fold_tree_functions.cc File Reference

methods for manipulating FoldTrees More...

#include <protocols/forge/methods/fold_tree_functions.hh>
#include <protocols/forge/methods/util.hh>
#include <core/types.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/Conformation.hh>
#include <core/chemical/VariantType.hh>
#include <utility/graph/DisjointSets.hh>
#include <core/kinematics/Edge.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/pose/Pose.hh>
#include <basic/Tracer.hh>
#include <numeric/random/random.hh>
#include <utility/exit.hh>
#include <algorithm>
#include <map>
#include <set>
#include <sstream>
#include <string>
#include <vector>
#include <core/pose/variant_util.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
static basic::Tracer	protocols::forge::methods::TR ("protocols.forge.methods.fold_tree_functions")
bool	protocols::forge::methods::order (core::kinematics::Edge &e)
	enforce Edge has start <= stop (swap 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...
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)