Working with documents and nodes#
Documents#
SAMSON documents are hierarchies of SAMSON nodes. A document hierarchy is visible in the Document view.
SAMSON documents (SBDocument) may contain cameras (SBCamera), folders (SBFolder), files (SBFile),
structural nodes (e.g. molecules, residues, groups, atoms, bonds, conformations, paths, etc.),
labels (SBLabel), notes (SBNote), visual models (SBVisualModel), simulators (SBSimulator), etc.
SAMSON maintains the information about models (structural nodes, visual models, etc), cameras, simulators, etc., in the document’s data graph.
See User guide - Node types for the description of types of nodes in SAMSON documents.
In one SAMSON instance you can simultaneously have multiple opened documents, but only one document is active at any given time - the one you see in the Document view. The loaded or created molecules are placed in the active document.
document = SAMSON.getActiveDocument()
Moving around#
Each document has at least one camera (SBCamera).
A camera provides a 3D view of visualizable objects.
Basically, you may consider your screen as a camera pointing into the viewport and yourself as an operator seeing through the camera.
Cameras and their positions and properties are saved and loaded together with a document.
# change the active camera's view using commands
SAMSON.runCommand("Top view")
# change the view directly via the active camera
# get the active camera
camera = SAMSON.getActiveCamera()
# change the view of the camera
camera.topView()
Having multiple cameras in a document might be useful if you want to switch fast between different views (e.g., positions, projections, close-up views, and a full view) in the same document. To switch between cameras in the document:
# get all cameras in the document
cameraIndexer = document.getNodes("node.type camera")
# make the operation undoable
SAMSON.beginHolding("Change camera")
# change the document's active camera to the first camera in the document
SAMSON.getActiveDocument().setActiveCamera(cameraIndexer[0])
# stop holding
SAMSON.endHolding()
You can also access and modify other camera’s attributes. See SBCamera for more information and examples.
Working with nodes#
Each node has one and only one parent, and possibly some children or references to other nodes. See the following sections to learn how to work with nodes:
See also
User Guide: Node types