The FoldTree is a residue-based tree-like representation of a molecule. More...
#include <FoldTree.hh>
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 VirtualBase. 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
◆ const_iterator
| typedef EdgeList::const_iterator core::kinematics::FoldTree::const_iterator |
◆ EdgeList
| typedef std::vector< Edge > core::kinematics::FoldTree::EdgeList |
◆ iterator
| typedef EdgeList::iterator core::kinematics::FoldTree::iterator |
Constructor & Destructor Documentation
◆ ~FoldTree()
|
overridedefault |
Automatically generated virtual destructor for class deriving directly from VirtualBase.
◆ FoldTree() [1/3]
|
inline |
constructor
◆ FoldTree() [2/3]
|
inline |
Constructs a simple FoldTree.
ft = FoldTree( nres_in )
int nres_in /the number of residues in this simple tree
References simple_tree().
◆ FoldTree() [3/3]
|
default |
Member Function Documentation
◆ add_edge() [1/4]
| 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
References protocols::loops::start, and protocols::loops::stop.
Referenced by protocols::forge::methods::add_edges(), protocols::antibody_legacy::Antibody::all_cdr_fold_tree(), protocols::antibody_legacy::AntibodyModeler::all_cdr_VL_VH_fold_tree(), protocols::chemically_conjugated_docking::UBQ_GTPaseMover::analyze_and_filter(), protocols::metal_interface::ZincHeterodimerMover::apply(), protocols::protein_interface_design::movers::SetAtomTree::apply(), protocols::simple_moves::ResetFoldTree::apply(), protocols::simple_moves::SetTorsion::apply(), protocols::simple_moves::SwitchChainOrderMover::apply(), protocols::simple_moves::FoldTreeFromMotif::apply(), protocols::backbone_moves::local_backbone_mover::GapCloser::apply_closure(), protocols::fold_from_loops::movers::NubInitioLoopClosureMover::apply_closure_trust(), protocols::loophash::BackboneSegment::apply_to_pose(), protocols::pose_length_moves::PossibleLoop::assign_phi_psi_omega_from_lookback(), protocols::fold_from_loops::utils::attach_n_and_c_unfolded_poses_to_pose(), protocols::metal_interface::MatchGrafter::build_combined_pose_with_zinc_overlay(), protocols::symmetric_docking::SymDockProtocol::calc_fnat(), protocols::symmetric_docking::SymDockProtocol::calc_Irms(), protocols::analysis::LoopAnalyzerMover::calculate_all_chainbreaks(), protocols::protein_interface_design::movers::copy_hotspot_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::pose_length_moves::NearNativeLoopCloser::extendRegion(), protocols::pose_length_moves::PossibleLoop::extendRegion(), protocols::pose_length_moves::InsertResMover::extendRegion(), protocols::loophash::LoopHashLibrary::extract_data_from_pose(), protocols::splice::Splice::fold_tree(), protocols::splice::SpliceManager::fold_tree(), protocols::denovo_design::components::FoldGraph::fold_tree(), protocols::loops::fold_tree_from_loops(), protocols::forge::methods::fold_tree_from_pose(), 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(), core::kinematics::get_foldtree_which_partitions(), 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(), protocols::grafting::insert_pose_into_pose(), protocols::pose_length_moves::PossibleLoop::kic_closure(), protocols::denovo_design::linear_chainbreak(), core::kinematics::linearize_fold_tree(), protocols::protein_interface_design::make_hotspot_foldtree(), protocols::forge::methods::make_star_foldtree(), protocols::forge::methods::merge(), protocols::pose_length_moves::PossibleLoop::minimize_loop(), protocols::enzdes::EnzdesFlexibleRegion::minimize_region(), protocols::protein_interface_design::MinimizeInterface(), protocols::forge::build::BuildManager::modify(), protocols::forge::build::SegmentInsert::modify_impl(), protocols::forge::build::SegmentRebuild::modify_impl(), protocols::ub_e2c::ubi_e2c_modeler::monoub_fold_tree(), partition_by_jump(), protocols::protein_interface_design::movers::PlaceStubMover::place_stub(), protocols::cyclic_peptide::PeptideStubMover::preserve_old_mainchain_torsions(), protocols::protein_interface_design::movers::PlacementMinimizationMover::refresh_bbstub_constraints(), core::kinematics::remodel_fold_tree_to_account_for_insertion(), protocols::denovo_design::remove_all_jump_atoms(), protocols::jumping::remove_cut(), protocols::denovo_design::remove_missing_jump_atoms(), protocols::ligand_docking::LigandBaseProtocol::reorder_foldtree_around_mobile_regions(), protocols::analysis::InterfaceAnalyzerMover::reorder_foldtree_find_jump(), protocols::forge::methods::replace(), protocols::relax::RepeatProteinRelax::seal_jumps(), protocols::protein_interface_design::movers::SetAtomTree::set_ab_fold_tree(), protocols::ub_e2c::ubi_e2c_modeler::set_e2g2_diubi_fold_tree(), protocols::splice::RBInMover::set_fold_tree(), protocols::splice::Splice::set_fold_tree(), protocols::anchored_design::AnchoredDesignMover::set_fold_tree_and_cutpoints(), core::pose::set_reasonable_fold_tree(), protocols::ub_e2c::ubi_e2c_modeler::setup_complex_fold_tree(), 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::ncbb::setup_pert_foldtree(), protocols::rbsegment_relax::setup_pose_from_rbsegs(), protocols::antibody_legacy::AntibodyModeler::setup_simple_fold_tree(), protocols::ub_e2c::ubi_e2c_modeler::setup_simple_fold_tree(), protocols::grafting::setup_single_loop_double_arm_remodeling_foldtree(), protocols::grafting::setup_single_loop_single_arm_remodeling_foldtree(), protocols::forge::methods::shift_jumps(), protocols::antibody::simple_fold_tree(), protocols::antibody_legacy::simple_fold_tree(), protocols::antibody::simple_one_loop_fold_tree(), protocols::antibody_legacy::simple_one_loop_fold_tree(), protocols::denovo_design::slide_jump(), protocols::protein_interface_design::star_fold_tree(), protocols::comparative_modeling::steal_ligands(), protocols::denovo_design::symmetric_fold_tree(), protocols::splice::Splice::tail_fold_tree(), protocols::loophash::LoopHashLibrary::test_loop_sample(), protocols::legacy_sewing::Assembly::to_pose(), and protocols::hybridization::HybridizeFoldtreeDynamic::update().
◆ add_edge() [2/4]
| 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
◆ add_edge() [3/4]
| 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.
References protocols::loops::start, and protocols::loops::stop.
◆ add_edge() [4/4]
| 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.
References protocols::loops::start, and protocols::loops::stop.
◆ add_vertex()
|
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.
◆ append_residue()
| 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.
◆ append_residue_by_chemical_bond()
| 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.
◆ apply_sequence_mapping()
| 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
◆ begin()
|
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(), protocols::denovo_design::find_jump_rec(), protocols::denovo_design::components::FoldGraph::fold_tree(), is_root(), protocols::forge::build::SegmentInsert::modify_impl(), protocols::forge::build::SegmentRebuild::modify_impl(), core::pose::symmetry::partition_by_symm_jumps(), core::energy_methods::FastDensEnergy::pose_is_setup_for_density_scoring(), protocols::topology_broker::TMHTopologySamplerClaimer::pre_process(), protocols::forge::methods::replace(), core::pose::set_reasonable_fold_tree(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_fold_tree_through_build_full_model_info(), core::energy_methods::ElecDensAllAtomCenEnergy::setup_for_scoring(), core::energy_methods::ElecDensAtomwiseEnergy::setup_for_scoring(), core::energy_methods::ElecDensCenEnergy::setup_for_scoring(), core::energy_methods::ElecDensEnergy::setup_for_scoring(), core::energy_methods::FastDensEnergy::setup_for_scoring(), protocols::denovo_design::slide_jump(), protocols::hybridization::FoldTreeHybridize::superimpose_strand_pairings_to_templates(), and protocols::hybridization::HybridizeFoldtreeDynamic::update().
◆ boundary_left()
Return the starting residue of the first kinematic Edge to which res belongs.
References get_residue_edge(), and core::kinematics::Edge::start().
Referenced by protocols::fold_from_loops::movers::NubInitioLoopClosureMover::apply_closure_trust().
◆ boundary_right()
Return the ending residue of the first kinematic Edge to which res belongs.
References get_residue_edge(), and core::kinematics::Edge::stop().
Referenced by protocols::fold_from_loops::movers::NubInitioLoopClosureMover::apply_closure_trust().
◆ check_edges_for_atom_info()
| 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().
◆ check_fold_tree()
| 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::denovo_design::movers::FoldTreeFromFoldGraphMover::apply(), protocols::frag_picker::nonlocal::NonlocalFrags::apply(), protocols::nonlocal::SingleFragmentMover::apply(), protocols::simple_moves::FoldTreeFromMotif::apply(), protocols::loops::apply_sequence_mapping(), protocols::jumping::JumpSample::apply_to(), protocols::symmetric_docking::SymDockProtocol::calc_fnat(), protocols::symmetric_docking::SymDockProtocol::calc_Irms(), protocols::analysis::LoopAnalyzerMover::calculate_all_chainbreaks(), core::conformation::membrane::MembraneInfo::check_membrane_fold_tree(), protocols::splice::Splice::fold_tree(), protocols::splice::SpliceManager::fold_tree(), protocols::denovo_design::components::FoldGraph::fold_tree(), protocols::splice::RBOutMover::get_disulf_jump(), protocols::antibody::AntibodyInfo::get_FoldTree_L_HA(), protocols::antibody::AntibodyInfo::get_FoldTree_LA_H(), protocols::antibody::AntibodyInfo::get_FoldTree_LH_A(), core::kinematics::get_foldtree_which_partitions(), 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(), protocols::ligand_docking::LigandBaseProtocol::reorder_foldtree_around_mobile_regions(), protocols::protein_interface_design::movers::SetAtomTree::set_ab_fold_tree(), protocols::rigid::RigidBodyMotionMover::set_fold_tree(), protocols::splice::RBInMover::set_fold_tree(), protocols::splice::Splice::set_fold_tree(), protocols::docking::setup_foldtree(), protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover::setup_foldtree_around_anchor_invrot(), protocols::hotspot_hashing::HotspotStubSet::setup_hotspot_foldtree_(), protocols::ncbb::setup_pert_foldtree(), protocols::denovo_design::slide_jump(), and protocols::splice::Splice::tail_fold_tree().
◆ check_order()
|
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().
◆ check_topology()
|
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().
