ParticleSystem¶
This class describes a particle system in SAMSON, i.e. a dynamical system composed of particles. A particle system has two buffers - a position buffer and a momentum buffer - which may be used to write adaptive simulation algorithms.
You can get a number of changed momenums and a momentum of a particle in the particle system:
particleSystem.numberOfChangedMomentums
particleSystem.getMomentum(i)
# the same can be done for positions
particleSystem.numberOfChangedPositions
particleSystem.getPosition(i)
You can get the index of i-th changed momentum. Assume for example that particle 17, 32, and 529 have had their momentum changed since the last flush of the momentum buffer. Then the following code:
for i in range(particleSystem.numberOfChangedMomentums):
# changedMomentumIndex is the index of the i-th changed momentum
changedMomentumIndex = particleSystem.getChangedMomentumIndex(i)
print(changedMomentumIndex)
This will result in the following output:
17
32
529
You can use these indeces in adaptive simulation algorithms for example together with samson.Modeling.InteractionModel.ParticleSystem
.
See also
SAMSON API: SBMDynamicalModelParticleSystem
- class samson.Modeling.DynamicalModel.ParticleSystem(*args, **kwargs)¶
Bases:
samson.Modeling.DynamicalModel.DynamicalModel
This class describes a dynamical particle system.
Overloaded function.
__init__(self: samson.Modeling.DynamicalModel.ParticleSystem) -> None
Constructs a dynamical particle system
__init__(self: samson.Modeling.DynamicalModel.ParticleSystem, nodeIndexer: samson.DataModel.DataGraph.NodeIndexer) -> None
Constructs a dynamical particle system based in nodeIndexer
- class NodeType(self: samson.DataModel.DataGraph.Node.NodeType, value: int) None ¶
Bases:
pybind11_builtins.pybind11_object
Members:
Undefined
StructuralModel
StructuralModelNode
Conformation
StructuralModelConformation
Path
StructuralModelPath
StructuralGroup
StructuralModelNodeGroup
Root
StructuralModelNodeRoot
StructuralParticle
StructuralModelNodeParticle
Atom
StructuralModelNodeAtom
PseudoAtom
StructuralModelNodePseudoAtom
Bond
StructuralModelNodeBond
PseudoBond
StructuralModelNodePseudoBond
HydrogenBond
StructuralModelNodeHydrogenBond
HydrogenBondGroup
StructuralModelNodeHydrogenBondGroup
Residue
StructuralModelNodeResidue
Segment
StructuralModelNodeSegment
Protein
StructuralModelNodeProtein
Chain
StructuralModelNodeChain
Molecule
StructuralModelNodeMolecule
Backbone
StructuralModelNodeBackbone
SideChain
StructuralModelNodeSideChain
VisualModel
Mesh
VisualModelMesh
DynamicalModel
ParticleSystem
DynamicalModelParticleSystem
RigidBodySystem
DynamicalModelRigidBodySystem
ArticulatedBodySystem
DynamicalModelArticulatedBodySystem
DynamicalNode
DynamicalModelNode
DynamicalGroup
DynamicalModelNodeGroup
DynamicalRoot
DynamicalModelNodeRoot
DynamicalParticle
DynamicalModelNodeParticle
RigidBody
DynamicalModelNodeRigidBody
ArticulatedBody
DynamicalModelNodeArticulatedBody
InteractionModel
InteractionModelParticleSystem
InteractionModelRigidBodySystem
InteractionModelArticulatedBodySystem
PropertyModel
PropertyModelFunction
Simulator
SimulatorParticleSystem
SimulatorRigidBodySystem
SimulatorArticulatedBodySystem
StateUpdater
StateUpdaterParticleSystem
StateUpdaterRigidBodySystem
StateUpdaterArticulatedBodySystem
DocumentManager
Document
Folder
Camera
Label
Note
Animation
Presentation
DataGraphNodeGroup
NodeGroup
Controller
ControllerNode
Asset
- Animation = <NodeType.Animation: 26>¶
- ArticulatedBody = <NodeType.ArticulatedBody: 603>¶
