Classes
struct	Line
	struct More...

class	ABEGO
	abego elments More...

class	ABEGOManager
	manager for abego More...

class	Aligner

class	AlignerFactory

class	AnnotatedSequence

class	SimpleSequenceCreator

class	SequenceProfileCreator

class	SequenceCouplingCreator

class	CompositeSequenceCreator

class	ChemicalShiftSequenceCreator

struct	CharPairHash

struct	Blosum62Map

class	ChemicalShiftScoringScheme

class	ChemicalShiftSequence

class	CompassScoringScheme

class	CompositeScoringScheme

class	CompositeSequence

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	Cell

class	DP_Matrix

class	DPScoringScheme

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	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< 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)

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< 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)

utility::vector1< Size >	strip_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

◆ ABEGOManagerCOP

typedef utility::pointer::shared_ptr<ABEGOManager const> core::sequence::ABEGOManagerCOP

◆ ABEGOManagerOP

typedef utility::pointer::shared_ptr<ABEGOManager> core::sequence::ABEGOManagerOP

◆ AlignerCOP

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

◆ AlignerOP

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

◆ CellOP

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

◆ ChemicalShiftSequenceCOP

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

◆ ChemicalShiftSequenceOP

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

◆ CompositeScoringSchemeOP

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

◆ CompositeSequenceCOP

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

◆ CompositeSequenceOP

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

◆ DerivedSequenceMappingCOP

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

◆ DerivedSequenceMappingOP

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

◆ NWAlignerCOP

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

◆ NWAlignerOP

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

◆ PairScoringSchemeOP

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

◆ ScoringSchemeOP

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

◆ SequenceAlignmentCOP

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

◆ SequenceAlignmentOP

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

◆ SequenceCOP

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

◆ SequenceCouplingCOP

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

◆ SequenceCouplingOP

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

◆ SequenceCreatorCOP

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

◆ SequenceCreatorOP

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

◆ SequenceOP

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

◆ SequenceProfileCOP

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

◆ SequenceProfileOP

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

◆ SSManagerCOP

typedef utility::pointer::shared_ptr<SSManager const> core::sequence::SSManagerCOP

◆ SSManagerOP

typedef utility::pointer::shared_ptr<SSManager> core::sequence::SSManagerOP

◆ SWAlignerCOP

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

◆ SWAlignerOP

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

Enumeration Type Documentation

◆ AlignMove

enum core::sequence::AlignMove

Enumerator
diagonal
left
above
end

Function Documentation

◆ align_naive()

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

Generate a naive sequence alignment between two sequences.

References core::sequence::SWAligner::align().

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

◆ align_poses_naive()

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

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

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

◆ alignment_from_pose()

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

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

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

◆ alignment_into_pose()

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

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

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

◆ calpha_superimpose_with_mapping()

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

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

Referenced by protocols::constraint_generator::CoordinateConstraintGenerator::align_reference_pose(), and protocols::relax::AtomCoordinateCstMover::generate_constraints().

◆ convert_to_fasta()

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().

◆ 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().

◆ create_map_for_Blosum62Map()

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

inline

References blosum_62_map_tr().

◆ get_abego()

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

utility for getting abego

References core::sequence::ABEGOManager::get_symbols().

Referenced by protocols::pose_length_moves::PossibleLoop::check_loop_abego(), protocols::fldsgn::filters::SheetTopologyFilter::compute(), protocols::denovo_design::filters::PreProlineFilter::compute_simple(), protocols::fldsgn::SheetConstraintGenerator::get_abego(), protocols::pose_length_moves::NearNativeLoopCloser::get_additional_output_with_rmsd(), and protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::loop_info_from_subset().

◆ get_concatenated_sequence() [1/2]

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

Return a string of concatenated SequenceCOP sequences.

◆ get_concatenated_sequence() [2/2]

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().

◆ get_conventional_chains_and_numbering()

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
	)

looks for tab-delimited tags like 'chain:A' and 'res_num:5-20' in fasta IDs.

References core::chemical::rings::q, core::pose::rna::remove_bracketed(), and tr().

Referenced by core::import_pose::get_sequence_information(), and core::pose::full_model_info::FullModelParameters::read_global_seq_info().

◆ get_design_sequence_motif_syntax()

std::string core::sequence::get_design_sequence_motif_syntax ( )

Return the description of the syntax for a design sequence motif.

Referenced by protocols::calc_taskop_movers::CreateSequenceMotifMover::provide_xml_schema(), and protocols::task_operations::SequenceMotifTaskOperation::provide_xml_schema().

◆ get_maximum_scores()

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

◆ get_motif_length()

core::Size core::sequence::get_motif_length ( std::string const & motif )

References split_sequence_motif().

Referenced by protocols::calc_taskop_movers::CreateSequenceMotifMover::initialize_objects().

◆ get_sequence_object()

SequenceOP core::sequence::get_sequence_object	(	std::string const &	current_id,
		std::string const &	current_sequence
	)

References strip_spacers(), and core::chemical::orbitals::strip_whitespace().

Referenced by read_fasta_file().

◆ map_seq1_seq2()

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::SWAligner::align(), 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().

