#include <PairingLibrary.hh>

Inheritance diagram for protocols::jumping::PairingLibrary:

[legend]

Public Types
typedef std::vector< PairingTemplate >	PairingTemplateList

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

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 override
	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) override

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

Private Attributes
PairingTemplateMap	pairings_

core::Size	num_of_pairings_

Member Typedef Documentation

◆ PairingTemplateList

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

◆ PairingTemplateMap

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

Constructor & Destructor Documentation

◆ PairingLibrary()

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

inline

Member Function Documentation

◆ create_jump_fragments()

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

overridevirtual

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

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

◆ 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
	)

overridevirtual

Implements protocols::jumping::BasePairingLibrary.

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().

◆ get_random_beta_sheet_jump()

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

classic rosetta++ accessor

References pairings_, core::scoring::rg, and protocols::hybridization::t.

◆ get_random_tmh_jump()

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

classic rosetta++ accessor

References pairings_, core::scoring::rg, and protocols::hybridization::t.

◆ read_from_file()

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

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 protocols::hybridization::t.

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

◆ read_from_file_no_filters()

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

References protocols::abinitio::filename(), num_of_pairings_, pairings_, and protocols::hybridization::t.

◆ set_tmh_jump()

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

References core::pose::Pose::conformation(), core::pose::named_stub_id_to_stub_id(), pairings_, core::scoring::rg, core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), core::pose::Pose::set_secstruct(), core::conformation::Conformation::set_stub_transform(), and protocols::hybridization::t.

◆ size()

core::Size protocols::jumping::PairingLibrary::size ( ) const

inline

References num_of_pairings_.

Member Data Documentation

◆ num_of_pairings_

core::Size protocols::jumping::PairingLibrary::num_of_pairings_

private

Referenced by read_from_file(), read_from_file_no_filters(), and size().

◆ pairings_

PairingTemplateMap protocols::jumping::PairingLibrary::pairings_