The FoldTree is a residue-based tree-like representation of a molecule. More...

#include <FoldTree.hh>

Inheritance diagram for core::kinematics::FoldTree:

Public Types
typedef std::vector< Edge >	EdgeList

typedef EdgeList::iterator	iterator

typedef EdgeList::const_iterator	const_iterator

Public Member Functions
	~FoldTree () override
	Automatically generated virtual destructor for class deriving directly from ReferenceCount. More...

	FoldTree ()
	constructor More...

	FoldTree (int const nres_in)
	Constructs a simple FoldTree. More...

	FoldTree (FoldTree const &)=default

FoldTree &	operator= (FoldTree const &src)
	operator= More...

FoldTree	clone ()

Size	boundary_left (Size res) const
	Return the starting residue of the first kinematic Edge to which res belongs. More...

Size	boundary_right (Size res) const
	Return the ending residue of the first kinematic Edge to which res belongs. More...

int	size () const
	Returns the number of edges in the FoldTree. More...

const_iterator	begin () const
	begin iterator of the edge_list More...

const_iterator	end () const
	end iterator of the edge_list More...

void	show (std::ostream &out) const
	Displays the FoldTree information. More...

void	add_edge (core::Size const start, core::Size const stop, int const label)
	Adds an edge from <start> to <stop> More...

void	add_edge (Size const start, Size const stop, std::string const &start_atom, std::string const &stop_atom)
	Especially useful version of add_edge for chemical edge construction. More...

void	add_edge (Size const start, Size const stop, int const label, std::string const &start_atom, std::string const &stop_atom)
	Especially useful version of add_edge for chemical edge construction. More...

void	add_edge (Edge const &new_edge)
	Add the edge <new_edge> More...

void	prepend_edge (Edge const &new_edge)
	Prepend the edge <new_edge>. Useful alternative to add_edge for setting root. More...

void	replace_edge (Edge const &old_edge, Edge const &replacement_edge)
	Find and replace an Edge in the FoldTree. More...

void	delete_edge (iterator edge)
	Deletes the edge <edge> in the FoldTree by iterator. More...

void	delete_edge (Edge const &edge)
	Delete the edge <edge> in the fold tree by example edge. More...

void	delete_unordered_edge (Size const start, Size const stop, int const label)
	Find an edge in fold tree and delete it. More...

void	update_edge_label (Size const start, Size const stop, int const old_label, int const new_label)
	Changes the label of an edge in fold tree. More...

int	edge_label (Size const start, Size const stop)
	Returns the edge label of the edge from <start> to <stop> More...

void	split_existing_edge_at_residue (Size const resNo)
	Splits an edge into two at a specified position. More...

void	clear ()
	Deletes all edge in the FoldTree. More...

void	renumber_jumps ()
	Renumbers the jump edges in the FoldTree How? More...

void	renumber_jumps_ordered ()
	Renumbers the jump edges in the FoldTree while. More...

void	delete_self_edges ()
	Deletes edges with start==stop allowable 1->1 edge for single residue FoldTree. More...

void	delete_extra_vertices ()
	Delete vertices that are no longer necessary any more How is this determined? More...

void	delete_segment (Size const seg_begin, Size const seg_end)
	Deletes a continuous segment from <seq_begin> to <seq_end> More...

void	delete_seqpos (Size const seqpos)
	Deletes the residue <seqpos> from the FoldTree. Will rearrange topology if necessary. More...

void	insert_polymer_residue (Size const seqpos, bool const join_lower, bool const join_upper)
	Inserts a polymer residue at position <seqpos> How? More...

void	insert_residue_by_chemical_bond (Size const seqpos, Size const anchor_residue, std::string const &anchor_atom, std::string const &root_atom)
	Inserts a bonded residue at position <seqpos> More...

void	insert_residue_by_jump (Size const seqpos, Size anchor_pos, std::string const &anchor_atom="", std::string const &root_atomno="")
	Inserts a residue attached only by a jump. precondition is that seqpos-1 is a cutpoint. More...

void	insert_fold_tree_by_jump (FoldTree const &subtree, Size const insert_seqpos, Size const insert_jumppos, Size const anchor_pos, Size anchor_jump_number=0, std::string const &anchor_atom="", std::string const &root_atom="")
	Inserts a fold_tree as a subtree. More...

void	apply_sequence_mapping (id::SequenceMapping const &old2new)
	Renumber all vertices according to an input sequence mapping. More...

core::Size	new_jump (Size const jump_pos1, Size const jump_pos2, Size const cutpoint)
	Adds a new jump edge from <pos1> to <pos2> with cutpoint <cutpoint> More...

void	new_chemical_bond (Size const anchor_pos, Size const root_pos, std::string const &anchor_atom, std::string const &root_atom, Size const new_cutpoint)

void	simple_tree (Size const nres_in)
	Produces a 1-edge FoldTree that is <nres_in> long No jumps or extraneous features. More...

bool	is_simple_tree () const
	Returns true if the FoldTree has 1-edge (non-jump) More...

bool	random_tree_from_jump_points (Size const nres_in, Size const num_jump_in, ObjexxFCL::FArray2D< Size > const &jump_point, ObjexxFCL::FArray1D_float const &cut_bias, Size const root_in=1, bool const allow_jump_at_1_or_NRES=false)
	Builds a FoldTree from a list of <jump_points> and random cut points based on some biased probability Returns bool about success. More...

bool	random_tree_from_jump_points (Size const nres_in, Size const num_jump_in, ObjexxFCL::FArray2D< Size > const &jump_point, std::vector< Size > const &obligate_cut_points, ObjexxFCL::FArray1D_float const &cut_bias, Size const root_in=1, bool const allow_jump_at_1_or_NRES=false)
	Builds a FoldTree from a list of <jump_points> and random cut points based on some biased probability and any user-defined obligate cutpoints Returns bool about success. More...

bool	tree_from_jumps_and_cuts (Size const nres_in, Size const num_jump_in, ObjexxFCL::FArray2D< Size > const &jump_point, ObjexxFCL::FArray1D< Size > const &cuts, Size const root_in=1, bool const verbose=false)
	Constructs a FoldTree from listed <jump point>=""> and <cuts> Returns bool about success. More...

void	append_residue (bool const attach_by_jump=false, core::Size const jump_anchor_residue=0, std::string const &jump_upstream_atom="", std::string const &jump_downstream_atom="")
	Appends a new residue to the tree, either by a jump or as a continuation of a peptide segment. More...

void	append_residue_by_chemical_bond (core::Size const anchor_residue, std::string const &anchor_atom, std::string const &root_atom)
	Appends a new residue to the tree using a chemical (APL-style) connection. More...

bool	reorder (Size const start_residue, bool const verbose_if_fail=true)
	Reorders the FoldTree to start at residue <start_residue> More...

bool	check_fold_tree () const
	Returns true if this is a valid FoldTree. More...

bool	connected () const
	Returns true if the FoldTree is connected. More...

bool	check_edges_for_atom_info () const
	chemical edges should have atom info More...

Size	upstream_jump_residue (Size const jump_number) const
	the starting residue for this jump More...

Size	downstream_jump_residue (Size const jump_number) const
	the stopping residue for this jump More...

void	partition_by_jump (Size const jump_number, FoldTree &f1, FoldTree &f2) const
	partition into two foldtrees by cutting at jump= jump_number More...

void	partition_by_jump (Size const jump_number, ObjexxFCL::FArray1D_bool &partner1) const
	partition the fold tree in two parts if the jump is disconnected. More...

utility::vector1< bool >	partition_by_jump (Size const jump_nr) const
	partition the fold tree in two parts if the jump is disconnected. More...

utility::vector1< Size >	partition_coloring (utility::vector1< Size > const &jump_numbers) const
	partition the fold tree into n parts based on specified jumps. More...

void	partition_by_residue (Size const seqpos, ObjexxFCL::FArray1D_bool &partner1) const
	partition the fold tree in two parts if a cut would be introduced between seqpos and seqpos+1 More...

Size	cutpoint_by_jump (Size const jump_number) const
	Returns the corresponding cutpoint position for jump <jump_number> WARNING: if you look for all cutpoints by cycling thru jump_numbers you may be dissapointed you will get most likely the same cutpoint for several different jump_numbers however: the method cutpoint( nr ) will give you the number you are looking for. More...

std::string	upstream_atom (Size const jump_number) const
	the jump atom on the staring side More...

std::string	downstream_atom (Size const jump_number) const
	the jump atom on the stopping side More...

int	get_polymer_residue_direction (Size const seqpos) const
	Returns the direction (n2c, c2n) in which the given (peptide) residue is built during folding. More...

bool	residue_is_in_fold_tree (Size seqpos) const
	Check if the seqpos is covered by an edge in the FoldTree (Mainly useful for FoldTrees as they are being built.) More...

Edge const &	get_residue_edge (Size const seqpos) const
	Returns the edge that builds the residue <seqpos> Does not work for root atom (will fail) More...

utility::vector1< Edge >	get_outgoing_edges (Size const seqpos) const
	Returns all edges that build a residue directly off of <seqpos> More...

utility::vector1< Edge >	get_jump_edges () const
	Return all jump Edges from the FoldTree. More...

utility::vector1< Edge >	get_chemical_edges () const
	Returns all chemical edges from fold tree. More...

core::Size	get_jump_that_builds_residue (Size const seqpos) const
	Get the number of the jump that builds (connects to) a given residue It's an error if the residue isn't built directly by a jump. More...

core::Size	get_parent_residue (Size const seqpos, bool &connected_by_jump) const
	Get the residue that is immediately upstream of this residue (and tell us whether connection is jump or bond). More...

core::Size	get_parent_residue (Size const seqpos) const
	Get the residue that is immediately upstream of this residue. More...

void	set_jump_atoms (Size const jump_number, std::string const &upstream_atom, std::string const &downstream_atom, bool bKeepStubInResidue=false)
	define the specific atoms that should be connected by this jump More...

void	set_jump_atoms (Size const jump_number, core::Size res1, std::string const &atom1, core::Size res2, std::string const &atom2, bool bKeepStubInResidue=false)

void	put_jump_stubs_intra_residue ()
	this reorganizes upstream/downstream atoms of all jumps such that stubs are N-CA-C More...

void	reassign_atoms_for_intra_residue_stubs ()
	this reorganizes upstream/downstream atoms of jumps that have flag keep_stub_in_resiue = true such that stubs are N-CA-C More...

std::size_t	hash_value () const
	computes a fixed-length, hash-based identifier for this FoldTree, permitting efficient comparison between a pair of FoldTrees More...

std::string	to_string () const
	easy output of string More...

Size	nres () const
	Returns the number of residues in the FoldTree. More...

Size	num_jump () const
	Returns the number of jumps in the FoldTree. More...

Size	jump_point (Size const lower_higher, Size const jump_number) const
	starting or stopping residue of a jump edge More...

bool	is_jump_point (Size const seqpos) const
	Returns true if <seqpos> is a starting or stopping residue of a jump edge. More...

Size	cutpoint (Size const cut) const
	Returns the cutpoint position of jump number <cut> More...

Size	num_cutpoint () const
	Returns the number of cutpoints in the FoldTree. More...

bool	is_cutpoint (Size const seqpos) const
	Returns true is position <seqpos> is a cutpoint. More...

Size	cutpoint_map (Size const seqpos) const
	cutpoint number for this residue More...

Edge const &	jump_edge (Size const jump_number) const
	Returns the jump edge with jump number <jump_number> (const) More...

Edge &	jump_edge (Size const jump_number)
	Returns the jump edge with jump number <jump_number> (non-const) More...

core::Size	jump_nr (core::Size upstream_res, core::Size downstream_res) const
	get the jump_nr connected to jump upstream->downstream, returns 0 if not found More...

bool	empty () const
	Returns true if the FoldTree is empty. More...

bool	is_root (Size const seqpos) const
	Returns true if <seqpos> the the root. More...

bool	possible_root (Size const &seqpos) const
	Returns true if <seqpos> is the root. More...

