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Typedefs | Functions
rna_graft.cc File Reference
#include <core/scoring/rms_util.hh>
#include <core/types.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/import_pose/import_pose.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/pose/Pose.hh>
#include <core/pose/annotated_sequence.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/variant_util.hh>
#include <core/pose/rna/util.hh>
#include <protocols/rna/denovo/util.hh>
#include <protocols/rna/movers/RNA_LoopCloser.hh>
#include <protocols/stepwise/modeler/align/util.hh>
#include <protocols/viewer/viewers.hh>
#include <devel/init.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <utility/vector1.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/string.functions.hh>
#include <fstream>
#include <iostream>
#include <sstream>
#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 <basic/options/option_macros.hh>

Typedefs

using Matrix = numeric::xyzMatrix< Real >
 

Functions

void unvirtualize_phosphates (pose::Pose &pose, utility::vector1< Size > const &unvirtualize_phosphate_residues)
 
void get_pose_and_numbering (std::string const &pdb_file, pose::Pose &pose, utility::vector1< Size > &resnum)
 
Size find_index (Size const val, utility::vector1< Size > const &vec)
 
bool is_subset (utility::vector1< Size > const &vec_sub, utility::vector1< Size >const &vec_big)
 
std::map< Size, Size > calculate_res_map (utility::vector1< Size > const &superimpose_resnum, utility::vector1< Size > const &resnum1, utility::vector1< Size > const &resnum2)
 
void superimpose_pdb (pose::Pose &pose1, pose::Pose &pose2, utility::vector1< Size > const &resnum1, utility::vector1< Size > const &resnum2)
 
void output_superimposed_pdb (pose::Pose const &pose2, std::string const &pdb_file2)
 
void graft_in_positions (pose::Pose const &pose1, pose::Pose &pose_target, utility::vector1< Size > const &resnum1, utility::vector1< Size > const &resnum_target, utility::vector1< Size > const &resnum_graft, bool const graft_backbone_only)
 
void graft_in_positions (pose::Pose const &pose1, pose::Pose &pose_target, utility::vector1< Size > const &resnum1, utility::vector1< Size > const &resnum_target)
 
void close_loops (core::pose::Pose &pose, utility::vector1< Size > const &resnum)
 
void graft_pdb (pose::Pose const &pose1, pose::Pose const &pose2, utility::vector1< Size > const &resnum1, utility::vector1< Size > const &resnum2, pose::Pose &pose_target, utility::vector1< Size > &resnum_target)
 
void rna_superimpose_and_graft_test ()
 
void * my_main (void *)
 
int main (int argc, char *argv[])
 

Typedef Documentation

using Matrix = numeric::xyzMatrix<Real>

Function Documentation

std::map< Size, Size > calculate_res_map ( utility::vector1< Size > const &  superimpose_resnum,
utility::vector1< Size > const &  resnum1,
utility::vector1< Size > const &  resnum2 
)
void close_loops ( core::pose::Pose pose,
utility::vector1< Size > const &  resnum 
)
Size find_index ( Size const  val,
utility::vector1< Size > const &  vec 
)
void get_pose_and_numbering ( std::string const &  pdb_file,
pose::Pose pose,
utility::vector1< Size > &  resnum 
)
void graft_in_positions ( pose::Pose const &  pose1,
pose::Pose pose_target,
utility::vector1< Size > const &  resnum1,
utility::vector1< Size > const &  resnum_target,
utility::vector1< Size > const &  resnum_graft,
bool const  graft_backbone_only 
)
void graft_in_positions ( pose::Pose const &  pose1,
pose::Pose pose_target,
utility::vector1< Size > const &  resnum1,
utility::vector1< Size > const &  resnum_target 
)

References graft_in_positions().

void graft_pdb ( pose::Pose const &  pose1,
pose::Pose const &  pose2,
utility::vector1< Size > const &  resnum1,
utility::vector1< Size > const &  resnum2,
pose::Pose pose_target,
utility::vector1< Size > &  resnum_target 
)
bool is_subset ( utility::vector1< Size > const &  vec_sub,
utility::vector1< Size >const &  vec_big 
)

References find_index().

Referenced by calculate_res_map().

int main ( int  argc,
char *  argv[] 
)
void* my_main ( void *  )
void output_superimposed_pdb ( pose::Pose const &  pose2,
std::string const &  pdb_file2 
)
void rna_superimpose_and_graft_test ( )
void superimpose_pdb ( pose::Pose pose1,
pose::Pose pose2,
utility::vector1< Size > const &  resnum1,
utility::vector1< Size > const &  resnum2 
)
void unvirtualize_phosphates ( pose::Pose pose,
utility::vector1< Size > const &  unvirtualize_phosphate_residues 
)

Referenced by graft_pdb(), and superimpose_pdb().