util.cc File Reference

#include <protocols/jumping/util.hh>
#include <core/scoring/dssp/Dssp.hh>
#include <core/pose/Pose.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/kinematics/util.hh>
#include <core/fragment/JumpingFrame.hh>
#include <core/fragment/BBTorsionSRFD.hh>
#include <core/fragment/JumpSRFD.hh>
#include <core/conformation/util.hh>
#include <core/pose/symmetry/util.hh>
#include <core/conformation/symmetry/util.hh>
#include <core/conformation/symmetry/SymmetryInfo.hh>
#include <protocols/loops/loop_closure/ccd/SlidingWindowLoopClosure.hh>
#include <protocols/loops/Exceptions.hh>
#include <protocols/checkpoint/CheckPointer.hh>
#include <basic/Tracer.hh>
#include <list>
#include <core/chemical/ResidueType.hh>
#include <utility/vector1.hh>
#include <ObjexxFCL/string.functions.hh>
#include <core/fragment/FragData.hh>

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

Typedefs
using	protocols::jumping::PointList = utility::vector1< PointPosition >

Functions
static basic::Tracer	protocols::jumping::tr ("protocols.jumping")
void	protocols::jumping::close_chainbreaks (loops::loop_closure::ccd::SlidingWindowLoopClosureOP closure_protocol, Pose &open_pose, protocols::checkpoint::CheckPointer &checkpoint, const std::string &decoy_tag, core::kinematics::FoldTree const &final_fold_tree_in)
bool	protocols::jumping::remove_cut (core::Size cutpoint, Pose &pose, FoldTree const &final_fold_tree)
bool	protocols::jumping::remove_cut (core::Size cutpoint, FoldTree &new_fold_tree, FoldTree const &final_fold_tree)
void	protocols::jumping::safe_secstruct (pose::Pose &pose)
core::fragment::JumpingFrameOP	protocols::jumping::generate_empty_jump_frame (core::Size startpos, core::Size endpos, core::Size length)
core::fragment::JumpingFrameOP	protocols::jumping::generate_jump_frame (core::Size startpos, core::Size endpos, bool bWithTorsion)
void	protocols::jumping::get_CA_vectors (PointList const &ca1, PointList const &ca2, Vector &a, Vector &b, Vector &c)
void	protocols::jumping::get_pairing_geometry (pose::Pose const &pose, core::Size const res1, core::Size const res2, Real &orientation, Real &pleating1, Real &pleating2)
void	protocols::jumping::get_pleating (pose::Pose const &pose, core::Size const pos1, core::Size const pos2, core::Size &orientation, core::Size &pleating)
void	protocols::jumping::assign_ss_dssp (core::pose::Pose &pose)
	Assign secondary structure using DSSP. More...

Detailed Description

Author

Oliver Lange