rna_score.cc File Reference

#include <core/types.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/io/silent/util.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/rms_util.hh>
#include <core/energy_methods/RNA_ChemicalMappingEnergy.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/pose/full_model_info/FullModelInfo.hh>
#include <core/pose/extra_pose_info_util.hh>
#include <devel/init.hh>
#include <core/import_pose/import_pose.hh>
#include <core/import_pose/FullModelPoseBuilder.hh>
#include <utility/vector1.hh>
#include <protocols/stepwise/modeler/align/util.hh>
#include <core/io/rna/RNA_DataReader.hh>
#include <core/pose/PDBInfo.hh>
#include <core/scoring/ScoreType.hh>
#include <core/scoring/etable/EtableEnergy.hh>
#include <core/scoring/ScoringManager.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/etable/count_pair/CountPairGeneric.hh>
#include <core/scoring/etable/atom_pair_energy_inline.hh>
#include <core/util/SwitchResidueTypeSet.hh>
#include <protocols/moves/Mover.hh>
#include <iostream>
#include <string>
#include <numeric/conversions.hh>
#include <basic/Tracer.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/full_model.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/rna.OptionKeys.gen.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <basic/options/keys/stepwise.OptionKeys.gen.hh>
#include <protocols/jd2/util.hh>
#include <protocols/jd2/internal_util.hh>
#include <protocols/jd2/JobDistributor.hh>
#include <utility/excn/Exceptions.hh>
#include <core/pose/util.hh>

Classes
class	RNA_ScoreMover

Functions
void	do_color_by_score (core::pose::Pose &pose)
Real	calc_dihedral_rms (core::pose::Pose const &pose, core::pose::Pose const &native_pose, bool verbose=false)
void *	my_main (void *)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("apps.public.rna.util.rna_score")

Function Documentation

calc_dihedral_rms()

Real calc_dihedral_rms	(	core::pose::Pose const &	pose,
		core::pose::Pose const &	native_pose,
		bool	verbose = false
	)

References count, create_a3b_hbs::ii, beta_nonlocal::jj, docking::native_pose, beta_nonlocal::pose, TR, utility_exit_with_message, and basic::options::OptionKeys::sc::verbose.

Referenced by RNA_ScoreMover::apply().

do_color_by_score()

void do_color_by_score

(

core::pose::Pose &

pose

)

References test.T200_Scoring::emap, create_a3b_hbs::i, create_a3b_hbs::j, kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, basic::options::option, options, beta_nonlocal::pose, erraser_analysis::res1, erraser_analysis::res2, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::dna::specificity::soft_rep, TR, and basic::options::OptionKeys::sc::weight.

Referenced by RNA_ScoreMover::apply().

main()

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

References argv, full_model::cutpoint_open(), basic::options::OptionKeys::motifs::data_file, test.T009_Exceptions::e, in::file::fasta(), basic::init(), in::file::input_res(), score::just_calc_rmsd(), my_main(), in::file::native(), NEW_OPT, option, out::overwrite(), basic::options::OptionKeys::flexPepDocking::params_file, register_options(), basic::options::OptionKeys::abinitio::rmsd_residues, in::file::s(), in::file::silent(), basic::options::OptionKeys::dna::specificity::soft_rep, in::file::tags(), TR, viewer_main(), basic::options::OptionKeys::stepwise::virtualize_free_moieties_in_native, and score::weights().

my_main()

void* my_main

(

void *

)

References utility::io::oc::cerr, basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, pyrosetta::create_score_function, data, utility::options::OptionKeys::options::exit, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, in::file::native(), docking::native_pose, basic::options::option, option, basic::options::OptionKeys::full_model::other_poses, full_model::other_poses(), out::overwrite(), oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, utility::excn::Exception::show(), basic::options::OptionKeys::in::file::silent, out::file::silent(), basic::options::OptionKeys::inout::dbms::user, basic::options::OptionKeys::stepwise::virtualize_free_moieties_in_native, and basic::options::OptionKeys::score::weights.

Referenced by main().

Variable Documentation

TR

basic::Tracer TR("apps.public.rna.util.rna_score") ( "apps.public.rna.util.rna_score"  )

static

Referenced by RNA_ScoreMover::apply(), calc_dihedral_rms(), do_color_by_score(), and main().