Path¶
This class describes a structural path, i.e. a trajectory of structural particles (smason.Modeling.StructuralModel.Particle
).
You can add, insert, and remove conformation and parts of a path from a path using samson.Modeling.StructuralModel.Path.add()
, samson.Modeling.StructuralModel.Path.insert()
, and samson.Modeling.StructuralModel.Path.remove()
functions respectively.
You can also add, insert, and remove structural particles from a conformation using samson.Modeling.StructuralModel.Path.addStructuralParticle()
, samson.Modeling.StructuralModel.Path.insertStructuralParticle()
, and samson.Modeling.StructuralModel.Path.removeStructuralParticle()
functions respectively.
You can also get and set position, velocity, and force data for all structural particles in a path or for a particular structural particle.
You can get a node indexer of structural particles in the conformation:
# get all paths in the active document
pathIndexer = SAMSON.getNodes('node.type path')
# get the first conformation
path = pathIndexer[0]
# get an indexer of structural particles in the path
structuralParticleIndexer = path.getStructuralParticleIndexer()
You can create a conformation from a path for a particular step:
# create a conformation from the first step in the path
conformationIndexer = path.createConformation(0)
conformation = conformationIndexer[0]
# name the conformation
conformation.name = "Initial state"
# turn the undo system on
SAMSON.beginHolding("Add new conformation")
# hold the cloned folder instance
SAMSON.hold(conformation)
# create the cloned folder
conformation.create()
# add the conformation to the active document
SAMSON.getActiveDocument().addChild(conformation)
# turn the undo system off
SAMSON.endHolding()
You can set the current step in a path:
# set the current step of the path to 10
path.currentStep = 10
You can go through a path to visualize it in SAMSON’s viewport as follows:
# set the step duration in seconds
path.stepDuration = Quantity.second(0.05)
# go through all the steps in the path
for step in range(path.numberOfSteps):
path.currentStep = step
# request SAMSON to process events
SAMSON.processEvents()
See also
SAMSON API: SBMStructuralModelPath
- class samson.Modeling.StructuralModel.Path(*args, **kwargs)¶
Bases:
samson.DataModel.DataGraph.Node
This class describes a structural path.
Overloaded function.
__init__(self: samson.Modeling.StructuralModel.Path) -> None
Constructs a structural model path
__init__(self: samson.Modeling.StructuralModel.Path, name: str, nodeIndexer: samson.DataModel.DataGraph.NodeIndexer) -> None
Constructs a structural model path with name from the nodes in nodeIndexer
- class AnimationType(self: samson.Modeling.StructuralModel.Path.AnimationType, value: int) None ¶
Bases:
pybind11_builtins.pybind11_object
Members:
Once
Loop
Bounce
- Bounce = <AnimationType.Bounce: 3>¶
- Loop = <AnimationType.Loop: 2>¶
- Once = <AnimationType.Once: 1>¶
- property name¶
- property value¶
- 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¶
- add(*args, **kwargs)¶
Overloaded function.
add(self: samson.Modeling.StructuralModel.Path, conformation: samson.Modeling.StructuralModel.Conformation) -> bool
Adds a frame to the path
add(self: samson.Modeling.StructuralModel.Path, path: samson.Modeling.StructuralModel.Path) -> bool
Adds frames to the path
add(self: samson.Modeling.StructuralModel.Path, positionData: List[samson.DataModel.Type.vector3], energy: samson.DataModel.Quantity.unitsSI = 0,000000 (dimensionless), time: samson.DataModel.Quantity.unitsSI = 0,000000 (dimensionless), velocityData: List[samson.DataModel.Type.vector3] = [], forceData: List[samson.DataModel.Type.vector3] = []) -> bool
Adds a frame to the path
add(self: samson.Modeling.StructuralModel.Path, positionData: List[List[samson.DataModel.Type.vector3]], energyData: List[samson.DataModel.Quantity.unitsSI] = [], timeData: List[samson.DataModel.Quantity.unitsSI] = [], velocityData: List[List[samson.DataModel.Type.vector3]] = [], forceData: List[List[samson.DataModel.Type.vector3]] = []) -> bool
Adds frames to the path
- addChild(self: samson.DataModel.DataGraph.Node, node: samson.DataModel.DataGraph.Node, nextNode: samson.DataModel.DataGraph.Node = None) bool ¶
Adds a child to the node
- addStructuralParticle(self: samson.Modeling.StructuralModel.Path, structuralParticle: SBMStructuralModelNodeParticle, structuralParticlePositionVector: List[samson.DataModel.Type.vector3] = [], structuralParticleVelocityVector: List[samson.DataModel.Type.vector3] = [], structuralParticleForceVector: List[samson.DataModel.Type.vector3] = []) bool ¶
Adds a structuralParticle to the path
- 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.DataModel.DataGraph.Node) samson.DataModel.DataGraph.Node ¶
Returns a copy of the node and its descendants
- copy(self: samson.Modeling.StructuralModel.Path, firstStep: int, lastStep: int) samson.Modeling.StructuralModel.Path ¶
Copies frames from the path to create a new path
- 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
- createConformation(self: samson.Modeling.StructuralModel.Path, step: int) samson.DataModel.DataGraph.NodeIndexer ¶
Create a conformation corresponding to a specific step
- createConformations(self: samson.Modeling.StructuralModel.Path) samson.DataModel.DataGraph.NodeIndexer ¶
Create conformations corresponding to all steps
- createStructuralModels(*args, **kwargs)¶
Overloaded function.
