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Contains the libXpertMassCore documentation. More...
| Header: | #include <libXpertMassCore> |
| namespace | Enums |
| int | ATOM_DEC_PLACES |
| std::map<MsXpS::libXpertMassCore::Enums::CleavageAction, QString> | CleavageActionMap |
| int | FWHM_PEAK_SPAN_FACTOR |
| int | OLIGOMER_DEC_PLACES |
| int | PKA_PH_PI_DEC_PLACES |
| int | POLYMER_DEC_PLACES |
| const int | POL_CHEM_DEF_FILE_FORMAT_VERSION |
| const int | POL_SEQ_FILE_FORMAT_VERSION |
| std::map<MsXpS::libXpertMassCore::Enums::CapType, QString> | capTypeMap |
| std::map<MsXpS::libXpertMassCore::Enums::ChemicalEntity, QString> | chemicalEntityMap |
| std::map<MsXpS::libXpertMassCore::Enums::ChemicalGroupFate, QString> | chemicalGroupFateMap |
| std::map<MsXpS::libXpertMassCore::Enums::ChemicalGroupTrapped, QString> | chemicalGroupTrappedMap |
| std::map<MsXpS::libXpertMassCore::Enums::CrossLinkEncompassed, QString> | crossLinkEncompassedMap |
| std::map<MsXpS::libXpertMassCore::Enums::FragEnd, QString> | fragEndMap |
| std::map<MsXpS::libXpertMassCore::Enums::IonizationOutcome, QString> | ionizationOutcomeMap |
| std::map<MsXpS::libXpertMassCore::Enums::LocationType, QString> | locationTypeMap |
| std::map<MsXpS::libXpertMassCore::Enums::MassDataType, QString> | massDataTypeMap |
| std::map<MsXpS::libXpertMassCore::Enums::MassPeakShapeType, QString> | massPeakShapeTypeMap |
| std::map<MsXpS::libXpertMassCore::Enums::MassPeakWidthLogic, QString> | massPeakWidthLogicMap |
| std::map<MsXpS::libXpertMassCore::Enums::MassToleranceType, QString> | massToleranceTypeMap |
| std::map<MsXpS::libXpertMassCore::Enums::MassType, QString> | massTypeMap |
| std::map<MsXpS::libXpertMassCore::Enums::PolymerEnd, QString> | polymerEndMap |
| std::map<MsXpS::libXpertMassCore::Enums::SelectionType, QString> | selectionTypeMap |
The CalcOptions class provides the specifications that configure the way masses are calculated for Oligomers, Polymers and product ions. More...
The ChemicalGroup class provides a model for specifying the acido-basic behaviour of a chemical group of either a Monomer object or of a Modif object. More...
The ChemicalGroupProp class provides a Prop instance of which the member data points to a dynamically allocated ChemicalGroup instance. More...
The ChemicalGroupRule class provides a model for refining the acido-basic behaviour of a chemical group of either a Monomer object or of a Modif object. More...
The CleavageAgent class provides a model for specifying aqueous cleavage specifications (patterns) of Polymer Sequences. More...
The CleavageConfig class derives from CleavageAgent to provide a model for specifying aqueous cleavage specifications (patterns) of Polymer Sequences along with instructions on the way the cleavage must occur. More...
The CleavageMotif class provides a model for specifying aqueous cleavage motfis of Polymer Sequences. More...
The CleavageRule class provides a model for specifying aqueous cleavage rules for refining cleavage agent specifications (CleavageAgent) of Polymer Sequences. More...
The Cleaver class provides a model for performing aqueous cleavage reactions involving CleavageAgent objects and Polymer Sequences. More...
The CrossLink class provides abstractions to work with a cross-link entity between Monomer instances. More...
The CrossLinkedRegion class provides abstractions to work with cross-links and detect the region of oligomers that are linked together. More...
The CrossLinker class provides abstractions to define the chemical basis of a cross-linking reaction. More...
The DoubleProp class is the specialized class for properties that hold data in the form of double values. More...
