#include <JumpSample.hh>

Public Member Functions
	JumpSample ()

	~JumpSample ()=default

	JumpSample (JumpSetup const &)

	JumpSample (core::Size total_residue, core::Size njump, ObjexxFCL::FArray2D_int jumps, ObjexxFCL::FArray1D_int cuts, core::Size root=1)

	JumpSample (core::Size total_residue, core::Size njump, ObjexxFCL::FArray2D_int jumps, ObjexxFCL::FArray2D< std::string > jump_atoms, ObjexxFCL::FArray1D_int cuts, core::Size root=1)

	JumpSample (core::Size total_residue, core::scoring::dssp::PairingsList const &jumps, ObjexxFCL::FArray1D_float const &cut_probability, core::Size root=1)

	JumpSample (core::Size total_residue, core::scoring::dssp::PairingsList const &jumps, core::fragment::SecondaryStructure const &ss_def, core::Size root=1)

	JumpSample (core::kinematics::FoldTree const &f)

	JumpSample (core::kinematics::FoldTreeOP f)

bool	is_valid () const

void	resize (core::Size njump)

void	set_fold_tree_in_pose (core::pose::Pose &pose) const

void	safe_secstruct (core::pose::Pose &pose) const

void	transfer_jumps (core::pose::Pose &pose, core::pose::Pose &native_pose) const

void	steal_jumps (core::pose::Pose &native_pose, core::fragment::FrameIterator const &begin, core::fragment::FrameIterator const &end) const

void	generate_jump_frames (core::fragment::FrameList &, core::kinematics::MoveMap const &, bool bWithTorsion=true) const

void	steal_orientation_and_pleating (core::pose::Pose &native_pose)

void	generate_jump_frags (PairingLibrary const &pairings, core::kinematics::MoveMap const &, bool bWithTorsion, core::fragment::FrameList &) const

void	add_chainbreaks (core::pose::Pose &pose) const

void	add_chainbreaks (core::pose::Pose &pose, core::Size max_dist, core::kinematics::ShortestPathInFoldTree const &) const

void	add_chainbreaks_as_distance_constraint (core::pose::Pose &pose) const

void	add_chainbreaks_as_distance_constraint (core::pose::Pose &pose, core::Size max_dist, core::kinematics::ShortestPathInFoldTree const &sp) const

void	remove_chainbreaks (core::pose::Pose &pose) const

void	set_fold_tree_and_chainbreaks (core::pose::Pose &pose) const

core::Size	downstream_res_nr (core::Size jump_nr) const

core::Size	size () const

ObjexxFCL::FArray2D< core::Size > const &	jumps () const

ObjexxFCL::FArray1D< core::Size > const &	cuts () const

ObjexxFCL::FArray2D< std::string > const &	jump_atoms () const

bool	has_orientation_and_pleating () const

core::kinematics::FoldTree const &	fold_tree () const

core::Size	total_residue () const

void	dump_pymol (std::string fn) const
	dump file with little pymol script that shows jumps and cuts More...

core::scoring::dssp::Pairing	get_pairing (core::Size res1, core::Size res2) const

Private Member Functions
void	generate_tree_from_jumps_and_cuts (core::Size root=1)

void	generate_random_tree_from_jumps (ObjexxFCL::FArray1D_float const &prob, core::Size root=1)

void	apply_to (core::kinematics::FoldTreeOP f)

void	jumps2pairings ()

void	correct_jump_atoms_for_fragments () const

Private Attributes
core::Size	total_residue_

core::Size	njump_

core::scoring::dssp::PairingsList	jump_pairings_

ObjexxFCL::FArray2D< core::Size >	jumps_

ObjexxFCL::FArray2D< std::string >	jump_atoms_

ObjexxFCL::FArray1D< core::Size >	cuts_

core::kinematics::FoldTreeOP	fold_tree_

bool	bValidTree_

Friends
std::ostream &	operator<< (std::ostream &os, JumpSample const &t)
	output operator More...