Size	root () const
	Returns the root vertex position of the FoldTree. More...

bool	jump_exists (Size const pos1, Size const pos2) const
	Return true if a jump exists between <pos1> and <pos2> More...

Size	count_fixed_residues (Size const begin_res, Size const size, Size &min_edge_count_out) const

utility::vector1< Size >	cutpoints () const
	get all cutpoints More...

bool	is_equivalent (FoldTree const &b) const
	Check if the two FoldTrees build in a similar fashion That is, if their roots are the same and if all edges correspond to each other – Does not necessarily check that the order of the edges are the same. More...

void	slide_cutpoint (Size const current_cut, Size const target_cut)
	Slide a polymer cutpoint from one location to another. More...

void	slide_jump (Size const jump_number, Size const new_res1, Size const new_res2)
	change an existing jump to start and end in new positions More...

void	delete_jump_and_intervening_cutpoint (Size jump_begin, Size jump_end, Size cut=0)
	Useful for removing a loop modeling jump+cut. More...

void	delete_jump_and_intervening_cutpoint (Size const jump_number)
	Useful for removing a loop modeling jump+cut. More...

bool	cut_edge (Size const cut_point)
	helper function to try cutting an edge in a tree. More...

Private Member Functions
void	delete_seqpos_simple (Size const seqpos)
	delete a polymer residue (non-jump,non-root) More...

void	delete_jump_seqpos (Size const seqpos)
	delete a root/jump_point residue More...

iterator	nc_begin ()
	non-const begin iterator of edge_list More...

iterator	nc_end ()
	non-const end iterator of edge_list More...

void	add_vertex (Size const v)
	Helper function. More...

bool	check_topology () const
	update fold tree topology (when edges are changed) if necessary More...

bool	check_order () const
	update fold tree order (when edges are same but the order in the edge_list is changed) if necessary More...

void	update_nres () const
	update total number residues in the fold tree More...

void	update_num_jump () const
	update number of jumps in the fold tree More...

void	update_jump_points () const
	update jump residues list More...

void	update_jump_edge () const
	update the index of jump edges in the edge list More...

void	update_cutpoints () const
	update cutpoints info in the fold tree More...

void	setup_edge_counts () const
	update edge counts info More...

void	update_edge_labels ()
	update edge labels based on whether edges are separating or not. More...

bool	cut_random_edge (ObjexxFCL::FArray1D_float const &cut_bias_sum, Size const nres_in)
	cut an edge randomly based on probability without disconnecting fold tree More...

Private Attributes
EdgeList	edge_list_

bool	new_topology
	edges in the edge_list_ have been changed. More...

bool	new_order
	edges in the edge_list_ have been reordered. More...

Size	nres_
	just the largest vertex in edge_list_ More...

Size	num_jump_
	number of jump edges (edges in edge_list_ with label>0) More...

Size	num_cutpoint_
	number of cutpoints in the fold tree. More...

utility::vector1< std::pair < Size, Size > >	jump_point_
	jump number to jump residue number. dimensioned as (2,num_jump_) More...

utility::vector1< bool >	is_jump_point_
	whehter a residue is a jump_point, dimensioned as nres_ More...

utility::vector1< Size >	cutpoint_
	cutpoint number to cutpoint residue number, dimesioned as num_cutpoint_. More...

utility::vector1< Size >	cutpoint_map_
	residue number of cutpoint number, 0 if it is not a cutpoint. dimensioned as nres_. More...

ObjexxFCL::FArray1D_bool	is_cutpoint_
	whether a residue is a cutpoint, dimensioned as nres_ More...

utility::vector1< Size >	jump_edge_
	jump number to edge index number in the edge_list_, dimensioned as num_jump_. More...

utility::vector1< Size >	edge_count
	dimensioned as nres_, see setup_edge_counts for more info More...

Size	min_edge_count
	the minimum number in edge_count and jump_edge_count. More...

utility::vector1< Size >	jump_edge_count
	dimensioned as num_jump, see setup_edge_counts for more info More...

ObjexxFCL::FArray1D_bool	linked_
	Used as scratch space by a couple of functions. More...

ObjexxFCL::FArray1D_bool	seen_

boost::hash< std::string >	hasher
	computes fixed-size identifier for a string input More...

Friends
std::istream &	operator>> (std::istream &is, FoldTree &t)
	input operator More...

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

bool	operator== (FoldTree const &a, FoldTree const &b)
	equal to operator More...

bool	operator!= (FoldTree const &a, FoldTree const &b)
	Not equal to operator. More...

Detailed Description

The FoldTree is a residue-based tree-like representation of a molecule.

Note: all the derived data is "mutable", so that we can update them as needed on the fly inside "const" member functions this emphasizes that the core data is just the edge_list_; see FoldTree overview and concepts for details

Common Methods: FoldTree.check_fold_tree FoldTree.clear FoldTree.new_jump FoldTree.nres FoldTree.num_jump FoldTree.simple_tree Foldtree.size

Member Typedef Documentation

typedef EdgeList::const_iterator core::kinematics::FoldTree::const_iterator

typedef std::vector< Edge > core::kinematics::FoldTree::EdgeList

typedef EdgeList::iterator core::kinematics::FoldTree::iterator

Constructor & Destructor Documentation

core::kinematics::FoldTree::~FoldTree ( )

overridedefault

Automatically generated virtual destructor for class deriving directly from ReferenceCount.

core::kinematics::FoldTree::FoldTree ( )

inline

constructor

core::kinematics::FoldTree::FoldTree ( int const nres_in )

inline

Constructs a simple FoldTree.

ft = FoldTree( nres_in )

int nres_in /the number of residues in this simple tree

References simple_tree().

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

default

Member Function Documentation

void core::kinematics::FoldTree::add_edge	(	core::Size const	start,
		core::Size const	stop,
		int const	label
	)

Adds an edge from <start> to <stop>

do not allow self edge and do not order the edge list here

Referenced by protocols::forge::methods::add_edges(), protocols::simple_moves::ResetFoldTree::apply(), protocols::simple_moves::SwitchChainOrderMover::apply(), protocols::protein_interface_design::movers::SetAtomTree::apply(), protocols::metal_interface::ZincHeterodimerMover::apply(), protocols::simple_moves::SetTorsion::apply(), protocols::pose_length_moves::PossibleLoop::assign_phi_psi_omega_from_lookback(), protocols::fold_from_loops::utils::attach_n_and_c_unfolded_poses_to_pose(), core::pose::create_chemical_edge(), protocols::pose_length_moves::NearNativeLoopCloser::create_maximum_length_pose(), protocols::loop_modeling::LoopBuilder::do_apply(), protocols::stepwise::monte_carlo::mover::ensure_appropriate_foldtree_for_move(), protocols::star::Extender::extend_unaligned(), protocols::loophash::LoopHashLibrary::extract_data_from_pose(), protocols::splice::SpliceManager::fold_tree(), protocols::splice::Splice::fold_tree(), protocols::loops::fold_tree_from_loops(), protocols::denovo_design::components::FoldGraph::fold_tree_rec(), protocols::simple_moves::CutChainMover::foldTree(), core::conformation::symmetry::get_asymm_unit_fold_tree(), protocols::splice::RBOutMover::get_disulf_jump(), protocols::rna::denovo::get_rnp_docking_fold_tree(), protocols::loophash::get_rt_over_leap(), protocols::loophash::get_rt_over_leap_fast(), protocols::denovo_design::insert_peptide_edges(), core::kinematics::linearize_fold_tree(), protocols::features::PoseConformationFeatures::load_fold_tree(), protocols::enzdes::EnzdesFlexibleRegion::minimize_region(), protocols::protein_interface_design::MinimizeInterface(), partition_by_jump(), protocols::protein_interface_design::movers::PlaceStubMover::place_stub(), core::kinematics::remodel_fold_tree_to_account_for_insertion(), protocols::denovo_design::remove_all_jump_atoms(), protocols::denovo_design::remove_missing_jump_atoms(), protocols::ligand_docking::LigandBaseProtocol::reorder_foldtree_around_mobile_regions(), protocols::relax::RepeatProteinRelax::seal_jumps(), protocols::splice::RBInMover::set_fold_tree(), protocols::anchored_design::AnchoredDesignMover::set_fold_tree_and_cutpoints(), protocols::docking::setup_dock_jump(), protocols::docking::setup_edges_for_partner(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_fold_tree_through_build_full_model_info(), protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover::setup_foldtree_around_anchor_invrot(), protocols::denovo_design::slide_jump(), protocols::protein_interface_design::star_fold_tree(), protocols::comparative_modeling::steal_ligands(), protocols::loophash::LoopHashLibrary::test_loop_sample(), protocols::legacy_sewing::Assembly::to_pose(), and protocols::hybridization::HybridizeFoldtreeDynamic::update().

void core::kinematics::FoldTree::add_edge	(	Size const	start,
		Size const	stop,
		std::string const &	start_atom,
		std::string const &	stop_atom
	)

Especially useful version of add_edge for chemical edge construction.

This 'add_edge' calls the edge constructor with the same args and is used to form chemical edges.

void core::kinematics::FoldTree::add_edge	(	Size const	start,
		Size const	stop,
		int const	label,
		std::string const &	start_atom,
		std::string const &	stop_atom
	)

Especially useful version of add_edge for chemical edge construction.

Allows label.

Author: Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org)

void core::kinematics::FoldTree::add_edge ( Edge const & new_edge )

Add the edge <new_edge>

example(s): ft.add_edge(edge1) See also: FoldTree FoldTree.check_fold_tree FoldTree.delete_edge FoldTree.jump_edge FoldTree.nres FoldTree.num_jump

Does not ensure proper folding order

void core::kinematics::FoldTree::add_vertex ( Size const v )

private

Helper function.

After this call you're guaranteed that v is a vertex of the tree, ie not contained in the interior of a peptide edge

References protocols::mean_field::max(), protocols::mean_field::min(), protocols::make_rot_lib::PEPTIDE, protocols::loops::start, and protocols::loops::stop.

void core::kinematics::FoldTree::append_residue	(	bool const	attach_by_jump = `false`,
		core::Size const	jump_anchor_residue = `0`,
		std::string const &	jump_upstream_atom = `""`,
		std::string const &	jump_downstream_atom = `""`
	)

Appends a new residue to the tree, either by a jump or as a continuation of a peptide segment.

Add a new residue – either polymer or jump – to the end of the tree if the new residue is appended by polymer connection, add it at the end of polymer. if the new residue is appended by jump connection, the cutpoint is the original polymer end

References protocols::make_rot_lib::PEPTIDE.

void core::kinematics::FoldTree::append_residue_by_chemical_bond	(	core::Size const	anchor_residue,
		std::string const &	anchor_atom,
		std::string const &	root_atom
	)

Appends a new residue to the tree using a chemical (APL-style) connection.

void core::kinematics::FoldTree::apply_sequence_mapping ( id::SequenceMapping const & old2new )

Renumber all vertices according to an input sequence mapping.

Renumber all vertices according to an input sequence mapping

const_iterator core::kinematics::FoldTree::begin ( ) const

inline

begin iterator of the edge_list

References edge_list_.