- ArticulatedBodySystem = <NodeType.ArticulatedBodySystem: 502>¶
- Asset = <NodeType.Asset: 50>¶
- Atom = <NodeType.Atom: 20100>¶
- Backbone = <NodeType.Backbone: 209>¶
- Bond = <NodeType.Bond: 202>¶
- Camera = <NodeType.Camera: 23>¶
- Chain = <NodeType.Chain: 207>¶
- Conformation = <NodeType.Conformation: 28>¶
- Controller = <NodeType.Controller: 40>¶
- ControllerNode = <NodeType.ControllerNode: 41>¶
- DataGraphNodeGroup = <NodeType.DataGraphNodeGroup: 30>¶
- Document = <NodeType.Document: 21>¶
- DocumentManager = <NodeType.DocumentManager: 20>¶
- DynamicalGroup = <NodeType.DynamicalGroup: 600>¶
- DynamicalModel = <NodeType.DynamicalModel: 5>¶
- DynamicalModelArticulatedBodySystem = <NodeType.ArticulatedBodySystem: 502>¶
- DynamicalModelNode = <NodeType.DynamicalNode: 6>¶
- DynamicalModelNodeArticulatedBody = <NodeType.ArticulatedBody: 603>¶
- DynamicalModelNodeGroup = <NodeType.DynamicalGroup: 600>¶
- DynamicalModelNodeParticle = <NodeType.DynamicalParticle: 601>¶
- DynamicalModelNodeRigidBody = <NodeType.RigidBody: 602>¶
- DynamicalModelNodeRoot = <NodeType.DynamicalRoot: 60000>¶
- DynamicalModelParticleSystem = <NodeType.ParticleSystem: 500>¶
- DynamicalModelRigidBodySystem = <NodeType.RigidBodySystem: 501>¶
- DynamicalNode = <NodeType.DynamicalNode: 6>¶
- DynamicalParticle = <NodeType.DynamicalParticle: 601>¶
- DynamicalRoot = <NodeType.DynamicalRoot: 60000>¶
- Folder = <NodeType.Folder: 22>¶
- HydrogenBond = <NodeType.HydrogenBond: 20202>¶
- HydrogenBondGroup = <NodeType.HydrogenBondGroup: 20203>¶
- InteractionModel = <NodeType.InteractionModel: 7>¶
- InteractionModelArticulatedBodySystem = <NodeType.InteractionModelArticulatedBodySystem: 702>¶
- InteractionModelParticleSystem = <NodeType.InteractionModelParticleSystem: 700>¶
- InteractionModelRigidBodySystem = <NodeType.InteractionModelRigidBodySystem: 701>¶
- Label = <NodeType.Label: 24>¶
- Mesh = <NodeType.Mesh: 300>¶
- Molecule = <NodeType.Molecule: 208>¶
- NodeGroup = <NodeType.DataGraphNodeGroup: 30>¶
- Note = <NodeType.Note: 25>¶
- ParticleSystem = <NodeType.ParticleSystem: 500>¶
- Path = <NodeType.Path: 29>¶
- Presentation = <NodeType.Presentation: 27>¶
- PropertyModel = <NodeType.PropertyModel: 9>¶
- PropertyModelFunction = <NodeType.PropertyModelFunction: 900>¶
- Protein = <NodeType.Protein: 206>¶
- PseudoAtom = <NodeType.PseudoAtom: 20101>¶
- PseudoBond = <NodeType.PseudoBond: 20201>¶
- Residue = <NodeType.Residue: 204>¶
- RigidBody = <NodeType.RigidBody: 602>¶
- RigidBodySystem = <NodeType.RigidBodySystem: 501>¶
- Root = <NodeType.Root: 20000>¶
- Segment = <NodeType.Segment: 205>¶
- SideChain = <NodeType.SideChain: 210>¶
- Simulator = <NodeType.Simulator: 11>¶
- SimulatorArticulatedBodySystem = <NodeType.SimulatorArticulatedBodySystem: 1102>¶
- SimulatorParticleSystem = <NodeType.SimulatorParticleSystem: 1100>¶
- SimulatorRigidBodySystem = <NodeType.SimulatorRigidBodySystem: 1101>¶
- StateUpdater = <NodeType.StateUpdater: 15>¶
- StateUpdaterArticulatedBodySystem = <NodeType.StateUpdaterArticulatedBodySystem: 1503>¶
- StateUpdaterParticleSystem = <NodeType.StateUpdaterParticleSystem: 1501>¶
- StateUpdaterRigidBodySystem = <NodeType.StateUpdaterRigidBodySystem: 1502>¶
- StructuralGroup = <NodeType.StructuralGroup: 200>¶
- StructuralModel = <NodeType.StructuralModel: 1>¶
- StructuralModelConformation = <NodeType.Conformation: 28>¶
- StructuralModelNode = <NodeType.StructuralModelNode: 2>¶
- StructuralModelNodeAtom = <NodeType.Atom: 20100>¶
- StructuralModelNodeBackbone = <NodeType.Backbone: 209>¶
