Enums Namespace

Type Documentation

enum class Enums::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 class Enums::ChemicalEntity

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 class Enums::ChemicalGroupFate

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 class Enums::ChemicalGroupTrapped

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 class Enums::CleavageAction

This enum specifies the cleavage operation to be carried out.

This enum is typically used when CleavageMotif objects are configured, either for cleavage (after arginine, for Trypsin) or not-for-cleavage, at K/P, for Trypsin).

enum class Enums::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 Enums::FragEnd

This enum specifies the end of the polymer that is found in a fragment.

This enum is typically used to tell what polymer end is found in a fragment ion product. For example, in protein fragmentations, the a, b, c fragments contain the left end of the peptide that was fragmented, while the x, y, z fragments contain the right end of the fragmented peptide.

enum class Enums::HashAccountData

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

enum Enums::IonizationOutcome

This enum specifies the outcome of an ionization or deionization process.

enum class Enums::LocationType

This enum type specified the kind of location:

enum class Enums::MassDataType

This enum type specifies the kind of mass data that are encoded in a CBOR container.

enum class Enums::MassPeakShapeType

This enum specifies how the peak shape needs to be computed.

enum class Enums::MassPeakWidthLogic

This enum specifies how the peak shape needs to be computed.

enum class Enums::MassToleranceType

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

enum class Enums::MassType

This enum type specifies the type of mass:

enum class Enums::PolymerEnd

This enum specifies the polymer end.

enum class Enums::SelectionType

This enum specifies the selection type in a polymer sequence.