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util.cc File Reference
#include <protocols/toolbox/sample_around/util.hh>
#include <protocols/toolbox/rigid_body/util.hh>
#include <core/scoring/rms_util.hh>
#include <core/types.hh>
#include <core/chemical/AA.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/util.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/ScoringManager.hh>
#include <core/chemical/rna/util.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/Jump.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/kinematics/Stub.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/io/silent/BinarySilentStruct.hh>
#include <utility/io/ozstream.hh>
#include <core/pose/util.hh>
#include <core/pose/Pose.hh>
#include <core/init/init.hh>
#include <utility/vector1.hh>
#include <utility/io/izstream.hh>
#include <numeric/xyzVector.hh>
#include <numeric/conversions.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/string.functions.hh>
#include <core/import_pose/import_pose.hh>
#include <protocols/viewer/viewers.hh>
#include <basic/options/option.hh>
#include <basic/options/option_macros.hh>
#include <basic/options/keys/sample_around.OptionKeys.gen.hh>
#include <fstream>
#include <iostream>
#include <string>
#include <basic/Tracer.hh>

Namespaces

 protocols
 The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.
 
 protocols::toolbox
 
 protocols::toolbox::sample_around
 

Typedefs

using Matrix = numeric::xyzMatrix< Real >
 

Functions

static basic::Tracer TR ("protocols.toolbox.sample_around.util")
 
void protocols::toolbox::sample_around::add_virtual_res (core::pose::Pose &pose, bool set_res_as_root)
 
void protocols::toolbox::sample_around::add_another_virtual_res (core::pose::Pose &pose)
 
void protocols::toolbox::sample_around::rotate_into_nucleobase_frame (core::pose::Pose &pose)
 
void protocols::toolbox::sample_around::rotate_into_phosphate_frame (core::pose::Pose &pose, core::Size const n, bool const center_on_OP2)
 
Real protocols::toolbox::sample_around::centroid_dist (core::pose::Pose &pose, bool const sample_another_adenosine_)
 
Real protocols::toolbox::sample_around::sample_all_rotations_at_jump (pose::Pose &pose, core::Size const num_jump, scoring::ScoreFunctionOP scorefxn)
 
Real protocols::toolbox::sample_around::do_scoring (pose::Pose &pose, scoring::ScoreFunctionOP scorefxn, bool const &sample_rotations, core::Size const probe_jump_num)
 
void protocols::toolbox::sample_around::do_xy_scan (pose::Pose &pose, scoring::ScoreFunctionOP scorefxn, std::string const &outfile, Real const z, core::Size const probe_jump_num, Real const box_bins, Real const translation_increment, bool const sample_rotations)
 

Detailed Description

Author
Rhiju Das, rhiju.nosp@m.@sta.nosp@m.nford.nosp@m..edu

Typedef Documentation

using Matrix = numeric::xyzMatrix<Real>

Function Documentation

static basic::Tracer TR ( "protocols.toolbox.sample_around.util"  )
static