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>. 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< SequenceOP >	read_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< SequenceOP >	seqs_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< Real >	get_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

typedef utility::pointer::owning_ptr< Aligner const > core::sequence::AlignerCOP

Definition at line 24 of file Aligner.fwd.hh.

typedef utility::pointer::owning_ptr< Aligner > core::sequence::AlignerOP

Definition at line 22 of file Aligner.fwd.hh.

typedef utility::pointer::access_ptr< CacheableSequenceProfile > core::sequence::CacheableSequenceProfileAP

Definition at line 29 of file CacheableSequenceProfile.fwd.hh.

typedef utility::pointer::access_ptr< CacheableSequenceProfile const > core::sequence::CacheableSequenceProfileCAP

Definition at line 30 of file CacheableSequenceProfile.fwd.hh.

typedef utility::pointer::owning_ptr< CacheableSequenceProfile const > core::sequence::CacheableSequenceProfileCOP

Definition at line 28 of file CacheableSequenceProfile.fwd.hh.

typedef utility::pointer::owning_ptr< CacheableSequenceProfile > core::sequence::CacheableSequenceProfileOP

Definition at line 26 of file CacheableSequenceProfile.fwd.hh.

typedef utility::pointer::owning_ptr< Cell > core::sequence::CellOP

Definition at line 37 of file DP_Matrix.hh.

typedef utility::pointer::owning_ptr< ChemicalShiftSequence const > core::sequence::ChemicalShiftSequenceCOP

Definition at line 24 of file ChemicalShiftSequence.fwd.hh.

typedef utility::pointer::owning_ptr< ChemicalShiftSequence > core::sequence::ChemicalShiftSequenceOP

Definition at line 22 of file ChemicalShiftSequence.fwd.hh.

typedef utility::pointer::owning_ptr< CompositeScoringScheme > core::sequence::CompositeScoringSchemeOP

Definition at line 22 of file CompositeScoringScheme.fwd.hh.

typedef utility::pointer::owning_ptr< CompositeSequence const > core::sequence::CompositeSequenceCOP

Definition at line 24 of file CompositeSequence.fwd.hh.

typedef utility::pointer::owning_ptr< CompositeSequence > core::sequence::CompositeSequenceOP

Definition at line 22 of file CompositeSequence.fwd.hh.

typedef utility::pointer::owning_ptr< DerivedSequenceMapping const > core::sequence::DerivedSequenceMappingCOP

Definition at line 25 of file DerivedSequenceMapping.fwd.hh.

typedef utility::pointer::owning_ptr< DerivedSequenceMapping > core::sequence::DerivedSequenceMappingOP

Definition at line 23 of file DerivedSequenceMapping.fwd.hh.

typedef utility::pointer::owning_ptr< NWAligner const > core::sequence::NWAlignerCOP

Definition at line 24 of file NWAligner.fwd.hh.

typedef utility::pointer::owning_ptr< NWAligner > core::sequence::NWAlignerOP

Definition at line 22 of file NWAligner.fwd.hh.

typedef utility::pointer::owning_ptr< PairScoringScheme > core::sequence::PairScoringSchemeOP

Definition at line 22 of file PairScoringScheme.fwd.hh.

typedef utility::pointer::owning_ptr< ScoringScheme > core::sequence::ScoringSchemeOP

Definition at line 22 of file ScoringScheme.fwd.hh.

typedef utility::pointer::owning_ptr< SequenceAlignment const > core::sequence::SequenceAlignmentCOP

Definition at line 24 of file SequenceAlignment.fwd.hh.

typedef utility::pointer::owning_ptr< SequenceAlignment > core::sequence::SequenceAlignmentOP

Definition at line 22 of file SequenceAlignment.fwd.hh.

typedef utility::pointer::owning_ptr< Sequence const > core::sequence::SequenceCOP

Definition at line 24 of file Sequence.fwd.hh.