- StructuralModelNodeBond = <NodeType.Bond: 202>¶
- StructuralModelNodeChain = <NodeType.Chain: 207>¶
- StructuralModelNodeGroup = <NodeType.StructuralGroup: 200>¶
- StructuralModelNodeHydrogenBond = <NodeType.HydrogenBond: 20202>¶
- StructuralModelNodeHydrogenBondGroup = <NodeType.HydrogenBondGroup: 20203>¶
- StructuralModelNodeMolecule = <NodeType.Molecule: 208>¶
- StructuralModelNodeParticle = <NodeType.StructuralParticle: 201>¶
- StructuralModelNodeProtein = <NodeType.Protein: 206>¶
- StructuralModelNodePseudoAtom = <NodeType.PseudoAtom: 20101>¶
- StructuralModelNodePseudoBond = <NodeType.PseudoBond: 20201>¶
- StructuralModelNodeResidue = <NodeType.Residue: 204>¶
- StructuralModelNodeRoot = <NodeType.Root: 20000>¶
- StructuralModelNodeSegment = <NodeType.Segment: 205>¶
- StructuralModelNodeSideChain = <NodeType.SideChain: 210>¶
- StructuralModelPath = <NodeType.Path: 29>¶
- StructuralParticle = <NodeType.StructuralParticle: 201>¶
- Undefined = <NodeType.Undefined: 0>¶
- VisualModel = <NodeType.VisualModel: 3>¶
- VisualModelMesh = <NodeType.Mesh: 300>¶
- property name¶
- property value¶
- addChild(self: samson.DataModel.DataGraph.Node, node: samson.DataModel.DataGraph.Node, nextNode: samson.DataModel.DataGraph.Node = None) bool ¶
Adds a child to the node
- addParticle(self: samson.Modeling.DynamicalModel.ParticleSystem, particle: samson.Modeling.StructuralModel.Particle) int ¶
Adds a particle to the particle system
- 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
- canHaveDescendantType(self: samson.DataModel.DataGraph.Node, nodeType: SBDDataGraphNode::Type) bool ¶
Returns whether this node can have a node with type nodeType as a descendant
- 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
- castToMesh(self: samson.DataModel.DataGraph.Node) SBMVisualModelMesh ¶
Casts (if possible) from SBDDataGraphNode to SBMVisualModelMesh
- castToVisualModel(self: samson.DataModel.DataGraph.Node) SBMVisualModel ¶
Casts (if possible) from SBDDataGraphNode to SBMVisualModel
- clone(self: samson.Modeling.DynamicalModel.DynamicalModel) samson.Modeling.DynamicalModel.DynamicalModel ¶
Returns a copy of the node and its descendants
- correctDistanceWithPBC(self: samson.Modeling.DynamicalModel.ParticleSystem, distance: samson.DataModel.Type.vector3) None ¶
- countNodes(*args, **kwargs)¶
Overloaded function.
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
countNodes(self: samson.DataModel.DataGraph.Node, nodeType: SBDDataGraphNode::Type, selectedNodesOnly: bool = False, visitString: str = ‘*’, includeDependencies: bool = False) -> int
- Count nodes into nodeIndexer, based on a nodeType, a selection status and a visitPredicate, with our without dependencies).
For visitString use Node Specification Language (SAMSON API: Node Specification Language
- create(self: samson.DataModel.DataGraph.Node) None ¶
Creates the node
- descendsFrom(*args, **kwargs)¶
Overloaded function.
descendsFrom(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
descendsFrom(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
- enforcePeriodicBoundaryConditions(self: samson.Modeling.DynamicalModel.DynamicalModel) bool ¶
Enforces the periodic boundary conditions
- erase(self: samson.DataModel.DataGraph.Node) None ¶
Erases the node
- flushMomentumBuffer(self: samson.Modeling.DynamicalModel.ParticleSystem) None ¶
Flushes the momentum buffer
- flushPositionBuffer(self: samson.Modeling.DynamicalModel.DynamicalModel) None ¶
Flushes the position buffer
- getActivityFlag(*args, **kwargs)¶
Overloaded function.
