swa_rna_main.cc File Reference

#include <protocols/stepwise/legacy/modeler/rna/StepWiseRNA_PoseSetupFromCommandLine.hh>
#include <protocols/stepwise/modeler/StepWiseModeler.hh>
#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/chemical.OptionKeys.gen.hh>
#include <basic/options/keys/cluster.OptionKeys.gen.hh>
#include <basic/options/keys/stepwise.OptionKeys.gen.hh>
#include <basic/options/keys/rna.OptionKeys.gen.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <basic/options/keys/edensity.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/copydofs/util.hh>
#include <core/pose/rna/util.hh>
#include <core/io/pdb/pdb_writer.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/util.hh>
#include <protocols/farna/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/VirtualSugarSamplerFromStringList.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/legacy/modeler/rna/StepWiseRNA_Clusterer.hh>
#include <protocols/stepwise/modeler/rna/checker/RNA_VDW_BinChecker.hh>
#include <protocols/stepwise/modeler/rna/checker/RNA_BaseCentroidChecker.hh>
#include <protocols/stepwise/modeler/util.hh>
#include <protocols/stepwise/modeler/working_parameters/StepWiseWorkingParameters.hh>
#include <protocols/stepwise/legacy/modeler/rna/util.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 <unistd.h>
#include <libgen.h>
#include <list>
#include <stdio.h>
#include <math.h>

Macros
#define	GetCurrentDir   getcwd

Typedefs
typedef numeric::xyzMatrix< Real >	Matrix

Functions
static THREAD_LOCAL basic::Tracer	TR ("swa_rna_main")
void	swa_rna_sample ()
void	swa_rna_cluster ()
void	rna_sample_virtual_sugar ()
void	filter_combine_long_loop ()
void	post_rebuild_bulge_assembly ()
	Oct 22, 2011. More...
void *	my_main (void *)
int	main (int argc, char *argv[])

Detailed Description

Author

Parin Sripakdeevong (sripa.nosp@m.kpa@.nosp@m.stanf.nosp@m.ord..nosp@m.edu), Rhiju Das (rhiju.nosp@m.@sta.nosp@m.nford.nosp@m..edu)

Macro Definition Documentation

#define GetCurrentDir   getcwd

Typedef Documentation

typedef numeric::xyzMatrix< Real > Matrix

Function Documentation

void filter_combine_long_loop

(

)

References basic::options::OptionKeys::chemical::chemical, basic::options::OptionKeys::stepwise::rna::combine_helical_silent_file, utility::io::oc::cout, utility::file::file_exists(), basic::options::OptionKeys::stepwise::rna::filter_output_filename, option, clean_pdb_keep_ligand::outfile, basic::options::OptionKeys::stepwise::rna::parin_favorite_output, app.surface_docking.surface_docking::pose, basic::options::OptionKeys::full_model::rna::rna, runtime_assert, basic::options::OptionKeys::frags::scoring::scoring, in::file::silent(), and basic::options::OptionKeys::inout::dbms::user.

Referenced by my_main().

int main	(	int	argc,
		char *	argv[]
	)

References basic::options::OptionKeys::stepwise::rna::allow_base_pair_only_centroid_screen, basic::options::OptionKeys::stepwise::rna::allow_bulge_at_chainbreak, basic::options::OptionKeys::stepwise::rna::centroid_screen, basic::options::OptionKeys::stepwise::choose_random, basic::options::OptionKeys::stepwise::rna::combine_long_loop_mode, basic::options::OptionKeys::rna::corrected_geo, utility::io::oc::cout, basic::options::OptionKeys::stepwise::rna::distinguish_pucker, basic::options::OptionKeys::stepwise::rna::do_not_sample_multiple_virtual_sugar, basic::options::OptionKeys::rna::farna::erraser::erraser, basic::options::OptionKeys::rna::farna::erraser::fixed_res, basic::options::OptionKeys::stepwise::rna::force_centroid_interaction, basic::init(), basic::options::OptionKeys::magnesium::integration_test, basic::options::OptionKeys::stepwise::rna::minimize_and_score_native_pose, basic::options::OptionKeys::stepwise::rna::minimize_and_score_sugar, basic::options::OptionKeys::stepwise::rna::minimizer_rename_tag, utility::excn::EXCN_Base::msg(), my_main(), basic::options::OptionKeys::stepwise::rna::native_edensity_score_cutoff, NEW_OPT, basic::options::OptionKeys::stepwise::num_pose_minimize, basic::options::OptionKeys::stepwise::num_random_samples, basic::options::OptionKeys::stepwise::rna::o2prime_legacy_mode, option, options, basic::options::OptionKeys::stepwise::rna::parin_favorite_output, basic::options::OptionKeys::stepwise::rna::PBP_clustering_at_chain_closure, basic::options::OptionKeys::cluster::radius, basic::options::OptionKeys::stepwise::rna::reinitialize_CCD_torsions, basic::options::OptionKeys::stepwise::rna::rm_virt_phosphate, basic::options::OptionKeys::stepwise::rna::sample_both_sugar_base_rotamer, basic::options::OptionKeys::stepwise::rna::sample_ONLY_multiple_virtual_sugar, basic::options::OptionKeys::stepwise::rna::sampler_allow_syn_pyrimidine, basic::options::OptionKeys::stepwise::rna::sampler_assert_no_virt_sugar_sampling, basic::options::OptionKeys::stepwise::rna::sampler_extra_beta_rotamer, basic::options::OptionKeys::stepwise::rna::sampler_extra_chi_rotamer, basic::options::OptionKeys::stepwise::rna::sampler_extra_epsilon_rotamer, basic::options::OptionKeys::stepwise::rna::sampler_include_torsion_value_in_tag, basic::options::OptionKeys::stepwise::rna::sampler_num_pose_kept, basic::options::OptionKeys::stepwise::rna::sampler_try_sugar_instantiation, basic::options::OptionKeys::cluster::score_diff_cut, basic::options::OptionKeys::rna::farna::erraser::skip_minimize, basic::options::OptionKeys::stepwise::use_green_packer, basic::options::OptionKeys::stepwise::rna::VDW_atr_rep_screen, basic::options::OptionKeys::stepwise::rna::VDW_rep_alignment_RMSD_CUTOFF, basic::options::OptionKeys::stepwise::rna::VDW_rep_delete_matching_res, basic::options::OptionKeys::stepwise::rna::VDW_rep_screen_info, basic::options::OptionKeys::stepwise::rna::VDW_rep_screen_physical_pose_clash_dist_cutoff, basic::options::OptionKeys::stepwise::VERBOSE, basic::options::OptionKeys::stepwise::rna::virtual_sugar_keep_base_fixed, and basic::options::OptionKeys::stepwise::rna::virtual_sugar_legacy_mode.

