util.cc File Reference

#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/conformation/Conformation.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/Energies.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/kinematics/FoldTree.hh>
#include <protocols/jd2/util.hh>
#include <protocols/moves/MoverContainer.hh>
#include <protocols/moves/TrialMover.hh>
#include <protocols/moves/MonteCarlo.hh>
#include <protocols/minimization_packing/MinMover.hh>
#include <protocols/minimization_packing/PackRotamersMover.hh>
#include <protocols/minimization_packing/TaskAwareMinMover.hh>
#include <protocols/rigid/RigidBodyMover.hh>
#include <basic/MetricValue.hh>
#include <core/pose/metrics/simple_calculators/SasaCalculatorLegacy.hh>
#include <core/pose/metrics/CalculatorFactory.hh>
#include <protocols/simple_pose_metric_calculators/NumberHBondsCalculator.hh>
#include <protocols/simple_pose_metric_calculators/BuriedUnsatisfiedPolarsCalculator.hh>
#include <protocols/pose_metric_calculators/PackstatCalculator.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/run.OptionKeys.gen.hh>
#include <basic/datacache/DataMap.hh>
#include <basic/Tracer.hh>
#include <utility/tag/Tag.hh>
#include <utility/tag/XMLSchemaGeneration.hh>
#include <utility/excn/Exceptions.hh>
#include <string>
#include <core/pack/task/ResidueLevelTask.hh>

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

Functions
static basic::Tracer	TR ("NCBB")
Size	protocols::ncbb::give_dihedral_index (core::Size n, utility::vector1< char > uniqs, std::string dihedral_pattern, std::string alpha_beta_pattern)
Size	protocols::ncbb::get_number_dihedrals (utility::vector1< char > uniqs, std::string const &dihedral_pattern, std::string const &alpha_beta_pattern)
void	protocols::ncbb::count_uniq_char (std::string pattern, core::Size &num, utility::vector1< char > &uniqs)
void	protocols::ncbb::ncbb_design_main_loop (core::Size loop_num, core::Size pert_num, core::pose::Pose pose, TrialMoverOP pert_trial, utility::vector1< core::Size > designable_positions, core::Size pep_start, core::Size pep_end, TaskAwareMinMoverOP desn_ta_min, core::scoring::ScoreFunctionOP score_fxn, MonteCarloOP mc)
void	protocols::ncbb::final_design_min (core::pose::Pose &pose, ScoreFunctionOP score_fxn_, core::pack::task::TaskFactoryOP desn_tf)
void	protocols::ncbb::calculate_statistics (core::pose::Pose const &pose, core::scoring::ScoreFunctionOP score_fxn)
	Calculate various statistics, and add them to the current JD2 job. More...
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_, core::Size &pert_pep_num_rep_, core::Size &pert_num_, core::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_)
void	protocols::ncbb::add_attributes_for_common_options (AttributeList &attlist)

Function Documentation

TR()

static basic::Tracer TR ( "NCBB"  )

static