Functions
core::Real	linear_chainbreak (core::pose::Pose const &pose, core::Size const pos)
	evaluate linear chainbreak at a position More...

core::Real	linear_chainbreak (core::pose::Pose &pose, core::Size const pos)
	evaluate linear chainbreak at a position More...

core::Real	overlap_chainbreak (core::pose::Pose const &pose, core::Size const pos)
	evaluate overlap chainbreak at a position More...

core::Real	overlap_chainbreak (core::pose::Pose &pose, core::Size const pos)
	evaluate overlap chainbreak at a position More...

core::Real	quadratic_chainbreak (core::pose::Pose const &pose, core::Size const pos)
	evaluate quadratic chainbreak at a position More...

core::Real	quadratic_chainbreak (core::pose::Pose &pose, core::Size const pos)
	evaluate quadratic chainbreak at a position More...

static basic::Tracer	TR ("protocols.forge.methods.fold_tree_functions")

bool	order (core::kinematics::Edge &e)
	enforce Edge has start <= stop (swap if necessary) More...

core::Size	closest_larger_peptide_vertex (core::Size const v, core::kinematics::FoldTree const &ft, core::Size const k)
	find the k'th closest larger peptide vertex of given vertex in fold tree More...

core::Size	closest_smaller_peptide_vertex (core::Size const v, core::kinematics::FoldTree const &ft, core::Size const k)
	find the k'th closest smaller peptide vertex of given vertex in fold tree More...

bool	vertex_exists (core::Size const v, core::kinematics::FoldTree const &ft)
	query if vertex already exists in fold tree More...

utility::vector1< core::kinematics::Edge >	jumps_connected_to_position (core::Size const pos, core::kinematics::FoldTree const &ft)
	find all jump edges whose start or stop lands on the given position More...

core::Size	find_connecting_jump (core::Size const u, core::Size const v, core::kinematics::FoldTree const &ft)
	find the jump connecting two continuous segments of a fold tree More...

bool	remove_cutpoint (core::Size const v, core::kinematics::FoldTree &ft)
	remove a cutpoint, merging the two sections that are adjacent to the cut More...

void	remove_cutpoints (utility::vector1< core::Size > const &cutpoints, core::kinematics::FoldTree &ft)
	seal a fold tree by removing all specified cutpoints More...

core::kinematics::FoldTree	shift_jumps (core::kinematics::FoldTree const &ft, core::kinematics::MoveMap const &mm)
	attempt to shift jumps in a fold tree based on fixed positions in a MoveMap More...

core::kinematics::FoldTree	fold_tree_from_pose (core::pose::Pose const &pose, core::Size const ft_root, core::kinematics::MoveMap const &mm)
	construct a fold tree from Pose wrt chain endings and residue types More...

core::kinematics::FoldTree	merge (core::kinematics::FoldTree const &left_tree, core::kinematics::FoldTree const &right_tree)
	merge two fold trees by jump between their roots More...

core::kinematics::FoldTree	merge (core::kinematics::FoldTree const &left_tree, core::Size const left_position, core::kinematics::FoldTree const &right_tree, core::Size const right_position)
	merge two fold trees connecting by jump via specified positions More...

core::kinematics::FoldTree	merge (core::kinematics::FoldTree const &left_tree, core::Size const left_position, std::string const &left_jump_atom, core::kinematics::FoldTree const &right_tree, core::Size const right_position, std::string const &right_jump_atom, bool const keep_stub_in_residue)
	merge two fold trees connecting by jump via specified positions More...

core::kinematics::FoldTree	replace (core::kinematics::FoldTree const &original_tree, core::Size const replace_begin, core::Size const replace_end, core::kinematics::MoveMap const &movemap, core::kinematics::FoldTree const &replacement_tree)
	replace a section of one fold tree with another fold tree, connecting by jump between their roots More...

void	make_star_foldtree (core::pose::Pose &pose, protocols::loops::Loops loops)

void	jumps_and_cuts_from_pose (core::pose::Pose &pose, utility::vector1< std::pair< core::Size, core::Size > > &jumps, utility::vector1< core::Size > &cuts)

template<typename EdgeIterator >
void	add_edges (EdgeIterator begin, EdgeIterator end, core::kinematics::FoldTree &ft)
	add a set of Edges to a FoldTree More...

template<typename EdgeIterator >
EdgeIterator	regular_facet_containing_position (core::Size const pos, EdgeIterator const begin, EdgeIterator const end)
	find regular facet (non-jump edge sans face vertices) that contains given position More...

template<typename EdgeList >
bool	add_vertex (core::Size const v, EdgeList &edges)
	add a vertex, splitting edges if necessary More...

template<typename EdgeIterator >
EdgeIterator	facet_containing_position (core::Size const pos, EdgeIterator const begin, EdgeIterator const end, int const label=core::kinematics::Edge::PEPTIDE)
	find facet (edge sans face vertices) that contains given position More...

template<typename EdgeIterator >
utility::vector1< core::kinematics::Edge >	regular_edges_within_interval (core::Size const left, core::Size const right, EdgeIterator const begin, EdgeIterator const end)
	find regular (non-jump) edges contained within the interval [left, right] More...

template<typename EdgeIterator >
utility::vector1< core::kinematics::Edge >	edges_within_interval (core::Size const left, core::Size const right, int const edge_type, EdgeIterator const begin, EdgeIterator const end)
	find specific type of edges contained within the interval [left, right] More...

core::fragment::ConstantLengthFragSetOP	smallmer_from_largemer (core::fragment::ConstFrameIterator begin, core::fragment::ConstFrameIterator end, core::Size const smallmer_size, bool const all_possible_smallmers)
	create small-mers from large-mers More...

static basic::Tracer	TR ("protocols.forge.methods.pose_mod")

bool	add_cutpoint_variants (core::pose::Pose &pose, core::Size const pos)
	add cutpoint variants at a specific position More...

bool	remove_cutpoint_variants (core::pose::Pose &pose, core::Size const pos)
	remove cutpoint variants at a specific position More...

void	restore_residues (std::map< core::Size, core::Size > const &old2new, core::pose::Pose &archive_pose, core::pose::Pose &pose)
	restore residues (i.e. sidechains) More...

void	restore_residues (core::pose::Pose &archive_pose, core::pose::Pose &pose)
	restore residues (i.e. sidechains) More...

template<typename ResidueOPIterator >
core::Size	grow_left_r (core::pose::Pose &pose, core::Size anchor, ResidueOPIterator begin, ResidueOPIterator end, bool const correct_terminus=true, bool const use_existing_crd=false)
	grow a series of residues to the left of a position More...

template<typename ResidueTypeOPIterator >
core::Size	grow_left_rtype (core::pose::Pose &pose, core::Size anchor, ResidueTypeOPIterator begin, ResidueTypeOPIterator end, bool const correct_terminus=true)
	grow a series of residues to the left of a position More...

template<typename ResidueOPIterator >
core::Size	grow_right_r (core::pose::Pose &pose, core::Size anchor, ResidueOPIterator begin, ResidueOPIterator end, bool const correct_terminus=true, bool const use_existing_crd=false)
	grow a series of residues to the right of a position More...