getActivityFlag(self: samson.Modeling.DynamicalModel.ParticleSystem, particle: samson.Modeling.StructuralModel.Particle) -> bool
returns activity flag of a particle
getActivityFlag(self: samson.Modeling.DynamicalModel.ParticleSystem, particleIndex: int) -> bool
returns activity flag of a particle
- getChangedMomentumIndex(self: samson.Modeling.DynamicalModel.ParticleSystem, i: int) int ¶
Returns the index of a changed momentum
- getChangedPositionIndex(self: samson.Modeling.DynamicalModel.DynamicalModel, i: int) int ¶
Returns the index of a changed position
- getDocument(self: samson.DataModel.DataGraph.Node) SBDDocument ¶
Returns the document the node belongs to
- getDynamicalRoot(self: samson.Modeling.DynamicalModel.DynamicalModel) SBMDynamicalModelNodeRoot ¶
Returns the root of the dynamical model
- getFlags(self: samson.DataModel.DataGraph.Node) int ¶
Returns the flags
- getHierarchyString(self: samson.DataModel.DataGraph.Node, separator: str = ' / ', includeNodeType: bool = False) str ¶
Returns a string with hierarchical information on the node and its parents names
- getInheritedFlags(self: samson.DataModel.DataGraph.Node) int ¶
Returns the inherited flags
- getInverseMass(*args, **kwargs)¶
Overloaded function.
getInverseMass(self: samson.Modeling.DynamicalModel.ParticleSystem, particle: samson.Modeling.StructuralModel.Particle) -> samson.DataModel.Quantity.unitsSI
returns inverse mass of a particle
getInverseMass(self: samson.Modeling.DynamicalModel.ParticleSystem, particleIndex: int) -> samson.DataModel.Quantity.unitsSI
returns inverse mass of a particle
- getMass(*args, **kwargs)¶
Overloaded function.
getMass(self: samson.Modeling.DynamicalModel.ParticleSystem, particle: samson.Modeling.StructuralModel.Particle) -> samson.DataModel.Quantity.unitsSI
returns mass of a particle
getMass(self: samson.Modeling.DynamicalModel.ParticleSystem, particleIndex: int) -> samson.DataModel.Quantity.unitsSI
returns mass of a particle
- 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
- getMomentum(self: samson.Modeling.DynamicalModel.ParticleSystem, i: int) samson.DataModel.Type.vector3 ¶
Returns the momentum of a particle
- getNextModel(self: samson.Modeling.Model.Model) samson.Modeling.Model.Model ¶
Returns the next model in the parent
- getNextNode(*args, **kwargs)¶
Overloaded function.
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
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
- getNode(self: int) samson.DataModel.DataGraph.Node ¶
Returns the unique node corresponding to the node index nodeIndex
- getNodes(*args, **kwargs)¶
Overloaded function.
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
getNodes(self: samson.DataModel.DataGraph.Node, nodeType: SBDDataGraphNode::Type, selectedNodesOnly: bool = False, visitString: str = ‘*’, includeDependencies: bool = False) -> SBDDataGraphNodeIndexer
- Returns nodes (in a node indexer), based on a nodeType, a selection status and a visitString, with our without dependencies).
For visitString use Node Specification Language (SAMSON API: Node Specification Language
- getNumberOfChangedPositions(self: samson.Modeling.DynamicalModel.DynamicalModel) int ¶
Returns the number of changed positions
- getParent(self: samson.DataModel.DataGraph.Node) samson.DataModel.DataGraph.Node ¶
Returns the parent of the node
- getPeriodicBoundaryConditions(self: samson.Modeling.DynamicalModel.DynamicalModel) samson.DataModel.Type.intervalVector3 ¶
Returns the periodic boundary conditions
- getPosition(self: samson.Modeling.DynamicalModel.ParticleSystem, i: int) samson.DataModel.Type.vector3 ¶
Returns the position of a particle
- getPositionChanged(self: samson.Modeling.DynamicalModel.ParticleSystem, i: int) bool ¶
Returns whether momentum i has been changed since the last flush
- getPreviousModel(self: samson.Modeling.Model.Model) samson.Modeling.Model.Model ¶
Returns the previous model in the parent
- getPreviousNode(*args, **kwargs)¶
Overloaded function.
