Atom

class samson.Modeling.StructuralModel.Atom(*args, **kwargs)

Bases: samson.Modeling.StructuralModel.Particle

This class describes an atom in a structural model

SAMSON API: SBMStructuralModelNodeAtom

Overloaded function.

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

Constructs an atom of a default type (default position = (0,0,0))

2. __init__(self: samson.Modeling.StructuralModel.Atom, element: samson.Modeling.Element.Element.ElementType) -> None

Constructs an atom of a given type (default position = (0,0,0))

3. __init__(self: samson.Modeling.StructuralModel.Atom, element: samson.Modeling.Element.Element.ElementType, x: samson.DataModel.Quantity.unitsSI, y: samson.DataModel.Quantity.unitsSI, z: samson.DataModel.Quantity.unitsSI) -> None

Constructs an atom of a given type at position = (x,y,z)

4. __init__(self: samson.Modeling.StructuralModel.Atom, element: samson.Modeling.Element.Element.ElementType, p: samson.DataModel.Type.vector3) -> None

Constructs an atom of a given type at position p

5. __init__(self: samson.Modeling.StructuralModel.Atom, element: samson.Modeling.Element.Element.ElementType, n: str, p: samson.DataModel.Type.vector3) -> None

Constructs an atom of a given type with name n at position p

class NodeType(self: samson.DataModel.DataGraph.Node.NodeType, arg0: int) → None

Bases: pybind11_builtins.pybind11_object

ArticulatedBody = NodeType.DynamicalModelNodeArticulatedBody

ArticulatedBodySystem = NodeType.DynamicalModelArticulatedBodySystem

Atom = NodeType.Atom

Backbone = NodeType.StructuralModelNodeBackbone

Bond = NodeType.StructuralModelNodeBond

Camera = NodeType.Camera

Chain = NodeType.StructuralModelNodeChain

Conformation = NodeType.StructuralModelConformation

Controller = NodeType.Controller

ControllerNode = NodeType.ControllerNode

DataGraphNodeGroup = NodeType.DataGraphNodeGroup

Document = NodeType.Document

DocumentManager = NodeType.DocumentManager

DynamicalGroup = NodeType.DynamicalModelNodeGroup

DynamicalModel = NodeType.DynamicalModel

DynamicalModelArticulatedBodySystem = NodeType.DynamicalModelArticulatedBodySystem

DynamicalModelNode = NodeType.DynamicalModelNode

DynamicalModelNodeArticulatedBody = NodeType.DynamicalModelNodeArticulatedBody

DynamicalModelNodeGroup = NodeType.DynamicalModelNodeGroup

DynamicalModelNodeParticle = NodeType.DynamicalModelNodeParticle

DynamicalModelNodeRigidBody = NodeType.DynamicalModelNodeRigidBody

DynamicalModelNodeRoot = NodeType.DynamicalModelNodeRoot

DynamicalModelParticleSystem = NodeType.DynamicalModelParticleSystem

DynamicalModelRigidBodySystem = NodeType.DynamicalModelRigidBodySystem

DynamicalNode = NodeType.DynamicalModelNode

DynamicalParticle = NodeType.DynamicalModelNodeParticle

DynamicalRoot = NodeType.DynamicalModelNodeRoot

Folder = NodeType.Folder

InteractionModel = NodeType.InteractionModel

InteractionModelArticulatedBodySystem = NodeType.InteractionModelArticulatedBodySystem

