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
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 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, labels, and notes.
- A note may contain text (including html) e.g. describing the current document, molecules, experiments, etc.
- A presentation contains animations.
- A structural model may contain atoms, backbones, bonds, chain, molecules, pseudo-atoms, residues, segments, side chains and structural groups.
- 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 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 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.