check_frag_rmsd.cc File Reference

#include <core/types.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/ResidueType.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/rms_util.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/util.hh>
#include <core/init/init.hh>
#include <core/pose/annotated_sequence.hh>
#include <core/import_pose/import_pose.hh>
#include <basic/database/open.hh>
#include <utility/vector1.hh>
#include <core/fragment/rna/RNA_MatchType.hh>
#include <core/fragment/rna/RNA_Fragments.hh>
#include <core/fragment/rna/FragmentLibrary.hh>
#include <core/fragment/rna/TorsionSet.hh>
#include <core/import_pose/libraries/RNA_LibraryManager.hh>
#include <core/pose/toolbox/AtomLevelDomainMap.hh>
#include <core/pose/copydofs/util.hh>
#include <iostream>
#include <string>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/rna.OptionKeys.gen.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <utility/excn/Exceptions.hh>
#include <utility/stream_util.hh>

Functions
std::string	figure_out_secstruct (pose::Pose &pose)
utility::vector1< Real >	get_min_frag_rmsd (std::string const &in_file, core::fragment::rna::RNA_Fragments const &fragments, std::string const &exclusion_match_type="MATCH_EXACT")
void	test ()
void *	my_main (void *)
int	main (int argc, char *argv[])

Function Documentation

figure_out_secstruct()

std::string figure_out_secstruct

(

pose::Pose &

pose

)

References utility::io::oc::cout, create_a3b_hbs::i, beta_nonlocal::pose, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, and secstruct().

Referenced by get_min_frag_rmsd(), and output_minipose_coords_test().

get_min_frag_rmsd()

utility::vector1< Real > get_min_frag_rmsd	(	std::string const &	in_file,
		core::fragment::rna::RNA_Fragments const &	fragments,
		std::string const &	exclusion_match_type = "MATCH_EXACT"
	)

References basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, basic::options::OptionKeys::rna::denovo::exclusion_match_type, figure_out_secstruct(), demo.D080_Loop_modeling::frag_length, basic::options::OptionKeys::in::path::fragments, create_a3b_hbs::i, create_a3b_hbs::ii, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, option, beta_nonlocal::pose, average_rmsds::rmsd, basic::options::OptionKeys::full_model::rna::rna, basic::options::OptionKeys::frags::scoring::scoring, secstruct(), basic::options::OptionKeys::relax::sequence, superimpose_pose(), basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.

Referenced by test().

main()

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

References argv, utility::io::oc::cout, test.T009_Exceptions::e, basic::options::OptionKeys::rna::denovo::fragment_homology_rmsd, basic::init(), my_main(), in::file::native(), NEW_OPT, option, in::file::s(), in::file::silent(), in::file::tags(), viewer_main(), and score::weights().

my_main()

void* my_main

(

void *

)

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

Referenced by main().

test()

void test

(

)

References utility::io::oc::cout, basic::database::full_name(), get_min_frag_rmsd(), create_a3b_hbs::i, pilot_app_settings::libraries, surface_app::native, option, basic::options::OptionKeys::full_model::rna::rna, and value.

Referenced by my_main().