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

#include <FoldTree.hh>

Inheritance diagram for core::kinematics::FoldTree:

Collaboration 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
virtual	~FoldTree ()

	FoldTree ()
	constructor More...

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

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

Size	boundary_left (Size res) const
	Returns the starting residue of the kinematic chunk to which res belongs. More...

Size	boundary_right (Size res) const
	Returns the ending residue of the kinematic chunk 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 (int const start, int const stop, int const label)
	Adds an edge from <start> to <stop> More...

void	add_edge (int const start, int 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 (Edge const &new_edge)
	Add the edge <new_edge> 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 (int const start, int const stop, int const label)
	Find an edge in fold tree and delete it. More...

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

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

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

void	renumber_jumps ()
	Renumbers the jump edges in the FoldTree How? 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 (int const seg_begin, int const seg_end)
	Deletes a continuous segment from <seq_begin> to <seq_end> More...

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

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

void	insert_residue_by_jump (int const seqpos, int 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, int const insert_seqpos, int const insert_jumppos, int const anchor_pos, int 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...

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

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

void	simple_tree (int 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 (int const nres_in, int const num_jump_in, ObjexxFCL::FArray2D_int const &jump_point, ObjexxFCL::FArray1D_float const &cut_bias, int 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 (int const nres_in, int const num_jump_in, ObjexxFCL::FArray2D_int const &jump_point, std::vector< int > const &obligate_cut_points, ObjexxFCL::FArray1D_float const &cut_bias, int 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 (int const nres_in, int const num_jump_in, ObjexxFCL::FArray2D_int const &jump_point, ObjexxFCL::FArray1D_int const &cuts, int 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, int 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 (int 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 (int const start_residue)
	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...

int	upstream_jump_residue (int const jump_number) const
	the staring residue for this jump More...

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

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

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

void	partition_by_residue (int 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...

int	cutpoint_by_jump (int 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 (int const jump_number) const
	the jump atom on the staring side More...

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

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

Edge const &	get_residue_edge (int 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 (int const seqpos) const
	Returns all edges that build a residue directly off of <seqpos> More...

int	get_jump_that_builds_residue (int const seqpos) const
	Get the number of the jump that builds (connects to) a given residue. More...

void	set_jump_atoms (int 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 (int 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...

size_t	hash_value () const

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...

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

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

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

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

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

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

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

Edge &	jump_edge (int 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 (int const seqpos) const
	Returns true if <seqpos> the the root. More...

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

bool	jump_exists (int const pos1, int 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< int >	cutpoints () const
	get all cutpoints 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 (int jump_begin, int jump_end)
	Useful for removing a loop modeling jump+cut. More...

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

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

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

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

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

void	add_vertex (int 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_edge (int const cut_point)
	helper function to try cutting an edge in a tree. More...

bool	cut_random_edge (ObjexxFCL::FArray1D_float const &cut_bias_sum, int 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 reorderd. More...

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

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

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

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

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

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

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

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

boost::hash< std::string >	hasher

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

Detailed Description

The FoldTree is a residue-based treelike 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

Definition at line 65 of file FoldTree.hh.

Member Typedef Documentation

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

Definition at line 74 of file FoldTree.hh.

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

Definition at line 72 of file FoldTree.hh.

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

Definition at line 73 of file FoldTree.hh.

Constructor & Destructor Documentation

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

virtual

Definition at line 50 of file FoldTree.cc.

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

inline

constructor

Definition at line 81 of file FoldTree.hh.

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

Definition at line 93 of file FoldTree.hh.

References simple_tree().

Member Function Documentation

void core::kinematics::FoldTree::add_edge	(	int const	start,
		int 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

Definition at line 702 of file FoldTree.cc.

Referenced by protocols::forge::methods::add_edges(), protocols::simple_moves::SwitchChainOrderMover::apply(), protocols::protein_interface_design::movers::SetAtomTree::apply(), protocols::star::Extender::extend_unaligned(), protocols::loophash::LoopHashLibrary::extract_data_from_pose(), protocols::protein_interface_design::movers::Splice::fold_tree(), protocols::loops::fold_tree_from_loops(), protocols::simple_moves::CutChainMover::foldTree(), core::conformation::symmetry::get_asymm_unit_fold_tree(), protocols::loophash::get_rt_over_leap(), protocols::loophash::get_rt_over_leap_fast(), core::kinematics::linearize_fold_tree(), protocols::features::PoseConformationFeatures::load_fold_tree(), protocols::enzdes::EnzdesFlexibleRegion::minimize_region(), MinimizeInterface(), partition_by_jump(), protocols::protein_interface_design::movers::PlaceStubMover::place_stub(), core::kinematics::remodel_fold_tree_to_account_for_insertion(), protocols::ligand_docking::LigandBaseProtocol::reorder_foldtree_around_mobile_regions(), protocols::anchored_design::AnchoredDesignMover::set_fold_tree_and_cutpoints(), protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover::setup_foldtree_around_anchor_invrot(), protocols::protein_interface_design::star_fold_tree(), protocols::comparative_modeling::steal_ligands(), protocols::loophash::LoopHashLibrary::test_loop_sample(), and protocols::hybridization::HybridizeFoldtreeDynamic::update().

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

Especially useful version of add_edge for chemical edge construction.

Definition at line 717 of file FoldTree.cc.

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

Definition at line 734 of file FoldTree.cc.

void core::kinematics::FoldTree::add_vertex ( int 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

Definition at line 1137 of file FoldTree.cc.

References protocols::loops::start, and protocols::loops::stop.

void core::kinematics::FoldTree::append_residue	(	bool const	attach_by_jump = `false`,
		int 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

Definition at line 651 of file FoldTree.cc.

void core::kinematics::FoldTree::append_residue_by_chemical_bond	(	int 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.

Definition at line 681 of file FoldTree.cc.

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

Definition at line 421 of file FoldTree.cc.

References core::sequence::end.

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

inline

begin iterator of the edge_list

Definition at line 154 of file FoldTree.hh.

