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