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Rosetta
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Utilities for working with sequence motifs. More...
#include <core/sequence/util.hh>#include <algorithm>#include <string>#include <basic/Tracer.hh>#include <basic/options/option.hh>#include <basic/options/keys/in.OptionKeys.gen.hh>#include <ObjexxFCL/string.functions.hh>#include <utility/io/izstream.hh>#include <utility/tools/make_vector1.hh>#include <utility/vector1.hh>#include <utility/exit.hh>#include <utility/string_util.hh>#include <core/types.hh>#include <core/id/AtomID.hh>#include <core/id/AtomID_Map.hh>#include <core/id/SequenceMapping.hh>#include <core/pose/Pose.hh>#include <core/pose/annotated_sequence.hh>#include <core/pose/rna/util.hh>#include <core/pose/PDBInfo.hh>#include <core/pose/extra_pose_info_util.hh>#include <core/scoring/rms_util.hh>#include <core/sequence/SWAligner.hh>#include <core/sequence/ScoringScheme.hh>#include <core/sequence/ScoringScheme.fwd.hh>#include <core/sequence/SimpleScoringScheme.hh>#include <core/sequence/Sequence.hh>#include <core/sequence/SequenceProfile.hh>#include <core/sequence/SequenceAlignment.hh>#include <core/sequence/DerivedSequenceMapping.hh>#include <core/pose/init_id_map.hh>#include <utility/stream_util.hh>Namespaces | |
| core | |
| A class for reading in the atom type properties. | |
| core::sequence | |
Functions | |
| static basic::Tracer | core::sequence::tr ("core.sequence") |
| 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>. More... | |
| void | core::sequence::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 > | core::sequence::read_fasta_file_str (std::string const &filename) |
| SequenceOP | core::sequence::get_sequence_object (std::string const ¤t_id, std::string const ¤t_sequence) |
| vector1< SequenceOP > | core::sequence::read_fasta_file (std::string const &filename) |
| Read in sequences from a fasta-formatted file. More... | |
| std::string | core::sequence::read_fasta_file_return_str (std::string const &filename) |
| std::string | core::sequence::read_fasta_file_section (std::string const &filename, std::string const §ion_) |
| 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 | 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. More... | |
| std::string | core::sequence::get_concatenated_sequence (vector1< SequenceCOP > const &fasta_sequences) |
| Return a string of concatenated SequenceCOP sequences. More... | |
| std::string | core::sequence::read_fasta_file_and_concatenate (std::string const &filename) |
| Read fasta file and concatenate sequences. More... | |
| 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. More... | |
| utility::vector1< SequenceOP > | core::sequence::seqs_from_cmd_lines () |
| utility::vector1< SequenceAlignment > | core::sequence::read_aln (std::string const &format, std::string const &filename) |
| utility::vector1< SequenceAlignment > | core::sequence::read_general_aln (std::istream &input) |
| read generalized alignment format. More... | |
| 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) |
| Size | core::sequence::n_correctly_aligned_positions (SequenceAlignment &candidate_aln, SequenceAlignment &true_aln) |
| 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. More... | |
| SequenceAlignment | core::sequence::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 | 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. More... | |
| 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. More... | |
| core::sequence::SequenceAlignment | core::sequence::align_naive (core::sequence::SequenceOP seq1, core::sequence::SequenceOP seq2) |
| Generate a naive sequence alignment between two sequences. More... | |
| core::sequence::SequenceAlignment | core::sequence::align_poses_naive (core::pose::Pose &pose1, core::pose::Pose &pose2) |
| utility::vector1< Real > | core::sequence::get_maximum_scores (core::sequence::ScoringSchemeOP ss, core::sequence::SequenceOP seq) |
| 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< Size > | core::sequence::strip_spacers (std::string &sequence, bool const annotations_in_brackets) |
| std::map< Size, std::string > | core::sequence::parse_out_non_standard_residues (vector1< core::sequence::SequenceOP > &fasta_sequences) |
| std::map< Size, std::string > | core::sequence::parse_out_non_standard_residues (std::string &sequence) |
| 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. More... | |
| 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. More... | |
| void | core::sequence::output_fasta_file (std::string const &fasta_filename, core::pose::Pose const &pose) |
Variables | |
| vector1< char > | core::sequence::spacers = utility::tools::make_vector1( '+','*',' ',',' ) |
Utilities for working with sequence motifs.
small bundle of utilities for dealing with sequences
1.9.1