◆ mapping_to_alignment()

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(), core::id::SequenceMapping::reverse(), and core::id::SequenceMapping::size1().

◆ n_correctly_aligned_positions()

core::Size core::sequence::n_correctly_aligned_positions	(	SequenceAlignment &	candidate_aln,
		SequenceAlignment &	true_aln
	)

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

◆ operator<()

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

◆ operator<<() [1/6]

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

◆ operator<<() [2/6]

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

References core::conformation::membrane::out, and core::sequence::CompositeSequence::to_string().

◆ operator<<() [3/6]

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

◆ operator<<() [4/6]

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

◆ operator<<() [5/6]

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

◆ operator<<() [6/6]

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

◆ operator>>() [1/2]

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

◆ operator>>() [2/2]

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

◆ output_fasta_file()

void core::sequence::output_fasta_file	(	std::string const &	fasta_filename,
		core::pose::Pose const &	pose
	)

References core::pose::Pose::annotated_sequence(), core::pose::Pose::pdb_info(), core::pose::Pose::size(), and core::pose::tag_from_pose().

◆ parse_out_non_standard_residues() [1/3]

std::map< core::Size, std::string > core::sequence::parse_out_non_standard_residues ( std::string & sequence )

References core::pose::parse_sequence().

◆ parse_out_non_standard_residues() [2/3]

std::map< Size, std::string > core::sequence::parse_out_non_standard_residues ( utility::vector1< core::sequence::SequenceOP > & fasta_sequences )

◆ parse_out_non_standard_residues() [3/3]

std::map< Size, std::string > core::sequence::parse_out_non_standard_residues ( vector1< core::sequence::SequenceOP > & fasta_sequences )

Referenced by core::import_pose::RNA_HelixAssembler::apply(), core::import_pose::RNA_DeNovoSetup::de_novo_setup_from_options(), protocols::stepwise::legacy::modeler::rna::full_length_rmsd_over_residue_list(), core::import_pose::get_sequence_information(), core::import_pose::libraries::RNA_ChunkLibrary::initialize_rna_chunk_library(), protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::initialize_sequence_information(), and core::import_pose::just_modeling_RNA().

◆ read_alignment_file()

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(), protocols::abinitio::filename(), core::id::SequenceMapping::push_back(), core::id::SequenceMapping::size1(), core::id::SequenceMapping::size2(), and tr().

◆ read_all_alignments()

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().

◆ read_aln()

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

References protocols::abinitio::filename(), 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(), read_all_alignments(), and protocols::comparative_modeling::ThreadingJobInputter::ThreadingJobInputter().

◆ read_fasta_file()

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

Read in sequences from a fasta-formatted file.

References protocols::abinitio::filename(), and get_sequence_object().

Referenced by protocols::topology_broker::add_cmdline_claims(), protocols::comparative_modeling::AlignmentClustering::AlignmentClustering(), protocols::trRosetta_protocols::movers::trRosettaProtocolMover::apply(), protocols::evolution::AlignmentAAFinder::apply(), protocols::evolution::AlignmentGapInserter::apply(), core::import_pose::get_sequence_information(), protocols::membrane::HelixFromSequence::init_from_cmd(), protocols::abinitio::IterativeBase::IterativeBase(), protocols::frag_picker::FragmentPicker::parse_command_line(), protocols::pose_creation::ExtendedPoseMover::parse_my_tag(), protocols::pose_creation::PoseFromSequenceMover::parse_my_tag(), protocols::comparative_modeling::ThreadingJobInputter::pose_from_job(), protocols::topology_broker::SequenceClaimer::read_fasta_file(), read_fasta_file_and_concatenate(), read_fasta_file_section(), read_fasta_file_str(), core::pose::full_model_info::FullModelParameters::read_global_seq_info(), protocols::abinitio::run_boinc_debug(), seqs_from_cmd_lines(), protocols::abinitio::AbrelaxApplication::setup(), protocols::frag_picker::FragmentScoreFilter::setup_fragment_picker(), and core::import_pose::pose_stream::streams_from_cmd_line().

◆ read_fasta_file_and_concatenate()

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

Read fasta file and concatenate sequences.

References protocols::abinitio::filename(), get_concatenated_sequence(), and read_fasta_file().

Referenced by protocols::stepwise::legacy::modeler::rna::setup_rna_working_parameters(), and protocols::stepwise::legacy::modeler::rna::setup_simple_full_length_rna_working_parameters().

◆ read_fasta_file_return_str()

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

References protocols::abinitio::filename(), and read_fasta_file_str().

Referenced by core::import_pose::RNA_DeNovoSetup::de_novo_setup_from_command_line_legacy(), and core::import_pose::just_modeling_RNA().

◆ read_fasta_file_section()

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, protocols::abinitio::filename(), read_fasta_file(), core::chemical::element::S, and protocols::sparta::section().

◆ read_fasta_file_str()

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

References protocols::abinitio::filename(), and read_fasta_file().