typedef utility::pointer::owning_ptr< SequenceCoupling const > core::sequence::SequenceCouplingCOP

Definition at line 24 of file SequenceCoupling.fwd.hh.

typedef utility::pointer::owning_ptr< SequenceCoupling > core::sequence::SequenceCouplingOP

Definition at line 22 of file SequenceCoupling.fwd.hh.

typedef utility::pointer::owning_ptr< SequenceCreator const > core::sequence::SequenceCreatorCOP

Definition at line 28 of file SequenceCreator.fwd.hh.

typedef utility::pointer::owning_ptr< SequenceCreator > core::sequence::SequenceCreatorOP

Definition at line 25 of file SequenceCreator.fwd.hh.

typedef utility::pointer::owning_ptr< Sequence > core::sequence::SequenceOP

Definition at line 22 of file Sequence.fwd.hh.

typedef utility::pointer::owning_ptr< SequenceProfile const > core::sequence::SequenceProfileCOP

Definition at line 24 of file SequenceProfile.fwd.hh.

typedef utility::pointer::owning_ptr< SequenceProfile > core::sequence::SequenceProfileOP

Definition at line 22 of file SequenceProfile.fwd.hh.

typedef utility::pointer::owning_ptr< SWAligner const > core::sequence::SWAlignerCOP

Definition at line 24 of file SWAligner.fwd.hh.

typedef utility::pointer::owning_ptr< SWAligner > core::sequence::SWAlignerOP

Definition at line 22 of file SWAligner.fwd.hh.

Enumeration Type Documentation

enum core::sequence::AlignMove

Enumerator
diagonal
left
above
end

Definition at line 28 of file DP_Matrix.hh.

Function Documentation

core::sequence::SequenceAlignment core::sequence::align_naive	(	core::sequence::SequenceOP	seq1,
		core::sequence::SequenceOP	seq2
	)

Generate a naive sequence alignment between two sequences.

Definition at line 679 of file util.cc.

Referenced by align_poses_naive(), protocols::evaluation::AlignEvaluator::get_alignment(), and protocols::hybridization::get_gdtmm().

core::sequence::SequenceAlignment core::sequence::align_poses_naive	(	core::pose::Pose &	pose1,
		core::pose::Pose &	pose2
	)

Definition at line 694 of file util.cc.

References align_naive(), and core::pose::Pose::sequence().

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

static numeric::random::RandomGenerator core::sequence::align_RG ( 31882 )

static

Referenced by core::sequence::MCAligner::align().

core::sequence::SequenceAlignment core::sequence::alignment_from_pose ( core::pose::Pose & pose)

Definition at line 722 of file util.cc.

References core::sequence::SequenceAlignment::add_sequence(), core::pose::get_comment(), and tr().

Referenced by protocols::relax::MiniRelax::apply(), and protocols::comparative_modeling::LoopRelaxThreadingMover::apply().

void core::sequence::alignment_into_pose	(	core::sequence::SequenceAlignment const &	aln,
		core::pose::Pose &	pose
	)

Definition at line 758 of file util.cc.

References core::pose::add_comment(), and core::sequence::SequenceAlignment::sequence().

Referenced by protocols::comparative_modeling::ThreadingJobInputter::pose_from_job().

core::Real core::sequence::calpha_superimpose_with_mapping	(	core::pose::Pose &	mod_pose,
		core::pose::Pose const &	ref_pose,
		core::id::SequenceMapping const &	mapping
	)

Definition at line 767 of file util.cc.

References core::conformation::Residue::atom_index(), core::id::BOGUS_ATOM_ID, core::conformation::Residue::has(), core::pose::initialize_atomid_map(), core::pose::Pose::residue(), core::id::AtomID_Map< T >::set(), core::scoring::superimpose_pose(), and core::pose::Pose::total_residue().