References edge_list_.

Referenced by core::kinematics::ShortestPathInFoldTree::build_peptide_table(), core::conformation::build_tree(), protocols::forge::methods::closest_larger_peptide_vertex(), protocols::forge::methods::closest_smaller_peptide_vertex(), core::kinematics::ShortestPathInFoldTree::compute_dist_map(), protocols::viewer::dump_foldtree_kinemage(), protocols::forge::methods::find_connecting_jump(), core::conformation::symmetry::get_asymm_unit_fold_tree(), insert_fold_tree_by_jump(), is_root(), protocols::forge::methods::jumps_connected_to_position(), core::kinematics::linearize_fold_tree(), core::scoring::dssp::StrandPairingSet::merge(), protocols::forge::methods::merge(), protocols::enzdes::EnzdesFlexibleRegion::minimize_region(), protocols::forge::build::SegmentRebuild::modify_impl(), protocols::forge::build::SegmentInsert::modify_impl(), core::kinematics::operator<<(), core::pose::symmetry::partition_by_symm_jumps(), core::kinematics::remodel_fold_tree_to_account_for_insertion(), protocols::ligand_docking::LigandBaseProtocol::reorder_foldtree_around_mobile_regions(), protocols::forge::methods::replace(), core::scoring::electron_density::PattersonCorrEnergy::setup_for_scoring(), 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::forge::methods::shift_jumps(), protocols::hybridization::HybridizeFoldtreeDynamic::update(), and protocols::forge::methods::vertex_exists().

iterator core::kinematics::FoldTree::begin ( )

inlineprivate

non-const begin iterator of edge_list

Definition at line 809 of file FoldTree.hh.

References edge_list_.

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

inline

Returns the starting residue of the kinematic chunk to which res belongs.

Definition at line 116 of file FoldTree.hh.

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

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

inline

Returns the ending residue of the kinematic chunk to which res belongs.

Definition at line 124 of file FoldTree.hh.

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

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

chemical edges should have atom info

Definition at line 2440 of file FoldTree.cc.

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.

Definition at line 2396 of file FoldTree.cc.

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

Referenced by protocols::frag_picker::nonlocal::NonlocalFrags::apply(), protocols::nonlocal::SingleFragmentMover::apply(), protocols::loops::apply_sequence_mapping(), protocols::jumping::JumpSample::apply_to(), core::fragment::make_pose_from_frags(), protocols::enzdes::EnzdesFlexibleRegion::minimize_region(), core::kinematics::operator>>(), and protocols::rigid::RigidBodyMotionMover::set_fold_tree().

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

see details for check_topology

Definition at line 976 of file FoldTree.hh.

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.

Definition at line 956 of file FoldTree.hh.

References new_order, new_topology, setup_edge_counts(), 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

Definition at line 249 of file FoldTree.hh.

References edge_list_, and new_topology.

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

Returns true if the FoldTree is connected.

Is the tree connected? returns true if fold_tree is connected doesnt assume that the fold_tree is in valid folding order, or even a tree

Definition at line 1633 of file FoldTree.cc.

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

Definition at line 2556 of file FoldTree.cc.

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

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

private

helper function to try cutting an edge in a tree.

Definition at line 1497 of file FoldTree.cc.

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

bool core::kinematics::FoldTree::cut_random_edge	(	ObjexxFCL::FArray1D_float const &	cut_bias_sum,
		int 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.

Definition at line 1587 of file FoldTree.cc.

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

int core::kinematics::FoldTree::cutpoint ( int 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

Definition at line 1027 of file FoldTree.hh.

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::ChainbreakEnergy::finalize_total_energy(), core::scoring::methods::DistanceChainbreakEnergy::finalize_total_energy(), protocols::abinitio::find_sampling_cuts(), core::fragment::FindBoundaries(), protocols::swa::rna::floating_base_chain_closure_setup(), protocols::abinitio::AbrelaxApplication::fold(), core::conformation::symmetry::get_component_contiguous_foldtree(), protocols::topology_broker::TopologyBroker::initialize_cuts(), protocols::medal::invalidate_residues_spanning_cuts(), protocols::swa::rna::Output_fold_tree_info(), protocols::toolbox::pose_manipulation::remove_chainbreaks_according_to_jumps(), protocols::loops::remove_cutpoint_variants(), protocols::jumping::MembraneJump::setup_fold_tree(), core::fragment::steal_constant_length_frag_set_from_pose(), protocols::rigid::RigidBodyMotionMover::update_chunks(), and protocols::nonlocal::BiasedFragmentMover::verify_probabilities_or_die().

int core::kinematics::FoldTree::cutpoint_by_jump ( int 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.

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.

Definition at line 1926 of file FoldTree.cc.

References TR().

Referenced by core::pack::task::operation::DockingNoRepack1::apply(), core::pack::task::operation::DockingNoRepack2::apply(), protocols::docking::InterfaceSidechainMinMover::apply(), protocols::docking::DockTaskFactory::create_and_attach_task_factory(), protocols::docking::DockingEnsemblePrepackProtocol::finalize_setup(), protocols::docking::DockingProtocol::finalize_setup(), protocols::scoring::Interface::set_pack(), and protocols::docking::DockingHighResLegacy::setup_packing().

int core::kinematics::FoldTree::cutpoint_map ( int 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)

Definition at line 1064 of file FoldTree.hh.

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

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

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

get all cutpoints

Fill a vector of cutpoints.

Note: Slow: just for convenience routines...

Definition at line 1527 of file FoldTree.cc.

Referenced by protocols::abinitio::MembraneAbinitio::add_spanning_region(), protocols::seeded_abinitio::CAcstGenerator::apply(), protocols::seeded_abinitio::GrowPeptides::apply(), protocols::loophash::BackboneSegment::apply_to_pose(), protocols::electron_density::findLoopFromDensity(), 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::hybridization::HybridizeFoldtreeDynamic::jumps_and_cuts_from_foldtree(), protocols::forge::methods::jumps_and_cuts_from_pose(), protocols::rna::remove_cutpoint_closed(), 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

Definition at line 747 of file FoldTree.cc.

