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util.cc File Reference

Kinematics utility functions. More...

#include <core/kinematics/util.hh>
#include <core/kinematics/AtomTree.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/tree/JumpAtom.hh>
#include <core/kinematics/tree/BondedAtom.hh>
#include <core/id/TorsionID.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/kinematics/types.hh>
#include <basic/Tracer.hh>
#include <utility/excn/Exceptions.hh>
#include <numeric/random/random.hh>
#include <cassert>
#include <utility/vector1.hh>
#include <ObjexxFCL/format.hh>

Classes

struct  core::kinematics::Node
 
struct  core::kinematics::TreeVizBuilder
 

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.
 

Functions

static
numeric::random::RandomGenerator 
core::kinematics::RG (62457)
 
static basic::Tracer core::kinematics::TR ("core.kinematics.util")
 
tree::AtomOP core::kinematics::add_atom (int const atomno, int const seqpos, Links const &links, AtomPointer1D &atom_ptr, bool const add_jump_atom)
 
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_cloned_atom (tree::AtomCOP, utility::vector1< id::AtomID > const &)
 helper function for setup_backrub_atom_tree 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...
 
void core::kinematics::replace_substr (std::string &str, const std::string from, const std::string to)
 
std::string core::kinematics::operator* (std::string const s, size_t n)
 
std::string core::kinematics::pad_dash (Size npad, std::string s)
 
std::string core::kinematics::pad_dash_left (Size npad, std::string s)
 
std::string core::kinematics::pad_dash_right (Size npad, std::string s)
 
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)
 
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)
 
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