◆ 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::protein_interface_design::movers::SetAtomTree::apply(), protocols::simple_moves::ResetFoldTree::apply(), protocols::simple_moves::SetTorsion::apply(), protocols::simple_moves::SwitchChainOrderMover::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::NearNativeLoopCloser::extendRegion(), protocols::pose_length_moves::PossibleLoop::extendRegion(), protocols::splice::Splice::fold_tree(), protocols::splice::SpliceManager::fold_tree(), protocols::loops::fold_tree_from_loops(), protocols::simple_moves::CutChainMover::foldTree(), protocols::splice::RBOutMover::get_disulf_jump(), protocols::antibody::AntibodyInfo::get_FoldTree_L_HA(), protocols::antibody::AntibodyInfo::get_FoldTree_LA_H(), protocols::antibody::AntibodyInfo::get_FoldTree_LH_A(), core::kinematics::get_foldtree_which_partitions(), protocols::seeded_abinitio::GrowPeptides::grow_from_vertices(), protocols::topology_broker::AsymFoldandDockClaimer::initialize_dofs(), protocols::grafting::insert_pose_into_pose(), protocols::pose_length_moves::PossibleLoop::kic_closure(), 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(), protocols::ub_e2c::ubi_e2c_modeler::monoub_fold_tree(), 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::analysis::InterfaceAnalyzerMover::reorder_foldtree_find_jump(), 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::ub_e2c::ubi_e2c_modeler::set_e2g2_diubi_fold_tree(), protocols::splice::RBInMover::set_fold_tree(), protocols::splice::Splice::set_fold_tree(), core::conformation::symmetry::set_fold_tree_from_symm_data(), protocols::ub_e2c::ubi_e2c_modeler::setup_complex_fold_tree(), protocols::flexpep_docking::FlexPepDockingProtocol::setup_foldtree(), protocols::docking::setup_foldtree(), protocols::ncbb::setup_pert_foldtree(), protocols::rbsegment_relax::setup_pose_rbsegs_keep_loops(), protocols::antibody_legacy::AntibodyModeler::setup_simple_fold_tree(), protocols::ub_e2c::ubi_e2c_modeler::setup_simple_fold_tree(), 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_legacy::simple_fold_tree(), protocols::antibody::simple_one_loop_fold_tree(), protocols::antibody_legacy::simple_one_loop_fold_tree(), protocols::protein_interface_design::star_fold_tree(), core::conformation::symmetry::symmetrize_fold_tree(), protocols::splice::Splice::tail_fold_tree(), and protocols::hybridization::HybridizeFoldtreeDynamic::update().
◆ clone()
|
inline |
Referenced by protocols::docking::calc_CA_Irmsd(), protocols::docking::calc_Fnat(), protocols::symmetric_docking::SymDockProtocol::calc_fnat(), protocols::docking::calc_Fnonnat(), protocols::docking::calc_Irmsd(), protocols::docking::calc_Irmsd_legacy(), protocols::abinitio::AbrelaxApplication::fold(), protocols::splice::min_seg(), and protocols::enzdes::EnzdesFlexibleRegion::minimize_region().
◆ connected()
| 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
Referenced by core::kinematics::get_foldtree_which_partitions(), protocols::jumping::remove_cut(), and protocols::ligand_docking::LigandBaseProtocol::reorder_foldtree_around_mobile_regions().
◆ count_fixed_residues()
◆ cut_edge()
| bool core::kinematics::FoldTree::cut_edge | ( | Size const | cut_point | ) |
helper function to try cutting an edge in a tree.
References protocols::loops::cut_point, protocols::mean_field::max(), protocols::mean_field::min(), protocols::make_rot_lib::PEPTIDE, protocols::loops::start, protocols::loops::stop, and TR().
◆ cut_random_edge()
|
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().
◆ cutpoint()
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::topology_broker::TopologyBroker::apply(), protocols::loop_grower::LoopGrower::apply(), protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspots::apply(), protocols::RBSegmentRelaxImpl::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(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::determine_loop(), core::energy_methods::DistanceChainbreakEnergy::finalize_total_energy(), protocols::abinitio::find_sampling_cuts(), core::fragment::FindBoundaries(), protocols::abinitio::AbrelaxApplication::fold(), core::conformation::symmetry::get_component_contiguous_foldtree(), core::kinematics::TreeVizBuilder::get_ft_node_bounds(), protocols::environment::inherit_cuts(), protocols::topology_broker::TopologyBroker::initialize_cuts(), core::scoring::motif::Xfrag::insert(), protocols::medal::invalidate_residues_spanning_cuts(), protocols::fold_from_loops::movers::NubInitioLoopClosureMover::make_cutpoints_coherent_to_foldtree(), 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(), protocols::jumping::MembraneJump::rt_templates(), core::import_pose::RNA_JumpMover::sample_alternative_chain_connection(), core::fragment::steal_constant_length_frag_set_from_pose(), protocols::rigid::RigidBodyMotionMover::update_chunks(), and protocols::nonlocal::BiasedFragmentMover::verify_probabilities_or_die().
◆ cutpoint_by_jump()
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::docking::InterfaceSidechainMinMover::apply(), protocols::loop_grower::LoopGrower::apply(), protocols::simple_task_operations::DockingNoRepack1::apply(), protocols::simple_task_operations::DockingNoRepack2::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().
◆ cutpoint_map()
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().
◆ cutpoints()
| 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::CAcstGenerator::apply(), protocols::seeded_abinitio::GrowPeptides::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::loophash::BackboneSegment::apply_to_pose(), protocols::symmetric_docking::SymDockProtocol::calc_fnat(), protocols::symmetric_docking::SymDockProtocol::calc_Irms(), protocols::peptide_deriver::PeptideDeriverFilter::derive_peptide(), protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockMoveRbJumpMover::find_new_jump_residue(), core::pose::symmetry::find_new_symmetric_jump_residues(), protocols::electron_density::findLoopFromDensity(), core::environment::FoldTreeSketch::FoldTreeSketch(), protocols::topology_broker::AsymFoldandDockClaimer::generate_claims(), protocols::topology_broker::FibrilModelingClaimer::generate_claims(), protocols::topology_broker::FoldandDockClaimer::generate_claims(), protocols::loophash::get_rt_over_leap(), 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(), protocols::rbsegment_relax::setup_pose_rbsegs_keep_loops(), and core::conformation::symmetry::symmetrize_fold_tree().
◆ delete_edge() [1/2]
| 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().
◆ delete_edge() [2/2]
| 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::fold_from_loops::movers::NubInitioLoopClosureMover::apply_closure_trust(), protocols::denovo_design::components::FoldGraph::fold_tree(), protocols::denovo_design::insert_peptide_edges(), protocols::forge::methods::merge(), protocols::forge::build::SegmentInsert::modify_impl(), protocols::forge::build::SegmentRebuild::modify_impl(), protocols::forge::methods::replace(), and protocols::anchored_design::AnchoredDesignMover::set_fold_tree_and_cutpoints().
◆ delete_extra_vertices()
| 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::fold_from_loops::movers::NubInitioLoopClosureMover::apply_closure_trust(), protocols::denovo_design::components::FoldGraph::fold_tree(), protocols::enzdes::EnzdesFlexibleRegion::minimize_region(), protocols::jumping::remove_cut(), protocols::ligand_docking::LigandBaseProtocol::reorder_foldtree_around_mobile_regions(), and protocols::denovo_design::symmetric_fold_tree().
◆ delete_jump_and_intervening_cutpoint() [1/2]
| 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()
◆ delete_jump_and_intervening_cutpoint() [2/2]
| 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::fold_from_loops::movers::NubInitioLoopClosureMover::make_final_tree(), 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().
◆ delete_jump_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(), protocols::loops::start, core::kinematics::Edge::stop(), protocols::loops::stop, TR(), and core::kinematics::Edge::valid().
◆ delete_segment()
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().
◆ delete_self_edges()
| 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::protein_interface_design::movers::SetAtomTree::apply(), protocols::analysis::LoopAnalyzerMover::calculate_all_chainbreaks(), protocols::splice::Splice::fold_tree(), protocols::splice::SpliceManager::fold_tree(), protocols::splice::RBOutMover::get_disulf_jump(), protocols::protein_interface_design::make_hotspot_foldtree(), protocols::protein_interface_design::movers::PlaceStubMover::place_stub(), protocols::forge::methods::replace(), protocols::protein_interface_design::movers::SetAtomTree::set_ab_fold_tree(), protocols::splice::RBInMover::set_fold_tree(), protocols::splice::Splice::set_fold_tree(), and protocols::docking::setup_foldtree().
◆ delete_seqpos()
| 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().
◆ delete_seqpos_simple()
|
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().
◆ delete_unordered_edge()
| 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().
Referenced by protocols::antibody_legacy::AntibodyModeler::all_cdr_VL_VH_fold_tree(), protocols::metal_interface::ZincHeterodimerMover::apply(), protocols::jumping::remove_cut(), and protocols::splice::Splice::tail_fold_tree().
◆ downstream_atom()
| 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(), protocols::stepwise::modeler::fix_protein_jump_atom(), protocols::stepwise::sampler::protein::ProteinBetaAntiParallelStepWiseSampler::get_antiparallel_beta_jumps(), core::conformation::symmetry::get_component_contiguous_foldtree(), protocols::stepwise::modeler::get_jump_partners_from_pose(), protocols::recces::sampler::rna::MC_RNA_OneJump::MC_RNA_OneJump(), protocols::stepwise::legacy::modeler::rna::output_fold_tree_info(), protocols::rna::denovo::movers::RNA_Minimizer::setup_movemap(), protocols::stepwise::modeler::slice(), and protocols::magnesium::update_mg_hoh_fold_tree().