Referenced by protocols::topology_broker::MembraneTopologyClaimer::addVirtualResAsRootMembrane(), protocols::topology_broker::TMHTopologySamplerClaimer::build_fold_tree(), core::kinematics::ShortestPathInFoldTree::build_peptide_table(), protocols::viewer::dump_foldtree_kinemage(), is_root(), core::scoring::dssp::StrandPairingSet::merge(), protocols::forge::build::SegmentRebuild::modify_impl(), protocols::forge::build::SegmentInsert::modify_impl(), core::pose::symmetry::partition_by_symm_jumps(), core::scoring::electron_density::FastDensEnergy::pose_is_setup_for_density_scoring(), protocols::topology_broker::TMHTopologySamplerClaimer::pre_process(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_fold_tree_through_build_full_model_info(), core::scoring::electron_density::ElecDensEnergy::setup_for_scoring(), core::scoring::electron_density::FastDensEnergy::setup_for_scoring(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::setup_for_scoring(), core::scoring::electron_density::ElecDensCenEnergy::setup_for_scoring(), core::scoring::electron_density_atomwise::ElecDensAtomwiseEnergy::setup_for_scoring(), protocols::denovo_design::slide_jump(), and protocols::hybridization::HybridizeFoldtreeDynamic::update().

Size core::kinematics::FoldTree::boundary_left ( Size res ) const

inline

Return the starting residue of the first kinematic Edge to which res belongs.

References get_residue_edge(), and core::kinematics::Edge::start().

Size core::kinematics::FoldTree::boundary_right ( Size res ) const

inline

Return the ending residue of the first kinematic Edge to which res belongs.

References get_residue_edge(), and core::kinematics::Edge::stop().

bool core::kinematics::FoldTree::check_edges_for_atom_info ( ) const

chemical edges should have atom info

References TR().

Referenced by protocols::ligand_docking::MinimizeBackbone::apply(), and protocols::ligand_docking::MinimizeBackbone::reorder_foldtree_around_mobile_regions().

bool core::kinematics::FoldTree::check_fold_tree ( ) const

Returns true if this is a valid FoldTree.

example(s): ft.check_fold_tree() See also: FoldTree FoldTree.check_fold_tree FoldTree.clear FoldTree.is_simple_tree FoldTree.new_jump FoldTree.nres FoldTree.num_jump FoldTree.simple_tree

Check to see if a foldtree is in valid folding order. To be valid, a fold tree needs to be connected, but not cyclic. So the tree is traversed from the root residue and if any residue has not been visited or has been visited multiple times, the fold tree is bad.

References protocols::loops::start, protocols::loops::stop, and TR().

Referenced by protocols::denovo_design::movers::AlignResiduesMover::align_residues(), protocols::frag_picker::nonlocal::NonlocalFrags::apply(), protocols::denovo_design::movers::FoldTreeFromFoldGraphMover::apply(), protocols::nonlocal::SingleFragmentMover::apply(), protocols::loops::apply_sequence_mapping(), protocols::jumping::JumpSample::apply_to(), core::conformation::membrane::MembraneInfo::check_membrane_fold_tree(), protocols::splice::SpliceManager::fold_tree(), protocols::splice::RBOutMover::get_disulf_jump(), core::fragment::make_pose_from_frags(), protocols::enzdes::EnzdesFlexibleRegion::minimize_region(), protocols::denovo_design::components::modify_ft_for_residue_insertion(), protocols::denovo_design::movers::new_jump_and_cutpoint(), core::kinematics::operator>>(), protocols::splice::RBInMover::set_fold_tree(), protocols::rigid::RigidBodyMotionMover::set_fold_tree(), protocols::docking::setup_foldtree(), and protocols::denovo_design::slide_jump().

bool core::kinematics::FoldTree::check_order ( ) const

inlineprivate

update fold tree order (when edges are same but the order in the edge_list is changed) if necessary

returns true if order has changed see details for check_topology

References check_topology(), new_order, and update_jump_edge().

bool core::kinematics::FoldTree::check_topology ( ) const

inlineprivate

update fold tree topology (when edges are changed) if necessary

check_topology and check_order handle the updating of data that depends on tree topology and/or tree order.

any routine that depends on the stored derived data (eg any of the access methods ) should call check_topology() or check_order() at the beginning.

Note: also, any method function that changes the tree topology or order should set the private data members new_topology and/or new_topology to true.

References new_order, new_topology, update_cutpoints(), update_jump_points(), update_nres(), and update_num_jump().

Referenced by check_order(), cutpoint(), cutpoint_map(), is_cutpoint(), is_jump_point(), nres(), num_cutpoint(), and num_jump().

void core::kinematics::FoldTree::clear ( )

inline

Deletes all edge in the FoldTree.

example(s): ft.clear() See also: FoldTree FoldTree.add_edge FoldTree.check_fold_tree FoldTree.delete_edge FoldTree.new_jump FoldTree.nres FoldTree.num_jump FoldTree.simple_tree FoldTree.size

References edge_list_, and new_topology.

Referenced by protocols::antibody_legacy::Antibody::all_cdr_fold_tree(), protocols::chemically_conjugated_docking::UBQ_GTPaseMover::analyze_and_filter(), protocols::simple_moves::ResetFoldTree::apply(), protocols::simple_moves::SwitchChainOrderMover::apply(), protocols::protein_interface_design::movers::SetAtomTree::apply(), protocols::simple_moves::SetTorsion::apply(), protocols::antibody_legacy::LoopRlxMover::apply(), protocols::pose_length_moves::PossibleLoop::assign_phi_psi_omega_from_lookback(), protocols::metal_interface::MatchGrafter::build_combined_pose_with_zinc_overlay(), protocols::analysis::LoopAnalyzerMover::calculate_all_chainbreaks(), protocols::protein_interface_design::movers::copy_hotspot_to_pose(), protocols::pose_length_moves::NearNativeLoopCloser::create_maximum_length_pose(), protocols::pose_length_moves::PossibleLoop::extendRegion(), protocols::pose_length_moves::NearNativeLoopCloser::extendRegion(), protocols::splice::SpliceManager::fold_tree(), protocols::splice::Splice::fold_tree(), protocols::loops::fold_tree_from_loops(), protocols::simple_moves::CutChainMover::foldTree(), protocols::splice::RBOutMover::get_disulf_jump(), core::kinematics::get_foldtree_which_partitions(), protocols::topology_broker::AsymFoldandDockClaimer::initialize_dofs(), protocols::grafting::insert_pose_into_pose(), protocols::pose_length_moves::PossibleLoop::kic_closure(), protocols::antibody_legacy::CDRH3Modeler::loop_centroid_relax(), protocols::antibody_legacy::CDRH3Modeler::loop_fa_relax(), protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover::make_disjointed_foldtree(), protocols::protein_interface_design::make_hotspot_foldtree(), protocols::pose_length_moves::PossibleLoop::minimize_loop(), protocols::protein_interface_design::MinimizeInterface(), partition_by_jump(), protocols::protein_interface_design::movers::PlaceStubMover::place_stub(), core::import_pose::atom_tree_diffs::pose_from_atom_tree_diff(), protocols::cyclic_peptide::PeptideStubMover::preserve_old_mainchain_torsions(), protocols::protein_interface_design::movers::PlacementMinimizationMover::refresh_bbstub_constraints(), protocols::grafting::return_region(), protocols::relax::RepeatProteinRelax::seal_jumps(), core::pose::symmetry::sealed_symmetric_fold_tree(), protocols::protein_interface_design::movers::SetAtomTree::set_ab_fold_tree(), protocols::splice::RBInMover::set_fold_tree(), protocols::splice::Splice::set_fold_tree(), core::conformation::symmetry::set_fold_tree_from_symm_data(), protocols::flexpep_docking::FlexPepDockingProtocol::setup_foldtree(), protocols::docking::setup_foldtree(), protocols::rbsegment_relax::setup_pose_rbsegs_keep_loops(), protocols::grafting::setup_single_loop_double_arm_remodeling_foldtree(), protocols::grafting::setup_single_loop_single_arm_remodeling_foldtree(), protocols::antibody::simple_fold_tree(), protocols::antibody::simple_one_loop_fold_tree(), protocols::protein_interface_design::star_fold_tree(), core::conformation::symmetry::symmetrize_fold_tree(), and protocols::hybridization::HybridizeFoldtreeDynamic::update().

FoldTree core::kinematics::FoldTree::clone ( )

inline

Referenced by protocols::docking::calc_CA_Irmsd(), protocols::docking::calc_Fnat(), protocols::docking::calc_Fnonnat(), protocols::docking::calc_Irmsd(), protocols::docking::calc_Irmsd_legacy(), protocols::abinitio::AbrelaxApplication::fold(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::get_working_pose(), protocols::splice::min_seg(), and protocols::enzdes::EnzdesFlexibleRegion::minimize_region().

bool core::kinematics::FoldTree::connected ( ) const

Returns true if the FoldTree is connected.

Is the tree connected? returns true if fold_tree is connected doesn't assume that the fold_tree is in valid folding order, or even a tree

Size core::kinematics::FoldTree::count_fixed_residues	(	Size const	begin_res,
		Size const	size,
		Size &	min_edge_count_out
	)		const

Referenced by protocols::simple_moves::ClassicFragmentMover::end_bias_check().

bool core::kinematics::FoldTree::cut_edge ( Size const cut_point )

helper function to try cutting an edge in a tree.

References protocols::mean_field::max(), protocols::mean_field::min(), protocols::make_rot_lib::PEPTIDE, protocols::loops::start, protocols::loops::stop, and TR().

bool core::kinematics::FoldTree::cut_random_edge	(	ObjexxFCL::FArray1D_float const &	cut_bias_sum,
		Size const	nres_in
	)

private

cut an edge randomly based on probability without disconnecting fold tree

Cuts a random edge chosen with per-rsd frequency given by cut_bias_sum. private: returns true if success, false if failure. operates on the edge_list_. doesnt assume any derived data is up-to-date. only an non-separating edge (label==-2) can be cut, otherwise fold tree will not be valid.

References protocols::loops::cut_point, core::kinematics::pick_loopy_cutpoint(), and TR().

Size core::kinematics::FoldTree::cutpoint ( Size const cut ) const

inline

Returns the cutpoint position of jump number <cut>

example(s): ft.cutpoint(1) See also: FoldTree FoldTree.jump_edge FoldTree.is_cutpoint FoldTree.is_jump_point FoldTree.num_cutpoint FoldTree.num_jump

References check_topology(), and cutpoint_.

Referenced by protocols::toolbox::pose_manipulation::add_chainbreaks_according_to_jumps(), protocols::loops::add_cutpoint_variants(), protocols::RBSegmentRelaxImpl::apply(), protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspots::apply(), protocols::topology_broker::TopologyBroker::apply(), protocols::loops::apply_sequence_mapping(), protocols::jumping::JumpSample::apply_to(), protocols::jumping::close_chainbreaks(), protocols::abinitio::AbrelaxMover::close_with_idealization(), protocols::medal::cutpoint_probabilities(), core::scoring::methods::DistanceChainbreakEnergy::finalize_total_energy(), protocols::abinitio::find_sampling_cuts(), core::fragment::FindBoundaries(), protocols::abinitio::AbrelaxApplication::fold(), core::conformation::symmetry::get_component_contiguous_foldtree(), protocols::environment::inherit_cuts(), protocols::topology_broker::TopologyBroker::initialize_cuts(), core::scoring::motif::Xfrag::insert(), protocols::medal::invalidate_residues_spanning_cuts(), protocols::stepwise::legacy::modeler::rna::output_fold_tree_info(), protocols::toolbox::pose_manipulation::remove_chainbreaks_according_to_jumps(), protocols::loops::remove_cutpoint_variants(), protocols::hybridization::HybridizeFoldtreeDynamic::reset(), core::fragment::steal_constant_length_frag_set_from_pose(), protocols::rigid::RigidBodyMotionMover::update_chunks(), and protocols::nonlocal::BiasedFragmentMover::verify_probabilities_or_die().

Size core::kinematics::FoldTree::cutpoint_by_jump ( Size const jump_number ) const

Returns the corresponding cutpoint position for jump <jump_number> WARNING: if you look for all cutpoints by cycling thru jump_numbers you may be dissapointed you will get most likely the same cutpoint for several different jump_numbers however: the method cutpoint( nr ) will give you the number you are looking for.