References TR().

Referenced by 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

Definition at line 760 of file FoldTree.cc.

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

Definition at line 933 of file FoldTree.cc.

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	(	int	jump_begin,
		int	jump_end
	)

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()

Definition at line 149 of file FoldTree.cc.

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

Referenced by protocols::forge::methods::remove_cutpoint(), and protocols::forge::methods::remove_cutpoints().

void core::kinematics::FoldTree::delete_jump_and_intervening_cutpoint ( int 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()

Definition at line 141 of file FoldTree.cc.

void core::kinematics::FoldTree::delete_jump_seqpos ( int 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

Definition at line 272 of file FoldTree.cc.

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(), 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	(	int const	seg_begin,
		int 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.

Definition at line 803 of file FoldTree.cc.

References protocols::rigid::c2n, protocols::rigid::n2c, core::io::serialization::size(), 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

Definition at line 104 of file FoldTree.cc.

void core::kinematics::FoldTree::delete_seqpos ( int 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.

Definition at line 128 of file FoldTree.cc.

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

void core::kinematics::FoldTree::delete_seqpos_simple ( int 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.

Definition at line 381 of file FoldTree.cc.

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

void core::kinematics::FoldTree::delete_unordered_edge	(	int const	start,
		int 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.

Definition at line 770 of file FoldTree.cc.

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

std::string core::kinematics::FoldTree::downstream_atom ( int 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.

Definition at line 2536 of file FoldTree.cc.

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

Referenced by core::conformation::symmetry::get_component_contiguous_foldtree(), protocols::swa::rna::Output_fold_tree_info(), and protocols::rna::RNA_Minimizer::setup_movemap().

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

the stopping residue for this jump

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

Definition at line 996 of file FoldTree.cc.

Referenced by protocols::abinitio::MembraneAbinitio::add_spanning_region(), protocols::ligand_docking::append_multi_residue_ligand_RMSD(), protocols::enzdes::DetectProteinLigandInterface::apply(), protocols::jumping::JumpSample::apply_to(), core::optimization::symmetry::atom_tree_get_atompairE_deriv(), protocols::rna::RNA_ChunkLibrary::check_connections(), protocols::rna::ChunkSet::check_fold_tree_OK(), protocols::rna::RNA_ChunkLibrary::check_jump_match(), protocols::enzdes::EnzdesBaseProtocol::create_enzdes_movemap(), protocols::ligand_docking::MinimizeBackbone::create_fold_tree_with_ligand_jumps_from_attach_pts(), core::conformation::symmetry::SymmetryInfo::dependent_dofs(), protocols::swa::rna::StepWiseRNA_Minimizer::Figure_out_moving_residues(), protocols::swa::Figure_out_moving_residues(), protocols::rna::RNA_StructureParameters::fill_in_default_jump_atoms(), protocols::enzdes::SecondaryMatchProtocol::find_all_allowed_positions(), protocols::ligand_docking::find_attach_pt(), core::pose::symmetry::find_symmetric_basejump_anchor(), protocols::swa::rna::floating_base_chain_closure_setup(), core::conformation::symmetry::fold_tree_entry_point(), protocols::jumping::JumpSample::generate_jump_frags(), protocols::jumping::JumpSample::generate_jump_frames(), core::pose::get_chain_id_from_jump_id(), core::pose::get_jump_id_from_chain_id(), protocols::ligand_docking::LigandBaseProtocol::get_ligand_id(), protocols::hybridization::InsertChunkMover::get_local_sequence_mapping(), protocols::rna::get_rigid_body_jumps(), protocols::rna::RNA_StructureParameters::insert_base_pair_jumps(), protocols::hybridization::HybridizeFoldtreeDynamic::jumps_and_cuts_from_foldtree(), protocols::forge::methods::jumps_and_cuts_from_pose(), protocols::swa::rna::make_cut_at_moving_suite(), core::pose::symmetry::make_symmetric_movemap(), protocols::swa::rna::move_jump_atom_to_base(), protocols::swa::rna::Output_movemap(), protocols::enzdes::PredesignPerturbMover::parse_my_tag(), protocols::hybridization::ChunkTrialMover::pick_random_chunk(), protocols::rna::remove_cutpoint_closed(), protocols::simple_filters::AlaScan::report(), core::pose::symmetry::sealed_symmetric_fold_tree(), protocols::hybridization::InsertChunkMover::set_bb_xyz_aligned(), core::conformation::symmetry::SymmetricConformation::set_dof(), protocols::analysis::InterfaceAnalyzerMover::set_pose_info(), protocols::swa::rna::StepWiseRNA_JobParameters_Setup::setup_fold_tree(), protocols::rna::MultipleDomainMover::setup_jump_numbers_and_partner(), protocols::rna::RNA_Minimizer::setup_movemap(), core::pose::swap_transform(), core::conformation::symmetry::symmetrize_fold_tree(), protocols::rna::translate_virtual_anchor_to_first_rigid_body(), protocols::rna::MultipleDomainMover::try_to_slide_into_contact(), and core::kinematics::visualize_fold_tree().

int core::kinematics::FoldTree::edge_label	(	int const	start,
		int 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

Definition at line 902 of file FoldTree.cc.

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

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

Definition at line 679 of file FoldTree.hh.

References edge_list_.

Referenced by root().

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

inline

end iterator of the edge_list

Definition at line 162 of file FoldTree.hh.

References edge_list_.

iterator core::kinematics::FoldTree::end ( )

inlineprivate

non-const end iterator of edge_list

Definition at line 817 of file FoldTree.hh.

References edge_list_.

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

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

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

Definition at line 368 of file FoldTree.cc.

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::enzdes::DiversifyStoredRBConfs::diversify_all_confs(), core::conformation::symmetry::SymmetryInfo::dof_is_independent(), core::conformation::symmetry::SymmetryInfo::get_dof_derivative_weight(), protocols::enzdes::MinimizeStoredRBConfs::rb_minimize_all_confs(), and protocols::enzdes::RepackLigandSiteWithoutLigandMover::separate_protein_and_ligand().

utility::vector1< Edge > core::kinematics::FoldTree::get_outgoing_edges ( int 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

Definition at line 2117 of file FoldTree.cc.

