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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>
#include <utility/excn/Exceptions.hh>
#include <numeric/random/random.hh>
#include <utility/assert.hh>
#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
 

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::Sizecore::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::Sizecore::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 ***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...
 
utility::vector1< core::Sizecore::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::Sizecore::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::Sizecore::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