MedalExchangeMover.cc File Reference

#include <protocols/medal/MedalExchangeMover.hh>
#include <iostream>
#include <string>
#include <basic/options/option.hh>
#include <basic/options/keys/OptionKeys.hh>
#include <basic/options/keys/abinitio.OptionKeys.gen.hh>
#include <basic/options/keys/cm.OptionKeys.gen.hh>
#include <basic/options/keys/constraints.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/Tracer.hh>
#include <numeric/prob_util.hh>
#include <utility/vector1.hh>
#include <core/types.hh>
#include <core/conformation/Conformation.hh>
#include <core/id/AtomID.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/constraints/Constraint.hh>
#include <core/scoring/constraints/ConstraintIO.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/constraints/CoordinateConstraint.hh>
#include <core/scoring/func/HarmonicFunc.hh>
#include <core/fragment/FragmentIO.hh>
#include <core/fragment/FragSet.hh>
#include <core/fragment/SecondaryStructure.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/pose/Pose.hh>
#include <core/scoring/Energies.hh>
#include <core/util/kinematics_util.hh>
#include <protocols/comparative_modeling/ThreadingJob.hh>
#include <protocols/loops/Loop.hh>
#include <protocols/loops/Loops.hh>
#include <protocols/medal/util.hh>
#include <protocols/nonlocal/BiasedFragmentMover.hh>
#include <protocols/nonlocal/Policy.hh>
#include <protocols/nonlocal/PolicyFactory.hh>
#include <protocols/nonlocal/TreeBuilder.hh>
#include <protocols/nonlocal/TreeBuilderFactory.hh>
#include <protocols/nonlocal/util.hh>
#include <protocols/simple_moves/rational_mc/RationalMonteCarlo.hh>
#include <protocols/star/Extender.hh>

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

Functions
static thread_local basic::Tracer	protocols::medal::TR ("protocols.medal.MedalExchangeMover")
protocols::loops::LoopsCOP	protocols::medal::combine_loops (LoopsCOP aligned, LoopsCOP unaligned)
	Combines both sets of loops, sorting the result in increasing order of start position More...
void	protocols::medal::setup_coordinate_constraints (const Pose &pose, LoopsCOP aligned, ConstraintSetOP constraints)
	Create coordinate constraints restraining aligned residues to their initial positions More...
void	protocols::medal::setup_atom_pair_constraints (const Pose &pose, LoopsCOP aligned, ConstraintSetOP constraints)
	Retain user-specified distance restraints that operate on pairs of aligned residues More...
void	protocols::medal::setup_constraints (const Pose &pose, LoopsCOP aligned, ConstraintSetOP constraints)

Detailed Description

Author

Christopher Miles (cmile.nosp@m.s@uw.nosp@m..edu)