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Node types

SAMSON document are composed of nodes.

The image below shows some of the possible node types and their corresponding icons in the Document view.

Document nodes

See also: Models

Hierarchy#

SAMSON Documents have a hierarchical structure: each node has one and only one parent, and possibly some children or references to other nodes.

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

  • A document can contain the same node types as the folder, it is basically the root folder. Additionally, it can contain cameras.
  • A folder can contain folders, files, Python scripts, structural models, visual models, dynamical models, interaction models, property models, simulators, labels, notes, render presets.
  • A presentation contains animations.
  • A structural model can contain atoms, backbones, bonds, chain, molecules, residues, segments, side chains, and structural groups.
  • A structural group can contain atoms, backbones, bonds, chain, molecules, residues, segments, side chains, and structural groups.
  • A molecule can contain structural groups, chains, segments, residues, atoms, and bonds.
  • A chain can contain structural groups, segments, residues, atoms, and bonds.
  • A segment can contain atoms, bonds, structural groups, and residues.
  • A residue can contain a single backbone and a single side chain.
  • A backbone can contain atoms and bonds.
  • A side chain can contain atoms and bonds.
  • A simulator can contain a state updater.

The following nodes cannot have children:

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

  • A bond references two atoms.
  • A node group references the nodes contained in the group.
  • A H-bond group contains H-bonds that reference two to three atoms (an acceptor, a donor, a hydrogen), but are not the parent of the referenced atoms.
  • A conformation references a group of atoms with their position saved.
  • A path is a trajectory of a group of atoms and references this group of atoms.
  • A dynamical model references structural nodes.
  • An interaction model references a dynamical model.
  • A simulator references a dynamical model and an interaction model.

Some other types of nodes:

  • A file represents any type of an embedded file, e.g. a PDF, an image, some data file, some structure file, etc., basically, any type of file.
  • A script represents a Python script file, it can be opened via Code editor and launched using the integrated Python console.
  • A note can contain text (including html), e.g. describing the current document, molecules, experiments, etc.
  • A render preset contains rendering settings.