protocols::ncbb Namespace Reference

Namespaces
	oop

Classes
class	NcbbDockDesignProtocol
class	NcbbDockDesignProtocolCreator

Typedefs
typedef utility::pointer::shared_ptr < NcbbDockDesignProtocol >	NcbbDockDesignProtocolOP
typedef utility::pointer::shared_ptr < NcbbDockDesignProtocol const >	NcbbDockDesignProtocolCOP
typedef utility::pointer::shared_ptr < NcbbDockDesignProtocolCreator >	NcbbDockDesignProtocolCreatorOP
typedef utility::pointer::shared_ptr < NcbbDockDesignProtocolCreator const >	NcbbDockDesignProtocolCreatorCOP

Functions
void	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	calculate_statistics (protocols::jd2::JobOP curr_job, core::pose::Pose pose, core::scoring::ScoreFunctionOP score_fxn)
void	setup_pert_foldtree (core::pose::Pose &pose)
void	setup_filter_stats ()
void	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_)

Typedef Documentation

typedef utility::pointer::shared_ptr< NcbbDockDesignProtocol const > protocols::ncbb::NcbbDockDesignProtocolCOP

typedef utility::pointer::shared_ptr< NcbbDockDesignProtocolCreator const > protocols::ncbb::NcbbDockDesignProtocolCreatorCOP

typedef utility::pointer::shared_ptr< NcbbDockDesignProtocolCreator > protocols::ncbb::NcbbDockDesignProtocolCreatorOP

typedef utility::pointer::shared_ptr< NcbbDockDesignProtocol > protocols::ncbb::NcbbDockDesignProtocolOP

Function Documentation

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

References core::pose::Pose::energies(), hbond_bb_sc, hbond_lr_bb, hbond_sc, hbond_sr_bb, core::pose::Pose::metric(), option, core::scoring::Energies::total_energies(), protocols::toolbox::rigid_body::translate(), and basic::MetricValue< T >::value().

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_
	)

References basic::datacache::DataMap::get_ptr(), and basic::datacache::DataMap::has().

Referenced by protocols::ncbb::NcbbDockDesignProtocol::parse_my_tag(), and protocols::ncbb::oop::OopDockDesignProtocol::parse_my_tag().

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
	)

References core::conformation::Residue::aa(), aa_cys, aa_gly, aa_pro, core::pose::Pose::residue(), and core::conformation::TR().

void protocols::ncbb::setup_filter_stats

(

)

References core::pose::metrics::CalculatorFactory::Instance(), and core::pose::metrics::CalculatorFactory::register_calculator().

void protocols::ncbb::setup_pert_foldtree

(

core::pose::Pose &

pose

)

References core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), core::pose::Pose::fold_tree(), and core::pose::residue_center_of_mass().

Referenced by protocols::ncbb::NcbbDockDesignProtocol::apply(), and protocols::ncbb::oop::OopDockDesignProtocol::apply().