rna_minimize.cc File Reference

#include <core/types.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/io/silent/BinarySilentStruct.hh>
#include <core/io/silent/SilentFileOptions.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/io/silent/util.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/constraints/ConstraintSet.fwd.hh>
#include <core/scoring/constraints/ConstraintIO.hh>
#include <basic/options/option.hh>
#include <basic/options/option_macros.hh>
#include <protocols/viewer/viewers.hh>
#include <core/pose/Pose.hh>
#include <core/pose/rna/RNA_SecStruct.hh>
#include <core/pose/rna/util.hh>
#include <core/pose/extra_pose_info_util.hh>
#include <core/pose/annotated_sequence.hh>
#include <devel/init.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/import_pose/import_pose.hh>
#include <core/import_pose/FullModelPoseBuilder.hh>
#include <core/import_pose/pose_stream/PoseInputStream.hh>
#include <core/import_pose/pose_stream/PoseInputStream.fwd.hh>
#include <core/import_pose/pose_stream/PDBPoseInputStream.hh>
#include <core/import_pose/pose_stream/SilentFilePoseInputStream.hh>
#include <utility/vector1.hh>
#include <protocols/rna/denovo/RNA_DeNovoPoseInitializer.hh>
#include <protocols/rna/denovo/movers/RNA_Minimizer.hh>
#include <core/import_pose/options/RNA_MinimizerOptions.hh>
#include <protocols/rna/denovo/util.hh>
#include <protocols/stepwise/modeler/align/util.hh>
#include <core/pose/toolbox/AtomLevelDomainMap.hh>
#include <iostream>
#include <string>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/rna.OptionKeys.gen.hh>
#include <basic/options/keys/stepwise.OptionKeys.gen.hh>
#include <basic/options/keys/constraints.OptionKeys.gen.hh>
#include <basic/options/keys/full_model.OptionKeys.gen.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <utility/excn/Exceptions.hh>
#include <core/pose/full_model_info/FullModelParameters.hh>

Functions
void	rna_fullatom_minimize_test ()
void *	my_main (void *)
int	main (int argc, char *argv[])

Function Documentation

main()

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

References argv, utility::io::oc::cout, basic::options::OptionKeys::constraints::cst_fa_file, basic::options::OptionKeys::rna::denovo::minimize::deriv_check, test.T009_Exceptions::e, basic::init(), basic::options::OptionKeys::dna::specificity::min_type, basic::options::OptionKeys::loops::minimize_max_iter, basic::options::OptionKeys::rna::denovo::minimize::minimize_nblist_auto_update, in::file::minimize_res(), basic::options::OptionKeys::rna::denovo::minimize::minimize_use_nblist, my_main(), NEW_OPT, option, basic::options::OptionKeys::flexPepDocking::params_file, out::pdb(), basic::options::OptionKeys::rna::denovo::minimize::skip_coord_constraints, basic::options::OptionKeys::rna::denovo::minimize::skip_o2prime_trials, basic::options::OptionKeys::rna::vary_geometry, viewer_main(), and score::weights().

my_main()

void* my_main

(

void *

)

References utility::options::OptionKeys::options::exit, and rna_fullatom_minimize_test().

Referenced by main().

rna_fullatom_minimize_test()

void rna_fullatom_minimize_test

(

)

References align_pose(), basic::options::OptionKeys::chemical::chemical, basic::options::OptionKeys::constraints::constraints, utility::io::oc::cout, basic::options::OptionKeys::constraints::cst_fa_file, basic::options::OptionKeys::rna::denovo::denovo, basic::options::OptionKeys::matdes::dock::dump_pdb, basic::options::OptionKeys::in::file::fasta, create_a3b_hbs::i, gaussian-sampling::input, in::file::minimize_res(), pyrosetta.distributed.docs::movers, in::file::native(), docking::native_pose, option, options, basic::options::OptionKeys::full_model::other_poses, full_model::other_poses(), out::overwrite(), basic::options::OptionKeys::templates::pairings, basic::options::OptionKeys::flexPepDocking::params_file, out::pdb(), make_symmdef_file_denovo::pos, beta_nonlocal::pose, average_rmsds::rmsd, basic::options::OptionKeys::stepwise::rmsd_screen, docking::s, in::file::s(), basic::options::OptionKeys::frags::scoring::scoring, secstruct(), basic::options::OptionKeys::rna::denovo::secstruct_file, basic::options::OptionKeys::relax::sequence, basic::options::OptionKeys::recces::thermal_sampling::setup_base_pair_constraints, in::file::silent(), out::file::silent(), basic::options::OptionKeys::stepwise::stepwise, basic::options::OptionKeys::stepwise::superimpose_over_all, tag, tag_from_pose(), in::file::tags(), create_a3b_hbs::test_pose, basic::options::OptionKeys::inout::dbms::user, utility_exit_with_message, and value.

Referenced by my_main().