template<typename ResidueTypeOPIterator >
core::Size	grow_right_rtype (core::pose::Pose &pose, core::Size anchor, ResidueTypeOPIterator begin, ResidueTypeOPIterator end, bool const correct_terminus=true)
	grow a series of residues to the right of a position More...

static basic::Tracer	TR ("protocols.forge.methods.util")

void	union_interval (core::Size const root, core::Size const left, core::Size const right, utility::graph::DisjointSets &uf)
	perform union( root, i ) for all 'i' within the closed interval [left, right] More...

core::Size	find_cutpoint (core::pose::Pose const &pose, core::Size left, core::Size right)
	moving left to right, find the first true cutpoint within specified extent More...

core::Size	count_cutpoints (core::pose::Pose const &pose, core::Size left, core::Size right)
	moving left to right, count the number of true cutpoints within the specified extent More...

void	trans_omega (core::Size const left, core::Size const right, core::pose::Pose &pose)
	set omega to 180 for a range of residues [left, right] More...

protocols::loops::Loop	interval_to_loop (protocols::forge::build::Interval const &interval)
	create Loop object w/ random cutpoint from an Interval More...

core::kinematics::FoldTree	fold_tree_from_loops (core::pose::Pose const &pose, protocols::loops::Loops const &loops)
	create fold tree from loops More...

void	set_single_loop_fold_tree (core::pose::Pose &pose, protocols::loops::Loop const &loop)
	set a single loop fold tree More...

utility::vector1< bool >	parse_resfile_string_with_no_lockdown (core::pose::Pose const &pose, core::pack::task::PackerTask &the_task, std::string const &resfile_string)

core::pack::task::TaskFactoryOP	remodel_generic_taskfactory ()

void	fill_non_loop_cst_set (core::pose::Pose &pose, protocols::loops::Loops loops)

utility::vector1< core::Real > const	calc_rsd_sasa (core::pose::Pose const &pose)
	return accessible surface area for each residue More...

void	apply_transformation (core::pose::Pose &mod_pose, std::list< core::Size > const &residue_list, numeric::xyzMatrix< core::Real > const &R, numeric::xyzVector< core::Real > const &preT, numeric::xyzVector< core::Real > const &postT)

template<typename T >
std::set< T >	closed_range (T const left, T const right, T const increment=1)
	return a set containing values in the closed interval [left, right] filled by looping from left -> right with the given increment More...

template<typename T >
void	insert_closed_range (T const left, T const right, std::set< T > &s, T const increment=1)
	add the values in the closed interval [left, right] to a set by looping from left -> right with the given increment More...

template<typename T >
std::set< T >	half_open_range (T const left, T const right, T const increment=1)
	return a set containing values in the half-open interval [left, right) filled by looping from left -> right with the given increment More...

template<typename T >
void	insert_half_open_range (T const left, T const right, std::set< T > &s, T const increment=1)
	add the values in the half-open interval [left, right) to a set by looping from left -> right with the given increment More...

template<typename IntervalIterator >
protocols::loops::Loops	intervals_to_loops (IntervalIterator begin, IntervalIterator end)
	create Loops object w/ random cutpoints from a collection of Intervals More...

template<typename IntervalIterator >
protocols::loops::Loops	intervals_to_confirmation_loops (IntervalIterator begin, IntervalIterator end, core::Size nres)
	create Loops object w/ random cutpoints from a collection of Intervals for KIC confirmation purpose More...

Function Documentation

◆ add_cutpoint_variants()

bool protocols::forge::methods::add_cutpoint_variants	(	core::pose::Pose &	pose,
		core::Size const	pos
	)

add cutpoint variants at a specific position

Parameters

[in,out]	Pose	to modify
[in]	position	at which to add cutpoint variants

Returns: true if cutpoint variants added, false if position not a topological cutpoint or cutpoint variants already exist

Parameters

[in,out]	Pose	to modify
[in]	position	at which to add cutpoint variants

Returns: true if cutpoint variants added, false if position not a topological cutpoint

References core::pose::add_variant_type_to_pose_residue(), core::conformation::Residue::atom_name(), core::pose::Pose::conformation(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::conformation::Conformation::declare_chemical_bond(), core::pose::Pose::fold_tree(), core::conformation::Residue::has_variant_type(), core::kinematics::FoldTree::is_cutpoint(), core::conformation::Residue::lower_connect_atom(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Residue::upper_connect_atom().

Referenced by protocols::forge::remodel::RemodelLoopMover::abinitio_stage(), protocols::protein_interface_design::movers::LoopMoverFromCommandLine::apply(), protocols::protein_interface_design::movers::LoopRemodel::apply(), protocols::forge::remodel::RemodelLoopMover::boost_closure_stage(), protocols::forge::remodel::RemodelLoopMover::independent_stage(), linear_chainbreak(), protocols::denovo_design::linear_chainbreak(), protocols::forge::remodel::RemodelLoopMover::loophash_stage(), overlap_chainbreak(), quadratic_chainbreak(), protocols::forge::remodel::RemodelLoopMover::set_segment_stage(), protocols::forge::remodel::RemodelLoopMover::simultaneous_stage(), and protocols::forge::remodel::RemodelLoopMover::small_move_stage().

◆ add_edges()

template<typename EdgeIterator >

void protocols::forge::methods::add_edges	(	EdgeIterator	begin,
		EdgeIterator	end,
		core::kinematics::FoldTree &	ft
	)

add a set of Edges to a FoldTree

Parameters

[in]	begin	iterator pointing to the first edge to add
[in]	end	iterator pointing just past the last edge to add
	[out	ft the FoldTree to modify

References core::kinematics::FoldTree::add_edge(), and core::sequence::end.

◆ add_vertex()

template<typename EdgeList >

bool protocols::forge::methods::add_vertex	(	core::Size const	v,
		EdgeList &	edges
	)

add a vertex, splitting edges if necessary

Parameters

[in]	v	the vertex to add
[in,out]	edges	the list of edges to modify

Returns: true if vertex was added and an edge was split, false otherwise

References core::sequence::left, order(), regular_facet_containing_position(), and core::kinematics::Edge::start().

Referenced by core::chemical::convert_residuetype_to_light_graph(), core::kinematics::FoldTree::insert_fold_tree_by_jump(), core::kinematics::FoldTree::new_chemical_bond(), core::kinematics::FoldTree::new_jump(), core::io::pose_from_sfr::remap_names_on_geometry(), shift_jumps(), core::kinematics::FoldTree::slide_cutpoint(), and core::kinematics::FoldTree::split_existing_edge_at_residue().

◆ apply_transformation()

void protocols::forge::methods::apply_transformation	(	core::pose::Pose &	mod_pose,
		std::list< core::Size > const &	residue_list,
		numeric::xyzMatrix< core::Real > const &	R,
		numeric::xyzVector< core::Real > const &	preT,
		numeric::xyzVector< core::Real > const &	postT
	)

References core::pose::Pose::batch_set_xyz(), core::pose::Pose::residue_type(), and core::pose::Pose::xyz().

