OpenMS
2.4.0
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Representation of a peptide/protein sequence. More...
#include <OpenMS/CHEMISTRY/AASequence.h>
Classes | |
class | ConstIterator |
ConstIterator for AASequence. More... | |
class | Iterator |
Iterator class for AASequence. More... | |
Public Member Functions | |
AASequence & | operator= (const AASequence &rhs) |
assignment operator More... | |
bool | empty () const |
check if sequence is empty More... | |
Constructors and Destructors | |
AASequence () | |
default constructor More... | |
AASequence (const AASequence &rhs) | |
copy constructor More... | |
virtual | ~AASequence () |
destructor More... | |
Accessors | |
String | toString () const |
returns the peptide as string with modifications embedded in brackets More... | |
String | toUnmodifiedString () const |
returns the peptide as string without any modifications More... | |
String | toUniModString () const |
returns the peptide as string with UniMod-style modifications embedded in brackets More... | |
String | toBracketString (bool integer_mass=true, const std::vector< String > &fixed_modifications=std::vector< String >()) const |
create a TPP compatible string of the modified sequence using bracket notation. More... | |
void | setModification (Size index, const String &modification) |
void | setNTerminalModification (const String &modification) |
sets the N-terminal modification More... | |
const String & | getNTerminalModificationName () const |
returns the name (ID) of the N-terminal modification, or an empty string if none is set More... | |
const ResidueModification * | getNTerminalModification () const |
returns a pointer to the N-terminal modification, or zero if none is set More... | |
void | setCTerminalModification (const String &modification) |
sets the C-terminal modification More... | |
const String & | getCTerminalModificationName () const |
returns the name (ID) of the C-terminal modification, or an empty string if none is set More... | |
const ResidueModification * | getCTerminalModification () const |
returns a pointer to the C-terminal modification, or zero if none is set More... | |
const Residue & | getResidue (Size index) const |
returns a pointer to the residue at position index More... | |
EmpiricalFormula | getFormula (Residue::ResidueType type=Residue::Full, Int charge=0) const |
returns the formula of the peptide More... | |
double | getAverageWeight (Residue::ResidueType type=Residue::Full, Int charge=0) const |
returns the average weight of the peptide More... | |
double | getMonoWeight (Residue::ResidueType type=Residue::Full, Int charge=0) const |
const Residue & | operator[] (Size index) const |
returns a pointer to the residue at given position More... | |
AASequence | operator+ (const AASequence &peptide) const |
adds the residues of the peptide More... | |
AASequence & | operator+= (const AASequence &) |
adds the residues of a peptide More... | |
AASequence | operator+ (const Residue *residue) const |
adds the residues of the peptide More... | |
AASequence & | operator+= (const Residue *) |
adds the residues of a peptide More... | |
Size | size () const |
returns the number of residues More... | |
AASequence | getPrefix (Size index) const |
returns a peptide sequence of the first index residues More... | |
AASequence | getSuffix (Size index) const |
returns a peptide sequence of the last index residues More... | |
AASequence | getSubsequence (Size index, UInt number) const |
returns a peptide sequence of number residues, beginning at position index More... | |
void | getAAFrequencies (Map< String, Size > &frequency_table) const |
compute frequency table of amino acids More... | |
Predicates | |
bool | has (const Residue &residue) const |
returns true if the peptide contains the given residue More... | |
bool | hasSubsequence (const AASequence &peptide) const |
bool | hasPrefix (const AASequence &peptide) const |
bool | hasSuffix (const AASequence &peptide) const |
bool | hasNTerminalModification () const |
predicate which is true if the peptide is N-term modified More... | |
bool | hasCTerminalModification () const |
predicate which is true if the peptide is C-term modified More... | |
bool | isModified () const |
returns true if any of the residues or termini are modified More... | |
bool | operator== (const AASequence &rhs) const |
equality operator. Two sequences are equal iff all amino acids including PTMs are equal More... | |
bool | operator< (const AASequence &rhs) const |
lesser than operator which compares the C-term mods, sequence including PTMS and N-term mods; can be used for maps More... | |
bool | operator!= (const AASequence &rhs) const |
