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StepWiseRNA_PoseSetupFromCommandLine.cc File Reference
#include <core/types.hh>
#include <core/chemical/AA.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/VariantType.hh>
#include <core/chemical/util.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/conformation/ResidueMatcher.hh>
#include <core/conformation/Conformation.hh>
#include <core/scoring/ScoringManager.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/chemical/rna/RNA_FittedTorsionInfo.hh>
#include <core/chemical/rna/util.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/EnergyGraph.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/EnergyMap.hh>
#include <core/scoring/EnergyMap.fwd.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/func/CharmmPeriodicFunc.hh>
#include <core/scoring/constraints/DihedralConstraint.hh>
#include <core/sequence/util.hh>
#include <core/sequence/Sequence.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/tree/Atom.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/id/AtomID_Map.hh>
#include <core/id/AtomID.hh>
#include <core/id/DOF_ID.hh>
#include <core/init/init.hh>
#include <utility/file/file_sys_util.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/rna.OptionKeys.gen.hh>
#include <basic/options/keys/stepwise.OptionKeys.gen.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <basic/options/keys/full_model.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/OptionKeys.hh>
#include <basic/options/option_macros.hh>
#include <basic/Tracer.hh>
#include <protocols/idealize/idealize.hh>
#include <core/optimization/AtomTreeMinimizer.hh>
#include <core/optimization/MinimizerOptions.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <utility/vector1.hh>
#include <utility/io/ozstream.hh>
#include <utility/io/izstream.hh>
#include <utility/excn/Exceptions.hh>
#include <numeric/xyzVector.hh>
#include <numeric/conversions.hh>
#include <core/pose/MiniPose.hh>
#include <core/pose/util.hh>
#include <core/pose/rna/util.hh>
#include <core/io/silent/SilentStruct.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/io/silent/util.hh>
#include <core/import_pose/pose_stream/SilentFilePoseInputStream.hh>
#include <core/import_pose/import_pose.hh>
#include <protocols/viewer/viewers.hh>
#include <protocols/rna/movers/RNA_LoopCloser.hh>
#include <protocols/stepwise/modeler/rna/StepWiseRNA_OutputData.hh>
#include <protocols/stepwise/modeler/rna/StepWiseRNA_CombineLongLoopFilterer.hh>
#include <protocols/stepwise/modeler/rna/StepWiseRNA_CombineLongLoopFilterer.fwd.hh>
#include <protocols/stepwise/modeler/rna/sugar/VirtualSugarSampler.hh>
#include <protocols/stepwise/legacy/modeler/rna/StepWiseRNA_Minimizer.hh>
#include <protocols/stepwise/legacy/modeler/rna/StepWiseRNA_PoseSetup.fwd.hh>
#include <protocols/stepwise/legacy/modeler/rna/StepWiseRNA_PoseSetup.hh>
#include <protocols/stepwise/legacy/modeler/rna/StepWiseRNA_WorkingParametersSetup.hh>
#include <protocols/stepwise/modeler/working_parameters/StepWiseWorkingParameters.hh>
#include <protocols/stepwise/legacy/modeler/rna/StepWiseRNA_Clusterer.hh>
#include <protocols/stepwise/legacy/modeler/rna/util.hh>
#include <protocols/stepwise/modeler/rna/checker/RNA_VDW_BinChecker.hh>
#include <protocols/stepwise/modeler/rna/checker/RNA_BaseCentroidChecker.hh>
#include <ObjexxFCL/string.functions.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/FArray1D.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <fstream>
#include <iostream>
#include <sstream>
#include <string>
#include <algorithm>
#include <cctype>
#include <iomanip>
#include <map>
#include <cstdlib>
#include <ctime>
#include <libgen.h>
#include <unistd.h>
#include <list>
#include <cstdio>
#include <cmath>

Namespaces

 protocols
 The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.
 
 protocols::stepwise
 
 protocols::stepwise::legacy
 
 protocols::stepwise::legacy::modeler
 
 protocols::stepwise::legacy::modeler::rna
 

Macros

#define GetCurrentDir   getcwd
 

Typedefs

using Matrix = numeric::xyzMatrix< Real >
 

Functions

static basic::Tracer TR ("protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetupFromCommandLine")
 
void protocols::stepwise::legacy::modeler::rna::apply_chi_cst (core::pose::Pose &pose, core::pose::Pose const &ref_pose)
 
std::string protocols::stepwise::legacy::modeler::rna::get_working_directory ()
 
utility::vector1< core::Sizeprotocols::stepwise::legacy::modeler::rna::get_fixed_res (core::Size const nres)
 
bool protocols::stepwise::legacy::modeler::rna::is_nonempty_input_silent_file (std::string const &input_silent_file, std::string const &exit_key_string)
 
utility::vector1< core::Sizeprotocols::stepwise::legacy::modeler::rna::get_input_res (core::Size const nres, std::string const &pose_num)
 
utility::vector1< std::string > protocols::stepwise::legacy::modeler::rna::get_silent_file_tags ()
 
core::scoring::ScoreFunctionOP protocols::stepwise::legacy::modeler::rna::create_scorefxn ()
 
stepwise::modeler::working_parameters::StepWiseWorkingParametersOP protocols::stepwise::legacy::modeler::rna::setup_simple_full_length_rna_working_parameters ()
 
stepwise::modeler::working_parameters::StepWiseWorkingParametersOP protocols::stepwise::legacy::modeler::rna::setup_rna_working_parameters (bool check_for_previously_closed_cutpoint_with_input_pose)
 
void protocols::stepwise::legacy::modeler::rna::setup_copy_DOF_input (StepWiseRNA_PoseSetupOP &stepwise_rna_pose_setup)
 
StepWiseRNA_PoseSetupOP protocols::stepwise::legacy::modeler::rna::setup_pose_setup_class (stepwise::modeler::working_parameters::StepWiseWorkingParametersOP &working_parameters, bool const copy_DOF)
 
bool protocols::stepwise::legacy::modeler::rna::get_tag_and_silent_file_for_struct (std::string &swa_silent_file, std::string &out_tag, core::Size const &n, bool const &multiple_shots, std::string const &silent_file)
 
void protocols::stepwise::legacy::modeler::rna::ensure_directory_for_out_silent_file_exists ()
 

Detailed Description

Author
Rhiju Das, rhiju.nosp@m.@sta.nosp@m.nford.nosp@m..edu, based on Parin Sripakdeevong's work

Macro Definition Documentation

#define GetCurrentDir   getcwd

Typedef Documentation

using Matrix = numeric::xyzMatrix<Real>

Function Documentation

static basic::Tracer TR ( "protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetupFromCommandLine"  )
static