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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