add_delete_monte_carlo.cc File Reference

#include <core/types.hh>
#include <core/chemical/AA.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/ResidueTypeSelector.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/Conformation.hh>
#include <protocols/moves/MonteCarlo.hh>
#include <core/scoring/ScoringManager.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/chemical/rna/RNA_FittedTorsionInfo.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/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/types.hh>
#include <core/id/TorsionID.hh>
#include <core/id/AtomID_Map.hh>
#include <core/id/AtomID.hh>
#include <core/id/DOF_ID.hh>
#include <devel/init.hh>
#include <core/pose/datacache/CacheableDataType.hh>
#include <basic/datacache/BasicDataCache.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <basic/options/option.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 <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/tools/make_vector1.hh>
#include <utility/io/ozstream.hh>
#include <utility/io/izstream.hh>
#include <numeric/xyzVector.hh>
#include <numeric/conversions.hh>
#include <core/pose/MiniPose.hh>
#include <core/pose/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/BinarySilentStruct.hh>
#include <core/import_pose/pose_stream/SilentFilePoseInputStream.hh>
#include <core/import_pose/import_pose.hh>
#include <protocols/viewer/viewers.hh>
#include <protocols/rna/denovo/util.hh>
#include <protocols/rna/movers/RNA_LoopCloser.hh>
#include <protocols/stepwise/legacy/modeler/rna/StepWiseRNA_PoseSetupFromCommandLine.hh>
#include <protocols/stepwise/modeler/rna/StepWiseRNA_OutputData.hh>
#include <protocols/stepwise/modeler/rna/StepWiseRNA_ResidueSampler.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/rna/StepWiseWorkingParameters.hh>
#include <protocols/stepwise/modeler/rna/StepWiseWorkingParametersUtil.hh>
#include <core/pose/full_model_info/FullModelInfo.hh>
#include <protocols/stepwise/monte_carlo/rna/RNA_AddMover.hh>
#include <protocols/stepwise/monte_carlo/rna/RNA_DeleteMover.hh>
#include <protocols/stepwise/monte_carlo/rna/RNA_AddOrDeleteMover.hh>
#include <protocols/stepwise/monte_carlo/rna/RNA_FromScratchMover.hh>
#include <protocols/stepwise/monte_carlo/rna/RNA_O2PrimeMover.hh>
#include <protocols/stepwise/monte_carlo/rna/RNA_TorsionMover.hh>
#include <protocols/stepwise/monte_carlo/rna/RNA_AddDeleteMonteCarlo.hh>
#include <protocols/stepwise/monte_carlo/SWA_Move.hh>
#include <numeric/random/random.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 <list>
#include <stdio.h>
#include <math.h>

Typedefs
typedef numeric::xyzMatrix< Real >	Matrix

Functions
OPT_KEY(Boolean, add_virt_root) using namespace protocols void	swa_rna_sample ()
void *	my_main (void *)
int	main (int argc, char *argv[])

Typedef Documentation

Matrix

typedef numeric::xyzMatrix< Real > Matrix

Function Documentation

main()

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

References basic::options::OptionKeys::stepwise::rna::add_virt_root, basic::options::OptionKeys::stepwise::rna::alignment_res, 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::allow_chain_boundary_jump_partner_right_at_fixed_BP, basic::options::OptionKeys::stepwise::rna::allow_fixed_res_at_moving_res, argv, basic::options::OptionKeys::full_model::rna::bulge_res, basic::options::OptionKeys::stepwise::rna::centroid_screen, basic::options::OptionKeys::stepwise::rna::combine_helical_silent_file, basic::options::OptionKeys::full_model::cutpoint_closed, basic::options::OptionKeys::full_model::cutpoint_open, basic::options::OptionKeys::stepwise::rna::distinguish_pucker, basic::options::OptionKeys::stepwise::rna::do_not_sample_multiple_virtual_sugar, test.T009_Exceptions::e, basic::options::OptionKeys::dna::specificity::fast, basic::options::OptionKeys::stepwise::rna::filter_output_filename, basic::options::OptionKeys::stepwise::rna::filter_user_alignment_res, basic::options::OptionKeys::rna::erraser::fixed_res, basic::options::OptionKeys::stepwise::rna::floating_base, basic::options::OptionKeys::full_model::rna::force_north_sugar_list, basic::options::OptionKeys::full_model::rna::force_south_sugar_list, basic::options::OptionKeys::full_model::rna::force_syn_chi_res_list, basic::options::OptionKeys::stepwise::rna::global_sample_res_list, basic::init(), basic::options::OptionKeys::in::file::input_res, basic::options::OptionKeys::stepwise::input_res2, basic::options::OptionKeys::magnesium::integration_test, basic::options::OptionKeys::stepwise::rna::job_queue_ID, basic::options::OptionKeys::stepwise::rna::jump_point_pairs, basic::options::OptionKeys::relax::range::kT, basic::options::OptionKeys::in::file::minimize_res, basic::options::OptionKeys::stepwise::rna::missing_res, basic::options::OptionKeys::stepwise::rna::missing_res2, my_main(), basic::options::OptionKeys::stepwise::protein::n_sample, basic::options::OptionKeys::stepwise::rna::native_alignment_res, basic::options::OptionKeys::stepwise::rna::native_virtual_res, NEW_OPT, basic::options::OptionKeys::stepwise::rna::output_extra_RMSDs, output_pdb(), basic::options::OptionKeys::stepwise::rna::parin_favorite_output, basic::options::OptionKeys::stepwise::rna::PBP_clustering_at_chain_closure, basic::options::OptionKeys::stepwise::rna::protonated_H1_adenosine_list, basic::options::OptionKeys::stepwise::rna::rebuild_bulge_mode, basic::options::OptionKeys::stepwise::rna::reinitialize_CCD_torsions, basic::options::OptionKeys::stepwise::rna::rmsd_res, basic::options::OptionKeys::stepwise::rna::sample_both_sugar_base_rotamer, basic::options::OptionKeys::stepwise::rna::sample_ONLY_multiple_virtual_sugar, basic::options::OptionKeys::full_model::sample_res, basic::options::OptionKeys::stepwise::rna::sampler_allow_syn_pyrimidine, basic::options::OptionKeys::stepwise::rna::sampler_extra_beta_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::simple_append_map, basic::options::OptionKeys::full_model::rna::terminal_res, basic::options::OptionKeys::stepwise::VERBOSE, viewer_main(), and basic::options::OptionKeys::full_model::virtual_res.

my_main()

void* my_main

(

void *

)

References utility::io::oc::cout, utility::options::OptionKeys::options::exit, and swa_rna_sample().

Referenced by main().

swa_rna_sample()

OPT_KEY ( Boolean, add_virt_root ) using namespace protocols void swa_rna_sample

(

)

References basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, pyrosetta.io::create_score_function, basic::options::OptionKeys::full_model::cutpoint_open, pyrosetta.distributed.io::get_score_function(), basic::options::OptionKeys::in::file::input_res, basic::options::OptionKeys::relax::range::kT, basic::options::OptionKeys::ddg::legacy, basic::options::OptionKeys::stepwise::protein::n_sample, out::file::o(), option, beta_nonlocal::pose, basic::options::OptionKeys::full_model::rna::rna, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, setup_pose_setup_class(), setup_rna_working_parameters(), basic::options::OptionKeys::in::file::silent, out::file::silent(), basic::options::OptionKeys::inout::dbms::user, and score::weights().

Referenced by my_main().