StructuralModel

See also

SAMSON API: SBMStructuralModel

class samson.Modeling.StructuralModel.StructuralModel(self: samson.Modeling.StructuralModel.StructuralModel) → None

Bases: samson.Modeling.Model.Model

This class describes a structural model.

Constructs a structural model

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

static bondExists(atom1: SBMStructuralModelNodeAtom, atom2: SBMStructuralModelNodeAtom) → bool

Checks whether the bond between atoms atom1 and atom2 exists

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

centerTransform(self: samson.Modeling.StructuralModel.StructuralModel) → None

Centers the pivot of the transform on the center of mass of the particles contained in the structural model

clearConnectivityAnnotationInformation(self: samson.Modeling.StructuralModel.StructuralModel) → None

Clears the model’s connectivity annotation information

clearCrystallographicAndTransformationInformation(self: samson.Modeling.StructuralModel.StructuralModel) → None

Clears the model’s transformation information

clearHeterogenInformation(self: samson.Modeling.StructuralModel.StructuralModel) → None

Clears the model’s heterogen information

clearMiscellaneousInformation(self: samson.Modeling.StructuralModel.StructuralModel) → None

Clears the model’s miscellaneous information

clearPrimaryStructureInformation(self: samson.Modeling.StructuralModel.StructuralModel) → None

Clears the model’s primary structure information

clearSecondaryStructureInformation(self: samson.Modeling.StructuralModel.StructuralModel) → None

Clears the model’s secondary structure information

clearTitleInformation(self: samson.Modeling.StructuralModel.StructuralModel) → None

Clears the model’s title information

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

Returns a copy of the node and its descendants

static computeDomain(nodeIndexer: samson.DataModel.DataGraph.NodeIndexer) → samson.DataModel.Type.spatialDomain

Computes the domain containing the atoms and bond atoms in the node indexer

computeSecondaryStructure(self: samson.Modeling.StructuralModel.StructuralModel, forceUpdate: bool = False) → List[bool]

Computes the secondary structure for all residues in the structural model. Returns a list: 1st element - true if everything went well; 2nd element - true if and only if the secondary structure was changed compared to the previous call.

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

static createBond(atom1: SBMStructuralModelNodeAtom, atom2: SBMStructuralModelNodeAtom, bondOrder: float, bondType: SBMStructuralModelNodeBond::BondType) → bool

Creates a bond between atom1 and atom2 if there is none; sets the bond order to bondOrder and the bond type to bondType

createCovalentBonds(self: samson.Modeling.StructuralModel.StructuralModel) → None

Builds covalent bonds for the atoms belonging to the structural model according to the inter-atomic distances

createCovalentBondsByResidueType(*args, **kwargs)

Overloaded function.

  1. createCovalentBondsByResidueType(self: samson.Modeling.StructuralModel.StructuralModel) -> int

Builds covalent bonds for the atoms belonging to the structural model according to the residue types, regardless of inter-atomic distances. If the bonds are already present, it sets the order of covalent bonds for the atoms belonging to the structural model according to the residue types.

  1. createCovalentBondsByResidueType(self: samson.Modeling.StructuralModel.StructuralModel, residueIndexer: samson.DataModel.DataGraph.NodeIndexer) -> int

Builds covalent bonds for the atoms belonging to the given residues of the structural model according to the residue types, regardless of inter-atomic distances. If the bonds are already present, it sets the order of covalent bonds for the atoms belonging to the structural model according to the residue types.

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

static findAtom(*args, **kwargs)

Overloaded function.

  1. findAtom(nodeIndexer: samson.DataModel.DataGraph.NodeIndexer, elementType: samson.Modeling.Element.Element.ElementType, name: str) -> SBMStructuralModelNodeAtom

Returns, if found, an atom from a node indexer nodeIndexer with the element type elementType and name name; else returns null.

