Analyze RNA motifs docked onto proteins to try to design protein binding structures. More...

#include <core/types.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <core/scoring/ScoreFunctionFactory.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/extra_pose_info_util.hh>
#include <core/init/init.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 <basic/Tracer.hh>
#include <iostream>
#include <string>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <utility/excn/Exceptions.hh>
#include <core/conformation/Residue.hh>
#include <utility/stream_util.hh>

Functions
void	get_contacts (core::pose::Pose const &pose, std::string const &tag)

void	get_RNA_binding_residues (core::pose::Pose const &pose, std::string const &tag)

void	count_contacts ()

void *	my_main (void *)

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

Variables
static basic::Tracer	TR ("apps.pilot.kkappel.analyze_docked_RNA_motifs")

Detailed Description

Analyze RNA motifs docked onto proteins to try to design protein binding structures.

Function Documentation

◆ count_contacts()

void count_contacts ( )

References basic::options::OptionKeys::chemical::chemical, pyrosetta::create_score_function, get_contacts(), get_RNA_binding_residues(), gaussian-sampling::input, basic::options::option, option, beta_nonlocal::pose, in::file::s(), oop_conformations::scorefxn, basic::options::OptionKeys::in::file::silent, in::file::silent(), tag, tag_from_pose(), in::file::tags(), basic::options::OptionKeys::inout::dbms::user, and basic::options::OptionKeys::score::weights.

Referenced by my_main().

◆ get_contacts()

void get_contacts	(	core::pose::Pose const &	pose,
		std::string const &	tag
	)

References basic::Tracer::Blue, basic::options::OptionKeys::chemical::chemical, build_jacobian::distance, create_a3b_hbs::i, numeric::xyzVector< T >::length(), natoms(), option, beta_nonlocal::pose, basic::options::OptionKeys::in::file::silent, subloop_histogram::size, tag, and TR.

Referenced by count_contacts().

◆ get_RNA_binding_residues()

void get_RNA_binding_residues	(	core::pose::Pose const &	pose,
		std::string const &	tag
	)

References basic::Tracer::Blue, basic::options::OptionKeys::chemical::chemical, build_jacobian::distance, numeric::xyzVector< T >::length(), natoms(), beta_nonlocal::pose, basic::options::OptionKeys::in::file::silent, tag, and TR.

Referenced by count_contacts().

◆ main()

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

References argv, utility::io::oc::cout, test.T009_Exceptions::e, 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 count_contacts(), and utility::options::OptionKeys::options::exit.

Referenced by main().

Variable Documentation

◆ TR

basic::Tracer TR("apps.pilot.kkappel.analyze_docked_RNA_motifs") ( "apps.pilot.kkappel.analyze_docked_RNA_motifs" )

static

Referenced by get_contacts(), and get_RNA_binding_residues().

Functions

Variables