hatchlings

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CloningNode ​

A CloningNode represents a DNA construct at any stage in a cloning workflow — either a starting material (source vector, insert, donor) or a derived product created by a cloning operation.

Overview ​

Cloning data in hatchlings is modeled as a tree of CloningNode objects. Each node describes a construct (name, size, topology, features) and optionally a source that records how it was made.

  • Leaf nodes have no source — they are starting materials (vectors, inserts, PCR templates)
  • Derived nodes have a source containing the CloningAction and input nodes that produced them
Final Product (root)
├── source.action: Gibson Assembly
├── source.inputs[0].node: Backbone (leaf)
└── source.inputs[1].node: Insert
    ├── source.action: PCR
    ├── source.inputs[0].node: Template (leaf)

Interface Reference ​

ts
import type { CloningNode } from '@molbiohive/hatchlings';
FieldTypeRequiredDescription
idstringyesUnique identifier for this node
namestringyesConstruct name (e.g. 'pUC19', 'GFP insert')
sizenumberyesTotal length in base pairs
topology'circular' | 'linear'noDefaults to 'circular' for most vectors
sequencestringnoFull nucleotide sequence (sense strand, 5'→3')
partsPart[]noFeature annotations (genes, promoters, primers)
cutSitesCutSite[]noRestriction enzyme cut sites
descriptionstringnoFree-text description
sourceCloningSourcenoHow this node was produced (absent for starting materials)

Leaf Node (Source Material) ​

A leaf node has no source. It represents raw starting material:

ts
const backbone: CloningNode = {
  id: 'puc19',
  name: 'pUC19',
  size: 2686,
  topology: 'circular',
  parts: [
    { name: 'AmpR', type: 'CDS', start: 1629, end: 2489, strand: -1, color: '#4dc3ff' },
    { name: 'ori', type: 'rep_origin', start: 836, end: 1424, strand: -1, color: '#9467bd' },
    { name: 'lacZa', type: 'CDS', start: 217, end: 508, strand: 1, color: '#e6a24c' },
  ],
  cutSites: [
    { enzyme: 'EcoRI', position: 396, end: 402, strand: 1, cutPosition: 1, complementCutPosition: 5 },
    { enzyme: 'BamHI', position: 417, end: 423, strand: 1, cutPosition: 1, complementCutPosition: 5 },
  ],
};

Derived Node (Cloned Product) ​

A derived node has a source describing the operation and inputs:

ts
const product: CloningNode = {
  id: 'puc19-gfp',
  name: 'pUC19-GFP',
  size: 3403,
  topology: 'circular',
  parts: [
    { name: 'AmpR', type: 'CDS', start: 1629, end: 2489, strand: -1, color: '#4dc3ff' },
    { name: 'GFP', type: 'CDS', start: 396, end: 1113, strand: 1, color: '#58b56a' },
    { name: 'ori', type: 'rep_origin', start: 836, end: 1424, strand: -1, color: '#9467bd' },
  ],
  source: {
    action: {
      paradigm: 'restriction',
      enzymes: ['EcoRI', 'BamHI'],
    },
    inputs: [
      { node: backbone, label: 'Vector' },
      { node: gfpInsert, label: 'Insert' },
    ],
  },
};

Relationship to PlasmidData ​

CloningNode shares the same Part[] and CutSite[] types as PlasmidData. A CloningNode can be directly rendered by PlasmidViewer by mapping to PlasmidData:

ts
import type { PlasmidData, CloningNode } from '@molbiohive/hatchlings';

function toPlasmidData(node: CloningNode): PlasmidData {
  return {
    name: node.name,
    size: node.size,
    topology: node.topology ?? 'circular',
    seq: node.sequence,
    parts: node.parts ?? [],
    cutSites: node.cutSites ?? [],
  };
}