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core::sequence Namespace Reference

Classes

class  ABEGO
 abego elments More...
 
class  ABEGOManager
 manager for abego More...
 
class  Aligner
 
class  AlignerFactory
 
class  AnnotatedSequence
 
struct  Blosum62Map
 
class  Cell
 
struct  CharPairHash
 
class  ChemicalShiftScoringScheme
 
class  ChemicalShiftSequence
 
class  ChemicalShiftSequenceCreator
 
class  CompassScoringScheme
 
class  CompositeScoringScheme
 
class  CompositeSequence
 
class  CompositeSequenceCreator
 
class  DerivedSequenceMapping
 This is quite possibly the laziest form of class naming ever. What does the name of this class tell you about it? It's a SequenceMapping, and it's derived from SequenceMapping. Oops, it said it twice. What is different about this sequence mapping from the parent class? Who knows! When should you use it? Who knows!</snark> More...
 
class  DP_Matrix
 
class  DPScoringScheme
 
class  L1ScoringScheme
 
struct  Line
 struct More...
 
class  MatrixScoringScheme
 
class  MCAligner
 
class  NWAligner
 
class  PairScoringScheme
 
class  ProfSimScoringScheme
 
class  ScoringScheme
 
class  ScoringSchemeFactory
 
class  Sequence
 
class  SequenceAlignment
 
struct  SequenceAlignmentHasher
 
class  SequenceCoupling
 
class  SequenceCouplingCreator
 
class  SequenceCreator
 Abstract base class for a Mover factory; the Creator class is responsible for creating a particular mover class. More...
 
class  SequenceFactory
 
class  SequenceProfile
 
class  SequenceProfileCreator
 
class  SequenceRegistrator
 This templated class will register an instance of an SequenceCreator (class T) with the SequenceFactory. It will ensure that no SequenceCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place. More...
 
class  SimpleScoringScheme
 
class  SimpleSequenceCreator
 
class  SSManager
 struct More...
 
class  SWAligner
 

Typedefs

typedef
utility::pointer::shared_ptr
< ABEGOManager
ABEGOManagerOP
 
typedef
utility::pointer::shared_ptr
< ABEGOManager const > 
ABEGOManagerCOP
 
typedef
utility::pointer::shared_ptr
< Aligner
AlignerOP
 
typedef
utility::pointer::shared_ptr
< Aligner const > 
AlignerCOP
 
typedef
utility::pointer::shared_ptr
< ChemicalShiftSequence
ChemicalShiftSequenceOP
 
typedef
utility::pointer::shared_ptr
< ChemicalShiftSequence const > 
ChemicalShiftSequenceCOP
 
typedef
utility::pointer::shared_ptr
< CompositeScoringScheme
CompositeScoringSchemeOP
 
typedef
utility::pointer::shared_ptr
< CompositeSequence
CompositeSequenceOP
 
typedef
utility::pointer::shared_ptr
< CompositeSequence const > 
CompositeSequenceCOP
 
typedef
utility::pointer::shared_ptr
< DerivedSequenceMapping
DerivedSequenceMappingOP
 
typedef
utility::pointer::shared_ptr
< DerivedSequenceMapping const > 
DerivedSequenceMappingCOP
 
typedef
utility::pointer::shared_ptr
< Cell
CellOP
 
typedef
utility::pointer::shared_ptr
< NWAligner
NWAlignerOP
 
typedef
utility::pointer::shared_ptr
< NWAligner const > 
NWAlignerCOP
 
typedef
utility::pointer::shared_ptr
< PairScoringScheme
PairScoringSchemeOP
 
typedef
utility::pointer::shared_ptr
< ScoringScheme
ScoringSchemeOP
 
typedef
utility::pointer::shared_ptr
< Sequence
SequenceOP
 
typedef
utility::pointer::shared_ptr
< Sequence const > 
SequenceCOP
 
typedef
utility::pointer::shared_ptr
< SequenceAlignment
SequenceAlignmentOP
 
typedef
utility::pointer::shared_ptr
< SequenceAlignment const > 
SequenceAlignmentCOP
 
