libXpertMass Namespace

Type Documentation

enum libXpertMass::CapType

This enum specifies the type of cap (the chemical entities that are set to the polymer ends so as to finish its polymerization state from a chain of residues to an actual polymer molecule.

enum libXpertMass::ChemicalGroupRuleFate

This enum specifies how the chemical group behaves when the chemical entity that it holds polymerizes into a Polymer.

This example clarifies the concept:

<monomer>
  <code>C</code>
  <mnmchemgroup>
    <name>N-term NH2</name>
    <pka>9.6</pka>
    <acidcharged>TRUE</acidcharged>
    <polrule>left_trapped</polrule>
    <chemgrouprule>
      <entity>LE_PLM_MODIF</entity>
      <name>Acetylation</name>
      <outcome>LOST</outcome>
    </chemgrouprule>
  </mnmchemgroup>

When the Cysteine's amino group is modified because the Cys residue on on the N-terminal end of the polymer, if it gets acetylated, then the amino group is lost because it is trapped in the amide bond. It is thus not accounted for when computing the pI of the protein.

enum libXpertMass::ChemicalGroupTrapping

This enum specifies how the chemical group behaves when the chemical entity that it holds polymerizes into a Polymer.

One example will clear things out:

An amino acid has a amino group and a carboxylic acid group. The amino group gets entrapped in the monomer-to-monomer bond (the peptide bond) if the polymerization occurs at the left of the monomer. That means that if the Monomer holding this ChemicalGroup is N-terminal, then the amino group should be accounted for because it is intact. Conversely, the carboxylic acid group gets entrapped in the peptide bond if the polymerization occurs at the right of the monomer. That means that if the Monomer holding this ChemicalGroup is C-terminal, then the carboxylic acid group should be accounted for because it is intact.

enum libXpertMass::CrossLinkEncompassed

This enum type specifies the manner in which a sequence region in a Polymer or in an Oligomer contains fully, or partially not does not contain all the monomers involved in a CrossLink:

enum class libXpertMass::FormulaSplitResult

This enum type specifies the result of an actionformula parsing process:

enum libXpertMass::FragEnd

This enum specifies the end of the Oligomer that will be contained in the fragment resulting from its fragmentation. In protein chemistry, for example, a,b and x fragments are N-terminal fragments, that is, they contain the left end of the framgented Oligomer's sequence.

enum libXpertMass::HashAccountData

This enum specifies the chemical entites to account for when calculating a hash.

enum class libXpertMass::IsotopeFields

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 Isotope::initialize().

enum class libXpertMass::IsotopicDataType

This enum specifies the type of isotopic data.

enum class libXpertMass::MassPeakShapeType

This enum specifies the type of mass peak shape to be computed around a m/z peak centroid.

enum class libXpertMass::MassPeakWidthLogic

This enum specifies the logic used to computed the width of the mass peak shape around a m/z peak centroid.

enum libXpertMass::MassToleranceType

This enum type specifies the kind of mass tolerance to use for a mass calculation or a mass comparison.

enum libXpertMass::MassType

This enum type specifies the type of mass:

enum libXpertMass::MonomerChemEnt

This enum specifies the monomer chemical entities to account for in a calculation.

This enum is typically used when mass calculations need to account or not for the various chemical entities that are attached to a given monomer.

enum libXpertMass::PolymerChemEnt

This enum specifies the polymer sequence chemical entities to account for in a calculation.

This enum is typically used when mass calculations need to account or not for the various chemical entities that are attached to a given polymer.

enum libXpertMass::PolymerEnd

This enum specifies the polymer end.

enum libXpertMass::SelectionType

This enum specifies the selection type in a polymer sequence.

                    Centroid value
                     ^
                     |
[ m/z - (2 * FWHM) <-|-> m/z + (2 * FWHM) ]
<----- width of the whole peak shape ----->

"([+-]?)([A-Z][a-z]*)(\\d*[\\.]?\\d*)"