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

To keep the fold tree non-cyclic, for each jump added, there should be a corresponding cutpoint. First call partition_by_jump() and the cutpoint for this jump would be those two sequentially adjacent residues which are not connected any more if the jump is disconnected.

Note: This cutpoint is not necessarily unique if the foldtree is sufficiently complex. Chooses the first cutpoint with the desired property, starting at the N-terminus. Will be unique eg if the jump is the intra-template jump used to support a single loop region during loop modeling.

References protocols::mean_field::max(), protocols::mean_field::min(), and TR().

Referenced by protocols::simple_task_operations::DockingNoRepack1::apply(), protocols::docking::InterfaceSidechainMinMover::apply(), protocols::simple_task_operations::DockingNoRepack2::apply(), protocols::loop_grower::LoopGrower::apply(), protocols::docking::DockTaskFactory::create_and_attach_task_factory(), protocols::loop_grower::LoopComparator::fill_pose(), protocols::docking::DockingEnsemblePrepackProtocol::finalize_setup(), protocols::docking::DockingProtocol::finalize_setup(), protocols::scoring::Interface::set_pack(), protocols::docking::DockingHighResLegacy::setup_packing(), and protocols::loop_grower::LoopGrower::update_and_writelps().

Size core::kinematics::FoldTree::cutpoint_map ( Size const seqpos ) const

inline

cutpoint number for this residue

cutpoint_map is the inverse of cutpoint_, ie it assigns each sequence position that is a cutpoint to the cutpoint number associated with that cutpoint (cutpoints are numbered in increasing residue number from the beginning of the chain)

References check_topology(), cutpoint_, cutpoint_map_, and is_cutpoint_.

Referenced by protocols::topology_broker::TopologyBroker::initialize_cuts().

utility::vector1< Size > core::kinematics::FoldTree::cutpoints ( ) const

get all cutpoints

Fill a vector of cutpoints.

Note: Slow: just for convenience routines...

Referenced by protocols::abinitio::MembraneAbinitio::add_spanning_region(), protocols::seeded_abinitio::GrowPeptides::apply(), protocols::seeded_abinitio::CAcstGenerator::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::loophash::BackboneSegment::apply_to_pose(), protocols::peptide_deriver::PeptideDeriverFilter::derive_peptide(), protocols::electron_density::findLoopFromDensity(), core::environment::FoldTreeSketch::FoldTreeSketch(), protocols::topology_broker::FoldandDockClaimer::generate_claims(), protocols::topology_broker::AsymFoldandDockClaimer::generate_claims(), protocols::topology_broker::FibrilModelingClaimer::generate_claims(), protocols::loophash::get_rt_over_leap_fast(), protocols::rbsegment_relax::guess_rbsegs_from_pose(), protocols::hybridization::HybridizeFoldtreeDynamic::jumps_and_cuts_from_foldtree(), protocols::forge::methods::jumps_and_cuts_from_pose(), core::import_pose::remove_cutpoint_closed(), protocols::environment::EnvClaimBroker::render_fold_tree(), core::pose::symmetry::sealed_symmetric_fold_tree(), and core::conformation::symmetry::symmetrize_fold_tree().

void core::kinematics::FoldTree::delete_edge ( FoldTree::iterator edge )

Deletes the edge <edge> in the FoldTree by iterator.

die if the iterator is out of range

References TR().

Referenced by protocols::denovo_design::insert_peptide_edges(), and protocols::anchored_design::AnchoredDesignMover::set_fold_tree_and_cutpoints().

void core::kinematics::FoldTree::delete_edge ( Edge const & edge )

Delete the edge <edge> in the fold tree by example edge.

example(s): ft.delete_edge(edge1) See also: FoldTree FoldTree.add_edge FoldTree.check_fold_tree FoldTree.jump_edge FoldTree.nres FoldTree.num_jump

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

void core::kinematics::FoldTree::delete_extra_vertices ( )

Delete vertices that are no longer necessary any more How is this determined?

after deleting a jump, there may be vertices of the tree which are neither jumps nor cutpoints. So delete them! this will combine two adjacent short edges into a long one

References protocols::make_rot_lib::PEPTIDE.

Referenced by protocols::enzdes::EnzdesFlexibleRegion::minimize_region(), and protocols::ligand_docking::LigandBaseProtocol::reorder_foldtree_around_mobile_regions().

void core::kinematics::FoldTree::delete_jump_and_intervening_cutpoint	(	Size	jump_begin,
		Size	jump_end,
		Size	cut = `0`
	)

Useful for removing a loop modeling jump+cut.

Useful for removing a loop modeling jump+cut

Note: This will trigger a renumbering of the jumps if jump number < num_jump()

References protocols::make_rot_lib::PEPTIDE, and TR().

Referenced by protocols::indexed_structure_store::append_pose_with_overlap(), protocols::loop_grower::LoopGrower::apply(), protocols::loop_grower::LoopComparator::fill_pose(), protocols::stepwise::legacy::modeler::rna::remove_chain_break_jump_point(), protocols::forge::methods::remove_cutpoint(), protocols::forge::methods::remove_cutpoints(), and protocols::stepwise::monte_carlo::mover::TransientCutpointHandler::take_out_cutpoints().

void core::kinematics::FoldTree::delete_jump_and_intervening_cutpoint ( Size const jump_number )

Useful for removing a loop modeling jump+cut.

Useful for removing a loop modeling jump+cut

Note: This will trigger a renumbering of the jumps if jump_number < num_jump()

void core::kinematics::FoldTree::delete_jump_seqpos ( Size const seqpos )

private

delete a root/jump_point residue

Delete a position from the foldtree that is either a jump_point or the root. Will require some rearranging of the topology. LOGIC: note that there are 0 or 1 incoming edges to this vertex need a replacement vertex for edges involving this guy: (note that this number will have to be adjusted) I. if seqpos is polymer residue (ie contained in a polymer edge)

if there's an incoming polymer segment, choose the previous rsd in this segment
choose the next residue in the first outgoing polymer edge II. if there's an incoming edge, choose the start of this edge III. (non-polymer root residue) choose stop of first edge in foldtree

References protocols::loops::apply_sequence_mapping(), core::id::SequenceMapping::delete_target_residue(), core::sequence::end, core::kinematics::Edge::is_jump(), core::kinematics::Edge::is_polymer(), core::kinematics::Edge::label(), protocols::make_rot_lib::PEPTIDE, core::kinematics::Edge::polymer_direction(), core::kinematics::Edge::start(), core::kinematics::Edge::stop(), TR(), and core::kinematics::Edge::valid().

void core::kinematics::FoldTree::delete_segment	(	Size const	seg_begin,
		Size const	seg_end
	)

Deletes a continuous segment from <seq_begin> to <seq_end>

example(s): ft.delete_segment(13,37) See also: FoldTree FoldTree.check_fold_tree FoldTree.delete_edge FoldTree.new_jump FoldTree.nres FoldTree.simple_tree

it assumes that the segment is completely contained in a single edge of the tree. Only edge_list is updated and new topology is set true. No derived data is updated.

References protocols::rigid::c2n, protocols::rigid::n2c, and TR().

void core::kinematics::FoldTree::delete_self_edges ( )

Deletes edges with start==stop allowable 1->1 edge for single residue FoldTree.

Delete self-edges in the foldtree, allowing the edge 1->1 for a single residue tree

Referenced by protocols::splice::SpliceManager::fold_tree(), protocols::splice::RBOutMover::get_disulf_jump(), protocols::splice::RBInMover::set_fold_tree(), and protocols::docking::setup_foldtree().

void core::kinematics::FoldTree::delete_seqpos ( Size const seqpos )

Deletes the residue <seqpos> from the FoldTree. Will rearrange topology if necessary.

example(s): ft.delete_seqpos(3) See also: FoldTree FoldTree.check_fold_tree FoldTree.clear FoldTree.new_jump FoldTree.nres FoldTree.num_jump FoldTree.simple_tree

Delete a sequence position from a foldtree. If the residue is a jump point or the root of the tree, we will have to rearrange the topology.

Referenced by protocols::forge::methods::replace().

void core::kinematics::FoldTree::delete_seqpos_simple ( Size const seqpos )

private

delete a polymer residue (non-jump,non-root)

Delete a sequence position from a foldtree. This will not work at positions that are jump points, ie start or stop vertices for jump edges. (or the root of the tree!) So basically only works for polymer residues.

References protocols::loops::apply_sequence_mapping(), core::id::SequenceMapping::delete_target_residue(), and TR().

void core::kinematics::FoldTree::delete_unordered_edge	(	Size const	start,
		Size const	stop,
		int const	label
	)

Find an edge in fold tree and delete it.

needs to match start residue number, end residue number and label index. abort if the edge is not found.

References protocols::loops::start, protocols::loops::stop, and TR().

std::string core::kinematics::FoldTree::downstream_atom ( Size const jump_number ) const

the jump atom on the stopping side

Get the downstream connection atomno (connection atom # at the "stop" vertex) If it hasn't been set return 0. Also see set_jump_atoms, which sets this data.

References core::kinematics::Edge::downstream_atom(), and core::kinematics::Edge::has_atom_info().

Referenced by protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::calculate_jump(), core::conformation::symmetry::get_component_contiguous_foldtree(), protocols::stepwise::legacy::modeler::rna::output_fold_tree_info(), and protocols::rna::denovo::movers::RNA_Minimizer::setup_movemap().

Size core::kinematics::FoldTree::downstream_jump_residue ( Size const jump_number ) const

the stopping residue for this jump

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

Get the sequence position of the downstream vertex of the jump indicated by the jump_number argument. Downstream means that if we traverse the tree starting at the root then we hit that vertex second.

return 0 if failed

int core::kinematics::FoldTree::edge_label	(	Size const	start,
		Size const	stop
	)

Returns the edge label of the edge from <start> to <stop>

this is an internal function, used for testing if an edge is separating

References protocols::loops::start, protocols::loops::stop, and TR().

Referenced by protocols::docking::setup_foldtree().

bool core::kinematics::FoldTree::empty ( ) const

inline

Returns true if the FoldTree is empty.

example(s): ft.empty() See also: FoldTree FoldTree.check_fold_tree FoldTree.clear FoldTree.nres FoldTree.simple_tree FoldTree.size

References edge_list_.

Referenced by protocols::topology_broker::TMHTopologySamplerClaimer::build_fold_tree(), and root().

const_iterator core::kinematics::FoldTree::end ( ) const

inline

end iterator of the edge_list

References edge_list_.

Referenced by protocols::topology_broker::TMHTopologySamplerClaimer::build_fold_tree(), core::kinematics::ShortestPathInFoldTree::build_peptide_table(), protocols::viewer::dump_foldtree_kinemage(), protocols::forge::build::SegmentRebuild::modify_impl(), protocols::forge::build::SegmentInsert::modify_impl(), core::pose::symmetry::partition_by_symm_jumps(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_fold_tree_through_build_full_model_info(), protocols::rbsegment_relax::setup_pose_from_rbsegs(), protocols::denovo_design::slide_jump(), and protocols::hybridization::HybridizeFoldtreeDynamic::update().

utility::vector1< Edge > core::kinematics::FoldTree::get_chemical_edges ( ) const

Returns all chemical edges from fold tree.

Author: Morgan Nance

Referenced by protocols::docking::setup_foldtree(), and core::kinematics::visualize_fold_tree().

utility::vector1< Edge > core::kinematics::FoldTree::get_jump_edges ( ) const

Return all jump Edges from the FoldTree.

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

Author: Labonte JWLab.nosp@m.onte.nosp@m.@jhu..nosp@m.edu

Referenced by protocols::fold_from_loops::movers::DisplayPoseLabelsMover::is_nubinitio_tree(), and protocols::docking::setup_foldtree().

Size core::kinematics::FoldTree::get_jump_that_builds_residue ( Size const seqpos ) const

Get the number of the jump that builds (connects to) a given residue It's an error if the residue isn't built directly by a jump.

