rna_database.cc File Reference

#include <core/types.hh>
#include <core/chemical/AA.hh>
#include <core/conformation/Residue.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/io/silent/BinarySilentStruct.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/chemical/rna/util.hh>
#include <core/scoring/rna/RNA_ScoringInfo.hh>
#include <core/scoring/constraints/ConstraintSet.fwd.hh>
#include <basic/options/option.hh>
#include <basic/options/option_macros.hh>
#include <protocols/viewer/viewers.hh>
#include <protocols/stepwise/modeler/util.hh>
#include <protocols/stepwise/setup/util.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/pose/rna/util.hh>
#include <core/pose/rna/RNA_BasePairClassifier.hh>
#include <core/pose/PDBInfo.hh>
#include <core/init/init.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <utility/vector1.hh>
#include <utility/tools/make_vector1.hh>
#include <utility/io/ozstream.hh>
#include <utility/file/file_sys_util.hh>
#include <numeric/conversions.hh>
#include <ObjexxFCL/string.functions.hh>
#include <ObjexxFCL/format.hh>
#include <protocols/farna/util.hh>
#include <protocols/farna/libraries/BasePairStepLibrary.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/rna.OptionKeys.gen.hh>
#include <core/import_pose/import_pose.hh>
#include <core/kinematics/Jump.hh>
#include <numeric/xyz.functions.hh>
#include <core/scoring/EnergyGraph.hh>
#include <utility/excn/Exceptions.hh>

Typedefs
typedef numeric::xyzMatrix< Real >	Matrix

Functions
void	create_rna_vall_torsions_test ()
bool	check_for_contacts (pose::Pose &pose, Size const i, Vector const &atom_j, Vector const dir_vector, char &edge_i, char &orientation)
void	check_for_contacts_and_output_jump_o2prime (pose::Pose &pose, Size const i, Size const j, utility::io::ozstream &dataout)
void	check_for_contacts_and_output_jump_phosphate (pose::Pose &pose, Size const i, Size const j, utility::io::ozstream &dataout)
void	create_bp_jump_database_test ()
std::string	get_bps_seq (utility::vector1< Size > const &base_pair_res, std::string const &sequence)
std::string	get_bps_tag (utility::vector1< Size > const &base_pair_res, std::string const &infile, pose::Pose const &pose)
std::string	get_bps_sub_dir (int const seq_sep)
std::string	get_bps_sub_dir (utility::vector1< Size > const &base_pair_res)
void	write_base_pair_step_to_silent_struct (pose::Pose const &pose, utility::vector1< int > base_pair_res, std::string const &intag, bool const use_sub_directories=true)
void	write_base_pair_step_to_silent_struct (pose::Pose const &pose, Size const &i, Size const &j, std::string const &intag)
void	output_canonical_base_pair_steps (pose::Pose &pose, std::string const &intag)
void	output_general_base_pair_steps (pose::Pose const &pose, std::string const &intag)
void	create_base_pair_step_database_test ()
void *	my_main (void *)
int	main (int argc, char *argv[])

Typedef Documentation

typedef numeric::xyzMatrix< Real > Matrix

Function Documentation

bool check_for_contacts	(	pose::Pose &	pose,
		Size const	i,
		Vector const &	atom_j,
		Vector const	dir_vector,
		char &	edge_i,
		char &	orientation
	)

References ObjexxFCL::abs(), numeric::xyzMatrix< typename >::col_x(), numeric::xyzMatrix< typename >::col_y(), numeric::xyzMatrix< typename >::col_z(), numeric::conversions::degrees(), ObjexxFCL::dot(), ObjexxFCL::dot_product(), and test.T200_Scoring::ii.

Referenced by check_for_contacts_and_output_jump_o2prime(), and check_for_contacts_and_output_jump_phosphate().

void check_for_contacts_and_output_jump_o2prime	(	pose::Pose &	pose,
		Size const	i,
		Size const	j,
		utility::io::ozstream &	dataout
	)

References check_for_contacts(), and ObjexxFCL::format::I().

Referenced by create_bp_jump_database_test().

void check_for_contacts_and_output_jump_phosphate	(	pose::Pose &	pose,
		Size const	i,
		Size const	j,
		utility::io::ozstream &	dataout
	)

References check_for_contacts(), ObjexxFCL::cross(), and ObjexxFCL::format::I().

Referenced by create_bp_jump_database_test().

void create_base_pair_step_database_test

(

)

References basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, basic::options::OptionKeys::cluster::exclude_res, basic::options::OptionKeys::rna::farna::farna, option, options, output_canonical_base_pair_steps(), output_general_base_pair_steps(), in::path::pdb(), make_symmdef_file_denovo::pos, app.surface_docking.surface_docking::pose, basic::options::OptionKeys::full_model::rna::rna, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::relax::sequence, and basic::options::OptionKeys::stepwise::stepwise.

Referenced by my_main().

void create_bp_jump_database_test

(

)

References check_for_contacts_and_output_jump_o2prime(), check_for_contacts_and_output_jump_phosphate(), basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, pyrosetta::create_score_function, basic::options::OptionKeys::cluster::exclude_res, basic::options::OptionKeys::rna::farna::farna, ObjexxFCL::format::I(), basic::options::OptionKeys::frags::j, basic::options::OptionKeys::rna::farna::lores_scorefxn, out::file::o(), option, options, clean_pdb_keep_ligand::outfile, app.surface_docking.surface_docking::pose, basic::options::OptionKeys::full_model::rna::rna, in::file::s(), and basic::options::OptionKeys::frags::scoring::scoring.

Referenced by my_main().

void create_rna_vall_torsions_test

(

)

References basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, basic::options::OptionKeys::cluster::exclude_res, out::file::o(), option, options, clean_pdb_keep_ligand::outfile, app.surface_docking.surface_docking::pose, in::file::s(), basic::options::OptionKeys::inout::dbms::user, and basic::options::OptionKeys::rna::farna::vall_torsions.

Referenced by my_main().

std::string get_bps_seq	(	utility::vector1< Size > const &	base_pair_res,
		std::string const &	sequence
	)

References runtime_assert.

Referenced by write_base_pair_step_to_silent_struct().

std::string get_bps_sub_dir

(

int const

seq_sep

)

References ObjexxFCL::format::I().

Referenced by get_bps_sub_dir(), and write_base_pair_step_to_silent_struct().

std::string get_bps_sub_dir

(

utility::vector1< Size > const &

base_pair_res

)

References get_bps_sub_dir().

std::string get_bps_tag	(	utility::vector1< Size > const &	base_pair_res,
		std::string const &	infile,
		pose::Pose const &	pose
	)

References BuildPackagedBindings::format.

Referenced by write_base_pair_step_to_silent_struct().

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

References basic::options::OptionKeys::rna::farna::db::bps_database, utility::io::oc::cout, basic::options::OptionKeys::cluster::exclude_res, basic::init(), basic::options::OptionKeys::rna::farna::db::jump_database, utility::excn::EXCN_Base::msg(), my_main(), NEW_OPT, option, options, and basic::options::OptionKeys::rna::farna::vall_torsions.

void* my_main

(

void *

)

References basic::options::OptionKeys::rna::farna::db::bps_database, utility::io::oc::cout, create_base_pair_step_database_test(), create_bp_jump_database_test(), create_rna_vall_torsions_test(), basic::options::OptionKeys::out::path::db, utility::options::OptionKeys::options::exit, basic::options::OptionKeys::rna::farna::farna, basic::options::OptionKeys::rna::farna::db::jump_database, option, options, basic::options::OptionKeys::inout::dbms::user, and basic::options::OptionKeys::rna::farna::vall_torsions.

Referenced by main().

void output_canonical_base_pair_steps	(	pose::Pose &	pose,
		std::string const &	intag
	)

References basic::options::OptionKeys::frags::j, PDBInfo::partner(), and write_base_pair_step_to_silent_struct().

Referenced by create_base_pair_step_database_test().

void output_general_base_pair_steps	(	pose::Pose const &	pose,
		std::string const &	intag
	)

References ObjexxFCL::abs(), basic::options::OptionKeys::frags::j, utility::tools::make_vector1(), basic::options::option, runtime_assert, and write_base_pair_step_to_silent_struct().

Referenced by create_base_pair_step_database_test().

void write_base_pair_step_to_silent_struct	(	pose::Pose const &	pose,
		utility::vector1< int >	base_pair_res,
		std::string const &	intag,
		bool const	use_sub_directories = true
	)

References utility::io::oc::cout, utility::file::create_directory_recursive(), utility::file::file_exists(), get_bps_seq(), get_bps_sub_dir(), get_bps_tag(), basic::options::OptionKeys::in::file::s, and basic::options::OptionKeys::in::file::silent.

Referenced by output_canonical_base_pair_steps(), output_general_base_pair_steps(), and write_base_pair_step_to_silent_struct().

void write_base_pair_step_to_silent_struct	(	pose::Pose const &	pose,
		Size const &	i,
		Size const &	j,
		std::string const &	intag
	)

References utility::tools::make_vector1(), and write_base_pair_step_to_silent_struct().