The Formula class provides sophisticated abstractions to work with formulas. More...
The FragmentationConfig class derives from FragmentationPathway and adds functionality to configure the way the fragmentation occurs in the Oligomer Sequence. More...
The FragmentationPathway class provides a model for specifying gas phase fragmentation pathways of Oligomer Sequences. More...
The FragmentationRule class provides a model for specifying gas phase fragmentation rules for refining fragmentation pathway specifications (FragmentationPathway) of Oligomer Sequences. More...
The Fragmenter class provides a model for performing gas phase fragmentation reactions involving FragmentationPathway objects and Polymer Sequences. More...
The IndexRange class provides a range of indices that delimit a region of interest in a Polymer's Sequence instance. More...
The IndexRangeCollection class provides a collection of IndexRange instances that enable delimiting Sequence regions of interest in a given Polymer instance. More...
The IntProp class is the specialized class for properties that hold data in the form of integer values. More...
The Ionizer class provides abstractions to ionize analytes. More...
The Isotope class models an isotope. More...
The IsotopicClusterGenerator class provides the features needed to model isotopic clusters starting from (elemental-composition, charge) pairs. More...
The IsotopicClusterShaper class provides the features needed to shape sets of (peak centroid m/z, intensity) pairs associated to a given charge into a mass spectral pappso;:Trace. More...
The IsotopicData class provides a collection of Isotopes and associated methods to access them in various ways. More...
The IsotopicDataBaseHandler class features basic handling of IsotopicData. More...
The IsotopicDataLibraryHandler class handles IsotopicData from the IsoSpec element data tables directly from the library's data. These are the reference, pristine, unmodified, isotopic data. More...
The IsotopicDataManualConfigHandler class handles a peculiar kind of IsotopicData that cannot be handled with the other handlers. More...
The IsotopicDataUserConfigHandler class handles user-defined IsotopicData. More...
The MassCollection class provides a container for masses (as double values) and for text representing thoses values. More...
The MassDataCborBaseHandler class provides features to handle mass spectrometric data using the CBOR (Concise Binary Object Representation) container streaming classes. More...
The MassDataCborMassSpectrumHandler class provides features to handle mass spectrum data using the CBOR (Concise Binary Object Representation) container streaming classes. More...
The MassDataClient class provides a network client. More...
The MassDataServer class provides a network server. More...
The MassPeakShaper class provides the features needed to shape a mass peak. More...
The MassPeakShaperConfig class provides the features required to configure the shaping of a mass peak centroid into a Gaussian or a Lorentzian fully profiled shape. More...
The Modif class provides abstractions to work with chemical modifications. More...
The Monomer class provides abstractions to work with monomers. More...
The MonomerDictionary class provides a Monomer code dictionary allowing the user to automatically translate Monomer codes from x-letter codes to y-letter codes. For example, a monomer dictionary file can define how to translate 3-letter monomer codes to 1-letter codes. This is typically useful when working on Protein Database (PDB) file. More...
The NoDeletePointerProp class provides a pointer property. More...
The Oligomer class provides abstractions to work with an oligomer molecule (peptide or oligonucleotide, for example). More...
The OligomerCollection class provides abstractions to work with Oligomer instances that have been produced in specific contexts, like Polymer cleavages or Oligomer fragmentations. More...
The OligomerPair class provides abstractions to work with a pair of Oligomer instances. More...
The PkaPhPi class provides a model for specifying the acido-basic properties of a chemical entity. More...
The PkaPhPiDataParser class provides a file reader for the pKa, pH, pI data XML file. More...
The PolChemDef class provides a complete set of chemical entities fully qualifying a polymer chemistry definition, like Proteins, Saccharides or Nucleic acids. More...
The PolChemDefSpec class provides metadata for accessing a given polymer chemistry definition's data on disk. More...
The Polymer class provides abstractions to work with a polymer molecule (protein or saccharide , for example). More...
The Prop class is the abstract base class for a number of specialized properties. More...