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

Get the number of the jump that builds (connects to) a given residue

References core::kinematics::Edge::is_jump(), and core::kinematics::Edge::label().

Referenced by core::optimization::symmetry::SymMinimizerMap::asymmetric_dof(), core::optimization::symmetry::atom_tree_get_atompairE_deriv(), core::conformation::symmetry::SymmetryInfo::dependent_dofs(), protocols::peptide_deriver::PeptideDeriverFilter::derive_peptide(), protocols::enzdes::DiversifyStoredRBConfs::diversify_all_confs(), protocols::simple_ddg::ddG::do_minimize(), core::conformation::symmetry::SymmetryInfo::dof_is_independent(), protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::estimate_Stors(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_cartligmin(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_exact_cartmin(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_exact_scmin(), protocols::magnesium::fix_water_jump(), protocols::stepwise::modeler::freeze_waters(), core::conformation::symmetry::SymmetryInfo::get_dof_derivative_weight(), protocols::cyclic_peptide::CrosslinkerMover::get_jump_index_for_crosslinker(), protocols::cyclic_peptide::CrosslinkerMover::get_jump_indices_for_symmetric_crosslinker(), core::optimization::symmetry::SymAtomTreeMinimizer::make_asymmetric_movemap(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::make_starting_pose_for_virtual_screening(), protocols::enzdes::MinimizeStoredRBConfs::rb_minimize_all_confs(), protocols::enzdes::RepackLigandSiteWithoutLigandMover::separate_protein_and_ligand(), protocols::stepwise::monte_carlo::mover::ResampleMover::slide_jump_randomly(), and protocols::magnesium::update_jump_atoms_for_mg_bound_water().

utility::vector1< Edge > core::kinematics::FoldTree::get_outgoing_edges ( Size const seqpos ) const

Returns all edges that build a residue directly off of <seqpos>

Returns all edges that build a residue directly off of seqpos

Referenced by core::scoring::electron_density::ElectronDensity::compute_symm_rotations(), protocols::electron_density::dockPoseIntoMap(), protocols::hybridization::downstream_residues_from_jump(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensCenEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensEnergy::eval_atom_derivative(), core::scoring::electron_density::FastDensEnergy::eval_residue_pair_derivatives(), and core::conformation::get_residue_connections().

Size core::kinematics::FoldTree::get_parent_residue	(	Size const	seqpos,
		bool &	connected_by_jump
	)		const

Get the residue that is immediately upstream of this residue (and tell us whether connection is jump or bond).

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

Size core::kinematics::FoldTree::get_parent_residue ( Size const seqpos ) const

Get the residue that is immediately upstream of this residue.

int core::kinematics::FoldTree::get_polymer_residue_direction ( Size const seqpos ) const

Returns the direction (n2c, c2n) in which the given (peptide) residue is built during folding.

Returns the folding direction of a given polymer (peptide) residue. If the residue is in a peptide edge this is the direction in which that edge is traveled if we traverse the tree starting at the root. Will die if residue is root or if residue is built by jump or chemical bond.

Edge const & core::kinematics::FoldTree::get_residue_edge ( Size const seqpos ) const

Returns the edge that builds the residue <seqpos> Does not work for root atom (will fail)

Referenced by boundary_left(), boundary_right(), protocols::ligand_docking::MoveMapBuilder::build(), core::conformation::build_residue_tree(), protocols::stepwise::monte_carlo::mover::ensure_appropriate_foldtree_for_move(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensCenEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensEnergy::eval_atom_derivative(), core::scoring::electron_density::FastDensEnergy::eval_residue_pair_derivatives(), core::conformation::get_anchor_atomno(), core::conformation::get_residue_connections(), core::conformation::symmetry::SymmetricConformation::get_upstream_vrt(), protocols::ligand_docking::LigandBaseProtocol::make_movemap(), protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::prepare_foldtree(), core::conformation::replace_residue_in_atom_tree(), and protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::store_target_icoors().

size_t core::kinematics::FoldTree::hash_value ( ) const

computes a fixed-length, hash-based identifier for this FoldTree, permitting efficient comparison between a pair of FoldTrees

Computes a fixed-length, hash-based identifier for this FoldTree, permitting efficient comparison of a pair of FoldTrees. The need for this functionality arose from a desire to reuse an object that was unaware of changes to the FoldTree. Rather than perform a costly deep comparison by evaluating edge lists, we wanted a simple method for quickly testing whether the naive object should be reinstantiated. This method is most useful in situations where there are many edges in the FoldTree.

References core::id::to_string().

void core::kinematics::FoldTree::insert_fold_tree_by_jump	(	FoldTree const &	subtree,
		Size const	insert_seqpos,
		Size const	insert_jumppos,
		Size const	anchor_pos,
		Size	anchor_jump_number = `0`,
		std::string const &	anchor_atom = `""`,
		std::string const &	root_atom = `""`
	)

Inserts a fold_tree as a subtree.

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

Insert another fold_tree as a subtree. Residues are inserted as a contiguous block beginning at insert_seqpos. Jumps are inserted as a contiguous block beginning at insert_jumppos. Note that insert_seqpos could be equal to nres()+1, ie subtree is being appended at the end. The jump anchoring subtree runs from the residue currently numbered "anchor_pos" to the residue insert_seqpos + subtree.root() - 1, and has label/number anchor_jump_number

References protocols::forge::methods::add_vertex(), nres(), num_jump(), root(), and TR().

Referenced by protocols::fold_from_loops::utils::append_pose_to_pose_keep_fold_tree().

void core::kinematics::FoldTree::insert_polymer_residue	(	Size const	seqpos,
		bool const	join_lower,
		bool const	join_upper
	)

Inserts a polymer residue at position <seqpos> How?

(ie between current rsds seqpos-1 and seqpos, so that the sequence position of the new residue is seqpos) if seqpos-1 is a cutpoint in the current fold_tree – we have a choice about how to connect the new residue: it could be joined to the preceding peptide segment (join to seqpos-1) or to the following segment (joined to the residue currently at seqpos). join_upper and join_lower control the behavior in this case.

Note: seqpos may be greater than current nres, ie we may be "inserting" at end

References protocols::make_rot_lib::PEPTIDE.

void core::kinematics::FoldTree::insert_residue_by_chemical_bond	(	Size const	seqpos,
		Size const	anchor_residue,
		std::string const &	anchor_atom,
		std::string const &	root_atom
	)

Inserts a bonded residue at position <seqpos>

(ie between current rsds seqpos-1 and seqpos, so that the sequence position of the new residue is seqpos) if seqpos-1 is a cutpoint in the current fold_tree – we have a choice about how to connect the new residue: it could be joined to the preceding peptide segment (join to seqpos-1) or to the following segment (joined to the residue currently at seqpos). join_upper and join_lower control the behavior in this case.

Note: seqpos may be greater than current nres, ie we may be "inserting" at end

void core::kinematics::FoldTree::insert_residue_by_jump	(	Size const	seqpos,
		Size	anchor_pos,
		std::string const &	anchor_atom = `""`,
		std::string const &	root_atom = `""`
	)

Inserts a residue attached only by a jump. precondition is that seqpos-1 is a cutpoint.

Note: that anchor_pos is wrt the current numbering system (ie before insertion)

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

Insert a new residue into the tree at position seqpos, anchoring it to the rest of the tree by a jump

the residue at position seqpos moves to position seqpos+1

vertices remapped, only question is cutpoint at seqpos-1, should it move to seqpos?

bool core::kinematics::FoldTree::is_cutpoint ( Size const seqpos ) const

inline

Returns true is position <seqpos> is a cutpoint.

example(s): ft.is_cutpoint(37) See also: FoldTree FoldTree.cutpoint FoldTree.new_jump FoldTree.nres FoldTree.num_cutpoint FoldTree.num_jump

References check_topology(), cutpoint_, cutpoint_map_, is_cutpoint_, and nres_.

bool core::kinematics::FoldTree::is_equivalent ( FoldTree const & b ) const

Check if the two FoldTrees build in a similar fashion That is, if their roots are the same and if all edges correspond to each other – Does not necessarily check that the order of the edges are the same.

References edge_list_, and root().

bool core::kinematics::FoldTree::is_jump_point ( Size const seqpos ) const

inline

Returns true if <seqpos> is a starting or stopping residue of a jump edge.

is seqpos a jump-point?

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

example(s): ft.is_jump_point() See also: FoldTree FoldTree.is_cutpoint FoldTree.new_jump FoldTree.num_jump

References check_topology(), and is_jump_point_.

Referenced by protocols::protein_interface_design::movers::LoopLengthChange::apply(), protocols::cyclic_peptide::PeptideStubMover::apply(), protocols::simple_moves::PeptideStapleMover::apply(), core::fragment::DownJumpSRFD::apply(), core::conformation::membrane::MembraneInfo::check_membrane_fold_tree(), protocols::jumping::close_chainbreaks(), core::conformation::get_root_residue_root_atomno(), protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::prepare_foldtree(), core::kinematics::remodel_fold_tree_to_account_for_insertion(), core::conformation::replace_residue_in_atom_tree(), core::import_pose::atom_tree_diffs::rms_error_with_noise(), protocols::moves::PyMOLMover::send_foldtree(), protocols::fold_from_loops::movers::DisplayPoseLabelsMover::simple_visualize_fold_tree(), core::kinematics::simple_visualize_fold_tree(), core::kinematics::simple_visualize_fold_tree_and_movemap(), core::kinematics::simple_visualize_fold_tree_and_movemap_bb_chi(), protocols::loop_grower::LoopGrower::store_sheets(), and protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::store_target_icoors().

bool core::kinematics::FoldTree::is_root ( Size const seqpos ) const

inline

Returns true if <seqpos> the the root.

example(s): ft.empty() See also: FoldTree FoldTree.is_cutpoint FoldTree.is_jump_point FoldTree.nres

References begin(), and edge_list_.

Referenced by core::scoring::electron_density::ElecDensAllAtomCenEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensCenEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensEnergy::eval_atom_derivative(), core::scoring::electron_density::FastDensEnergy::eval_residue_pair_derivatives(), core::conformation::get_residue_connections(), protocols::membrane::is_membrane_fixed(), protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::prepare_foldtree(), core::conformation::replace_residue_in_atom_tree(), and protocols::fold_from_loops::movers::DisplayPoseLabelsMover::simple_visualize_fold_tree().

bool core::kinematics::FoldTree::is_simple_tree ( ) const

Returns true if the FoldTree has 1-edge (non-jump)

Returns true if this tree is a simple 1->total_residue FoldTree, returns false otherwise.

example(s): ft.is_simple_tree() See also: FoldTree FoldTree.check_fold_tree FoldTree.num_jump FoldTree.simple_tree

Referenced by protocols::fldsgn::potentials::sspot::get_foldtree_seqsep(), core::scoring::SecondaryStructurePotential::get_foldtree_seqsep(), and core::io::silent::BinarySilentStruct::resize().

