Simulator

Initialize and add simulator in the active document

To add a simulator in SAMSON you need to create and add a dynamical model, an interaction model, and a state updater. In the following example we will apply a simulator to a molecular system in the active document using the Brenner interaction model and the Interactive modeling state updater.

# Apply a simulator to a molecule in the active document

# get a node indexer of all structural models in the active document
nodeIndexer = SAMSON.getNodes('n.t sm')

# UUID of the Brenner SAMSON Element
IMuuid = sam.Core.Container.UUID('AD608CB6-6971-7CD4-6FCC-34531998E743')

# UUID of the State Updater pack SAMSON Element
SUuuid = sam.Core.Container.UUID('F912F119-7CBB-B5BD-972A-0A02DFCF683D')

# make an instance of a simulator by providing class names of an interaction model and a state updater
simulator = SAMSON.makeSimulator(nodeIndexer, 'SMMBrennerInteractionModel', IMuuid, 'SESInteractiveModelingUpdater', SUuuid)

# now we need to create a dynamical model, an interaction model, and a state updater

# get the dynamical model from the simulator
dynamicalModel = simulator.getDynamicalModel()
# create the dynamical model
dynamicalModel.create()

# get the interaction model from the simulator
interactionModel = simulator.getInteractionModel()
# create the interaction model
interactionModel.create()
# show a window with interaction model properties
SAMSON.showProperties(interactionModel)
# initialize interaction model
interactionModel.initializeInteractions()

# get the state updater from the simulator
stateUpdater = simulator.getStateUpdater()
# create the state updater
stateUpdater.create()
# show a window with state updator properties
SAMSON.showProperties(stateUpdater)

# create the simulator
simulator.create()

# get the active document
document = SAMSON.getActiveDocument()

# turn the undo system on
SAMSON.beginHolding('Add simulator')

# hold an object for undo/redo
SAMSON.hold(dynamicalModel)
# add the dynamical model to the active document
document.addChild(dynamicalModel)

# hold an object for undo/redo
SAMSON.hold(interactionModel)
# add the interaction model to the active document in SAMSON
document.addChild(interactionModel)

# hold an object for undo/redo
SAMSON.hold(simulator)
# add the simulator to the active document
document.addChild(simulator)

# turn the undo system off
SAMSON.endHolding()

You can start and stop simulation using the SAMSON Facade (samson.Facade.SAMSON):

# start simulation
SAMSON.startSimulation()

# check until the simulation is done
# ...

# stop simulation
SAMSON.stopSimulation()

See also

SAMSON API: SBSSimulator

class samson.Simulation.Simulator.Simulator

Bases: samson.DataModel.DataGraph.Node

This class is the base class of simulators.

class NodeType(self: samson.DataModel.DataGraph.Node.NodeType, arg0: int) → None

Bases: pybind11_builtins.pybind11_object

ArticulatedBody = NodeType.DynamicalModelNodeArticulatedBody

ArticulatedBodySystem = NodeType.DynamicalModelArticulatedBodySystem

Atom = NodeType.Atom

Backbone = NodeType.StructuralModelNodeBackbone

Bond = NodeType.StructuralModelNodeBond

Camera = NodeType.Camera

Chain = NodeType.StructuralModelNodeChain

Conformation = NodeType.StructuralModelConformation

Controller = NodeType.Controller

ControllerNode = NodeType.ControllerNode

DataGraphNodeGroup = NodeType.DataGraphNodeGroup

Document = NodeType.Document

DocumentManager = NodeType.DocumentManager

DynamicalGroup = NodeType.DynamicalModelNodeGroup

DynamicalModel = NodeType.DynamicalModel

DynamicalModelArticulatedBodySystem = NodeType.DynamicalModelArticulatedBodySystem

DynamicalModelNode = NodeType.DynamicalModelNode

DynamicalModelNodeArticulatedBody = NodeType.DynamicalModelNodeArticulatedBody

DynamicalModelNodeGroup = NodeType.DynamicalModelNodeGroup

DynamicalModelNodeParticle = NodeType.DynamicalModelNodeParticle

DynamicalModelNodeRigidBody = NodeType.DynamicalModelNodeRigidBody

DynamicalModelNodeRoot = NodeType.DynamicalModelNodeRoot

DynamicalModelParticleSystem = NodeType.DynamicalModelParticleSystem

DynamicalModelRigidBodySystem = NodeType.DynamicalModelRigidBodySystem

DynamicalNode = NodeType.DynamicalModelNode

DynamicalParticle = NodeType.DynamicalModelNodeParticle

DynamicalRoot = NodeType.DynamicalModelNodeRoot

Folder = NodeType.Folder

InteractionModel = NodeType.InteractionModel

InteractionModelArticulatedBodySystem = NodeType.InteractionModelArticulatedBodySystem

