#include <HybridizeFoldtreeDynamic.hh>

Public Member Functions
	HybridizeFoldtreeDynamic ()

void	initialize (core::pose::Pose &pose, protocols::loops::Loops const &core_chunks, utility::vector1< std::pair< core::Size, core::Size > > const &strand_pairs, std::set< core::Size > const &strand_pair_library_positions)

void	reset (core::pose::Pose &pose)

utility::vector1< core::Size >	get_anchors ()

Private Member Functions
core::Size	choose_anchor_position (const protocols::loops::Loop &chunk) const

void	update (core::pose::Pose &pose)

void	set_core_chunks (const protocols::loops::Loops &chunks)

void	jumps_and_cuts_from_foldtree (core::kinematics::FoldTree &foldtree, utility::vector1< std::pair< core::Size, core::Size > > &jumps, utility::vector1< core::Size > &cuts)

utility::vector1< core::Size >	decide_cuts (core::pose::Pose &pose, core::Size n_residues)

void	choose_anchors ()

void	make_complete_chunks (utility::vector1< core::Size > cut_positions, core::Size n_residues)

void	get_pair_core_chunks (core::Size const chunk_index, utility::vector1< core::Size > &pair_chunks, utility::vector1< std::pair< core::Size, core::Size > > &pair_chunks_pairs)

void	get_core_chunk_index_from_position (core::Size const position, core::Size &index)

void	add_overlapping_pair_chunks (core::Size const index, utility::vector1< core::Size > &cuts, utility::vector1< std::pair< core::Size, core::Size > > &jumps, std::set< core::Size > &rooted_chunk_indices)

void	remove_cut (core::Size const cut, utility::vector1< core::Size > &cuts)

Private Attributes
protocols::loops::Loops	chunks_

protocols::loops::Loops	core_chunks_

utility::vector1< core::Size >	anchor_positions_

int	virtual_res_
	index of the virtual residue we added to the pose in set_up() More...

core::Size	num_nonvirt_residues_ = 0

core::Size	num_polymer_residues_ = 0

core::kinematics::FoldTree	initial_asymm_foldtree_

core::kinematics::FoldTree	saved_ft_

core::Size	saved_n_residue_

utility::vector1< std::pair< core::Size, core::Size > >	strand_pairs_

std::set< core::Size >	strand_pair_library_positions_

std::set< core::Size >	template_core_chunk_indices_

std::set< core::Size >	rooted_chunk_indices_

Constructor & Destructor Documentation

◆ HybridizeFoldtreeDynamic()

protocols::hybridization::HybridizeFoldtreeDynamic::HybridizeFoldtreeDynamic ( )

Member Function Documentation

◆ add_overlapping_pair_chunks()

void protocols::hybridization::HybridizeFoldtreeDynamic::add_overlapping_pair_chunks	(	core::Size const	index,
		utility::vector1< core::Size > &	cuts,
		utility::vector1< std::pair< core::Size, core::Size > > &	jumps,
		std::set< core::Size > &	rooted_chunk_indices
	)

private

References chunks_, get_pair_core_chunks(), core::scoring::pair, protocols::loops::Loops::push_back(), rooted_chunk_indices_, protocols::loops::stop, and protocols::hybridization::TR().

Referenced by update().

◆ choose_anchor_position()

core::Size protocols::hybridization::HybridizeFoldtreeDynamic::choose_anchor_position ( const protocols::loops::Loop & chunk ) const

private

References protocols::loops::Loop::length(), core::conformation::membrane::normal, protocols::loops::Loop::start(), and protocols::loops::Loop::stop().

Referenced by choose_anchors().

◆ choose_anchors()

void protocols::hybridization::HybridizeFoldtreeDynamic::choose_anchors ( )

private

References anchor_positions_, choose_anchor_position(), core_chunks_, and protocols::loops::Loops::num_loop().

Referenced by initialize().

◆ decide_cuts()

utility::vector1< core::Size > protocols::hybridization::HybridizeFoldtreeDynamic::decide_cuts	(	core::pose::Pose &	pose,
		core::Size	n_residues
	)

private

References core_chunks_, initial_asymm_foldtree_, jumps_and_cuts_from_foldtree(), core::conformation::membrane::normal, protocols::loops::Loops::num_loop(), core::scoring::rg, core::pose::Pose::secstruct(), protocols::loops::start, and protocols::hybridization::TR().

Referenced by initialize().

◆ get_anchors()

utility::vector1< core::Size > protocols::hybridization::HybridizeFoldtreeDynamic::get_anchors ( )

inline

References anchor_positions_.

Referenced by protocols::hybridization::FoldTreeHybridize::get_jump_anchors().

