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::Size >	protocols::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::Size >	protocols::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

Referenced by protocols::stepwise::legacy::modeler::rna::get_working_directory().

Typedef Documentation

using Matrix = numeric::xyzMatrix<Real>

Function Documentation

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

static

Referenced by protocols::stepwise::legacy::modeler::rna::create_scorefxn(), protocols::stepwise::legacy::modeler::rna::ensure_directory_for_out_silent_file_exists(), protocols::stepwise::legacy::modeler::rna::get_fixed_res(), protocols::stepwise::legacy::modeler::rna::get_input_res(), protocols::stepwise::legacy::modeler::rna::get_silent_file_tags(), protocols::stepwise::legacy::modeler::rna::get_tag_and_silent_file_for_struct(), protocols::stepwise::legacy::modeler::rna::is_nonempty_input_silent_file(), protocols::stepwise::legacy::modeler::rna::setup_copy_DOF_input(), protocols::stepwise::legacy::modeler::rna::setup_pose_setup_class(), protocols::stepwise::legacy::modeler::rna::setup_rna_working_parameters(), and protocols::stepwise::legacy::modeler::rna::setup_simple_full_length_rna_working_parameters().