Additional Data Handling

In the Biomolecule Toolkit, additional data can be assigned to entities and macromolecule types.

Entities

Monomer
The building blocks that are assemble macromolecules.

Macromolecule
An entity that can be composed of monomers, domains, components and/or additional data. Examples for macromolecule types: peptide, oligonucleotide, protein etc.

Component
The distinguished compartment(s) of the macromolecule (e.g. CHEMs, PEPTIDEs, RNAs, BLOBs)

Domain
The structurally and functionally distinct segment of the biological sequences.

Macromolecule Type

Macromolecules that are belonging a certain modality group. Can be standard custom or modality type (e.g peptide, oligonucleotide, protein, ADC etc.)

To define additional data, attributes have to be configured and assigned directly to a given entity type in order to be in use by an entity or a specific monomer.

Reserved attributes

The following reserved attributes are utilized in certain features in the Biomolecule Toolkit and BioEddie:

  • name: appears in the component box if it is defined in a macromolecule’s component in BioEddie

  • Mw: molar mass range of a monomer (value1-value2). If it is defined, then the Biomolecule Toolkit can calculate the molar mass on macromolecules.

Set options for monomer grouping

The options for monomer grouping are dedicated to enable grouping by properties in BioEddie, the JS macromolecule sketcher.

Monomers can be grouped based on their default (e.g. functional type, natural analogue etc.) and custom (registered) attributes.
For the monomer grouping, it is mandatory to assign attributes to monomer entities.
If the attributes are assigned, then the following options have to be defined.

propertyName
The registered attribute which is assigned to the monomer entity.

attribute
Checks whether the attribute is custom or default.

type
The type of the attribute’s value (string or number).

label
The title of the grouping category.

intervals
If a number is associated with the corresponding attribute, then intervals with a label (name of the group), lower bound and upper bound have to be set.
The intervals option is not required if the associated attribute’s datatype is a string.