  1. findAtom(nodeIndexer: samson.DataModel.DataGraph.NodeIndexer, elementType: samson.Modeling.Element.Element.ElementType, name: str, altLoc: str) -> SBMStructuralModelNodeAtom

Returns, if found, an atom from a node indexer nodeIndexer with the element type elementType and name name, and an alternate location altLoc (if the atom has an alternate location); else returns null.

static getAsphericity(nodeIndexer: samson.DataModel.DataGraph.NodeIndexer) → float

Returns true if all atoms in nodeIndexer are in the same plane

static getCenterOfMass(nodeIndexer: samson.DataModel.DataGraph.NodeIndexer) → samson.DataModel.Type.vector3

Returns the center of mass of atoms in the nodeIndexer

static getCentroid(nodeIndexer: samson.DataModel.DataGraph.NodeIndexer) → samson.DataModel.Type.vector3

Returns the centroid (the geometric center) of atoms in the nodeIndexer

getChildren(self: samson.Modeling.StructuralModel.StructuralModel) → samson.DataModel.DataGraph.NodeIndexer

Returns the children of the structural model

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

Returns the document the node belongs to

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

static getInertiaTensor(nodeIndexer: samson.DataModel.DataGraph.NodeIndexer) → samson.DataModel.Type.matrix33

Returns the inertia tensor of the system of atoms (based on their positions and masses) in the nodeIndexer

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

static getMolecularWeightForNodeIndexer(nodeIndexer: samson.DataModel.DataGraph.NodeIndexer) → samson.DataModel.Quantity.unitsSI

Returns the cumulative molecular weight of atoms in the nodeIndexer

getNextModel(self: samson.Modeling.Model.Model) → samson.Modeling.Model.Model

Returns the next model in the parent

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

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

getOrientation(self: samson.Modeling.StructuralModel.StructuralModel) → samson.DataModel.Type.matrix33

Returns the orientation of the structural model

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

Returns the parent of the node

getPosition(self: samson.Modeling.StructuralModel.StructuralModel) → samson.DataModel.Type.vector3

Returns the position of the structural model

getPreviousModel(self: samson.Modeling.Model.Model) → samson.Modeling.Model.Model

Returns the previous model in the parent

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

static getPrincipalAxes(nodeIndexer: samson.DataModel.DataGraph.NodeIndexer) → samson.DataModel.Type.matrix33

Returns the principal axes of the inertia tensor of the system of atoms (based on their positions and masses) in the nodeIndexer

static getRadiusOfGyration(nodeIndexer: samson.DataModel.DataGraph.NodeIndexer) → samson.DataModel.Quantity.unitsSI

Returns the radius of gyration based on atoms in the nodeIndexer

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

Returns the root of the hierarchy the node belongs to

static getShapeParameter(nodeIndexer: samson.DataModel.DataGraph.NodeIndexer) → float

Returns the shape parameter of the system of atoms (based on their positions and masses) in nodeIndexer. The shape parameter, S, changes in the [-0.25, 2] interval, where 0 corresponds to a sphere, negative values correspond to oblate ellipsoid, possitive values correspond to prolate ellipsoid.

static getSolventAccessibleSurfaceArea(nodeIndexer: samson.DataModel.DataGraph.NodeIndexer, probeRadius: samson.DataModel.Quantity.unitsSI, numberOfPointsOnSphere: int) → samson.DataModel.Quantity.unitsSI

Returns the solvent-accessible surface area (SASA) based on atoms in nodeIndexer with the probe radius probeRadius, and the number of points on a sphere numberOfPointsOnSphere

static getSpatialTransform(nodeIndexer: samson.DataModel.DataGraph.NodeIndexer) → samson.DataModel.Type.spatialTransform

Returns the spatial transform based on the inertia tensor of the system of atoms (based on their positions and masses) in the nodeIndexer

getStructuralRoot(self: samson.Modeling.StructuralModel.StructuralModel) → SBMStructuralModelNodeRoot

Returns the root

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

Returns the pointer to this node

getTransform(self: samson.Modeling.StructuralModel.StructuralModel) → samson.DataModel.Type.spatialTransform

Returns the spatial transform of the structural model

static getTypeString(type: SBDDataGraphNode::Type) → str

Returns a string describing the type of the data graph node

getWater(self: samson.Modeling.StructuralModel.StructuralModel) → samson.DataModel.DataGraph.NodeIndexer

Finds water nodes in the structural model

static getWaterFromNodeIndexer(nodeIndexer: samson.DataModel.DataGraph.NodeIndexer) → samson.DataModel.DataGraph.NodeIndexer

Finds water nodes in the nodeIndexer

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

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

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

Returns true when the node is a dynamical model

isIn(*args, **kwargs)

Overloaded function.