References core::sequence::end, and protocols::loops::start.

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::FastDensEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensEnergy::eval_atom_derivative(), and core::conformation::get_residue_connections().

int core::kinematics::FoldTree::get_polymer_residue_direction ( int 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.

Definition at line 2137 of file FoldTree.cc.

References core::sequence::end, and protocols::loops::start.

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

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

Definition at line 2099 of file FoldTree.cc.

References core::sequence::end, and protocols::loops::start.

Referenced by boundary_left(), boundary_right(), protocols::ligand_docking::MoveMapBuilder::build(), core::conformation::build_residue_tree(), 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_atom_derivative(), core::conformation::get_anchor_atomno(), core::conformation::get_residue_connections(), core::conformation::symmetry::SymmetricConformation::get_upstream_vrt(), protocols::ligand_docking::LigandBaseProtocol::make_movemap(), and core::conformation::replace_residue_in_atom_tree().

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

Definition at line 87 of file FoldTree.cc.

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

Inserts a fold_tree as a subtree.

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

Definition at line 555 of file FoldTree.cc.

References protocols::forge::methods::add_vertex(), begin(), end(), core::kinematics::Edge::is_jump(), core::kinematics::Edge::label(), nres(), num_jump(), root(), core::kinematics::Edge::start(), core::kinematics::Edge::stop(), and TR().

void core::kinematics::FoldTree::insert_polymer_residue	(	int 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

Definition at line 449 of file FoldTree.cc.

void core::kinematics::FoldTree::insert_residue_by_jump	(	int const	seqpos,
		int	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)

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?

Definition at line 515 of file FoldTree.cc.

bool core::kinematics::FoldTree::is_cutpoint ( int 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

Definition at line 1078 of file FoldTree.hh.

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

Referenced by protocols::topology_broker::TopologyBroker::add_chainbreak_variants(), protocols::forge::methods::add_cutpoint_variants(), protocols::simple_moves::MissingDensityToJumpMover::apply(), protocols::rbsegment_relax::RBSegmentRelax::apply(), protocols::hybridization::CartesianHybridize::apply(), protocols::hybridization::CartesianSampler::apply_frame(), protocols::loops::apply_sequence_mapping(), protocols::swa::rna::apply_virtual_rna_residue_variant_type(), protocols::toolbox::AllowInsert::calculate_atom_id_map(), protocols::topology_broker::TopologyBroker::check_chainbreak_variants(), protocols::jumping::close_chainbreaks(), protocols::topology_broker::copy_internal_coords(), protocols::hybridization::create_fragment_set(), protocols::rna::create_rna_vall_torsions(), protocols::anchored_design::dump_cutpoint_info(), core::scoring::methods::ChainbreakEnergy::eval_atom_derivative(), core::scoring::methods::CartesianBondedEnergy::eval_intraresidue_dof_derivative(), core::scoring::methods::CartesianBondedEnergy::eval_residue_pair_derivatives(), protocols::coarse_rna::CoarseRNA_LoopCloser::figure_out_dof_ids_and_offsets(), protocols::swa::protein::StepWiseProteinLoopBridger::figure_out_loop(), protocols::swa::rna::StepWiseRNA_JobParameters_Setup::figure_out_partition_definition(), protocols::swa::StepWisePoseSetup::figure_out_Prepend_Internal(), protocols::coarse_rna::CoarseRNA_LoopCloser::figure_out_which_cutpoints_were_affected(), protocols::electron_density::findLoopFromDensity(), protocols::electron_density::findLoopFromPatterson(), protocols::rna::RNA_ChunkLibrary::get_component_sequences(), protocols::swa::rna::get_default_allowed_bulge_res(), protocols::seeded_abinitio::GrowPeptides::grow_from_verteces(), protocols::loops::Loops::grow_loop(), protocols::loops::Loops::grow_loop_away_from_sheets(), protocols::seeded_abinitio::SegmentHybridizer::hybridize(), core::conformation::idealize_position(), protocols::nonlocal::SingleFragmentMover::initialize_chunks(), core::conformation::insert_ideal_bonds_at_polymer_junction(), core::scoring::rna::is_cutpoint_open(), core::conformation::is_ideal_position(), core::scoring::methods::is_lower_cutpoint(), core::scoring::methods::is_upper_cutpoint(), protocols::forge::methods::linear_chainbreak(), protocols::forge::methods::make_star_foldtree(), core::scoring::electron_density::ElectronDensity::matchRes(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::model_loop(), protocols::forge::build::Bridge::modify_impl(), protocols::forge::build::SegmentRebuild::modify_impl(), protocols::forge::build::SegmentInsert::modify_impl(), protocols::swa::monte_carlo::RNA_SWA_MonteCarloMover::output_silent_file(), protocols::forge::methods::overlap_chainbreak(), protocols::swa::pdbslice(), protocols::swa::rna::possible_root(), protocols::rna::possible_root(), protocols::forge::methods::quadratic_chainbreak(), protocols::forge::methods::remove_cutpoint(), protocols::forge::methods::remove_cutpoint_variants(), protocols::rna::remove_cutpoints_closed(), protocols::features::ProteinBondGeometryFeatures::report_interres_angles(), protocols::features::ProteinBondGeometryFeatures::report_interres_lengths(), core::scoring::methods::CartesianBondedEnergy::residue_pair_energy_sorted(), protocols::rna::RNA_StructureParameters::setup_chainbreak_variants(), protocols::rna::RNA_StructureParameters::setup_virtual_phosphate_variants_OLD(), 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::rna::RNA_Minimizer::update_allow_insert_with_extra_minimize_res(), and protocols::rna::virtualize_5prime_phosphates().

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

inline

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

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

Definition at line 1017 of file FoldTree.hh.