Referenced by protocols::relax::RelaxProtocolBase::set_up_constraints().

utility::vector1< Real > core::sequence::get_maximum_scores	(	core::sequence::ScoringSchemeOP	ss,
		core::sequence::SequenceOP	seq
	)

Definition at line 706 of file util.cc.

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.

Definition at line 637 of file util.cc.

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

Definition at line 563 of file util.cc.

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
	)

Definition at line 436 of file util.cc.

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

bool core::sequence::operator<	(	SequenceAlignment const &	lhs,
		SequenceAlignment const &	rhs
	)

Definition at line 467 of file SequenceAlignment.cc.

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

std::ostream& core::sequence::operator<<	(	std::ostream &	out,
		const CompositeSequence &	p
	)

Definition at line 35 of file CompositeSequence.cc.

References core::sequence::CompositeSequence::to_string().

std::ostream& core::sequence::operator<<	(	std::ostream &	out,
		const DP_Matrix &	m
	)

Definition at line 82 of file DP_Matrix.cc.

References protocols::comparative_modeling::features::A, core::sequence::DP_Matrix::cols(), core::io::raw_data::precision(), core::sequence::DP_Matrix::rows(), core::sequence::DP_Matrix::xlab(), and core::sequence::DP_Matrix::ylab().

std::ostream& core::sequence::operator<<	(	std::ostream &	out,
		const ChemicalShiftSequence &	p
	)

Definition at line 191 of file ChemicalShiftSequence.cc.

References core::sequence::Sequence::length(), core::io::raw_data::precision(), core::sequence::SequenceProfile::prof_row(), core::sequence::Sequence::to_string(), and core::sequence::SequenceProfile::width().

std::ostream& core::sequence::operator<<	(	std::ostream &	out,
		const Sequence &	seq
	)

Definition at line 196 of file Sequence.cc.

References core::sequence::Sequence::to_string().

std::ostream& core::sequence::operator<<	(	std::ostream &	out,
		const SequenceProfile &	p
	)

Definition at line 359 of file SequenceProfile.cc.

References core::sequence::Sequence::length(), core::io::raw_data::precision(), core::sequence::SequenceProfile::prof_row(), core::sequence::Sequence::to_string(), and core::sequence::SequenceProfile::width().

std::ostream& core::sequence::operator<<	(	std::ostream &	out,
		const SequenceAlignment &	sa
	)

Definition at line 413 of file SequenceAlignment.cc.

References core::sequence::SequenceAlignment::gapped_positions(), core::sequence::SequenceAlignment::identities(), core::sequence::SequenceAlignment::length(), core::sequence::SequenceAlignment::score(), core::sequence::SequenceAlignment::sequence(), and core::sequence::SequenceAlignment::size().

std::istream& core::sequence::operator>>	(	std::istream &	in,
		Sequence &	seq
	)

Definition at line 205 of file Sequence.cc.

References core::sequence::Sequence::read_data().

std::istream& core::sequence::operator>>	(	std::istream &	in,
		SequenceAlignment &	aln
	)

Definition at line 431 of file SequenceAlignment.cc.

References core::sequence::SequenceAlignment::read_data().

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

Definition at line 78 of file util.cc.

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>.

Definition at line 59 of file util.cc.

References read_aln().

utility::vector1< SequenceAlignment > core::sequence::read_aln	(	std::string const &	format,
		std::string const &	filename
	)

Definition at line 302 of file util.cc.

References read_general_aln_file(), read_grishin_aln_file(), and tr().

Referenced by protocols::comparative_modeling::AlignRmsdTargetEvaluatorCreator::add_evaluators(), protocols::comparative_modeling::AlignmentClustering::AlignmentClustering(), protocols::frag_picker::FragmentPicker::nonlocal_pairs(), protocols::comparative_modeling::PartialThreadingMover::parse_my_tag(), read_all_alignments(), and protocols::comparative_modeling::ThreadingJobInputter::ThreadingJobInputter().

utility::vector1< SequenceOP > core::sequence::read_fasta_file ( std::string const & filename)

Read in sequences from a fasta-formatted file.

