D060_Folding.py File Reference

Namespaces
	demo.D060_Folding

Functions
def	demo.D060_Folding.sample_folding
	Methods. More...
def	demo.D060_Folding.guess_disulfides
	if you create a custom protocol, you may have additional variables to reset, such as kT More...

Variables
tuple	demo.D060_Folding.scorefxn_low = create_score_function('score3')
	AddPyMolObserver(test_pose, True) More...
tuple	demo.D060_Folding.scorefxn_high = get_fa_scorefxn()
tuple	demo.D060_Folding.folding_mover = SequenceMover()
	add any other moves you desire More...
tuple	demo.D060_Folding.mc = MonteCarlo(test_pose, scorefxn_low, kT)
tuple	demo.D060_Folding.trial = TrialMover(folding_mover, mc)
tuple	demo.D060_Folding.folding = RepeatMover(trial, cycles)
	for each trajectory, try cycles number of applications More...
tuple	demo.D060_Folding.jd = PyJobDistributor(job_output, jobs, scorefxn_high)
list	demo.D060_Folding.scores = [0]
int	demo.D060_Folding.counter = 0
tuple	demo.D060_Folding.parser = optparse.OptionParser()
	INTERPRETING RESULTS. More...
string	demo.D060_Folding.default = '../test/data/test_in.pdb'
string	demo.D060_Folding.help = 'the PDB file containing the protein to fold'
tuple	demo.D060_Folding.pose = Pose()
	demo.D060_Folding.fasta_filename = options.fasta_filename
tuple	demo.D060_Folding.f = open(fasta_filename, 'r')
tuple	demo.D060_Folding.sequence = f.readlines()
	demo.D060_Folding.pdb_filename = options.pdb_filename;
	demo.D060_Folding.long_frag_filename = options.long_frag_filename
tuple	demo.D060_Folding.long_frag_length = int(options.long_frag_length)
	demo.D060_Folding.short_frag_filename = options.short_frag_filename
tuple	demo.D060_Folding.short_frag_length = int(options.short_frag_length)
tuple	demo.D060_Folding.kT = float(options.kT)
tuple	demo.D060_Folding.long_inserts = int(options.long_inserts)
tuple	demo.D060_Folding.short_inserts = int(options.short_inserts)
tuple	demo.D060_Folding.cycles = int(options.cycles)
tuple	demo.D060_Folding.jobs = int(options.jobs)
	demo.D060_Folding.job_output = options.job_output