References check_topology(), and is_jump_point_.

Referenced by protocols::simple_moves::PeptideStapleMover::apply(), core::fragment::DownJumpSRFD::apply(), protocols::jumping::close_chainbreaks(), core::conformation::get_root_residue_root_atomno(), 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(), core::kinematics::simple_visualize_fold_tree(), core::kinematics::simple_visualize_fold_tree_and_movemap(), and core::kinematics::simple_visualize_fold_tree_and_movemap_bb_chi().

bool core::kinematics::FoldTree::is_root ( int 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

Definition at line 696 of file FoldTree.hh.

References begin(), and edge_list_.

Referenced by boundary_left(), boundary_right(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensCenEnergy::eval_atom_derivative(), core::scoring::electron_density::FastDensEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensEnergy::eval_atom_derivative(), core::conformation::get_residue_connections(), core::conformation::replace_residue_in_atom_tree(), and protocols::relax::RelaxProtocolBase::set_up_constraints().

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

Definition at line 1119 of file FoldTree.cc.

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

Edge const & core::kinematics::FoldTree::jump_edge ( int 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

Definition at line 2079 of file FoldTree.cc.

Referenced by protocols::seeded_abinitio::CoordinateCst::apply(), protocols::protein_interface_design::movers::SpinMover::apply(), protocols::rigid::RotateJumpAxisMover::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_atom_derivative(), core::io::silent::BinaryProteinSilentStruct::fill_pose(), protocols::forge::methods::find_connecting_jump(), core::conformation::get_root_residue_root_atomno(), protocols::simple_filters::JumpEvaluator::JumpEvaluator(), protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue(), protocols::anchored_design::AnchoredDesignMover::set_fold_tree_and_cutpoints(), core::kinematics::simple_visualize_fold_tree(), core::kinematics::simple_visualize_fold_tree_and_movemap(), core::kinematics::simple_visualize_fold_tree_and_movemap_bb_chi(), and core::pose::transfer_jumps().

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

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

Definition at line 2089 of file FoldTree.cc.

bool core::kinematics::FoldTree::jump_exists	(	int const	pos1,
		int 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

Definition at line 732 of file FoldTree.hh.

References jump_point(), and num_jump().

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

Definition at line 1047 of file FoldTree.hh.

References jump_point(), and num_jump().

Referenced by protocols::topology_broker::TopologyBroker::initialize_dofs(), and core::pose::transfer_jumps().

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

starting or stopping residue of a jump edge

Definition at line 1894 of file FoldTree.cc.

Referenced by jump_exists(), jump_nr(), and protocols::swa::rna::Output_fold_tree_info().

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

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

Definition at line 1198 of file FoldTree.cc.

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

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

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

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

Definition at line 1161 of file FoldTree.cc.

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

Referenced by protocols::frag_picker::nonlocal::NonlocalFrags::apply(), protocols::loops::loop_closure::ccd::ShortLoopClosure::apply(), protocols::simple_moves::MissingDensityToJumpMover::apply(), protocols::rna::RNA_HelixAssembler::apply(), protocols::hybridization::DomainAssembly::apply(), protocols::swa::StepWiseScreener::figure_out_fold_tree(), protocols::swa::protein::StepWiseProteinScreener::figure_out_fold_tree(), protocols::rna::figure_out_reasonable_rna_fold_tree(), protocols::swa::protein::generate_beta_database_test(), protocols::enzdes::EnzdesFlexBBProtocol::generate_ensemble_for_region(), protocols::rna::RNA_HelixAssembler::get_rid_of_capping_base_pairs(), protocols::forge::methods::linear_chainbreak(), protocols::swa::make_cut_at_moving_suite(), protocols::swa::rna::make_cut_at_moving_suite(), protocols::forge::build::SegmentSwap::modify_impl(), protocols::forge::methods::overlap_chainbreak(), protocols::forge::methods::quadratic_chainbreak(), and protocols::rna::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

Definition at line 997 of file FoldTree.hh.

References check_topology(), and nres_.

Referenced by protocols::jumping::JumpSample::apply_to(), boundary_left(), boundary_right(), core::kinematics::ShortestPathInFoldTree::build_peptide_table(), protocols::jumping::close_chainbreaks(), core::pose::create_subpose(), protocols::forge::methods::find_connecting_jump(), core::fragment::FindBoundaries(), core::conformation::Conformation::fold_tree(), core::conformation::symmetry::fold_tree_entry_point(), protocols::loops::fold_tree_from_loops(), core::conformation::symmetry::get_component_contiguous_foldtree(), insert_fold_tree_by_jump(), core::conformation::insert_residue_into_atom_tree(), protocols::forge::methods::merge(), protocols::swa::rna::possible_root(), protocols::rna::possible_root(), protocols::forge::methods::remove_cutpoint(), protocols::forge::methods::remove_cutpoints(), protocols::forge::methods::replace(), protocols::loops::set_single_loop_fold_tree(), protocols::forge::methods::shift_jumps(), 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().

int 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

Definition at line 1038 of file FoldTree.hh.

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::loops::apply_sequence_mapping(), protocols::forge::remodel::RemodelLoopMover::boost_closure_stage(), protocols::jumping::close_chainbreaks(), protocols::abinitio::AbrelaxMover::close_with_idealization(), protocols::medal::cutpoint_probabilities(), core::scoring::methods::ChainbreakEnergy::finalize_total_energy(), 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::medal::invalidate_residues_spanning_cuts(), protocols::forge::methods::linear_chainbreak(), protocols::swa::rna::move_jump_atom_to_base(), protocols::swa::rna::Output_fold_tree_info(), protocols::forge::methods::overlap_chainbreak(), protocols::forge::methods::quadratic_chainbreak(), protocols::loops::remove_cutpoint_variants(), protocols::swa::rna::StepWiseRNA_JobParameters_Setup::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.

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

Definition at line 1006 of file FoldTree.hh.

References check_topology(), and num_jump_.

