backrub Namespace Reference

Functions
BooleanOptionKey const	backrub ("backrub")
IntegerVectorOptionKey const	pivot_residues ("backrub:pivot_residues")
StringVectorOptionKey const	pivot_atoms ("backrub:pivot_atoms")
IntegerOptionKey const	min_atoms ("backrub:min_atoms")
IntegerOptionKey const	max_atoms ("backrub:max_atoms")
IntegerOptionKey const	ntrials ("backrub:ntrials")
RealOptionKey const	sc_prob ("backrub:sc_prob")
RealOptionKey const	sm_prob ("backrub:sm_prob")
RealOptionKey const	sc_prob_uniform ("backrub:sc_prob_uniform")
RealOptionKey const	sc_prob_withinrot ("backrub:sc_prob_withinrot")
RealOptionKey const	mc_kt ("backrub:mc_kt")
RealOptionKey const	mm_bend_weight ("backrub:mm_bend_weight")
BooleanOptionKey const	initial_pack ("backrub:initial_pack")
FileOptionKey const	minimize_movemap ("backrub:minimize_movemap")
BooleanOptionKey const	trajectory ("backrub:trajectory")
BooleanOptionKey const	trajectory_gz ("backrub:trajectory_gz")
IntegerOptionKey const	trajectory_stride ("backrub:trajectory_stride")

Variables
tuple	parser = optparse.OptionParser()
string	help = "number of Monte Carlo trials to run"
list	rosetta_args = [" ".join(sys.argv[:sys.argv.index("--")+1])]
tuple	import_time_start = time.time()
tuple	import_time_end = time.time()
tuple	main_task_factory = core.pack.task.TaskFactory()
tuple	score_fxn = core.scoring.get_score_function()
tuple	energymethodoptions = score_fxn.energy_method_options()
tuple	backrubmover = protocols.moves.BackrubMover()
tuple	smallmover = protocols.moves.SmallMover()
tuple	movemap = core.kinematics.MoveMap()
tuple	sidechainmover = protocols.moves.SidechainMover()
tuple	packrotamersmover = protocols.moves.PackRotamersMover()
tuple	input_jobs = protocols.jobdist.load_s_and_l()
	custom_fold_tree = False
tuple	input_pose = core.pose.Pose()

Function Documentation

BooleanOptionKey const backrub::backrub

(

"backrub"

)

BooleanOptionKey const backrub::initial_pack

(

"backrub:initial_pack"

)

Referenced by main().

IntegerOptionKey const backrub::max_atoms

(

"backrub:max_atoms"

)

Referenced by main().

RealOptionKey const backrub::mc_kt

(

"backrub:mc_kt"

)

Referenced by main().

IntegerOptionKey const backrub::min_atoms

(

"backrub:min_atoms"

)

Referenced by main().

FileOptionKey const backrub::minimize_movemap

(

"backrub:minimize_movemap"

)

Referenced by main().

RealOptionKey const backrub::mm_bend_weight

(

"backrub:mm_bend_weight"

)

Referenced by main().

IntegerOptionKey const backrub::ntrials

(

"backrub:ntrials"

)

Referenced by main().

StringVectorOptionKey const backrub::pivot_atoms

(

"backrub:pivot_atoms"

)

Referenced by CoupledMovesProtocol::CoupledMovesProtocol(), and main().

IntegerVectorOptionKey const backrub::pivot_residues

(

"backrub:pivot_residues"

)

Referenced by main().

RealOptionKey const backrub::sc_prob

(

"backrub:sc_prob"

)

Referenced by main().

RealOptionKey const backrub::sc_prob_uniform

(

"backrub:sc_prob_uniform"

)

Referenced by main().

RealOptionKey const backrub::sc_prob_withinrot

(

"backrub:sc_prob_withinrot"

)

Referenced by main().

RealOptionKey const backrub::sm_prob

(

"backrub:sm_prob"

)

Referenced by main().

BooleanOptionKey const backrub::trajectory

(

"backrub:trajectory"

)

Referenced by main().

BooleanOptionKey const backrub::trajectory_gz

(

"backrub:trajectory_gz"

)

Referenced by main().

IntegerOptionKey const backrub::trajectory_stride

(

"backrub:trajectory_stride"

)

Referenced by main().

Variable Documentation

tuple backrub.backrubmover = protocols.moves.BackrubMover()

backrub.custom_fold_tree = False

tuple backrub.energymethodoptions = score_fxn.energy_method_options()

Referenced by supercharge.apply(), HDdesignMover.calc_bb_E(), CoupledMovesProtocol.CoupledMovesProtocol(), supercharge.design_supercharge(), supercharge.design_supercharge_AvNAPSA(), and supercharge.prepack_input_structure().

string backrub.help = "number of Monte Carlo trials to run"

Referenced by utility::options::OptionCollection.add_built_in_options(), and utility::options::OptionCollection.load().

tuple backrub.import_time_end = time.time()

tuple backrub.import_time_start = time.time()

tuple backrub.input_jobs = protocols.jobdist.load_s_and_l()

Referenced by main(), and match_main().

tuple backrub.input_pose = core.pose.Pose()

Referenced by main().

tuple backrub.main_task_factory = core.pack.task.TaskFactory()

Referenced by main().

tuple backrub.movemap = core.kinematics.MoveMap()

tuple backrub.packrotamersmover = protocols.moves.PackRotamersMover()

tuple backrub.parser = optparse.OptionParser()

list backrub.rosetta_args = [" ".join(sys.argv[:sys.argv.index("--")+1])]

tuple backrub.score_fxn = core.scoring.get_score_function()

Referenced by HbsDesignMover.apply(), PeptoidDesignMover.apply(), OopDesignMover.apply(), DougsDockDesignMinimizeMagicMover.apply(), find_close_motifs(), and main().

tuple backrub.sidechainmover = protocols.moves.SidechainMover()

tuple backrub.smallmover = protocols.moves.SmallMover()