#include <PairingLibrary.hh>

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::FragDataOPs &) 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_

Member Typedef Documentation

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

private

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

private

Constructor & Destructor Documentation

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

inline

Member Function Documentation

void protocols::jumping::PairingLibrary::create_jump_fragments	(	int const	orientation,
		int const	pleating,
		bool	bWithTorsion,
		core::fragment::FragDataOPs &	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.

References key, pairings_, runtime_assert, protocols::loops::start, protocols::loops::stop, and templates.

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.

References create_jump_fragments(), frame(), protocols::jumping::generate_empty_jump_frame(), core::kinematics::MoveMap::get_bb(), has_orientation_and_pleating(), jump_nr, length, runtime_assert, and utility_exit_with_message.

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

References key, pairings_, protocols::jumping::RG, protocols::jumping::PairingTemplate::rt_, runtime_assert, t, templates, and numeric::random::RandomGenerator::uniform().

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

classic rosetta++ accessor

References pairings_, protocols::jumping::RG, protocols::jumping::PairingTemplate::rt_, t, templates, and numeric::random::RandomGenerator::uniform().

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

References filename(), getline(), num_of_pairings_, o, 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(), runtime_assert, t, and tag.

Referenced by protocols::jumping::StandardPairingLibrary::create_singleton_instance().

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

References filename(), getline(), num_of_pairings_, o, protocols::jumping::PairingTemplate::omega, pairings_, protocols::jumping::PairingTemplate::phi, protocols::jumping::PairingTemplate::psi, protocols::jumping::PairingTemplate::rt_, protocols::jumping::PairingTemplate::secstruct, ss1, ss2, t, tag, numeric::xyzVector< class >::x(), numeric::xyzVector< class >::y(), and numeric::xyzVector< class >::z().

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