◆ get_core_chunk_index_from_position()

void protocols::hybridization::HybridizeFoldtreeDynamic::get_core_chunk_index_from_position	(	core::Size const	position,
		core::Size &	index
	)

private

References core_chunks_, protocols::loops::Loops::num_loop(), protocols::loops::start, and protocols::loops::stop.

Referenced by get_pair_core_chunks(), and update().

◆ get_pair_core_chunks()

void protocols::hybridization::HybridizeFoldtreeDynamic::get_pair_core_chunks	(	core::Size const	chunk_index,
		utility::vector1< core::Size > &	pair_chunks,
		utility::vector1< std::pair< core::Size, core::Size > > &	pair_chunks_pairs
	)

private

References core_chunks_, get_core_chunk_index_from_position(), protocols::loops::start, protocols::loops::stop, and strand_pairs_.

Referenced by add_overlapping_pair_chunks().

◆ initialize()

void protocols::hybridization::HybridizeFoldtreeDynamic::initialize	(	core::pose::Pose &	pose,
		protocols::loops::Loops const &	core_chunks,
		utility::vector1< std::pair< core::Size, core::Size > > const &	strand_pairs,
		std::set< core::Size > const &	strand_pair_library_positions
	)

References core::chemical::ResidueTypeBase::aa(), core::chemical::aa_vrt, protocols::loops::add_cutpoint_variants(), core::pose::addVirtualResAsRoot(), choose_anchors(), chunks_, core::pose::Pose::conformation(), decide_cuts(), core::conformation::Conformation::fold_tree(), core::conformation::symmetry::get_asymm_unit_fold_tree(), initial_asymm_foldtree_, core::conformation::Residue::is_polymer(), core::pose::symmetry::is_symmetric(), make_complete_chunks(), protocols::loops::Loops::num_loop(), num_nonvirt_residues_, num_polymer_residues_, protocols::loops::Loops::push_back(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), saved_ft_, saved_n_residue_, set_core_chunks(), core::pose::Pose::size(), protocols::loops::Loops::size(), protocols::loops::start, protocols::loops::stop, strand_pair_library_positions_, strand_pairs_, template_core_chunk_indices_, protocols::hybridization::TR(), update(), and virtual_res_.

Referenced by protocols::mpi_refinement::WorkUnit_PartialAbinitio::run(), and protocols::hybridization::FoldTreeHybridize::setup_foldtree().

◆ jumps_and_cuts_from_foldtree()

void protocols::hybridization::HybridizeFoldtreeDynamic::jumps_and_cuts_from_foldtree	(	core::kinematics::FoldTree &	foldtree,
		utility::vector1< std::pair< core::Size, core::Size > > &	jumps,
		utility::vector1< core::Size > &	cuts
	)

private

References core::kinematics::FoldTree::cutpoints(), core::kinematics::FoldTree::downstream_jump_residue(), core::kinematics::FoldTree::num_jump(), and core::kinematics::FoldTree::upstream_jump_residue().

Referenced by decide_cuts(), and update().

◆ make_complete_chunks()

void protocols::hybridization::HybridizeFoldtreeDynamic::make_complete_chunks	(	utility::vector1< core::Size >	cut_positions,
		core::Size	n_residues
	)

private

References chunks_, core_chunks_, protocols::loops::Loops::num_loop(), and protocols::loops::Loops::size().

Referenced by initialize().

◆ remove_cut()

void protocols::hybridization::HybridizeFoldtreeDynamic::remove_cut	(	core::Size const	cut,
		utility::vector1< core::Size > &	cuts
	)

private

Referenced by update().

◆ reset()

void protocols::hybridization::HybridizeFoldtreeDynamic::reset ( core::pose::Pose & pose )

References core::pose::Pose::conformation(), core::pose::Pose::constraint_set(), core::kinematics::FoldTree::cutpoint(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::conformation::Conformation::delete_residue_range_slow(), core::conformation::Conformation::fold_tree(), core::pose::Pose::fold_tree(), core::conformation::Residue::has_variant_type(), core::pose::remove_variant_type_from_pose_residue(), core::pose::Pose::residue(), saved_ft_, saved_n_residue_, and core::pose::Pose::size().

Referenced by protocols::hybridization::FoldTreeHybridize::restore_original_foldtree().

◆ set_core_chunks()

void protocols::hybridization::HybridizeFoldtreeDynamic::set_core_chunks ( const protocols::loops::Loops & chunks )

private

References core_chunks_.

Referenced by initialize().

