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RNA_StubCoordinateEnergy.cc File Reference
#include <core/energy_methods/RNA_StubCoordinateEnergy.hh>
#include <core/energy_methods/RNA_StubCoordinateEnergyCreator.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/EnergyGraph.hh>
#include <core/scoring/DenseEnergyContainer.hh>
#include <basic/Tracer.hh>
#include <core/pose/Pose.hh>
#include <core/pose/rna/util.hh>
#include <core/pose/full_model_info/FullModelInfo.hh>
#include <core/pose/full_model_info/FullModelParameters.hh>
#include <core/conformation/Residue.hh>
#include <core/chemical/AtomType.hh>
#include <core/kinematics/Stub.hh>
#include <core/kinematics/RT.hh>
#include <core/scoring/func/HarmonicFunc.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/rna.OptionKeys.gen.hh>
#include <numeric/xyzMatrix.hh>
#include <numeric/xyzVector.hh>
#include <core/id/AtomID.hh>
#include <utility/vector1.hh>

Namespaces

 core
 A class for reading in the atom type properties.
 
 core::energy_methods
 

Functions

static basic::Tracer TR ("core.energy_methods.RNA_StubCoordinateEnergy")
 

Function Documentation

static basic::Tracer TR ( "core.energy_methods.RNA_StubCoordinateEnergy"  )
static

Computes penalty for having an O5' atom far from a target location, as defined by the O3' stub of a previous residue.

Using this for umbrella sampling of end-to-end geometries of RNA loops with rna_denovo– the resulting six-dimensional potential will go into an improved loop_close term for stepwise and other RNA modeling applications

TODO: Ideally, would make a clean version that lives in StubCoordinateConstraint and handles derivatives. Probably could sub-class from CoordinateConstraint.

TODO: Could also use this framework to align rotations of coordinate frames. See notes below.

TODO: Setup still copies a ton of code from RNA_FragmentMonteCarlo. Could be unified if we use Constraint above.

– rhiju, 2017