Bond¶

This class describes a bond in a structural model.

A bond has links to two atoms: the left one and the right one. You can get these atoms as follows:

bond.leftAtom
bond.rightAtom

# get the atom opposite to the given one in a bond
bond.getOppositeAtom(bond.leftAtom)

You can also get some parameters of a bond, such as its type, length, or the middle point position:

bond.bondType
bond.length
bond.midPoint

To construct a new bond you need to provide the left and the right atoms, you can also specify the bond order:

bond = sam.Modeling.StructuralModel.Bond(leftAtom, rightAtom, Quantity.dimensionless(2.0))

# turn the undo system on
SAMSON.beginHolding("Add new bond")
# hold the bond instance
SAMSON.hold(bond)

# create the bond
bond.create()

# add the bond to a structural model
structuralModel.addChild(bond)

# turn the undo system off
SAMSON.endHolding()

See also

SAMSON API: SBMStructuralModelNodeBond

class samson.Modeling.StructuralModel.Bond(*args, **kwargs)¶

Bases: samson.Modeling.StructuralModel.Node

This class describes a bond in a structural model.

Overloaded function.

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

Constructs a bond

__init__(self: samson.Modeling.StructuralModel.Bond, leftAtom: samson.Modeling.StructuralModel.Atom, rightAtom: samson.Modeling.StructuralModel.Atom, order: samson.DataModel.Quantity.unitsSI = 1,000000 (dimensionless)) -> None

Constructs a bond between atoms leftAtom and rightAtom and a specific bond order

class BondType(self: samson.Modeling.StructuralModel.Bond.BondType, value: int) → None¶

Bases: pybind11_builtins.pybind11_object

Members:

Undefined

Single

Double

Triple

Amide

Aromatic

Dummy

Amide = <BondType.Amide: 4>¶

Aromatic = <BondType.Aromatic: 5>¶

Double = <BondType.Double: 2>¶

Dummy = <BondType.Dummy: 6>¶

Single = <BondType.Single: 1>¶

Triple = <BondType.Triple: 3>¶

Undefined = <BondType.Undefined: 0>¶

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¶

addChild(self: samson.DataModel.DataGraph.Node, node: samson.DataModel.DataGraph.Node, nextNode: samson.DataModel.DataGraph.Node = None) → bool¶: Adds a child to the node

canAddChild(self: samson.DataModel.DataGraph.Node, node: samson.DataModel.DataGraph.Node, nextNode: samson.DataModel.DataGraph.Node = None) → bool¶: Returns whether this node can add node as a child

canAddChildType(self: samson.DataModel.DataGraph.Node, nodeType: SBDDataGraphNode::Type) → bool¶: Returns whether this node can add a node with type nodeType as a child

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

clearCustomType(self: samson.Modeling.StructuralModel.Bond) → None¶: Clears the bond’s custom type

clearStatusBit(self: samson.Modeling.StructuralModel.Bond) → None¶: Clears the bond’s status bit

clone(self: samson.DataModel.DataGraph.Node) → samson.DataModel.DataGraph.Node¶: Returns a copy of the node and its descendants

countNodes(*args, **kwargs)¶

Overloaded function.

countNodes(self: samson.DataModel.DataGraph.Node, selectionString: str = ‘*’, visitString: str = ‘*’, includeDependencies: bool = False) -> int

Count nodes into nodeIndexer, based on a selectionPredicate and a visitPredicate, with our without dependencies).: For selectionString and visitString use Node Specification Language (SAMSON API: Node Specification Language

countNodes(self: samson.DataModel.DataGraph.Node, nodeType: SBDDataGraphNode::Type, selectedNodesOnly: bool = False, visitString: str = ‘*’, includeDependencies: bool = False) -> int

Count nodes into nodeIndexer, based on a nodeType, a selection status and a visitPredicate, with our without dependencies).: For visitString use Node Specification Language (SAMSON API: Node Specification Language

create(self: samson.DataModel.DataGraph.Node) → None¶: Creates the node

descendsFrom(*args, **kwargs)¶

Overloaded function.

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

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

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

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

erase(self: samson.DataModel.DataGraph.Node) → None¶: Erases the node

getChildren(self: samson.Modeling.StructuralModel.Node) → samson.DataModel.DataGraph.NodeIndexer¶: Returns the children of the node

getDisplacement(self: samson.Modeling.StructuralModel.Bond) → samson.DataModel.Type.vector3¶: Returns the displacement used for display when multiple bond rendering is turned on

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

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

getModel(self: samson.Modeling.StructuralModel.Node) → samson.Modeling.StructuralModel.StructuralModel¶

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

getNextStructuralNode(self: samson.Modeling.StructuralModel.Node) → samson.Modeling.StructuralModel.Node¶

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

getOppositeAtom(self: samson.Modeling.StructuralModel.Bond, atom: samson.Modeling.StructuralModel.Atom) → samson.Modeling.StructuralModel.Atom¶: Returns the pointer to the atom opposite atom, when atom is either the left atom or the right atom of the bond

getParent(self: samson.DataModel.DataGraph.Node) → samson.DataModel.DataGraph.Node¶: Returns the parent of the node

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

getPreviousStructuralNode(self: samson.Modeling.StructuralModel.Node) → samson.Modeling.StructuralModel.Node¶

getRoot(self: samson.DataModel.DataGraph.Node) → samson.DataModel.DataGraph.Node¶: Returns the root of the hierarchy the node belongs to

getThisNode(self: samson.DataModel.DataGraph.Node) → samson.DataModel.DataGraph.Node¶: Returns the pointer to this node

static getTypeString(type: SBDDataGraphNode::Type) → str¶: Returns a string describing the type of the data graph node

hasOneOf(self: samson.DataModel.DataGraph.Node, nodeIndexer: SBDDataGraphNodeIndexer) → bool¶: Returns true if and only if this node is one of the nodes of the nodeIndexer, or is the ancestor of one of them

isDynamicalModel(self: samson.DataModel.DataGraph.Node) → bool¶: Returns true when the node is a dynamical model

isIn(*args, **kwargs)¶

Overloaded function.