createStructuralModels(self: samson.Modeling.StructuralModel.Path, step: int) -> samson.DataModel.DataGraph.NodeIndexer
Create structural models corresponding to a specific step
createStructuralModels(self: samson.Modeling.StructuralModel.Path) -> samson.DataModel.DataGraph.NodeIndexer
Create structural models corresponding to all steps
- 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
- erase(self: samson.DataModel.DataGraph.Node) None ¶
Erases the node
- getDocument(self: samson.DataModel.DataGraph.Node) SBDDocument ¶
Returns the document the node belongs to
- getEnergy(self: samson.Modeling.StructuralModel.Path, step: int) samson.DataModel.Quantity.unitsSI ¶
Returnes the energy for a specific step
- getEnergyData(self: samson.Modeling.StructuralModel.Path) List[samson.DataModel.Quantity.unitsSI] ¶
Returnes the energy data
- getFlags(self: samson.DataModel.DataGraph.Node) int ¶
Returns the flags
- getForce(*args, **kwargs)¶
Overloaded function.
getForce(self: samson.Modeling.StructuralModel.Path, step: int, structuralParticleIndex: int) -> samson.DataModel.Type.vector3
Returnes the force of structural particle structuralParticleIndex for a specific step
getForce(self: samson.Modeling.StructuralModel.Path, step: int, structuralParticle: SBMStructuralModelNodeParticle) -> samson.DataModel.Type.vector3
Returnes the force of structural particle structuralParticle for a specific step
- getForceData(self: samson.Modeling.StructuralModel.Path) List[List[samson.DataModel.Type.vector3]] ¶
Returns the force array: 2D array, (number of timesteps) x (number of structural nodes)
- 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
- 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.
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
- getNextPath(self: samson.Modeling.StructuralModel.Path) samson.Modeling.StructuralModel.Path ¶
Returns the next path in the document
- 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
- getParent(self: samson.DataModel.DataGraph.Node) samson.DataModel.DataGraph.Node ¶
Returns the parent of the node
- getPosition(*args, **kwargs)¶
Overloaded function.
getPosition(self: samson.Modeling.StructuralModel.Path, step: int, structuralParticleIndex: int) -> samson.DataModel.Type.vector3
Returnes the position of structural particle structuralParticleIndex for a specific step
getPosition(self: samson.Modeling.StructuralModel.Path, step: int, structuralParticle: SBMStructuralModelNodeParticle) -> samson.DataModel.Type.vector3
Returnes the position of structural particle structuralParticle for a specific step
- getPositionData(self: samson.Modeling.StructuralModel.Path) List[List[samson.DataModel.Type.vector3]] ¶
Returns the position array: 2D array, (number of timesteps) x (number of structural nodes)
- 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
- getPreviousPath(self: samson.Modeling.StructuralModel.Path) samson.Modeling.StructuralModel.Path ¶
Returns the previous path in the document
- getRoot(self: samson.DataModel.DataGraph.Node) samson.DataModel.DataGraph.Node ¶
Returns the root of the hierarchy the node belongs to
- getStructuralParticleIndexer(self: samson.Modeling.StructuralModel.Path) samson.DataModel.DataGraph.NodeIndexer ¶
Returns the indexer of structural particles for which a position is saved
- getThisNode(self: samson.DataModel.DataGraph.Node) samson.DataModel.DataGraph.Node ¶
Returns the pointer to this node
- getTime(self: samson.Modeling.StructuralModel.Path, step: int) samson.DataModel.Quantity.unitsSI ¶
Returnes the time for a specific step
- getTimeData(self: samson.Modeling.StructuralModel.Path) List[samson.DataModel.Quantity.unitsSI] ¶
Returnes the time data
- static getTypeString(type: SBDDataGraphNode::Type) str ¶
Returns a string describing the type of the data graph node
- getVelocity(*args, **kwargs)¶
Overloaded function.
