protocols::motifs::IRCollection Class Reference

#include <IRCollection.hh>

Collaboration diagram for protocols::motifs::IRCollection:

Public Member Functions
	IRCollection ()
	IRCollection (core::pose::Pose &pose, MotifLibrary &motifs, utility::vector1< core::Size > const &build_sites)
core::Size	nirotamers () const
void	find_closest_backbone (core::pose::Pose &pose, protocols::loops::LoopsOP const flexible_positions, utility::vector1< core::Size > &closest_pos, utility::vector1< core::Real > &closest_rmsd)
void	incorporate_motifs (core::pose::Pose &pose, protocols::loops::LoopsOP const flexible_positions)
void	try_for_more (core::pose::Pose &pose, protocols::loops::LoopsOP const flexible_positions, std::map< core::Size, MotifCOP > setpos, std::map< core::Size, core::conformation::ResidueCOP > setpos_ir, std::map< core::Size, bool > setpos_forward_info, core::Size start_depth)
bool	successful_loop_closure (core::pose::Pose &pose, protocols::loops::LoopsOP flexible_regions, std::map< core::Size, MotifCOP > &setpos, std::map< core::Size, core::conformation::ResidueCOP > &setpos_ir, std::map< core::Size, bool > &setpos_forward_info, core::conformation::Residue const &this_rotamer, core::Size const this_pos, MotifCOP this_motif, bool const this_forward_info)
std::string	make_motif_filename (std::map< core::Size, MotifCOP > &setpos, std::map< core::Size, bool > &setpos_forward_info, core::pose::Pose &pose)
core::Size	unique_id ()
void	reset_unique_id ()
void	increment_unique_id ()

Private Attributes
core::Size	unique_id_
MotifCOPs	motif_source_
utility::vector1< bool >	motif_forward_
utility::vector1< core::Size >	target_positions_
utility::vector1 < core::pack::rotamer_set::RotamerSetOP >	rotamer_sets_

Detailed Description

Definition at line 34 of file IRCollection.hh.

Constructor & Destructor Documentation

protocols::motifs::IRCollection::IRCollection

(

)

Definition at line 54 of file IRCollection.cc.

protocols::motifs::IRCollection::IRCollection	(	core::pose::Pose &	pose,
		MotifLibrary &	motifs,
		utility::vector1< core::Size > const &	build_sites
	)

Definition at line 56 of file IRCollection.cc.

References protocols::motifs::MotifLibrary::begin(), protocols::motifs::MotifLibrary::end(), motif_forward_, motif_source_, rotamer_sets_, and target_positions_.

Member Function Documentation

void protocols::motifs::IRCollection::find_closest_backbone	(	core::pose::Pose &	pose,
		protocols::loops::LoopsOP const	flexible_positions,
		utility::vector1< core::Size > &	closest_pos,
		utility::vector1< core::Real > &	closest_rmsd
	)

Definition at line 97 of file IRCollection.cc.

References protocols::motifs::backbone_stub_match(), core::pose::Pose::residue(), rotamer_sets_, and core::pose::Pose::total_residue().

Referenced by try_for_more().

void protocols::motifs::IRCollection::incorporate_motifs	(	core::pose::Pose &	pose,
		protocols::loops::LoopsOP const	flexible_positions
	)

Definition at line 133 of file IRCollection.cc.

References protocols::loops::loop_mover::refine::LoopMover_Refine_Backrub::apply(), core::scoring::ScoreFunctionFactory::create_score_function(), core::pose::Pose::dump_pdb(), core::scoring::methods::EnergyMethodOptions::exclude_DNA_DNA(), protocols::motifs::mutate_loops_for_search(), reset_unique_id(), and try_for_more().

void protocols::motifs::IRCollection::increment_unique_id ( )

inline

Definition at line 77 of file IRCollection.hh.

Referenced by try_for_more().

std::string protocols::motifs::IRCollection::make_motif_filename	(	std::map< core::Size, MotifCOP > &	setpos,
		std::map< core::Size, bool > &	setpos_forward_info,
		core::pose::Pose &	pose
	)

Definition at line 389 of file IRCollection.cc.

