rna_features.cc File Reference

#include <core/types.hh>
#include <core/chemical/AA.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/conformation/Residue.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <core/scoring/sasa.hh>
#include <core/scoring/ScoringManager.hh>
#include <core/scoring/rna/data/RNA_DMS_Potential.hh>
#include <core/scoring/rna/data/RNA_DMS_LowResolutionPotential.hh>
#include <core/io/rna/RDAT.hh>
#include <core/id/AtomID_Map.hh>
#include <core/id/AtomID.hh>
#include <core/id/NamedAtomID.hh>
#include <devel/init.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/PDBInfo.fwd.hh>
#include <core/pose/util.hh>
#include <core/import_pose/import_pose.hh>
#include <protocols/rna/denovo/util.hh>
#include <protocols/viewer/viewers.hh>
#include <basic/options/option.hh>
#include <utility/vector1.hh>
#include <utility/tools/make_vector1.hh>
#include <utility/io/izstream.hh>
#include <utility/file/FileName.hh>
#include <numeric/xyzMatrix.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/string.functions.hh>
#include <iostream>
#include <string>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>

Typedefs
using	Matrix = numeric::xyzMatrix< core::Real >

Functions
void	save_feature (vector1< std::string > &feature_names, vector1< core::Real > &feature_vals, Size &feature_counter, std::string const &feature_name, core::Real const feature_val)
Size	rna_features_from_pose (core::io::rna::RDAT &rdat, pose::Pose &pose)
void	rhiju_pdbstats ()
void *	my_main (void *)
int	main (int argc, char *argv[])

Detailed Description

Author

Rhiju, rhiju.nosp@m.@sta.nosp@m.nford.nosp@m..edu

Typedef Documentation

Matrix

using Matrix = numeric::xyzMatrix<core::Real>

Function Documentation

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::options::OptionKeys::options::exit, and rhiju_pdbstats().

Referenced by main().

rhiju_pdbstats()

void rhiju_pdbstats

(

)

References utility::io::oc::cerr, basic::options::OptionKeys::chemical::chemical, count, utility::io::oc::cout, utility::exit(), erraser::file_path, getline(), test.T110_numeric::I, in::file::l(), line, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, out::file::o(), option, lactamize::outfile, in::path::pdb(), bur_nodon_tyr::pdb_list, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, rna_features_from_pose(), in::file::s(), and basic::options::OptionKeys::inout::dbms::user.

Referenced by my_main().

rna_features_from_pose()

Size rna_features_from_pose	(	core::io::rna::RDAT &	rdat,
		pose::Pose &	pose
	)

References chains, basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, data, basic::options::OptionKeys::rna::denovo::denovo, ObjexxFCL::format::F(), benchmark_ns::hbonded, create_a3b_hbs::i, test.T110_numeric::I, create_a3b_hbs::k, kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, utility::tools::make_vector1(), create_a3b_hbs::nres, create_a3b_hbs::pdb_info, beta_nonlocal::pose, bur_nodon_tyr::probe_radius, basic::options::OptionKeys::full_model::rna::rna, runtime_assert, save_feature(), basic::options::OptionKeys::frags::scoring::scoring, ObjexxFCL::strip_whitespace(), and tag.

Referenced by rhiju_pdbstats().

save_feature()

void save_feature	(	vector1< std::string > &	feature_names,
		vector1< core::Real > &	feature_vals,
		Size &	feature_counter,
		std::string const &	feature_name,
		core::Real const	feature_val
	)

References runtime_assert.

Referenced by rna_features_from_pose().