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util.cc File Reference

small bundle of utilities for dealing with sequences 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/vector1.hh>
#include <utility/exit.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/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/util.tmpl.hh>

Namespaces

 core
 A class for defining atom parameters, known as atom_types.
 
 core::sequence
 

Constant Groups

 core
 A class for defining atom parameters, known as atom_types.
 
 core::sequence
 

Functions

static basic::Tracer core::sequence::tr ("core.sequence")
 
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>. 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)
 
vector1< SequenceOPcore::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)
 
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< SequenceOPcore::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< Realcore::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)
 

Detailed Description

small bundle of utilities for dealing with sequences

Author
James Thompson