Constructor & Destructor Documentation

◆ JumpSample() [1/8]

protocols::jumping::JumpSample::JumpSample ( )

inline

◆ ~JumpSample()

protocols::jumping::JumpSample::~JumpSample ( )

default

◆ JumpSample() [2/8]

protocols::jumping::JumpSample::JumpSample ( JumpSetup const & def )

References protocols::jumping::JumpSetup::begin(), bValidTree_, cuts_, protocols::jumping::JumpSetup::end(), generate_tree_from_jumps_and_cuts(), jump_atoms_, jumps2pairings(), jumps_, resize(), protocols::jumping::JumpSetup::size(), and protocols::jumping::tr().

◆ JumpSample() [3/8]

protocols::jumping::JumpSample::JumpSample	(	core::Size	total_residue,
		core::Size	njump,
		ObjexxFCL::FArray2D_int	jumps,
		ObjexxFCL::FArray1D_int	cuts,
		core::Size	root = `1`
	)

◆ JumpSample() [4/8]

protocols::jumping::JumpSample::JumpSample	(	core::Size	total_residue,
		core::Size	njump,
		ObjexxFCL::FArray2D_int	jumps,
		ObjexxFCL::FArray2D< std::string >	jump_atoms,
		ObjexxFCL::FArray1D_int	cuts,
		core::Size	root = `1`
	)

◆ JumpSample() [5/8]

protocols::jumping::JumpSample::JumpSample	(	core::Size	total_residue,
		core::scoring::dssp::PairingsList const &	jumps,
		ObjexxFCL::FArray1D_float const &	cut_probability,
		core::Size	root = `1`
	)

◆ JumpSample() [6/8]

protocols::jumping::JumpSample::JumpSample	(	core::Size	total_residue,
		core::scoring::dssp::PairingsList const &	jumps,
		core::fragment::SecondaryStructure const &	ss_def,
		core::Size	root = `1`
	)

References core::fragment::SecondaryStructure::extend(), generate_random_tree_from_jumps(), jump_atoms_, jumps_, core::fragment::SecondaryStructure::loop_fraction(), njump_, resize(), core::fragment::SecondaryStructure::total_residue(), and total_residue().

◆ JumpSample() [7/8]

protocols::jumping::JumpSample::JumpSample ( core::kinematics::FoldTree const & f )

References apply_to(), and correct_jump_atoms_for_fragments().

◆ JumpSample() [8/8]

protocols::jumping::JumpSample::JumpSample ( core::kinematics::FoldTreeOP f )

References apply_to(), and correct_jump_atoms_for_fragments().

Member Function Documentation

◆ add_chainbreaks() [1/2]

void protocols::jumping::JumpSample::add_chainbreaks ( core::pose::Pose & pose ) const

References core::pose::add_variant_type_to_pose_residue(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, cuts_, core::chemical::LOWER_TERMINUS_VARIANT, njump_, core::pose::Pose::residue_type(), protocols::jumping::tr(), and core::chemical::UPPER_TERMINUS_VARIANT.

Referenced by set_fold_tree_and_chainbreaks().

◆ add_chainbreaks() [2/2]

void protocols::jumping::JumpSample::add_chainbreaks	(	core::pose::Pose &	pose,
		core::Size	max_dist,
		core::kinematics::ShortestPathInFoldTree const &	sp
	)		const

References core::pose::add_variant_type_to_pose_residue(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, cuts_, core::kinematics::ShortestPathInFoldTree::dist(), core::chemical::LOWER_TERMINUS_VARIANT, njump_, core::pose::Pose::residue(), core::pose::Pose::residue_type(), protocols::jumping::tr(), and core::chemical::UPPER_TERMINUS_VARIANT.

◆ add_chainbreaks_as_distance_constraint() [1/2]

void protocols::jumping::JumpSample::add_chainbreaks_as_distance_constraint ( core::pose::Pose & pose ) const

References core::pose::Pose::add_constraint(), cuts_, njump_, and core::pose::Pose::residue().

