rna_motif.cc File Reference

check if we can annotate U-turns, A-minor motifs, etc. in an RNA More...

#include <core/chemical/ChemicalManager.hh>
#include <core/conformation/Residue.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/rna/RNA_Motif.hh>
#include <core/scoring/rna/RNA_LowResolutionPotential.hh>
#include <core/pose/rna/RNA_FilteredBaseBaseInfo.hh>
#include <core/scoring/rna/RNA_ScoringInfo.hh>
#include <core/import_pose/pose_stream/PoseInputStream.hh>
#include <core/import_pose/pose_stream/PDBPoseInputStream.hh>
#include <core/import_pose/pose_stream/SilentFilePoseInputStream.hh>
#include <core/pose/Pose.hh>
#include <devel/init.hh>
#include <protocols/viewer/viewers.hh>
#include <basic/Tracer.hh>
#include <basic/options/option.hh>
#include <basic/options/option_macros.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <utility/io/ozstream.hh>
#include <ObjexxFCL/string.functions.hh>

Functions
static THREAD_LOCAL basic::Tracer	TR ("rna_motif")
void	output_motifs_to_pymol (std::ostream &out, pose::Pose const &pose, RNA_Motifs const &rna_motifs)
void	rna_motif_test ()
void *	my_main (void *)
int	main (int argc, char *argv[])

Variables
std::map< RNA_MotifType, std::string >	motif_color

Detailed Description

check if we can annotate U-turns, A-minor motifs, etc. in an RNA

Function Documentation

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

References utility::io::oc::cout, devel::init(), utility::excn::EXCN_Base::msg(), and my_main().

void* my_main

(

void *

)

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

Referenced by main().

void output_motifs_to_pymol	(	std::ostream &	out,
		pose::Pose const &	pose,
		RNA_Motifs const &	rna_motifs
	)

References motif_color, utility::replace_in(), res, and tag.

Referenced by rna_motif_test().

void rna_motif_test

(

)

References basic::options::OptionKeys::chemical::chemical, utility::io::ozstream::close(), utility::io::oc::cout, pyrosetta::create_score_function, basic::options::option, options, output_motifs_to_pymol(), demo.D010_Pose_structure::pose, basic::options::OptionKeys::full_model::rna::rna, basic::options::OptionKeys::in::file::s, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::in::file::silent, basic::options::OptionKeys::in::file::tags, basic::options::TR(), and basic::options::OptionKeys::inout::dbms::user.

Referenced by my_main().

static THREAD_LOCAL basic::Tracer TR ( "rna_motif"  )

static

Variable Documentation

std::map< RNA_MotifType, std::string > motif_color

Initial value:

=
{ {U_TURN, "lightblue"},
{UA_HANDLE, "marine" },
{T_LOOP, "tv_blue" },
{INTERCALATED_T_LOOP, "deepblue" },
{LOOP_E_SUBMOTIF, "salmon" },
{BULGED_G, "red" },
{GNRA_TETRALOOP, "ruby"},  
{STRICT_WC_STACKED_PAIR, "gray20"},
{WC_STACKED_PAIR, "gray50"},
{A_MINOR, "gold"},
{PLATFORM, "sand"},
{TL_RECEPTOR, "limon"},
{TETRALOOP_TL_RECEPTOR, "orange"}
}

Referenced by output_motifs_to_pymol().