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

Referenced by try_for_more().

core::Size protocols::motifs::IRCollection::nirotamers

(

)

const

Definition at line 88 of file IRCollection.cc.

References rotamer_sets_.

Referenced by try_for_more().

void protocols::motifs::IRCollection::reset_unique_id ( )

inline

Definition at line 76 of file IRCollection.hh.

References unique_id_.

Referenced by incorporate_motifs().

bool protocols::motifs::IRCollection::successful_loop_closure	(	core::pose::Pose &	pose,
		protocols::loops::LoopsOP	flexible_regions,
		std::map< core::Size, MotifCOP > &	setpos,
		std::map< core::Size, core::conformation::ResidueCOP > &	setpos_ir,
		std::map< core::Size, bool > &	setpos_forward_info,
		core::conformation::Residue const &	this_rotamer,
		core::Size const	this_pos,
		MotifCOP	this_motif,
		bool const	this_forward_info
	)

Definition at line 291 of file IRCollection.cc.

References protocols::motifs::add_motif_bb_constraints(), protocols::motifs::add_motif_sc_constraints(), protocols::loops::loop_mover::refine::LoopMover_Refine_Backrub::apply(), core::pose::Pose::constraint_set(), core::scoring::coordinate_constraint, core::scoring::ScoreFunctionFactory::create_score_function(), core::pose::Pose::energies(), core::scoring::methods::EnergyMethodOptions::exclude_DNA_DNA(), protocols::motifs::irt(), core::pose::Pose::remove_constraints(), core::pose::Pose::replace_residue(), and core::scoring::Energies::total_energies().

Referenced by try_for_more().

void protocols::motifs::IRCollection::try_for_more	(	core::pose::Pose &	pose,
		protocols::loops::LoopsOP const	flexible_positions,
		std::map< core::Size, MotifCOP >	setpos,
		std::map< core::Size, core::conformation::ResidueCOP >	setpos_ir,
		std::map< core::Size, bool >	setpos_forward_info,
		core::Size	start_depth
	)

Definition at line 171 of file IRCollection.cc.

References core::scoring::ScoreFunctionFactory::create_score_function(), core::pose::Pose::dump_scored_pdb(), core::scoring::methods::EnergyMethodOptions::exclude_DNA_DNA(), protocols::abinitio::filename(), find_closest_backbone(), increment_unique_id(), protocols::motifs::irt(), make_motif_filename(), motif_forward_, motif_source_, nirotamers(), rotamer_sets_, successful_loop_closure(), and unique_id().

Referenced by incorporate_motifs().

core::Size protocols::motifs::IRCollection::unique_id ( )

inline

Definition at line 75 of file IRCollection.hh.

References unique_id_.

Referenced by try_for_more().

Member Data Documentation

utility::vector1< bool > protocols::motifs::IRCollection::motif_forward_

private

Definition at line 82 of file IRCollection.hh.

Referenced by IRCollection(), and try_for_more().

MotifCOPs protocols::motifs::IRCollection::motif_source_

private

Definition at line 81 of file IRCollection.hh.

Referenced by IRCollection(), and try_for_more().

utility::vector1< core::pack::rotamer_set::RotamerSetOP > protocols::motifs::IRCollection::rotamer_sets_

private

Definition at line 84 of file IRCollection.hh.

Referenced by find_closest_backbone(), IRCollection(), nirotamers(), and try_for_more().

utility::vector1< core::Size > protocols::motifs::IRCollection::target_positions_

private

Definition at line 83 of file IRCollection.hh.

Referenced by IRCollection().

core::Size protocols::motifs::IRCollection::unique_id_

private

Definition at line 77 of file IRCollection.hh.

Referenced by reset_unique_id(), and unique_id().

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The documentation for this class was generated from the following files:

• src/protocols/motifs/IRCollection.hh
• src/protocols/motifs/IRCollection.cc