Kinematics utility functions. More...

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

Classes
struct	core::kinematics::Node

struct	core::kinematics::TreeVizBuilder

Namespaces
	core
	A class for reading in the atom type properties.

	core::kinematics

Typedefs
using	core::kinematics::NodeOP = utility::pointer::shared_ptr< Node >

using	core::kinematics::NodeAP = utility::pointer::weak_ptr< Node >

Functions
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...

core::Size	core::kinematics::jump_which_partitions (FoldTree const &fold_tree, utility::vector1< bool > residues)
	Return the jump which separates the residues in the passed residue selection from all the ones which are not. If no such jump exists (e.g. there's a mixture of included/excluded residues on both sides of every jump) then return zero. Note that upstream/downstream is not specified - you can check this later. More...

FoldTree	core::kinematics::get_foldtree_which_partitions (FoldTree const &fold_tree, utility::vector1< bool > residues)
	Return a new FoldTree where a single jump separates the residues in the passed set from those not in the passed set. More...

utility::vector1< core::Size >	core::kinematics::residues_upstream_of_jump (FoldTree const &fold_tree, core::Size jump_id)
	Return a list of residue numbers which are on the upstream side of the jump. More...

utility::vector1< core::Size >	core::kinematics::residues_downstream_of_jump (FoldTree const &fold_tree, core::Size jump_id)
	Return a list of residue numbers which are on the downstream side of the jump. More...

void	core::kinematics::simple_visualize_fold_tree (FoldTree const &fold_tree, std::ostream &out)
	prints something like this *1C1*****2C*****3C2****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 *1C1*****2C*****3C2****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 *1C1*****2C*****3C2****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...

utility::vector1< core::Size >	core::kinematics::get_residues_from_movemap_with_id (id::TorsionType query_torsion, MoveMap const &movemap)
	Get a vector of residues matching the id from a movemap. More...

utility::vector1< core::Size >	core::kinematics::get_residues_from_movemap_bb_any_torsion (MoveMap const &movemap, Size total_resnum)
	Get a vector of residues that have any of their BB torsions on - either by way of the full bb or torsion ID setting in Movemap. More...

utility::vector1< core::Size >	core::kinematics::get_residues_from_movemap_bb_or_chi (MoveMap const &movemap, Size total_resnum)
	Get residues that are on in the movemap, either for BB, Any Specific torsion (up to 4) or CHI. More...

Detailed Description

Kinematics utility functions.

Author: Phil Bradley

Classes

Namespaces

Typedefs

Functions

Detailed Description