Edge const & core::kinematics::FoldTree::jump_edge ( Size const jump_number ) const

Returns the jump edge with jump number <jump_number> (const)

example(s): ft.jump_edge(1) See also: FoldTree FoldTree.new_jump FoldTree.num_jump

Referenced by protocols::seeded_abinitio::CoordinateCst::apply(), protocols::protein_interface_design::movers::SpinMover::apply(), protocols::topology_broker::RigidBodyRandomTMHMover::apply(), protocols::rigid::RotateJumpAxisMover::apply(), protocols::cryst::UpdateCrystInfo::apply(), protocols::denovo_design::movers::RotateSegmentMover::apply(), core::optimization::symmetry::SymMinimizerMap::asymmetric_dof(), core::kinematics::ShortestPathInFoldTree::build_jumpres_distmap(), protocols::hybridization::downstream_residues_from_jump(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensCenEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensEnergy::eval_atom_derivative(), core::scoring::electron_density::FastDensEnergy::eval_residue_pair_derivatives(), core::io::silent::BinarySilentStruct::fill_pose(), protocols::topology_broker::MembraneTopologyClaimer::generate_claims(), core::kinematics::get_foldtree_which_partitions(), core::conformation::get_root_residue_root_atomno(), protocols::simple_filters::JumpEvaluator::JumpEvaluator(), protocols::topology_broker::TMHTopologySamplerClaimer::move_spans(), protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue(), protocols::moves::PyMOLMover::send_foldtree(), protocols::anchored_design::AnchoredDesignMover::set_fold_tree_and_cutpoints(), protocols::docking::setup_dock_jump(), protocols::docking::setup_foldtree(), protocols::fold_from_loops::movers::DisplayPoseLabelsMover::simple_visualize_fold_tree(), core::kinematics::simple_visualize_fold_tree(), core::kinematics::simple_visualize_fold_tree_and_movemap(), core::kinematics::simple_visualize_fold_tree_and_movemap_bb_chi(), protocols::denovo_design::slide_jump(), and core::pose::transfer_jumps().

Edge & core::kinematics::FoldTree::jump_edge ( Size const jump_number )

Returns the jump edge with jump number <jump_number> (non-const)

bool core::kinematics::FoldTree::jump_exists	(	Size const	pos1,
		Size const	pos2
	)		const

inline

Return true if a jump exists between <pos1> and <pos2>

example(s): ft.empty() See also: FoldTree FoldTree.check_fold_tree FoldTree.jump_edge FoldTree.new_jump FoldTree.nres

References jump_point(), and num_jump().

Referenced by protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::check_for_intramolecular_submotif_jump(), core::import_pose::update_fixed_domain_from_extra_minimize_jump_pairs(), and protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::update_fold_tree_at_virtual_sugars().

core::Size core::kinematics::FoldTree::jump_nr	(	core::Size	upstream_res,
		core::Size	downstream_res
	)		const

inline

get the jump_nr connected to jump upstream->downstream, returns 0 if not found

whether a jump exists between these residues

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

References jump_point(), and num_jump().

Size core::kinematics::FoldTree::jump_point	(	Size const	lower_higher,
		Size const	jump_number
	)		const

starting or stopping residue of a jump edge

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

Referenced by jump_exists(), jump_nr(), and protocols::stepwise::legacy::modeler::rna::output_fold_tree_info().

iterator core::kinematics::FoldTree::nc_begin ( )

inlineprivate

non-const begin iterator of edge_list

References edge_list_.

iterator core::kinematics::FoldTree::nc_end ( )

inlineprivate

non-const end iterator of edge_list

References edge_list_.

void core::kinematics::FoldTree::new_chemical_bond	(	Size const	anchor_pos,
		Size const	root_pos,
		std::string const &	anchor_atom,
		std::string const &	root_atom,
		Size const	new_cutpoint
	)

Add a new jump to an existing fold tree, returns the jump_number of the new jump.

References protocols::forge::methods::add_vertex(), core::kinematics::Edge::is_chemical_bond(), and protocols::make_rot_lib::PEPTIDE.

Size core::kinematics::FoldTree::new_jump	(	Size const	jump_pos1,
		Size const	jump_pos2,
		Size const	new_cutpoint
	)

Adds a new jump edge from <pos1> to <pos2> with cutpoint <cutpoint>

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

Add a new jump to an existing fold tree, returns the jump_number of the new jump.

References protocols::forge::methods::add_vertex(), and protocols::make_rot_lib::PEPTIDE.

Referenced by protocols::grafting::simple_movers::DeleteRegionMover::apply(), protocols::frag_picker::nonlocal::NonlocalFrags::apply(), protocols::loops::loop_closure::ccd::ShortLoopClosure::apply(), protocols::simple_moves::MissingDensityToJumpMover::apply(), protocols::hybridization::DomainAssembly::apply(), core::import_pose::RNA_HelixAssembler::build_init_pose(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::figure_out_fold_tree(), core::pose::rna::figure_out_reasonable_rna_fold_tree(), protocols::stepwise::sampler::protein::generate_beta_database_test(), protocols::enzdes::EnzdesFlexBBProtocol::generate_ensemble_for_region(), core::import_pose::RNA_HelixAssembler::get_rid_of_capping_base_pairs(), protocols::stepwise::monte_carlo::submotif::SubMotifLibrary::initialize_from_jump_library(), protocols::forge::methods::linear_chainbreak(), protocols::stepwise::modeler::make_cut_at_moving_suite(), protocols::forge::build::SegmentSwap::modify_impl(), protocols::denovo_design::movers::new_jump_and_cutpoint(), protocols::forge::methods::overlap_chainbreak(), protocols::recces::pose_setup_from_file(), core::import_pose::put_in_cutpoint(), protocols::forge::methods::quadratic_chainbreak(), and protocols::rna::movers::RNA_LoopCloser::rna_ccd_close().

Size core::kinematics::FoldTree::nres ( ) const

inline

Returns the number of residues in the FoldTree.

routines for retrieving the derived data will call check_topology and/or check_order first

example(s): ft.nres() See also: FoldTree FoldTree.check_fold_tree FoldTree.num_jump FoldTree.simple_tree FoldTree.size

References check_topology(), and nres_.

Referenced by protocols::jumping::JumpSample::apply_to(), core::kinematics::ShortestPathInFoldTree::build_peptide_table(), protocols::jumping::close_chainbreaks(), protocols::ligand_docking::MinimizeBackbone::create_fold_tree_with_ligand_jumps_from_attach_pts(), core::pose::create_subpose(), protocols::forge::methods::find_connecting_jump(), protocols::stepwise::modeler::find_first_root_residue(), protocols::denovo_design::find_jump_rec(), protocols::stepwise::modeler::find_root_without_virtual_ribose(), core::fragment::FindBoundaries(), core::conformation::Conformation::fold_tree(), core::conformation::symmetry::fold_tree_entry_point(), protocols::loops::fold_tree_from_loops(), core::environment::FoldTreeSketch::FoldTreeSketch(), protocols::topology_broker::MembraneTopologyClaimer::generate_claims(), core::conformation::symmetry::get_component_contiguous_foldtree(), core::kinematics::get_foldtree_which_partitions(), insert_fold_tree_by_jump(), core::conformation::insert_residue_into_atom_tree(), core::kinematics::jump_which_partitions(), protocols::forge::methods::merge(), possible_root(), protocols::backrub::read_fold_tree_from_file(), protocols::forge::methods::remove_cutpoint(), protocols::forge::methods::remove_cutpoints(), protocols::environment::Environment::remove_nonpermenant_features(), protocols::forge::methods::replace(), protocols::rbsegment_relax::setup_disconnected(), protocols::rbsegment_relax::setup_pose_rbsegs_keep_loops(), protocols::forge::methods::shift_jumps(), protocols::fold_from_loops::movers::DisplayPoseLabelsMover::simple_visualize_fold_tree(), core::kinematics::simple_visualize_fold_tree(), core::kinematics::simple_visualize_fold_tree_and_movemap(), core::kinematics::simple_visualize_fold_tree_and_movemap_bb_chi(), protocols::hybridization::HybridizeFoldtreeDynamic::update(), and core::kinematics::visualize_fold_tree().

Size core::kinematics::FoldTree::num_cutpoint ( ) const

inline

Returns the number of cutpoints in the FoldTree.

example(s): ft.num_cutpoint() See also: FoldTree FoldTree.cutpoint FoldTree.is_cutpoint FoldTree.nres FoldTree.num_jump

References check_topology(), and num_cutpoint_.

Referenced by protocols::loops::add_cutpoint_variants(), protocols::abinitio::MembraneAbinitio::add_spanning_region(), protocols::RBSegmentRelaxImpl::apply(), protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspots::apply(), protocols::topology_broker::TopologyBroker::apply(), protocols::loop_grower::LoopGrower::apply(), protocols::loops::apply_sequence_mapping(), protocols::abinitio::abscript::AbscriptLoopCloserCM::attempt_idealize(), protocols::forge::remodel::RemodelLoopMover::boost_closure_stage(), protocols::jumping::close_chainbreaks(), protocols::abinitio::AbrelaxMover::close_with_idealization(), protocols::medal::cutpoint_probabilities(), core::scoring::methods::DistanceChainbreakEnergy::finalize_total_energy(), protocols::abinitio::find_sampling_cuts(), core::fragment::FindBoundaries(), protocols::abinitio::AbrelaxApplication::fold(), core::conformation::symmetry::get_component_contiguous_foldtree(), protocols::forge::remodel::RemodelLoopMover::independent_stage(), protocols::environment::inherit_cuts(), core::scoring::motif::Xfrag::insert(), protocols::medal::invalidate_residues_spanning_cuts(), protocols::forge::methods::linear_chainbreak(), protocols::denovo_design::linear_chainbreak(), protocols::stepwise::legacy::modeler::rna::output_fold_tree_info(), protocols::forge::methods::overlap_chainbreak(), protocols::rna::movers::ErraserMinimizerMover::pose_preliminaries(), protocols::forge::methods::quadratic_chainbreak(), protocols::loops::remove_cutpoint_variants(), protocols::hybridization::HybridizeFoldtreeDynamic::reset(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::setup_fold_tree(), protocols::forge::remodel::RemodelLoopMover::simultaneous_stage(), core::fragment::steal_constant_length_frag_set_from_pose(), protocols::rigid::RigidBodyMotionMover::update_chunks(), and protocols::nonlocal::BiasedFragmentMover::verify_probabilities_or_die().

Size core::kinematics::FoldTree::num_jump ( ) const

inline

Returns the number of jumps in the FoldTree.

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

example(s): ft.num_jump() See also: FoldTree FoldTree.check_fold_tree FoldTree.jump_edge FoldTree.new_jump FoldTree.nres

References check_topology(), and num_jump_.

FoldTree& core::kinematics::FoldTree::operator= ( FoldTree const & src )

inline

operator=

Note: this version doesn't copy any of the derived data! will this be too slow? it will trigger re-calculating of everything every time we reject a move....

References edge_list_, and new_topology.

void core::kinematics::FoldTree::partition_by_jump	(	Size const	jump_number,
		FoldTree &	f1,
		FoldTree &	f2
	)		const

partition into two foldtrees by cutting at jump= jump_number

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

Create two new foldtrees f1 and f2 by splitting myself at jump jump_number Uses the following routine to figure out which vertices should be in each tree.

Note: The N-terminal vertex of jump "jump_number" goes to tree f1

References add_edge(), and clear().

