_cycles_low = 5 , |
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init_temp_low = 2.0 , |
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final_temp_low = 0.8 , |
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outer_cycles_high = 5 , |
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inner_cycles_high = 10 , |
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init_temp_high = 2.2 , |
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final_temp_high = 0.6 , |
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jobs = 1 , |
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job_output = 'loop_output' |
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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.
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 |