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util.hh File Reference

miscellaneous utility functions for forge More...

#include <core/types.hh>
#include <protocols/forge/build/Interval.fwd.hh>
#include <core/kinematics/FoldTree.fwd.hh>
#include <utility/graph/DisjointSets.fwd.hh>
#include <core/pose/Pose.fwd.hh>
#include <protocols/loops/Loop.hh>
#include <protocols/loops/Loops.hh>
#include <core/pack/task/PackerTask.fwd.hh>
#include <core/pack/task/TaskFactory.fwd.hh>
#include <set>
#include <list>
#include <iosfwd>
#include <utility/vector1.hh>
#include <numeric/xyzMatrix.hh>
#include <numeric/xyzVector.hh>
#include <numeric/xyz.functions.hh>

Namespaces

 protocols
 The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.
 
 protocols::forge
 
 protocols::forge::methods
 

Functions

template<typename T >
std::set< T > protocols::forge::methods::closed_range (T const left, T const right, T const increment=1)
 return a set containing values in the closed interval [left, right] filled by looping from left -> right with the given increment More...
 
template<typename T >
void protocols::forge::methods::insert_closed_range (T const left, T const right, std::set< T > &s, T const increment=1)
 add the values in the closed interval [left, right] to a set by looping from left -> right with the given increment More...
 
template<typename T >
std::set< T > protocols::forge::methods::half_open_range (T const left, T const right, T const increment=1)
 return a set containing values in the half-open interval [left, right) filled by looping from left -> right with the given increment More...
 
template<typename T >
void protocols::forge::methods::insert_half_open_range (T const left, T const right, std::set< T > &s, T const increment=1)
 add the values in the half-open interval [left, right) to a set by looping from left -> right with the given increment More...
 
void protocols::forge::methods::union_interval (core::Size const root, core::Size const left, core::Size const right, utility::graph::DisjointSets &uf)
 perform union( root, i ) for all 'i' within the closed interval [left, right] More...
 
core::Size protocols::forge::methods::find_cutpoint (core::pose::Pose const &pose, core::Size left, core::Size right)
 moving left to right, find the first true cutpoint within specified extent More...
 
core::Size protocols::forge::methods::count_cutpoints (core::pose::Pose const &pose, core::Size left, core::Size right)
 moving left to right, count the number of true cutpoints within the specified extent More...
 
void protocols::forge::methods::trans_omega (core::Size const left, core::Size const right, core::pose::Pose &pose)
 set omega to 180 for a range of residues [left, right] More...
 
protocols::loops::Loop protocols::forge::methods::interval_to_loop (protocols::forge::build::Interval const &interval)
 create Loop object w/ random cutpoint from an Interval More...
 
template<typename IntervalIterator >
protocols::loops::Loops protocols::forge::methods::intervals_to_loops (IntervalIterator begin, IntervalIterator end)
 create Loops object w/ random cutpoints from a collection of Intervals More...
 
template<typename IntervalIterator >
protocols::loops::Loops protocols::forge::methods::intervals_to_confirmation_loops (IntervalIterator begin, IntervalIterator end, core::Size nres)
 create Loops object w/ random cutpoints from a collection of Intervals for KIC confirmation purpose More...
 
core::kinematics::FoldTree protocols::forge::methods::fold_tree_from_loops (core::pose::Pose const &pose, protocols::loops::Loops const &loops)
 create fold tree from loops More...
 
void protocols::forge::methods::set_single_loop_fold_tree (core::pose::Pose &pose, protocols::loops::Loop const &loop)
 set a single loop fold tree More...
 
utility::vector1< boolprotocols::forge::methods::parse_resfile_string_with_no_lockdown (core::pose::Pose const &pose, core::pack::task::PackerTask &the_task, std::string const &resfile_string)
 
core::pack::task::TaskFactoryOP protocols::forge::methods::remodel_generic_taskfactory ()
 
void protocols::forge::methods::fill_non_loop_cst_set (core::pose::Pose &pose, protocols::loops::Loops loops)
 
utility::vector1< core::Real >
const 
protocols::forge::methods::calc_rsd_sasa (core::pose::Pose const &pose)
 return accessible surface area for each residue More...
 
void protocols::forge::methods::apply_transformation (core::pose::Pose &mod_pose, std::list< core::Size > const &residue_list, numeric::xyzMatrix< core::Real > const &R, numeric::xyzVector< core::Real > const &preT, numeric::xyzVector< core::Real > const &postT)
 

Detailed Description

miscellaneous utility functions for forge

Author
Yih-En Andrew Ban (yab@u.nosp@m..was.nosp@m.hingt.nosp@m.on.e.nosp@m.du)