homolog_finder_farna.cc File Reference

#include <core/types.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/pose/copydofs/util.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/ScoreFunction.hh>
#include <devel/init.hh>
#include <core/id/AtomID.hh>
#include <core/pose/Pose.hh>
#include <core/import_pose/import_pose.hh>
#include <core/pose/annotated_sequence.hh>
#include <core/import_pose/options/RNA_FragmentMonteCarloOptions.hh>
#include <core/fragment/rna/FullAtomRNA_Fragments.hh>
#include <core/fragment/rna/FragmentLibrary.hh>
#include <core/fragment/rna/TorsionSet.hh>
#include <core/pose/rna/util.hh>
#include <protocols/rna/denovo/util.hh>
#include <core/pose/toolbox/AtomLevelDomainMap.hh>
#include <protocols/viewer/viewers.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/Tracer.hh>
#include <iostream>
#include <string>

Functions
utility::vector1< std::pair< Size, std::string > >	split_segments_longer_than_6mers (utility::vector1< std::pair< Size, std::string > > const &secstruct_segments)
void	obtain_secstruct_segments (utility::vector1< std::pair< Size, std::string > > &secstruct_segments, std::string const &secstruct)
std::string	figure_out_secstruct (pose::Pose &pose)
void	homolog_finder ()
void *	my_main (void *)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("apps.pilot.rhiju.homolog_finder_farna")

Function Documentation

figure_out_secstruct()

std::string figure_out_secstruct

(

pose::Pose &

pose

)

References create_a3b_hbs::i, beta_nonlocal::pose, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, secstruct(), and TR.

Referenced by homolog_finder().

homolog_finder()

void homolog_finder

(

)

References basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, build_restypes::elem, figure_out_secstruct(), foo(), demo.D080_Loop_modeling::frag_length, basic::options::OptionKeys::in::path::fragments, create_a3b_hbs::i, basic::options::OptionKeys::epr_deer::input_files, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, out::file::o(), obtain_secstruct_segments(), option, options, lactamize::outfile, beta_nonlocal::pose, average_rmsds::rmsd, basic::options::OptionKeys::full_model::rna::rna, in::file::s(), basic::options::OptionKeys::frags::scoring::scoring, secstruct(), basic::options::OptionKeys::relax::sequence, split_segments_longer_than_6mers(), superimpose_pose(), and TR.

Referenced by my_main().

main()

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

References argv, test.T009_Exceptions::e, basic::init(), my_main(), and viewer_main().

my_main()

void* my_main

(

void *

)

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

Referenced by main().

obtain_secstruct_segments()

void obtain_secstruct_segments	(	utility::vector1< std::pair< Size, std::string > > &	secstruct_segments,
		std::string const &	secstruct
	)

References create_a3b_hbs::ii, make_symmdef_file_denovo::pos, secstruct(), erraser_analysis::temp, and TR.

Referenced by homolog_finder().

split_segments_longer_than_6mers()

utility::vector1< std::pair< Size, std::string > > split_segments_longer_than_6mers

(

utility::vector1< std::pair< Size, std::string > > const &

secstruct_segments

)

References create_a3b_hbs::ii.

Referenced by homolog_finder().

Variable Documentation

TR

basic::Tracer TR("apps.pilot.rhiju.homolog_finder_farna") ( "apps.pilot.rhiju.homolog_finder_farna"  )

static

Referenced by figure_out_secstruct(), homolog_finder(), and obtain_secstruct_segments().