#include <JumpSample.hh>

Collaboration diagram for protocols::jumping::JumpSample:

Public Member Functions
	JumpSample ()

	~JumpSample ()

	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_int const &	jumps () const

ObjexxFCL::FArray1D_int 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_int	jumps_

ObjexxFCL::FArray2D< std::string >	jump_atoms_

ObjexxFCL::FArray1D_int	cuts_

core::kinematics::FoldTreeOP	fold_tree_

bool	bValidTree_

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

Detailed Description

Definition at line 63 of file JumpSample.hh.

Constructor & Destructor Documentation

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

inline

Definition at line 65 of file JumpSample.hh.

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

inline

Definition at line 70 of file JumpSample.hh.

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

Definition at line 98 of file JumpSample.cc.

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().

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

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`
	)

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

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

Definition at line 145 of file JumpSample.cc.

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().

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

Definition at line 253 of file JumpSample.cc.

References apply_to(), and correct_jump_atoms_for_fragments().

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

Definition at line 258 of file JumpSample.cc.

References apply_to(), and correct_jump_atoms_for_fragments().

Member Function Documentation

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

Definition at line 512 of file JumpSample.cc.

References core::pose::add_variant_type_to_pose_residue(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, cuts_, core::chemical::ResidueType::has_variant_type(), core::chemical::LOWER_TERMINUS, njump_, core::pose::Pose::residue_type(), protocols::jumping::tr(), and core::chemical::UPPER_TERMINUS.

Referenced by set_fold_tree_and_chainbreaks().

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

Definition at line 523 of file JumpSample.cc.

References core::pose::add_variant_type_to_pose_residue(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, cuts_, core::kinematics::ShortestPathInFoldTree::dist(), core::chemical::ResidueType::has_variant_type(), core::conformation::Residue::is_polymer(), core::chemical::LOWER_TERMINUS, njump_, core::pose::Pose::residue(), core::pose::Pose::residue_type(), protocols::jumping::tr(), and core::chemical::UPPER_TERMINUS.

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

Definition at line 539 of file JumpSample.cc.

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

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

Definition at line 552 of file JumpSample.cc.

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

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

private

Definition at line 264 of file JumpSample.cc.

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().

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

Definition at line 199 of file JumpSample.cc.

References bValidTree_, fold_tree_, jump_atoms_, and njump_.

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

ObjexxFCL::FArray1D_int const& protocols::jumping::JumpSample::cuts ( ) const

inline

Definition at line 183 of file JumpSample.hh.

References cuts_.

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

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

inline

Definition at line 170 of file JumpSample.hh.

References fold_tree_.

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

dump file with little pymol script that shows jumps and cuts

Definition at line 590 of file JumpSample.cc.

References cuts_, jumps_, and size().

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

inline

Definition at line 196 of file JumpSample.hh.

References fold_tree_.

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

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

Definition at line 444 of file JumpSample.cc.

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().

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

Definition at line 358 of file JumpSample.cc.

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

Referenced by protocols::abinitio::TemplateJumpSetup::clean_jumps(), protocols::topology_broker::JumpClaimer::generate_claims(), protocols::abinitio::TemplateJumpSetup::generate_jump_frags(), and protocols::topology_broker::JumpClaimer::init_jumps().

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

private

Definition at line 227 of file JumpSample.cc.

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

Referenced by JumpSample().

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

private

Definition at line 211 of file JumpSample.cc.

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

Referenced by JumpSample().

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

Definition at line 432 of file JumpSample.cc.

References has_orientation_and_pleating(), and jump_pairings_.

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

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

Definition at line 427 of file JumpSample.cc.

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

Referenced by generate_jump_frags(), and get_pairing().

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

inline

Definition at line 93 of file JumpSample.hh.

References bValidTree_.

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

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

inline

Definition at line 187 of file JumpSample.hh.

References jump_atoms_.

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

ObjexxFCL::FArray2D_int const& protocols::jumping::JumpSample::jumps ( ) const

inline

Definition at line 179 of file JumpSample.hh.

References jumps_.

Referenced by protocols::hybridization::FoldTreeHybridize::add_strand_pairings(), protocols::topology_broker::JumpClaimer::generate_claims(), protocols::jumping::ResiduePairJumpSetup::generate_jump_frags(), and protocols::topology_broker::JumpClaimer::init_jumps().

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

private

Definition at line 219 of file JumpSample.cc.

References jump_pairings_, jumps_, and size().

Referenced by apply_to(), and JumpSample().

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

Definition at line 571 of file JumpSample.cc.

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().

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

Definition at line 289 of file JumpSample.cc.

References cuts_, jump_atoms_, jump_pairings_, and jumps_.

Referenced by apply_to(), and JumpSample().

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

Definition at line 305 of file JumpSample.cc.

References core::pose::Pose::fold_tree(), fold_tree_, jumps_, core::pose::Pose::secstruct(), core::pose::Pose::set_secstruct(), size(), core::pose::Pose::total_residue(), and total_residue_.

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

inline

Definition at line 164 of file JumpSample.hh.

References add_chainbreaks(), and set_fold_tree_in_pose().

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

Definition at line 298 of file JumpSample.cc.

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

Referenced by set_fold_tree_and_chainbreaks(), and steal_jumps().

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

inline

Definition at line 174 of file JumpSample.hh.

References njump_.

Referenced by protocols::hybridization::FoldTreeHybridize::add_strand_pairings(), dump_pymol(), protocols::topology_broker::JumpClaimer::generate_claims(), generate_jump_frags(), protocols::jumping::ResiduePairJumpSetup::generate_jump_frags(), generate_jump_frames(), protocols::topology_broker::JumpClaimer::init_jumps(), jumps2pairings(), protocols::jumping::operator<<(), safe_secstruct(), steal_orientation_and_pleating(), and transfer_jumps().

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