protocols::ncbb Namespace Reference

Namespaces
	oop

Classes
class	NcbbDockDesignProtocol
class	NcbbDockDesignProtocolCreator
class	ResidueReplacementRebuildMover
	A simple method to mutate a pose fairly destructively, and barely recover. More...
class	ResidueReplacementRebuildMoverCreator
class	SecStructFinder
class	SecStructFinderCreator
class	SecStructMinimizeMover
class	SecStructMinimizeMoverCreator
class	SecStructMinimizeMultiFunc
	class for fitting a length of secondary structure keeping the same dihedrals More...

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
typedef utility::pointer::shared_ptr< ResidueReplacementRebuildMover >	ResidueReplacementRebuildMoverOP
typedef utility::pointer::shared_ptr< ResidueReplacementRebuildMover const >	ResidueReplacementRebuildMoverCOP
typedef utility::pointer::shared_ptr< SecStructFinder >	SecStructFinderOP
typedef utility::pointer::shared_ptr< SecStructFinder const >	SecStructFinderCOP
typedef utility::pointer::shared_ptr< SecStructFinderCreator >	SecStructFinderCreatorOP
typedef utility::pointer::shared_ptr< SecStructFinderCreator const >	SecStructFinderCreatorCOP
typedef utility::pointer::shared_ptr< SecStructMinimizeMover >	SecStructMinimizeMoverOP
typedef utility::pointer::shared_ptr< SecStructMinimizeMover const >	SecStructMinimizeMoverCOP
typedef utility::pointer::shared_ptr< SecStructMinimizeMoverCreator >	SecStructMinimizeMoverCreatorOP
typedef utility::pointer::shared_ptr< SecStructMinimizeMoverCreator const >	SecStructMinimizeMoverCreatorCOP

Functions
std::ostream &	operator<< (std::ostream &os, ResidueReplacementRebuildMover const &mover)
	private methods /// More...
bool	increment_dihedrals (utility::vector1< Real > &dihedrals, Real const dihedral_min_, Real const dihedral_max_, Real const bin_size_)
Size	give_dihedral_index (core::Size n, utility::vector1< char > uniqs, std::string dihedral_pattern, std::string alpha_beta_pattern)
Size	get_number_dihedrals (utility::vector1< char > uniqs, std::string const &dihedral_pattern, std::string const &alpha_beta_pattern)
void	count_uniq_char (std::string pattern, core::Size &num, utility::vector1< char > &uniqs)
void	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	final_design_min (core::pose::Pose &pose, ScoreFunctionOP score_fxn_, core::pack::task::TaskFactoryOP desn_tf)
void	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	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_, 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	add_attributes_for_common_options (AttributeList &attlist)
void	add_attributes_for_common_options (utility::tag::AttributeList &attlist)

Typedef Documentation

NcbbDockDesignProtocolCOP

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

NcbbDockDesignProtocolCreatorCOP

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

NcbbDockDesignProtocolCreatorOP

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

NcbbDockDesignProtocolOP

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

ResidueReplacementRebuildMoverCOP

typedef utility::pointer::shared_ptr< ResidueReplacementRebuildMover const > protocols::ncbb::ResidueReplacementRebuildMoverCOP

ResidueReplacementRebuildMoverOP

typedef utility::pointer::shared_ptr< ResidueReplacementRebuildMover > protocols::ncbb::ResidueReplacementRebuildMoverOP

SecStructFinderCOP

typedef utility::pointer::shared_ptr< SecStructFinder const > protocols::ncbb::SecStructFinderCOP

SecStructFinderCreatorCOP

typedef utility::pointer::shared_ptr< SecStructFinderCreator const > protocols::ncbb::SecStructFinderCreatorCOP

SecStructFinderCreatorOP

typedef utility::pointer::shared_ptr< SecStructFinderCreator > protocols::ncbb::SecStructFinderCreatorOP

SecStructFinderOP

typedef utility::pointer::shared_ptr< SecStructFinder > protocols::ncbb::SecStructFinderOP