Referenced by protocols::forge::remodel::RemodelGlobalFrame::align_segment(), protocols::forge::remodel::RemodelGlobalFrame::setup_CM_helical_constraint(), and protocols::forge::remodel::RemodelGlobalFrame::setup_helical_constraint().

◆ calc_rsd_sasa()

utility::vector1< core::Real > const protocols::forge::methods::calc_rsd_sasa ( core::pose::Pose const & pose )

return accessible surface area for each residue

References core::scoring::calc_per_atom_sasa(), core::pose::initialize_atomid_map(), core::id::AtomID_Map< T >::set(), and core::pose::Pose::size().

Referenced by protocols::forge::remodel::RemodelDesignMover::reduce_task().

◆ closed_range()

template<typename T >

std::set< T > protocols::forge::methods::closed_range	(	T const	left,
		T const	right,
		T const	increment = `1`
	)

return a set containing values in the closed interval [left, right] filled by looping from left -> right with the given increment

References core::sequence::left.

◆ closest_larger_peptide_vertex()

core::Size protocols::forge::methods::closest_larger_peptide_vertex	(	core::Size const	v,
		core::kinematics::FoldTree const &	ft,
		core::Size const	k
	)

find the k'th closest larger peptide vertex of given vertex in fold tree

Parameters

[in]	v	the given vertex
[in]	ft	fold tree to search
[in]	k	find the k'th closest, must be > 0

Returns: 0 if no such vertex

References core::kinematics::Edge::PEPTIDE.

Referenced by protocols::forge::build::SegmentRebuild::modify_impl().

◆ closest_smaller_peptide_vertex()

core::Size protocols::forge::methods::closest_smaller_peptide_vertex	(	core::Size const	v,
		core::kinematics::FoldTree const &	ft,
		core::Size const	k
	)

find the k'th closest smaller peptide vertex of given vertex in fold tree

Parameters

[in]	v	the given vertex
[in]	ft	fold tree to search
[in]	k	find the k'th closest, must be > 0

Returns: 0 if no such vertex

References core::kinematics::Edge::PEPTIDE.

Referenced by protocols::forge::build::SegmentRebuild::modify_impl().

◆ count_cutpoints()

core::Size protocols::forge::methods::count_cutpoints	(	core::pose::Pose const &	pose,
		core::Size	left,
		core::Size	right
	)

moving left to right, count the number of true cutpoints within the specified extent

0, pose.size(), and any cutpoint with lower/upper terminus are not counted as cutpoints

References core::pose::Pose::fold_tree(), core::kinematics::FoldTree::is_cutpoint(), core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_upper_terminus(), core::sequence::left, core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by protocols::forge::components::VarLengthBuild::centroid_build().

◆ edges_within_interval()

template<typename EdgeIterator >

utility::vector1< core::kinematics::Edge > protocols::forge::methods::edges_within_interval	(	core::Size const	left,
		core::Size const	right,
		int const	edge_type,
		EdgeIterator const	begin,
		EdgeIterator const	end
	)

find specific type of edges contained within the interval [left, right]

References core::sequence::end, core::sequence::left, order(), core::kinematics::Edge::start(), and core::kinematics::Edge::stop().

◆ facet_containing_position()

template<typename EdgeIterator >

EdgeIterator protocols::forge::methods::facet_containing_position	(	core::Size const	pos,
		EdgeIterator const	begin,
		EdgeIterator const	end,
		int const	label = `core::kinematics::Edge::PEPTIDE`
	)

find facet (edge sans face vertices) that contains given position

Parameters

[in]	pos	position
[in]	begin	iterator pointing to the first edge to search
[in]	end	iterator pointing just past the last edge to search
[in]	label	the types of Edge to search, default PEPTIDE

Returns: iterator pointing to the Edge defining the facet that contains the position; if vertex lies on the face of an edge or vertex not found, returns 'end'

References core::sequence::end.

Referenced by merge(), and replace().

◆ fill_non_loop_cst_set()

void protocols::forge::methods::fill_non_loop_cst_set	(	core::pose::Pose &	pose,
		protocols::loops::Loops	loops
	)

References core::pose::Pose::constraint_set(), core::pose::symmetry::is_symmetric(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), core::pose::symmetry::symmetry_info(), and core::conformation::Residue::xyz().

Referenced by protocols::forge::remodel::RemodelMover::design_refine_cart_relax(), and protocols::forge::remodel::RemodelMover::design_refine_seq_relax().

◆ find_connecting_jump()

core::Size protocols::forge::methods::find_connecting_jump	(	core::Size const	u,
		core::Size const	v,
		core::kinematics::FoldTree const &	ft
	)

find the jump connecting two continuous segments of a fold tree

Parameters

[in]	u	Any vertex on the first segment.
[in]	v	Any vertex on the second segment.
[in]	ft	The fold tree to query.

Returns: the jump number connecting the two segments, 0 if no such jump

References core::kinematics::FoldTree::jump_edge(), core::kinematics::FoldTree::nres(), core::kinematics::FoldTree::num_jump(), order(), core::kinematics::Edge::start(), core::kinematics::Edge::stop(), protocols::hybridization::u, and union_interval().

Referenced by protocols::forge::build::SegmentInsert::modify_impl(), and protocols::forge::build::SegmentRebuild::modify_impl().

◆ find_cutpoint()

core::Size protocols::forge::methods::find_cutpoint	(	core::pose::Pose const &	pose,
		core::Size	left,
		core::Size	right
	)

moving left to right, find the first true cutpoint within specified extent

moving left to right, find the first true cutpoint within the specified extent

Returns: the cutpoint position, otherwise 0 if not found

0, pose.size(), and any cutpoint with lower/upper terminus are not counted as cutpoints

Returns: the cutpoint position, otherwise 0 if not found

References core::pose::Pose::fold_tree(), core::kinematics::FoldTree::is_cutpoint(), core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_upper_terminus(), core::sequence::left, core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by protocols::forge::components::VarLengthBuild::centroid_build(), and protocols::forge::build::SegmentInsert::modify_impl().

◆ fold_tree_from_loops()

core::kinematics::FoldTree protocols::forge::methods::fold_tree_from_loops	(	core::pose::Pose const &	pose,
		protocols::loops::Loops const &	loops
	)

create fold tree from loops

Remarks: This is a generic replacement function for the one in protocols::loops and will be moved there in the near future.

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::id::BB, core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::id::CHI, core::pose::Pose::conformation(), core::pose::Pose::fold_tree(), fold_tree_from_pose(), core::kinematics::MoveMap::get_bb(), core::kinematics::FoldTree::new_jump(), core::conformation::Conformation::num_chains(), core::pose::Pose::residue(), core::scoring::rg, core::kinematics::FoldTree::root(), core::pose::Pose::size(), and protocols::loops::Loops::switch_movemap().

