StarAbinitio.cc File Reference

#include <protocols/star/StarAbinitio.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/options/keys/jumps.OptionKeys.gen.hh>
#include <basic/Tracer.hh>
#include <numeric/interpolate.hh>
#include <numeric/prob_util.hh>
#include <numeric/xyzVector.hh>
#include <ObjexxFCL/FArray1D.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <utility/exit.hh>
#include <utility/vector1.hh>
#include <core/types.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/conformation/Conformation.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/util.hh>
#include <core/fragment/FragmentIO.hh>
#include <core/fragment/FragSet.hh>
#include <core/fragment/SecondaryStructure.hh>
#include <core/id/AtomID.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/ShortestPathInFoldTree.hh>
#include <core/optimization/MinimizerOptions.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/constraints/AtomPairConstraint.hh>
#include <core/scoring/constraints/Constraint.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/constraints/util.hh>
#include <core/sequence/SequenceAlignment.hh>
#include <core/util/kinematics_util.hh>
#include <protocols/constraints_additional/MaxSeqSepConstraintSet.hh>
#include <protocols/comparative_modeling/ThreadingJob.hh>
#include <protocols/comparative_modeling/util.hh>
#include <protocols/loops/Loop.hh>
#include <protocols/loops/Loops.hh>
#include <protocols/loops/util.hh>
#include <protocols/medal/util.hh>
#include <protocols/moves/Mover.hh>
#include <protocols/nonlocal/BiasedFragmentMover.hh>
#include <protocols/nonlocal/Policy.hh>
#include <protocols/nonlocal/PolicyFactory.hh>
#include <protocols/nonlocal/util.hh>
#include <protocols/simple_moves/SaneMinMover.hh>
#include <protocols/simple_moves/rational_mc/RationalMonteCarlo.hh>
#include <protocols/star/Extender.hh>
#include <protocols/star/util.hh>

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

Typedefs
typedef utility::vector1< double >	protocols::star::Probabilities

Functions
static thread_local basic::Tracer	protocols::star::TR ("protocols.star.StarAbinitio")
void	protocols::star::compute_per_residue_probabilities (Size num_residues, Size fragment_len, const FoldTree &tree, Probabilities *probs)
void	protocols::star::update_sequence_separation (Size distance, Pose *pose)
void	protocols::star::setup_constraints (const Loops &aligned, Pose *pose)
void	protocols::star::tear_down_constraints (Pose *pose)
ScoreFunctionOP	protocols::star::setup_score (const std::string &weights, Real cb)
void	protocols::star::configure_rmc (MoverOP mover, ScoreFunctionOP score, Size num_cycles, Real temperature, bool recover_low, RationalMonteCarlo *rmc)

Detailed Description

Author

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