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 <core/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 <iostream>
#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, core::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< bool >	protocols::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)
void	protocols::forge::methods::cyclize_pose (core::pose::Pose &pose)

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)