Referenced by protocols::protein_interface_design::movers::LoopMoverFromCommandLine::apply(), protocols::protein_interface_design::movers::LoopRemodel::apply(), protocols::forge::components::BDR::design_refine(), protocols::forge::remodel::RemodelLoopMover::insert_random_smallestmer_per_loop(), protocols::seeded_abinitio::CloseFold::quick_closure(), protocols::forge::remodel::RemodelLoopMover::randomize_stage(), protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue(), protocols::forge::remodel::RemodelLoopMover::repeat_propagation(), set_single_loop_fold_tree(), and protocols::forge::remodel::RemodelLoopMover::simultaneous_stage().

◆ fold_tree_from_pose()

core::kinematics::FoldTree protocols::forge::methods::fold_tree_from_pose	(	core::pose::Pose const &	pose,
		core::Size const	ft_root,
		core::kinematics::MoveMap const &	mm
	)

construct a fold tree from Pose wrt chain endings and residue types

Remarks: Determines edge types from residues (polymer vs non-polymer). Each chain will end up as one edge in the fold tree. Jumps will be made from the new root to a random fixed backbone residue as specified by the movemap. If all residues in a chain are moveable, will choose any random residue.

Parameters

[in]	pose	Pose.
[in]	ft_root	Root of the new fold tree.
[in]	mm	MoveMap used to select jump positions.

Returns: fold tree wrt chain endings and residue types

Referenced by protocols::forge::components::VarLengthBuild::apply(), protocols::forge::remodel::RemodelLoopMover::apply(), fold_tree_from_loops(), linear_chainbreak(), overlap_chainbreak(), quadratic_chainbreak(), and protocols::fldsgn::CircularPermutation::split_chains().

◆ grow_left_r()

template<typename ResidueOPIterator >

core::Size protocols::forge::methods::grow_left_r	(	core::pose::Pose &	pose,
		core::Size	anchor,
		ResidueOPIterator	begin,
		ResidueOPIterator	end,
		bool const	correct_terminus = `true`,
		bool const	use_existing_crd = `false`
	)

grow a series of residues to the left of a position

Parameters

[in,out]	pose	Pose the pose to modify
[in]	anchor	the anchor position
[in]	begin	iterator that points to the first ResidueOP
[in]	end	iterator that points just beyond the last ResidueOP
[in]	correct_terminus	re-add lower terminus if found, default true
[in]	use_existing_crd	No idealization: place residues with existing coordinates, default false.

Returns: the left endpoint of the new growth or zero if nothing to do

Remarks: Use a reverse iterator to grow right -> left along vector containers.

References core::pose::add_lower_terminus_type_to_pose_residue(), core::pose::Pose::conformation(), core::sequence::end, core::conformation::Residue::is_lower_terminus(), core::pose::Pose::residue(), and core::conformation::Conformation::safely_prepend_polymer_residue_before_seqpos().

Referenced by grow_left_rtype(), and protocols::forge::build::SegmentInsert::modify_impl().

◆ grow_left_rtype()

template<typename ResidueTypeOPIterator >

core::Size protocols::forge::methods::grow_left_rtype	(	core::pose::Pose &	pose,
		core::Size	anchor,
		ResidueTypeOPIterator	begin,
		ResidueTypeOPIterator	end,
		bool const	correct_terminus = `true`
	)

grow a series of residues to the left of a position

Parameters

[in,out]	pose	Pose the pose to modify
[in]	anchor	the anchor position
[in]	begin	iterator that points to the first ResidueTypeOP
[in]	end	iterator that points just beyond the last ResidueTypeOP
[in]	correct_terminus	re-add lower terminus if found, default true

Returns: the left endpoint of the new growth or zero if nothing to do

Remarks: Use a reverse iterator to grow right -> left along vector containers.

References core::pose::Pose::begin(), core::conformation::ResidueFactory::create_residue(), core::sequence::end, and grow_left_r().

Referenced by protocols::forge::build::GrowLeft::modify_impl(), protocols::forge::build::SegmentInsert::modify_impl(), and protocols::forge::build::SegmentRebuild::modify_impl().

◆ grow_right_r()

template<typename ResidueOPIterator >

core::Size protocols::forge::methods::grow_right_r	(	core::pose::Pose &	pose,
		core::Size	anchor,
		ResidueOPIterator	begin,
		ResidueOPIterator	end,
		bool const	correct_terminus = `true`,
		bool const	use_existing_crd = `false`
	)

grow a series of residues to the right of a position

Parameters

[in,out]	pose	Pose the pose to modify
[in]	anchor	the anchor position, can be 0 if operating on empty Pose
[in]	begin	iterator that points to the first ResidueOP
[in]	end	iterator that points just beyond the last ResidueOP
[in]	correct_terminus	re-add upper terminus if found, default true
[in]	use_existing_crd	No idealization: place residues with existing coordinates, default false.

Returns: the right endpoint of the new growth or zero if nothing to do

References core::pose::add_upper_terminus_type_to_pose_residue(), core::pose::Pose::append_residue_by_bond(), core::pose::Pose::conformation(), core::sequence::end, core::conformation::Residue::is_upper_terminus(), core::pose::Pose::residue(), and core::conformation::Conformation::safely_append_polymer_residue_after_seqpos().

Referenced by grow_right_rtype(), and protocols::forge::build::SegmentInsert::modify_impl().

◆ grow_right_rtype()

template<typename ResidueTypeOPIterator >

core::Size protocols::forge::methods::grow_right_rtype	(	core::pose::Pose &	pose,
		core::Size	anchor,
		ResidueTypeOPIterator	begin,
		ResidueTypeOPIterator	end,
		bool const	correct_terminus = `true`
	)

grow a series of residues to the right of a position

Parameters

[in,out]	pose	Pose the pose to modify
[in]	anchor	the anchor position, can be 0 if operating on empty Pose
[in]	begin	iterator that points to the first ResidueTypeOP
[in]	end	iterator that points just beyond the last ResidueTypeOP
[in]	correct_terminus	re-add upper terminus if found, default true

Returns: the right endpoint of the new growth or zero if nothing to do

References core::pose::Pose::begin(), core::conformation::ResidueFactory::create_residue(), core::sequence::end, and grow_right_r().

Referenced by protocols::forge::build::GrowRight::modify_impl(), protocols::forge::build::SegmentInsert::modify_impl(), and protocols::forge::build::SegmentRebuild::modify_impl().

◆ half_open_range()

template<typename T >

std::set< T > protocols::forge::methods::half_open_range	(	T const	left,
		T const	right,
		T const	increment = `1`
	)

return a set containing values in the half-open interval [left, right) filled by looping from left -> right with the given increment

References core::sequence::left.

◆ insert_closed_range()

template<typename T >

void protocols::forge::methods::insert_closed_range	(	T const	left,
		T const	right,
		std::set< T > &	s,
		T const	increment = `1`
	)

add the values in the closed interval [left, right] to a set by looping from left -> right with the given increment

References core::sequence::left.

Referenced by protocols::forge::build::BuildManager::positions(), protocols::forge::build::SegmentInsert::undefined_positions(), and protocols::forge::build::BuildManager::union_of_intervals_containing_undefined_positions().

