rna_minimize.cc File Reference

#include <core/types.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/id/NamedAtomID.hh>
#include <core/id/AtomID.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/ScoreFunctionFactory.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/constraints/ConstraintSet.fwd.hh>
#include <core/scoring/constraints/ConstraintIO.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/rms_util.hh>
#include <basic/database/open.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 <utility/file/file_sys_util.hh>
#include <ObjexxFCL/string.functions.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/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>

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

Function Documentation

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

References utility::options::OptionCollection::add_relevant(), utility::io::oc::cout, basic::options::OptionKeys::constraints::cst_fa_file, basic::options::OptionKeys::rna::denovo::minimize::deriv_check, test.T009_Exceptions::e, devel::init(), basic::options::OptionKeys::rna::denovo::minimize::min_type, basic::options::OptionKeys::rna::denovo::minimize::minimize_max_iter, basic::options::OptionKeys::rna::denovo::minimize::minimize_nblist_auto_update, basic::options::OptionKeys::in::file::minimize_res, basic::options::OptionKeys::rna::denovo::minimize::minimize_use_nblist, utility::excn::Exception::msg(), my_main(), NEW_OPT, basic::options::option, options, basic::options::OptionKeys::flexPepDocking::params_file, basic::options::OptionKeys::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, and basic::options::OptionKeys::score::weights.

void* my_main

(

void *

)

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

Referenced by main().

void rna_fullatom_minimize_test

(

)

References 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, basic::options::OptionKeys::in::file::minimize_res, pyrosetta.distributed.docs::movers, basic::options::OptionKeys::in::file::native, test.Workshop7test::native_pose, basic::options::option, options, basic::options::OptionKeys::full_model::other_poses, basic::options::OptionKeys::out::overwrite, basic::options::OptionKeys::templates::pairings, basic::options::OptionKeys::flexPepDocking::params_file, basic::options::OptionKeys::out::pdb, make_symmdef_file_denovo::pos, demo.D010_Pose_structure::pose, basic::options::OptionKeys::AnchoredDesign::rmsd, basic::options::OptionKeys::in::file::s, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::rna::denovo::secstruct, local::secstruct, basic::options::OptionKeys::rna::denovo::secstruct_file, basic::options::OptionKeys::relax::sequence, basic::options::OptionKeys::recces::thermal_sampling::setup_base_pair_constraints, basic::options::OptionKeys::out::file::silent, basic::options::OptionKeys::in::file::silent, basic::options::OptionKeys::stepwise::stepwise, basic::options::OptionKeys::stepwise::superimpose_over_all, tag, basic::options::OptionKeys::in::file::tags, test.T220_AtomAtomPairEnergies::test_pose, basic::options::OptionKeys::inout::dbms::user, utility_exit_with_message, and value.

Referenced by my_main().