Rosetta 3.5
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Namespaces | Constant Groups | Typedefs | Functions
util.hh File Reference

Kinematics utility functions. More...

#include <core/kinematics/tree/Atom.fwd.hh>
#include <core/kinematics/FoldTree.fwd.hh>
#include <core/kinematics/AtomPointer.fwd.hh>
#include <core/id/AtomID.fwd.hh>
#include <core/kinematics/MoveMap.fwd.hh>
#include <ObjexxFCL/FArray1D.fwd.hh>
#include <core/types.hh>
#include <string>
#include <map>

Namespaces

 core
 A class for defining atom parameters, known as atom_types.
 
 core::kinematics
 See AtomTree overview and FoldTree overview for details.
 

Constant Groups

 core
 A class for defining atom parameters, known as atom_types.
 
 core::kinematics
 See AtomTree overview and FoldTree overview for details.
 

Typedefs

typedef utility::vector1
< utility::vector1< Size > > 
core::kinematics::Links
 

Functions

tree::AtomOP core::kinematics::add_atom (int const atomno, int const seqpos, utility::vector1< utility::vector1< Size > > const &links, AtomPointer1D &atom_ptr, bool const add_jump_atom)
 creat an atom and add it to the residue atom-tree based on information stored in links. More...
 
int core::kinematics::pick_loopy_cutpoint (Size const n_res, ObjexxFCL::FArray1D_float const &cut_bias_sum)
 pick a postion in n_res as the cutpoint More...
 
tree::AtomOP core::kinematics::setup_backrub_atom_tree (utility::vector1< AtomID >, AtomID const &, AtomPointer2D const &, utility::vector1< std::pair< Size, Size > > const &, Size const )
 
void core::kinematics::simple_visualize_fold_tree (FoldTree const &fold_tree, std::ostream &out)
 prints something like this ***1***C***1*********2***C********3****C****2********3***** More...
 
void core::kinematics::simple_visualize_fold_tree_and_movemap (FoldTree const &fold_tree, MoveMap const &mm, std::ostream &out)
 prints something like this ***1***C***1*********2***C********3****C****2********3***** **********xxxxxxxxxxxxx************************************ More...
 
void core::kinematics::simple_visualize_fold_tree_and_movemap_bb_chi (FoldTree const &fold_tree, MoveMap const &mm, std::ostream &out)
 prints something like this ***1***C***1*********2***C********3****C****2********3***** **********xxxxxxxxxxxxx************************************ More...
 
core::kinematics::FoldTree core::kinematics::linearize_fold_tree (core::kinematics::FoldTree const &tree)
 linearizes (or defoliates, if you prefer) a FoldTree. "default" FoldTrees produced by the PDB reader have all chains (peptide edges) starting from jumps relative to residue 1. This code modifies the tree to instead have all the jumps be relative to the preceding edge. It is not tested with ligands and will not work with "functional" jumps. From A to B: A:FOLD_TREE EDGE 1 78 -1 EDGE 1 79 1 EDGE 79 454 -1 EDGE 1 455 2 EDGE 455 540 -1 EDGE 1 541 3 EDGE 541 697 -1 B:FOLD_TREE EDGE 1 78 -1 EDGE 78 79 1 EDGE 79 454 -1 EDGE 454 455 2 EDGE 455 540 -1 EDGE 540 541 3 EDGE 541 697 -1 More...
 
std::string core::kinematics::visualize_fold_tree (FoldTree const &fold_tree)
 sheffler More...
 
std::string core::kinematics::visualize_fold_tree (FoldTree const &ft, std::map< Size, std::string > const &node_labels_partial)
 
std::string core::kinematics::visualize_fold_tree (FoldTree const &ft, std::map< Size, char > const &mark_jump_to_res)
 
std::string core::kinematics::visualize_fold_tree (FoldTree const &ft, std::map< Size, std::string > const &node_labels_partial_in, std::map< Size, char > const &mark_jump_to_res, std::map< Size, Size > const &jump_follows)
 
core::kinematics::FoldTree core::kinematics::remodel_fold_tree_to_account_for_insertion (core::kinematics::FoldTree const &input_tree, core::Size insert_after, core::Size insert_size)
 remodel a fold tree to account for a large insertion by adding the size of the insert to upstream positions More...
 

Detailed Description

Kinematics utility functions.

Author
Phil Bradley