Rosetta Core  2014.35
Classes | Typedefs | Enumerations | Functions | Variables
core::sequence Namespace Reference

Classes

class  Aligner
 
class  AlignerFactory
 
class  AnnotatedSequence
 
class  CacheableSequenceProfile
 
class  Cell
 
class  ChemicalShiftScoringScheme
 
class  ChemicalShiftSequence
 
class  ChemicalShiftSequenceCreator
 
class  CompassScoringScheme
 
class  CompositeScoringScheme
 
class  CompositeSequence
 
class  CompositeSequenceCreator
 
class  DerivedSequenceMapping
 
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  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  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

std::ostream & operator<< (std::ostream &out, const ChemicalShiftSequence &p)
 
std::ostream & operator<< (std::ostream &out, const CompositeSequence &p)
 
std::ostream & operator<< (std::ostream &out, const DP_Matrix &m)
 
std::ostream & operator<< (std::ostream &out, const Sequence &seq)
 
std::istream & operator>> (std::istream &in, Sequence &seq)
 
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)
 
std::ostream & operator<< (std::ostream &out, const SequenceProfile &p)
 
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>. 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)
 
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)
 
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)
 

Variables

static basic::Tracer tr ("core.sequence.ChemicalShiftSequence")
 
static basic::Tracer tr ("core.sequence.CompositeSequence")
 
static basic::Tracer tr ("core.sequence.MatrixScoringScheme")
 
static
numeric::random::RandomGenerator 
align_RG (31882)
 
static basic::Tracer tr ("core.sequence.SequenceAlignment")
 
static basic::Tracer tr ("core.sequence.SequenceCoupling")
 
static basic::Tracer tr ("core.sequence.SequenceFactory")
 
static basic::Tracer tr ("core.sequence.SequenceProfile")
 
static basic::Tracer tr ("core.sequence")
 

Typedef Documentation

Enumeration Type Documentation

Enumerator
diagonal 
left 
above 
end 

Function Documentation

Generate a naive sequence alignment between two sequences.

References ss.

Referenced by align_poses_naive().

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 
)
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(), ss, and tr.

Referenced by 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(), length, runtime_assert, 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::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(), getline(), core::id::SequenceMapping::push_back(), runtime_assert, core::id::SequenceMapping::size1(), core::id::SequenceMapping::size2(), and basic::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)

References end, and read_fasta_file().

utility::vector1< SequenceAlignment > core::sequence::read_general_aln ( std::istream &  input)

read generalized alignment format.

References getline(), 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(), and utility_exit_with_message.

Referenced by read_aln().

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

References getline(), method, score, start, and utility_exit_with_message.

Referenced by read_aln().

utility::vector1< SequenceOP > core::sequence::seqs_from_cmd_lines ( )
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, getline(), core::id::SequenceMapping::insert_aligned_residue_safe(), resi, resj, core::sequence::DerivedSequenceMapping::seq1(), core::sequence::DerivedSequenceMapping::seq2(), core::io::serialization::size(), core::sequence::DerivedSequenceMapping::start_seq2(), tag, tr, type, and utility_exit_with_message.

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(), length, core::sequence::SequenceAlignment::length(), runtime_assert, sequence, core::sequence::SequenceAlignment::sequence(), core::sequence::SequenceAlignment::size(), start, and utility_exit_with_message.

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().

Variable Documentation

numeric::random::RandomGenerator core::sequence::align_RG(31882)
static
basic::Tracer core::sequence::tr("core.sequence.CompositeSequence")
static
basic::Tracer core::sequence::tr("core.sequence.SequenceFactory")
static
basic::Tracer core::sequence::tr("core.sequence.SequenceCoupling")
static
basic::Tracer core::sequence::tr("core.sequence.ChemicalShiftSequence")
static
basic::Tracer core::sequence::tr("core.sequence.MatrixScoringScheme")
static
basic::Tracer core::sequence::tr("core.sequence.SequenceAlignment")
static
basic::Tracer core::sequence::tr("core.sequence.SequenceProfile")
static
basic::Tracer core::sequence::tr("core.sequence")
static