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.

  1. __init__(self: samson.Modeling.StructuralModel.Path) -> None

Constructs a structural model path

  1. __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.

  1. add(self: samson.Modeling.StructuralModel.Path, conformation: samson.Modeling.StructuralModel.Conformation) -> bool

Adds a frame to the path

  1. add(self: samson.Modeling.StructuralModel.Path, path: samson.Modeling.StructuralModel.Path) -> bool

Adds frames to the path

  1. 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

  1. 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.

  1. 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

  1. 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.

  1. createStructuralModels(self: samson.Modeling.StructuralModel.Path, step: int) -> samson.DataModel.DataGraph.NodeIndexer

Create structural models corresponding to a specific step

  1. createStructuralModels(self: samson.Modeling.StructuralModel.Path) -> samson.DataModel.DataGraph.NodeIndexer

Create structural models corresponding to all steps

descendsFrom(*args, **kwargs)

Overloaded function.

  1. 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

  1. 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.

  1. 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

  1. 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.

  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

  1. 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.

  1. 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

  1. 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.

  1. 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

  1. 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.

  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

  1. 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.

  1. 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

  1. 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.

  1. insert(self: samson.Modeling.StructuralModel.Path, step: int, conformation: samson.Modeling.StructuralModel.Conformation) -> bool

Inserts a frame to the path at the step

  1. insert(self: samson.Modeling.StructuralModel.Path, step: int, path: samson.Modeling.StructuralModel.Path) -> bool

Inserts frames to the path starting from the step

  1. 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

  1. 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.

  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, or belongs to a group stored in node

  1. 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.

  1. remove(self: samson.Modeling.StructuralModel.Path, step: int) -> samson.Modeling.StructuralModel.Conformation

Remove a frame from the path to create a conformation

  1. 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.

  1. 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

  1. 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.

  1. 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

  1. 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.

  1. 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

  1. 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