typedef
utility::pointer::shared_ptr
< SequenceCoupling
SequenceCouplingOP
 
typedef
utility::pointer::shared_ptr
< SequenceCoupling const > 
SequenceCouplingCOP
 
typedef
utility::pointer::shared_ptr
< SequenceCreator
SequenceCreatorOP
 
typedef
utility::pointer::shared_ptr
< SequenceCreator const > 
SequenceCreatorCOP
 
typedef
utility::pointer::shared_ptr
< SequenceProfile
SequenceProfileOP
 
typedef
utility::pointer::shared_ptr
< SequenceProfile const > 
SequenceProfileCOP
 
typedef
utility::pointer::shared_ptr
< SSManager
SSManagerOP
 
typedef
utility::pointer::shared_ptr
< SSManager const > 
SSManagerCOP
 
typedef
utility::pointer::shared_ptr
< SWAligner
SWAlignerOP
 
typedef
utility::pointer::shared_ptr
< SWAligner const > 
SWAlignerCOP
 

Enumerations

enum  AlignMove { diagonal = 1, left, above, end }
 

Functions

utility::vector1< std::string > get_abego (core::pose::Pose const &pose, core::Size const level)
 utility for getting abego More...
 
std::unordered_map< std::pair
< char, char >, int,
CharPairHash
create_map_for_Blosum62Map ()
 
static basic::Tracer tr ("core.sequence.ChemicalShiftSequence")
 
std::ostream & operator<< (std::ostream &out, const ChemicalShiftSequence &p)
 
static basic::Tracer tr ("core.sequence.CompositeSequence")
 
std::ostream & operator<< (std::ostream &out, const CompositeSequence &p)
 
std::ostream & operator<< (std::ostream &out, const DP_Matrix &m)
 
static basic::Tracer tr ("core.sequence.MatrixScoringScheme")
 
std::ostream & operator<< (std::ostream &out, const Sequence &seq)
 
std::istream & operator>> (std::istream &in, Sequence &seq)
 
static basic::Tracer tr ("core.sequence.sequence_motif")
 
utility::vector1< std::string > split_sequence_motif (std::string const &motif)
 Splits the sequence motif (Ex. N[^P]-[STN]A) into strings of commands for individual positions Example: ["N", "^P", "-", "STN","A",] for the three positions specified. More...
 
core::Size get_motif_length (std::string const &motif)
 
std::string get_design_sequence_motif_syntax ()
 Return the description of the syntax for a design sequence motif. More...
 
static basic::Tracer tr ("core.sequence.SequenceAlignment")
 
std::ostream & operator<< (std::ostream &out, const SequenceAlignment &sa)
 
std::istream & operator>> (std::istream &in, SequenceAlignment &aln)
 
bool operator< (SequenceAlignment const &lhs, SequenceAlignment const &rhs)
 
static basic::Tracer tr ("core.sequence.SequenceCoupling")
 
static basic::Tracer tr ("core.sequence.SequenceFactory")
 
static basic::Tracer tr ("core.sequence.SequenceProfile")
 
std::ostream & operator<< (std::ostream &out, const SequenceProfile &p)
 
static basic::Tracer tr ("core.sequence")
 
void read_all_alignments (std::string const &format, utility::vector1< std::string > const &files, utility::vector1< SequenceAlignment > &alignments)
 Populates the non-null vector <alignments> with all of the sequence alignments found in <files>. Each alignment is required to have format <format>. More...
 
void read_alignment_file (std::string const &filename, std::string &seq1, std::string &seq2, core::sequence::DerivedSequenceMapping &mapping)
 helper function for reading a SequenceMapping from an alignment file. More...
 
vector1< string > read_fasta_file_str (std::string const &filename)
 
