#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/import_pose/import_pose.hh>
#include <core/conformation/Conformation.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/operation/TaskOperation.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/constraints/util.hh>
#include <core/scoring/ScoringManager.hh>
#include <core/chemical/VariantType.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/MoveMap.hh>
#include <utility/pointer/owning_ptr.hh>
#include <protocols/jd2/JobDistributor.hh>
#include <protocols/jd2/Job.hh>
#include <protocols/moves/MoverContainer.hh>
#include <protocols/moves/TrialMover.hh>
#include <protocols/moves/MonteCarlo.hh>
#include <protocols/moves/PyMolMover.hh>
#include <protocols/moves/RepeatMover.hh>
#include <protocols/simple_moves/MinMover.hh>
#include <protocols/simple_moves/PackRotamersMover.hh>
#include <protocols/simple_moves/RotamerTrialsMover.hh>
#include <protocols/simple_moves/TaskAwareMinMover.hh>
#include <protocols/simple_moves/BackboneMover.fwd.hh>
#include <protocols/simple_moves/BackboneMover.hh>
#include <protocols/simple_moves/hbs/HbsPatcher.hh>
#include <protocols/rigid/RigidBodyMover.hh>
#include <protocols/rigid/RB_geometry.hh>
#include <basic/MetricValue.hh>
#include <core/pose/metrics/CalculatorFactory.hh>
#include <core/pose/metrics/simple_calculators/SasaCalculatorLegacy.hh>
#include <protocols/toolbox/pose_metric_calculators/NumberHBondsCalculator.hh>
#include <protocols/toolbox/pose_metric_calculators/BuriedUnsatisfiedPolarsCalculator.hh>
#include <protocols/toolbox/pose_metric_calculators/PackstatCalculator.hh>
#include <basic/options/util.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/run.OptionKeys.gen.hh>
#include <basic/datacache/DataMap.hh>
#include <basic/Tracer.hh>
#include <utility/exit.hh>
#include <utility/excn/Exceptions.hh>
#include <string>
#include <sstream>

Namespaces
	protocols
	The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.

	protocols::ncbb

Functions
void	protocols::ncbb::ncbb_design_main_loop (Size loop_num, Size pert_num, core::pose::Pose pose, TrialMoverOP pert_trial, utility::vector1< Size > designable_positions, Size pep_start, Size pep_end, TaskAwareMinMoverOP desn_ta_min, core::scoring::ScoreFunctionOP score_fxn, MonteCarloOP mc)

void	protocols::ncbb::calculate_statistics (protocols::jd2::JobOP curr_job, core::pose::Pose pose, core::scoring::ScoreFunctionOP score_fxn)

void	protocols::ncbb::setup_pert_foldtree (core::pose::Pose &pose)

void	protocols::ncbb::setup_filter_stats ()

void	protocols::ncbb::init_common_options (utility::tag::TagCOP tag, basic::datacache::DataMap &data, ScoreFunctionOP score_fxn_, Real &mc_temp_, Real &pert_mc_temp_, Real &pert_dock_rot_mag_, Real &pert_dock_trans_mag_, Real &pert_pep_small_temp_, Real &pert_pep_small_H_, Real &pert_pep_small_L_, Real &pert_pep_small_E_, Real &pert_pep_shear_temp_, Real &pert_pep_shear_H_, Real &pert_pep_shear_L_, Real &pert_pep_shear_E_, Size &pert_pep_num_rep_, Size &pert_num_, Size &dock_design_loop_num_, bool &no_design_, bool &final_design_min_, bool &use_soft_rep_, bool &mc_initial_pose_, bool &pymol_, bool &keep_history_)

Namespaces

Functions