The PropListHolder class is the base class for a number of classes that need storing Prop instances. More...
The Sequence class provides abstractions to work with a simple sequence of Monomers. More...
The StringProp class is the specialized class for properties that hold data in the form of string objects. More...
The Utils class provides a number of utilitary features that may be of use anywhere in the XpertMass source code tree. More...
[alias] CleavageAgentCstSPtrSynonym for std::shared_ptr<const CleavageAgent>.
[alias] CleavageAgentSPtrSynonym for std::shared_ptr<CleavageAgent>.
Synonym for std::shared_ptr<const CrossLink>.
Synonym for std::weak_ptr<const CrossLink>.
Synonym for std::shared_ptr<CrossLink>.
Synonym for std::weak_ptr<CrossLink>.
Synonym for std::vector<QString> ErrorList.
[alias] libXpertMassCore::FormulaChargePairAlias for std::pair<QString, int>.
Synonym for std::shared_ptr<const Isotope>.
This enum type documents the various member data in Isotope.
The values assigned to the various enum members are used to specify the columsn in the GUI table view. They are also used to access substrings in the proper order in the overloaded initialize() function.
| Constant | Value | Description |
|---|---|---|
MsXpS::libXpertMassCore::IsotopeFields::NAME | 0 | Indicates Isotope::m_name. |
MsXpS::libXpertMassCore::IsotopeFields::SYMBOL | 1 | Indicates the Isotope::m_symbol. |
MsXpS::libXpertMassCore::IsotopeFields::MASS | 2 | Indicates the Isotope::m_mass. |
MsXpS::libXpertMassCore::IsotopeFields::PROBABILITY | 3 | Indicates the Isotope::m_probability. |
[alias] libXpertMassCore::IsotopeListCstIteratorAlias for QList<IsotopeQSPtr>::const_iterator.
[alias] libXpertMassCore::IsotopeListCstIteratorPairAlias for std::pair<IsotopeListCstIterator, IsotopeListCstIterator>.
[alias] libXpertMassCore::IsotopeListIteratorAlias for QList<IsotopeQSPtr>::iterator.
Synonym for std::shared_ptr<Isotope>.
[alias] libXpertMassCore::IsotopicClusterChargePairAlias for std::pair<pappso::TraceCstSPtr, int>.
Synonym for std::shared_ptr<const IsotopicClusterGenerator>.
Synonym for std::shared_ptr<IsotopicClusterGenerator>.
Synonym for std::shared_ptr<const IsotopicData>.
Synonym for std::shared_ptr<const IsotopicDataLibraryHandler>.
Synonym for std::shared_ptr<IsotopicDataLibraryHandler>.
Synonym for std::shared_ptr<const IsotopicDataManualConfigHandler>.
Synonym for std::shared_ptr<IsotopicDataManualConfigHandler>.
Synonym for std::shared_ptr<IsotopicData>.
This enum specifies the type of isotopic data.
| Constant | Value | Description |
|---|---|---|
MsXpS::libXpertMassCore::IsotopicDataType::NOT_SET | 0 | : Not configured. . |
MsXpS::libXpertMassCore::IsotopicDataType::LIBRARY_CONFIG | 1 | : The isotopic data are loaded intact from the IsoSpec library data and are considered pristine natural abundance data. . |
MsXpS::libXpertMassCore::IsotopicDataType::USER_CONFIG | 2 | : The isotopic data are in the same format as for LIBRARY_CONFIG but might have been modified by the user to configure new abundances. . |
MsXpS::libXpertMassCore::IsotopicDataType::MANUAL_CONFIG | 3 | : The isotopic data are in a specific format, different than the two above, that actually crafts the isotopes starting from scratch. |
Synonym for std::shared_ptr<MassPeakShaper>.
Synonym for const Monomer *.
[alias] MonomerCstSPtrSynonym for std::shared_ptr<const Monomer>.
Synonym for std::unique_ptr<const Monomer>.
Synonym for std::weak_ptr<const Monomer>.
Synonym for Monomer *.