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

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

static isPlanar(nodeIndexer: samson.DataModel.DataGraph.NodeIndexer) → bool

Returns true if all atoms in nodeIndexer are in the same plane

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

populateChainIDs(self: samson.Modeling.StructuralModel.StructuralModel, forceRenumbering: bool = False) → bool

Populates the chain IDs for all chains in the structural 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

static replaceAtom(oldAtom: SBMStructuralModelNodeAtom, newAtom: SBMStructuralModelNodeAtom, preserveOldAtomPosition: bool = False) → None

Replaces atom oldAtom with atom newAtom. All bonds from the old atom are transferred to the new atom

static replaceBond(oldBond: SBMStructuralModelNodeBond, newBond: SBMStructuralModelNodeBond, flipBond: bool = False, preserveOldBondPosition: bool = False) → None

Replaces bond oldBond with bond newBond. All neighboring bonds from the old bond are transferred to the new bond

rotate(self: samson.Modeling.StructuralModel.StructuralModel, axis: samson.DataModel.Type.vector3, angle: samson.DataModel.Quantity.unitsSI) → None

Rotates the structural model

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

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

Sets the material for the node.

Args:

material (Material): material to set

setOrientation(*args, **kwargs)

Overloaded function.

  1. setOrientation(self: samson.Modeling.StructuralModel.StructuralModel, orientation: samson.DataModel.Type.matrix33) -> None

Sets the orientation of the structural model

  1. setOrientation(self: samson.Modeling.StructuralModel.StructuralModel, orientation: samson.DataModel.Type.matrix33, transformParticles: bool) -> None

Sets the orientation of the structural model

setPosition(*args, **kwargs)

Overloaded function.

  1. setPosition(self: samson.Modeling.StructuralModel.StructuralModel, position: samson.DataModel.Type.vector3) -> None

Sets the position of the structural model

  1. setPosition(self: samson.Modeling.StructuralModel.StructuralModel, position: samson.DataModel.Type.vector3, transformParticles: bool) -> None

Sets the position of the structural model

setTransform(*args, **kwargs)

Overloaded function.

  1. setTransform(self: samson.Modeling.StructuralModel.StructuralModel, transform: samson.DataModel.Type.spatialTransform) -> None

Sets the spatial transform of the structural model

  1. setTransform(self: samson.Modeling.StructuralModel.StructuralModel, transform: samson.DataModel.Type.spatialTransform, transformParticles: bool) -> None

Sets the spatial transform of the structural model

toString(self: samson.Modeling.StructuralModel.StructuralModel) → str

A string representation

transform(self: samson.Modeling.StructuralModel.StructuralModel, transform: samson.DataModel.Type.spatialTransform) → None

Applies a spatial transform to the structural model

translate(self: samson.Modeling.StructuralModel.StructuralModel, translation: samson.DataModel.Type.vector3) → None

Translates the structural 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 connectivityAnnotationInformation

model’s connectivity annotation information

property crystallographicAndTransformationInformation

model’s transformation information

property defaultOpacity

Returns the default opacity

property defaultTransparency

Returns the default transparency

property hasConnectivityAnnotationInformation

Returns true when the model’s connectivity annotation information is set

property hasCrystallographicAndTransformationInformation

Returns true when the model’s transformation information is set

property hasHeterogenInformation

Returns true when the model’s heterogen information is set

property hasMaterial

Returns whether the node has a material (by itself, or inherited)

property hasMiscellaneousInformation

Returns true when the model’s miscellaneous information is set

property hasOpacityRange

Returns whether the node has opacity range

property hasPrimaryStructureInformation

Returns true when the model’s primary structure information is set

property hasSecondaryStructureInformation

Returns true when the model’s secondary structure information is set

property hasTitleInformation

Returns true when the model’s title information is set

property hasTransparencyRange

Returns whether the node has transparency range

property heterogenInformation

model’s heterogen information

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 miscellaneousInformation

model’s miscellaneous information

property modelType

Returns 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 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 primaryStructureInformation

model’s primary structure information

property secondaryStructureInformation

model’s secondary structure information

property selectionFlag

Selection flag

property sumOfFormalCharges

Returns the sum of formal charges

property sumOfPartialCharges

Returns the sum of partial charges

property titleInformation

model’s title information

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