Rosetta 3.4
Classes | Typedefs | Enumerations | Functions
core::sequence Namespace Reference

Classes

class  Aligner
class  AlignerFactory
class  AnnotatedSequence
class  SimpleSequenceCreator
class  SequenceProfileCreator
class  SequenceCouplingCreator
class  CompositeSequenceCreator
class  ChemicalShiftSequenceCreator
class  CacheableSequenceProfile
class  ChemicalShiftScoringScheme
class  ChemicalShiftSequence
class  CompassScoringScheme
class  CompositeScoringScheme
class  CompositeSequence
class  DerivedSequenceMapping
class  Cell
class  DP_Matrix
class  DPScoringScheme
class  ExtendAlignerSW
class  L1ScoringScheme
class  MatrixScoringScheme
class  MCAligner
class  NWAligner
class  PairScoringScheme
class  ProfSimScoringScheme
class  ScoringScheme
class  ScoringSchemeFactory
class  Sequence
class  SequenceAlignment
struct  SequenceAlignmentHasher
class  SequenceCoupling
class  SequenceCreator
 Abstract base class for a Mover factory; the Creator class is responsible for creating a particular mover class. More...
class  SequenceFactory
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  SequenceProfile
class  SimpleScoringScheme
class  SWAligner

Typedefs

typedef
utility::pointer::owning_ptr
< Aligner
AlignerOP
typedef
utility::pointer::owning_ptr
< Aligner const > 
AlignerCOP
typedef
utility::pointer::owning_ptr
< CacheableSequenceProfile
CacheableSequenceProfileOP
typedef
utility::pointer::owning_ptr
< CacheableSequenceProfile
const > 
CacheableSequenceProfileCOP
typedef
utility::pointer::access_ptr
< CacheableSequenceProfile
CacheableSequenceProfileAP
typedef
utility::pointer::access_ptr
< CacheableSequenceProfile
const > 
CacheableSequenceProfileCAP
typedef
utility::pointer::owning_ptr
< ChemicalShiftSequence
ChemicalShiftSequenceOP
typedef
utility::pointer::owning_ptr
< ChemicalShiftSequence const > 
ChemicalShiftSequenceCOP
typedef
utility::pointer::owning_ptr
< CompositeScoringScheme
CompositeScoringSchemeOP
typedef
utility::pointer::owning_ptr
< CompositeSequence
CompositeSequenceOP
typedef
utility::pointer::owning_ptr
< CompositeSequence const > 
CompositeSequenceCOP
typedef
utility::pointer::owning_ptr
< DerivedSequenceMapping
DerivedSequenceMappingOP
typedef
utility::pointer::owning_ptr
< DerivedSequenceMapping const > 
DerivedSequenceMappingCOP
typedef
utility::pointer::owning_ptr
< Cell
CellOP
typedef
utility::pointer::owning_ptr
< NWAligner
NWAlignerOP
typedef
utility::pointer::owning_ptr
< NWAligner const > 
NWAlignerCOP
typedef
utility::pointer::owning_ptr
< PairScoringScheme
PairScoringSchemeOP
typedef
utility::pointer::owning_ptr
< ScoringScheme
ScoringSchemeOP
typedef
utility::pointer::owning_ptr
< Sequence
SequenceOP
typedef
utility::pointer::owning_ptr
< Sequence const > 
SequenceCOP
typedef
utility::pointer::owning_ptr
< SequenceAlignment
SequenceAlignmentOP
typedef
utility::pointer::owning_ptr
< SequenceAlignment const > 
SequenceAlignmentCOP
typedef
utility::pointer::owning_ptr
< SequenceCoupling
SequenceCouplingOP
typedef
utility::pointer::owning_ptr
< SequenceCoupling const > 
SequenceCouplingCOP
typedef
utility::pointer::owning_ptr
< SequenceCreator
SequenceCreatorOP
typedef
utility::pointer::owning_ptr
< SequenceCreator const > 
SequenceCreatorCOP
typedef
utility::pointer::owning_ptr
< SequenceProfile
SequenceProfileOP
typedef
utility::pointer::owning_ptr
< SequenceProfile const > 
SequenceProfileCOP
typedef
utility::pointer::owning_ptr
< SWAligner
SWAlignerOP
typedef
utility::pointer::owning_ptr
< SWAligner const > 
SWAlignerCOP

Enumerations

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

Functions

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")
static
numeric::random::RandomGenerator 
align_RG (31882)
std::ostream & operator<< (std::ostream &out, const Sequence &seq)
std::istream & operator>> (std::istream &in, Sequence &seq)
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 (const std::string &format, const utility::vector1< std::string > &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>.
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.
vector1< string > read_fasta_file_str (std::string const &filename)
vector1< SequenceOPread_fasta_file (std::string const &filename)
 Read in sequences from a fasta-formatted file.
std::string read_fasta_file_return_str (std::string const &filename)
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.
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.
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.
SequenceAlignment mapping_to_alignment (core::id::SequenceMapping const &mapping, SequenceOP seq1, SequenceOP seq2)
 Constructs a SequenceAlignment from the given SequenceMapping and the two sequences.
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.
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.
core::sequence::SequenceAlignment align_naive (core::sequence::SequenceOP seq1, core::sequence::SequenceOP seq2)
 Generate a naive sequence alignment between two sequences.
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)

Typedef Documentation


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 
)
static numeric::random::RandomGenerator core::sequence::align_RG ( 31882  ) [static]
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 
)
utility::vector1< Real > core::sequence::get_maximum_scores ( core::sequence::ScoringSchemeOP  ss,
core::sequence::SequenceOP  seq 
)
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().

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 Sequence &  seq 
)
std::ostream& core::sequence::operator<< ( std::ostream &  out,
const SequenceProfile &  p 
)
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 SequenceAlignment &  sa 
)
std::ostream& core::sequence::operator<< ( std::ostream &  out,
const ChemicalShiftSequence &  p 
)
std::istream& core::sequence::operator>> ( std::istream &  in,
Sequence &  seq 
)
std::istream& core::sequence::operator>> ( std::istream &  in,
SequenceAlignment &  aln 
)
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 core::pack::interaction_graph::T().

void core::sequence::read_all_alignments ( const std::string &  format,
const utility::vector1< std::string > &  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_return_str ( std::string const &  filename)
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)
utility::vector1< SequenceAlignment > core::sequence::read_general_aln_file ( std::string const &  filename)
utility::vector1< SequenceAlignment > core::sequence::read_grishin_aln_file ( std::string const &  filename)
utility::vector1< SequenceOP > core::sequence::seqs_from_cmd_lines ( )

References end, and 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(), core::sequence::DerivedSequenceMapping::seq1(), core::sequence::DerivedSequenceMapping::seq2(), core::sequence::DerivedSequenceMapping::start_seq2(), and tr().

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

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(), and core::sequence::SequenceAlignment::size().

static basic::Tracer core::sequence::tr ( "core.sequence.ChemicalShiftSequence"  ) [static]
static basic::Tracer core::sequence::tr ( "core.sequence.SequenceProfile"  ) [static]
static basic::Tracer core::sequence::tr ( "core.sequence.SequenceCoupling"  ) [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.CompositeSequence"  ) [static]
static basic::Tracer core::sequence::tr ( "core.sequence.SequenceFactory"  ) [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::ThreadingMover::get_qt_mapping(), and protocols::comparative_modeling::ExtraThreadingMover::get_qt_mapping().

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