inequality operator. Complement of equality operator. More... | |
Iterators | |
Iterator | begin () |
ConstIterator | begin () const |
Iterator | end () |
ConstIterator | end () const |
Static Public Member Functions | |
static AASequence | fromString (const String &s, bool permissive=true) |
create AASequence object by parsing an OpenMS string More... | |
static AASequence | fromString (const char *s, bool permissive=true) |
create AASequence object by parsing a C string (character array) More... | |
Static Protected Member Functions | |
static String::ConstIterator | parseModRoundBrackets_ (const String::ConstIterator str_it, const String &str, AASequence &aas, const ResidueModification::TermSpecificity &specificity) |
Parses modifications in round brackets (an identifier) More... | |
static String::ConstIterator | parseModSquareBrackets_ (const String::ConstIterator str_it, const String &str, AASequence &aas, const ResidueModification::TermSpecificity &specificity) |
Parses modifications in square brackets (a mass) More... | |
static void | parseString_ (const String &peptide, AASequence &aas, bool permissive=true) |
Protected Attributes | |
std::vector< const Residue * > | peptide_ |
const ResidueModification * | n_term_mod_ |
const ResidueModification * | c_term_mod_ |
Friends | |
Stream operators | |
std::ostream & | operator<< (std::ostream &os, const AASequence &peptide) |
writes a peptide to an output stream More... | |
std::istream & | operator>> (std::istream &is, const AASequence &peptide) |
reads a peptide from an input stream More... | |
Representation of a peptide/protein sequence.
This class represents amino acid sequences in OpenMS. An AASequence instance primarily contains a sequence of residues. The sequence is represented as a vector of pointers to instances of Residue. Each amino acid has only one instance, which is accessible using the ResidueDB instance (singleton).
To create an AASequence instance for a specific amino acid sequence, use the AASequence::fromString function. For example, AASequence::fromString(".DFPIANGER.")
produces an instance of AASequence for the peptide "DFPIANGER". Please note that both the N- and the C-terminal are explicitly represented by dots.
A critical property of amino acid sequences is that they can be modified. Which means that one or more amino acids are chemically modified, e.g. oxidized. This is represented via Residue instances which carry a ResidueModification object. This is also handled in the ResidueDB.
Modifications are specified using a unique string identifier present in the ModificationsDB in round brackets after the modified amino acid or by providing the mass of the residue in square brackets. For example AASequence::fromString(".DFPIAM(Oxidation)GER.")
creates an instance of the peptide "DFPIAMGER" with an oxidized methionine (AASequence::fromString(".DFPIAM(UniMod:35)GER.")
, AASequence::fromString(".DFPIAM[+16]GER.")
and AASequence::fromString(".DFPIAM[147]GER.")
are all equivalent). N- and C-terminal modifications are represented by brackets to the right of the dots terminating the sequence. For example, ".(Dimethyl)DFPIAMGER."
and ".DFPIAMGER.(Label:18O(2))"
represent the labelling of the N- and C-terminus respectively, but ".DFPIAMGER(Phospho)."
will be interpreted as a phosphorylation of the last arginine at its side chain.
Note there is a subtle difference between AASequence::fromString(".DFPIAM[+16]GER.")
and AASequence::fromString(".DFPIAM[+15.9949]GER.")
– while the former will try to find the first modification matching to a mass difference of 16 +/- 0.5, the latter will try to find the closest matching modification to the exact mass. This usually gives the intended results while the first approach may not.
Arbitrary/unknown amino acids (usually due to an unknown modification) can be specified using tags preceded by X: "X[weight]". This indicates a new amino acid ("X") with the specified weight, e.g. "RX[148.5]T"". Note that this tag does not alter the amino acids to the left (R) or right (T). Rather, X represents an amino acid on its own. Be careful when converting such AASequence objects to an EmpiricalFormula using getFormula(), as tags will not be considered in this case (there exists no formula for them). However, they have an influence on getMonoWeight() and getAverageWeight()!
AASequence | ( | ) |
default constructor
AASequence | ( | const AASequence & | rhs | ) |
copy constructor
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destructor
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bool empty | ( | ) | const |
check if sequence is empty
Referenced by OPXLDataStructs::ProteinProteinCrossLink::getType().