◆ downstream_jump_residue()
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
Referenced by core::import_pose::RNA_JumpMover::add_new_RNA_jump(), protocols::abinitio::LoopJumpFoldCst::add_rigidity_jumps(), protocols::abinitio::MembraneAbinitio::add_spanning_region(), protocols::enzdes::PredesignPerturbMover::apply(), protocols::indel::IndelOptimizationMover::apply(), protocols::membrane::FlipMover::apply(), core::select::jump_selector::InterchainJumpSelector::apply(), protocols::enzdes::DetectProteinLigandInterface::apply(), protocols::jumping::JumpSample::apply_to(), core::optimization::symmetry::atom_tree_get_atompairE_deriv(), protocols::scoring::Interface::calculate(), protocols::simple_ddg::ddG::calculate(), core::import_pose::libraries::ChunkSet::check_fold_tree_OK(), protocols::simple_filters::InterfaceHbondsFilter::compute_hbonds(), 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::topology_broker::AsymFoldandDockClaimer::docking_jump(), protocols::toolbox::rigid_body::figure_out_moving_partition_res(), protocols::stepwise::modeler::figure_out_moving_partition_res_for_jump(), protocols::stepwise::modeler::working_parameters::figure_out_rebuild_bulge_mode(), protocols::toolbox::rigid_body::figure_out_reference_res_for_jump(), core::pose::rna::fill_in_default_jump_atoms(), protocols::enzdes::SecondaryMatchProtocol::find_all_allowed_positions(), protocols::ligand_docking::find_attach_pt(), protocols::stepwise::modeler::find_jump_number_at_suite(), protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockMoveRbJumpMover::find_new_jump_residue(), core::pose::symmetry::find_new_symmetric_jump_residues(), core::pose::symmetry::find_symmetric_basejump_anchor(), protocols::stepwise::modeler::fix_protein_jump_atom(), core::conformation::symmetry::fold_tree_entry_point(), core::environment::FoldTreeSketch::FoldTreeSketch(), protocols::loop_grower::SheetSampler::generate_jump_frags(), protocols::jumping::JumpSample::generate_jump_frags(), protocols::jumping::JumpSample::generate_jump_frames(), protocols::stepwise::modeler::rna::get_anchor_res(), core::import_pose::get_anchor_rsd(), protocols::stepwise::sampler::protein::ProteinBetaAntiParallelStepWiseSampler::get_antiparallel_beta_jumps(), core::pose::get_chain_from_jump_id(), core::pose::get_chain_id_from_jump_id(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_docking_split_move_elements(), core::kinematics::TreeVizBuilder::get_ft_node_subroot(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_intramolecular_split_move_elements(), core::pose::get_jump_ids_from_chain(), core::pose::get_jump_ids_from_chain_ids(), core::kinematics::TreeVizBuilder::get_jump_num_to_contig_of_resi(), protocols::stepwise::modeler::get_jump_partners_from_pose(), protocols::ligand_docking::LigandBaseProtocol::get_ligand_id(), protocols::hybridization::InsertChunkMover::get_local_sequence_mapping(), protocols::magnesium::MgMinimizer::get_mg_hoh_minimize_move_map(), core::pose::rna::get_rigid_body_jumps(), protocols::recces::sampler::initialize_sampler(), core::scoring::motif::Xfrag::insert(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::insert_base_pair_jumps(), protocols::hybridization::HybridizeFoldtreeDynamic::jumps_and_cuts_from_foldtree(), protocols::forge::methods::jumps_and_cuts_from_pose(), protocols::stepwise::modeler::look_for_unique_jump_to_moving_res(), core::optimization::symmetry::SymAtomTreeMinimizer::make_asymmetric_movemap(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::make_pose(), core::pose::symmetry::make_symmetric_movemap(), protocols::recces::sampler::rna::MC_RNA_OneJump::MC_RNA_OneJump(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::minimize_sugar(), protocols::rna::movers::ErraserMinimizerMover::movemap_setup(), protocols::stepwise::modeler::output_movemap(), protocols::hybridization::ChunkTrialMover::pick_random_chunk(), core::import_pose::put_in_cutpoint(), core::import_pose::RNA_JumpMover::random_jump_change(), protocols::rna::denovo::movers::RNA_DeNovoMasterMover::randomize_rnp_rigid_body_orientations(), core::conformation::symmetry::SymmetricConformation::recalculate_transforms(), core::import_pose::remove_cutpoint_closed(), protocols::ligand_docking::LigandBaseProtocol::reorder_foldtree_around_mobile_regions(), protocols::simple_ddg::AlaScan::report(), core::kinematics::residues_downstream_of_jump(), core::import_pose::RNA_BasePairHandler::RNA_BasePairHandler(), core::import_pose::RNA_JumpMover::sample_alternative_chain_connection(), core::pose::symmetry::sealed_symmetric_fold_tree(), protocols::rna::denovo::movers::RNA_DeNovoMasterMover::search_rigid_body_orientation(), protocols::hybridization::InsertChunkMover::set_bb_xyz_aligned(), core::conformation::symmetry::SymmetricConformation::set_dof(), protocols::rna::denovo::movers::RNA_HelixMover::set_pose(), protocols::analysis::InterfaceAnalyzerMover::set_pose_info(), protocols::hydrate::set_task_and_movemap(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::setup_fold_tree(), protocols::rna::denovo::coarse::MultipleDomainMover::setup_jump_numbers_and_partner(), protocols::rna::denovo::movers::RNA_Minimizer::setup_movemap(), protocols::rna::denovo::movers::RNA_DeNovoMasterMover::setup_rna_protein_docking_mover(), protocols::stepwise::modeler::slice(), protocols::membrane::split_topology_by_jump_noshift(), core::pose::swap_transform(), core::conformation::symmetry::symmetrize_fold_tree(), protocols::rna::denovo::coarse::MultipleDomainMover::try_to_slide_into_contact(), core::import_pose::update_fixed_domain_from_extra_minimize_jump_pairs(), protocols::magnesium::update_jump_atoms_for_mg_bound_water(), protocols::magnesium::update_mg_hoh_fold_tree(), protocols::environment::CoMTrackerCM::update_tracking_residue(), core::kinematics::visualize_fold_tree(), and protocols::environment::claims::VirtResClaim::yield_elements().
◆ edge_label()
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().
◆ empty()
|
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().
◆ end()
|
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::denovo_design::find_jump_rec(), protocols::forge::build::SegmentInsert::modify_impl(), protocols::forge::build::SegmentRebuild::modify_impl(), core::pose::symmetry::partition_by_symm_jumps(), protocols::forge::methods::replace(), core::pose::set_reasonable_fold_tree(), 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(), protocols::hybridization::FoldTreeHybridize::superimpose_strand_pairings_to_templates(), protocols::hybridization::MRMover::trim_target_pose(), and protocols::hybridization::HybridizeFoldtreeDynamic::update().
◆ get_chemical_edges()
| utility::vector1< Edge > core::kinematics::FoldTree::get_chemical_edges | ( | ) | const |
Returns all chemical edges from fold tree.
Referenced by protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_intramolecular_split_move_elements(), protocols::docking::setup_foldtree(), protocols::glycopeptide_docking::setup_glycosylation_foldtree(), and core::kinematics::visualize_fold_tree().
◆ get_jump_edges()
| 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.
Referenced by protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::EntropyEstimator(), protocols::ligand_docking::ga_ligand_dock::get_ligand_jumpid(), protocols::fold_from_loops::movers::DisplayPoseLabelsMover::is_nubinitio_tree(), protocols::docking::setup_foldtree(), and protocols::glycopeptide_docking::setup_glycosylation_foldtree().
◆ get_jump_that_builds_residue()
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(), protocols::simple_filters::BuriedUnsatHbondFilter::compute(), 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::GALigandDock::final_exact_cartmin(), core::pose::symmetry::find_new_symmetric_jump_residues(), 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(), core::pose::symmetry::rotate_anchor_to_x_axis(), protocols::enzdes::RepackLigandSiteWithoutLigandMover::separate_protein_and_ligand(), protocols::stepwise::monte_carlo::mover::AddMover::setup_initial_jump(), protocols::stepwise::monte_carlo::mover::ResampleMover::slide_jump_randomly(), and protocols::magnesium::update_jump_atoms_for_mg_bound_water().
◆ get_outgoing_edges()
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::create_minimize_pose_into_density_options(), protocols::electron_density::dockPoseIntoMap(), protocols::hybridization::downstream_residues_from_jump(), core::energy_methods::ElecDensAllAtomCenEnergy::eval_atom_derivative(), core::energy_methods::ElecDensCenEnergy::eval_atom_derivative(), core::energy_methods::ElecDensEnergy::eval_atom_derivative(), core::energy_methods::FastDensEnergy::eval_residue_pair_derivatives(), and core::conformation::get_residue_connections().
◆ get_parent_residue() [1/2]
Get the residue that is immediately upstream of this residue.
◆ get_parent_residue() [2/2]
| 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().
Referenced by protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::define_moving_res(), protocols::stepwise::monte_carlo::mover::ensure_appropriate_foldtree_for_move(), protocols::stepwise::modeler::protein::figure_out_protein_modeling_info(), protocols::stepwise::modeler::figure_out_reference_res_for_suite(), protocols::stepwise::modeler::figure_out_root_and_moving_partition_res(), protocols::magnesium::find_bound_waters_that_are_daughters_in_fold_tree(), protocols::stepwise::modeler::find_downstream_connection_res(), protocols::stepwise::modeler::get_domain_boundary_res(), protocols::stepwise::monte_carlo::mover::ResampleMover::get_remodel_res(), protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::moves_for_pose(), protocols::rna::denovo::RNA_FragmentMonteCarlo::reroot_pose_before_align_and_return_moving_res(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::reverse_add_move(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::reverse_add_submotif_move(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::reverse_delete_move(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::reverse_resample_move(), protocols::stepwise::modeler::revise_root_and_moving_res(), protocols::stepwise::modeler::revise_root_and_moving_res_list(), protocols::stepwise::monte_carlo::mover::AddMover::setup_initial_jump(), protocols::magnesium::MgHydrater::setup_virtual_waters_around_magnesiums(), protocols::stepwise::modeler::working_parameters::setup_working_parameters_explicit(), protocols::stepwise::modeler::working_parameters::setup_working_parameters_for_swa(), protocols::stepwise::modeler::split_pose(), and protocols::loop_grower::LoopGrower::store_sheets().
◆ get_polymer_residue_direction()
| 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.
◆ get_residue_edge()
Returns the edge that builds the residue <seqpos> Does not work for root atom (will fail)
Referenced by protocols::fold_from_loops::movers::NubInitioLoopClosureMover::apply_closure_trust(), boundary_left(), boundary_right(), protocols::ligand_docking::MoveMapBuilder::build(), core::conformation::build_residue_tree(), protocols::stepwise::modeler::check_jump_to_next_residue_in_chain(), protocols::stepwise::modeler::check_jump_to_previous_residue_in_chain(), protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::default_target_icoors(), protocols::stepwise::monte_carlo::mover::ensure_appropriate_foldtree_for_move(), core::energy_methods::ElecDensAllAtomCenEnergy::eval_atom_derivative(), core::energy_methods::ElecDensCenEnergy::eval_atom_derivative(), core::energy_methods::ElecDensEnergy::eval_atom_derivative(), core::energy_methods::FastDensEnergy::eval_residue_pair_derivatives(), protocols::stepwise::modeler::movemap::figure_out_stepwise_movemap(), core::conformation::get_anchor_atomno(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_intramolecular_split_move_elements(), core::conformation::get_residue_connections(), core::conformation::symmetry::SymmetricConformation::get_upstream_vrt(), protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::init_apply(), protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_generic_polymer_bond_sampler(), protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_protein_bond_sampler(), protocols::stepwise::modeler::make_cut_at_moving_suite(), protocols::ligand_docking::LigandBaseProtocol::make_movemap(), protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::prepare_foldtree(), core::conformation::replace_residue_in_atom_tree(), core::pose::toolbox::AtomLevelDomainMap::setup_movemap(), and protocols::stepwise::modeler::slice().
◆ hash_value()
| 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().
◆ insert_fold_tree_by_jump()
| 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(), and protocols::denovo_design::symmetric_fold_tree().
◆ insert_polymer_residue()
| 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.
◆ insert_residue_by_chemical_bond()
| 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
◆ insert_residue_by_jump()
| 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?
◆ is_cutpoint()
|
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_.