getVelocity(self: samson.Modeling.StructuralModel.Path, step: int, structuralParticleIndex: int) -> samson.DataModel.Type.vector3
Returnes the velocity of structural particle structuralParticleIndex for a specific step
getVelocity(self: samson.Modeling.StructuralModel.Path, step: int, structuralParticle: SBMStructuralModelNodeParticle) -> samson.DataModel.Type.vector3
Returnes the velocity of structural particle structuralParticle for a specific step
- getVelocityData(self: samson.Modeling.StructuralModel.Path) List[List[samson.DataModel.Type.vector3]] ¶
Returns the velocity array: 2D array, (number of timesteps) x (number of structural nodes)
- 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
- insert(*args, **kwargs)¶
Overloaded function.
insert(self: samson.Modeling.StructuralModel.Path, step: int, conformation: samson.Modeling.StructuralModel.Conformation) -> bool
Inserts a frame to the path at the step
insert(self: samson.Modeling.StructuralModel.Path, step: int, path: samson.Modeling.StructuralModel.Path) -> bool
Inserts frames to the path starting from the step
insert(self: samson.Modeling.StructuralModel.Path, step: int, positionData: List[samson.DataModel.Type.vector3], energy: samson.DataModel.Quantity.unitsSI = 0,000000 (dimensionless), time: samson.DataModel.Quantity.unitsSI = 0,000000 (dimensionless), velocityData: List[samson.DataModel.Type.vector3] = [], forceData: List[samson.DataModel.Type.vector3] = []) -> bool
Inserts a frame in the path at position step
insert(self: samson.Modeling.StructuralModel.Path, step: int, positionData: List[List[samson.DataModel.Type.vector3]], energyData: List[samson.DataModel.Quantity.unitsSI] = [], timeData: List[samson.DataModel.Quantity.unitsSI] = [], velocityData: List[List[samson.DataModel.Type.vector3]] = [], forceData: List[List[samson.DataModel.Type.vector3]] = []) -> bool
Inserts frames in the path at position step
- insertStructuralParticle(self: samson.Modeling.StructuralModel.Path, structuralParticleIndex: int, structuralParticle: SBMStructuralModelNodeParticle, structuralParticlePositionVector: List[samson.DataModel.Type.vector3] = [], structuralParticleVelocityVector: List[samson.DataModel.Type.vector3] = [], structuralParticleForceVector: List[samson.DataModel.Type.vector3] = []) bool ¶
Inserts a structuralParticle at index structuralParticleIndex to the path
- 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
- remove(*args, **kwargs)¶
Overloaded function.
remove(self: samson.Modeling.StructuralModel.Path, step: int) -> samson.Modeling.StructuralModel.Conformation
Remove a frame from the path to create a conformation
remove(self: samson.Modeling.StructuralModel.Path, firstStep: int, lastStep: int) -> samson.Modeling.StructuralModel.Path
Removes frames from the path to create a new path
- 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
- removeStructuralParticle(self: samson.Modeling.StructuralModel.Path, structuralParticle: SBMStructuralModelNodeParticle) bool ¶
Removes a structural particle from the path
- 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
- setEnergy(self: samson.Modeling.StructuralModel.Path, step: int, energy: samson.DataModel.Quantity.unitsSI) None ¶
Sets the energy for a specific step
- setEnergyData(self: samson.Modeling.StructuralModel.Path, energyData: List[samson.DataModel.Quantity.unitsSI]) None ¶
Sets the energy data
- setForce(*args, **kwargs)¶
Overloaded function.