SecStructMinimizeMoverCOP

typedef utility::pointer::shared_ptr< SecStructMinimizeMover const > protocols::ncbb::SecStructMinimizeMoverCOP

SecStructMinimizeMoverCreatorCOP

typedef utility::pointer::shared_ptr< SecStructMinimizeMoverCreator const > protocols::ncbb::SecStructMinimizeMoverCreatorCOP

SecStructMinimizeMoverCreatorOP

typedef utility::pointer::shared_ptr< SecStructMinimizeMoverCreator > protocols::ncbb::SecStructMinimizeMoverCreatorOP

SecStructMinimizeMoverOP

typedef utility::pointer::shared_ptr< SecStructMinimizeMover > protocols::ncbb::SecStructMinimizeMoverOP

Function Documentation

add_attributes_for_common_options() [1/2]

void protocols::ncbb::add_attributes_for_common_options

(

AttributeList &

attlist

)

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

add_attributes_for_common_options() [2/2]

void protocols::ncbb::add_attributes_for_common_options

(

utility::tag::AttributeList &

attlist

)

calculate_statistics()

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.

References protocols::jd2::add_string_real_pair_to_current_job(), core::pose::Pose::energies(), core::scoring::hbond_bb_sc, core::scoring::hbond_lr_bb, core::scoring::hbond_sc, core::scoring::hbond_sr_bb, core::pose::Pose::metric(), core::scoring::Energies::total_energies(), and protocols::toolbox::rigid_body::translate().

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

count_uniq_char()

void protocols::ncbb::count_uniq_char	(	std::string	pattern,
		core::Size &	num,
		utility::vector1< char > &	uniqs
	)

Referenced by protocols::ncbb::SecStructFinder::apply(), protocols::ncbb::SecStructMinimizeMover::apply(), and protocols::ncbb::SecStructMinimizeMultiFunc::SecStructMinimizeMultiFunc().

final_design_min()

void protocols::ncbb::final_design_min	(	core::pose::Pose &	pose,
		ScoreFunctionOP	score_fxn_,
		core::pack::task::TaskFactoryOP	desn_tf
	)

References core::pose::Pose::size().

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

get_number_dihedrals()

core::Size protocols::ncbb::get_number_dihedrals	(	utility::vector1< char >	uniqs,
		std::string const &	dihedral_pattern,
		std::string const &	alpha_beta_pattern
	)

Referenced by protocols::ncbb::SecStructFinder::apply(), and protocols::ncbb::SecStructMinimizeMover::apply().

give_dihedral_index()

core::Size protocols::ncbb::give_dihedral_index	(	core::Size	n,
		utility::vector1< char >	uniqs,
		std::string	dihedral_pattern,
		std::string	alpha_beta_pattern
	)

Referenced by protocols::ncbb::SecStructMinimizeMover::add_dihedral_constraints_to_pose(), protocols::ncbb::SecStructFinder::apply(), and protocols::ncbb::SecStructFinder::show_current_dihedrals().

increment_dihedrals()

bool protocols::ncbb::increment_dihedrals	(	utility::vector1< Real > &	dihedrals,
		Real const	dihedral_min_,
		Real const	dihedral_max_,
		Real const	bin_size_
	)

Referenced by protocols::ncbb::SecStructFinder::apply().

init_common_options()

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_
	)

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

ncbb_design_main_loop()

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
	)

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

operator<<()

std::ostream & protocols::ncbb::operator<<	(	std::ostream &	os,
		ResidueReplacementRebuildMover const &	mover
	)

private methods ///

References protocols::ncbb::ResidueReplacementRebuildMover::show().

setup_filter_stats()

void protocols::ncbb::setup_filter_stats

(

)

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

setup_pert_foldtree()

void protocols::ncbb::setup_pert_foldtree

(

core::pose::Pose &

pose

)

References core::kinematics::FoldTree::add_edge(), core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::kinematics::FoldTree::check_fold_tree(), core::kinematics::FoldTree::clear(), core::pose::Pose::conformation(), core::pose::Pose::fold_tree(), core::kinematics::FoldTree::num_jump(), core::kinematics::FoldTree::reorder(), and core::pose::residue_center_of_mass().

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