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create AASequence object by parsing an OpenMS string
s | Input string |
permissive | If set, skip spaces and replace stop codon symbols ("*", "#", "+") by "X" (unknown amino acid) during parsing |
Exception::ParseError | if an invalid string representation of an AA sequence is passed |
Referenced by MetaProSIPDecomposition::calculateIsotopePatternsFor13CRange(), MetaProSIPDecomposition::calculateIsotopePatternsFor15NRange(), MetaProSIPDecomposition::calculateIsotopePatternsFor18ORange(), MetaProSIPDecomposition::calculateIsotopePatternsFor2HRange(), MetaProSIPDecomposition::getNumberOfLabelingElements(), SimpleSearchEngine::main_(), RNPxlSearch::main_(), TOPPMetaProSIP::main_(), IDFilter::DigestionFilter::operator()(), SimpleSearchEngine::postProcessHits_(), RNPxlSearch::postProcessHits_(), RNPxlSearch::postScoreHits_(), and TOPPViewBase::showSpectrumGenerationDialog().
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create AASequence object by parsing a C string (character array)
s | Input string |
permissive | If set, skip spaces and replace stop codon symbols ("*", "#", "+") by "X" (unknown amino acid) during parsing |
Exception::ParseError | if an invalid string representation of an AA sequence is passed |
compute frequency table of amino acids
double getAverageWeight | ( | Residue::ResidueType | type = Residue::Full , |
Int | charge = 0 |
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) | const |
returns the average weight of the peptide
const ResidueModification* getCTerminalModification | ( | ) | const |
returns a pointer to the C-terminal modification, or zero if none is set
const String& getCTerminalModificationName | ( | ) | const |
returns the name (ID) of the C-terminal modification, or an empty string if none is set
EmpiricalFormula getFormula | ( | Residue::ResidueType | type = Residue::Full , |
Int | charge = 0 |
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) | const |
returns the formula of the peptide
Referenced by MetaProSIPDecomposition::calculateIsotopePatternsFor13CRange(), MetaProSIPDecomposition::calculateIsotopePatternsFor15NRange(), MetaProSIPDecomposition::calculateIsotopePatternsFor18ORange(), MetaProSIPDecomposition::calculateIsotopePatternsFor2HRange(), MetaProSIPDecomposition::getNumberOfLabelingElements(), and TOPPMetaProSIP::main_().
double getMonoWeight | ( | Residue::ResidueType | type = Residue::Full , |
Int | charge = 0 |
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) | const |
returns the mono isotopic weight of the peptide in the given ionic form
Referenced by TOPPOpenPepXLLF::main_(), SimpleSearchEngine::main_(), TOPPOpenPepXL::main_(), RNPxlSearch::main_(), TOPPMetaProSIP::main_(), and TOPPViewBase::showSpectrumGenerationDialog().
const ResidueModification* getNTerminalModification | ( | ) | const |
returns a pointer to the N-terminal modification, or zero if none is set
const String& getNTerminalModificationName | ( | ) | const |
returns the name (ID) of the N-terminal modification, or an empty string if none is set
AASequence getPrefix | ( | Size | index | ) | const |
returns a peptide sequence of the first index residues
Referenced by RNPxlSearch::postScoreHits_().
AASequence getSubsequence | ( | Size | index, |
UInt | number | ||
) | const |
returns a peptide sequence of number residues, beginning at position index
AASequence getSuffix | ( | Size | index | ) | const |
returns a peptide sequence of the last index residues
Referenced by RNPxlSearch::postScoreHits_().
bool has | ( | const Residue & | residue | ) | const |
returns true if the peptide contains the given residue
bool hasCTerminalModification | ( | ) | const |
predicate which is true if the peptide is C-term modified
bool hasNTerminalModification | ( | ) | const |
predicate which is true if the peptide is N-term modified
bool hasPrefix | ( | const AASequence & | peptide | ) | const |
returns true if the peptide has the given prefix n-term mod is also checked (c-term as well, if prefix is of same length)
bool hasSubsequence | ( | const AASequence & | peptide | ) | const |
returns true if the peptide contains the given peptide
bool hasSuffix | ( | const AASequence & | peptide | ) | const |
returns true if the peptide has the given suffix c-term mod is also checked (n-term as well, if suffix is of same length)
bool isModified | ( | ) | const |
returns true if any of the residues or termini are modified
bool operator!= | ( | const AASequence & | rhs | ) | const |
inequality operator. Complement of equality operator.
