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util.cc File Reference
#include <protocols/stepwise/modeler/rna/util.hh>
#include <protocols/stepwise/modeler/rna/rigid_body/util.hh>
#include <protocols/stepwise/sampler/rna/RNA_NucleosideStepWiseSampler.hh>
#include <protocols/stepwise/modeler/output_util.hh>
#include <core/chemical/rna/RNA_FittedTorsionInfo.hh>
#include <core/chemical/rna/util.hh>
#include <protocols/rna/movers/RNA_LoopCloser.hh>
#include <protocols/stepwise/modeler/working_parameters/StepWiseWorkingParameters.hh>
#include <protocols/stepwise/modeler/rna/checker/RNA_VDW_BinChecker.hh>
#include <protocols/toolbox/rigid_body/util.hh>
#include <protocols/stepwise/sampler/rigid_body/EulerAngles.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/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::modeler
 
 protocols::stepwise::modeler::rna
 
 protocols::stepwise::modeler::rna::rigid_body
 

Functions

static basic::Tracer TR ("protocols.stepwise.modeler.rna.rigid_body.util")
 
core::Real protocols::stepwise::modeler::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::modeler::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, core::Size const gap_size_to_anchor)
 
utility::vector1
< core::pose::PoseOP
protocols::stepwise::modeler::rna::rigid_body::setup_pose_with_moving_residue_alternative_list (pose::Pose const &pose, core::Size const &moving_res, bool const extra_chi, bool const use_phenix_geo)
 
int protocols::stepwise::modeler::rna::rigid_body::DOF_bin_value (BaseBin const &base_bin, std::string const &DOF)
 
Real protocols::stepwise::modeler::rna::rigid_body::DOF_bin_size (std::string const &DOF)
 
void protocols::stepwise::modeler::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::modeler::rna::rigid_body::analyze_base_bin_map (std::map< BaseBin, int, compare_base_bin > const &base_bin_map, std::string const &foldername)
 

Function Documentation

static basic::Tracer TR ( "protocols.stepwise.modeler.rna.rigid_body.util"  )
static