SequenceOP get_sequence_object (std::string const &current_id, std::string const &current_sequence)
 
vector1< SequenceOPread_fasta_file (std::string const &filename)
 Read in sequences from a fasta-formatted file. More...
 
std::string read_fasta_file_return_str (std::string const &filename)
 
std::string read_fasta_file_section (std::string const &filename, std::string const &section_)
 read sequence from particular section of fasta file (comment starting with '> section'), terminate with failure if section not found Note: section detection string is case insensitive More...
 
void get_conventional_chains_and_numbering (utility::vector1< SequenceCOP > const &fasta_sequences, utility::vector1< char > &conventional_chains, utility::vector1< int > &conventional_numbering, utility::vector1< std::string > &conventional_segids)
 looks for tab-delimited tags like 'chain:A' and 'res_num:5-20' in fasta IDs. More...
 
std::string get_concatenated_sequence (vector1< SequenceCOP > const &fasta_sequences)
 Return a string of concatenated SequenceCOP sequences. More...
 
std::string read_fasta_file_and_concatenate (std::string const &filename)
 Read fasta file and concatenate sequences. More...
 
core::sequence::DerivedSequenceMapping simple_mapping_from_file (std::string const &filename)
 Read in a SequenceMapping from a file. File format is super-simple, it just contains single lines like this that claim that residue resi and resj are aligned: resi resj. More...
 
utility::vector1< SequenceOPseqs_from_cmd_lines ()
 
utility::vector1
< SequenceAlignment
read_aln (std::string const &format, std::string const &filename)
 
utility::vector1
< SequenceAlignment
read_general_aln (std::istream &input)
 read generalized alignment format. More...
 
utility::vector1
< SequenceAlignment
read_general_aln_file (std::string const &filename)
 
utility::vector1
< SequenceAlignment
read_grishin_aln_file (std::string const &filename)
 
Size n_correctly_aligned_positions (SequenceAlignment &candidate_aln, SequenceAlignment &true_aln)
 
SequenceAlignment steal_alignment (SequenceAlignment aln_to_steal, utility::vector1< SequenceOP > seqs)
 takes the sequences in the provided vector1 and makes them match the alignment in aln_to_steal by matching gaps. This assumes that the ungapped sequences at index j in the vector1< SequenceOP > match the ungapped sequences at index j in aln_to_steal. More...
 
SequenceAlignment mapping_to_alignment (core::id::SequenceMapping const &mapping, SequenceOP seq1, SequenceOP seq2)
 Constructs a SequenceAlignment from the given SequenceMapping and the two sequences. More...
 
core::id::SequenceMapping transitive_map (core::id::SequenceMapping const &map1, core::id::SequenceMapping const &map2)
 Assuming that map1 maps sequence A to sequence B, and map2 maps sequence B to sequence C, this function returns the SequenceMapping representing the direct map of sequence A to sequence C. More...
 
core::id::SequenceMapping map_seq1_seq2 (core::sequence::SequenceOP seq1, core::sequence::SequenceOP seq2)
 Generates a mapping of sequence 1 onto sequence 2 using dynamic programming with a simple scoring framework. More...
 
core::sequence::SequenceAlignment align_naive (core::sequence::SequenceOP seq1, core::sequence::SequenceOP seq2)
 Generate a naive sequence alignment between two sequences. More...
 