Referenced by protocols::ligand_docking::LigandDockProtocol::append_ligand_docking_scores(), protocols::protein_interface_design::movers::BackrubDDMover::apply(), protocols::protein_interface_design::movers::DesignMinimizeHbonds::apply(), core::select::residue_selector::JumpUpstreamSelector::apply(), core::select::residue_selector::JumpDownstreamSelector::apply(), protocols::simple_task_operations::RestrictToInterface::apply(), protocols::rna::denovo::coarse::CoarseRNA_LoopCloser::apply_after_jump_change(), protocols::simple_filters::EnergyPerResidueFilter::apply_helper(), core::scoring::sc::ElectrostaticComplementarityCalculator::Calc(), core::scoring::sc::MolecularSurfaceCalculator::Calc(), protocols::docking::calc_Fnat(), protocols::docking::calc_Fnonnat(), protocols::docking::calc_Lrmsd(), protocols::docking::calc_P1rmsd(), protocols::docking::calc_P2rmsd(), protocols::geometry::centroids_by_jump(), protocols::geometry::centroids_by_jump_int(), protocols::matdes::InterfacePackingFilter::compute(), protocols::protein_interface_design::filters::AtomicContactCountFilter::compute(), protocols::matdes::OligomericAverageDegreeFilter::compute(), protocols::simple_ddg::ddG::compute_rmsd_with_super(), protocols::optimize_weights::IterativeOptEDriver::compute_rotamers_around_ligands(), protocols::simple_ddg::ddG::duplicate_waters_across_jump(), protocols::toolbox::rigid_body::figure_out_moving_partition_res(), protocols::ligand_docking::LigandBaseProtocol::find_interface_backbone(), protocols::ligand_docking::LigandBaseProtocol::find_interface_rsds(), core::select::util::find_jump_partners_within_CB_cutoff(), core::pose::symmetry::get_full_intracomponent_and_neighbor_subs(), protocols::docking::EllipsoidalRandomizationMover::get_interface_residues(), core::pose::symmetry::get_intracomponent_and_neighbor_subs(), protocols::ligand_docking::LigandBaseProtocol::get_ligand_id(), protocols::stepwise::modeler::get_partition_definition_by_jump(), core::pose::symmetry::get_symdof_subunits(), core::pose::symmetry::intracomponent_contact(), core::kinematics::jump_which_partitions(), core::pose::partition_pose_by_jump(), core::import_pose::remove_cutpoint_closed(), core::kinematics::residues_downstream_of_jump(), core::kinematics::residues_upstream_of_jump(), protocols::calc_taskop_movers::DesignRepackMover::setup_packer_and_movemap(), core::import_pose::update_fixed_domain_from_extra_minimize_jump_pairs(), and protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::virtualize_distal_partition().

void core::kinematics::FoldTree::partition_by_jump	(	Size const	jump_number,
		ObjexxFCL::FArray1D_bool &	partner1
	)		const

partition the fold tree in two parts if the jump is disconnected.

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

utility::vector1< bool > core::kinematics::FoldTree::partition_by_jump ( Size const jump_nr ) const

partition the fold tree in two parts if the jump is disconnected.

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

when a jump edge is removed, the fold tree is separated into two parts. This fucntion is to find all residues connecting to the jump starting residue and flag them in the partner1(n_res) array as true. The residues on the other side are flagged as false. Useful to distinguish two docking partners when fold tree is properly set up.

void core::kinematics::FoldTree::partition_by_residue	(	Size const	seqpos,
		ObjexxFCL::FArray1D_bool &	partner1
	)		const

partition the fold tree in two parts if a cut would be introduced between seqpos and seqpos+1

partition the fold tree in two parts if a cut would be introduced between seqpos and seqpos+1. Function is an analog to partition_by_jump() – its goal to find all residues connecting to the jump starting residue and flag them in the partner1(n_res) array as true. The residues on the other side are flagged as false. Useful to distinguish two docking partners when fold tree is properly set up.

References protocols::mean_field::max(), protocols::mean_field::min(), core::kinematics::Edge::start(), protocols::loops::start, core::kinematics::Edge::stop(), and protocols::loops::stop.

Referenced by protocols::rna::denovo::coarse::CoarseRNA_LoopCloser::apply(), protocols::stepwise::modeler::figure_out_moving_chain_break_res(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::figure_out_partition_definition(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::figure_out_partition_definition(), and protocols::stepwise::modeler::get_partition_definition().

utility::vector1< Size > core::kinematics::FoldTree::partition_coloring ( utility::vector1< Size > const & jump_numbers ) const

partition the fold tree into n parts based on specified jumps.

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

partition the fold tree into n parts based on specified jumps. Just uses partition_by_jump over and over again.

bool core::kinematics::FoldTree::possible_root ( Size const & seqpos ) const

inline

Returns true if <seqpos> is the root.

References is_cutpoint(), and nres().

Referenced by protocols::stepwise::modeler::find_first_root_residue(), protocols::stepwise::modeler::find_root_without_virtual_ribose(), core::pose::get_definite_terminal_root(), protocols::rna::denovo::possible_root(), core::pose::reroot(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::reroot_fold_tree(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::reroot_fold_tree(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::reroot_fold_tree_simple(), and protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_jumps().

void core::kinematics::FoldTree::prepend_edge ( Edge const & new_edge )

Prepend the edge <new_edge>. Useful alternative to add_edge for setting root.

Does not ensure proper folding order

void core::kinematics::FoldTree::put_jump_stubs_intra_residue ( )

this reorganizes upstream/downstream atoms of all jumps such that stubs are N-CA-C

Referenced by protocols::abinitio::LoopJumpFoldCst::add_rigidity_jumps(), core::io::silent::BinarySilentStruct::init_from_lines(), and protocols::jumping::MembraneJump::setup_fold_tree().

bool core::kinematics::FoldTree::random_tree_from_jump_points	(	Size const	nres_in,
		Size const	num_jump_in,
		ObjexxFCL::FArray2D< Size > const &	jump_point,
		ObjexxFCL::FArray1D_float const &	cut_bias,
		Size const	root_in = `1`,
		bool const	allow_jump_at_1_or_NRES = `false`
	)

Builds a FoldTree from a list of <jump_points> and random cut points based on some biased probability Returns bool about success.

Referenced by protocols::abinitio::LoopJumpFoldCst::add_rigidity_jumps(), protocols::jumping::MembraneJump::setup_fold_tree(), and protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_fold_tree_legacy().

bool core::kinematics::FoldTree::random_tree_from_jump_points	(	Size const	nres_in,
		Size const	num_jump_in,
		ObjexxFCL::FArray2D< Size > const &	jump_point,
		std::vector< Size > const &	obligate_cut_points,
		ObjexxFCL::FArray1D_float const &	cut_bias,
		Size const	root_in = `1`,
		bool const	allow_jump_at_1_or_NRES = `false`
	)

Builds a FoldTree from a list of <jump_points> and random cut points based on some biased probability and any user-defined obligate cutpoints Returns bool about success.

void core::kinematics::FoldTree::reassign_atoms_for_intra_residue_stubs ( )

this reorganizes upstream/downstream atoms of jumps that have flag keep_stub_in_resiue = true such that stubs are N-CA-C

References core::kinematics::Edge::is_jump(), core::kinematics::Edge::start(), protocols::loops::start, core::kinematics::Edge::stop(), core::chemical::orbitals::strip_whitespace(), and TR().

Referenced by protocols::stepwise::modeler::fix_up_jump_atoms(), and core::import_pose::get_tree().

void core::kinematics::FoldTree::renumber_jumps ( )

Renumbers the jump edges in the FoldTree How?

Assign new numbers to the jumps. after we delete a jump, we may want to re-number the others. note of course this will invalidate the jump_transform array of any pose with this fold_tree, so be sure to call jumps_from_positions or something

References TR().

Referenced by protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue(), and protocols::docking::setup_foldtree().

void core::kinematics::FoldTree::renumber_jumps_ordered ( )

Renumbers the jump edges in the FoldTree while.

Referenced by core::conformation::symmetry::get_asymm_unit_fold_tree().

bool core::kinematics::FoldTree::reorder	(	Size const	start_residue,
		bool const	verbose_if_fail = `true`
	)

Reorders the FoldTree to start at residue <start_residue>

Reorder the tree so that start_residue is the new root. returns false if no re-ordering allowed! To reorder successfully, start_residue needs to be a vertex in the original fold tree.

References core::kinematics::Edge::is_polymer(), protocols::mean_field::max(), protocols::mean_field::min(), core::kinematics::Edge::start(), core::kinematics::Edge::start_atom(), core::kinematics::Edge::stop(), core::kinematics::Edge::stop_atom(), and TR().

void core::kinematics::FoldTree::replace_edge	(	Edge const &	old_edge,
		Edge const &	replacement_edge
	)

Find and replace an Edge in the FoldTree.

This function is used primarily to restore CHEMICAL Edges that have been replaced by JUMPs after other FoldTree manipulations.

Author: Labonte JWLab.nosp@m.onte.nosp@m.@jhu..nosp@m.edu

References TR().

Referenced by protocols::docking::setup_foldtree().

bool core::kinematics::FoldTree::residue_is_in_fold_tree ( Size seqpos ) const

Check if the seqpos is covered by an edge in the FoldTree (Mainly useful for FoldTrees as they are being built.)

If true, seqpos is either the root or get_residue_edge() will return an edge.

Size core::kinematics::FoldTree::root ( ) const

inline

Returns the root vertex position of the FoldTree.

example(s): ft.empty() See also: FoldTree FoldTree.is_root FoldTree.clear FoldTree.simple_tree

References edge_list_, and empty().

void core::kinematics::FoldTree::set_jump_atoms	(	Size const	jump_number,
		std::string const &	upstream_atom,
		std::string const &	downstream_atom,
		bool	bKeepStubInResidue = `false`
	)

define the specific atoms that should be connected by this jump

This information can then be used in setting up the AtomTree from the FoldTree. Data is stored in the Edge corresponding to this Jump. If not specified, residue-specific defaults will be used.

Set connection atoms for a jump. This is not used by the foldtree, only to communicate to the AtomTree during construction of an atomtree from a foldtree.

References core::kinematics::Edge::downstream_atom(), core::kinematics::Edge::keep_stub_in_residue(), and core::kinematics::Edge::upstream_atom().

Referenced by protocols::stepwise::monte_carlo::mover::AddMover::append_residue(), protocols::frag_picker::nonlocal::NonlocalFrags::apply(), protocols::topology_broker::TMHTopologySamplerClaimer::build_fold_tree(), core::import_pose::RNA_HelixAssembler::build_init_pose(), core::pose::rna::figure_out_reasonable_rna_fold_tree(), core::pose::rna::fill_in_default_jump_atoms(), protocols::stepwise::modeler::fix_protein_jump_atom(), core::conformation::symmetry::get_component_contiguous_foldtree(), core::import_pose::RNA_HelixAssembler::get_rid_of_capping_base_pairs(), core::import_pose::get_tree(), core::import_pose::make_coarse_pose(), protocols::protein_interface_design::movers::PlaceStubMover::place_stub(), protocols::recces::pose_setup_from_file(), protocols::stepwise::monte_carlo::mover::AddMover::prepend_residue(), core::import_pose::put_in_cutpoint(), protocols::environment::Environment::remove_nonpermenant_features(), protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::setup_fold_tree(), and protocols::magnesium::update_jump_atoms_for_mg_bound_water().

void core::kinematics::FoldTree::set_jump_atoms	(	Size const	jump_number,
		core::Size	res1,
		std::string const &	atom1,
		core::Size	res2,
		std::string const &	atom2,
		bool	bKeepStubInResidue = `false`
	)

References core::kinematics::Edge::downstream_atom(), core::kinematics::Edge::keep_stub_in_residue(), core::kinematics::Edge::start(), core::kinematics::Edge::stop(), and core::kinematics::Edge::upstream_atom().

void core::kinematics::FoldTree::setup_edge_counts ( ) const

private

update edge counts info

edge_count(i): delete the edge (i-1,i), how many residues are in the component of the graph containing i-1?
jump_edge_count(i): delete jump_number i. How many residues are in the component of the graph containing the jump point on the N-terminal side of the jump.

Note: edge_count(cutpoint+1) doesn't really make sense currently set to 0 but routines should avoid looking at this value (see eg refold_reorder(...) ); Not checked out for chemical links

References protocols::mean_field::max(), protocols::mean_field::min(), protocols::loops::start, and protocols::loops::stop.

void core::kinematics::FoldTree::show ( std::ostream & out ) const

Displays the FoldTree information.

example(s): ft.show() See Also: Pose

References core::chemical::element::I.

void core::kinematics::FoldTree::simple_tree ( Size const nres_in )

Produces a 1-edge FoldTree that is <nres_in> long No jumps or extraneous features.

Make a simple, 1->total_residue tree.

example(s): ft.simple_tree() See also: FoldTree FoldTree.add_edge FoldTree.check_fold_tree FoldTree.clear FoldTree.delete_edge FoldTree.is_simple_tree FoldTree.new_jump FoldTree.nres FoldTree.num_jump FoldTree.size

References protocols::make_rot_lib::PEPTIDE.