InteractionModelParticleSystem = NodeType.InteractionModelParticleSystem

InteractionModelRigidBodySystem = NodeType.InteractionModelRigidBodySystem

Label = NodeType.Label

Molecule = NodeType.StructuralModelNodeMolecule

NodeGroup = NodeType.DataGraphNodeGroup

ParticleSystem = NodeType.DynamicalModelParticleSystem

Path = NodeType.StructuralModelPath

PropertyModel = NodeType.PropertyModel

PropertyModelFunction = NodeType.PropertyModelFunction

Protein = NodeType.StructuralModelNodeProtein

PseudoAtom = NodeType.StructuralModelNodePseudoAtom

Residue = NodeType.StructuralModelNodeResidue

RigidBody = NodeType.DynamicalModelNodeRigidBody

RigidBodySystem = NodeType.DynamicalModelRigidBodySystem

Root = NodeType.StructuralModelNodeRoot

Segment = NodeType.StructuralModelNodeSegment

SideChain = NodeType.StructuralModelNodeSideChain

Simulator = NodeType.Simulator

SimulatorArticulatedBodySystem = NodeType.SimulatorArticulatedBodySystem

SimulatorParticleSystem = NodeType.SimulatorParticleSystem

SimulatorRigidBodySystem = NodeType.SimulatorRigidBodySystem

StateUpdater = NodeType.StateUpdater

StateUpdaterArticulatedBodySystem = NodeType.StateUpdaterArticulatedBodySystem

StateUpdaterParticleSystem = NodeType.StateUpdaterParticleSystem

StateUpdaterRigidBodySystem = NodeType.StateUpdaterRigidBodySystem

StructuralGroup = NodeType.StructuralModelNodeGroup

StructuralModel = NodeType.StructuralModel

StructuralModelConformation = NodeType.StructuralModelConformation

StructuralModelNode = NodeType.StructuralModelNode

StructuralModelNodeAtom = NodeType.Atom

StructuralModelNodeBackbone = NodeType.StructuralModelNodeBackbone

StructuralModelNodeBond = NodeType.StructuralModelNodeBond

StructuralModelNodeChain = NodeType.StructuralModelNodeChain

StructuralModelNodeGroup = NodeType.StructuralModelNodeGroup

StructuralModelNodeMolecule = NodeType.StructuralModelNodeMolecule

StructuralModelNodeParticle = NodeType.StructuralModelNodeParticle

StructuralModelNodeProtein = NodeType.StructuralModelNodeProtein

StructuralModelNodePseudoAtom = NodeType.StructuralModelNodePseudoAtom

StructuralModelNodeResidue = NodeType.StructuralModelNodeResidue

StructuralModelNodeRoot = NodeType.StructuralModelNodeRoot

StructuralModelNodeSegment = NodeType.StructuralModelNodeSegment

StructuralModelNodeSideChain = NodeType.StructuralModelNodeSideChain

StructuralModelPath = NodeType.StructuralModelPath

StructuralParticle = NodeType.StructuralModelNodeParticle

Undefined = NodeType.Undefined

VisualModel = NodeType.VisualModel

addChild(self: samson.DataModel.DataGraph.Node, node: samson.DataModel.DataGraph.Node, nextNode: samson.DataModel.DataGraph.Node=None) → bool

Adds a child to the node

canAddChild(self: samson.DataModel.DataGraph.Node, node: samson.DataModel.DataGraph.Node, nextNode: samson.DataModel.DataGraph.Node=None) → bool

Returns whether this node can add node as a child

canAddChildType(self: samson.DataModel.DataGraph.Node, nodeType: SBDDataGraphNode::Type) → bool

Returns whether this node can add a node with type nodeType as a child

castToInteractionModelParticleSystem(self: samson.DataModel.DataGraph.Node) → SBMInteractionModelParticleSystem