core::sequence::SequenceAlignment align_poses_naive (core::pose::Pose &pose1, core::pose::Pose &pose2)
 
utility::vector1< Realget_maximum_scores (core::sequence::ScoringSchemeOP ss, core::sequence::SequenceOP seq)
 
core::sequence::SequenceAlignment alignment_from_pose (core::pose::Pose &pose)
 
void alignment_into_pose (core::sequence::SequenceAlignment const &aln, core::pose::Pose &pose)
 
core::Real calpha_superimpose_with_mapping (core::pose::Pose &mod_pose, core::pose::Pose const &ref_pose, core::id::SequenceMapping const &mapping)
 
utility::vector1< Sizestrip_spacers (std::string &sequence, bool const annotations_in_brackets)
 
std::map< Size, std::string > parse_out_non_standard_residues (vector1< core::sequence::SequenceOP > &fasta_sequences)
 
std::map< Size, std::string > parse_out_non_standard_residues (std::string &sequence)
 
std::string convert_to_fasta (std::string const &pname, std::string const &seq)
 Convert sequence string to fasta string with only 80 characters per line. More...
 
std::string create_fasta_file (std::string const &pname, std::string const &seq)
 Create fasta file from sequence string. Differs from output_fasta_file in that the output is in valid FASTA format, rather than including NTerm/CTerm tags. More...
 
void output_fasta_file (std::string const &fasta_filename, core::pose::Pose const &pose)
 
std::string get_concatenated_sequence (utility::vector1< SequenceCOP > const &fasta_sequences)
 Return a string of concatenated SequenceCOP sequences. More...
 
std::map< Size, std::string > parse_out_non_standard_residues (utility::vector1< core::sequence::SequenceOP > &fasta_sequences)
 

Variables

vector1< char > spacers = utility::tools::make_vector1( '+','*',' ',',' )
 

Typedef Documentation

typedef utility::pointer::shared_ptr<ABEGOManager const> core::sequence::ABEGOManagerCOP
typedef utility::pointer::shared_ptr<ABEGOManager> core::sequence::ABEGOManagerOP
typedef utility::pointer::shared_ptr< Aligner const > core::sequence::AlignerCOP
typedef utility::pointer::shared_ptr< Aligner > core::sequence::AlignerOP
typedef utility::pointer::shared_ptr< Cell > core::sequence::CellOP
typedef utility::pointer::shared_ptr< ChemicalShiftSequence const > core::sequence::ChemicalShiftSequenceCOP
typedef utility::pointer::shared_ptr< ChemicalShiftSequence > core::sequence::ChemicalShiftSequenceOP
typedef utility::pointer::shared_ptr< CompositeScoringScheme > core::sequence::CompositeScoringSchemeOP
typedef utility::pointer::shared_ptr< CompositeSequence const > core::sequence::CompositeSequenceCOP
typedef utility::pointer::shared_ptr< CompositeSequence > core::sequence::CompositeSequenceOP
typedef utility::pointer::shared_ptr< DerivedSequenceMapping const > core::sequence::DerivedSequenceMappingCOP
typedef utility::pointer::shared_ptr< DerivedSequenceMapping > core::sequence::DerivedSequenceMappingOP
typedef utility::pointer::shared_ptr< NWAligner const > core::sequence::NWAlignerCOP
typedef utility::pointer::shared_ptr< NWAligner > core::sequence::NWAlignerOP
typedef utility::pointer::shared_ptr< PairScoringScheme > core::sequence::PairScoringSchemeOP
typedef utility::pointer::shared_ptr< ScoringScheme > core::sequence::ScoringSchemeOP
typedef utility::pointer::shared_ptr< SequenceAlignment const > core::sequence::SequenceAlignmentCOP
typedef utility::pointer::shared_ptr< SequenceAlignment > core::sequence::SequenceAlignmentOP
typedef utility::pointer::shared_ptr< Sequence const > core::sequence::SequenceCOP
typedef utility::pointer::shared_ptr< SequenceCoupling const > core::sequence::SequenceCouplingCOP
typedef utility::pointer::shared_ptr< SequenceCoupling > core::sequence::SequenceCouplingOP
typedef utility::pointer::shared_ptr< SequenceCreator const > core::sequence::SequenceCreatorCOP
typedef utility::pointer::shared_ptr< SequenceCreator > core::sequence::SequenceCreatorOP
typedef utility::pointer::shared_ptr< Sequence > core::sequence::SequenceOP
typedef utility::pointer::shared_ptr< SequenceProfile const > core::sequence::SequenceProfileCOP
typedef utility::pointer::shared_ptr< SequenceProfile > core::sequence::SequenceProfileOP
typedef utility::pointer::shared_ptr<SSManager const> core::sequence::SSManagerCOP
typedef utility::pointer::shared_ptr<SSManager> core::sequence::SSManagerOP
typedef utility::pointer::shared_ptr< SWAligner const > core::sequence::SWAlignerCOP
typedef utility::pointer::shared_ptr< SWAligner > core::sequence::SWAlignerOP