[alias] MonomerSPtrSynonym for std::shared_ptr<Monomer>.
Synonym for std::unique_ptr<Monomer>.
Synonym for std::weak_ptr<Monomer>.
Synonym for std::shared_ptr<const OligomerCollection>.
Synonym for std::shared_ptr<OligomerCollection>.
Synonym for std::shared_ptr<const Oligomer>.
Synonym for std::shared_ptr<const OligomerPair>.
Synonym for std::shared_ptr<OligomerPair>.
Synonym for std::shared_ptr<Oligomer>.
Synonym for std::shared_ptr<const Polymer>.
Synonym for std::shared_ptr<Polymer>.
[alias] libXpertMassCore::SymbolCountMapAlias for to std::map<QString, int>.
[alias] UuidCrossLinkCstWPtrPairSynonym for std::pair<QString, CrossLinkCstWPtr>.
[alias] UuidCrossLinkWPtrPairSynonym for std::pair<QString, CrossLinkWPtr>.
These pairs are used to store a unique identifier (Uuid) string related to a std::shared_ptr<CrossLink> type. This kind of pair is used in a container in the Polymer class. The fact that the std::shared_ptr is converted to a std::weak_ptr is interesting because the item in the pair will not increase the reference count.
[alias] UuidMonomerCstWPtrPairSynonym for std::pair<QString, MonomerCstWPtr> items.
These pairs are used to store a unique identifier (Uuid) string related to a std::shared_ptr<const Monomer> type. This kind of pair is used in a container in the CrossLink class. The fact that the std::shared_ptr is converted to a std::weak_ptr is interesting because the item in the pair will not increase the reference count.
Number of decimal places after the decimal symbol for atom masses.
Map relating each CleavageAction member to a corresponding textual representation.
This variable holds the compounding factor to account for when shaping the sides of the peak.
The shape of the peak needs to reflect a real mass peak. In particular, the shape of the peak has to return, on each one of both sides, to the baseline, thus mimicking the baseline for a m/z distance equivalent to FWHM_PEAK_SPAN_FACTOR times the FWHM m/z range from left to right. That means that the simulated peak region at the left hand side of the centroid value will span (FWHM_PEAK_SPAN_FACTOR/2) times the FWHM and the same one right. Empirically, a good FWHM_PEAK_SPAN_FACTOR is 4, meaning that the left half of the peak (that is centered on the centroid) will have a size corresponding to two times the FHWM, and the same for the right half of the peak.
This is best exemplified as follows:
Centroid value
^
|
[ m/z - (2 * FWHM) <-|-> m/z + (2 * FWHM) ]
<----- width of the whole peak shape ----->
Number of decimal places after the decimal symbol for oligomer masses.
Number of decimal places after the decimal symbol for pH/pKa values.
Number of decimal places after the decimal symbol for polymer masses.
This variable holds the latest version of the format of the file containing the polymer chemistry definition.
Brought to 1 30 january 2023 for massXpert2 Brought to 2 10 november 2024 for massXpert2
Version number of the polymer sequence file format.
Map relating each CapType member to a corresponding textual representation.
Map relating each ChemicalEntity member to a corresponding textual representation.
Map relating each ChemicalGroupFate member to a corresponding textual representation.
Map relating each ChemicalGroupTrapped member to a corresponding textual representation.
Map relating each CrossLinkEncompassed member to a corresponding textual representation.
Map relating each FragEnd member to a corresponding textual representation.
Map relating each IonizationOutcome member to a corresponding textual representation.
Map relating each LocationType member to a corresponding textual representation.
Map relating each MassDataType member to a corresponding textual representation.
Map relating each MassPeakShapeType member to a corresponding textual representation.
Map relating each MassPeakWidthLogic member to a corresponding textual representation.
Map relating each MassToleranceType member to a corresponding textual representation.
Map relating each MassType member to a corresponding textual representation.
Map relating each PolymerEnd member to a corresponding textual representation.
Map relating each SelectionType member to a corresponding textual representation.