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 reading in the atom type properties.
	core::kinematics

Functions
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...

Variables
static numeric::random::RandomGenerator	core::kinematics::RG (62457)
static basic::Tracer	core::kinematics::TR ("core.kinematics.util")

Detailed Description

Kinematics utility functions.

Author

Phil Bradley