Definition at line 141 of file util.cc.

References strip_whitespace().

Referenced by protocols::topology_broker::add_cmdline_claims(), protocols::comparative_modeling::AlignmentClustering::AlignmentClustering(), protocols::abinitio::IterativeBase::IterativeBase(), protocols::frag_picker::FragmentPicker::parse_command_line(), protocols::comparative_modeling::ThreadingJobInputter::pose_from_job(), read_fasta_file_str(), protocols::topology_broker::SequenceClaimer::read_tag(), protocols::hybridization::FoldTreeHybridize::revert_loops_to_original(), protocols::abinitio::run_boinc_debug(), seqs_from_cmd_lines(), protocols::abinitio::AbrelaxApplication::setup(), and core::import_pose::pose_stream::streams_from_cmd_line().

std::string core::sequence::read_fasta_file_return_str ( std::string const & filename)

Definition at line 175 of file util.cc.

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

Definition at line 132 of file util.cc.

References end, and read_fasta_file().

Referenced by protocols::inputter::FastaInputter::get_nth_pose(), protocols::simple_moves::FavorSequenceProfile::parse_def(), protocols::toolbox::task_operations::JointSequenceOperation::parse_def(), protocols::simple_moves::FavorSequenceProfile::parse_my_tag(), protocols::toolbox::task_operations::JointSequenceOperation::parse_tag(), and protocols::comparative_modeling::GenericJobInputter::pose_from_job().

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

read generalized alignment format.

Definition at line 323 of file util.cc.

References tr().

Referenced by read_general_aln_file().

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

Definition at line 361 of file util.cc.

References read_general_aln().

Referenced by protocols::comparative_modeling::alignment_from_cmd_line(), and read_aln().

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

Definition at line 374 of file util.cc.

References protocols::loops::start.

Referenced by protocols::comparative_modeling::alignment_from_cmd_line(), and read_aln().

utility::vector1< SequenceOP > core::sequence::seqs_from_cmd_lines ( )

Definition at line 266 of file util.cc.

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.

Definition at line 205 of file util.cc.

References end, core::id::SequenceMapping::insert_aligned_residue_safe(), core::sequence::DerivedSequenceMapping::seq1(), core::sequence::DerivedSequenceMapping::seq2(), core::io::serialization::size(), 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.

Definition at line 467 of file util.cc.

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

static basic::Tracer core::sequence::tr ( "core.sequence.SequenceFactory" )

static

static basic::Tracer core::sequence::tr ( "core.sequence.CompositeSequence" )

static

static basic::Tracer core::sequence::tr ( "core.sequence.SequenceCoupling" )

static

static basic::Tracer core::sequence::tr ( "core.sequence.ChemicalShiftSequence" )

static

Referenced by alignment_from_pose(), core::sequence::SequenceAlignment::calculate_per_position_scores(), core::sequence::SequenceFactory::get_sequence(), map_seq1_seq2(), read_aln(), core::sequence::SequenceProfile::read_from_file(), read_general_aln(), core::sequence::SequenceProfile::rescale(), core::sequence::MatrixScoringScheme::score(), core::sequence::SequenceFactory::seq_from_file(), and simple_mapping_from_file().

static basic::Tracer core::sequence::tr ( "core.sequence.MatrixScoringScheme" )

static

static basic::Tracer core::sequence::tr ( "core.sequence.SequenceProfile" )

static

static basic::Tracer core::sequence::tr ( "core.sequence.SequenceAlignment" )

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.

Definition at line 622 of file util.cc.

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

Referenced by protocols::comparative_modeling::ExtraThreadingMover::get_qt_mapping(), and protocols::comparative_modeling::ThreadingMover::get_qt_mapping().

Classes

Typedefs

Enumerations

Functions

Typedef Documentation

Enumeration Type Documentation

Function Documentation