Casts (if possible) from SBDDataGraphNode to SBMInteractionModelParticleSystem

castToLabel(self: samson.DataModel.DataGraph.Node) → SBDDocumentLabel

Casts (if possible) from SBDDataGraphNode to SBDDocumentLabel

castToVisualModel(self: samson.DataModel.DataGraph.Node) → SBMVisualModel

Casts (if possible) from SBDDataGraphNode to SBMVisualModel

clone(self: samson.Simulation.Simulator.Simulator) → samson.Simulation.Simulator.Simulator

Returns a copy of the node and its descendants

countNodes(self: samson.DataModel.DataGraph.Node, selectionString: str='*', visitString: str='*', includeDependencies: bool=False) → int

Count nodes into nodeIndexer, based on a selectionPredicate and a visitPredicate, with our without dependencies).

For selectionString and visitString use Node Specification Language (SAMSON API: Node Specification Language

create(self: samson.DataModel.DataGraph.Node) → None

Creates the node

display(self: samson.Simulation.Simulator.Simulator) → None

Displays the interaction model

displayForSelection(self: samson.Simulation.Simulator.Simulator) → None

Displays the interaction model for selection purposes

displayForShadow(self: samson.Simulation.Simulator.Simulator) → None

Displays the interaction model for shadow purposes

erase(self: samson.DataModel.DataGraph.Node) → None

Erases the node

getDocument(self: samson.DataModel.DataGraph.Node) → SBDDocument

Returns the document the node belongs to

getFlags(self: samson.DataModel.DataGraph.Node) → int

Returns the flags

getInheritedFlags(self: samson.DataModel.DataGraph.Node) → int

Returns the inherited flags

getMaterial(self: samson.DataModel.DataGraph.Node) → SBDDataGraphNodeMaterial

Returns the material of the node

getMaterialOwner(self: samson.DataModel.DataGraph.Node) → samson.DataModel.DataGraph.Node

Returns the node whose material is inherited

getMemoryFootprint(self: samson.Core.Reference.ReferenceTarget) → int

Returns the memory footprint

getNextNode(*args, **kwargs)

Overloaded function.

1. getNextNode(self: samson.DataModel.DataGraph.Node) -> samson.DataModel.DataGraph.Node

Returns the pointer to the next node in the children of the node’s parent

2. getNextNode(self: samson.DataModel.DataGraph.Node, nodeType: SBDDataGraphNode::Type) -> samson.DataModel.DataGraph.Node

Returns the pointer to the next node with type nodeType in the children of the node’s parent

getNextSimulator(self: samson.Simulation.Simulator.Simulator) → samson.Simulation.Simulator.Simulator

Returns the next Simulator

getNode(self: int) → samson.DataModel.DataGraph.Node

Returns the unique node corresponding to the node index nodeIndex

getNodes(self: samson.DataModel.DataGraph.Node, selectionString: str='*', visitString: str='*', includeDependencies: bool=False) → SBDDataGraphNodeIndexer

Returns nodes (in a node indexer), based on a selectionString and a visitString, with our without dependencies).

For selectionString and visitString use Node Specification Language (SAMSON API: Node Specification Language

getParent(self: samson.DataModel.DataGraph.Node) → samson.DataModel.DataGraph.Node

Returns the parent of the node

getPreviousNode(*args, **kwargs)

Overloaded function.

1. getPreviousNode(self: samson.DataModel.DataGraph.Node) -> samson.DataModel.DataGraph.Node

Returns the pointer to the previous node in the children of the node’s parent

2. getPreviousNode(self: samson.DataModel.DataGraph.Node, nodeType: SBDDataGraphNode::Type) -> samson.DataModel.DataGraph.Node

Returns the pointer to the previous node with type nodeType in the children of the node’s parent

getPreviousSimulator(self: samson.Simulation.Simulator.Simulator) → samson.Simulation.Simulator.Simulator

Returns the previous Simulator

getRoot(self: samson.DataModel.DataGraph.Node) → samson.DataModel.DataGraph.Node

Returns the root of the hierarchy the node belongs to

getThisNode(self: samson.DataModel.DataGraph.Node) → samson.DataModel.DataGraph.Node

Returns the pointer to this node

getTypeString(type: SBDDataGraphNode::Type) → str

Returns a string describing the type of the data graph node

hasOneOf(self: samson.DataModel.DataGraph.Node, nodeIndexer: SBDDataGraphNodeIndexer) → bool

Returns true if and only if this node is one of the nodes of the nodeIndexer, or is the ancestor of one of them

isDynamicalModel(self: samson.DataModel.DataGraph.Node) → bool

Returns true when the node is a dynamical model

isIn(*args, **kwargs)

Overloaded function.

