D060_Folding.py File Reference

Namespaces
	demo.D060_Folding

Functions
def	demo.D060_Folding.sample_folding (sequence, long_frag_filename, long_frag_length, short_frag_filename, short_frag_length, kT=3.0, long_inserts=1, short_inserts=3, cycles=40, jobs=1, job_output='fold_output')
	Methods. More...
def	demo.D060_Folding.guess_disulfides (pose, cutoff=6.0)
	if you create a custom protocol, you may have additional variables to reset, such as kT More...

Variables
	demo.D060_Folding.extra_options
	demo.D060_Folding.scorefxn_low = create_score_function('score3')
	AddPyMOLObserver(test_pose, True) More...
	demo.D060_Folding.scorefxn_high = get_fa_scorefxn()
	demo.D060_Folding.folding_mover = protocols.moves.SequenceMover()
	add any other moves you desire More...
	demo.D060_Folding.mc = MonteCarlo(test_pose, scorefxn_low, kT)
	demo.D060_Folding.trial = TrialMover(folding_mover, mc)
	demo.D060_Folding.folding = protocols.moves.RepeatMover(trial, cycles)
	for each trajectory, try cycles number of applications More...
	demo.D060_Folding.jd = PyJobDistributor(job_output, jobs, scorefxn_high)
list	demo.D060_Folding.scores = [0]*(jobs + 1)
int	demo.D060_Folding.counter = 0
	demo.D060_Folding.parser = optparse.OptionParser()
	INTERPRETING RESULTS. More...
	demo.D060_Folding.dest
	demo.D060_Folding.default
	demo.D060_Folding.help
	demo.D060_Folding.options
	demo.D060_Folding.args
	demo.D060_Folding.pose = Pose()
	demo.D060_Folding.fasta_filename = options.fasta_filename
	demo.D060_Folding.f = open(fasta_filename, 'r')
	demo.D060_Folding.sequence = f.readlines()
	demo.D060_Folding.pdb_filename = options.pdb_filename;
	demo.D060_Folding.long_frag_filename = options.long_frag_filename
	demo.D060_Folding.long_frag_length = int(options.long_frag_length)
	demo.D060_Folding.short_frag_filename = options.short_frag_filename
	demo.D060_Folding.short_frag_length = int(options.short_frag_length)
	demo.D060_Folding.kT = float(options.kT)
	demo.D060_Folding.long_inserts = int(options.long_inserts)
	demo.D060_Folding.short_inserts = int(options.short_inserts)
	demo.D060_Folding.cycles = int(options.cycles)
	demo.D060_Folding.jobs = int(options.jobs)
	demo.D060_Folding.job_output = options.job_output