◆ add_chainbreaks_as_distance_constraint() [2/2]

void protocols::jumping::JumpSample::add_chainbreaks_as_distance_constraint	(	core::pose::Pose &	pose,
		core::Size	max_dist,
		core::kinematics::ShortestPathInFoldTree const &	sp
	)		const

References core::pose::Pose::add_constraint(), cuts_, core::kinematics::ShortestPathInFoldTree::dist(), njump_, core::pose::Pose::residue(), and protocols::jumping::tr().

◆ apply_to()

void protocols::jumping::JumpSample::apply_to ( core::kinematics::FoldTreeOP f )

private

References bValidTree_, core::kinematics::FoldTree::check_fold_tree(), core::kinematics::FoldTree::cutpoint(), cuts_, core::kinematics::FoldTree::downstream_jump_residue(), fold_tree_, jumps2pairings(), jumps_, njump_, core::kinematics::FoldTree::nres(), core::kinematics::FoldTree::num_jump(), resize(), total_residue_, and core::kinematics::FoldTree::upstream_jump_residue().

Referenced by JumpSample().

◆ correct_jump_atoms_for_fragments()

void protocols::jumping::JumpSample::correct_jump_atoms_for_fragments ( ) const

private

we want N-CA-C as the stub atoms for the jump to achieve that we have to set the upstream jump atom according to folding direction N2C --> JumpAtom C C2N --> JumpAtom N since the AtomTree automatically uses the parent and grand-parent as second and third stub atom

References bValidTree_, fold_tree_, jump_atoms_, and njump_.

Referenced by generate_random_tree_from_jumps(), generate_tree_from_jumps_and_cuts(), and JumpSample().

◆ cuts()

ObjexxFCL::FArray1D< core::Size > const& protocols::jumping::JumpSample::cuts ( ) const

inline

References cuts_.

Referenced by protocols::topology_broker::FragmentJumpClaimer::init_jumps().

◆ downstream_res_nr()

core::Size protocols::jumping::JumpSample::downstream_res_nr ( core::Size jump_nr ) const

inline

References fold_tree_.

◆ dump_pymol()

void protocols::jumping::JumpSample::dump_pymol ( std::string fn ) const

dump file with little pymol script that shows jumps and cuts

References cuts_, jumps_, core::conformation::membrane::out, and size().

◆ fold_tree()

core::kinematics::FoldTree const& protocols::jumping::JumpSample::fold_tree ( ) const

inline

References fold_tree_.

Referenced by protocols::hybridization::FoldTreeHybridize::add_strand_pairing(), protocols::abinitio::JumpingFoldConstraintsWrapper::apply(), generate_jump_frags(), generate_jump_frames(), protocols::abinitio::LoopJumpFoldCst::parse_jump_def(), and protocols::abinitio::abscript::JumpSampleData::write().

◆ generate_jump_frags()

void protocols::jumping::JumpSample::generate_jump_frags	(	PairingLibrary const &	pairings,
		core::kinematics::MoveMap const &	mm,
		bool	bWithTorsion,
		core::fragment::FrameList &	all_frames
	)		const

References protocols::jumping::PairingLibrary::create_jump_fragments(), core::kinematics::FoldTree::downstream_jump_residue(), fold_tree(), protocols::jumping::generate_empty_jump_frame(), core::kinematics::MoveMap::get_bb(), has_orientation_and_pleating(), jump_pairings_, jumps_, size(), protocols::jumping::tr(), and core::kinematics::FoldTree::upstream_jump_residue().

Referenced by protocols::jumping::BaseJumpSetup::generate_jump_frags(), and protocols::abinitio::LoopJumpFoldCst::parse_jump_def().

◆ generate_jump_frames()

void protocols::jumping::JumpSample::generate_jump_frames	(	core::fragment::FrameList &	all_frames,
		core::kinematics::MoveMap const &	mm,
		bool	bWithTorsion = `true`
	)		const

References core::kinematics::FoldTree::downstream_jump_residue(), fold_tree(), core::kinematics::MoveMap::get_bb(), jumps_, size(), protocols::loops::start, protocols::loops::stop, protocols::jumping::tr(), and core::kinematics::FoldTree::upstream_jump_residue().