1. isIn(self: samson.DataModel.DataGraph.Node, node: samson.DataModel.DataGraph.Node) -> bool

Returns true if and only if this node is node, or descends from it

2. isIn(self: samson.DataModel.DataGraph.Node, nodeIndexer: SBDDataGraphNodeIndexer) -> bool

Returns true if and only if this node is one of the nodes of the nodeIndexer, or descends from one of them

isInteractionModel(self: samson.DataModel.DataGraph.Node) → bool

Returns true when the node is a interaction model

isModel(self: samson.DataModel.DataGraph.Node) → bool

Returns true when the node is a model

isOneOf(self: samson.DataModel.DataGraph.Node, nodeIndexer: SBDDataGraphNodeIndexer) → bool

Returns true if and only if this node is one of the nodes of the nodeIndexer

isPropertyModel(self: samson.DataModel.DataGraph.Node) → bool

Returns true when the node is a property model

isSimulator(self: samson.DataModel.DataGraph.Node) → bool

Returns true when the node is a simulator

isStructuralModel(self: samson.DataModel.DataGraph.Node) → bool

Returns true when the node is a structural model

isStructuralParticle(self: samson.DataModel.DataGraph.Node) → bool

Returns true when the node is a structural particle (an atom or a pseudo-atom)

isType(self: samson.DataModel.DataGraph.Node, type: SBDDataGraphNode::Type) → bool

Returns true when the type of the node corresponds to type

isVisualModel(self: samson.DataModel.DataGraph.Node) → bool

Returns true when the node is a visual model

printDebugInfo(self: samson.Simulation.Simulator.Simulator, offset: int=0) → None

Prints some debugging information in stdout

removeChild(self: samson.DataModel.DataGraph.Node, node: samson.DataModel.DataGraph.Node) → bool

Removes a child from the node

removeMaterial(self: samson.DataModel.DataGraph.Node) → bool

Removes material from the node

setColor(self: samson.DataModel.DataGraph.Node, color: SBDColor) → bool

Sets the color for the node (modifies an existing material of the node or adds a material with a given color)

Args:

color (Color): color to set

setColorScheme(self: samson.DataModel.DataGraph.Node, colorScheme: SBDDataGraphNodeColorScheme) → bool

Sets the color scheme for the node (modifies an existing material of the node or adds a material with a given color scheme)

Args:

colorScheme (ColorScheme): color scheme to set

setMaterial(self: samson.DataModel.DataGraph.Node, material: SBDDataGraphNodeMaterial) → bool

Sets the material for the node.

Args:

material (Material): material to set

ArticulatedBody = NodeType.DynamicalModelNodeArticulatedBody

ArticulatedBodySystem = NodeType.DynamicalModelArticulatedBodySystem

Atom = NodeType.Atom

Backbone = NodeType.StructuralModelNodeBackbone

Bond = NodeType.StructuralModelNodeBond

Camera = NodeType.Camera

Chain = NodeType.StructuralModelNodeChain

Conformation = NodeType.StructuralModelConformation

Controller = NodeType.Controller

ControllerNode = NodeType.ControllerNode

DataGraphNodeGroup = NodeType.DataGraphNodeGroup

Document = NodeType.Document

DocumentManager = NodeType.DocumentManager

DynamicalGroup = NodeType.DynamicalModelNodeGroup

DynamicalModel = NodeType.DynamicalModel

DynamicalModelArticulatedBodySystem = NodeType.DynamicalModelArticulatedBodySystem