◆ insert_half_open_range()

template<typename T >

void protocols::forge::methods::insert_half_open_range	(	T const	left,
		T const	right,
		std::set< T > &	s,
		T const	increment = `1`
	)

add the values in the half-open interval [left, right) to a set by looping from left -> right with the given increment

References core::sequence::left.

◆ interval_to_loop()

protocols::loops::Loop protocols::forge::methods::interval_to_loop ( protocols::forge::build::Interval const & interval )

create Loop object w/ random cutpoint from an Interval

References protocols::forge::build::Interval::left, core::scoring::rg, and protocols::forge::build::Interval::right.

Referenced by intervals_to_loops().

◆ intervals_to_confirmation_loops()

template<typename IntervalIterator >

protocols::loops::Loops protocols::forge::methods::intervals_to_confirmation_loops	(	IntervalIterator	begin,
		IntervalIterator	end,
		core::Size	nres
	)

create Loops object w/ random cutpoints from a collection of Intervals for KIC confirmation purpose

References protocols::loops::Loops::add_loop(), and core::sequence::end.

Referenced by protocols::forge::remodel::RemodelMover::confirm_sequence().

◆ intervals_to_loops()

template<typename IntervalIterator >

protocols::loops::Loops protocols::forge::methods::intervals_to_loops	(	IntervalIterator	begin,
		IntervalIterator	end
	)

create Loops object w/ random cutpoints from a collection of Intervals

References protocols::loops::Loops::add_loop(), core::sequence::end, and interval_to_loop().

Referenced by protocols::forge::components::VarLengthBuild::apply(), protocols::forge::remodel::RemodelMover::centroid_build(), protocols::forge::components::BDR::design_refine(), protocols::forge::remodel::RemodelMover::design_refine(), protocols::forge::remodel::RemodelMover::design_refine_cart_relax(), and protocols::forge::remodel::RemodelMover::design_refine_seq_relax().

◆ jumps_and_cuts_from_pose()

void protocols::forge::methods::jumps_and_cuts_from_pose	(	core::pose::Pose &	pose,
		utility::vector1< std::pair< core::Size, core::Size > > &	jumps,
		utility::vector1< core::Size > &	cuts
	)

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

Referenced by protocols::forge::build::SegmentInsert::modify_impl(), and protocols::forge::build::SegmentRebuild::modify_impl().

◆ jumps_connected_to_position()

utility::vector1< core::kinematics::Edge > protocols::forge::methods::jumps_connected_to_position	(	core::Size const	pos,
		core::kinematics::FoldTree const &	ft
	)

find all jump edges whose start or stop lands on the given position

Parameters

[in]	pos	The position.
[in]	ft	The fold tree.

Returns: a list of jump edges

Parameters

[in]	pos	The position.
[in]	ft	The fold tree.

Returns: a list of jump edges

Remarks: jump edges start/stop will be ordered such that 'pos' will always be at 'start'.

Referenced by protocols::forge::build::SegmentRebuild::modify_impl().

◆ linear_chainbreak() [1/2]

core::Real protocols::forge::methods::linear_chainbreak	(	core::pose::Pose &	pose,
		core::Size const	pos
	)

evaluate linear chainbreak at a position

Remarks: If necessary, will evaluate using a copy of the Pose with a cut fold tree. If cutpoint variants are present at chainbreak, will use existing variants and not modify them. If cutpoint variants are not found will add them and then remove them once calculation is finished.; If necessary, will evaluate using a copy of the Pose with a cut fold tree.

References add_cutpoint_variants(), protocols::buns::energy, core::pose::Pose::fold_tree(), fold_tree_from_pose(), core::kinematics::FoldTree::is_cutpoint(), core::scoring::linear_chainbreak, core::kinematics::FoldTree::new_jump(), core::kinematics::FoldTree::num_cutpoint(), remove_cutpoint_variants(), core::kinematics::FoldTree::root(), and core::pose::Pose::size().

◆ linear_chainbreak() [2/2]

core::Real protocols::forge::methods::linear_chainbreak	(	core::pose::Pose const &	pose,
		core::Size const	pos
	)

evaluate linear chainbreak at a position

Remarks: Copies the Pose, if necessary swaps the Pose with a cut fold tree, then evaluates the chainbreak.

References core::pose::Pose::fold_tree(), fold_tree_from_pose(), core::kinematics::FoldTree::is_cutpoint(), core::kinematics::FoldTree::new_jump(), core::kinematics::FoldTree::num_cutpoint(), and core::kinematics::FoldTree::root().

◆ make_star_foldtree()

void protocols::forge::methods::make_star_foldtree	(	core::pose::Pose &	pose,
		protocols::loops::Loops	loops
	)

References core::kinematics::FoldTree::add_edge(), core::pose::add_variant_type_to_pose_residue(), core::conformation::Residue::atom_name(), core::pose::Pose::conformation(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::conformation::Conformation::declare_chemical_bond(), core::pose::Pose::fold_tree(), core::kinematics::FoldTree::is_cutpoint(), core::conformation::Residue::lower_connect_atom(), core::kinematics::Edge::PEPTIDE, core::kinematics::FoldTree::reorder(), core::pose::Pose::residue(), core::pose::Pose::size(), protocols::loops::Loops::size(), TR(), and core::conformation::Residue::upper_connect_atom().

Referenced by protocols::forge::build::BuildManager::modify().

◆ merge() [1/3]

core::kinematics::FoldTree protocols::forge::methods::merge	(	core::kinematics::FoldTree const &	left_tree,
		core::kinematics::FoldTree const &	right_tree
	)

merge two fold trees by jump between their roots

Parameters

[in]	left_tree
[in]	right_tree

Returns: Merged FoldTree with all vertices of right_tree placed to the right of vertices in left_tree. Jump labels in right_tree will be renumbered += left_tree.num_jump(). New tree is rooted in the same place as left_tree.

References core::kinematics::FoldTree::root().

Referenced by merge(), and protocols::forge::build::ConnectRight::modify_impl().

◆ merge() [2/3]

core::kinematics::FoldTree protocols::forge::methods::merge	(	core::kinematics::FoldTree const &	left_tree,
		core::Size const	left_position,
		core::kinematics::FoldTree const &	right_tree,
		core::Size const	right_position
	)

merge two fold trees connecting by jump via specified positions

Parameters

[in]	left_tree
[in]	left_position	position on left_tree to connect
[in]	right_tree
[in]	right_position	position on right_tree to connect

Returns: Merged FoldTree with all vertices of right_tree placed to the right of vertices in left_tree. Jump labels in right_tree will be renumbered += left_tree.num_jump(). New tree is rooted in the same place as left_tree.

References merge().