Referenced by protocols::topology_broker::TopologyBroker::add_chainbreak_variants(), protocols::environment::EnvClaimBroker::add_chainbreak_variants(), protocols::splice::Splice::add_coordinate_constraints(), protocols::splice::SpliceManager::add_coordinate_constraints(), protocols::protein_interface_design::movers::SetAtomTree::add_cutpoint_variants(), protocols::forge::methods::add_cutpoint_variants(), core::import_pose::add_virtual_sugar_res(), core::import_pose::RNA_HelixAssembler::append_Aform_residue(), protocols::grafting::simple_movers::DeleteRegionMover::apply(), protocols::hybridization::CartesianHybridize::apply(), protocols::loop_grower::LoopGrower::apply(), protocols::protein_interface_design::movers::AddChainBreak::apply(), protocols::rbsegment_relax::OptimizeThreadingMover::apply(), protocols::rbsegment_relax::RBSegmentRelax::apply(), protocols::simple_moves::MissingDensityToJumpMover::apply(), protocols::stepwise::modeler::precomputed::PrecomputedLibraryMover::apply(), protocols::fold_from_loops::selectors::CutpointResidueSelector::apply(), protocols::hybridization::CartesianSampler::apply_fragcsts(), protocols::loops::apply_sequence_mapping(), core::pose::rna::apply_virtual_rna_residue_variant_type(), protocols::idealize::basic_idealize(), core::pose::toolbox::AtomID_Mapper::calculate_atom_id_map(), protocols::hybridization::FragmentBiasAssigner::chainbreak(), protocols::topology_broker::TopologyBroker::check_chainbreak_variants(), protocols::rna::denovo::RNA_FragmentMonteCarlo::check_fold_tree_cutpoints_ok(), core::scoring::loop_graph::LoopGraph::check_for_unexpected_cutpoints(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::check_from_scratch(), core::scoring::rna::check_rna_loop(), protocols::jumping::close_chainbreaks(), protocols::score_filters::GeometryFilter::compute(), core::scoring::ResidualDipolarCoupling::compute_dipscore(), core::scoring::ResidualDipolarCoupling::compute_dipscore_nls(), protocols::hybridization::FragmentBiasAssigner::compute_frag_bias(), protocols::loop_grower::LoopGrower::coordinate_filter(), protocols::topology_broker::copy_internal_coords(), protocols::stepwise::modeler::rna::phosphate::copy_over_phosphate_variants(), core::pose::correctly_add_cutpoint_variants(), protocols::forge::methods::count_cutpoints(), protocols::hybridization::create_fragment_set(), protocols::hybridization::create_fragment_set_no_ssbias(), protocols::rna::denovo::create_rna_vall_torsions(), protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::current_closed_as_target(), protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::default_target_icoors(), core::import_pose::define_chains(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::determine_loop(), protocols::stepwise::modeler::align::StepWisePoseAligner::do_checks(), protocols::anchored_design::dump_cutpoint_info(), protocols::cyclic_peptide::dump_debug_output(), protocols::rna::denovo::coarse::CoarseRNA_LoopCloser::figure_out_dof_ids_and_offsets(), protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger::figure_out_loop(), protocols::stepwise::modeler::figure_out_moving_chain_break_res(), protocols::stepwise::modeler::figure_out_moving_chain_breaks(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::figure_out_partition_definition(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::figure_out_Prepend_Internal(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::figure_out_prepend_internal(), protocols::stepwise::modeler::working_parameters::figure_out_rebuild_bulge_mode(), protocols::rna::denovo::coarse::CoarseRNA_LoopCloser::figure_out_which_cutpoints_were_affected(), core::io::silent::BinarySilentStruct::fill_struct(), protocols::forge::methods::find_cutpoint(), protocols::electron_density::findLoopFromDensity(), core::pose::fix_up_residue_type_variants(), protocols::loop_grower::LoopGrower::GDThatonative(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_attachments(), protocols::stepwise::modeler::align::StepWisePoseAligner::get_calc_rms_atom_id_map(), core::import_pose::RNA_HelixAssembler::get_cutpoint(), protocols::rna::denovo::get_default_allowed_bulge_res(), protocols::stepwise::modeler::get_domain_boundary_suites(), protocols::stepwise::modeler::get_endpoints_from_pose(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_intramolecular_add_move_elements(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_intramolecular_split_move_elements(), protocols::stepwise::monte_carlo::submotif::SubMotifLibrary::get_matches_for_one_submotif_sequence_set(), protocols::recces::sampler::get_recces_turner_sampler_from_secstruct(), protocols::recces::sampler::get_recces_turner_sampler_legacy(), protocols::stepwise::monte_carlo::submotif::SubMotifLibrary::get_submotif_sequence_set(), protocols::hybridization::CartesianSampler::get_transform(), protocols::seeded_abinitio::GrowPeptides::grow_from_vertices(), protocols::loops::Loops::grow_loop(), protocols::loops::Loops::grow_loop_away_from_sheets(), protocols::stepwise::modeler::precomputed::PrecomputedLibraryMover::has_precomputed_move(), protocols::seeded_abinitio::SegmentHybridizer::hybridize(), core::conformation::idealize_position(), protocols::abinitio::abscript::RigidChunkCM::initialize(), protocols::nonlocal::SingleFragmentMover::initialize_chunks(), core::import_pose::libraries::BasePairStepLibrary::initialize_data(), protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::initialize_phosphate_move_list(), protocols::recces::sampler::initialize_sampler(), protocols::recces::sampler::initialize_thermal_sampler(), core::conformation::insert_ideal_bonds_at_polymer_junction(), protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::instantiate_sugars_at_cutpoint_closed(), core::pose::rna::is_cutpoint_open(), core::conformation::is_ideal_position(), core::scoring::methods::is_lower_cutpoint(), core::pose::rna::is_torsion_valid(), core::scoring::methods::is_upper_cutpoint(), protocols::forge::methods::linear_chainbreak(), protocols::stepwise::modeler::rna::sugar::look_for_non_jump_reference_to_next(), protocols::stepwise::modeler::rna::sugar::look_for_non_jump_reference_to_previous(), protocols::stepwise::modeler::make_cut_at_moving_suite(), protocols::forge::methods::make_star_foldtree(), core::scoring::electron_density::ElectronDensity::matchRes(), protocols::stepwise::modeler::merge_two_poses(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::model_loop(), protocols::stepwise::sampler::rna::modeler_sugar_at_five_prime(), protocols::stepwise::sampler::rna::modeler_sugar_at_three_prime(), protocols::forge::build::Bridge::modify_impl(), protocols::forge::build::SegmentInsert::modify_impl(), protocols::forge::build::SegmentRebuild::modify_impl(), protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo::output_silent_file(), core::pose::rna::output_stems(), protocols::forge::methods::overlap_chainbreak(), core::pose::pdbslice(), possible_root(), protocols::fold_from_loops::NubInitioMover::post_process(), protocols::stepwise::monte_carlo::mover::TransientCutpointHandler::prepare_fold_tree_for_erraser(), protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::prepare_foldtree(), core::import_pose::RNA_HelixAssembler::prepend_Aform_residue(), protocols::forge::methods::quadratic_chainbreak(), protocols::rbsegment_relax::OptimizeThreadingMover::rebuild_unaligned(), protocols::loop_grower::LoopGrower::refine_cycle(), protocols::jumping::remove_cut(), protocols::forge::methods::remove_cutpoint(), core::util::remove_cutpoint_variants(), protocols::forge::methods::remove_cutpoint_variants(), core::import_pose::remove_cutpoints_closed(), protocols::electron_density::remove_occupied_density_from_density(), protocols::features::ProteinBondGeometryFeatures::report_interres_angles(), protocols::features::ProteinBondGeometryFeatures::report_interres_lengths(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::reverse_delete_move(), protocols::loop_grower::LoopGrower::RMStonative(), core::import_pose::RNA_BasePairHandler::RNA_BasePairHandler(), protocols::moves::PyMOLMover::send_foldtree(), protocols::recces::set_gaussian_stdevs_recces_turner_from_secstruct(), protocols::recces::set_gaussian_stdevs_recces_turner_legacy(), protocols::loops::set_loop_cutpoint_in_pose_fold_tree(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_chainbreak_variants(), core::import_pose::setup_fold_trees(), protocols::stepwise::modeler::working_parameters::setup_working_parameters_explicit(), 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::stepwise::modeler::slice(), protocols::stepwise::modeler::split_pose(), protocols::loop_grower::transform_to_closest_symmunit(), protocols::hybridization::MRMover::trim_target_pose(), core::import_pose::libraries::RNA_ChunkLibrary::update_atom_level_domain_map(), protocols::rna::denovo::movers::RNA_Minimizer::update_atom_level_domain_map_with_extra_minimize_res(), protocols::rna::denovo::movers::RNA_FragmentMover::update_insert_map(), protocols::magnesium::update_mg_hoh_fold_tree(), core::pose::rna::virtualize_5prime_phosphates(), and core::pose::rna::virtualize_free_rna_moieties().
◆ is_equivalent()
| 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 protocols::match::upstream::b.
◆ is_jump_point()
|
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::simple_moves::PeptideStapleMover::apply(), protocols::protein_interface_design::movers::LoopLengthChange::apply(), core::fragment::DownJumpSRFD::apply(), core::conformation::membrane::MembraneInfo::check_membrane_fold_tree(), protocols::jumping::close_chainbreaks(), protocols::score_filters::GeometryFilter::compute(), protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::default_target_icoors(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::determine_loop(), core::import_pose::atom_tree_diffs::dump_atom_tree_diff(), protocols::cyclic_peptide::dump_debug_output(), protocols::cyclic_peptide::CrosslinkerMover::get_jump_index_for_crosslinker(), protocols::cyclic_peptide::CrosslinkerMover::get_jump_indices_for_symmetric_crosslinker(), core::conformation::get_root_residue_root_atomno(), protocols::simple_filters::SSElementMotifContactFilter::get_SSelements_in_contact(), core::scoring::motif::Xfrag::insert(), protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::prepare_foldtree(), core::kinematics::remodel_fold_tree_to_account_for_insertion(), protocols::jumping::remove_cut(), 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(), and protocols::loop_grower::LoopGrower::store_sheets().
◆ is_root()
|
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(), edge_list_, and protocols::loops::start.
Referenced by core::energy_methods::ElecDensAllAtomCenEnergy::eval_atom_derivative(), core::energy_methods::ElecDensCenEnergy::eval_atom_derivative(), core::energy_methods::ElecDensEnergy::eval_atom_derivative(), core::energy_methods::FastDensEnergy::eval_residue_pair_derivatives(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_exact_cartmin(), 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(), protocols::fold_from_loops::movers::DisplayPoseLabelsMover::simple_visualize_fold_tree(), and protocols::stepwise::modeler::slice().
◆ is_simple_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().
◆ jump_edge() [1/2]
Returns the jump edge with jump number <jump_number> (non-const)
◆ jump_edge() [2/2]
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::cryst::UpdateCrystInfo::apply(), protocols::protein_interface_design::movers::SpinMover::apply(), protocols::rigid::RotateJumpAxisMover::apply(), protocols::seeded_abinitio::CoordinateCst::apply(), protocols::topology_broker::RigidBodyRandomTMHMover::apply(), protocols::denovo_design::movers::RotateSegmentMover::apply(), core::select::residue_selector::JumpDownstreamSelector::apply(), protocols::fold_from_loops::movers::NubInitioLoopClosureMover::apply_closure_trust(), core::kinematics::inverse::assert_atoms_are_downstream_of_jump(), core::kinematics::inverse::assert_atoms_are_upstream_of_jump(), core::optimization::symmetry::SymMinimizerMap::asymmetric_dof(), core::kinematics::ShortestPathInFoldTree::build_jumpres_distmap(), protocols::hybridization::downstream_residues_from_jump(), core::energy_methods::ElecDensAllAtomCenEnergy::eval_atom_derivative(), core::energy_methods::ElecDensCenEnergy::eval_atom_derivative(), core::energy_methods::ElecDensEnergy::eval_atom_derivative(), core::energy_methods::FastDensEnergy::eval_residue_pair_derivatives(), core::io::silent::BinarySilentStruct::fill_pose(), protocols::forge::methods::find_connecting_jump(), 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::fold_from_loops::movers::NubInitioLoopClosureMover::make_cutpoints_coherent_to_foldtree(), protocols::fold_from_loops::movers::NubInitioLoopClosureMover::make_final_tree(), protocols::forge::build::SegmentInsert::modify_impl(), protocols::forge::build::SegmentRebuild::modify_impl(), protocols::topology_broker::TMHTopologySamplerClaimer::move_spans(), protocols::glycan_docking::GlycanDockProtocol::record_pose_metrics(), protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue(), protocols::jumping::safe_secstruct(), 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(), protocols::denovo_design::symmetric_fold_tree(), and core::pose::transfer_jumps().
◆ jump_exists()
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().
◆ jump_nr()
|
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().
Referenced by protocols::stepwise::monte_carlo::mover::AddMover::append_residue(), protocols::fold_from_loops::movers::NubInitioLoopClosureMover::apply_closure_trust(), protocols::stepwise::modeler::check_jump_to_next_residue_in_chain(), protocols::stepwise::modeler::check_jump_to_previous_residue_in_chain(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::define_moving_res(), protocols::stepwise::modeler::working_parameters::figure_out_rebuild_bulge_mode(), protocols::stepwise::modeler::figure_out_root_and_moving_partition_res(), protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::get_base_atr_rep_score(), core::import_pose::get_tree(), protocols::topology_broker::TopologyBroker::initialize_dofs(), protocols::stepwise::modeler::rna::sugar::look_for_jumps_to_next(), protocols::stepwise::modeler::rna::sugar::look_for_jumps_to_previous(), core::optimization::symmetry::SymAtomTreeMinimizer::make_asymmetric_movemap(), protocols::stepwise::monte_carlo::mover::TransientCutpointHandler::prepare_fold_tree_for_erraser(), protocols::stepwise::monte_carlo::mover::AddMover::prepend_residue(), protocols::stepwise::legacy::modeler::rna::remove_chain_break_jump_point(), protocols::rna::denovo::RNA_FragmentMonteCarlo::reroot_pose_before_align_and_return_moving_res(), protocols::stepwise::modeler::revise_root_and_moving_res_list(), protocols::stepwise::legacy::modeler::rna::setup_bulge_jump_point(), protocols::stepwise::modeler::working_parameters::setup_working_parameters_for_swa(), protocols::stepwise::modeler::slice(), protocols::stepwise::modeler::split_pose(), core::pose::transfer_jumps(), core::import_pose::update_fixed_domain_from_extra_minimize_jump_pairs(), and protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::virtualize_distal_partition().
