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Typedefs | Functions | Variables
swa_rna_util.cc File Reference
#include <core/types.hh>
#include <core/chemical/AA.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/VariantType.hh>
#include <core/chemical/util.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/AtomType.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueMatcher.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/scoring/ScoringManager.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/sequence/util.hh>
#include <core/sequence/Sequence.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/tree/Atom.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/id/AtomID_Map.hh>
#include <core/id/AtomID.hh>
#include <core/id/DOF_ID.hh>
#include <devel/init.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/pose/variant_util.hh>
#include <core/pose/util.tmpl.hh>
#include <core/pose/annotated_sequence.hh>
#include <core/import_pose/pose_stream/SilentFilePoseInputStream.hh>
#include <core/import_pose/pose_stream/SilentFilePoseInputStream.fwd.hh>
#include <core/import_pose/import_pose.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/chemical.OptionKeys.gen.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/OptionKeys.hh>
#include <basic/options/option_macros.hh>
#include <basic/Tracer.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/rna/util.hh>
#include <core/chemical/rna/RNA_FittedTorsionInfo.hh>
#include <core/scoring/EnergyGraph.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/EnergyMap.hh>
#include <core/scoring/EnergyMap.fwd.hh>
#include <core/scoring/constraints/util.hh>
#include <core/scoring/rms_util.tmpl.hh>
#include <core/pack/pack_rotamers.hh>
#include <core/pack/rotamer_trials.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <utility/vector1.hh>
#include <utility/io/ozstream.hh>
#include <utility/io/izstream.hh>
#include <utility/file/file_sys_util.hh>
#include <utility/excn/Exceptions.hh>
#include <numeric/xyzVector.hh>
#include <numeric/conversions.hh>
#include <protocols/viewer/viewers.hh>
#include <protocols/rna/denovo/movers/RNA_Minimizer.hh>
#include <core/import_pose/options/RNA_MinimizerOptions.hh>
#include <protocols/rna/denovo/util.hh>
#include <protocols/stepwise/modeler/output_util.hh>
#include <protocols/stepwise/modeler/rna/util.hh>
#include <protocols/stepwise/modeler/rna/StepWiseRNA_ResidueInfo.hh>
#include <protocols/stepwise/modeler/working_parameters/StepWiseWorkingParameters.hh>
#include <protocols/stepwise/legacy/modeler/rna/util.hh>
#include <protocols/rna/movers/RNA_LoopCloser.hh>
#include <protocols/rna/movers/RNA_LoopCloser.fwd.hh>
#include <core/pose/rna/RNA_BaseDoubletClasses.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/string.functions.hh>
#include <core/io/silent/BinarySilentStruct.hh>
#include <core/io/silent/SilentFileOptions.hh>
#include <fstream>
#include <iostream>
#include <sstream>
#include <string>
#include <algorithm>
#include <cctype>
#include <iomanip>
#include <map>
#include <cstdlib>
#include <ctime>
#include <list>
#include <cstdio>
#include <cmath>

Typedefs

using Matrix = numeric::xyzMatrix< Real >
 

Functions

core::scoring::ScoreFunctionOP create_scorefxn ()
 
void align_pose_general (core::pose::Pose const &static_pose, std::string const &static_tag, core::pose::Pose &moving_pose, std::string const &moving_tag, utility::vector1< std::pair< Size, Size > > const &alignment_res_pair_list, bool const base_only)
 Jan 01, 2012: SHOULD INTEGRATE THIS WITH THE VERSION in protocols/stepwise/modeler/rna/util.hh. More...
 
core::Real check_alignment_RMSD_cutoff (core::pose::Pose const &static_pose, std::string const &static_tag, core::pose::Pose &moving_pose, std::string const &moving_tag, utility::vector1< std::pair< Size, Size > > const &alignment_res_pair_list, bool const base_only, core::Real const alignment_RMSD_cutoff)
 
