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Rosetta
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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) |
methods for manipulating FoldTrees
1.9.1