Public Member Functions |
| | DigestedPeptide (const std::string &sequence) |
| | DigestedPeptide (const char *sequence) |
| | DigestedPeptide (std::string::const_iterator begin, std::string::const_iterator end, size_t offset, size_t missedCleavages, bool NTerminusIsSpecific, bool CTerminusIsSpecific, std::string NTerminusPrefix="", std::string CTerminusSuffix="") |
| | DigestedPeptide (const Peptide &peptide, size_t offset, size_t missedCleavages, bool NTerminusIsSpecific, bool CTerminusIsSpecific, std::string NTerminusPrefix="", std::string CTerminusSuffix="") |
| | DigestedPeptide (const DigestedPeptide &) |
| DigestedPeptide & | operator= (const DigestedPeptide &) |
| virtual | ~DigestedPeptide () |
| size_t | offset () const |
| | returns the zero-based offset of the N terminus of the peptide in the polypeptide from which it was digested
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| size_t | missedCleavages () const |
| | returns the number of missed cleavage sites in the peptide
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| size_t | specificTermini () const |
| | returns the number of termini that matched to the digestion rules
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| bool | NTerminusIsSpecific () const |
| | returns true iff the N terminus matched the digestion rules
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| bool | CTerminusIsSpecific () const |
| | returns true iff the C terminus matched the digestion rules
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| std::string | NTerminusPrefix () const |
| | returns residue preceding digestion site
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| std::string | CTerminusSuffix () const |
| | returns residue following digestion site
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| bool | operator== (const DigestedPeptide &rhs) const |
| | returns true iff peptide sequences, masses, and all digestion metadata are equal
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| | Peptide (const std::string &sequence="", MODIFICATION_PARSING_ARGUMENTS) |
| | Peptide (const char *sequence, MODIFICATION_PARSING_ARGUMENTS) |
| | Peptide (std::string::const_iterator begin, std::string::const_iterator end, MODIFICATION_PARSING_ARGUMENTS) |
| | Peptide (const char *begin, const char *end, MODIFICATION_PARSING_ARGUMENTS) |
| | Peptide (const Peptide &) |
| Peptide & | operator= (const Peptide &) |
| virtual | ~Peptide () |
| const std::string & | sequence () const |
| | returns the sequence of amino acids making up the peptide
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| chemistry::Formula | formula (bool modified=false) const |
| | if modified = false: returns the composition formula of sequence()+water if modified = true: returns the composition formula of sequence()+modifications()+water throws an exception if modified = true and any modification has only mass information
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| double | monoisotopicMass (int charge=0, bool modified=true) const |
| | if charge = 0: returns neutral mass if charge > 0: returns charged m/z if modified = false: returns the monoisotopic mass of sequence()+water if modified = true: returns the monoisotopic mass of sequence()+modifications()+water
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| double | molecularWeight (int charge=0, bool modified=true) const |
| | if charge = 0: returns neutral mass if charge > 0: returns charged m/z if modified = false: returns the molecular weight of sequence()+water if modified = true: returns the molecular weight of sequence()+modifications()+water
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| ModificationMap & | modifications () |
| | the map of sequence offsets (0-based) to modifications; modifications can be added or removed from the peptide with this map
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| const ModificationMap & | modifications () const |
| | the map of sequence offsets (0-based) to modifications
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| Fragmentation | fragmentation (bool monoisotopic=true, bool modified=true) const |
| | returns a fragmentation model for the peptide; fragment masses can calculated as mono/avg and as modified/unmodified
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| bool | operator== (const Peptide &rhs) const |
| | returns true iff peptide sequences and modifications are equal
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| bool | operator< (const Peptide &rhs) const |
| | returns true iff this peptide has a lesser sequence length, sequence, modifications length, or modifications
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peptide subclass that contains extra metadata provided by digestion
Definition at line 48 of file Digestion.hpp.
Public Member Functions inherited from pwiz::proteome::Peptide