| | |
Contains non-GUI classes for the modelling of linear polymer chemistries. More...
Features to use the Averagine concept | |
This struct describes a calculated isotopic cluster's centroid for a calculated isotopic cluster that was binned so as to remove hyperfine isotopic structure centroids that would be of no use during the matching of centroids with the input mass spectrum centroids | |
The specifications that configure the way masses are calculated for Oligomers, Polymers and product ions | |
This struct holds the data describing an input mass spectrum centroid with a given tested charge | |
Model for specifying the acido-basic behaviour of a chemical group of either a Monomer object or of a Modif object | |
Prop instance of which the member data points to a dynamically allocated ChemicalGroup instance | |
Model for refining the acido-basic behaviour of a chemical group of either a Monomer object or of a Modif object | |
Model for specifying aqueous cleavage specifications (patterns) of Polymer Sequences | |
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 | |
Model for specifying aqueous cleavage motfis of Polymer Sequences | |
Model for specifying aqueous cleavage rules for refining cleavage agent specifications (CleavageAgent) of Polymer Sequences | |
Model for performing aqueous cleavage reactions involving CleavageAgent objects and Polymer Sequences | |
Abstractions to work with a cross-link entity between Monomer instances | |
Abstractions to work with cross-links and detect the region of oligomers that are linked together | |
Abstractions to define the chemical basis of a cross-linking reaction | |
Struct provides a cubic spline model of a mass spectrometric data peak | |
This struct holds the data about an analyte's neutral mass and intensity as defined by the deconvolution of one or more isotopic clusters representing different ionization levels of the same analyte | |
The mechanics that performs matches between analyte ID : molecular mass dictionary entries and the masses obtained by deconvolution of a mass spectrum | |
The specialized class for properties that hold data in the form of double values | |
This struct holds the metric data about the matches between the calculated isotopic cluster's centroids and those from the input centroided mass spectrum. This struct is mainly for use in the reporting to the user | |
Sophisticated abstractions to work with formulas | |
Derives from FragmentationPathway and adds functionality to configure the way the fragmentation occurs in the Oligomer Sequence | |
Model for specifying gas phase fragmentation pathways of Oligomer Sequences | |
Model for specifying gas phase fragmentation rules for refining fragmentation pathway specifications (FragmentationPathway) of Oligomer Sequences | |
Model for performing gas phase fragmentation reactions involving FragmentationPathway objects and Polymer Sequences | |
Provides a peak picking feature for data acquired on high resolving power instruments | |
Provides parameters for the HighResPeakPicker peak picking feature | |
Range of indices that delimit a region of interest in a Polymer's Sequence instance | |
Collection of IndexRange instances that enable delimiting Sequence regions of interest in a given Polymer instance | |
The specialized class for properties that hold data in the form of integer values | |
Abstractions to ionize analytes | |
Struct describes a match between a theoretical isotopic cluster centroid and a centroid of the input centroided mass spectrum (observed) | |
The features needed to model isotopic clusters starting from (elemental-composition, charge) pairs. Neutral analytes can have their isotopic cluster modelle by setting the charge to 0 | |
The features needed to shape sets of (peak centroid m/z, intensity) pairs associated to a given charge into a mass spectral pappso::Trace | |
Collection of Isotopes and associated methods to access them in various ways | |
Features basic handling of IsotopicData | |
Handles IsotopicData from the IsoSpec element data tables directly from the library's data. These are the reference, pristine, unmodified, isotopic data | |
Handles a peculiar kind of IsotopicData that cannot be handled with the other handlers | |
Handles user-defined IsotopicData | |
Struct encapsulates all the parameters needed to configure the low mass deconvolving process | |
Container for masses (as double values) and for text representing thoses values | |
Features to handle mass spectrometric data using the CBOR (Concise Binary Object Representation) container streaming classes | |
Features to handle mass spectrum data using the CBOR (Concise Binary Object Representation) container streaming classes | |
Network client | |
Network server | |
The features needed to shape a mass peak | |
The features required to configure the shaping of a mass peak centroid into a Gaussian or a Lorentzian fully profiled shape | |
Abstractions to work with chemical modifications | |
Abstractions to work with monomers | |
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 | |
Pointer property | |
Abstractions to work with an oligomer molecule (peptide or oligonucleotide, for example) | |
Abstractions to work with Oligomer instances that have been produced in specific contexts, like Polymer cleavages or Oligomer fragmentations | |
Abstractions to work with a pair of Oligomer instances | |
Model for specifying the acido-basic properties of a chemical entity | |
File reader for the pKa, pH, pI data XML file | |
Complete set of chemical entities fully qualifying a polymer chemistry definition, like Proteins, Saccharides or Nucleic acids | |
Metadata for accessing a given polymer chemistry definition's data on disk | |
Abstractions to work with a polymer molecule (protein or saccharide , for example) | |
The abstract base class for a number of specialized properties | |
The base class for a number of classes that need storing Prop instances | |
Abstractions to work with a simple sequence of Monomers | |
The specialized class for properties that hold data in the form of string objects | |
Struct encapsulates an input mass spectrum's monoisotopic centroid of a cluster that was succesfully matched to a corresponding calculated cluster | |
Number of utilitary features that may be of use anywhere in the XpertMass source code tree |
The libXpertMassCore module provides classes to model all the chemical entities required to fully characterize the behaviour of polymer chemistries both in solution and in the gas phase. It offers both high-level classes such as Polymer and low-level classes such as Isotope. Other classes define how polymers of a given polymer chemistry might be modified, either in solution or in the gas phase (cleavages or fragmentations). Other classes define ways to process mass data (centroidation, deconvolutions...).