◆ jump_point()
| 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(), protocols::stepwise::legacy::modeler::rna::output_fold_tree_info(), protocols::jumping::remove_cut(), and core::import_pose::RNA_JumpMover::sample_alternative_chain_connection().
◆ nc_begin()
|
inlineprivate |
non-const begin iterator of edge_list
References edge_list_.
◆ nc_end()
|
inlineprivate |
non-const end iterator of edge_list
References edge_list_.
◆ new_chemical_bond()
| 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.
Referenced by protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::semiexpl_water_hbgeom_score().
◆ new_jump()
| 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::dna::SeparateDnaFromNonDna::apply(), protocols::frag_picker::nonlocal::NonlocalFrags::apply(), protocols::grafting::simple_movers::DeleteRegionMover::apply(), protocols::hybridization::DomainAssembly::apply(), protocols::protein_interface_design::movers::AddChainBreak::apply(), protocols::simple_moves::ChainSplitMover::apply(), protocols::simple_moves::MissingDensityToJumpMover::apply(), protocols::loops::loop_closure::ccd::ShortLoopClosure::apply(), protocols::simple_moves::FoldTreeFromMotif::apply(), protocols::loops::apply_sequence_mapping(), protocols::idealize::basic_idealize(), core::import_pose::RNA_HelixAssembler::build_init_pose(), protocols::membrane::create_membrane_docking_foldtree_from_partners(), protocols::membrane::create_membrane_foldtree_from_anchors(), protocols::membrane::create_specific_membrane_foldtree(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::figure_out_fold_tree(), core::pose::rna::figure_out_reasonable_rna_fold_tree(), protocols::forge::methods::fold_tree_from_loops(), protocols::stepwise::sampler::protein::generate_beta_database_test(), protocols::enzdes::EnzdesFlexBBProtocol::generate_ensemble_for_region(), protocols::antibody::AntibodyInfo::get_FoldTree_L_HA(), protocols::antibody::AntibodyInfo::get_FoldTree_LA_H(), protocols::antibody::AntibodyInfo::get_FoldTree_LH_A(), core::import_pose::RNA_HelixAssembler::get_rid_of_capping_base_pairs(), protocols::seeded_abinitio::GrowPeptides::grow_from_vertices(), protocols::topology_broker::AsymFoldandDockClaimer::initialize_dofs(), protocols::stepwise::monte_carlo::submotif::SubMotifLibrary::initialize_from_jump_library(), protocols::denovo_design::linear_chainbreak(), protocols::forge::methods::linear_chainbreak(), protocols::stepwise::modeler::make_cut_at_moving_suite(), core::fragment::make_pose_from_frags(), protocols::forge::build::SegmentInsert::modify_impl(), protocols::forge::build::SegmentRebuild::modify_impl(), 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(), protocols::stepwise::monte_carlo::mover::TransientCutpointHandler::prepare_fold_tree_for_erraser(), core::import_pose::put_in_cutpoint(), protocols::forge::methods::quadratic_chainbreak(), protocols::rna::movers::RNA_LoopCloser::rna_ccd_close(), protocols::loops::set_loop_cutpoint_in_pose_fold_tree(), protocols::stepwise::legacy::modeler::rna::setup_bulge_jump_point(), protocols::membrane::setup_foldtree_from_anchors(), protocols::magnesium::MgMonteCarlo::setup_mg_water_fold_tree(), protocols::relax::membrane::MPFastRelaxMover::setup_relax_foldtree(), protocols::relax::RepeatProteinRelax::setup_repeat_pose_jumping(), and protocols::fldsgn::CircularPermutation::split_chains().
◆ nres()
|
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::loops::loop_closure::ccd::SlidingWindowLoopClosure::determine_loop(), 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(), core::conformation::symmetry::get_component_contiguous_foldtree(), core::kinematics::get_foldtree_which_partitions(), core::kinematics::TreeVizBuilder::get_ft_node_bounds(), core::kinematics::TreeVizBuilder::get_res_nodenames(), core::scoring::motif::Xfrag::insert(), insert_fold_tree_by_jump(), core::conformation::insert_residue_into_atom_tree(), core::kinematics::jump_which_partitions(), protocols::forge::methods::merge(), core::import_pose::atom_tree_diffs::pose_from_atom_tree_diff(), possible_root(), core::import_pose::read_additional_pdb_data(), protocols::backrub::read_fold_tree_from_file(), protocols::jumping::remove_cut(), protocols::forge::methods::remove_cutpoint(), protocols::forge::methods::remove_cutpoints(), protocols::environment::Environment::remove_nonpermenant_features(), protocols::ligand_docking::LigandBaseProtocol::reorder_foldtree_around_mobile_regions(), 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(), core::kinematics::TreeVizBuilder::TreeVizBuilder(), protocols::hybridization::HybridizeFoldtreeDynamic::update(), and core::kinematics::visualize_fold_tree().
◆ num_cutpoint()
|
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::abinitio::MembraneAbinitio::add_spanning_region(), protocols::topology_broker::TopologyBroker::apply(), protocols::loop_grower::LoopGrower::apply(), protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspots::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(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::determine_loop(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::figure_out_is_residue_prepend(), core::energy_methods::DistanceChainbreakEnergy::finalize_total_energy(), protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockMoveRbJumpMover::find_new_jump_residue(), core::pose::symmetry::find_new_symmetric_jump_residues(), protocols::abinitio::find_sampling_cuts(), core::fragment::FindBoundaries(), protocols::abinitio::AbrelaxApplication::fold(), core::conformation::symmetry::get_component_contiguous_foldtree(), core::kinematics::TreeVizBuilder::get_ft_node_bounds(), protocols::forge::remodel::RemodelLoopMover::independent_stage(), protocols::environment::inherit_cuts(), protocols::medal::invalidate_residues_spanning_cuts(), protocols::denovo_design::linear_chainbreak(), protocols::forge::methods::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::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().
◆ num_jump()
|
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_.
Referenced by protocols::cryst::MakeLatticeMover::add_monomers_to_lattice(), protocols::cryst::MakeLayerMover::add_monomers_to_layer(), protocols::abinitio::LoopJumpFoldCst::add_rigidity_jumps(), protocols::denovo_design::components::add_to_pose(), protocols::antibody_legacy::AntibodyModeler::all_cdr_VL_VH_fold_tree(), protocols::cryst::MakeLatticeMover::apply(), protocols::cryst::MakeLayerMover::apply(), protocols::indel::IndelOptimizationMover::apply(), protocols::loop_grower::LoopGrower::apply(), protocols::magnesium::MgMonteCarlo::apply(), protocols::membrane::AddMembraneMover::apply(), core::select::jump_selector::JumpIndexSelector::apply(), protocols::simple_ddg::ddG::apply(), protocols::splice::Splice::apply(), protocols::splice::SpliceOut::apply(), protocols::enzdes::DetectProteinLigandInterface::apply(), protocols::jumping::JumpSample::apply_to(), protocols::topology_broker::TMHTopologySamplerClaimer::build_fold_tree(), core::kinematics::ShortestPathInFoldTree::build_jumpres_distmap(), protocols::cryst::MakeLatticeMover::build_lattice_of_virtuals(), protocols::cryst::MakeLayerMover::build_layer_of_virtuals(), protocols::ligand_docking::MinimizeBackbone::create_fold_tree_with_ligand_jumps_from_attach_pts(), protocols::topology_broker::AsymFoldandDockClaimer::docking_jump(), protocols::abinitio::KinematicAbinitio::dump_jump_log(), protocols::toolbox::rigid_body::figure_out_moving_partition_res(), protocols::stepwise::modeler::working_parameters::figure_out_rebuild_bulge_mode(), protocols::toolbox::rigid_body::figure_out_reference_res_for_jump(), core::pose::rna::fill_in_default_jump_atoms(), protocols::loop_grower::LoopComparator::fill_pose(), core::io::silent::BinarySilentStruct::fill_pose(), core::io::silent::RNA_SilentStruct::fill_pose(), core::io::silent::ScoreJumpFileSilentStruct::fill_pose(), core::io::silent::BinarySilentStruct::fill_struct(), core::io::silent::RNA_SilentStruct::fill_struct(), core::io::silent::ScoreJumpFileSilentStruct::fill_struct(), protocols::forge::methods::find_connecting_jump(), protocols::stepwise::modeler::find_jump_number_at_suite(), protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockMoveRbJumpMover::find_new_jump_residue(), core::pose::symmetry::find_new_symmetric_jump_residues(), core::pose::symmetry::find_symmetric_basejump_anchor(), protocols::stepwise::modeler::fix_protein_jump_atom(), core::conformation::symmetry::SymmetricConformation::fold_tree(), protocols::denovo_design::components::FoldGraph::fold_tree(), core::conformation::symmetry::fold_tree_entry_point(), protocols::loops::fold_tree_from_loops(), protocols::denovo_design::components::FoldGraph::fold_tree_rec(), core::environment::FoldTreeSketch::FoldTreeSketch(), protocols::topology_broker::MembraneTopologyClaimer::generate_claims(), protocols::stepwise::sampler::protein::ProteinBetaAntiParallelStepWiseSampler::get_antiparallel_beta_jumps(), core::conformation::symmetry::get_component_contiguous_foldtree(), core::kinematics::get_foldtree_which_partitions(), core::kinematics::TreeVizBuilder::get_ft_node_subroot(), core::kinematics::TreeVizBuilder::get_jump_num_to_contig_of_resi(), protocols::stepwise::modeler::get_jump_partners_from_pose(), protocols::magnesium::MgMinimizer::get_mg_hoh_minimize_move_map(), core::conformation::get_root_residue_root_atomno(), core::io::silent::ProteinSilentStruct_Template< T >::init_from_lines(), core::io::silent::RigidBodySilentStruct::init_from_lines(), core::io::silent::RNA_SilentStruct::init_from_lines(), core::io::silent::ScoreJumpFileSilentStruct::init_from_lines(), core::io::silent::BinarySilentStruct::init_from_lines(), protocols::topology_broker::AsymFoldandDockClaimer::initialize_dofs(), core::conformation::symmetry::MirrorSymmetricConformation::insert_conformation_by_jump(), core::conformation::symmetry::SymmetricConformation::insert_conformation_by_jump(), insert_fold_tree_by_jump(), protocols::membrane::is_membrane_moveable_by_itself(), protocols::motif_grafting::movers::MotifGraftMover::join_two_poses_by_jump(), jump_exists(), jump_nr(), core::kinematics::jump_which_partitions(), protocols::hybridization::HybridizeFoldtreeDynamic::jumps_and_cuts_from_foldtree(), protocols::forge::methods::jumps_and_cuts_from_pose(), protocols::stepwise::modeler::look_for_unique_jump_to_moving_res(), protocols::fold_from_loops::movers::NubInitioLoopClosureMover::make_cutpoints_coherent_to_foldtree(), protocols::fold_from_loops::movers::NubInitioLoopClosureMover::make_final_tree(), protocols::forge::methods::merge(), protocols::enzdes::EnzdesFlexibleRegion::minimize_region(), protocols::rna::movers::ErraserMinimizerMover::movemap_setup(), protocols::denovo_design::components::num_strands(), core::io::silent::BinarySilentStruct::print_conformation(), core::io::silent::RNA_SilentStruct::print_conformation(), core::io::silent::ScoreJumpFileSilentStruct::print_conformation(), protocols::rna::denovo::movers::RNA_DeNovoMasterMover::randomize_rnp_rigid_body_orientations(), core::io::serialization::read_binary(), core::conformation::symmetry::SymmetricConformation::recalculate_transforms(), protocols::jumping::remove_cut(), core::import_pose::remove_cutpoint_closed(), protocols::environment::Environment::remove_nonpermenant_features(), protocols::ligand_docking::LigandBaseProtocol::reorder_foldtree_around_mobile_regions(), protocols::forge::methods::replace(), protocols::features::PoseConformationFeatures::report_features_implementation(), core::import_pose::RNA_BasePairHandler::RNA_BasePairHandler(), protocols::jumping::safe_secstruct(), core::import_pose::RNA_JumpMover::sample_alternative_chain_connection(), core::pose::symmetry::sealed_symmetric_fold_tree(), protocols::rna::denovo::movers::RNA_DeNovoMasterMover::search_rigid_body_orientation(), protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::semiexpl_water_hbgeom_score(), protocols::moves::PyMOLMover::send_foldtree(), protocols::hydrate::set_task_and_movemap(), 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::ncbb::setup_pert_foldtree(), protocols::simple_moves::PeriodicBoxMover::setup_pose(), protocols::rna::denovo::movers::RNA_DeNovoMasterMover::setup_rna_protein_docking_mover(), core::conformation::symmetry::setup_symmetric_conformation(), core::kinematics::ShortestPathInFoldTree::ShortestPathInFoldTree(), 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::stepwise::modeler::slice(), protocols::denovo_design::slide_jump(), protocols::denovo_design::symmetric_fold_tree(), core::conformation::symmetry::symmetrize_fold_tree(), core::conformation::symmetry::MirrorSymmetricConformation::synch_mirror_jumps_with_atomtree(), protocols::splice::Splice::tail_fold_tree(), protocols::magnesium::update_mg_hoh_fold_tree(), core::kinematics::visualize_fold_tree(), and protocols::environment::claims::VirtResClaim::yield_elements().
