#include <PairingLibrary.hh>

Inheritance diagram for protocols::jumping::PairingLibrary:

Collaboration diagram for protocols::jumping::PairingLibrary:

Public Member Functions
	PairingLibrary ()

void	read_from_file (std::string const &fn)

void	read_from_file_no_filters (std::string const &fn)

core::kinematics::RT	get_random_beta_sheet_jump (int const orientation, int const pleating) const
	classic rosetta++ accessor More...

core::kinematics::RT	get_random_tmh_jump (int const orientation, int const pos1, int const pos2) const
	classic rosetta++ accessor More...

void	set_tmh_jump (core::pose::Pose pose, int const jump_number, int const orientation, int const pos1, int const pos2) const

void	create_jump_fragments (int const orientation, int const pleating, bool bWithTorsion, core::fragment::FragDataList &) const
	puts all jump-geometries that fit the orientation and pleating into list of FragData's. Try to reuse these FragData for different Frames that have same orientation and pleating This creates Fragments with single JumpSRFD — PairingLibrary also stores phi/psi/omega of start and end residue use bWithTorsion = true to get FragData with BBTorsionSRFD and JumpSRFD length of single FragData is noTorsion 1 withTorsion 3 bWithTorsion = true length of single FragData is 3 start jump end More...

core::Size	size () const

void	generate_jump_frags (core::scoring::dssp::PairingsList const &pairings, core::kinematics::MoveMap const &mm, bool bWithTorsion, core::fragment::FragSet &frags_accumulator)

Public Member Functions inherited from protocols::jumping::BasePairingLibrary
virtual	~BasePairingLibrary ()

Private Types
typedef std::vector < PairingTemplate >	PairingTemplateList

typedef std::map< std::pair < int, int > , PairingTemplateList >	PairingTemplateMap

Private Attributes
PairingTemplateMap	pairings_

core::Size	num_of_pairings_

Detailed Description

Definition at line 101 of file PairingLibrary.hh.

Member Typedef Documentation

typedef std::vector< PairingTemplate > protocols::jumping::PairingLibrary::PairingTemplateList

private

Definition at line 102 of file PairingLibrary.hh.

typedef std::map< std::pair< int, int >, PairingTemplateList > protocols::jumping::PairingLibrary::PairingTemplateMap

private

Definition at line 103 of file PairingLibrary.hh.

Constructor & Destructor Documentation

protocols::jumping::PairingLibrary::PairingLibrary ( )

inline

Definition at line 105 of file PairingLibrary.hh.

Member Function Documentation

void protocols::jumping::PairingLibrary::create_jump_fragments	(	int const	orientation,
		int const	pleating,
		bool	bWithTorsion,
		core::fragment::FragDataList &	frags
	)		const

virtual

puts all jump-geometries that fit the orientation and pleating into list of FragData's. Try to reuse these FragData for different Frames that have same orientation and pleating This creates Fragments with single JumpSRFD — PairingLibrary also stores phi/psi/omega of start and end residue use bWithTorsion = true to get FragData with BBTorsionSRFD and JumpSRFD length of single FragData is noTorsion 1 withTorsion 3 bWithTorsion = true length of single FragData is 3 start jump end

puts all jump-geometries that fit the orientation and pleating into list of FragData's. Try to reuse these FragData for different Frames that have same orientation and pleating

Implements protocols::jumping::BasePairingLibrary.

Definition at line 612 of file PairingLibrary.cc.

References pairings_, protocols::loops::start, and protocols::loops::stop.

Referenced by protocols::jumping::JumpSample::generate_jump_frags(), and generate_jump_frags().

void protocols::jumping::PairingLibrary::generate_jump_frags	(	core::scoring::dssp::PairingsList const &	pairings,
		core::kinematics::MoveMap const &	mm,
		bool	bWithTorsion,
		core::fragment::FragSet &	frags_accumulator
	)

virtual

Implements protocols::jumping::BasePairingLibrary.

Definition at line 664 of file PairingLibrary.cc.

References core::fragment::FragSet::add(), create_jump_fragments(), protocols::jumping::generate_empty_jump_frame(), core::kinematics::MoveMap::get_bb(), and core::scoring::dssp::has_orientation_and_pleating().

Referenced by protocols::abinitio::TemplateJumpSetup::generate_jump_frags().

kinematics::RT protocols::jumping::PairingLibrary::get_random_beta_sheet_jump	(	int const	orientation,
		int const	pleating
	)		const

classic rosetta++ accessor

Definition at line 492 of file PairingLibrary.cc.

References pairings_, protocols::jumping::RG(), protocols::jumping::PairingTemplate::rt_, and core::scoring::hbonds::t().

kinematics::RT protocols::jumping::PairingLibrary::get_random_tmh_jump	(	int const	orientation,
		int const	pos1,
		int const	pos2
	)		const

classic rosetta++ accessor

Definition at line 518 of file PairingLibrary.cc.

References pairings_, protocols::jumping::RG(), protocols::jumping::PairingTemplate::rt_, and core::scoring::hbonds::t().

void protocols::jumping::PairingLibrary::read_from_file ( std::string const & fn)

Definition at line 318 of file PairingLibrary.cc.

References protocols::abinitio::filename(), num_of_pairings_, protocols::jumping::PairingTemplate::omega, pairings_, protocols::jumping::PairingTemplate::phi, protocols::jumping::PairingTemplate::psi, core::kinematics::RT::reverse(), protocols::jumping::PairingTemplate::rt_, protocols::jumping::RT_from_epos(), and core::scoring::hbonds::t().

void protocols::jumping::PairingLibrary::read_from_file_no_filters ( std::string const & fn)

Definition at line 397 of file PairingLibrary.cc.

References protocols::abinitio::filename(), num_of_pairings_, protocols::jumping::PairingTemplate::omega, pairings_, protocols::jumping::PairingTemplate::phi, protocols::jumping::PairingTemplate::psi, protocols::jumping::PairingTemplate::rt_, protocols::jumping::PairingTemplate::secstruct, and core::scoring::hbonds::t().

void protocols::jumping::PairingLibrary::set_tmh_jump	(	core::pose::Pose	pose,
		int const	jump_number,
		int const	orientation,
		int const	pos1,
		int const	pos2
	)		const