MembraneEnergyLandscapeSampler.cc File Reference

Sample a protein energy landscape as a function of orientation in the membrane. More...

#include <protocols/membrane_benchmark/MembraneEnergyLandscapeSampler.hh>
#include <protocols/membrane_benchmark/MembraneEnergyLandscapeSamplerCreator.hh>
#include <protocols/membrane/TransformIntoMembraneMover.hh>
#include <protocols/membrane/TranslationRotationMover.hh>
#include <protocols/membrane/util.hh>
#include <protocols/rigid/RigidBodyMover.hh>
#include <protocols/simple_moves/MutateResidue.hh>
#include <core/pose/Pose.hh>
#include <core/types.hh>
#include <core/pose/PDBInfo.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/ScoreType.hh>
#include <core/scoring/Energies.hh>
#include <core/energy_methods/pHEnergy.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/kinematics/Jump.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/task/PackerTask.fwd.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <protocols/minimization_packing/PackRotamersMover.hh>
#include <core/pack/task/operation/TaskOperation.hh>
#include <core/pack/palette/DefaultPackerPalette.hh>
#include <core/conformation/membrane/SpanningTopology.hh>
#include <core/conformation/membrane/Span.hh>
#include <core/conformation/membrane/MembraneInfo.hh>
#include <core/conformation/Conformation.hh>
#include <core/conformation/Residue.hh>
#include <core/scoring/MembranePotential.hh>
#include <core/scoring/MembraneTopology.hh>
#include <core/conformation/util.hh>
#include <core/chemical/AA.hh>
#include <basic/Tracer.hh>
#include <utility/tag/Tag.hh>
#include <utility/io/ozstream.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <basic/options/keys/mp.OptionKeys.gen.hh>
#include <basic/options/keys/pH.OptionKeys.gen.hh>
#include <numeric/conversions.hh>
#include <numeric/xyzVector.io.hh>
#include <numeric/constants.hh>
#include <numeric/HomogeneousTransform.hh>
#include <numeric/xyzMatrix.hh>
#include <numeric/random/random.hh>
#include <utility/pointer/owning_ptr.hh>
#include <utility/down_cast.hh>
#include <utility/vector1.hh>
#include <utility/tag/XMLSchemaGeneration.hh>
#include <protocols/moves/mover_schemas.hh>
#include <ostream>
#include <protocols/rosetta_scripts/util.hh>
#include <utility/string_util.hh>

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

Functions
static basic::Tracer	TR ("protocols.membrane_benchmark.MembraneEnergyLandscapeSampler")
std::ostream &	protocols::membrane_benchmark::operator<< (std::ostream &os, MembraneEnergyLandscapeSampler const &mover)
	private methods /// More...

Detailed Description

Sample a protein energy landscape as a function of orientation in the membrane.

Orientation is sampled as a function of three degrees of freedom: helix tilt relative to the membrane normal, azimuthal angle about its own axis and distance between the membrane center and peptide residue center of mass.

Author

Rebecca F. Alford (rfalf.nosp@m.ord1.nosp@m.2@gma.nosp@m.il.c.nosp@m.om) The code is modified on Sept 26th by Rituparna Samanta (ritup.nosp@m.arna.nosp@m.@utex.nosp@m.as.e.nosp@m.du) An additional degree of freedom is included while sampling the orientation: azimuthal angle beside helix tilt relative to the membrane normal, distance between the membrane center and peptide residue center of mass. Unit headers In this version we have first aligned the peptide to the center of the membrane and along the z-axis. The definition of center is the average of all CA atoms or the center of the axis joining the upper disk and lower disk.

Function Documentation

TR()

static basic::Tracer TR ( "protocols.membrane_benchmark.MembraneEnergyLandscapeSampler"  )

static