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| DigestedPeptide (const std::string &sequence) |
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| DigestedPeptide (const char *sequence) |
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| 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="") |
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| DigestedPeptide (const Peptide &peptide, size_t offset, size_t missedCleavages, bool NTerminusIsSpecific, bool CTerminusIsSpecific, std::string NTerminusPrefix="", std::string CTerminusSuffix="") |
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| DigestedPeptide (const DigestedPeptide &) |
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DigestedPeptide & | operator= (const DigestedPeptide &) |
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virtual | ~DigestedPeptide () |
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size_t | offset () const |
| returns the zero-based offset of the N terminus of the peptide in the polypeptide from which it was digested More...
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size_t | missedCleavages () const |
| returns the number of missed cleavage sites in the peptide More...
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size_t | specificTermini () const |
| returns the number of termini that matched to the digestion rules More...
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bool | NTerminusIsSpecific () const |
| returns true iff the N terminus matched the digestion rules More...
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bool | CTerminusIsSpecific () const |
| returns true iff the C terminus matched the digestion rules More...
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std::string | NTerminusPrefix () const |
| returns residue preceding digestion site More...
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std::string | CTerminusSuffix () const |
| returns residue following digestion site More...
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bool | operator== (const DigestedPeptide &rhs) const |
| returns true iff peptide sequences, masses, and all digestion metadata are equal More...
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| Peptide (const std::string &sequence="", MODIFICATION_PARSING_ARGUMENTS) |
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| Peptide (const char *sequence, MODIFICATION_PARSING_ARGUMENTS) |
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| Peptide (std::string::const_iterator begin, std::string::const_iterator end, MODIFICATION_PARSING_ARGUMENTS) |
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| Peptide (const char *begin, const char *end, MODIFICATION_PARSING_ARGUMENTS) |
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| Peptide (const Peptide &) |
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Peptide & | operator= (const Peptide &) |
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virtual | ~Peptide () |
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const std::string & | sequence () const |
| returns the sequence of amino acids making up the peptide More...
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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 More...
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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 More...
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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 More...
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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 More...
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const ModificationMap & | modifications () const |
| the map of sequence offsets (0-based) to modifications More...
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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 More...
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bool | operator== (const Peptide &rhs) const |
| returns true iff peptide sequences and modifications are equal More...
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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 More...
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peptide subclass that contains extra metadata provided by digestion
Definition at line 47 of file Digestion.hpp.