Enumeration Type Documentation

Enumerator
diagonal 
left 
above 
end 

Function Documentation

core::sequence::SequenceAlignment core::sequence::align_poses_naive ( core::pose::Pose pose1,
core::pose::Pose pose2 
)
core::sequence::SequenceAlignment core::sequence::alignment_from_pose ( core::pose::Pose pose)
void core::sequence::alignment_into_pose ( core::sequence::SequenceAlignment const &  aln,
core::pose::Pose pose 
)
core::Real core::sequence::calpha_superimpose_with_mapping ( core::pose::Pose mod_pose,
core::pose::Pose const &  ref_pose,
core::id::SequenceMapping const &  mapping 
)
std::string core::sequence::convert_to_fasta ( std::string const &  pname,
std::string const &  seq 
)

Convert sequence string to fasta string with only 80 characters per line.

Referenced by create_fasta_file().

std::string core::sequence::create_fasta_file ( std::string const &  pname,
std::string const &  seq 
)

Create fasta file from sequence string. Differs from output_fasta_file in that the output is in valid FASTA format, rather than including NTerm/CTerm tags.

References convert_to_fasta(), and tr().

Referenced by protocols::frag_picker::FragmentScoreFilter::setup_fragment_picker().

std::unordered_map< std::pair< char, char >, int, CharPairHash > core::sequence::create_map_for_Blosum62Map ( )
inline

References blosum_62_map_tr().

utility::vector1< std::string > core::sequence::get_abego ( core::pose::Pose const &  pose,
core::Size const  level 
)
std::string core::sequence::get_concatenated_sequence ( vector1< SequenceCOP > const &  fasta_sequences)

Return a string of concatenated SequenceCOP sequences.

moved from stepwise/setup/FullModelInfoSetupFromCommandLine.cc

Referenced by core::import_pose::get_sequence_information(), and read_fasta_file_and_concatenate().

std::string core::sequence::get_concatenated_sequence ( vector1< SequenceCOP > const &  fasta_sequences)

Return a string of concatenated SequenceCOP sequences.

moved from stepwise/setup/FullModelInfoSetupFromCommandLine.cc

Referenced by core::import_pose::get_sequence_information(), and read_fasta_file_and_concatenate().

void core::sequence::get_conventional_chains_and_numbering ( utility::vector1< SequenceCOP > const &  fasta_sequences,
utility::vector1< char > &  conventional_chains,
utility::vector1< int > &  conventional_numbering,
utility::vector1< std::string > &  conventional_segids 
)
std::string core::sequence::get_design_sequence_motif_syntax ( )
utility::vector1< Real > core::sequence::get_maximum_scores ( core::sequence::ScoringSchemeOP  ss,
core::sequence::SequenceOP  seq 
)
core::Size core::sequence::get_motif_length ( std::string const &  motif)
SequenceOP core::sequence::get_sequence_object ( std::string const &  current_id,
std::string const &  current_sequence 
)
core::id::SequenceMapping core::sequence::map_seq1_seq2 ( core::sequence::SequenceOP  seq1,
core::sequence::SequenceOP  seq2 
)

Generates a mapping of sequence 1 onto sequence 2 using dynamic programming with a simple scoring framework.

References core::sequence::SequenceAlignment::identities(), core::sequence::SequenceAlignment::length(), core::sequence::SequenceAlignment::sequence_mapping(), and tr().

