Rosetta  2021.16
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Namespaces | Functions
AlignPDBInfoToSequences.cc File Reference

Realign poses to sequences after losing pdb_info. More...

#include <protocols/pdbinfo_manipulations/AlignPDBInfoToSequences.hh>
#include <protocols/pdbinfo_manipulations/AlignPDBInfoToSequencesCreator.hh>
#include <protocols/pdbinfo_manipulations/AlignPDBInfoToSequencesUtil.hh>
#include <core/id/SequenceMapping.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <core/sequence/Sequence.hh>
#include <core/sequence/SequenceAlignment.hh>
#include <core/sequence/SimpleScoringScheme.hh>
#include <core/sequence/SWAligner.hh>
#include <basic/Tracer.hh>
#include <utility/tag/Tag.hh>
#include <utility/string_util.hh>
#include <utility/pointer/memory.hh>
#include <utility/io/izstream.hh>
#include <utility/json_utilities.hh>
#include <utility/excn/Exceptions.hh>
#include <utility/tag/XMLSchemaGeneration.hh>
#include <protocols/moves/mover_schemas.hh>
#include <numeric>
#include <sstream>

Namespaces

 protocols
 The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.
 
 protocols::pdbinfo_manipulations
 

Functions

static basic::Tracer TR ("protocols.pdbinfo_manipulations.AlignPDBInfoToSequences")
 
AlignPDBInfoToSequencesMode protocols::pdbinfo_manipulations::get_alignpdbinfotosequencesmode_from_string (std::string const &str)
 
std::string protocols::pdbinfo_manipulations::alignpdbinfotosequencesmode_to_string (AlignPDBInfoToSequencesMode const &mode)
 
std::ostream & protocols::pdbinfo_manipulations::operator<< (std::ostream &os, SequenceSpecification const &ss)
 
void protocols::pdbinfo_manipulations::to_json (nlohmann::json &j, SequenceSpecification const &ss)
 serialization (json) of SequenceSpecification More...
 
void protocols::pdbinfo_manipulations::from_json (const json &j, SequenceSpecification &ss)
 
utility::vector1
< core::sequence::SequenceOP
protocols::pdbinfo_manipulations::get_pose_sequences (core::pose::Pose const &pose)
 
utility::vector1< std::string > protocols::pdbinfo_manipulations::split_string_based_on_inserts (std::string const &str_in)
 take something like -—HELLO-—MY—BOY— More...
 
std::string protocols::pdbinfo_manipulations::AlignPDBInfoToSequences_namer (std::string const &name)
 
std::ostream & protocols::pdbinfo_manipulations::operator<< (std::ostream &os, AlignPDBInfoToSequences const &mover)
 private methods /// More...
 

Detailed Description

Realign poses to sequences after losing pdb_info.

Author
Dan Farrell (danpf.nosp@m.@uw..nosp@m.edu)

Function Documentation

static basic::Tracer TR ( "protocols.pdbinfo_manipulations.AlignPDBInfoToSequences"  )
static