Referenced by protocols::toolbox::pose_manipulation::add_chainbreaks_according_to_jumps(), protocols::toolbox::pose_metric_calculators::append_rsd_by_jump_near_atom(), protocols::enzdes::DetectProteinLigandInterface::apply(), protocols::jumping::JumpSample::apply_to(), core::kinematics::ShortestPathInFoldTree::build_jumpres_distmap(), protocols::toolbox::pose_metric_calculators::dock_waters_to_atom(), protocols::abinitio::KinematicAbinitio::dump_jump_log(), protocols::swa::rna::StepWiseRNA_Minimizer::Figure_out_moving_residues(), protocols::swa::Figure_out_moving_residues(), protocols::rna::RNA_StructureParameters::fill_in_default_jump_atoms(), core::io::silent::BinaryProteinSilentStruct::fill_pose(), core::io::silent::RNA_SilentStruct::fill_pose(), core::io::silent::BinaryRNASilentStruct::fill_struct(), core::io::silent::BinaryProteinSilentStruct::fill_struct(), core::io::silent::RNA_SilentStruct::fill_struct(), protocols::forge::methods::find_connecting_jump(), core::pose::symmetry::find_symmetric_basejump_anchor(), protocols::swa::rna::floating_base_chain_closure_setup(), core::conformation::symmetry::SymmetricConformation::fold_tree(), core::conformation::symmetry::fold_tree_entry_point(), protocols::loops::fold_tree_from_loops(), core::conformation::symmetry::get_component_contiguous_foldtree(), protocols::rna::get_rigid_body_jumps(), core::conformation::get_root_residue_root_atomno(), core::io::silent::BinaryRNASilentStruct::init_from_lines(), core::io::silent::BinaryProteinSilentStruct::init_from_lines(), protocols::topology_broker::AsymFoldandDockClaimer::initialize_dofs(), core::conformation::symmetry::SymmetricConformation::insert_conformation_by_jump(), insert_fold_tree_by_jump(), jump_exists(), jump_nr(), protocols::hybridization::HybridizeFoldtreeDynamic::jumps_and_cuts_from_foldtree(), protocols::forge::methods::jumps_and_cuts_from_pose(), core::optimization::symmetry::SymAtomTreeMinimizer::make_assymetric_movemap(), protocols::swa::rna::make_cut_at_moving_suite(), core::optimization::symmetry::SymAtomTreeMinimizer::make_semisymmetric_movemap(), protocols::forge::methods::merge(), protocols::enzdes::EnzdesFlexibleRegion::minimize_region(), protocols::swa::rna::Output_movemap(), core::io::silent::BinaryRNASilentStruct::print_conformation(), core::io::silent::BinaryProteinSilentStruct::print_conformation(), core::io::silent::RNA_SilentStruct::print_conformation(), protocols::toolbox::pose_manipulation::remove_chainbreaks_according_to_jumps(), protocols::rna::remove_cutpoint_closed(), protocols::ligand_docking::LigandBaseProtocol::reorder_foldtree_around_mobile_regions(), core::pose::symmetry::sealed_symmetric_fold_tree(), protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::semiexpl_water_hbgeom_score(), protocols::rna::MultipleDomainMover::setup_jump_numbers_and_partner(), protocols::rna::RNA_Minimizer::setup_movemap(), core::conformation::symmetry::setup_symmetric_conformation(), core::kinematics::ShortestPathInFoldTree::ShortestPathInFoldTree(), core::kinematics::simple_visualize_fold_tree(), core::kinematics::simple_visualize_fold_tree_and_movemap(), core::kinematics::simple_visualize_fold_tree_and_movemap_bb_chi(), core::conformation::symmetry::symmetrize_fold_tree(), and core::kinematics::visualize_fold_tree().

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

inline

operator=

Note: this version doesnt copy any of the derived data! will this be too slow? it will trigger re-calculating of everything every time we reject a move....

Definition at line 106 of file FoldTree.hh.

References edge_list_, and new_topology.

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

partition into two foldtrees by cutting at jump= jump_number

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

Definition at line 1683 of file FoldTree.cc.

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

Referenced by protocols::ligand_docking::LigandDockProtocol::append_ligand_docking_scores(), protocols::ligand_docking::append_radius_of_gyration(), protocols::protein_interface_design::movers::BackrubDDMover::apply(), protocols::protein_interface_design::movers::DesignMinimizeHbonds::apply(), protocols::coarse_rna::CoarseRNA_LoopCloser::apply_after_jump_change(), core::scoring::sc::MolecularSurfaceCalculator::Calc(), protocols::docking::calc_Fnat(), protocols::docking::calc_Lrmsd(), protocols::geometry::centroids_by_jump(), protocols::geometry::centroids_by_jump_int(), protocols::protein_interface_design::filters::AtomicContactCountFilter::compute(), protocols::optimize_weights::IterativeOptEDriver::compute_rotamers_around_ligands(), protocols::swa::rna::StepWiseRNA_JobParameters_Setup::figure_out_partition_definition(), protocols::ligand_docking::LigandBaseProtocol::find_interface_backbone(), protocols::ligand_docking::LigandBaseProtocol::find_interface_rsds(), core::pack::task::operation::util::find_jump_partners_within_CB_cutoff(), protocols::ligand_docking::LigandBaseProtocol::get_ligand_id(), core::pose::symmetry::get_symdof_subunits(), core::pose::partition_pose_by_jump(), protocols::rna::remove_cutpoint_closed(), protocols::simple_filters::EnergyPerResidueFilter::report(), protocols::enzdes::LigInterfaceEnergyFilter::report(), and protocols::simple_moves::DesignRepackMover::setup_packer_and_movemap().

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

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

void core::kinematics::FoldTree::partition_by_residue	(	int 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.void

Definition at line 1818 of file FoldTree.cc.

References core::sequence::end, core::kinematics::Edge::start(), protocols::loops::start, core::kinematics::Edge::stop(), and protocols::loops::stop.

Referenced by protocols::coarse_rna::CoarseRNA_LoopCloser::apply(), and protocols::swa::StepWisePoseSetup::figure_out_partition_definition().

