util.cc File Reference

#include <protocols/rbsegment_relax/RBSegmentMover.hh>
#include <protocols/rbsegment_relax/util.hh>
#include <protocols/loops/Loop.hh>
#include <protocols/loops/Loops.hh>
#include <core/scoring/dssp/Dssp.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/pose/PDBInfo.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/scoring/constraints/Constraint.hh>
#include <core/scoring/constraints/BoundConstraint.hh>
#include <core/scoring/constraints/CoordinateConstraint.hh>
#include <core/scoring/constraints/AmbiguousConstraint.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/constraints/ConstraintSet.fwd.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/conformation/symmetry/util.hh>
#include <core/pose/symmetry/util.hh>
#include <core/chemical/VariantType.hh>
#include <core/kinematics/MoveMap.hh>
#include <basic/basic.hh>
#include <basic/Tracer.hh>
#include <numeric/xyzVector.io.hh>
#include <numeric/xyz.functions.hh>
#include <numeric/random/random.hh>
#include <ObjexxFCL/FArray1D.hh>
#include <string>
#include <core/id/NamedAtomID.hh>
#include <core/id/SequenceMapping.hh>

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

Functions
static thread_local basic::Tracer	protocols::rbsegment_relax::TR ("protocols::moves::RBSegmentMover")
void	protocols::rbsegment_relax::set_rb_constraints (core::pose::Pose &pose, core::pose::Pose const &cst_pose, utility::vector1< protocols::rbsegment_relax::RBSegment > const &rbsegs, core::id::SequenceMapping const &resmap, core::Real cst_width, core::Real cst_stdev, core::Size cst_seqwidth)
	set up constraints from RB segs currently uses bounded constraints on each CA ... make CST type flag-selectable???? More...
void	protocols::rbsegment_relax::set_constraints (core::pose::Pose &pose, core::pose::Pose const &cst_pose, core::Real cst_width, core::Real cst_stdev, core::Size cst_seqwidth)
	set up constraints on complete pose (not just RB segments) currently uses bounded constraints ... make CST type flag-selectable???? More...
utility::vector1< core::Size >	protocols::rbsegment_relax::setup_pose_rbsegs_keep_loops (core::pose::Pose &pose, utility::vector1< protocols::rbsegment_relax::RBSegment > const &rbsegs, loops::Loops const &loops, core::kinematics::MoveMapOP mm)
	Helper function to set up a pose; unlike alt version keep loops (use cutpoint variants) unlike version in loops_main, this uses RBSegment structure to build multi-level topology returns jump residues. More...
void	protocols::rbsegment_relax::setup_star_topology (core::pose::Pose &pose)
	setup star-topology fold tree More...
void	protocols::rbsegment_relax::setup_disconnected (core::pose::Pose &pose)
	build a pose where every residue is connected by jumps to vrt More...
void	protocols::rbsegment_relax::setup_pose_from_rbsegs (utility::vector1< protocols::rbsegment_relax::RBSegment > const &rbsegs, core::pose::Pose const &pose_in, core::pose::Pose &pose_out, core::id::SequenceMapping &resmap, core::kinematics::MoveMap &mm, bool fix_ligand)
	Helper function to set up a loop-removed pose. More...
void	protocols::rbsegment_relax::restore_pose_from_rbsegs (utility::vector1< protocols::rbsegment_relax::RBSegment > const &rbsegs, core::pose::Pose const &pose_in, core::pose::Pose &pose_out)
	Helper function to restore a fully-connected pose. More...
void	protocols::rbsegment_relax::guess_rbsegs_from_pose (core::pose::Pose const &pose, utility::vector1< RBSegment > &rigid_segs, utility::vector1< RBSegment > &rb_chunks, protocols::loops::Loops &loops)
	use DSSP and simple rules to guess the asignment of rigid-body segments More...
void	protocols::rbsegment_relax::remap_rb_segments (utility::vector1< RBSegment > const &rbsegs, utility::vector1< RBSegment > &rbsegs_remap, core::id::SequenceMapping const &resmap)
	res mapping to rbsegments More...

Detailed Description

Author

Frank DiMaio

Srivatsan Raman