◆ merge() [3/3]

core::kinematics::FoldTree protocols::forge::methods::merge	(	core::kinematics::FoldTree const &	left_tree,
		core::Size const	left_position,
		std::string const &	left_jump_atom,
		core::kinematics::FoldTree const &	right_tree,
		core::Size const	right_position,
		std::string const &	right_jump_atom,
		bool const	keep_stub_in_residue
	)

merge two fold trees connecting by jump via specified positions

Parameters

[in]	left_tree
[in]	left_position	position on left_tree to connect
[in]	left_jump_atom	Use this atom for the left side of the jump. Use empty string to indicate default setting.
[in]	right_tree
[in]	right_position	position on right_tree to connect
[in]	right_jump_atom	Use this atom for the right set of the jump. Use empty string to indicate default setting.
[in]	keep_stub_in_residue	Attempt to keep generated stubs of the jump within their respective residues. default False

Returns: Merged FoldTree with all vertices of right_tree placed to the right of vertices in left_tree. Jump labels in right_tree will be renumbered += left_tree.num_jump(). New tree is rooted in the same place as left_tree.

References core::kinematics::FoldTree::add_edge(), core::kinematics::FoldTree::delete_edge(), core::sequence::end, facet_containing_position(), core::kinematics::Edge::label(), core::kinematics::FoldTree::nres(), core::kinematics::FoldTree::num_jump(), core::kinematics::Edge::PEPTIDE, core::kinematics::FoldTree::reorder(), core::kinematics::FoldTree::root(), core::kinematics::Edge::start(), core::kinematics::Edge::stop(), and vertex_exists().

◆ order()

bool protocols::forge::methods::order ( core::kinematics::Edge & e )

enforce Edge has start <= stop (swap if necessary)

Returns: true if start and stop were swapped

References core::kinematics::Edge::start(), core::kinematics::Edge::start_atom(), core::kinematics::Edge::stop(), and core::kinematics::Edge::stop_atom().

Referenced by add_vertex(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::apply(), protocols::simple_moves::PSSM2BfactorMover::apply(), protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::close_at_cutpoint(), protocols::rna::denovo::coarse::CoarseRNA_LoopCloser::close_the_loop(), protocols::generalized_kinematic_closure::GeneralizedKIC::doKIC(), edges_within_interval(), find_connecting_jump(), protocols::generalized_kinematic_closure::GeneralizedKIC::generate_bridgeobjects_data_from_atomlist(), protocols::fold_from_loops::utils::Nub::get_nub_pieces(), protocols::simple_filters::SheetFilter::ingo_find_dir(), protocols::simple_filters::SheetFilter::ingo_find_ord(), protocols::simple_filters::SheetFilter::ingo_hand(), protocols::simple_filters::SheetFilter::ingo_lnl(), protocols::simple_filters::SheetFilter::ingo_sheet_stuff(), protocols::stepwise::sampler::rna::RNA_KinematicCloser::init(), core::chemical::gasteiger::PossibleAtomTypesForAtom::IsUnsaturated(), protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger::KIC_loop_close(), protocols::forge::build::SegmentInsert::modify_impl(), protocols::forge::build::SegmentRebuild::modify_impl(), core::fragment::picking_old::vall::VallResidue::order_vector(), protocols::frag_picker::VallResidue::order_vector(), protocols::pose_selectors::TopNByProperty::parse_my_tag(), core::sequence::MatrixScoringScheme::read_data(), core::sequence::SequenceProfile::read_from_binary_chk(), core::sequence::SequenceProfile::read_from_checkpoint(), core::sequence::ChemicalShiftSequence::read_from_file(), core::sequence::SequenceProfile::read_from_file(), regular_edges_within_interval(), remove_cutpoint(), remove_cutpoints(), replace(), protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger::sample_omega_recursively(), protocols::fldsgn::topology::SheetSet::set_sheet_number(), shift_jumps(), and protocols::kinematic_closure::ClosureProblem::solve().

◆ overlap_chainbreak() [1/2]

core::Real protocols::forge::methods::overlap_chainbreak	(	core::pose::Pose &	pose,
		core::Size const	pos
	)

evaluate overlap chainbreak at a position

Remarks: If necessary, will evaluate using a copy of the Pose with a cut fold tree. If cutpoint variants are present at chainbreak, will use existing variants and not modify them. If cutpoint variants are not found will add them and then remove them once calculation is finished.; If necessary, will evaluate using a copy of the Pose with a cut fold tree.

References add_cutpoint_variants(), protocols::buns::energy, core::pose::Pose::fold_tree(), fold_tree_from_pose(), core::kinematics::FoldTree::is_cutpoint(), core::kinematics::FoldTree::new_jump(), core::kinematics::FoldTree::num_cutpoint(), core::scoring::overlap_chainbreak, remove_cutpoint_variants(), core::kinematics::FoldTree::root(), and core::pose::Pose::size().

◆ overlap_chainbreak() [2/2]

core::Real protocols::forge::methods::overlap_chainbreak	(	core::pose::Pose const &	pose,
		core::Size const	pos
	)

evaluate overlap chainbreak at a position

Remarks: Copies the Pose, if necessary swaps the Pose with a cut fold tree, then evaluates the chainbreak.

References core::pose::Pose::fold_tree(), fold_tree_from_pose(), core::kinematics::FoldTree::is_cutpoint(), core::kinematics::FoldTree::new_jump(), core::kinematics::FoldTree::num_cutpoint(), and core::kinematics::FoldTree::root().

◆ parse_resfile_string_with_no_lockdown()

utility::vector1< bool > protocols::forge::methods::parse_resfile_string_with_no_lockdown	(	core::pose::Pose const &	pose,
		core::pack::task::PackerTask &	the_task,
		std::string const &	resfile_string
	)

References core::pack::task::comment_begin(), core::pack::task::create_command_map(), core::pack::task::get_token(), core::pack::task::onError(), core::pose::Pose::pdb_info(), core::pose::Pose::size(), core::pack::task::tokenize_line(), core::pack::task::PackerTask::total_residue(), and TR().

Referenced by protocols::forge::remodel::RemodelDesignMover::mode5_packertask().

◆ quadratic_chainbreak() [1/2]

core::Real protocols::forge::methods::quadratic_chainbreak	(	core::pose::Pose &	pose,
		core::Size const	pos
	)

evaluate quadratic chainbreak at a position

Remarks: If necessary, will evaluate using a copy of the Pose with a cut fold tree. If cutpoint variants are present at chainbreak, will use existing variants and not modify them. If cutpoint variants are not found will add them and then remove them once calculation is finished.; If necessary, will evaluate using a copy of the Pose with a cut fold tree.

References add_cutpoint_variants(), core::scoring::chainbreak, protocols::buns::energy, core::pose::Pose::fold_tree(), fold_tree_from_pose(), core::kinematics::FoldTree::is_cutpoint(), core::kinematics::FoldTree::new_jump(), core::kinematics::FoldTree::num_cutpoint(), remove_cutpoint_variants(), core::kinematics::FoldTree::root(), and core::pose::Pose::size().

◆ quadratic_chainbreak() [2/2]

core::Real protocols::forge::methods::quadratic_chainbreak	(	core::pose::Pose const &	pose,
		core::Size const	pos
	)

evaluate quadratic chainbreak at a position

Remarks: Copies the Pose, if necessary swaps the Pose with a cut fold tree, then evaluates the chainbreak.

References core::pose::Pose::fold_tree(), fold_tree_from_pose(), core::kinematics::FoldTree::is_cutpoint(), core::kinematics::FoldTree::new_jump(), core::kinematics::FoldTree::num_cutpoint(), and core::kinematics::FoldTree::root().