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
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
- getRoot(self: samson.DataModel.DataGraph.Node) samson.DataModel.DataGraph.Node ¶
Returns the root of the hierarchy the node belongs to
- getStructuralParticleIndexer(self: samson.Modeling.DynamicalModel.ParticleSystem) samson.DataModel.DataGraph.NodeIndexer ¶
Returns the particle index of the particle system
- getThisNode(self: samson.DataModel.DataGraph.Node) samson.DataModel.DataGraph.Node ¶
Returns the pointer to this node
- static 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.
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, or belongs to a group stored in node
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, or belongs to a group stored in one of the nodes of the nodeIndexer
- isInteractionModel(self: samson.DataModel.DataGraph.Node) bool ¶
Returns true when the node is a interaction model
- isMesh(self: samson.DataModel.DataGraph.Node) bool ¶
Returns true when the node is a mesh
- 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.DataModel.DataGraph.Node, 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
- removeParticle(*args, **kwargs)¶
Overloaded function.
removeParticle(self: samson.Modeling.DynamicalModel.ParticleSystem, particle: samson.Modeling.StructuralModel.Particle) -> None
Removes a particle from the particle system
removeParticle(self: samson.Modeling.DynamicalModel.ParticleSystem, particleIndex: int) -> None
Removes a particle from the particle system
- removeParticles(self: samson.Modeling.DynamicalModel.ParticleSystem, nodeIndexer: samson.DataModel.DataGraph.NodeIndexer) None ¶
Removes particles from a node indexer
- roundForPBC(self: samson.Modeling.DynamicalModel.ParticleSystem, length: samson.DataModel.Quantity.unitsSI) int ¶
- setActivityFlag(*args, **kwargs)¶
Overloaded function.
setActivityFlag(self: samson.Modeling.DynamicalModel.ParticleSystem, particle: samson.Modeling.StructuralModel.Particle, flag: bool) -> None
sets activity flag of a particle
setActivityFlag(self: samson.Modeling.DynamicalModel.ParticleSystem, particleIndex: int, flag: bool) -> None
sets activity flag of a particle
- setColor(self: samson.DataModel.DataGraph.Node, color: SBDTypeColor) 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
- setMass(*args, **kwargs)¶
Overloaded function.
setMass(self: samson.Modeling.DynamicalModel.ParticleSystem, particle: samson.Modeling.StructuralModel.Particle, flag: samson.DataModel.Quantity.unitsSI) -> None
sets mass of a particle
setMass(self: samson.Modeling.DynamicalModel.ParticleSystem, particleIndex: int, flag: samson.DataModel.Quantity.unitsSI) -> None
sets mass of a particle
- setMaterial(self: samson.DataModel.DataGraph.Node, material: SBDDataGraphNodeMaterial) bool ¶
Sets the material for the node.
- Args:
material (Material): material to set
- setMomentum(self: samson.Modeling.DynamicalModel.ParticleSystem, i: int, newMomentum: samson.DataModel.Type.vector3) None ¶
Updates the momentum of a particle
- setPeriodicBoundaryConditions(self: samson.Modeling.DynamicalModel.DynamicalModel, v: samson.DataModel.Type.intervalVector3) None ¶
Sets the periodic boundary conditions
- setPosition(self: samson.Modeling.DynamicalModel.ParticleSystem, i: int, newPosition: samson.DataModel.Type.vector3) None ¶
Updates the position of a particle
- toString(self: samson.Modeling.DynamicalModel.ParticleSystem) str ¶
A string representation
- updateStructuralNodes(self: samson.Modeling.DynamicalModel.DynamicalModel) None ¶
Updates structural nodes based on the state of the dynamical model
- Animation = <NodeType.Animation: 26>¶
- ArticulatedBody = <NodeType.ArticulatedBody: 603>¶
