StepWiseRNA_FloatingBaseSamplerUtil.cc File Reference

#include <protocols/stepwise/sampling/rna/StepWiseRNA_Util.hh>
#include <protocols/stepwise/sampling/rna/rigid_body/StepWiseRNA_FloatingBaseSamplerUtil.hh>
#include <protocols/rotamer_sampler/rna/RNA_NucleosideRotamer.hh>
#include <core/chemical/rna/RNA_FittedTorsionInfo.hh>
#include <core/chemical/rna/RNA_Util.hh>
#include <protocols/farna/RNA_LoopCloser.hh>
#include <protocols/stepwise/sampling/rna/StepWiseRNA_JobParameters.hh>
#include <protocols/stepwise/sampling/rna/checker/RNA_VDW_BinChecker.hh>
#include <protocols/rotamer_sampler/rigid_body/FloatingBaseUtil.hh>
#include <core/optimization/MinimizerOptions.hh>
#include <core/id/TorsionID.hh>
#include <basic/Tracer.hh>
#include <core/types.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/util.hh>
#include <core/chemical/VariantType.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/AtomType.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/pose/Pose.hh>
#include <core/io/pdb/pose_io.hh>
#include <core/scoring/rna/RNA_TorsionPotential.hh>
#include <core/scoring/rms_util.tmpl.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/constraints/ConstraintSet.fwd.hh>
#include <core/scoring/constraints/AtomPairConstraint.hh>
#include <core/scoring/constraints/AngleConstraint.hh>
#include <core/scoring/constraints/util.hh>
#include <set>
#include <numeric/conversions.hh>
#include <numeric/NumericTraits.hh>
#include <iostream>
#include <fstream>
#include <sstream>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/string.functions.hh>
#include <core/scoring/ScoreFunction.hh>

Namespaces
	protocols
	The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.
	protocols::stepwise
	protocols::stepwise::sampling
	protocols::stepwise::sampling::rna
	protocols::stepwise::sampling::rna::rigid_body

Functions
core::kinematics::Stub	protocols::stepwise::sampling::rna::rigid_body::get_sugar_stub (conformation::Residue const &rsd, bool const is_prepend, bool const verbose)
BaseBin	protocols::stepwise::sampling::rna::rigid_body::get_euler_stub_bin (numeric::xyzVector< core::Real > const &centroid, rotamer_sampler::rigid_body::EulerAngles const &euler_angles)
int	protocols::stepwise::sampling::rna::rigid_body::DOF_bin_value (std::map< BaseBin, int, compare_base_bin >::const_iterator const &base_bin_it, std::string const &DOF)
Real	protocols::stepwise::sampling::rna::rigid_body::DOF_bin_size (std::string const &DOF)
void	protocols::stepwise::sampling::rna::rigid_body::analyze_base_bin_map (std::map< BaseBin, int, compare_base_bin > const &base_bin_map, std::string const &DOF_one, std::string const &DOF_two, std::string const foldername)
void	protocols::stepwise::sampling::rna::rigid_body::analyze_base_bin_map (std::map< BaseBin, int, compare_base_bin > const &base_bin_map, std::string const foldername)
void	protocols::stepwise::sampling::rna::rigid_body::translate_then_rotate_pose (core::pose::Pose &pose, numeric::xyzVector< core::Real > const &vector, numeric::xyzMatrix< core::Real > const matrix, bool const verbose)
core::Real	protocols::stepwise::sampling::rna::rigid_body::get_max_centroid_to_atom_distance (utility::vector1< core::conformation::ResidueOP > const &rsd_at_origin_list, std::string const atom_name)
void	protocols::stepwise::sampling::rna::rigid_body::initialize_xyz_parameters (Distance &max_distance, Distance &max_distance_squared, int &centroid_bin_min, int &centroid_bin_max, utility::vector1< core::conformation::ResidueOP > const &moving_rsd_at_origin_list, Size const gap_size_to_anchor)
utility::vector1 < core::conformation::ResidueOP >	protocols::stepwise::sampling::rna::rigid_body::setup_residue_at_origin_list (pose::Pose const &pose, Size const &moving_res, bool const extra_chi, bool const use_phenix_geo)
utility::vector1 < core::pose::PoseOP >	protocols::stepwise::sampling::rna::rigid_body::setup_pose_at_origin_list (pose::Pose const &pose, Size const &moving_res, bool const extra_chi, bool const use_phenix_geo)
utility::vector1 < core::pose::PoseOP >	protocols::stepwise::sampling::rna::rigid_body::setup_pose_with_moving_residue_alternative_list (pose::Pose const &pose, Size const &moving_res, bool const extra_chi, bool const use_phenix_geo)

Variables
static basic::Tracer	TR ("protocols.stepwise.rna.StepWiseRNA_FloatingBaseSamplerUtil")

Variable Documentation

basic::Tracer TR("protocols.stepwise.rna.StepWiseRNA_FloatingBaseSamplerUtil")

static