void* my_main

(

void *

)

References utility::io::oc::cout, utility::options::OptionKeys::options::exit, filter_combine_long_loop(), option, options, post_rebuild_bulge_assembly(), basic::options::OptionKeys::full_model::rna::rna, rna_sample_virtual_sugar(), swa_rna_cluster(), swa_rna_sample(), and utility_exit_with_message.

Referenced by main().

void post_rebuild_bulge_assembly

(

)

Oct 22, 2011.

References ObjexxFCL::abs(), basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, create_scorefxn(), basic::options::OptionKeys::stepwise::dump, basic::options::OptionKeys::matdes::dock::dump_pdb, app.delta_score_per_mutation::mm, basic::options::OptionKeys::optimization::optimization, option, options, app.surface_docking.surface_docking::pose, basic::options::OptionKeys::stepwise::rna::protonated_H1_adenosine_list, basic::options::OptionKeys::full_model::rna::rna, runtime_assert, PyMOL_demo::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, in::file::silent(), basic::options::OptionKeys::in::file::silent, out::file::silent(), amino_acids::size, app.surface_docking.surface_docking::start_pose, ObjexxFCL::string_of(), in::file::tags(), TR(), basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.

Referenced by my_main().

void rna_sample_virtual_sugar

(

)

References basic::options::OptionKeys::chemical::chemical, basic::options::OptionKeys::stepwise::choose_random, basic::options::OptionKeys::rna::corrected_geo, create_scorefxn(), basic::options::OptionKeys::stepwise::rna::integration_test, option, app.surface_docking.surface_docking::pose, basic::options::OptionKeys::full_model::rna::rna, runtime_assert, PyMOL_demo::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, in::file::silent(), out::file::silent(), TR(), basic::options::OptionKeys::inout::dbms::user, and basic::options::OptionKeys::stepwise::rna::virtual_sugar_legacy_mode.

Referenced by my_main().

void swa_rna_cluster

(

)

References utility::io::oc::cout, basic::options::OptionKeys::stepwise::rna::distinguish_pucker, basic::options::OptionKeys::stepwise::dump, utility::file::file_exists(), option, clean_pdb_keep_ligand::outfile, basic::options::OptionKeys::stepwise::rna::PBP_clustering_at_chain_closure, basic::options::OptionKeys::stepwise::rna::rmsd_res, basic::options::OptionKeys::full_model::rna::rna, runtime_assert, basic::options::OptionKeys::cluster::score_diff_cut, in::file::silent(), out::file::silent(), ObjexxFCL::string_of(), TR(), basic::options::OptionKeys::inout::dbms::user, utility_exit_with_message, basic::options::OptionKeys::stepwise::rna::VDW_rep_alignment_RMSD_CUTOFF, basic::options::OptionKeys::stepwise::rna::VDW_rep_delete_matching_res, basic::options::OptionKeys::stepwise::rna::VDW_rep_screen_info, basic::options::OptionKeys::stepwise::rna::VDW_rep_screen_physical_pose_clash_dist_cutoff, basic::options::OptionKeys::stepwise::VERBOSE, and basic::options::OptionKeys::full_model::virtual_res.

Referenced by my_main().

void swa_rna_sample

(

)

References basic::Tracer::Blue, basic::options::OptionKeys::chemical::chemical, create_scorefxn(), in::file::native(), test.Workshop7test::native_pose, out::nstruct(), option, app.surface_docking.surface_docking::pose, basic::Tracer::Reset, basic::options::OptionKeys::full_model::rna::rna, PyMOL_demo::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, out::file::silent(), app.surface_docking.surface_docking::start_pose, basic::options::OptionKeys::stepwise::test_encapsulation, TR(), and basic::options::OptionKeys::inout::dbms::user.

Referenced by my_main().

static THREAD_LOCAL basic::Tracer TR ( "swa_rna_main"  )

static

Referenced by post_rebuild_bulge_assembly(), rna_sample_virtual_sugar(), swa_rna_cluster(), and swa_rna_sample().