Rosetta  2021.16
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Classes | Typedefs | Enumerations | Functions
protocols::pdbinfo_manipulations Namespace Reference

Classes

class  AlignPDBInfoToSequences
 Realign poses to sequences after losing pdb_info. More...
 
class  AlignPDBInfoToSequencesCreator
 
struct  SequenceSpecification
 Rosetta defines the pdbinfo of an object via possible chain IDs, segment IDs, and insertion codes. More...
 

Typedefs

using AlignPDBInfoToSequencesOP = utility::pointer::shared_ptr< AlignPDBInfoToSequences >
 
using AlignPDBInfoToSequencesCOP = utility::pointer::shared_ptr< AlignPDBInfoToSequences const >
 

Enumerations

enum  AlignPDBInfoToSequencesMode { AlignPDBInfoToSequencesMode::unset, AlignPDBInfoToSequencesMode::single, AlignPDBInfoToSequencesMode::multiple }
 

Functions

AlignPDBInfoToSequencesMode get_alignpdbinfotosequencesmode_from_string (std::string const &str)
 
std::string alignpdbinfotosequencesmode_to_string (AlignPDBInfoToSequencesMode const &mode)
 
std::ostream & operator<< (std::ostream &os, SequenceSpecification const &ss)
 
void to_json (nlohmann::json &j, SequenceSpecification const &ss)
 serialization (json) of SequenceSpecification More...
 
void from_json (const json &j, SequenceSpecification &ss)
 
utility::vector1
< core::sequence::SequenceOP
get_pose_sequences (core::pose::Pose const &pose)
 
utility::vector1< std::string > split_string_based_on_inserts (std::string const &str_in)
 take something like -—HELLO-—MY—BOY— More...
 
std::string AlignPDBInfoToSequences_namer (std::string const &name)
 
std::ostream & operator<< (std::ostream &os, AlignPDBInfoToSequences const &mover)
 private methods /// More...
 
void pad_sequences (std::string const &full_seq_1, core::sequence::SequenceOP const &aln_seq_1, std::string const &full_seq_2, core::sequence::SequenceOP const &aln_seq_2)
 Take two sequences that have been aligned, and their parent sequences and align/pad them with '-' as shown below: More...
 

Typedef Documentation

using protocols::pdbinfo_manipulations::AlignPDBInfoToSequencesCOP = typedef utility::pointer::shared_ptr< AlignPDBInfoToSequences const >

Enumeration Type Documentation

Enumerator
unset 
single 
multiple 

Function Documentation

std::string protocols::pdbinfo_manipulations::AlignPDBInfoToSequences_namer ( std::string const &  name)
std::string protocols::pdbinfo_manipulations::alignpdbinfotosequencesmode_to_string ( AlignPDBInfoToSequencesMode const &  mode)
void protocols::pdbinfo_manipulations::from_json ( const json &  j,
SequenceSpecification &  ss 
)
AlignPDBInfoToSequencesMode protocols::pdbinfo_manipulations::get_alignpdbinfotosequencesmode_from_string ( std::string const &  str)
utility::vector1< core::sequence::SequenceOP > protocols::pdbinfo_manipulations::get_pose_sequences ( core::pose::Pose const &  pose)
std::ostream & protocols::pdbinfo_manipulations::operator<< ( std::ostream &  os,
SequenceSpecification const &  ss 
)
std::ostream & protocols::pdbinfo_manipulations::operator<< ( std::ostream &  os,
AlignPDBInfoToSequences const &  mover 
)
void protocols::pdbinfo_manipulations::pad_sequences ( std::string const &  full_seq_1,
core::sequence::SequenceOP const &  aln_seq_1,
std::string const &  full_seq_2,
core::sequence::SequenceOP const &  aln_seq_2 
)

Take two sequences that have been aligned, and their parent sequences and align/pad them with '-' as shown below:

given to align from SWAlign: query: CLGIGSCNDFAGCGYAVVCFW target: XXXXXXXXXXXXXXCLGIGSCNDFAGCGXXXXXXYAVVCFWXXXXX

from: (aka a result from SWAlign) query 1 CLGIGSCNDFAGCG---—YAVVCFW target 15 CLGIGSCNDFAGCGXXXXXXYAVVCFW

to: query 1 -----------—CLGIGSCNDFAGCG---—YAVVCFW--— target 1 XXXXXXXXXXXXXXCLGIGSCNDFAGCGXXXXXXYAVVCFWXXXXX

References protocols::mean_field::max().

Referenced by protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::apply_multi_sequence(), and protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::apply_single_sequence().

utility::vector1< std::string > protocols::pdbinfo_manipulations::split_string_based_on_inserts ( std::string const &  str_in)

take something like -—HELLO-—MY—BOY—

Referenced by protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::apply_multi_sequence().

void protocols::pdbinfo_manipulations::to_json ( nlohmann::json &  j,
SequenceSpecification const &  ss 
)