StepWiseRNA_PoseSetupFromCommandLine.cc File Reference

#include <core/types.hh>
#include <core/chemical/AA.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/ResidueSelector.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/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/io/pdb/pose_io.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/farna/RNA_ProtocolUtil.hh>
#include <protocols/farna/RNA_LoopCloser.hh>
#include <protocols/stepwise/sampling/rna/StepWiseRNA_OutputData.hh>
#include <protocols/stepwise/sampling/rna/StepWiseRNA_CombineLongLoopFilterer.hh>
#include <protocols/stepwise/sampling/rna/StepWiseRNA_CombineLongLoopFilterer.fwd.hh>
#include <protocols/stepwise/sampling/rna/sugar/StepWiseRNA_VirtualSugarSampler.hh>
#include <protocols/stepwise/sampling/rna/StepWiseRNA_Minimizer.hh>
#include <protocols/stepwise/sampling/rna/StepWiseRNA_ResidueSampler.hh>
#include <protocols/stepwise/sampling/rna/StepWiseRNA_Modeler.hh>
#include <protocols/stepwise/sampling/rna/legacy/StepWiseRNA_PoseSetup.fwd.hh>
#include <protocols/stepwise/sampling/rna/legacy/StepWiseRNA_PoseSetup.hh>
#include <protocols/stepwise/sampling/rna/legacy/StepWiseRNA_JobParametersSetup.hh>
#include <protocols/stepwise/sampling/rna/StepWiseRNA_JobParameters.hh>
#include <protocols/stepwise/sampling/rna/StepWiseRNA_Clusterer.hh>
#include <protocols/stepwise/sampling/rna/checker/RNA_VDW_BinChecker.hh>
#include <protocols/stepwise/sampling/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 <stdio.h>
#include <math.h>

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::legacy

Macros
#define	GetCurrentDir   getcwd

Typedefs
typedef numeric::xyzMatrix< Real >	Matrix

Functions
void	protocols::stepwise::sampling::rna::legacy::apply_chi_cst (core::pose::Pose &pose, core::pose::Pose const &ref_pose)
std::string	protocols::stepwise::sampling::rna::legacy::get_working_directory ()
utility::vector1< core::Size >	protocols::stepwise::sampling::rna::legacy::get_fixed_res (core::Size const nres)
bool	protocols::stepwise::sampling::rna::legacy::is_nonempty_input_silent_file (std::string const input_silent_file, std::string const exit_key_string)
utility::vector1< core::Size >	protocols::stepwise::sampling::rna::legacy::get_input_res (core::Size const nres, std::string const pose_num)
utility::vector1< std::string >	protocols::stepwise::sampling::rna::legacy::get_silent_file_tags ()
core::scoring::ScoreFunctionOP	protocols::stepwise::sampling::rna::legacy::create_scorefxn ()
StepWiseRNA_JobParametersOP	protocols::stepwise::sampling::rna::legacy::setup_simple_full_length_rna_job_parameters ()
StepWiseRNA_JobParametersOP	protocols::stepwise::sampling::rna::legacy::setup_rna_job_parameters (bool check_for_previously_closed_cutpoint_with_input_pose)
void	protocols::stepwise::sampling::rna::legacy::setup_copy_DOF_input (StepWiseRNA_PoseSetupOP &stepwise_rna_pose_setup)
StepWiseRNA_PoseSetupOP	protocols::stepwise::sampling::rna::legacy::setup_pose_setup_class (StepWiseRNA_JobParametersOP &job_parameters, bool const copy_DOF)
void	protocols::stepwise::sampling::rna::legacy::check_if_silent_file_exists ()
bool	protocols::stepwise::sampling::rna::legacy::get_tag_and_silent_file_for_struct (std::string &swa_silent_file, std::string &out_tag, Size const &n, bool const &multiple_shots, std::string const &silent_file)
void	protocols::stepwise::sampling::rna::legacy::ensure_directory_for_out_silent_file_exists ()

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

Detailed Description

Detailed:

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::sampling::rna::legacy::get_working_directory().

Typedef Documentation

typedef numeric::xyzMatrix< Real > Matrix

Variable Documentation

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

static

Referenced by protocols::stepwise::sampling::rna::legacy::check_if_silent_file_exists(), protocols::stepwise::sampling::rna::legacy::create_scorefxn(), protocols::stepwise::sampling::rna::legacy::ensure_directory_for_out_silent_file_exists(), protocols::stepwise::sampling::rna::legacy::get_fixed_res(), protocols::stepwise::sampling::rna::legacy::get_input_res(), protocols::stepwise::sampling::rna::legacy::get_silent_file_tags(), protocols::stepwise::sampling::rna::legacy::get_tag_and_silent_file_for_struct(), protocols::stepwise::sampling::rna::legacy::is_nonempty_input_silent_file(), protocols::stepwise::sampling::rna::legacy::setup_copy_DOF_input(), protocols::stepwise::sampling::rna::legacy::setup_pose_setup_class(), protocols::stepwise::sampling::rna::legacy::setup_rna_job_parameters(), and protocols::stepwise::sampling::rna::legacy::setup_simple_full_length_rna_job_parameters().