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rna_rotamer_building_functions.cc File Reference

RNA nucleotide rotamer set class implementation. More...

#include <core/pack/rotamer_set/rotamer_building_functions.hh>
#include <core/pack/rotamer_set/RotamerCouplings.hh>
#include <core/pack/rotamer_set/RotamerSet.hh>
#include <core/pack/rotamer_set/RotamerSets.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/RotamerSampleOptions.hh>
#include <core/pack/task/rna/RNA_ResidueLevelTask.hh>
#include <core/pack/dunbrack/ChiSet.hh>
#include <core/pack/rotamers/SingleResidueRotamerLibrary.hh>
#include <core/pack/rotamers/SingleResidueRotamerLibraryFactory.hh>
#include <core/scoring/rna/RNA_TorsionPotential.hh>
#include <core/scoring/rna/RNA_EnergyMethodOptions.hh>
#include <core/chemical/AtomType.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/ResidueType.hh>
#include <core/chemical/rna/RNA_Info.hh>
#include <core/chemical/rna/util.hh>
#include <core/chemical/rna/RNA_SamplerUtil.hh>
#include <core/conformation/Atom.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueMatcher.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/kinematics/Stub.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/scoring/func/Func.hh>
#include <core/scoring/func/HarmonicFunc.hh>
#include <core/scoring/constraints/AtomPairConstraint.hh>
#include <core/scoring/constraints/AngleConstraint.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/chemical/rna/RNA_FittedTorsionInfo.hh>
#include <core/pose/Pose.hh>
#include <core/pose/variant_util.hh>
#include <basic/Tracer.hh>
#include <basic/datacache/BasicDataCache.hh>
#include <basic/database/open.hh>
#include <numeric/xyz.functions.hh>
#include <numeric/angle.functions.hh>
#include <numeric/constants.hh>
#include <utility/io/izstream.hh>
#include <utility/vector1.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/FArray3D.hh>
#include <string>
#include <iostream>
#include <fstream>

Namespaces

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

Functions

static basic::Tracer core::pack::rotamer_set::TR ("core.pack.rotamer_set.rna_rotamer_building_functions", basic::t_info)
 
void core::pack::rotamer_set::fill_chi_rotamers_with_center_and_stddev (conformation::ResidueOP const &rot, utility::vector1< conformation::ResidueOP > &rotamers, utility::vector1< Real > const &chi_steps, Real const &center, Real const &width)
 
void core::pack::rotamer_set::add_rna_chi_rotamers (conformation::ResidueOP const &rot, utility::vector1< conformation::ResidueOP > &rotamers, pack::task::ExtraRotSample const &level, utility::vector1< chemical::rna::GaussianParameter > const &gaussian_parameter_set)
 
void core::pack::rotamer_set::build_rna_chi_rotamers (Size const resid, pose::Pose const &pose, chemical::ResidueTypeCOP concrete_residue, pack::task::ExtraRotSample const &level, bool const sample_rna_chi, bool const &include_current, utility::vector1< conformation::ResidueOP > &rotamers)
 
void core::pack::rotamer_set::build_proton_chi_rotamers (Size const , pose::Pose const &pose, chemical::ResidueTypeCOP concrete_residue, pack::task::ResidueLevelTask const &residue_task, utility::vector1< conformation::ResidueOP > &rotamers)
 
void core::pack::rotamer_set::build_five_prime_phosphate_rotamers (utility::vector1< conformation::ResidueOP > &rotamers, pose::Pose const &pose, bool const allow_phosphate_virtualization)
 
void core::pack::rotamer_set::build_three_prime_phosphate_rotamers (utility::vector1< conformation::ResidueOP > &rotamers, pose::Pose const &pose, bool const allow_phosphate_virtualization)
 
void core::pack::rotamer_set::build_rna_rotamers (Size const resid, pose::Pose const &pose, chemical::ResidueTypeCOP concrete_residue, pack::task::PackerTask const &task, utility::vector1< conformation::ResidueOP > &new_rotamers, Size &id_for_current_rotamer)
 

Detailed Description

RNA nucleotide rotamer set class implementation.

Author
Rhiju Das (rhiju.nosp@m.@sta.nosp@m.nford.nosp@m..edu), Andrew Leaver-Fay (leave.nosp@m.rfa@.nosp@m.email.nosp@m..unc.nosp@m..edu)