Referenced by protocols::abinitio::KinematicAbinitio::apply(), protocols::abinitio::TemplateJumpSetup::clean_jumps(), protocols::topology_broker::FragmentJumpClaimer::generate_claims(), protocols::abinitio::TemplateJumpSetup::generate_jump_frags(), protocols::topology_broker::FragmentJumpClaimer::init_jumps(), and protocols::abinitio::abscript::FragmentJumpCM::setup_fragments().

◆ generate_random_tree_from_jumps()

void protocols::jumping::JumpSample::generate_random_tree_from_jumps	(	ObjexxFCL::FArray1D_float const &	prob,
		core::Size	root = `1`
	)

private

References bValidTree_, correct_jump_atoms_for_fragments(), cuts_, fold_tree_, jumps_, njump_, total_residue_, and protocols::jumping::tr().

Referenced by JumpSample().

◆ generate_tree_from_jumps_and_cuts()

void protocols::jumping::JumpSample::generate_tree_from_jumps_and_cuts ( core::Size root = 1 )

private

References bValidTree_, correct_jump_atoms_for_fragments(), cuts_, fold_tree_, jumps_, njump_, and total_residue_.

Referenced by JumpSample().

◆ get_pairing()

core::scoring::dssp::Pairing protocols::jumping::JumpSample::get_pairing	(	core::Size	res1,
		core::Size	res2
	)		const

References has_orientation_and_pleating(), and jump_pairings_.

Referenced by protocols::hybridization::FoldTreeHybridize::add_strand_pairings(), protocols::abinitio::KinematicAbinitio::apply(), protocols::abinitio::TemplateJumpSetup::clean_jumps(), and protocols::abinitio::TemplateJumpSetup::generate_jump_frags().

◆ has_orientation_and_pleating()

bool protocols::jumping::JumpSample::has_orientation_and_pleating ( ) const

References core::scoring::dssp::has_orientation_and_pleating(), and jump_pairings_.

Referenced by generate_jump_frags(), get_pairing(), and protocols::abinitio::AbrelaxApplication::setup_jumps().

◆ is_valid()

bool protocols::jumping::JumpSample::is_valid ( ) const

inline

References bValidTree_.

Referenced by protocols::hybridization::FoldTreeHybridize::add_strand_pairings(), protocols::abinitio::JumpingFoldConstraintsWrapper::apply(), protocols::abinitio::abscript::FragmentJumpCM::calculate_jump_sample(), protocols::jumping::SheetBuilder::create_jump_sample(), protocols::topology_broker::FragmentJumpClaimer::init_jumps(), and protocols::abinitio::LoopJumpFoldCst::parse_jump_def().

◆ jump_atoms()

ObjexxFCL::FArray2D< std::string > const& protocols::jumping::JumpSample::jump_atoms ( ) const

inline

References jump_atoms_.

Referenced by protocols::topology_broker::FragmentJumpClaimer::generate_claims().

◆ jumps()

ObjexxFCL::FArray2D< core::Size > const& protocols::jumping::JumpSample::jumps ( ) const

inline

References jumps_.

Referenced by protocols::hybridization::FoldTreeHybridize::add_strand_pairings(), protocols::abinitio::abscript::FragmentJumpCM::build_claims(), protocols::topology_broker::FragmentJumpClaimer::generate_claims(), protocols::jumping::ResiduePairJumpSetup::generate_jump_frags(), and protocols::topology_broker::FragmentJumpClaimer::init_jumps().

◆ jumps2pairings()

void protocols::jumping::JumpSample::jumps2pairings ( )

private

References jump_pairings_, jumps_, and size().

Referenced by apply_to(), and JumpSample().

◆ remove_chainbreaks()

void protocols::jumping::JumpSample::remove_chainbreaks ( core::pose::Pose & pose ) const

References core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, cuts_, njump_, and core::pose::remove_variant_type_from_pose_residue().