Referenced by protocols::jumping::close_chainbreaks(), protocols::abinitio::AbrelaxApplication::fold(), FoldTree(), core::io::silent::BinarySilentStruct::init_from_lines(), core::io::silent::RNA_SilentStruct::init_from_lines(), protocols::forge::remodel::RemodelLoopMover::loophash_stage(), protocols::loop_build::LoopMover_SlidingWindow::model_loop(), protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue(), core::io::silent::BinarySilentStruct::resize(), core::io::silent::RNA_SilentStruct::resize(), protocols::grafting::return_region(), protocols::relax::membrane::MPFastRelaxMover::setup_relax_foldtree(), and protocols::stepwise::legacy::modeler::rna::setup_simple_fold_tree().

int core::kinematics::FoldTree::size ( ) const

inline

Returns the number of edges in the FoldTree.

example(s): ft.size() See also: FoldTree FoldTree.add_edge FoldTree.check_fold_tree FoldTree.delete_edge FoldTree.jump_edge FoldTree.nres FoldTree.num_jump

References edge_list_.

Referenced by core::import_pose::get_tree(), core::fragment::make_pose_from_frags(), and core::io::silent::RNA_SilentStruct::print_conformation().

void core::kinematics::FoldTree::slide_cutpoint	(	Size const	current_cut,
		Size const	target_cut
	)

Slide a polymer cutpoint from one location to another.

Slide a cutpoint from one position to another.

References protocols::forge::methods::add_vertex(), protocols::make_rot_lib::PEPTIDE, and TR().

void core::kinematics::FoldTree::slide_jump	(	Size const	jump_number,
		Size const	new_res1,
		Size const	new_res2
	)

change an existing jump to start and end in new positions

Switches a given jump to connect two different residues.

References protocols::mean_field::max(), protocols::mean_field::min(), protocols::make_rot_lib::PEPTIDE, core::kinematics::Edge::start(), protocols::loops::start, protocols::loops::stop, and TR().

Referenced by protocols::stepwise::monte_carlo::mover::AddMover::append_residue(), protocols::stepwise::monte_carlo::mover::ensure_appropriate_foldtree_for_move(), protocols::stepwise::monte_carlo::mover::AddMover::prepend_residue(), protocols::flexpep_docking::FlexPepDockingProtocol::randomlySlidePeptideJump(), protocols::hotspot_hashing::HotspotStubSet::setup_hotspot_foldtree_(), and protocols::denovo_design::slide_jump().

void core::kinematics::FoldTree::split_existing_edge_at_residue ( Size const resNo )

Splits an edge into two at a specified position.

References protocols::forge::methods::add_vertex().

Referenced by protocols::fold_from_loops::utils::Nub::add_binders(), and protocols::docking::setup_edges_for_partner().

std::string core::kinematics::FoldTree::to_string ( ) const

easy output of string

Referenced by protocols::simple_moves::CopyDofMover::pose_string().

bool core::kinematics::FoldTree::tree_from_jumps_and_cuts	(	Size const	nres_in,
		Size const	num_jump_in,
		ObjexxFCL::FArray2D< Size > const &	jump_point,
		ObjexxFCL::FArray1D< Size > const &	cuts,
		Size const	root_in = `1`,
		bool const	verbose = `false`
	)

Constructs a FoldTree from listed <jump point>=""> and <cuts> Returns bool about success.

Construct a new tree (self) from a set of jump points and cutpoints this assumes that we can make a tree, ie that the number of cuts is equal to the number of jumps.

Note: The root vertex of new tree is 1.

References protocols::make_rot_lib::PEPTIDE, protocols::loops::start, protocols::loops::stop, and TR().

Referenced by protocols::hybridization::FoldTreeHybridize::add_strand_pairing(), protocols::loops::apply_sequence_mapping(), protocols::topology_broker::TMHTopologySamplerClaimer::build_fold_tree(), core::conformation::symmetry::get_component_contiguous_foldtree(), core::import_pose::get_tree(), protocols::dna::make_base_pair_aware_fold_tree(), core::fragment::make_simple_fold_tree_from_jump_frame(), core::import_pose::remove_cutpoint_closed(), core::environment::FoldTreeSketch::render(), core::pose::symmetry::sealed_symmetric_fold_tree(), protocols::anchored_design::AnchoredDesignMover::set_fold_tree_and_cutpoints(), protocols::nonlocal::StarTreeBuilder::set_up(), protocols::rbsegment_relax::setup_disconnected(), protocols::rna::movers::ErraserMinimizerMover::setup_fold_tree(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::setup_fold_tree(), protocols::star::StarAbinitio::setup_kinematics(), protocols::rbsegment_relax::setup_pose_rbsegs_keep_loops(), core::conformation::symmetry::symmetrize_fold_tree(), and protocols::hybridization::HybridizeFoldtreeDynamic::update().

void core::kinematics::FoldTree::update_cutpoints ( ) const

private

update cutpoints info in the fold tree

Internal routine for updating data that is derived from the edge list (which is the only primary data).

References protocols::mean_field::max(), and protocols::mean_field::min().

Referenced by check_topology().

void core::kinematics::FoldTree::update_edge_label	(	Size const	start,
		Size const	stop,
		int const	old_label,
		int const	new_label
	)

Changes the label of an edge in fold tree.

this is an internal function, used for testing if an edge is separating

References protocols::loops::start, protocols::loops::stop, and TR().

Referenced by protocols::docking::setup_dock_jump(), and protocols::docking::setup_foldtree().

void core::kinematics::FoldTree::update_edge_labels ( )

private

update edge labels based on whether edges are separating or not.

this routine assigns labels to the edges of a graph based on whether or not those edges are separating – ie whether they can be cut without disconnecting the graph. we know we have a tree when all the edges are separating

edge labels:

+N means that the edge corresponds to jump #N (=> uncuttable)
-2 means cuttable
-1 means separating == PEPTIDE
0 means cut

we assume that the only possible change in edge labeling that we need to make is from a -2 to a -1 ie, the -1's are still correct also, there shouldn't be any 0's before this is called 0's are for communicating between this function and the logical function connected_graph(g)

References protocols::make_rot_lib::PEPTIDE, and TR().

void core::kinematics::FoldTree::update_jump_edge ( ) const

private

update the index of jump edges in the edge list

fills jump_edge routines that use jump_edge should call check_order to ensure that its up to date

Note: that this is sensitive to the order of the tree so it's updated in check_order()

Internal routine for updating data that is derived from the edge list (which is the only primary data).

Referenced by check_order().

void core::kinematics::FoldTree::update_jump_points ( ) const

private

update jump residues list

Internal routine for updating data that is derived from the edge list (which is the only primary data). fills is_jump_point, jump_point

References protocols::mean_field::max(), and protocols::mean_field::min().

Referenced by check_topology().

void core::kinematics::FoldTree::update_nres ( ) const

private

update total number residues in the fold tree

Internal routine for updating data that is derived from the edge list (which is the only primary data).

References protocols::mean_field::max().

Referenced by check_topology().

void core::kinematics::FoldTree::update_num_jump ( ) const

private

update number of jumps in the fold tree

Internal routine for updating data that is derived from the edge list (which is the only primary data).

References protocols::mean_field::max(), and TR().

Referenced by check_topology().

std::string core::kinematics::FoldTree::upstream_atom ( Size const jump_number ) const

the jump atom on the staring side

Get the upstream connection resid (connection atom # at the "start" vertex) If it hasn't been set return 0. Also see set_jump_atoms, which sets this data.

References core::kinematics::Edge::has_atom_info(), and core::kinematics::Edge::upstream_atom().

Referenced by protocols::stepwise::legacy::modeler::rna::output_fold_tree_info(), and protocols::rna::denovo::movers::RNA_Minimizer::setup_movemap().

Size core::kinematics::FoldTree::upstream_jump_residue ( Size const jump_number ) const

the starting residue for this jump

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

Get the sequence position of the upstream vertex of the jump indicated by the jump_number argument. Upstream means that if we traverse the tree starting at the root then we hit that vertex first.

return 0 if failed

Friends And Related Function Documentation

bool operator!=	(	FoldTree const &	a,
		FoldTree const &	b
	)

friend

Not equal to operator.

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

friend

output operator

Foldtree output to stream

bool operator==	(	FoldTree const &	a,
		FoldTree const &	b
	)

friend

equal to operator

Checks that edges are in the same order and are equal That is, the order of the edges in the edge list is important to equality here

std::istream& operator>>	(	std::istream &	is,
		FoldTree &	t
	)

friend

input operator

Foldtree input from stream

Member Data Documentation

utility::vector1<Size> core::kinematics::FoldTree::cutpoint_

mutableprivate

cutpoint number to cutpoint residue number, dimesioned as num_cutpoint_.

Referenced by cutpoint(), cutpoint_map(), and is_cutpoint().

utility::vector1<Size> core::kinematics::FoldTree::cutpoint_map_

mutableprivate

residue number of cutpoint number, 0 if it is not a cutpoint. dimensioned as nres_.

Referenced by cutpoint_map(), and is_cutpoint().

utility::vector1<Size> core::kinematics::FoldTree::edge_count

mutableprivate

dimensioned as nres_, see setup_edge_counts for more info

EdgeList core::kinematics::FoldTree::edge_list_

private

Note: vector for fast traversal, but re-ordering, deleting are slow.

Referenced by begin(), clear(), empty(), end(), is_equivalent(), is_root(), nc_begin(), nc_end(), operator=(), core::kinematics::operator==(), core::kinematics::operator>>(), root(), and size().

boost::hash<std::string> core::kinematics::FoldTree::hasher

private

computes fixed-size identifier for a string input

ObjexxFCL::FArray1D_bool core::kinematics::FoldTree::is_cutpoint_

mutableprivate

whether a residue is a cutpoint, dimensioned as nres_

Referenced by cutpoint_map(), and is_cutpoint().

utility::vector1<bool> core::kinematics::FoldTree::is_jump_point_

mutableprivate

whehter a residue is a jump_point, dimensioned as nres_

Referenced by is_jump_point().

utility::vector1<Size> core::kinematics::FoldTree::jump_edge_

mutableprivate

jump number to edge index number in the edge_list_, dimensioned as num_jump_.

utility::vector1<Size> core::kinematics::FoldTree::jump_edge_count

mutableprivate

dimensioned as num_jump, see setup_edge_counts for more info

utility::vector1< std::pair< Size, Size > > core::kinematics::FoldTree::jump_point_

mutableprivate

jump number to jump residue number. dimensioned as (2,num_jump_)

ObjexxFCL::FArray1D_bool core::kinematics::FoldTree::linked_

mutableprivate

Used as scratch space by a couple of functions.

Size core::kinematics::FoldTree::min_edge_count

mutableprivate

the minimum number in edge_count and jump_edge_count.

bool core::kinematics::FoldTree::new_order

mutableprivate

edges in the edge_list_ have been reordered.

Referenced by check_order(), and check_topology().

bool core::kinematics::FoldTree::new_topology

mutableprivate

edges in the edge_list_ have been changed.

Referenced by check_topology(), clear(), operator=(), and core::kinematics::operator>>().

Size core::kinematics::FoldTree::nres_

mutableprivate

just the largest vertex in edge_list_

Referenced by is_cutpoint(), and nres().

Size core::kinematics::FoldTree::num_cutpoint_

mutableprivate

number of cutpoints in the fold tree.

Note: number_cutpoint_ == num_jump_ (if a connected tree)

Referenced by num_cutpoint().

Size core::kinematics::FoldTree::num_jump_

mutableprivate

number of jump edges (edges in edge_list_ with label>0)

Referenced by num_jump().

ObjexxFCL::FArray1D_bool core::kinematics::FoldTree::seen_

mutableprivate

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

src/core/kinematics/FoldTree.hh
src/core/kinematics/FoldTree.cc

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Friends

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation