src/apps/public/rna/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/scoring/Energies.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/rna/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 <core/pose/Pose.hh>
#include <protocols/init.hh>
#include <core/io/pdb/pose_io.hh>
#include <utility/vector1.hh>
#include <utility/io/ozstream.hh>
#include <numeric/conversions.hh>
#include <ObjexxFCL/string.functions.hh>
#include <protocols/rna/RNA_ProtocolUtil.hh>
#include <fstream>
#include <iostream>
#include <string>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <core/import_pose/import_pose.hh>
#include <core/kinematics/Jump.hh>
#include <core/scoring/constraints/Constraint.hh>
#include <numeric/xyz.functions.hh>
#include <ObjexxFCL/format.hh>

Namespaces
namespace	ObjexxFCL
	Objexx Fortran Compatibility Library.
namespace	ObjexxFCL::fmt
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_o2star (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 ()
void *	my_main (void *)
int	main (int argc, char *argv[])

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Detailed Description

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Typedef Documentation

typedef numeric::xyzMatrix< Real > Matrix

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

Referenced by check_for_contacts_and_output_jump_o2star(), and check_for_contacts_and_output_jump_phosphate().

void check_for_contacts_and_output_jump_o2star	(	pose::Pose &	pose,
		Size const	i,
		Size const	j,
		utility::io::ozstream &	dataout
	)

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

Referenced by create_bp_jump_database_test().

void create_bp_jump_database_test

(

)

References check_for_contacts_and_output_jump_o2star(), check_for_contacts_and_output_jump_phosphate(), basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, ObjexxFCL::fmt::I(), color_pdb::i, basic::options::OptionKeys::out::file::o, option, options, get_pdb::outfile, PyMOL_demo::pose, basic::options::OptionKeys::rna::rna, basic::options::OptionKeys::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::out::file::o, option, options, get_pdb::outfile, PyMOL_demo::pose, and basic::options::OptionKeys::in::file::s.

Referenced by my_main().

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

References src::init(), my_main(), NEW_OPT, and options.

void* my_main

(

void *

)

References utility::io::oc::cout, create_bp_jump_database_test(), create_rna_vall_torsions_test(), utility::options::OptionKeys::options::exit, option, and options.