- ArticulatedBodySystem = <NodeType.ArticulatedBodySystem: 502>¶
- Asset = <NodeType.Asset: 50>¶
- Atom = <NodeType.Atom: 20100>¶
- Backbone = <NodeType.Backbone: 209>¶
- Bond = <NodeType.Bond: 202>¶
- Camera = <NodeType.Camera: 23>¶
- Chain = <NodeType.Chain: 207>¶
- Conformation = <NodeType.Conformation: 28>¶
- Controller = <NodeType.Controller: 40>¶
- ControllerNode = <NodeType.ControllerNode: 41>¶
- DataGraphNodeGroup = <NodeType.DataGraphNodeGroup: 30>¶
- Document = <NodeType.Document: 21>¶
- DocumentManager = <NodeType.DocumentManager: 20>¶
- DynamicalGroup = <NodeType.DynamicalGroup: 600>¶
- DynamicalModel = <NodeType.DynamicalModel: 5>¶
- DynamicalModelArticulatedBodySystem = <NodeType.ArticulatedBodySystem: 502>¶
- DynamicalModelNode = <NodeType.DynamicalNode: 6>¶
- DynamicalModelNodeArticulatedBody = <NodeType.ArticulatedBody: 603>¶
- DynamicalModelNodeGroup = <NodeType.DynamicalGroup: 600>¶
- DynamicalModelNodeParticle = <NodeType.DynamicalParticle: 601>¶
- DynamicalModelNodeRigidBody = <NodeType.RigidBody: 602>¶
- DynamicalModelNodeRoot = <NodeType.DynamicalRoot: 60000>¶
- DynamicalModelParticleSystem = <NodeType.ParticleSystem: 500>¶
- DynamicalModelRigidBodySystem = <NodeType.RigidBodySystem: 501>¶
- DynamicalNode = <NodeType.DynamicalNode: 6>¶
- DynamicalParticle = <NodeType.DynamicalParticle: 601>¶
- DynamicalRoot = <NodeType.DynamicalRoot: 60000>¶
- Folder = <NodeType.Folder: 22>¶
- HydrogenBond = <NodeType.HydrogenBond: 20202>¶
- HydrogenBondGroup = <NodeType.HydrogenBondGroup: 20203>¶
- InteractionModel = <NodeType.InteractionModel: 7>¶
- InteractionModelArticulatedBodySystem = <NodeType.InteractionModelArticulatedBodySystem: 702>¶
- InteractionModelParticleSystem = <NodeType.InteractionModelParticleSystem: 700>¶
- InteractionModelRigidBodySystem = <NodeType.InteractionModelRigidBodySystem: 701>¶
- Label = <NodeType.Label: 24>¶
- Mesh = <NodeType.Mesh: 300>¶
- Molecule = <NodeType.Molecule: 208>¶
- NodeGroup = <NodeType.DataGraphNodeGroup: 30>¶
- Note = <NodeType.Note: 25>¶
- ParticleSystem = <NodeType.ParticleSystem: 500>¶
- Path = <NodeType.Path: 29>¶
- Presentation = <NodeType.Presentation: 27>¶
- PropertyModel = <NodeType.PropertyModel: 9>¶
- PropertyModelFunction = <NodeType.PropertyModelFunction: 900>¶
- Protein = <NodeType.Protein: 206>¶
- PseudoAtom = <NodeType.PseudoAtom: 20101>¶
- PseudoBond = <NodeType.PseudoBond: 20201>¶
- Residue = <NodeType.Residue: 204>¶
- RigidBody = <NodeType.RigidBody: 602>¶
- RigidBodySystem = <NodeType.RigidBodySystem: 501>¶
- Root = <NodeType.Root: 20000>¶
- Segment = <NodeType.Segment: 205>¶
- SideChain = <NodeType.SideChain: 210>¶
- Simulator = <NodeType.Simulator: 11>¶
- SimulatorArticulatedBodySystem = <NodeType.SimulatorArticulatedBodySystem: 1102>¶
- SimulatorParticleSystem = <NodeType.SimulatorParticleSystem: 1100>¶
- SimulatorRigidBodySystem = <NodeType.SimulatorRigidBodySystem: 1101>¶
- StateUpdater = <NodeType.StateUpdater: 15>¶
- StateUpdaterArticulatedBodySystem = <NodeType.StateUpdaterArticulatedBodySystem: 1503>¶
- StateUpdaterParticleSystem = <NodeType.StateUpdaterParticleSystem: 1501>¶
- StateUpdaterRigidBodySystem = <NodeType.StateUpdaterRigidBodySystem: 1502>¶
- StructuralGroup = <NodeType.StructuralGroup: 200>¶
- StructuralModel = <NodeType.StructuralModel: 1>¶
- StructuralModelConformation = <NodeType.Conformation: 28>¶
- StructuralModelNode = <NodeType.StructuralModelNode: 2>¶
- StructuralModelNodeAtom = <NodeType.Atom: 20100>¶
- StructuralModelNodeBackbone = <NodeType.Backbone: 209>¶
- StructuralModelNodeBond = <NodeType.Bond: 202>¶
- StructuralModelNodeChain = <NodeType.Chain: 207>¶
- StructuralModelNodeGroup = <NodeType.StructuralGroup: 200>¶
- StructuralModelNodeHydrogenBond = <NodeType.HydrogenBond: 20202>¶
