util.cc File Reference

miscellaneous utility functions for forge More...

#include <protocols/forge/methods/util.hh>
#include <protocols/forge/build/Interval.hh>
#include <protocols/forge/methods/fold_tree_functions.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/constraints/AtomPairConstraint.hh>
#include <core/scoring/constraints/CoordinateConstraint.hh>
#include <core/chemical/AA.hh>
#include <core/chemical/VariantType.hh>
#include <core/conformation/Conformation.hh>
#include <core/conformation/Residue.hh>
#include <core/graph/DisjointSets.hh>
#include <core/id/types.hh>
#include <core/types.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/pose/PDBInfo.hh>
#include <basic/Tracer.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/ResfileReader.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/task/operation/NoRepackDisulfides.hh>
#include <basic/options/keys/remodel.OptionKeys.gen.hh>
#include <basic/options/option.hh>
#include <protocols/toolbox/task_operations/LimitAromaChi2Operation.hh>
#include <protocols/loops/Loops.hh>
#include <core/scoring/sasa.hh>
#include <core/pose/PDBPoseMap.hh>
#include <numeric/random/random.hh>
#include <set>
#include <utility/vector1.hh>

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

Functions
static thread_local basic::Tracer	protocols::forge::methods::TR ("protocols.forge.methods.util")
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...
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)
void	protocols::forge::methods::fixH (core::pose::Pose &pose)
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)

Possu Huang (possu.nosp@m.@u.w.nosp@m.ashin.nosp@m.gton.nosp@m..edu)