DynamicalModelNode = NodeType.DynamicalModelNode

DynamicalModelNodeArticulatedBody = NodeType.DynamicalModelNodeArticulatedBody

DynamicalModelNodeGroup = NodeType.DynamicalModelNodeGroup

DynamicalModelNodeParticle = NodeType.DynamicalModelNodeParticle

DynamicalModelNodeRigidBody = NodeType.DynamicalModelNodeRigidBody

DynamicalModelNodeRoot = NodeType.DynamicalModelNodeRoot

DynamicalModelParticleSystem = NodeType.DynamicalModelParticleSystem

DynamicalModelRigidBodySystem = NodeType.DynamicalModelRigidBodySystem

DynamicalNode = NodeType.DynamicalModelNode

DynamicalParticle = NodeType.DynamicalModelNodeParticle

DynamicalRoot = NodeType.DynamicalModelNodeRoot

Folder = NodeType.Folder

InteractionModel = NodeType.InteractionModel

InteractionModelArticulatedBodySystem = NodeType.InteractionModelArticulatedBodySystem

InteractionModelParticleSystem = NodeType.InteractionModelParticleSystem

InteractionModelRigidBodySystem = NodeType.InteractionModelRigidBodySystem

Label = NodeType.Label

Molecule = NodeType.StructuralModelNodeMolecule

NodeGroup = NodeType.DataGraphNodeGroup

ParticleSystem = NodeType.DynamicalModelParticleSystem

Path = NodeType.StructuralModelPath

PropertyModel = NodeType.PropertyModel

PropertyModelFunction = NodeType.PropertyModelFunction

Protein = NodeType.StructuralModelNodeProtein

PseudoAtom = NodeType.StructuralModelNodePseudoAtom

Residue = NodeType.StructuralModelNodeResidue

RigidBody = NodeType.DynamicalModelNodeRigidBody

RigidBodySystem = NodeType.DynamicalModelRigidBodySystem

Root = NodeType.StructuralModelNodeRoot

Segment = NodeType.StructuralModelNodeSegment

SideChain = NodeType.StructuralModelNodeSideChain

Simulator = NodeType.Simulator

SimulatorArticulatedBodySystem = NodeType.SimulatorArticulatedBodySystem

SimulatorParticleSystem = NodeType.SimulatorParticleSystem

SimulatorRigidBodySystem = NodeType.SimulatorRigidBodySystem

StateUpdater = NodeType.StateUpdater

StateUpdaterArticulatedBodySystem = NodeType.StateUpdaterArticulatedBodySystem

StateUpdaterParticleSystem = NodeType.StateUpdaterParticleSystem

StateUpdaterRigidBodySystem = NodeType.StateUpdaterRigidBodySystem

StructuralGroup = NodeType.StructuralModelNodeGroup

StructuralModel = NodeType.StructuralModel

StructuralModelConformation = NodeType.StructuralModelConformation

StructuralModelNode = NodeType.StructuralModelNode

StructuralModelNodeAtom = NodeType.Atom

StructuralModelNodeBackbone = NodeType.StructuralModelNodeBackbone

StructuralModelNodeBond = NodeType.StructuralModelNodeBond

StructuralModelNodeChain = NodeType.StructuralModelNodeChain

StructuralModelNodeGroup = NodeType.StructuralModelNodeGroup

StructuralModelNodeMolecule = NodeType.StructuralModelNodeMolecule

StructuralModelNodeParticle = NodeType.StructuralModelNodeParticle

StructuralModelNodeProtein = NodeType.StructuralModelNodeProtein

StructuralModelNodePseudoAtom = NodeType.StructuralModelNodePseudoAtom

StructuralModelNodeResidue = NodeType.StructuralModelNodeResidue

StructuralModelNodeRoot = NodeType.StructuralModelNodeRoot

StructuralModelNodeSegment = NodeType.StructuralModelNodeSegment

StructuralModelNodeSideChain = NodeType.StructuralModelNodeSideChain

StructuralModelPath = NodeType.StructuralModelPath

StructuralParticle = NodeType.StructuralModelNodeParticle

Undefined = NodeType.Undefined

VisualModel = NodeType.VisualModel

activityFlag

The activity flag

highlightingFlag

isCreated

Returns true if and only if the node is created

isErased

Returns true if and only if the node is erased

isHighlighted

Returns whether the node is highlighted

isSelected

Returns whether the node is selected

isSerializable

Returns true when the class is serializable

isVisible

Returns whether the node is visible

name

The name of the simulator

nodeIndex

Returns the node index (unique in the whole data graph, but non-persistent)

selectionFlag

simulatorType

The type of the simulator

type

The type of the node

typeString

Returns a string describing the type of this data graph node

visibilityFlag