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

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

Definition at line 2652 of file FoldTree.cc.

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

bool core::kinematics::FoldTree::random_tree_from_jump_points	(	int const	nres_in,
		int const	num_jump_in,
		ObjexxFCL::FArray2D_int const &	jump_point,
		ObjexxFCL::FArray1D_float const &	cut_bias,
		int 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::RNA_StructureParameters::setup_jumps().

bool core::kinematics::FoldTree::random_tree_from_jump_points	(	int const	nres_in,
		int const	num_jump_in,
		ObjexxFCL::FArray2D_int const &	jump_point,
		std::vector< int > const &	obligate_cut_points,
		ObjexxFCL::FArray1D_float const &	cut_bias,
		int 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

Definition at line 2604 of file FoldTree.cc.

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

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

Definition at line 1613 of file FoldTree.cc.

References TR().

Referenced by core::conformation::symmetry::get_asymm_unit_fold_tree(), and protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue().

bool core::kinematics::FoldTree::reorder ( int const start_residue)

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.

Definition at line 1034 of file FoldTree.cc.

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

Referenced by protocols::swa::rna::StepWiseRNA_PoseSetup::add_aa_virt_rsd_as_root(), protocols::abinitio::LoopJumpFoldCst::add_rigidity_jumps(), core::pose::addVirtualResAsRoot(), protocols::topology_broker::MembraneTopologyClaimer::addVirtualResAsRootMembrane(), protocols::simple_moves::SwitchChainOrderMover::apply(), protocols::protein_interface_design::movers::SetAtomTree::apply(), protocols::idealize::IdealizeMover::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::loops::apply_sequence_mapping(), protocols::loops::fold_tree_from_loops(), core::conformation::symmetry::get_component_contiguous_foldtree(), protocols::rna::RNA_HelixAssembler::get_rid_of_capping_base_pairs(), MinimizeInterface(), protocols::forge::build::SegmentRebuild::modify_impl(), core::kinematics::operator>>(), protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue(), protocols::swa::rna::StepWiseRNA_JobParameters_Setup::reroot_fold_tree(), protocols::swa::StepWisePoseSetup::reroot_fold_tree(), protocols::swa::rna::StepWiseRNA_JobParameters_Setup::reroot_fold_tree_simple(), protocols::rbsegment_relax::restore_pose_from_rbsegs(), protocols::anchored_design::AnchoredDesignMover::set_fold_tree_and_cutpoints(), protocols::rna::RNA_StructureParameters::setup_jumps(), and protocols::protein_interface_design::star_fold_tree().

int 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

Definition at line 713 of file FoldTree.hh.

References edge_list_, and empty().

void core::kinematics::FoldTree::set_jump_atoms	(	int 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.

Definition at line 2460 of file FoldTree.cc.

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

Referenced by protocols::frag_picker::nonlocal::NonlocalFrags::apply(), protocols::rna::RNA_HelixAssembler::apply(), protocols::rna::figure_out_reasonable_rna_fold_tree(), protocols::rna::RNA_StructureParameters::fill_in_default_jump_atoms(), core::conformation::symmetry::get_component_contiguous_foldtree(), protocols::rna::RNA_HelixAssembler::get_rid_of_capping_base_pairs(), protocols::rna::make_coarse_pose(), protocols::swa::rna::move_jump_atom_to_base(), protocols::protein_interface_design::movers::PlaceStubMover::place_stub(), protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue(), and protocols::swa::rna::StepWiseRNA_JobParameters_Setup::setup_fold_tree().

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

Definition at line 2480 of file FoldTree.cc.

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

Definition at line 1963 of file FoldTree.cc.

References protocols::loops::start, and protocols::loops::stop.

Referenced by check_topology().

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

Displays the FoldTree information.

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

Definition at line 2318 of file FoldTree.cc.

References core::sequence::end.

Referenced by protocols::simple_filters::PoseInfoFilter::report().

void core::kinematics::FoldTree::simple_tree ( int 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

Definition at line 1107 of file FoldTree.cc.

Referenced by protocols::jumping::close_chainbreaks(), protocols::abinitio::AbrelaxApplication::fold(), FoldTree(), core::io::silent::BinaryRNASilentStruct::init_from_lines(), core::io::silent::BinaryProteinSilentStruct::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(), protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue(), core::io::silent::BinaryRNASilentStruct::resize(), core::io::silent::BinaryProteinSilentStruct::resize(), core::io::silent::RNA_SilentStruct::resize(), protocols::grafting::return_region(), and protocols::swa::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

Definition at line 146 of file FoldTree.hh.

References edge_list_.

Referenced by protocols::swa::rna::StepWiseRNA_JobParameters::fold_tree(), 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.

Definition at line 200 of file FoldTree.cc.

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

Definition at line 220 of file FoldTree.cc.

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

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::randomlySlidePeptideJump(), and protocols::hotspot_hashing::HotspotStubSet::setup_hotspot_foldtree_().

bool core::kinematics::FoldTree::tree_from_jumps_and_cuts	(	int const	nres_in,
		int const	num_jump_in,
		ObjexxFCL::FArray2D_int const &	jump_point,
		ObjexxFCL::FArray1D_int const &	cuts,
		int 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.

Definition at line 1233 of file FoldTree.cc.

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

Referenced by protocols::hybridization::FoldTreeHybridize::add_strand_pairing(), protocols::loops::apply_sequence_mapping(), core::conformation::symmetry::get_component_contiguous_foldtree(), protocols::dna::make_base_pair_aware_fold_tree(), core::fragment::make_simple_fold_tree_from_jump_frame(), protocols::rna::remove_cutpoint_closed(), core::pose::symmetry::sealed_symmetric_fold_tree(), protocols::anchored_design::AnchoredDesignMover::set_fold_tree_and_cutpoints(), protocols::nonlocal::StarTreeBuilder::set_up(), protocols::swa::rna::StepWiseRNA_JobParameters_Setup::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).

