rna_features.cc File Reference

#include <core/types.hh>
#include <core/chemical/AA.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/VariantType.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/scoring/func/HarmonicFunc.hh>
#include <core/chemical/rna/util.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/methods/EnergyMethodOptions.hh>
#include <core/scoring/sasa.hh>
#include <core/scoring/ScoringManager.hh>
#include <core/scoring/rna/RNA_LowResolutionPotential.hh>
#include <core/pose/rna/RNA_BaseDoubletClasses.hh>
#include <core/scoring/rna/RNA_CentroidInfo.hh>
#include <core/scoring/rna/RNA_ScoringInfo.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/scoring/hbonds/HBondSet.hh>
#include <core/scoring/hbonds/HBondOptions.hh>
#include <core/scoring/hbonds/hbonds.hh>
#include <core/id/AtomID_Map.hh>
#include <core/id/AtomID.hh>
#include <core/id/NamedAtomID.hh>
#include <core/id/DOF_ID.hh>
#include <core/init/init.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/kinematics/AtomTree.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/Jump.hh>
#include <core/kinematics/Stub.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/PDBInfo.fwd.hh>
#include <core/pose/util.hh>
#include <core/pose/rna/RNA_BasePairClassifier.hh>
#include <core/import_pose/import_pose.hh>
#include <devel/init.hh>
#include <protocols/farna/util.hh>
#include <protocols/viewer/viewers.hh>
#include <basic/options/option.hh>
#include <basic/options/option_macros.hh>
#include <basic/database/open.hh>
#include <utility/vector1.hh>
#include <utility/tools/make_vector1.hh>
#include <utility/io/ozstream.hh>
#include <utility/io/izstream.hh>
#include <utility/file/FileName.hh>
#include <numeric/xyzVector.hh>
#include <numeric/xyzMatrix.hh>
#include <numeric/conversions.hh>
#include <numeric/constants.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/FArray1D.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <ObjexxFCL/string.functions.hh>
#include <fstream>
#include <iostream>
#include <string>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/chemical.OptionKeys.gen.hh>
#include <core/conformation/Conformation.hh>
#include <core/scoring/constraints/Constraint.hh>
#include <numeric/xyz.functions.hh>

Namespaces
	ObjexxFCL
	ObjexxFCL::format

Typedefs
typedef numeric::xyzMatrix < core::Real >	Matrix

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

typedef numeric::xyzMatrix< core::Real > Matrix

Function Documentation

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

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

void* my_main

(

void *

)

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

Referenced by main().

void rhiju_pdbstats

(

)

References utility::io::oc::cerr, basic::options::OptionKeys::chemical::chemical, clean_pdb_keep_ligand::count, utility::io::oc::cout, utility::exit(), ObjexxFCL::getline(), ObjexxFCL::format::I(), in::file::l(), line, out::file::o(), option, options, clean_pdb_keep_ligand::outfile, in::path::pdb(), basic::options::OptionKeys::pepspec::pdb_list, app.surface_docking.surface_docking::pose, rna_features_from_pose(), in::file::s(), and basic::options::OptionKeys::inout::dbms::user.

Referenced by my_main().

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

References chains, basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, app.delta_score_per_mutation::data, ObjexxFCL::format::F(), basic::options::OptionKeys::rna::farna::farna, ObjexxFCL::format::I(), utility::tools::make_vector1(), clean_pdb_keep_ligand::nres, basic::options::OptionKeys::sasa::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().

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().