Rosetta  2019.47
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Typedefs | Functions
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/SilentFileOptions.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/subpose_manipulation_util.hh>
#include <core/pose/rna/util.hh>
#include <core/pose/rna/RNA_BasePairClassifier.hh>
#include <core/pose/PDBInfo.hh>
#include <devel/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/rna/denovo/util.hh>
#include <core/import_pose/libraries/BasePairStepLibrary.hh>
#include <core/import_pose/RNA_BasePairHandler.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

using Matrix = numeric::xyzMatrix< Real >
 

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

using Matrix = numeric::xyzMatrix<Real>

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 
)
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_base_pair_step_database_test ( )
void create_bp_jump_database_test ( )
void create_rna_vall_torsions_test ( )
std::string get_bps_seq ( utility::vector1< Size > const &  base_pair_res,
std::string const &  sequence 
)
std::string get_bps_sub_dir ( int const  seq_sep)
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 
)
int main ( int  argc,
char *  argv[] 
)
void* my_main ( void *  )
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 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 
)