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Typedefs | Functions
rna_thread.cc File Reference
#include <core/types.hh>
#include <core/chemical/AA.hh>
#include <core/conformation/Residue.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/VariantType.hh>
#include <core/chemical/util.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/import_pose/import_pose.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/sequence/Sequence.hh>
#include <core/sequence/util.hh>
#include <utility/string_util.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/tree/Atom.hh>
#include <core/id/AtomID_Map.hh>
#include <core/id/AtomID.hh>
#include <core/id/DOF_ID.hh>
#include <core/kinematics/AtomTree.hh>
#include <core/kinematics/Jump.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/pose/PDBInfo.hh>
#include <protocols/rna/denovo/util.hh>
#include <protocols/viewer/viewers.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/pose/rna/util.hh>
#include <devel/init.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <utility/vector1.hh>
#include <utility/io/ozstream.hh>
#include <utility/io/izstream.hh>
#include <numeric/xyzVector.hh>
#include <numeric/conversions.hh>
#include <ObjexxFCL/FArray1D.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/string.functions.hh>
#include <fstream>
#include <iostream>
#include <string>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/option_macros.hh>
#include <utility/excn/Exceptions.hh>

Typedefs

using Matrix = numeric::xyzMatrix< Real >
 

Functions

void setup_mask (ObjexxFCL::FArray1D_bool &sequence_mask, utility::vector1< sequence::SequenceOP > const &sequences_from_alignment)
 
void setup_alignment_map (std::map< Size, Size > &mapping, std::string const &sequence_from_alignment)
 
std::string remove_dashes (std::string const &s)
 
void prepare_threaded_model (pose::Pose &pose, std::string const &target_sequence_from_alignment, std::string const &template_sequence_from_alignment, ObjexxFCL::FArray1D_bool &sequence_mask, Size offset=0)
 
Size figure_out_which_sequence_is_template (utility::vector1< sequence::SequenceOP > const &sequences_from_alignment, pose::Pose const &template_pose, std::string const &template_file_name)
 
void rna_thread_test ()
 
void * my_main (void *)
 
int main (int argc, char *argv[])
 

Typedef Documentation

using Matrix = numeric::xyzMatrix<Real>

Function Documentation

Size figure_out_which_sequence_is_template ( utility::vector1< sequence::SequenceOP > const &  sequences_from_alignment,
pose::Pose const &  template_pose,
std::string const &  template_file_name 
)
int main ( int  argc,
char *  argv[] 
)
void* my_main ( void *  )
void prepare_threaded_model ( pose::Pose pose,
std::string const &  target_sequence_from_alignment,
std::string const &  template_sequence_from_alignment,
ObjexxFCL::FArray1D_bool sequence_mask,
Size  offset = 0 
)
std::string remove_dashes ( std::string const &  s)
void rna_thread_test ( )
void setup_alignment_map ( std::map< Size, Size > &  mapping,
std::string const &  sequence_from_alignment 
)
void setup_mask ( ObjexxFCL::FArray1D_bool sequence_mask,
utility::vector1< sequence::SequenceOP > const &  sequences_from_alignment 
)