EnergyBasedClusteringProtocol.cc File Reference

Performs the work done by the energy_based_clustering app. Uses an energy-biased cookie-cutter approach to cluster a large number of structures without generating an all-by-all RMSD matrix. More...

#include <protocols/energy_based_clustering/EnergyBasedClusteringProtocol.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreType.hh>
#include <core/scoring/func/HarmonicFunc.hh>
#include <core/scoring/func/CircularHarmonicFunc.hh>
#include <core/scoring/constraints/AtomPairConstraint.hh>
#include <core/scoring/constraints/AngleConstraint.hh>
#include <core/scoring/constraints/DihedralConstraint.hh>
#include <core/scoring/Energies.hh>
#include <core/id/NamedAtomID.hh>
#include <core/import_pose/pose_stream/MetaPoseInputStream.hh>
#include <core/import_pose/pose_stream/util.hh>
#include <core/pose/Pose.hh>
#include <core/pose/subpose_manipulation_util.hh>
#include <core/pose/variant_util.hh>
#include <core/chemical/ResidueType.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/Conformation.hh>
#include <core/id/TorsionID.hh>
#include <core/io/silent/SilentFileOptions.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/io/silent/SilentStruct.hh>
#include <core/io/silent/SilentStructFactory.hh>
#include <core/scoring/rms_util.hh>
#include <protocols/relax/FastRelax.hh>
#include <protocols/cyclic_peptide/CycpepSymmetryFilter.hh>
#include <protocols/cyclic_peptide/DeclareBond.hh>
#include <protocols/constraint_movers/ConstraintSetMover.hh>
#include <protocols/simple_moves/MutateResidue.hh>
#include <utility/vector1.hh>
#include <basic/Tracer.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/cluster.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <numeric/xyzVector.fwd.hh>
#include <numeric/angle.functions.hh>
#include <numeric/constants.hh>
#include <numeric/model_quality/rms.hh>
#include <set>

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

Macros
#define	CNCa_ANGLE   121.7
#define	CNH_ANGLE   119.15
#define	CaCN_ANGLE   116.2
#define	OCN_ANGLE   123.01

Functions
static basic::Tracer	TR ("protocols.cluster.energy_based_clustering.EnergyBasedClusteringProtocol")

Detailed Description

Performs the work done by the energy_based_clustering app. Uses an energy-biased cookie-cutter approach to cluster a large number of structures without generating an all-by-all RMSD matrix.

Author

Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

Macro Definition Documentation

#define CaCN_ANGLE   116.2

Referenced by protocols::energy_based_clustering::EnergyBasedClusteringProtocol::add_cyclic_constraints().

#define CNCa_ANGLE   121.7

Referenced by protocols::energy_based_clustering::EnergyBasedClusteringProtocol::add_cyclic_constraints().

#define CNH_ANGLE   119.15

#define OCN_ANGLE   123.01

Function Documentation

static basic::Tracer TR ( "protocols.cluster.energy_based_clustering.EnergyBasedClusteringProtocol"  )

static