◆ operator=()
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.
◆ partition_by_jump() [1/3]
| 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.
◆ partition_by_jump() [2/3]
| 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(), core::select::residue_selector::JumpDownstreamSelector::apply(), core::select::residue_selector::JumpUpstreamSelector::apply(), protocols::simple_task_operations::RestrictToInterface::apply(), protocols::protein_interface_design::movers::BackrubDDMover::apply(), protocols::protein_interface_design::movers::DesignMinimizeHbonds::apply(), protocols::rna::denovo::coarse::CoarseRNA_LoopCloser::apply_after_jump_change(), protocols::simple_filters::EnergyPerResidueFilter::apply_helper(), core::kinematics::inverse::assert_atoms_are_downstream_of_jump(), core::kinematics::inverse::assert_atoms_are_upstream_of_jump(), 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::scoring::Interface::calculate(), protocols::geometry::centroids_by_jump(), protocols::geometry::centroids_by_jump_int(), protocols::protein_interface_design::filters::AtomicContactCountFilter::compute(), protocols::matdes::InterfacePackingFilter::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(), protocols::enzdes::LigInterfaceEnergyFilter::report(), 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().
◆ partition_by_jump() [3/3]
| 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.
◆ partition_by_residue()
| 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::rna::StepWiseWorkingParametersSetup::figure_out_partition_definition(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::figure_out_partition_definition(), protocols::stepwise::modeler::get_partition_definition(), and protocols::stepwise::modeler::get_partition_definition_by_chemical_edge().
◆ partition_coloring()
| 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.
◆ possible_root()
|
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::stepwise::modeler::get_possible_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().
◆ prepend_edge()
| 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
◆ put_jump_stubs_intra_residue()
| 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().
◆ random_tree_from_jump_points() [1/2]
| 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().
◆ random_tree_from_jump_points() [2/2]
| 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.
◆ reassign_atoms_for_intra_residue_stubs()
| 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(), protocols::stepwise::sampler::protein::generate_beta_database_test(), core::import_pose::get_tree(), and protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::make_pose().
◆ renumber_jumps()
| 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::fold_from_loops::movers::NubInitioLoopClosureMover::apply_closure_trust(), protocols::fold_from_loops::movers::NubInitioLoopClosureMover::make_final_tree(), protocols::jumping::remove_cut(), protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue(), protocols::docking::setup_foldtree(), and protocols::hybridization::MRMover::trim_target_pose().
◆ renumber_jumps_ordered()
| 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().
◆ reorder()
| 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().
Referenced by protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::add_aa_virt_rsd_as_root(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::add_aa_virt_rsd_as_root(), protocols::fold_from_loops::utils::Nub::add_binders(), protocols::membrane::symmetry::SymmetricAddMembraneMover::add_membrane_virtual(), protocols::cryst::MakeLatticeMover::add_monomers_to_lattice(), protocols::cryst::MakeLayerMover::add_monomers_to_layer(), protocols::abinitio::LoopJumpFoldCst::add_rigidity_jumps(), protocols::denovo_design::components::add_to_pose(), protocols::toolbox::sample_around::add_virtual_res(), protocols::rna::movers::ErraserMinimizerMover::add_virtual_res(), core::pose::addVirtualResAsRoot(), protocols::topology_broker::MembraneTopologyClaimer::addVirtualResAsRootMembrane(), protocols::antibody_legacy::Antibody::all_cdr_fold_tree(), protocols::antibody_legacy::AntibodyModeler::all_cdr_VL_VH_fold_tree(), protocols::chemically_conjugated_docking::UBQ_GTPaseMover::analyze_and_filter(), protocols::loop_grower::LoopGrower::apply(), protocols::membrane::AddMPLigandMover::apply(), protocols::membrane::FlipMover::apply(), protocols::membrane::OptimizeMembranePositionMover::apply(), protocols::membrane::OptimizeProteinEmbeddingMover::apply(), protocols::membrane::TransformIntoMembraneMover::apply(), protocols::metal_interface::ZincHeterodimerMover::apply(), protocols::protein_interface_design::movers::SetAtomTree::apply(), protocols::rna::movers::RNAThreadAndMinimizeMover::apply(), protocols::simple_moves::SetTorsion::apply(), protocols::simple_moves::SwitchChainOrderMover::apply(), protocols::docking::membrane::MPDockingMover::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::idealize::IdealizeMover::apply(), protocols::membrane::MembranePositionFromTopologyMover::apply(), protocols::relax::membrane::MPRangeRelaxMover::apply(), protocols::simple_moves::FoldTreeFromMotif::apply(), protocols::loops::apply_sequence_mapping(), protocols::loophash::BackboneSegment::apply_to_pose(), protocols::metal_interface::MatchGrafter::build_combined_pose_with_zinc_overlay(), protocols::analysis::LoopAnalyzerMover::calculate_all_chainbreaks(), protocols::membrane::create_membrane_docking_foldtree_from_partners(), protocols::membrane::create_membrane_foldtree_from_anchors(), protocols::membrane::create_specific_membrane_foldtree(), protocols::stepwise::monte_carlo::mover::ensure_appropriate_foldtree_for_move(), protocols::loophash::LoopHashLibrary::extract_data_from_pose(), protocols::docking::membrane::QuickRelaxPartnersSeparately::finalize_setup(), protocols::relax::RangeRelaxMover::finalize_setup(), protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockMoveRbJumpMover::find_new_jump_residue(), core::pose::symmetry::find_new_symmetric_jump_residues(), protocols::splice::Splice::fold_tree(), protocols::splice::SpliceManager::fold_tree(), protocols::loops::fold_tree_from_loops(), protocols::forge::methods::fold_tree_from_pose(), core::conformation::symmetry::get_component_contiguous_foldtree(), protocols::splice::RBOutMover::get_disulf_jump(), protocols::antibody::AntibodyInfo::get_FoldTree_L_HA(), protocols::antibody::AntibodyInfo::get_FoldTree_LA_H(), protocols::antibody::AntibodyInfo::get_FoldTree_LH_A(), core::kinematics::get_foldtree_which_partitions(), core::import_pose::RNA_HelixAssembler::get_rid_of_capping_base_pairs(), protocols::rna::denovo::get_rnp_docking_fold_tree(), protocols::loophash::get_rt_over_leap(), protocols::loophash::get_rt_over_leap_fast(), core::scoring::motif::Xfrag::insert(), protocols::grafting::insert_pose_into_pose(), protocols::protein_interface_design::make_hotspot_foldtree(), protocols::forge::methods::make_star_foldtree(), protocols::forge::methods::merge(), protocols::stepwise::modeler::merge_two_poses(), protocols::protein_interface_design::MinimizeInterface(), protocols::forge::build::BuildManager::modify(), protocols::denovo_design::components::modify_ft_for_residue_insertion(), protocols::forge::build::SegmentInsert::modify_impl(), protocols::forge::build::SegmentRebuild::modify_impl(), protocols::ub_e2c::ubi_e2c_modeler::monoub_fold_tree(), protocols::protein_interface_design::movers::PlaceStubMover::place_stub(), protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::prepare_foldtree(), protocols::cyclic_peptide::PeptideStubMover::preserve_old_mainchain_torsions(), protocols::protein_interface_design::movers::PlacementMinimizationMover::refresh_bbstub_constraints(), protocols::jumping::remove_cut(), protocols::ligand_docking::LigandBaseProtocol::reorder_foldtree_around_mobile_regions(), protocols::analysis::InterfaceAnalyzerMover::reorder_foldtree_find_jump(), protocols::membrane::reorder_membrane_foldtree(), protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue(), protocols::forge::methods::replace(), 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(), protocols::rbsegment_relax::restore_pose_from_rbsegs(), protocols::protein_interface_design::movers::SetAtomTree::set_ab_fold_tree(), protocols::ub_e2c::ubi_e2c_modeler::set_e2g2_diubi_fold_tree(), protocols::splice::RBInMover::set_fold_tree(), protocols::splice::Splice::set_fold_tree(), protocols::anchored_design::AnchoredDesignMover::set_fold_tree_and_cutpoints(), protocols::ub_e2c::ubi_e2c_modeler::setup_complex_fold_tree(), protocols::rbsegment_relax::setup_disconnected(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_fold_tree_through_build_full_model_info(), protocols::docking::setup_foldtree(), protocols::membrane::setup_foldtree_from_anchors(), protocols::hotspot_hashing::HotspotStubSet::setup_hotspot_foldtree_(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_jumps(), protocols::ncbb::setup_pert_foldtree(), protocols::rbsegment_relax::setup_pose_from_rbsegs(), protocols::rbsegment_relax::setup_pose_rbsegs_keep_loops(), protocols::relax::membrane::MPFastRelaxMover::setup_relax_foldtree(), protocols::relax::RepeatProteinRelax::setup_repeat_pose(), protocols::relax::RepeatProteinRelax::setup_repeat_pose_jumping(), protocols::antibody_legacy::AntibodyModeler::setup_simple_fold_tree(), protocols::ub_e2c::ubi_e2c_modeler::setup_simple_fold_tree(), protocols::grafting::setup_single_loop_double_arm_remodeling_foldtree(), protocols::grafting::setup_single_loop_single_arm_remodeling_foldtree(), core::conformation::symmetry::setup_symmetric_conformation(), protocols::forge::methods::shift_jumps(), protocols::antibody::simple_fold_tree(), protocols::antibody_legacy::simple_fold_tree(), protocols::antibody::simple_one_loop_fold_tree(), protocols::antibody_legacy::simple_one_loop_fold_tree(), protocols::stepwise::modeler::slice(), protocols::protein_interface_design::star_fold_tree(), protocols::splice::Splice::tail_fold_tree(), protocols::loophash::LoopHashLibrary::test_loop_sample(), and protocols::hybridization::MRMover::trim_target_pose().