AASequence operator+ | ( | const AASequence & | peptide | ) | const |
adds the residues of the peptide
AASequence operator+ | ( | const Residue * | residue | ) | const |
adds the residues of the peptide
AASequence& operator+= | ( | const AASequence & | ) |
adds the residues of a peptide
AASequence& operator+= | ( | const Residue * | ) |
adds the residues of a peptide
bool operator< | ( | const AASequence & | rhs | ) | const |
lesser than operator which compares the C-term mods, sequence including PTMS and N-term mods; can be used for maps
AASequence& operator= | ( | const AASequence & | rhs | ) |
assignment operator
bool operator== | ( | const AASequence & | rhs | ) | const |
equality operator. Two sequences are equal iff all amino acids including PTMs are equal
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Parses modifications in round brackets (an identifier)
If dot notation is used it resolves cterm ambiguity based on the presence of the dot.
str_it | Current position in the string to be parsed |
str | Full input string |
aas | Current AASequence object (will be modified with the correct residue added) |
dot_notation | Whether "dot notation" is used (e.g. ".PEPTIDE.") |
dot_terminal | Whether the previous character was a dot |
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Parses modifications in square brackets (a mass)
If dot notation is used it resolves cterm ambiguity based on the presence of the dot.
str_it | Current position in the string to be parsed |
str | Full input string |
aas | Current AASequence object (will be modified with the correct residue added) |
specificity | Whether the current modification should be interpreted as N- or C-terminal |
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void setCTerminalModification | ( | const String & | modification | ) |
sets the C-terminal modification
set the modification of the residue at position index. if an empty string is passed replaces the residue with its unmodified version
void setNTerminalModification | ( | const String & | modification | ) |
sets the N-terminal modification
Size size | ( | ) | const |
returns the number of residues
Referenced by AAIndex::calculateGB(), TOPPOpenPepXLLF::main_(), TOPPOpenPepXL::main_(), and RNPxlSearch::postScoreHits_().
String toBracketString | ( | bool | integer_mass = true , |
const std::vector< String > & | fixed_modifications = std::vector< String >() |
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) | const |
create a TPP compatible string of the modified sequence using bracket notation.
Instead of using the modification names, it writes the modification masses in brackets
i.e.: n[35]RQLNK[162]LQHK[162]GEA
String toString | ( | ) | const |
returns the peptide as string with modifications embedded in brackets
Uses round brackets when possible (id is known) or square brackets for unknown modifications where only the mass is known.
i.e.: .n[43]PEPC(Carbamidomethyl)PEPM[147]PEPR.[16]
Referenced by MetaProSIPReporting::createPeptideCentricCSVReport(), TOPPOpenPepXLLF::main_(), TOPPOpenPepXL::main_(), TOPPMetaProSIP::main_(), and RNPxlSearch::postScoreHits_().
String toUniModString | ( | ) | const |
returns the peptide as string with UniMod-style modifications embedded in brackets
Uses round brackets when possible (id is known) or square brackets for unknown modifications where only the mass is known.
i.e.: .n[43]PEPC(UniMod:4)PEPM[147]PEPR.[16]
String toUnmodifiedString | ( | ) | const |
returns the peptide as string without any modifications
Referenced by MetaProSIPDecomposition::calculateIsotopePatternsFor13CRange(), MetaProSIPDecomposition::calculateIsotopePatternsFor15NRange(), MetaProSIPDecomposition::calculateIsotopePatternsFor18ORange(), MetaProSIPDecomposition::calculateIsotopePatternsFor2HRange(), MetaProSIPReporting::createCSVReport(), MetaProSIPDecomposition::getNumberOfLabelingElements(), IDFilter::PeptideDigestionFilter::operator()(), and RNPxlSearch::postScoreHits_().
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writes a peptide to an output stream
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friend |
reads a peptide from an input stream
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