Referenced by protocols::noesy_assign::CrossPeakList::calibrate(), and protocols::noesy_assign::CrossPeakList::update_decoy_compatibility_score().

◆ resize()

void protocols::jumping::JumpSample::resize ( core::Size njump )

References cuts_, jump_atoms_, jump_pairings_, jumps_, and njump_.

Referenced by apply_to(), and JumpSample().

◆ safe_secstruct()

void protocols::jumping::JumpSample::safe_secstruct ( core::pose::Pose & pose ) const

References core::pose::Pose::fold_tree(), fold_tree_, jumps_, protocols::mean_field::max(), protocols::mean_field::min(), core::pose::Pose::secstruct(), core::pose::Pose::set_secstruct(), core::pose::Pose::size(), size(), and total_residue_.

◆ set_fold_tree_and_chainbreaks()

void protocols::jumping::JumpSample::set_fold_tree_and_chainbreaks ( core::pose::Pose & pose ) const

inline

References add_chainbreaks(), and set_fold_tree_in_pose().

◆ set_fold_tree_in_pose()

void protocols::jumping::JumpSample::set_fold_tree_in_pose ( core::pose::Pose & pose ) const

References bValidTree_, core::pose::Pose::fold_tree(), and fold_tree_.

Referenced by set_fold_tree_and_chainbreaks(), and steal_jumps().

◆ size()

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

inline

References njump_.

Referenced by protocols::hybridization::FoldTreeHybridize::add_strand_pairings(), protocols::abinitio::abscript::FragmentJumpCM::build_claims(), dump_pymol(), protocols::topology_broker::FragmentJumpClaimer::generate_claims(), protocols::jumping::ResiduePairJumpSetup::generate_jump_frags(), generate_jump_frags(), generate_jump_frames(), protocols::topology_broker::FragmentJumpClaimer::init_jumps(), jumps2pairings(), safe_secstruct(), steal_orientation_and_pleating(), and transfer_jumps().

◆ steal_jumps()

void protocols::jumping::JumpSample::steal_jumps	(	core::pose::Pose &	native_pose,
		core::fragment::FrameIterator const &	begin,
		core::fragment::FrameIterator const &	end
	)		const

References core::sequence::end, and set_fold_tree_in_pose().

◆ steal_orientation_and_pleating()

void protocols::jumping::JumpSample::steal_orientation_and_pleating ( core::pose::Pose & native_pose )

References core::scoring::dssp::get_pleating(), jump_pairings_, core::scoring::dssp::Pairing::Orientation(), core::scoring::dssp::Pairing::Pleating(), core::scoring::dssp::Pairing::Pos1(), core::scoring::dssp::Pairing::Pos2(), size(), and protocols::jumping::tr().

Referenced by protocols::abinitio::KinematicAbinitio::apply(), and protocols::abinitio::AbrelaxApplication::setup_jumps().

◆ total_residue()

core::Size protocols::jumping::JumpSample::total_residue ( ) const

inline

References total_residue_.

Referenced by JumpSample().

◆ transfer_jumps()

void protocols::jumping::JumpSample::transfer_jumps	(	core::pose::Pose &	pose,
		core::pose::Pose &	native_pose
	)		const

References core::pose::Pose::fold_tree(), fold_tree_, core::pose::Pose::jump(), core::pose::Pose::set_jump(), size(), and protocols::jumping::tr().

Friends And Related Function Documentation

◆ operator<<

std::ostream& operator<<	(	std::ostream &	os,
		JumpSample const &	t
	)

friend

output operator

Member Data Documentation

◆ bValidTree_

bool protocols::jumping::JumpSample::bValidTree_

private

Referenced by apply_to(), correct_jump_atoms_for_fragments(), generate_random_tree_from_jumps(), generate_tree_from_jumps_and_cuts(), is_valid(), JumpSample(), and set_fold_tree_in_pose().