InteractionModelParticleSystem = NodeType.InteractionModelParticleSystem

InteractionModelRigidBodySystem = NodeType.InteractionModelRigidBodySystem

Label = NodeType.Label

Molecule = NodeType.StructuralModelNodeMolecule

NodeGroup = NodeType.DataGraphNodeGroup

ParticleSystem = NodeType.DynamicalModelParticleSystem

Path = NodeType.StructuralModelPath

PropertyModel = NodeType.PropertyModel

PropertyModelFunction = NodeType.PropertyModelFunction

Protein = NodeType.StructuralModelNodeProtein

PseudoAtom = NodeType.StructuralModelNodePseudoAtom

Residue = NodeType.StructuralModelNodeResidue

RigidBody = NodeType.DynamicalModelNodeRigidBody

RigidBodySystem = NodeType.DynamicalModelRigidBodySystem

Root = NodeType.StructuralModelNodeRoot

Segment = NodeType.StructuralModelNodeSegment

SideChain = NodeType.StructuralModelNodeSideChain

Simulator = NodeType.Simulator

SimulatorArticulatedBodySystem = NodeType.SimulatorArticulatedBodySystem

SimulatorParticleSystem = NodeType.SimulatorParticleSystem

SimulatorRigidBodySystem = NodeType.SimulatorRigidBodySystem

StateUpdater = NodeType.StateUpdater

StateUpdaterArticulatedBodySystem = NodeType.StateUpdaterArticulatedBodySystem

StateUpdaterParticleSystem = NodeType.StateUpdaterParticleSystem

StateUpdaterRigidBodySystem = NodeType.StateUpdaterRigidBodySystem

StructuralGroup = NodeType.StructuralModelNodeGroup

StructuralModel = NodeType.StructuralModel

StructuralModelConformation = NodeType.StructuralModelConformation

StructuralModelNode = NodeType.StructuralModelNode

StructuralModelNodeAtom = NodeType.Atom

StructuralModelNodeBackbone = NodeType.StructuralModelNodeBackbone

StructuralModelNodeBond = NodeType.StructuralModelNodeBond

StructuralModelNodeChain = NodeType.StructuralModelNodeChain

StructuralModelNodeGroup = NodeType.StructuralModelNodeGroup

StructuralModelNodeMolecule = NodeType.StructuralModelNodeMolecule

StructuralModelNodeParticle = NodeType.StructuralModelNodeParticle

StructuralModelNodeProtein = NodeType.StructuralModelNodeProtein

StructuralModelNodePseudoAtom = NodeType.StructuralModelNodePseudoAtom

StructuralModelNodeResidue = NodeType.StructuralModelNodeResidue

StructuralModelNodeRoot = NodeType.StructuralModelNodeRoot

StructuralModelNodeSegment = NodeType.StructuralModelNodeSegment

StructuralModelNodeSideChain = NodeType.StructuralModelNodeSideChain

StructuralModelPath = NodeType.StructuralModelPath

StructuralParticle = NodeType.StructuralModelNodeParticle

Undefined = NodeType.Undefined

VisualModel = NodeType.VisualModel

addChild(self: samson.DataModel.DataGraph.Node, node: samson.DataModel.DataGraph.Node, nextNode: samson.DataModel.DataGraph.Node=None) → bool

Adds a child to the node

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

Adds material 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

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

castToVisualModel(self: samson.DataModel.DataGraph.Node) → SBMVisualModel

Casts (if possible) from SBDDataGraphNode to SBMVisualModel

clearAltLocation(self: samson.Modeling.StructuralModel.Atom) → None

Clears the atom’s alternate location

clearAnisotropicTFactors(self: samson.Modeling.StructuralModel.Atom) → None

Clears the atom’s AnisotropicTFactors

clearAromaticity(self: samson.Modeling.StructuralModel.Atom) → None

Clears the atom’s Aromaticity

clearChain(self: samson.Modeling.StructuralModel.Atom) → None

Clears the atom’s chain

clearChainID(self: samson.Modeling.StructuralModel.Atom) → None

Clears the atom’s ChainID

clearComment(self: samson.Modeling.StructuralModel.Atom) → None

Clears the atom’s Comment

clearCustomType(self: samson.Modeling.StructuralModel.Atom) → None

Clears the atom’s CustomType

clearFormalCharge(self: samson.Modeling.StructuralModel.Atom) → None

Clears the atom’s FormalCharge

clearHybridization(self: samson.Modeling.StructuralModel.Atom) → None

Clears the atom’s Hybridization

clearInsertionCode(self: samson.Modeling.StructuralModel.Atom) → None

Clears the atom’s insertion code

clearMoleculeName(self: samson.Modeling.StructuralModel.Atom) → None

Clears the atom’s MoleculeName

clearName(self: samson.Modeling.StructuralModel.Atom) → None

Clears the atom’s full name

clearOccupancy(self: samson.Modeling.StructuralModel.Atom) → None

Clears the atom’s occupancy

clearOxydationState(self: samson.Modeling.StructuralModel.Atom) → None

Clears the atom’s OxydationState

clearPartialCharge(self: samson.Modeling.StructuralModel.Atom) → None

Clears the atom’s PartialCharge

clearRecordType(self: samson.Modeling.StructuralModel.Atom) → None

Clears the atom’s RecordType

clearResidueName(self: samson.Modeling.StructuralModel.Atom) → None

Clears the atom’s ResidueName

clearResidueSequenceNumber(self: samson.Modeling.StructuralModel.Atom) → None

Clears the atom’s ResidueSequenceNumber

clearResonance(self: samson.Modeling.StructuralModel.Atom) → None

Clears the atom’s Resonance

clearSYBYLType(self: samson.Modeling.StructuralModel.Atom) → None

Clears the atom’s SYBYLType

clearSegment(self: samson.Modeling.StructuralModel.Atom) → None

Clears the atom’s Segment

clearSerialNumber(self: samson.Modeling.StructuralModel.Atom) → None

Clears the atom’s serial number

clearStatusBit(self: samson.Modeling.StructuralModel.Atom) → None

Clears the atom’s StatusBit

clearSubstructureName(self: samson.Modeling.StructuralModel.Atom) → None

Clears the atom’s SubstructureName

clearSubstructureSequenceNumber(self: samson.Modeling.StructuralModel.Atom) → None