◆ regular_edges_within_interval()

template<typename EdgeIterator >

utility::vector1< core::kinematics::Edge > protocols::forge::methods::regular_edges_within_interval	(	core::Size const	left,
		core::Size const	right,
		EdgeIterator const	begin,
		EdgeIterator const	end
	)

find regular (non-jump) edges contained within the interval [left, right]

References core::sequence::end, core::sequence::left, order(), core::kinematics::Edge::start(), and core::kinematics::Edge::stop().

◆ regular_facet_containing_position()

template<typename EdgeIterator >

EdgeIterator protocols::forge::methods::regular_facet_containing_position	(	core::Size const	pos,
		EdgeIterator const	begin,
		EdgeIterator const	end
	)

find regular facet (non-jump edge sans face vertices) that contains given position

Parameters

[in]	pos	position
[in]	begin	iterator pointing to the first edge to search
[in]	end	iterator pointing just past the last edge to search

Returns: iterator pointing to the Edge defining the facet that contains the position; if vertex lies on the face of an edge or vertex not found, returns 'end'

References core::sequence::end.

Referenced by add_vertex().

◆ remodel_generic_taskfactory()

core::pack::task::TaskFactoryOP protocols::forge::methods::remodel_generic_taskfactory ( )

Referenced by protocols::forge::remodel::RemodelWorkingSet::manualPackerTaskGen(), protocols::forge::remodel::RemodelDesignMover::mode1_1_packertask(), protocols::forge::remodel::RemodelDesignMover::mode1_packertask(), protocols::forge::remodel::RemodelDesignMover::mode2_packertask(), protocols::forge::remodel::RemodelDesignMover::mode3_packertask(), and protocols::forge::remodel::RemodelDesignMover::mode5_packertask().

◆ remove_cutpoint()

bool protocols::forge::methods::remove_cutpoint	(	core::Size const	v,
		core::kinematics::FoldTree &	ft
	)

remove a cutpoint, merging the two sections that are adjacent to the cut

Returns: true if cutpoint removed, false if not a cutpoint

References core::kinematics::FoldTree::delete_jump_and_intervening_cutpoint(), core::kinematics::FoldTree::is_cutpoint(), core::kinematics::FoldTree::nres(), order(), core::kinematics::Edge::start(), core::kinematics::Edge::stop(), and union_interval().

Referenced by protocols::forge::build::Bridge::modify_impl().

◆ remove_cutpoint_variants()

bool protocols::forge::methods::remove_cutpoint_variants	(	core::pose::Pose &	pose,
		core::Size const	pos
	)

remove cutpoint variants at a specific position

Parameters

[in,out]	Pose	to modify
[in]	position	at which to remove cutpoint variants

Returns: true if cutpoint variants removed, false if no cutpoint variants found or position not a topological cutpoint

References core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::pose::Pose::fold_tree(), core::conformation::Residue::has_variant_type(), core::kinematics::FoldTree::is_cutpoint(), core::pose::remove_variant_type_from_pose_residue(), core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by linear_chainbreak(), protocols::forge::build::Bridge::modify_impl(), protocols::forge::build::SegmentRebuild::modify_impl(), overlap_chainbreak(), and quadratic_chainbreak().

◆ remove_cutpoints()

void protocols::forge::methods::remove_cutpoints	(	utility::vector1< core::Size > const &	cutpoints,
		core::kinematics::FoldTree &	ft
	)

seal a fold tree by removing all specified cutpoints

Parameters

[in]	cutpoints	Cutpoints to remove.
[in,out]	ft	The input tree.

Returns: A new tree with cutpoints removed and all other topology kept constant.

References core::kinematics::FoldTree::delete_jump_and_intervening_cutpoint(), core::kinematics::FoldTree::nres(), order(), core::kinematics::Edge::start(), core::kinematics::Edge::stop(), and union_interval().

◆ replace()

core::kinematics::FoldTree protocols::forge::methods::replace	(	core::kinematics::FoldTree const &	original_tree,
		core::Size const	replace_begin,
		core::Size const	replace_end,
		core::kinematics::MoveMap const &	movemap,
		core::kinematics::FoldTree const &	replacement_tree
	)

replace a section of one fold tree with another fold tree, connecting by jump between their roots

Parameters

[in]	original_tree
[in]	replace_begin	residue starting the section of original_tree to replace
[in]	replace_end	residue ending the section of original_tree to replace
[in]	movemap	MoveMap whose fixed backbone positions dictates where new jumps may be placed.
[in]	replacement_tree

Returns: FoldTree with section replaced.

Remarks: The procedure will attempt to honor the MoveMap as much as it can. The caveat is that sequences of calls to some FoldTree routines may shift the jumps internally in a way that is not easily predictable. If the procedure cannot find an allowed residue for a jump, it will make a jump to the median residue in the disconnected fold tree interval.

Referenced by core::io::silent::SilentStruct::add_energy(), core::scoring::power_diagram::PowerDiagram::add_single_atom_to_power_diagram(), core::io::silent::SilentStruct::add_string_value(), protocols::medal::MedalExchangeMover::apply(), protocols::flxbb::LayerDesignOperation::apply(), core::conformation::symmetry::comma_strings_to_map(), core::conformation::symmetry::comma_strings_to_pair_map(), core::conformation::symmetry::comma_strings_to_vector(), core::conformation::symmetry::comma_strings_to_vector_map(), core::io::silent::SilentStruct::copy_scores(), protocols::frag_picker::FragmentPicker::fragment_contacts(), protocols::forge::build::SegmentSwap::modify_impl(), protocols::frag_picker::FragmentPicker::nonlocal_pairs(), protocols::frag_picker::FragmentPicker::output_pair_counts(), core::conformation::symmetry::SymDof::read(), core::chemical::carbohydrates::CarbohydrateInfo::read_and_set_properties(), core::chemical::carbohydrates::replace_underscores_with_spaces(), and protocols::pockets::GenPharmacophore::ReplaceString().

◆ restore_residues() [1/2]

void protocols::forge::methods::restore_residues	(	core::pose::Pose &	archive_pose,
		core::pose::Pose &	pose
	)

restore residues (i.e. sidechains)

Parameters

[in]	archive_pose	the original Pose to take residues from
[out]	pose	the altered Pose that needs residue restoration

Remarks: length between two poses must be equal

References restore_residues(), and core::pose::Pose::size().

◆ restore_residues() [2/2]

void protocols::forge::methods::restore_residues	(	std::map< core::Size, core::Size > const &	old2new,
		core::pose::Pose &	archive_pose,
		core::pose::Pose &	pose
	)

restore residues (i.e. sidechains)

Parameters

[in]	old2new	map indicating residues to be transferred and the mapping from archive_pose position -> pose position
[in]	archive_pose	the original Pose to take residues from
[out]	pose	the altered Pose that needs residue restoration

References core::scoring::Energies::clear(), core::pose::Pose::conformation(), core::conformation::Conformation::detect_disulfides(), core::pose::Pose::energies(), core::scoring::get_score_function(), core::pose::Pose::is_fullatom(), core::pack::pack_rotamers(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by protocols::protein_interface_design::movers::DockWithHotspotMover::apply(), protocols::forge::components::VarLengthBuild::apply(), protocols::fldsgn::BluePrintBDR::centroid_build(), protocols::forge::components::BDR::centroid_build(), protocols::forge::remodel::RemodelMover::centroid_build(), and restore_residues().