setForce(self: samson.Modeling.StructuralModel.Path, step: int, structuralParticleIndex: int, force: samson.DataModel.Type.vector3) -> None
Sets the force of structural particle structuralParticleIndex to position for a specific step
setForce(self: samson.Modeling.StructuralModel.Path, step: int, structuralParticle: SBMStructuralModelNodeParticle, force: samson.DataModel.Type.vector3) -> None
Sets the force of structural particle structuralParticle to position for a specific step
- setForceData(self: samson.Modeling.StructuralModel.Path, forceData: List[List[samson.DataModel.Type.vector3]]) None ¶
Sets the force array: 2D array, (number of timesteps) x (number of structural nodes)
- setMaterial(self: samson.DataModel.DataGraph.Node, material: SBDDataGraphNodeMaterial) bool ¶
Sets the material for the node.
- Args:
material (Material): material to set
- setPosition(*args, **kwargs)¶
Overloaded function.
setPosition(self: samson.Modeling.StructuralModel.Path, step: int, structuralParticleIndex: int, position: samson.DataModel.Type.vector3) -> None
Sets the position of structural particle structuralParticleIndex to position for a specific step
setPosition(self: samson.Modeling.StructuralModel.Path, step: int, structuralParticle: SBMStructuralModelNodeParticle, position: samson.DataModel.Type.vector3) -> None
Sets the position of structural particle structuralParticle to position for a specific step
- setPositionData(self: samson.Modeling.StructuralModel.Path, positionData: List[List[samson.DataModel.Type.vector3]]) None ¶
Sets the position array: 2D array, (number of timesteps) x (number of structural nodes)
- setTime(self: samson.Modeling.StructuralModel.Path, step: int, time: samson.DataModel.Quantity.unitsSI) None ¶
Sets the time for a specific step
- setTimeData(self: samson.Modeling.StructuralModel.Path, timeData: List[samson.DataModel.Quantity.unitsSI]) None ¶
Sets the time data
- setVelocity(*args, **kwargs)¶
Overloaded function.
setVelocity(self: samson.Modeling.StructuralModel.Path, step: int, structuralParticleIndex: int, velocity: samson.DataModel.Type.vector3) -> None
Sets the velocity of structural particle structuralParticleIndex to position for a specific step
setVelocity(self: samson.Modeling.StructuralModel.Path, step: int, structuralParticle: SBMStructuralModelNodeParticle, velocity: samson.DataModel.Type.vector3) -> None
Sets the velocity of structural particle structuralParticle to position for a specific step
- setVelocityData(self: samson.Modeling.StructuralModel.Path, velocityData: List[List[samson.DataModel.Type.vector3]]) None ¶
Sets the velocity array: 2D array, (number of timesteps) x (number of structural nodes)
- toString(self: samson.Modeling.StructuralModel.Path) str ¶
A string representation
- updateState(self: samson.Modeling.StructuralModel.Path) None ¶
Updates the state along the path according to the animation parameters
- 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>¶
- Bounce = <AnimationType.Bounce: 3>¶
- 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>¶
- Loop = <AnimationType.Loop: 2>¶
- Mesh = <NodeType.Mesh: 300>¶
- Molecule = <NodeType.Molecule: 208>¶
- NodeGroup = <NodeType.DataGraphNodeGroup: 30>¶
- Note = <NodeType.Note: 25>¶
- Once = <AnimationType.Once: 1>¶
- 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 animationFlag¶
The animation flag
- property animationType¶
The animation type
- property currentEnergy¶
The current energy
- property currentStep¶
The current step along the path
- property currentTime¶
The current time
- property defaultOpacity¶
Returns the default opacity
- property defaultTransparency¶
Returns the default transparency
- property forwardFlag¶
The forward flag, which indicates when the animation is moving forward
- 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 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 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 numberOfSteps¶
The number of steps in the path
- property numberOfStructuralGroups¶
Returns the number of structural groups
- property numberOfStructuralModels¶
Returns the number of structural models
- property numberOfStructuralParticles¶
The number of structural particles for which a position is saved
- property numberOfSulfurs¶
Returns the number of sulfurs
- property opacity¶
Opacity
- property ownsMaterial¶
Returns whether the node owns a material
- property selectionFlag¶
Selection flag
- property smoothingWindowSize¶
The size of the smoothing window
- property stepDuration¶
The step duration
- property stride¶
The animation stride
- 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