◆ update()

void protocols::hybridization::HybridizeFoldtreeDynamic::update ( core::pose::Pose & pose )

private

References core::kinematics::FoldTree::add_edge(), add_overlapping_pair_chunks(), anchor_positions_, core::kinematics::FoldTree::begin(), chunks_, core::kinematics::FoldTree::clear(), core::pose::Pose::conformation(), protocols::loops::cut_point, core::kinematics::FoldTree::end(), core::conformation::symmetry::get_asymm_unit_fold_tree(), get_core_chunk_index_from_position(), initial_asymm_foldtree_, core::pose::symmetry::is_symmetric(), jumps_and_cuts_from_foldtree(), protocols::mean_field::max(), protocols::mean_field::min(), core::kinematics::FoldTree::nres(), protocols::loops::Loops::num_loop(), num_nonvirt_residues_, core::kinematics::Edge::PEPTIDE, protocols::loops::Loops::push_back(), remove_cut(), rooted_chunk_indices_, core::pose::symmetry::set_asymm_unit_fold_tree(), protocols::loops::Loops::size(), protocols::loops::start, protocols::loops::Loop::stop(), protocols::loops::stop, strand_pairs_, template_core_chunk_indices_, protocols::hybridization::TR(), and core::kinematics::FoldTree::tree_from_jumps_and_cuts().

Referenced by initialize().

Member Data Documentation

◆ anchor_positions_

utility::vector1< core::Size > protocols::hybridization::HybridizeFoldtreeDynamic::anchor_positions_

private

Referenced by choose_anchors(), get_anchors(), and update().

◆ chunks_

protocols::loops::Loops protocols::hybridization::HybridizeFoldtreeDynamic::chunks_

private

Referenced by add_overlapping_pair_chunks(), initialize(), make_complete_chunks(), and update().

◆ core_chunks_

protocols::loops::Loops protocols::hybridization::HybridizeFoldtreeDynamic::core_chunks_

private

Referenced by choose_anchors(), decide_cuts(), get_core_chunk_index_from_position(), get_pair_core_chunks(), make_complete_chunks(), and set_core_chunks().

◆ initial_asymm_foldtree_

core::kinematics::FoldTree protocols::hybridization::HybridizeFoldtreeDynamic::initial_asymm_foldtree_

private

Referenced by decide_cuts(), initialize(), and update().

◆ num_nonvirt_residues_

core::Size protocols::hybridization::HybridizeFoldtreeDynamic::num_nonvirt_residues_ = 0

private

Referenced by initialize(), and update().

◆ num_polymer_residues_

core::Size protocols::hybridization::HybridizeFoldtreeDynamic::num_polymer_residues_ = 0

private

Referenced by initialize().

◆ rooted_chunk_indices_

std::set<core::Size> protocols::hybridization::HybridizeFoldtreeDynamic::rooted_chunk_indices_

private

Referenced by add_overlapping_pair_chunks(), and update().

◆ saved_ft_

core::kinematics::FoldTree protocols::hybridization::HybridizeFoldtreeDynamic::saved_ft_

private

Referenced by initialize(), and reset().

◆ saved_n_residue_

core::Size protocols::hybridization::HybridizeFoldtreeDynamic::saved_n_residue_

private

Referenced by initialize(), and reset().

◆ strand_pair_library_positions_

std::set<core::Size> protocols::hybridization::HybridizeFoldtreeDynamic::strand_pair_library_positions_

private

Referenced by initialize().

◆ strand_pairs_

utility::vector1< std::pair< core::Size, core::Size > > protocols::hybridization::HybridizeFoldtreeDynamic::strand_pairs_

private

Referenced by get_pair_core_chunks(), initialize(), and update().

◆ template_core_chunk_indices_

std::set<core::Size> protocols::hybridization::HybridizeFoldtreeDynamic::template_core_chunk_indices_

private

Referenced by initialize(), and update().

◆ virtual_res_

int protocols::hybridization::HybridizeFoldtreeDynamic::virtual_res_

private

index of the virtual residue we added to the pose in set_up()

Referenced by initialize().

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

src/protocols/hybridization/HybridizeFoldtreeDynamic.hh
src/protocols/hybridization/HybridizeFoldtreeDynamic.cc

Public Member Functions

Private Member Functions

Private Attributes

Constructor & Destructor Documentation

◆ HybridizeFoldtreeDynamic()

Member Function Documentation

◆ add_overlapping_pair_chunks()

◆ choose_anchor_position()

◆ choose_anchors()

◆ decide_cuts()

◆ get_anchors()

◆ get_core_chunk_index_from_position()

◆ get_pair_core_chunks()

◆ initialize()

◆ jumps_and_cuts_from_foldtree()

◆ make_complete_chunks()

◆ remove_cut()

◆ reset()

◆ set_core_chunks()

◆ update()

Member Data Documentation

◆ anchor_positions_

◆ chunks_

◆ core_chunks_

◆ initial_asymm_foldtree_

◆ num_nonvirt_residues_

◆ num_polymer_residues_

◆ rooted_chunk_indices_

◆ saved_ft_

◆ saved_n_residue_

◆ strand_pair_library_positions_

◆ strand_pairs_

◆ template_core_chunk_indices_

◆ virtual_res_