◆ set_single_loop_fold_tree()

void protocols::forge::methods::set_single_loop_fold_tree	(	core::pose::Pose &	pose,
		protocols::loops::Loop const &	loop
	)

set a single loop fold tree

Remarks: This is a generic replacement function for the one in protocols::loops and will be moved there in the near future.

References protocols::loops::Loops::add_loop(), core::pose::Pose::fold_tree(), and fold_tree_from_loops().

Referenced by protocols::forge::remodel::RemodelLoopMover::boost_closure_stage(), protocols::LoopRebuild::build_loop_with_ccd_closure(), protocols::seeded_abinitio::CloseFold::fast_loopclose(), protocols::forge::remodel::RemodelLoopMover::independent_stage(), protocols::forge::remodel::RemodelLoopMover::loophash_stage(), protocols::loop_build::LoopMover_SlidingWindow::model_loop(), and protocols::forge::remodel::RemodelLoopMover::set_segment_stage().

◆ shift_jumps()

core::kinematics::FoldTree protocols::forge::methods::shift_jumps	(	core::kinematics::FoldTree const &	ft,
		core::kinematics::MoveMap const &	mm
	)

attempt to shift jumps in a fold tree based on fixed positions in a MoveMap

Parameters

[in]	ft	FoldTree to alter
[in]	movemap	MoveMap to try and honor

Returns: FoldTree with jumps shifted, if possible

Remarks: Procedure will shift a jump position on a continuous segment to a randomly selected fixed position on that segment specified by the MoveMap. No changes will be made to a jump point if it is contained within a segment lacking valid fixed positions. This procedure has the side effect of collapsing all jump points to a single point within segments that have fixed positions.

References core::kinematics::FoldTree::add_edge(), add_vertex(), core::kinematics::MoveMap::get_bb(), core::kinematics::FoldTree::nres(), order(), core::kinematics::FoldTree::reorder(), core::scoring::rg, core::kinematics::FoldTree::root(), and union_interval().

◆ smallmer_from_largemer()

core::fragment::ConstantLengthFragSetOP protocols::forge::methods::smallmer_from_largemer	(	core::fragment::ConstFrameIterator	begin,
		core::fragment::ConstFrameIterator	end,
		core::Size const	smallmer_size,
		bool const	all_possible_smallmers
	)

create small-mers from large-mers

Parameters

[in] all_possible_smallmers Default false. If true, grab all possible smallmers using every possible starting position in a largemer (you could end up with a lot of fragments per position). If false, grab smallmers using only the first position of a largemer as the starting position.

References core::sequence::end.

Referenced by protocols::forge::components::VarLengthBuild::pick_all_fragments(), and protocols::protein_interface_design::movers::LoopRemodel::pick_loop_frags().

◆ TR() [1/3]

static basic::Tracer protocols::forge::methods::TR ( "protocols.forge.methods.fold_tree_functions" )

static

Referenced by fold_tree_from_pose(), make_star_foldtree(), parse_resfile_string_with_no_lockdown(), and replace().

◆ TR() [2/3]

static basic::Tracer protocols::forge::methods::TR ( "protocols.forge.methods.pose_mod" )

static

◆ TR() [3/3]

static basic::Tracer protocols::forge::methods::TR ( "protocols.forge.methods.util" )

static

◆ trans_omega()

void protocols::forge::methods::trans_omega	(	core::Size const	left,
		core::Size const	right,
		core::pose::Pose &	pose
	)

set omega to 180 for a range of residues [left, right]

References core::sequence::left, and core::pose::Pose::set_omega().

Referenced by protocols::forge::build::GrowLeft::modify_impl(), protocols::forge::build::GrowRight::modify_impl(), protocols::forge::build::SegmentInsert::modify_impl(), protocols::forge::build::SegmentRebuild::modify_impl(), and protocols::kinematic_closure::perturbers::OmegaPerturber::perturb_subset().

◆ union_interval()

void protocols::forge::methods::union_interval	(	core::Size const	root,
		core::Size const	left,
		core::Size const	right,
		utility::graph::DisjointSets &	uf
	)

perform union( root, i ) for all 'i' within the closed interval [left, right]

Parameters

[in]	root	position to union with; can be any number, does not have to be a true root of a set
[in]	left	start of the interval
[in]	right	end of the interval
[in,out]	uf

References core::sequence::left.

Referenced by find_connecting_jump(), remove_cutpoint(), remove_cutpoints(), replace(), and shift_jumps().

◆ vertex_exists()

bool protocols::forge::methods::vertex_exists	(	core::Size const	v,
		core::kinematics::FoldTree const &	ft
	)

query if vertex already exists in fold tree

Referenced by merge().

Functions

Function Documentation

◆ add_cutpoint_variants()

◆ add_edges()

◆ add_vertex()

◆ apply_transformation()

◆ calc_rsd_sasa()

◆ closed_range()

◆ closest_larger_peptide_vertex()

◆ closest_smaller_peptide_vertex()

◆ count_cutpoints()

◆ edges_within_interval()

◆ facet_containing_position()

◆ fill_non_loop_cst_set()

◆ find_connecting_jump()

◆ find_cutpoint()

◆ fold_tree_from_loops()

◆ fold_tree_from_pose()

◆ grow_left_r()

◆ grow_left_rtype()

◆ grow_right_r()

◆ grow_right_rtype()

◆ half_open_range()

◆ insert_closed_range()

◆ insert_half_open_range()

◆ interval_to_loop()

◆ intervals_to_confirmation_loops()

◆ intervals_to_loops()

◆ jumps_and_cuts_from_pose()

◆ jumps_connected_to_position()

◆ linear_chainbreak() [1/2]

◆ linear_chainbreak() [2/2]

◆ make_star_foldtree()

◆ merge() [1/3]

◆ merge() [2/3]

◆ merge() [3/3]

◆ order()

◆ overlap_chainbreak() [1/2]

◆ overlap_chainbreak() [2/2]

◆ parse_resfile_string_with_no_lockdown()

◆ quadratic_chainbreak() [1/2]

◆ quadratic_chainbreak() [2/2]

◆ regular_edges_within_interval()

◆ regular_facet_containing_position()

◆ remodel_generic_taskfactory()

◆ remove_cutpoint()

◆ remove_cutpoint_variants()

◆ remove_cutpoints()

◆ replace()

◆ restore_residues() [1/2]

◆ restore_residues() [2/2]

◆ set_single_loop_fold_tree()

◆ shift_jumps()

◆ smallmer_from_largemer()

◆ TR() [1/3]

◆ TR() [2/3]

◆ TR() [3/3]

◆ trans_omega()

◆ union_interval()

◆ vertex_exists()