Referenced by protocols::antibody::cdr_backbone_rmsds(), and core::pose::sequence_map_from_pdbinfo().

SequenceAlignment core::sequence::mapping_to_alignment ( core::id::SequenceMapping const &  mapping,
SequenceOP  seq1_orig,
SequenceOP  seq2_orig 
)

Constructs a SequenceAlignment from the given SequenceMapping and the two sequences.

References core::sequence::SequenceAlignment::add_sequence(), and core::id::SequenceMapping::size1().

core::Size core::sequence::n_correctly_aligned_positions ( SequenceAlignment candidate_aln,
SequenceAlignment true_aln 
)
bool core::sequence::operator< ( SequenceAlignment const &  lhs,
SequenceAlignment const &  rhs 
)
std::ostream& core::sequence::operator<< ( std::ostream &  out,
const CompositeSequence &  p 
)
std::ostream& core::sequence::operator<< ( std::ostream &  out,
const DP_Matrix &  m 
)
std::ostream& core::sequence::operator<< ( std::ostream &  out,
const ChemicalShiftSequence &  p 
)
std::ostream& core::sequence::operator<< ( std::ostream &  out,
const Sequence &  seq 
)
std::ostream& core::sequence::operator<< ( std::ostream &  out,
const SequenceAlignment &  sa 
)
std::ostream& core::sequence::operator<< ( std::ostream &  out,
const SequenceProfile &  p 
)
std::istream& core::sequence::operator>> ( std::istream &  in,
Sequence &  seq 
)
std::istream& core::sequence::operator>> ( std::istream &  in,
SequenceAlignment &  aln 
)
void core::sequence::output_fasta_file ( std::string const &  fasta_filename,
core::pose::Pose const &  pose 
)
std::map< Size, std::string > core::sequence::parse_out_non_standard_residues ( utility::vector1< core::sequence::SequenceOP > &  fasta_sequences)
std::map< Size, std::string > core::sequence::parse_out_non_standard_residues ( vector1< core::sequence::SequenceOP > &  fasta_sequences)
std::map< core::Size, std::string > core::sequence::parse_out_non_standard_residues ( std::string &  sequence)
void core::sequence::read_alignment_file ( std::string const &  filename,
std::string &  seq1,
std::string &  seq2,
sequence::DerivedSequenceMapping &  mapping 
)

helper function for reading a SequenceMapping from an alignment file.

if position i in seq1 is aligned with position j in seq2, mapping[ i ] == j if position i in seq1 is unaligned, mapping[ i ] == 0

References core::id::SequenceMapping::clear(), core::id::SequenceMapping::push_back(), core::id::SequenceMapping::size1(), core::id::SequenceMapping::size2(), and tr().

void core::sequence::read_all_alignments ( std::string const &  format,
utility::vector1< std::string > const &  files,
utility::vector1< SequenceAlignment > &  alignments 
)

Populates the non-null vector <alignments> with all of the sequence alignments found in <files>. Each alignment is required to have format <format>.

References read_aln().

utility::vector1< SequenceAlignment > core::sequence::read_aln ( std::string const &  format,
std::string const &  filename 
)
utility::vector1< SequenceOP > core::sequence::read_fasta_file ( std::string const &  filename)
std::string core::sequence::read_fasta_file_and_concatenate ( std::string const &  filename)
std::string core::sequence::read_fasta_file_return_str ( std::string const &  filename)
std::string core::sequence::read_fasta_file_section ( std::string const &  filename,
std::string const &  section_ 
)

read sequence from particular section of fasta file (comment starting with '> section'), terminate with failure if section not found Note: section detection string is case insensitive

References end, read_fasta_file(), core::chemical::element::S, and protocols::sparta::section().

utility::vector1< std::string > core::sequence::read_fasta_file_str ( std::string const &  filename)
utility::vector1< SequenceAlignment > core::sequence::read_general_aln ( std::istream &  input)

read generalized alignment format.