◆ replace_edge()
| 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.
References TR().
Referenced by protocols::docking::EnsureExclusivelySharedJumpMover::apply(), and protocols::docking::setup_foldtree().
◆ residue_is_in_fold_tree()
| 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.
Referenced by protocols::stepwise::modeler::check_jump_to_next_residue_in_chain(), protocols::stepwise::modeler::check_jump_to_previous_residue_in_chain(), and core::pose::set_reasonable_fold_tree().
◆ root()
|
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().
Referenced by protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::add_aa_virt_rsd_as_root(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::add_aa_virt_rsd_as_root(), core::scoring::constraints::add_coordinate_constraints(), protocols::stepwise::modeler::align::StepWisePoseAligner::add_coordinate_constraints_from_map(), protocols::loops::add_coordinate_constraints_to_pose(), protocols::relax::add_coordinate_constraints_to_pose(), protocols::rbsegment_relax::ConfChangeMover::add_dihedral_csts(), protocols::chemically_conjugated_docking::add_extra_bodies(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::add_terminal_res_repulsion(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::add_terminal_res_repulsion(), protocols::toolbox::sample_around::add_virtual_res(), protocols::rna::movers::ErraserMinimizerMover::add_virtual_res(), core::pose::addVirtualResAsRoot(), protocols::topology_broker::MembraneTopologyClaimer::addVirtualResAsRootMembrane(), protocols::stepwise::modeler::align::align_pose_and_add_rmsd_constraints(), protocols::fold_from_loops::utils::append_pose_to_pose_keep_fold_tree(), protocols::docking::EnsureExclusivelySharedJumpMover::apply(), protocols::loop_grower::LoopGrower::apply(), protocols::relax::loop::LoopRelaxMover::apply(), protocols::rna::movers::RNAIdealizeMover::apply(), protocols::rna::movers::RNAThreadAndMinimizeMover::apply(), protocols::constraint_generator::CoordinateConstraintGenerator::apply(), protocols::forge::components::VarLengthBuild::apply(), protocols::forge::remodel::RemodelLoopMover::apply(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::apply(), protocols::simple_moves::VirtualRootMover::apply(), protocols::fold_from_loops::movers::NubInitioLoopClosureMover::apply_closure_trust(), protocols::loophash::BackboneSegment::apply_to_pose(), core::kinematics::ShortestPathInFoldTree::build_jumpres_distmap(), core::conformation::build_residue_tree(), core::conformation::build_tree(), protocols::stepwise::modeler::check_jump_to_next_residue_in_chain(), protocols::stepwise::modeler::check_jump_to_previous_residue_in_chain(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::check_superimpose_res(), protocols::ligand_docking::ga_ligand_dock::constraint_relax(), protocols::electron_density::create_minimize_pose_into_density_options(), protocols::electron_density::dockPoseIntoMap(), protocols::stepwise::monte_carlo::mover::ensure_appropriate_foldtree_for_move(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::figure_out_best_working_alignment(), protocols::stepwise::modeler::movemap::figure_out_stepwise_movemap(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_exact_cartmin(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_exact_ligmin_helper(), protocols::residue_optimization::MetapatchEnumeration::final_sampling(), protocols::denovo_design::find_jump_rec(), protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockMoveRbJumpMover::find_new_jump_residue(), core::pose::symmetry::find_new_symmetric_jump_residues(), core::conformation::symmetry::fold_tree_entry_point(), protocols::loops::fold_tree_from_loops(), protocols::forge::methods::fold_tree_from_loops(), protocols::topology_broker::MembraneTopologyClaimer::generate_claims(), protocols::relax::AtomCoordinateCstMover::generate_constraints(), core::conformation::get_anchor_atomno(), core::kinematics::get_foldtree_which_partitions(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_intramolecular_split_move_elements(), protocols::stepwise::modeler::align::StepWisePoseAligner::get_rmsd_res_and_superimpose_res_in_pose(), core::conformation::get_root_residue_root_atomno(), protocols::stepwise::modeler::align::StepWisePoseAligner::get_root_triad_atom_id_map(), protocols::loophash::get_rt_over_leap(), protocols::loophash::get_rt_over_leap_fast(), protocols::stepwise::modeler::get_unique_connection_res(), protocols::residue_optimization::MetapatchEnumeration::initial_sampling(), protocols::stepwise::modeler::rna::o2prime::O2PrimePacker::initialize_o2prime_green_packer(), protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::initialize_phosphate_move_list(), insert_fold_tree_by_jump(), protocols::forge::methods::linear_chainbreak(), protocols::forge::methods::merge(), protocols::forge::build::SegmentInsert::modify_impl(), protocols::forge::build::SegmentRebuild::modify_impl(), protocols::topology_broker::TMHTopologySamplerClaimer::output_membrane_vector(), protocols::forge::methods::overlap_chainbreak(), protocols::drug_design::place_new_restype_rotamer_align(), protocols::topology_broker::TMHTopologySamplerClaimer::pre_process(), protocols::constraint_generator::CoordinateConstraintGenerator::prepare_constraint_target_pose(), protocols::forge::methods::quadratic_chainbreak(), protocols::forge::methods::replace(), core::pose::reroot(), protocols::stepwise::modeler::reroot_based_on_full_model_info(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::reroot_fold_tree(), protocols::stepwise::modeler::revise_root_and_moving_res_list(), core::pose::symmetry::sealed_symmetric_fold_tree(), protocols::ligand_docking::ga_ligand_dock::LigandAligner::set_constraints(), protocols::ligand_docking::ga_ligand_dock::LigandAligner::set_hard_constraint_on_marked(), protocols::relax::RelaxProtocolBase::set_up_constraints(), protocols::rbsegment_relax::setup_disconnected(), core::pose::toolbox::AtomLevelDomainMap::setup_movemap(), protocols::rbsegment_relax::setup_pose_rbsegs_keep_loops(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::setup_using_user_input_VDW_pose(), protocols::forge::methods::shift_jumps(), protocols::stepwise::modeler::slice(), protocols::denovo_design::slide_jump(), protocols::fldsgn::CircularPermutation::split_chains(), protocols::hybridization::FoldTreeHybridize::superimpose_strand_pairings_to_templates(), protocols::denovo_design::symmetric_fold_tree(), core::conformation::symmetry::symmetrize_fold_tree(), protocols::hybridization::MRMover::trim_target_pose(), and protocols::environment::CoMTrackerCM::update_tracking_residue().
◆ set_jump_atoms() [1/2]
| 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 |
||
| ) |
◆ set_jump_atoms() [2/2]
| 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 core::import_pose::RNA_JumpMover::add_new_RNA_jump(), 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(), protocols::splice::Splice::fold_tree(), protocols::stepwise::sampler::protein::generate_beta_database_test(), 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::make_hotspot_foldtree(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::make_pose(), core::fragment::make_pose_from_frags(), protocols::protein_interface_design::movers::PlaceStubMover::place_stub(), protocols::recces::pose_setup_from_file(), protocols::stepwise::monte_carlo::mover::TransientCutpointHandler::prepare_fold_tree_for_erraser(), 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::rna::movers::RNA_LoopCloser::rna_ccd_close(), protocols::stepwise::legacy::modeler::rna::setup_bulge_jump_point(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::setup_fold_tree(), protocols::stepwise::modeler::slice(), protocols::stepwise::monte_carlo::mover::ResampleMover::slide_jump_randomly(), and protocols::magnesium::update_jump_atoms_for_mg_bound_water().
◆ setup_edge_counts()
|
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.
◆ show()
| 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, and core::conformation::membrane::out.
Referenced by protocols::membrane::AddMembraneMover::add_membrane_virtual(), protocols::docking::membrane::MPFindInterfaceMover::apply(), protocols::membrane::AddMembraneMover::apply(), protocols::membrane::AddMPLigandMover::apply(), protocols::membrane::FlipMover::apply(), protocols::membrane::MPQuickRelaxMover::apply(), protocols::membrane::OptimizeMembranePositionMover::apply(), protocols::membrane::OptimizeProteinEmbeddingMover::apply(), protocols::membrane::SetMembranePositionMover::apply(), protocols::membrane::SpinAroundPartnerMover::apply(), protocols::membrane::TiltMover::apply(), protocols::membrane::TransformIntoMembraneMover::apply(), protocols::membrane::TranslationMover::apply(), protocols::membrane::RotationMover::apply(), protocols::membrane::TranslationRotationMover::apply(), protocols::membrane::MPMutateRelaxMover::apply(), protocols::simple_moves::SetTorsion::apply(), protocols::docking::membrane::MPDockingMover::apply(), protocols::docking::membrane::MPDockingSetupMover::apply(), protocols::docking::membrane::QuickRelaxPartnersSeparately::apply(), protocols::membrane::MembranePositionFromTopologyMover::apply(), protocols::relax::membrane::MPRangeRelaxMover::apply(), protocols::relax::RangeRelaxMover::apply(), protocols::abinitio::FragmentSampler::check_loops(), protocols::membrane::create_membrane_docking_foldtree_from_partners(), protocols::membrane::create_membrane_foldtree_from_anchors(), protocols::membrane::create_specific_membrane_foldtree(), protocols::cyclic_peptide::dump_debug_output(), protocols::docking::membrane::QuickRelaxPartnersSeparately::finalize_setup(), protocols::relax::RangeRelaxMover::finalize_setup(), protocols::topology_broker::MembraneTopologyClaimer::generate_claims(), protocols::simple_filters::PoseInfoFilter::report(), protocols::membrane::setup_foldtree_from_anchors(), and protocols::relax::membrane::MPFastRelaxMover::setup_relax_foldtree().
◆ simple_tree()
| 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::membrane::create_membrane_docking_foldtree_from_partners(), protocols::membrane::create_membrane_foldtree_from_anchors(), protocols::membrane::create_specific_membrane_foldtree(), protocols::forge::remodel::RemodelMover::design_refine_cart_relax(), protocols::abinitio::AbrelaxApplication::fold(), FoldTree(), protocols::antibody::AntibodyInfo::get_FoldTree_L_HA(), protocols::antibody::AntibodyInfo::get_FoldTree_LA_H(), protocols::antibody::AntibodyInfo::get_FoldTree_LH_A(), core::io::silent::RNA_SilentStruct::init_from_lines(), core::io::silent::BinarySilentStruct::init_from_lines(), protocols::topology_broker::AsymFoldandDockClaimer::initialize_dofs(), protocols::forge::remodel::RemodelLoopMover::loophash_stage(), protocols::loop_build::LoopMover_SlidingWindow::model_loop(), protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue(), protocols::forge::remodel::RemodelLoopMover::repeat_propagation(), core::io::silent::BinarySilentStruct::resize(), core::io::silent::RNA_SilentStruct::resize(), protocols::grafting::return_region(), protocols::docking::DockingHighResLegacy::set_dock_mcm_protocol(), protocols::membrane::setup_foldtree_from_anchors(), and protocols::relax::membrane::MPFastRelaxMover::setup_relax_foldtree().
