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util.hh File Reference

small bundle of utilities for dealing with sequences More...

#include <utility/vector1.fwd.hh>
#include <core/types.hh>
#include <core/id/SequenceMapping.fwd.hh>
#include <core/sequence/Sequence.fwd.hh>
#include <core/sequence/ScoringScheme.fwd.hh>
#include <core/sequence/SequenceAlignment.fwd.hh>
#include <core/sequence/DerivedSequenceMapping.fwd.hh>
#include <core/pose/Pose.fwd.hh>
#include <utility/vector1.hh>
#include <map>


 A class for reading in the atom type properties.


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< SequenceOPcore::sequence::read_fasta_file (std::string const &filename)
 Read in sequences from a fasta-formatted file. More...
vector1< string > core::sequence::read_fasta_file_str (std::string const &filename)
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 &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 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 (utility::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...
< SequenceAlignment
core::sequence::read_aln (std::string const &format, std::string const &filename)
utility::vector1< SequenceOPcore::sequence::seqs_from_cmd_lines ()
< SequenceAlignment
core::sequence::read_general_aln (std::istream &input)
 read generalized alignment format. More...
< SequenceAlignment
core::sequence::read_grishin_aln_file (std::string const &filename)
< SequenceAlignment
core::sequence::read_general_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 (utility::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::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...
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...
void core::sequence::output_fasta_file (std::string const &fasta_filename, core::pose::Pose const &pose)

Detailed Description

small bundle of utilities for dealing with sequences

James Thompson
Sergey Lyskov