Definition at line 2157 of file FoldTree.cc.

Referenced by check_topology().

void core::kinematics::FoldTree::update_edge_label	(	int const	start,
		int 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

Definition at line 868 of file FoldTree.cc.

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

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 labelling 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)

Definition at line 1560 of file FoldTree.cc.

References 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).

Definition at line 2299 of file FoldTree.cc.

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

Definition at line 2255 of file FoldTree.cc.

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).

Definition at line 2205 of file FoldTree.cc.

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).

Definition at line 2223 of file FoldTree.cc.

References TR().

Referenced by check_topology().

std::string core::kinematics::FoldTree::upstream_atom ( int 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.

Definition at line 2518 of file FoldTree.cc.

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

Referenced by protocols::swa::rna::Output_fold_tree_info(), and protocols::rna::RNA_Minimizer::setup_movemap().

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

the staring residue for this jump

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

Definition at line 1013 of file FoldTree.cc.

Referenced by protocols::abinitio::MembraneAbinitio::add_spanning_region(), protocols::jumping::JumpSample::apply_to(), protocols::idealize::basic_idealize(), protocols::rna::RNA_ChunkLibrary::check_connections(), protocols::rna::ChunkSet::check_fold_tree_OK(), protocols::rna::RNA_ChunkLibrary::check_jump_match(), protocols::enzdes::EnzdesBaseProtocol::create_enzdes_movemap(), protocols::swa::rna::StepWiseRNA_Minimizer::Figure_out_moving_residues(), protocols::swa::Figure_out_moving_residues(), protocols::rna::RNA_StructureParameters::fill_in_default_jump_atoms(), core::pose::symmetry::find_symmetric_basejump_anchor(), protocols::swa::rna::floating_base_chain_closure_setup(), core::conformation::symmetry::fold_tree_entry_point(), protocols::jumping::JumpSample::generate_jump_frags(), protocols::jumping::JumpSample::generate_jump_frames(), protocols::rna::get_rigid_body_jumps(), protocols::rna::RNA_StructureParameters::insert_base_pair_jumps(), protocols::hybridization::HybridizeFoldtreeDynamic::jumps_and_cuts_from_foldtree(), protocols::forge::methods::jumps_and_cuts_from_pose(), protocols::swa::rna::make_cut_at_moving_suite(), core::pose::symmetry::make_symmetric_movemap(), protocols::swa::rna::move_jump_atom_to_base(), protocols::swa::rna::Output_movemap(), protocols::rna::RNA_StructureParameters::random_jump_change(), protocols::rna::remove_cutpoint_closed(), protocols::simple_filters::AlaScan::report(), core::pose::symmetry::sealed_symmetric_fold_tree(), protocols::analysis::InterfaceAnalyzerMover::set_pose_info(), protocols::swa::rna::StepWiseRNA_JobParameters_Setup::setup_fold_tree(), protocols::rna::MultipleDomainMover::setup_jump_numbers_and_partner(), protocols::rna::RNA_StructureParameters::setup_jumps(), protocols::rna::RNA_Minimizer::setup_movemap(), core::pose::swap_transform(), core::conformation::symmetry::symmetrize_fold_tree(), protocols::rna::translate_virtual_anchor_to_first_rigid_body(), protocols::rna::MultipleDomainMover::try_to_slide_into_contact(), and core::kinematics::visualize_fold_tree().

Friends And Related Function Documentation

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

friend

Not equal to operator.

Definition at line 76 of file FoldTree.cc.

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

friend

output operator

Foldtree output to stream

Definition at line 2338 of file FoldTree.cc.

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

friend

equal to operator

Checks that edges are in the same order and are equal

Definition at line 61 of file FoldTree.cc.

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

friend

input operator

Foldtree input from stream

Definition at line 2357 of file FoldTree.cc.

Member Data Documentation

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

mutableprivate

cutpoint number to cutpoint residue number, dimesioned as num_cutpoint_.

Definition at line 924 of file FoldTree.hh.

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

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

mutableprivate

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

Definition at line 926 of file FoldTree.hh.

Referenced by cutpoint_map(), and is_cutpoint().

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

mutableprivate

dimensioned as nres_, see setup_edge_counts for more info

Definition at line 932 of file FoldTree.hh.

EdgeList core::kinematics::FoldTree::edge_list_

private

the list of edges.

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

Definition at line 896 of file FoldTree.hh.

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

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

private

Definition at line 940 of file FoldTree.hh.

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

mutableprivate

whether a residue is a cutpoint, dimensioned as nres_

Definition at line 928 of file FoldTree.hh.

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_

Definition at line 922 of file FoldTree.hh.

Referenced by is_jump_point().

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

mutableprivate

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

Definition at line 930 of file FoldTree.hh.

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

mutableprivate

dimensioned as num_jump, see setup_edge_counts for more info

Definition at line 936 of file FoldTree.hh.

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

mutableprivate

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

Definition at line 920 of file FoldTree.hh.

int core::kinematics::FoldTree::min_edge_count

mutableprivate

the minimum number in edge_count and jump_edge_count.

Definition at line 934 of file FoldTree.hh.

bool core::kinematics::FoldTree::new_order

mutableprivate

edges in the edge_list_ have been reorderd.

Definition at line 902 of file FoldTree.hh.

Referenced by check_order(), and check_topology().

bool core::kinematics::FoldTree::new_topology

mutableprivate

edges in the edge_list_ have been changed.

Definition at line 900 of file FoldTree.hh.

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

int core::kinematics::FoldTree::nres_

mutableprivate

just the largest vertex in edge_list_

Definition at line 913 of file FoldTree.hh.

Referenced by is_cutpoint(), and nres().

int core::kinematics::FoldTree::num_cutpoint_

mutableprivate

number of cutpoints in the fold tree.

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

Definition at line 918 of file FoldTree.hh.

Referenced by num_cutpoint().

int core::kinematics::FoldTree::num_jump_

mutableprivate

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

Definition at line 915 of file FoldTree.hh.

Referenced by num_jump().

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