◆ size()
|
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::kinematics::get_foldtree_which_partitions(), core::import_pose::get_tree(), core::io::silent::RNA_SilentStruct::print_conformation(), protocols::forge::methods::replace(), and core::pose::set_reasonable_fold_tree().
◆ slide_cutpoint()
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().
Referenced by core::scoring::motif::Xfrag::insert(), protocols::forge::build::SegmentInsert::modify_impl(), and protocols::loops::set_loop_cutpoint_in_pose_fold_tree().
◆ slide_jump()
| 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::magnesium::fix_water_jump(), core::scoring::motif::Xfrag::insert(), protocols::stepwise::monte_carlo::mover::AddMover::prepend_residue(), protocols::flexpep_docking::FlexPepDockingProtocol::randomlySlidePeptideJump(), protocols::hotspot_hashing::HotspotStubSet::setup_hotspot_foldtree_(), protocols::denovo_design::slide_jump(), protocols::stepwise::monte_carlo::mover::ResampleMover::slide_jump_randomly(), and protocols::hybridization::MRMover::trim_target_pose().
◆ split_existing_edge_at_residue()
| 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().
◆ to_string()
| std::string core::kinematics::FoldTree::to_string | ( | ) | const |
easy output of string
easy output of string
Referenced by protocols::simple_moves::CopyDofMover::pose_string().
◆ tree_from_jumps_and_cuts()
| 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::loop_grower::LoopGrower::apply(), protocols::loops::apply_sequence_mapping(), protocols::topology_broker::TMHTopologySamplerClaimer::build_fold_tree(), protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockMoveRbJumpMover::find_new_jump_residue(), core::pose::symmetry::find_new_symmetric_jump_residues(), core::conformation::symmetry::get_component_contiguous_foldtree(), core::import_pose::get_tree(), protocols::dna::make_base_pair_aware_fold_tree(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::make_pose(), core::fragment::make_simple_fold_tree_from_jump_frame(), protocols::forge::build::SegmentInsert::modify_impl(), protocols::forge::build::SegmentRebuild::modify_impl(), core::import_pose::remove_cutpoint_closed(), core::environment::FoldTreeSketch::render(), core::import_pose::RNA_JumpMover::sample_alternative_chain_connection(), 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::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::setup_fold_tree(), protocols::rna::movers::ErraserMinimizerMover::setup_fold_tree(), protocols::flexpep_docking::FlexPepDockingProtocol::setup_foldtree(), protocols::star::StarAbinitio::setup_kinematics(), protocols::rbsegment_relax::setup_pose_rbsegs_keep_loops(), protocols::stepwise::modeler::slice(), core::conformation::symmetry::symmetrize_fold_tree(), and protocols::hybridization::HybridizeFoldtreeDynamic::update().
◆ update_cutpoints()
|
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().
◆ update_edge_label()
| 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::jumping::remove_cut(), protocols::docking::setup_dock_jump(), and protocols::docking::setup_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().
◆ update_jump_edge()
|
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().
◆ update_jump_points()
|
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().
◆ update_nres()
|
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().
◆ update_num_jump()
|
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().
◆ upstream_atom()
| 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::modeler::fix_protein_jump_atom(), protocols::stepwise::sampler::protein::ProteinBetaAntiParallelStepWiseSampler::get_antiparallel_beta_jumps(), protocols::stepwise::modeler::get_jump_partners_from_pose(), protocols::recces::sampler::rna::MC_RNA_OneJump::MC_RNA_OneJump(), protocols::stepwise::legacy::modeler::rna::output_fold_tree_info(), protocols::rna::denovo::movers::RNA_Minimizer::setup_movemap(), protocols::stepwise::modeler::slice(), and protocols::magnesium::update_mg_hoh_fold_tree().
◆ upstream_jump_residue()
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
Referenced by core::import_pose::RNA_JumpMover::add_new_RNA_jump(), protocols::abinitio::LoopJumpFoldCst::add_rigidity_jumps(), protocols::abinitio::MembraneAbinitio::add_spanning_region(), protocols::indel::IndelOptimizationMover::apply(), protocols::membrane::FlipMover::apply(), core::select::jump_selector::InterchainJumpSelector::apply(), protocols::jumping::JumpSample::apply_to(), protocols::idealize::basic_idealize(), protocols::scoring::Interface::calculate(), core::import_pose::libraries::ChunkSet::check_fold_tree_OK(), protocols::simple_filters::InterfaceHbondsFilter::compute_hbonds(), protocols::enzdes::EnzdesBaseProtocol::create_enzdes_movemap(), protocols::stepwise::monte_carlo::mover::ensure_appropriate_foldtree_for_move(), protocols::toolbox::rigid_body::figure_out_moving_partition_res(), protocols::stepwise::modeler::working_parameters::figure_out_rebuild_bulge_mode(), protocols::toolbox::rigid_body::figure_out_reference_res_for_jump(), core::pose::rna::fill_in_default_jump_atoms(), protocols::docking::membrane::QuickRelaxPartnersSeparately::finalize_setup(), protocols::stepwise::modeler::find_jump_number_at_suite(), protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockMoveRbJumpMover::find_new_jump_residue(), core::pose::symmetry::find_new_symmetric_jump_residues(), core::pose::symmetry::find_symmetric_basejump_anchor(), protocols::stepwise::modeler::fix_protein_jump_atom(), core::conformation::symmetry::fold_tree_entry_point(), core::environment::FoldTreeSketch::FoldTreeSketch(), protocols::loop_grower::SheetSampler::generate_jump_frags(), protocols::jumping::JumpSample::generate_jump_frags(), protocols::jumping::JumpSample::generate_jump_frames(), protocols::stepwise::modeler::rna::get_anchor_res(), core::import_pose::get_anchor_rsd(), protocols::stepwise::sampler::protein::ProteinBetaAntiParallelStepWiseSampler::get_antiparallel_beta_jumps(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_docking_split_move_elements(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_intramolecular_split_move_elements(), protocols::stepwise::modeler::get_jump_partners_from_pose(), protocols::magnesium::MgMinimizer::get_mg_hoh_minimize_move_map(), core::pose::rna::get_rigid_body_jumps(), core::scoring::motif::Xfrag::insert(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::insert_base_pair_jumps(), protocols::membrane::is_membrane_fixed(), protocols::hybridization::HybridizeFoldtreeDynamic::jumps_and_cuts_from_foldtree(), protocols::forge::methods::jumps_and_cuts_from_pose(), protocols::stepwise::modeler::rna::sugar::look_for_jumps_to_next(), protocols::stepwise::modeler::rna::sugar::look_for_jumps_to_previous(), protocols::stepwise::modeler::look_for_unique_jump_to_moving_res(), core::optimization::symmetry::SymAtomTreeMinimizer::make_asymmetric_movemap(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::make_pose(), core::pose::symmetry::make_symmetric_movemap(), protocols::recces::sampler::rna::MC_RNA_OneJump::MC_RNA_OneJump(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::minimize_sugar(), protocols::rna::movers::ErraserMinimizerMover::movemap_setup(), protocols::stepwise::modeler::output_movemap(), core::import_pose::put_in_cutpoint(), core::import_pose::RNA_JumpMover::random_jump_change(), protocols::rna::denovo::movers::RNA_DeNovoMasterMover::randomize_rnp_rigid_body_orientations(), protocols::flexpep_docking::FlexPepDockingProtocol::randomlySlidePeptideJump(), core::conformation::symmetry::SymmetricConformation::recalculate_transforms(), core::import_pose::remove_cutpoint_closed(), protocols::simple_ddg::AlaScan::report(), core::kinematics::residues_upstream_of_jump(), core::import_pose::RNA_BasePairHandler::RNA_BasePairHandler(), core::pose::symmetry::rotate_anchor_to_x_axis(), core::import_pose::RNA_JumpMover::sample_alternative_chain_connection(), core::pose::symmetry::sealed_symmetric_fold_tree(), protocols::rna::denovo::movers::RNA_DeNovoMasterMover::search_rigid_body_orientation(), protocols::rna::denovo::movers::RNA_HelixMover::set_pose(), protocols::analysis::InterfaceAnalyzerMover::set_pose_info(), protocols::rna::denovo::movers::RNA_DeNovoMasterMover::setup_dock_into_density_mover(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::setup_fold_tree(), protocols::rna::denovo::coarse::MultipleDomainMover::setup_jump_numbers_and_partner(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_jumps(), protocols::rna::denovo::movers::RNA_Minimizer::setup_movemap(), protocols::rna::denovo::movers::RNA_DeNovoMasterMover::setup_rna_protein_docking_mover(), protocols::stepwise::modeler::slice(), protocols::stepwise::monte_carlo::mover::ResampleMover::slide_jump_randomly(), core::pose::swap_transform(), core::conformation::symmetry::symmetrize_fold_tree(), protocols::rna::denovo::coarse::MultipleDomainMover::try_to_slide_into_contact(), protocols::magnesium::update_jump_atoms_for_mg_bound_water(), protocols::magnesium::update_mg_hoh_fold_tree(), protocols::environment::CoMTrackerCM::update_tracking_residue(), core::kinematics::visualize_fold_tree(), and protocols::environment::claims::VirtResClaim::yield_elements().
Friends And Related Function Documentation
◆ operator!=
◆ operator<<
|
friend |
output operator
Foldtree output to stream
◆ operator==
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
◆ operator>>
|
friend |
input operator
Foldtree input from stream
Member Data Documentation
◆ cutpoint_
|
mutableprivate |
cutpoint number to cutpoint residue number, dimesioned as num_cutpoint_.
Referenced by cutpoint(), cutpoint_map(), and is_cutpoint().
◆ 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().
◆ edge_count
|
mutableprivate |
dimensioned as nres_, see setup_edge_counts for more info
◆ edge_list_
|
private |
- Note
- vector for fast traversal, but re-ordering, deleting are slow.
Referenced by begin(), clear(), empty(), end(), is_root(), nc_begin(), nc_end(), operator=(), root(), and size().
◆ hasher
|
private |
computes fixed-size identifier for a string input
◆ is_cutpoint_
|
mutableprivate |
whether a residue is a cutpoint, dimensioned as nres_
Referenced by cutpoint_map(), and is_cutpoint().
◆ is_jump_point_
|
mutableprivate |
whehter a residue is a jump_point, dimensioned as nres_
Referenced by is_jump_point().
◆ jump_edge_
|
mutableprivate |
jump number to edge index number in the edge_list_, dimensioned as num_jump_.
◆ jump_edge_count
|
mutableprivate |
dimensioned as num_jump, see setup_edge_counts for more info
◆ jump_point_
jump number to jump residue number. dimensioned as (2,num_jump_)
◆ linked_
|
mutableprivate |
Used as scratch space by a couple of functions.
◆ min_edge_count
|
mutableprivate |
the minimum number in edge_count and jump_edge_count.
◆ new_order
|
mutableprivate |
edges in the edge_list_ have been reordered.
Referenced by check_order(), and check_topology().
◆ new_topology
|
mutableprivate |
edges in the edge_list_ have been changed.
Referenced by check_topology(), clear(), and operator=().
◆ nres_
|
mutableprivate |
just the largest vertex in edge_list_
Referenced by is_cutpoint(), and nres().
◆ num_cutpoint_
|
mutableprivate |
number of cutpoints in the fold tree.
- Note
- number_cutpoint_ == num_jump_ (if a connected tree)
Referenced by num_cutpoint().
◆ num_jump_
|
mutableprivate |
number of jump edges (edges in edge_list_ with label>0)
Referenced by num_jump().
◆ seen_
|
private |
The documentation for this class was generated from the following files:
- src/core/kinematics/FoldTree.hh
- src/core/kinematics/FoldTree.cc