References protocols::hybridization::score, and tr().

Referenced by read_general_aln_file().

utility::vector1< SequenceAlignment > core::sequence::read_general_aln_file ( std::string const &  filename)

References read_general_aln().

Referenced by read_aln().

utility::vector1< SequenceAlignment > core::sequence::read_grishin_aln_file ( std::string const &  filename)
utility::vector1< SequenceOP > core::sequence::seqs_from_cmd_lines ( )

References read_fasta_file().

core::sequence::DerivedSequenceMapping core::sequence::simple_mapping_from_file ( std::string const &  filename)

Read in a SequenceMapping from a file. File format is super-simple, it just contains single lines like this that claim that residue resi and resj are aligned: resi resj.

References end, core::id::SequenceMapping::insert_aligned_residue_safe(), protocols::mean_field::max(), core::sequence::DerivedSequenceMapping::seq1(), core::sequence::DerivedSequenceMapping::seq2(), core::sequence::DerivedSequenceMapping::start_seq2(), and tr().

Referenced by protocols::abinitio::Template::Template().

utility::vector1< std::string > core::sequence::split_sequence_motif ( std::string const &  motif)

Splits the sequence motif (Ex. N[^P]-[STN]A) into strings of commands for individual positions Example: ["N", "^P", "-", "STN","A",] for the three positions specified.

References core::pack::dunbrack::c, protocols::sparta::contains(), protocols::kinmatch::str(), and core::id::to_string().

Referenced by get_motif_length(), and core::pack::task::get_resfile_commands().

SequenceAlignment core::sequence::steal_alignment ( SequenceAlignment  aln_to_steal,
utility::vector1< SequenceOP seqs 
)

takes the sequences in the provided vector1 and makes them match the alignment in aln_to_steal by matching gaps. This assumes that the ungapped sequences at index j in the vector1< SequenceOP > match the ungapped sequences at index j in aln_to_steal.

References core::sequence::SequenceAlignment::add_sequence(), core::sequence::SequenceAlignment::length(), core::sequence::SequenceAlignment::sequence(), core::sequence::SequenceAlignment::size(), protocols::loops::start, and core::sequence::SequenceAlignment::to_string().

utility::vector1< core::Size > core::sequence::strip_spacers ( std::string &  sequence,
bool const  annotations_in_brackets 
)
static basic::Tracer core::sequence::tr ( "core.sequence.CompositeSequence"  )
static
static basic::Tracer core::sequence::tr ( "core.sequence.SequenceFactory"  )
static
static basic::Tracer core::sequence::tr ( "core.sequence.ChemicalShiftSequence"  )
static
static basic::Tracer core::sequence::tr ( "core.sequence.SequenceCoupling"  )
static
static basic::Tracer core::sequence::tr ( "core.sequence.sequence_motif"  )
static
static basic::Tracer core::sequence::tr ( "core.sequence.MatrixScoringScheme"  )
static
static basic::Tracer core::sequence::tr ( "core.sequence.SequenceAlignment"  )
static
static basic::Tracer core::sequence::tr ( "core.sequence.SequenceProfile"  )
static
static basic::Tracer core::sequence::tr ( "core.sequence"  )
static
core::id::SequenceMapping core::sequence::transitive_map ( core::id::SequenceMapping const &  map1,
core::id::SequenceMapping const &  map2 
)

Assuming that map1 maps sequence A to sequence B, and map2 maps sequence B to sequence C, this function returns the SequenceMapping representing the direct map of sequence A to sequence C.

References core::id::SequenceMapping::size1(), and core::id::SequenceMapping::size2().

Referenced by protocols::comparative_modeling::get_qt_mapping_general().

Variable Documentation

utility::vector1< char > core::sequence::spacers = utility::tools::make_vector1( '+','*',' ',',' )