- StructuralModelNodeHydrogenBondGroup = <NodeType.HydrogenBondGroup: 20203>¶
- StructuralModelNodeMolecule = <NodeType.Molecule: 208>¶
- StructuralModelNodeParticle = <NodeType.StructuralParticle: 201>¶
- StructuralModelNodeProtein = <NodeType.Protein: 206>¶
- StructuralModelNodePseudoAtom = <NodeType.PseudoAtom: 20101>¶
- StructuralModelNodePseudoBond = <NodeType.PseudoBond: 20201>¶
- StructuralModelNodeResidue = <NodeType.Residue: 204>¶
- StructuralModelNodeRoot = <NodeType.Root: 20000>¶
- StructuralModelNodeSegment = <NodeType.Segment: 205>¶
- StructuralModelNodeSideChain = <NodeType.SideChain: 210>¶
- StructuralModelPath = <NodeType.Path: 29>¶
- StructuralParticle = <NodeType.StructuralParticle: 201>¶
- Undefined = <NodeType.Undefined: 0>¶
- VisualModel = <NodeType.VisualModel: 3>¶
- VisualModelMesh = <NodeType.Mesh: 300>¶
- property defaultOpacity¶
Returns the default opacity
- property defaultTransparency¶
Returns the default transparency
- property dynamicalModelType¶
The dynamical model type
- property hasMaterial¶
Returns whether the node has a material (by itself, or inherited)
- property hasOpacityRange¶
Returns whether the node has opacity range
- property hasTransparencyRange¶
Returns whether the node has transparency range
- property highlightingFlag¶
Highlighting flag
- property isCreated¶
Returns true if and only if the node is created
- property isErased¶
Returns true if and only if the node is erased
- property isHighlighted¶
Returns whether the node is highlighted
- property isLocked¶
Returns whether the node is locked
- property isSelected¶
Returns whether the node is selected
- property isSerializable¶
Returns true when the class is serializable
- property isVisible¶
Returns whether the node is visible
- property lockedFlag¶
Locked flag
- property maximumOpacity¶
Returns the maximum opacity
- property maximumTransparency¶
Returns the maximum transparency
- property minimumOpacity¶
Returns the minimum opacity
- property minimumTransparency¶
Returns the minimum transparency
- property modelType¶
The model type
- property molecularWeight¶
Returns the molecular weight
- property name¶
The name of the node
- property nodeIndex¶
Returns the node index (unique in the whole data graph, but non-persistent)
- property numberOfAtoms¶
Returns the number of atoms
- property numberOfCarbons¶
Returns the number of carbons
- property numberOfChains¶
Returns the number of chains
- property numberOfChangedMomentums¶
Returns the number of changed momentum
- property numberOfHydrogens¶
Returns the number of hydrogens
- property numberOfMolecules¶
Returns the number of molecules
- property numberOfNitrogens¶
Returns the number of nitrogens
- property numberOfOtherAtoms¶
Returns the number of other atoms
- property numberOfOxygens¶
Returns the number of oxygens
- property numberOfResidues¶
Returns the number of residues
- property numberOfSegments¶
Returns the number of segments
- property numberOfStructuralGroups¶
Returns the number of structural groups
- property numberOfStructuralModels¶
Returns the number of structural models
- property numberOfSulfurs¶
Returns the number of sulfurs
- property opacity¶
Opacity
- property ownsMaterial¶
Returns whether the node owns a material
- property periodicBoundaryConditionsFlag¶
periodic boundary conditions flag
- property selectionFlag¶
Selection flag
- property sumOfFormalCharges¶
Returns the sum of formal charges
- property sumOfPartialCharges¶
Returns the sum of partial charges
- property transparency¶
Transparency
- property type¶
Returns the type of the data graph node
- property typeString¶
Returns a string describing the type of this data graph node
- property visibilityFlag¶
Visibility flag