Rosetta  2021.16
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fold_tree_functions.hh File Reference

methods for manipulating FoldTrees More...

#include <core/types.hh>
#include <core/kinematics/Edge.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/MoveMap.fwd.hh>
#include <core/pose/Pose.fwd.hh>
#include <string>
#include <protocols/loops/Loops.fwd.hh>
#include <utility/vector1.hh>

Namespaces

 protocols
 The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.
 
 protocols::forge
 
 protocols::forge::methods
 

Functions

bool protocols::forge::methods::order (core::kinematics::Edge &e)
 enforce Edge has start <= stop (swap if necessary) More...
 
template<typename EdgeIterator >
void protocols::forge::methods::add_edges (EdgeIterator begin, EdgeIterator end, core::kinematics::FoldTree &ft)
 add a set of Edges to a FoldTree More...
 
template<typename EdgeIterator >
EdgeIterator protocols::forge::methods::regular_facet_containing_position (core::Size const pos, EdgeIterator const begin, EdgeIterator const end)
 find regular facet (non-jump edge sans face vertices) that contains given position More...
 
template<typename EdgeList >
bool protocols::forge::methods::add_vertex (core::Size const v, EdgeList &edges)
 add a vertex, splitting edges if necessary More...
 
core::Size protocols::forge::methods::closest_larger_peptide_vertex (core::Size const v, core::kinematics::FoldTree const &ft, core::Size const k)
 find the k'th closest larger peptide vertex of given vertex in fold tree More...
 
core::Size protocols::forge::methods::closest_smaller_peptide_vertex (core::Size const v, core::kinematics::FoldTree const &ft, core::Size const k)
 find the k'th closest smaller peptide vertex of given vertex in fold tree More...
 
bool protocols::forge::methods::vertex_exists (core::Size const v, core::kinematics::FoldTree const &ft)
 query if vertex already exists in fold tree More...
 
template<typename EdgeIterator >
EdgeIterator protocols::forge::methods::facet_containing_position (core::Size const pos, EdgeIterator const begin, EdgeIterator const end, int const label=core::kinematics::Edge::PEPTIDE)
 find facet (edge sans face vertices) that contains given position More...
 
template<typename EdgeIterator >
utility::vector1
< core::kinematics::Edge
protocols::forge::methods::regular_edges_within_interval (core::Size const left, core::Size const right, EdgeIterator const begin, EdgeIterator const end)
 find regular (non-jump) edges contained within the interval [left, right] More...
 
template<typename EdgeIterator >
utility::vector1
< core::kinematics::Edge
protocols::forge::methods::edges_within_interval (core::Size const left, core::Size const right, int const edge_type, EdgeIterator const begin, EdgeIterator const end)
 find specific type of edges contained within the interval [left, right] More...
 
utility::vector1
< core::kinematics::Edge
protocols::forge::methods::jumps_connected_to_position (core::Size const pos, core::kinematics::FoldTree const &ft)
 find all jump edges whose start or stop lands on the given position More...
 
core::Size protocols::forge::methods::find_connecting_jump (core::Size const u, core::Size const v, core::kinematics::FoldTree const &ft)
 find the jump connecting two continuous segments of a fold tree More...
 
bool protocols::forge::methods::remove_cutpoint (core::Size const v, core::kinematics::FoldTree &ft)
 remove a cutpoint, merging the two sections that are adjacent to the cut More...
 
void protocols::forge::methods::remove_cutpoints (utility::vector1< core::Size > const &cutpoints, core::kinematics::FoldTree &ft)
 seal a fold tree by removing all specified cutpoints More...
 
core::kinematics::FoldTree protocols::forge::methods::shift_jumps (core::kinematics::FoldTree const &ft, core::kinematics::MoveMap const &mm)
 attempt to shift jumps in a fold tree based on fixed positions in a MoveMap More...
 
core::kinematics::FoldTree protocols::forge::methods::fold_tree_from_pose (core::pose::Pose const &pose, core::Size const ft_root, core::kinematics::MoveMap const &mm)
 construct a fold tree from Pose wrt chain endings and residue types More...
 
core::kinematics::FoldTree protocols::forge::methods::merge (core::kinematics::FoldTree const &left_tree, core::kinematics::FoldTree const &right_tree)
 merge two fold trees by jump between their roots More...
 
core::kinematics::FoldTree protocols::forge::methods::merge (core::kinematics::FoldTree const &left_tree, core::Size const left_position, core::kinematics::FoldTree const &right_tree, core::Size const right_position)
 merge two fold trees connecting by jump via specified positions More...
 
core::kinematics::FoldTree protocols::forge::methods::merge (core::kinematics::FoldTree const &left_tree, core::Size const left_position, std::string const &left_jump_atom, core::kinematics::FoldTree const &right_tree, core::Size const right_position, std::string const &right_jump_atom, bool const keep_stub_in_residue)
 merge two fold trees connecting by jump via specified positions More...
 
core::kinematics::FoldTree protocols::forge::methods::replace (core::kinematics::FoldTree const &original_tree, core::Size const replace_begin, core::Size const replace_end, core::kinematics::MoveMap const &movemap, core::kinematics::FoldTree const &replacement_tree)
 replace a section of one fold tree with another fold tree, connecting by jump between their roots More...
 
void protocols::forge::methods::make_star_foldtree (core::pose::Pose &pose, protocols::loops::Loops loops)
 
void protocols::forge::methods::jumps_and_cuts_from_pose (core::pose::Pose &pose, utility::vector1< std::pair< core::Size, core::Size > > &jumps, utility::vector1< core::Size > &cuts)
 

Detailed Description

methods for manipulating FoldTrees

Author
Yih-En Andrew Ban (yab@u.nosp@m..was.nosp@m.hingt.nosp@m.on.e.nosp@m.du)