◆ cuts_

ObjexxFCL::FArray1D< core::Size > protocols::jumping::JumpSample::cuts_

private

Referenced by add_chainbreaks(), add_chainbreaks_as_distance_constraint(), apply_to(), cuts(), dump_pymol(), generate_random_tree_from_jumps(), generate_tree_from_jumps_and_cuts(), JumpSample(), remove_chainbreaks(), and resize().

◆ fold_tree_

core::kinematics::FoldTreeOP protocols::jumping::JumpSample::fold_tree_

private

Referenced by apply_to(), correct_jump_atoms_for_fragments(), downstream_res_nr(), fold_tree(), generate_random_tree_from_jumps(), generate_tree_from_jumps_and_cuts(), safe_secstruct(), set_fold_tree_in_pose(), and transfer_jumps().

◆ jump_atoms_

ObjexxFCL::FArray2D< std::string > protocols::jumping::JumpSample::jump_atoms_

private

Referenced by correct_jump_atoms_for_fragments(), jump_atoms(), JumpSample(), and resize().

◆ jump_pairings_

core::scoring::dssp::PairingsList protocols::jumping::JumpSample::jump_pairings_

private

Referenced by generate_jump_frags(), get_pairing(), has_orientation_and_pleating(), jumps2pairings(), resize(), and steal_orientation_and_pleating().

◆ jumps_

ObjexxFCL::FArray2D< core::Size > protocols::jumping::JumpSample::jumps_

private

Referenced by apply_to(), dump_pymol(), generate_jump_frags(), generate_jump_frames(), generate_random_tree_from_jumps(), generate_tree_from_jumps_and_cuts(), jumps(), jumps2pairings(), JumpSample(), resize(), and safe_secstruct().

◆ njump_

core::Size protocols::jumping::JumpSample::njump_

private

Referenced by add_chainbreaks(), add_chainbreaks_as_distance_constraint(), apply_to(), correct_jump_atoms_for_fragments(), generate_random_tree_from_jumps(), generate_tree_from_jumps_and_cuts(), JumpSample(), remove_chainbreaks(), resize(), and size().

◆ total_residue_

core::Size protocols::jumping::JumpSample::total_residue_

private

Referenced by apply_to(), generate_random_tree_from_jumps(), generate_tree_from_jumps_and_cuts(), safe_secstruct(), and total_residue().

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

src/protocols/jumping/JumpSample.hh
src/protocols/jumping/JumpSample.cc

Public Member Functions

Private Member Functions

Private Attributes

Friends

Constructor & Destructor Documentation

◆ JumpSample() [1/8]

◆ ~JumpSample()

◆ JumpSample() [2/8]

◆ JumpSample() [3/8]

◆ JumpSample() [4/8]

◆ JumpSample() [5/8]

◆ JumpSample() [6/8]

◆ JumpSample() [7/8]

◆ JumpSample() [8/8]

Member Function Documentation

◆ add_chainbreaks() [1/2]

◆ add_chainbreaks() [2/2]

◆ add_chainbreaks_as_distance_constraint() [1/2]

◆ add_chainbreaks_as_distance_constraint() [2/2]

◆ apply_to()

◆ correct_jump_atoms_for_fragments()

◆ cuts()

◆ downstream_res_nr()

◆ dump_pymol()

◆ fold_tree()

◆ generate_jump_frags()

◆ generate_jump_frames()

◆ generate_random_tree_from_jumps()

◆ generate_tree_from_jumps_and_cuts()

◆ get_pairing()

◆ has_orientation_and_pleating()

◆ is_valid()

◆ jump_atoms()

◆ jumps()

◆ jumps2pairings()

◆ remove_chainbreaks()

◆ resize()

◆ safe_secstruct()

◆ set_fold_tree_and_chainbreaks()

◆ set_fold_tree_in_pose()

◆ size()

◆ steal_jumps()

◆ steal_orientation_and_pleating()

◆ total_residue()

◆ transfer_jumps()

Friends And Related Function Documentation

◆ operator<<

Member Data Documentation

◆ bValidTree_

◆ cuts_

◆ fold_tree_

◆ jump_atoms_

◆ jump_pairings_

◆ jumps_

◆ njump_

◆ total_residue_