Rosetta 3.4
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src/core/kinematics/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 <numeric/random/random.hh>
#include <cassert>
#include <utility/vector1.hh>

Namespaces

namespace  core
 

A class for defining atom parameters, known as atom_types.


namespace  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::Atom * 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
tree::Atom * core::kinematics::setup_cloned_atom (tree::Atom const *, utility::vector1< id::AtomID > const &)
tree::Atom * 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*****
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************************************
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************************************
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

Detailed Description

Kinematics utility functions.

Author:
Phil Bradley
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