Node types

SAMSON Document are composed of nodes.

The image below shows the twenty-six possible node types and their corresponding icon in the document view.

Document nodes


SAMSON documents have a hierarchical structure: each node has one and only one parent, and possibly some children.

Nodes of a given type may only have children of some specific types:

  • A document may contain cameras, folders, node groups, conformations and paths.
  • A folder may contain folders, structural models, visual models, dynamical models, interaction models, property models, simulators, and labels.
  • A structural model may contain a structural root.
  • A structural group may contain atoms, backbones, bonds, chain, molecules, pseudo-atoms, residues, segments, side chains and structural groups.
  • A molecule may contain structural groups, chains, segments, residues, atoms, pseudo-atoms, and bonds.
  • A chain may contain structural groups, segments, residues, atoms and bonds.
  • A segment may contain atoms, bonds, structural groups and residues.
  • A residue may contain a backbone and a side chain.
  • A backbone may contain atoms and bonds.
  • A side chain may contain atoms and bonds.
  • A simulator may contain a state updater

Cameras, visual models, dynamical models, interaction models, property models, state updaters, conformations and paths cannot have children.

Nodes may also reference other nodes that are not their children:

  • A bond references two atoms, but is not the parent of the referenced atoms.
  • A node group references the nodes contained in the group.
  • A conformation references a group of atoms or pseudo-atoms with their position saved.
  • A path is a trajectory of a group of atoms or pseudo-atoms.
  • A dynamical model references structural nodes.
  • An interaction model references a dynamical model.
  • A simulator references a dynamical model and an interaction model.