Real full_length_rmsd_over_reside_list_general (pose::Pose const &pose_one, pose::Pose const &pose_two, utility::vector1< std::pair< Size, Size > > const &rmsd_res_pair_list, bool const verbose, bool const ignore_virtual_atom)
 Jan 01, 2012: SHOULD INTEGRATE THIS WITH THE VERSION in protocols/stepwise/modeler/rna/util.hh. More...
 
void align_pdbs ()
 
void calculate_pairwise_RMSD ()
 
void import_and_dump_pdb ()
 
void o2prime_packer ()
 
void mutate_residue (pose::Pose &pose, Size const seq_num, std::string const &res_name)
 
std::string get_one_letter_name (std::string const &three_letter_name)
 
std::string get_three_letter_name (std::string const &one_letter_name)
 
utility::vector1< Residue_info > Convert_rebuild_residue_string_to_list (std::string const &rebuild_residue_string)
 
void output_residue_struct (Residue_info const &residue)
 
void mutate_residues_wrapper ()
 
void slice_ellipsoid_envelope ()
 
void slice_sample_res_and_surrounding ()
 
void pdb_to_silent_file ()
 
void * my_main (void *)
 
int main (int argc, char *argv[])
 

Variables

static basic::Tracer TR ("swa_rna_util")
 

Typedef Documentation

using Matrix = numeric::xyzMatrix<Real>

Function Documentation

void align_pdbs ( )
void align_pose_general ( core::pose::Pose const &  static_pose,
std::string const &  static_tag,
core::pose::Pose moving_pose,
std::string const &  moving_tag,
utility::vector1< std::pair< Size, Size > > const &  alignment_res_pair_list,
bool const  base_only 
)

Jan 01, 2012: SHOULD INTEGRATE THIS WITH THE VERSION in protocols/stepwise/modeler/rna/util.hh.

References utility::io::oc::cout, TR, and utility_exit_with_message.

Referenced by align_pdbs(), and calculate_pairwise_RMSD().

void calculate_pairwise_RMSD ( )
core::Real check_alignment_RMSD_cutoff ( core::pose::Pose const &  static_pose,
std::string const &  static_tag,
core::pose::Pose moving_pose,
std::string const &  moving_tag,
utility::vector1< std::pair< Size, Size > > const &  alignment_res_pair_list,
bool const  base_only,
core::Real const  alignment_RMSD_cutoff 
)
utility::vector1< Residue_info > Convert_rebuild_residue_string_to_list ( std::string const &  rebuild_residue_string)
core::scoring::ScoreFunctionOP create_scorefxn ( )
Real full_length_rmsd_over_reside_list_general ( pose::Pose const &  pose_one,
pose::Pose const &  pose_two,
utility::vector1< std::pair< Size, Size > > const &  rmsd_res_pair_list,
bool const  verbose,
bool const  ignore_virtual_atom 
)

Jan 01, 2012: SHOULD INTEGRATE THIS WITH THE VERSION in protocols/stepwise/modeler/rna/util.hh.

References utility::io::oc::cout, max(), basic::options::OptionKeys::AnchoredDesign::rmsd, ObjexxFCL::string_of(), TR, and utility_exit_with_message.

Referenced by calculate_pairwise_RMSD().

std::string get_one_letter_name ( std::string const &  three_letter_name)
std::string get_three_letter_name ( std::string const &  one_letter_name)
void import_and_dump_pdb ( )
int main ( int  argc,
char *  argv[] 
)
void mutate_residue ( pose::Pose pose,
Size const  seq_num,
std::string const &  res_name 
)
void mutate_residues_wrapper ( )
void* my_main ( void *  )
void o2prime_packer ( )
void output_residue_struct ( Residue_info const &  residue)
void pdb_to_silent_file ( )
void slice_ellipsoid_envelope ( )
void slice_sample_res_and_surrounding ( )

Variable Documentation

basic::Tracer TR("swa_rna_util")
static