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

Returns true if and only if this node is node, or descends from it, or belongs to a group stored in node

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

Returns true if and only if this node is one of the nodes of the nodeIndexer, or descends from one of them, or belongs to a group stored in one of the nodes of the nodeIndexer

isInteractionModel(self: samson.DataModel.DataGraph.Node) → bool¶: Returns true when the node is a interaction model

isLinking(self: samson.Modeling.StructuralModel.Bond, nodeIndexer: samson.DataModel.DataGraph.NodeIndexer) → bool¶: Returns true if and only if either atom is in nodeIndexer, or descends from a node of nodeIndexer

isMesh(self: samson.DataModel.DataGraph.Node) → bool¶: Returns true when the node is a mesh

isModel(self: samson.DataModel.DataGraph.Node) → bool¶: Returns true when the node is a model

isOneOf(self: samson.DataModel.DataGraph.Node, nodeIndexer: SBDDataGraphNodeIndexer) → bool¶: Returns true if and only if this node is one of the nodes of the nodeIndexer

isPropertyModel(self: samson.DataModel.DataGraph.Node) → bool¶: Returns true when the node is a property model

isSimulator(self: samson.DataModel.DataGraph.Node) → bool¶: Returns true when the node is a simulator

isStructuralModel(self: samson.DataModel.DataGraph.Node) → bool¶: Returns true when the node is a structural model

isStructuralParticle(self: samson.DataModel.DataGraph.Node) → bool¶: Returns true when the node is a structural particle (an atom or a pseudo-atom)

isType(self: samson.DataModel.DataGraph.Node, type: SBDDataGraphNode::Type) → bool¶: Returns true when the type of the node corresponds to type

isVisualModel(self: samson.DataModel.DataGraph.Node) → bool¶: Returns true when the node is a visual model

printDebugInfo(self: samson.DataModel.DataGraph.Node, offset: int = 0) → None¶: Prints some debugging information in stdout

removeChild(self: samson.DataModel.DataGraph.Node, node: samson.DataModel.DataGraph.Node) → bool¶: Removes a child from the node

removeMaterial(self: samson.DataModel.DataGraph.Node) → bool¶: Removes material from the node

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

toString(self: samson.Modeling.StructuralModel.Bond) → str¶: A string representation

Amide = <BondType.Amide: 4>¶

Animation = <NodeType.Animation: 26>¶

Aromatic = <BondType.Aromatic: 5>¶

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>¶

Double = <BondType.Double: 2>¶

Dummy = <BondType.Dummy: 6>¶

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>¶

Single = <BondType.Single: 1>¶

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>¶

Triple = <BondType.Triple: 3>¶

Undefined = <BondType.Undefined: 0>¶

VisualModel = <NodeType.VisualModel: 3>¶

VisualModelMesh = <NodeType.Mesh: 300>¶

property bondType¶: The bond type

property bondTypeString¶: Returns the string corresponding to the bondType

property customType¶: The bond’s custom type

property defaultOpacity¶: Returns the default opacity

property defaultTransparency¶: Returns the default transparency

property hasCustomType¶: Returns true when the bond’s custom type is set

property hasMaterial¶: Returns whether the node has a material (by itself, or inherited)

property hasOpacityRange¶: Returns whether the node has opacity range

property hasStatusBit¶: Returns true when the bond’s status bit is set

property hasTransparencyRange¶: Returns whether the node has transparency range

property highlightingFlag¶: Highlighting flag

property isAmideBond¶

N-C=O

Type: Returns true if the bond is an amide bond, i.e. between a Nytrogen and a carbonyl Carbon

property isCarbonylBond¶: Returns true if the bond is a carbonyl bond (C=O)

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 isEsterBond¶

O-C=O

Type: Returns true if the bond is an ester bond, i.e. between an Oxygen and a carbonyl Carbon

property isHighlighted¶: Returns whether the node is highlighted

property isLocked¶: Returns whether the node is locked

property isPrimaryAmideBond¶: Returns true if the bond is a primary amide bond, i.e. an amid bond where the Nytrogen atom has exactly one non-Hydronen bond

property isSecondaryAmideBond¶: Returns true if the bond is a secondary amide bond, i.e. an amid bond where the Nytrogen atom has exactly two non-Hydronen bonds

property isSelected¶: Returns whether the node is selected

property isSerializable¶: Returns true when the class is serializable

property isTertiaryAmideBond¶: Returns true if the bond is a tertiary amide bond, i.e. an amid bond where the Nytrogen atom has exactly three non-Hydronen bonds

property isVisible¶: Returns whether the node is visible

property leftAtom¶: Returns a pointer to the left atom

property length¶: The length of the bond

property lockedFlag¶: Locked flag

property maximumOpacity¶: Returns the maximum opacity

property maximumTransparency¶: Returns the maximum transparency

property midPoint¶: The mid point of the bond

property minimumOpacity¶: Returns the minimum opacity

property minimumTransparency¶: Returns the minimum transparency

property mobilityFlag¶: The node’s mobility flag

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 order¶: The bond order

property ownsMaterial¶: Returns whether the node owns a material

property rightAtom¶: Returns a pointer to the right atom

property selectionFlag¶: Selection flag

property statusBit¶: The bond’s status bit

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