Referenced by protocols::simple_moves::FavorSequenceProfile::parse_my_tag(), protocols::loop_grower::FragmentExtension::parse_my_tag(), protocols::task_operations::JointSequenceOperation::parse_tag(), protocols::comparative_modeling::GenericJobInputter::pose_from_job(), protocols::jd2::LargeNstructJobInputter::pose_from_job(), and read_fasta_file_return_str().

◆ read_general_aln()

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().

◆ read_general_aln_file()

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

References protocols::abinitio::filename(), and read_general_aln().

Referenced by read_aln().

◆ read_grishin_aln_file()

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

References protocols::abinitio::filename(), protocols::hybridization::score, and protocols::loops::start.

Referenced by read_aln().

◆ seqs_from_cmd_lines()

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

References read_fasta_file().

◆ simple_mapping_from_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, protocols::abinitio::filename(), 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().

◆ split_sequence_motif()

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 protocols::sparta::contains(), protocols::kinmatch::str(), and core::id::to_string().

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

◆ steal_alignment()

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().

◆ strip_spacers()

utility::vector1< core::Size > core::sequence::strip_spacers	(	std::string &	sequence,
		bool const	annotations_in_brackets
	)

References spacers.

Referenced by core::pose::rna::RNA_SecStruct::blank_secstruct(), core::pose::rna::RNA_SecStruct::check_compatible_with_sequence(), core::import_pose::RNA_DeNovoSetup::de_novo_setup_from_options(), get_sequence_object(), protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::initialize_sequence_information(), core::pose::rna::RNA_SecStruct::set_secstruct(), and protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::working_res_map().

◆ tr() [1/9]

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

static

◆ tr() [2/9]

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

static

Referenced by alignment_from_pose(), core::sequence::SequenceAlignment::calculate_per_position_scores(), create_fasta_file(), get_conventional_chains_and_numbering(), core::sequence::SequenceFactory::get_sequence(), map_seq1_seq2(), read_alignment_file(), read_aln(), core::sequence::SequenceProfile::read_from_binary_chk(), core::sequence::SequenceProfile::read_from_checkpoint(), 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().

◆ tr() [3/9]

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

static

◆ tr() [4/9]

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

static

◆ tr() [5/9]

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

static

◆ tr() [6/9]

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

static

◆ tr() [7/9]

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

static

◆ tr() [8/9]

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

static

◆ tr() [9/9]

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

static

◆ transitive_map()

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

◆ spacers

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

Referenced by core::pose::rna::RNA_SecStruct::set_basepairs_from_secstruct(), and strip_spacers().

Classes

Typedefs

Enumerations

Functions

Variables

Typedef Documentation

◆ ABEGOManagerCOP

◆ ABEGOManagerOP

◆ AlignerCOP

◆ AlignerOP

◆ CellOP

◆ ChemicalShiftSequenceCOP

◆ ChemicalShiftSequenceOP

◆ CompositeScoringSchemeOP

◆ CompositeSequenceCOP

◆ CompositeSequenceOP

◆ DerivedSequenceMappingCOP

◆ DerivedSequenceMappingOP

◆ NWAlignerCOP

◆ NWAlignerOP

◆ PairScoringSchemeOP

◆ ScoringSchemeOP

◆ SequenceAlignmentCOP

◆ SequenceAlignmentOP

◆ SequenceCOP

◆ SequenceCouplingCOP

◆ SequenceCouplingOP

◆ SequenceCreatorCOP

◆ SequenceCreatorOP

◆ SequenceOP

◆ SequenceProfileCOP

◆ SequenceProfileOP

◆ SSManagerCOP

◆ SSManagerOP

◆ SWAlignerCOP

◆ SWAlignerOP

Enumeration Type Documentation

◆ AlignMove

Function Documentation

◆ align_naive()

◆ align_poses_naive()

◆ alignment_from_pose()

◆ alignment_into_pose()

◆ calpha_superimpose_with_mapping()

◆ convert_to_fasta()

◆ create_fasta_file()

◆ create_map_for_Blosum62Map()

◆ get_abego()

◆ get_concatenated_sequence() [1/2]

◆ get_concatenated_sequence() [2/2]

◆ get_conventional_chains_and_numbering()

◆ get_design_sequence_motif_syntax()

◆ get_maximum_scores()

◆ get_motif_length()

◆ get_sequence_object()

◆ map_seq1_seq2()

◆ mapping_to_alignment()

◆ n_correctly_aligned_positions()

◆ operator<()

◆ operator<<() [1/6]

◆ operator<<() [2/6]

◆ operator<<() [3/6]

◆ operator<<() [4/6]

◆ operator<<() [5/6]

◆ operator<<() [6/6]

◆ operator>>() [1/2]

◆ operator>>() [2/2]

◆ output_fasta_file()

◆ parse_out_non_standard_residues() [1/3]

◆ parse_out_non_standard_residues() [2/3]

◆ parse_out_non_standard_residues() [3/3]

◆ read_alignment_file()

◆ read_all_alignments()

◆ read_aln()

◆ read_fasta_file()

◆ read_fasta_file_and_concatenate()

◆ read_fasta_file_return_str()

◆ read_fasta_file_section()

◆ read_fasta_file_str()

◆ read_general_aln()