Clears the atom’s SubstructureSequenceNumber

clearTemperatureFactor(self: samson.Modeling.StructuralModel.Atom) → None

Clears the atom’s TemperatureFactor

clearWaterFlag(self: samson.Modeling.StructuralModel.Atom) → None

Clears the atom’s WaterFlag

clone(self: samson.Modeling.StructuralModel.Atom) → samson.Modeling.StructuralModel.Atom

Returns a copy of the node and its descendants

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

create(self: samson.DataModel.DataGraph.Node) → None

Creates the node

erase(self: samson.DataModel.DataGraph.Node) → None

Erases the node

getBondList(self: samson.Modeling.StructuralModel.Atom) → SBCReferencePointerList<SBMStructuralModelNodeBond, SBCReferenceToTarget>

Returns the bond list

getBondTo(self: samson.Modeling.StructuralModel.Atom, atom: samson.Modeling.StructuralModel.Atom) → SBMStructuralModelNodeBond

Returns the bond to an atom (0 if no bond)

getChain(self: samson.Modeling.StructuralModel.Atom) → str

Returns the atom’s chain

getComment(self: samson.Modeling.StructuralModel.Atom) → str

Returns the atom’s comment

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

Gets all atoms in the connected component containing the atom

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

Returns the document the node belongs to

getFlags(self: samson.DataModel.DataGraph.Node) → int

Returns the flags

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

getMoleculeName(self: samson.Modeling.StructuralModel.Atom) → str

Returns the atom’s moleculeName

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

2. 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(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

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

Returns the parent of the node

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

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

2. 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

getRecordType(self: samson.Modeling.StructuralModel.Atom) → str

Returns the atom’s recordType

getResidueName(self: samson.Modeling.StructuralModel.Atom) → str

Returns the atom’s residueName

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

Returns the root of the hierarchy the node belongs to

getSYBYLType(self: samson.Modeling.StructuralModel.Atom) → str

Returns the atom’s SYBYLType

getSegment(self: samson.Modeling.StructuralModel.Atom) → str

Returns the atom’s segment

getStatusBit(self: samson.Modeling.StructuralModel.Atom) → str

Returns the atom’s statusBit

getSubstructureName(self: samson.Modeling.StructuralModel.Atom) → str

Returns the atom’s substructureName

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

Returns the pointer to this node

getTypeString(type: SBDDataGraphNode::Type) → str

Returns a string describing the type of the data graph node

getX(self: samson.Modeling.StructuralModel.Particle) → samson.DataModel.Quantity.unitsSI

getY(self: samson.Modeling.StructuralModel.Particle) → samson.DataModel.Quantity.unitsSI

getZ(self: samson.Modeling.StructuralModel.Particle) → samson.DataModel.Quantity.unitsSI

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

2. 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

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

Returns true when the node is a interaction model

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

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

setChain(self: samson.Modeling.StructuralModel.Atom, chain: str, size: int) → None

Set the atom’s chain

setColor(self: samson.DataModel.DataGraph.Node, color: SBDColor, applyToChildren: bool=False) → None

Sets the color for the node (removes an existing material from the node and adds a given material based on a given color)

Args:

color (Color): material to set

applyToChildren (boolean): if set to True goes through child nodes (default value: False)

setComment(self: samson.Modeling.StructuralModel.Atom, comment: str, size: int) → None

Set the atom’s comment

setMaterial(self: samson.DataModel.DataGraph.Node, material: SBDDataGraphNodeMaterial, applyToChildren: bool=False) → None

Sets the material for the node (removes an existing material from the node and adds a given material)

Args:

material (Material): material to set

applyToChildren (boolean): if set to True goes through child nodes (default value: False)

setMoleculeName(self: samson.Modeling.StructuralModel.Atom, moleculeName: str, size: int) → None

Set the atom’s moleculeName

setPosition(self: samson.Modeling.StructuralModel.Particle, arg0: samson.DataModel.Type.vector3) → None

setRecordType(self: samson.Modeling.StructuralModel.Atom, recordType: str, size: int) → None

Set the atom’s RecordType

setResidueName(self: samson.Modeling.StructuralModel.Atom, residueName: str, size: int) → None

Set the atom’s residueName

setSYBYLType(self: samson.Modeling.StructuralModel.Atom, SYBYLType: str, size: int) → None

Set the atom’s SYBYLType

setSegment(self: samson.Modeling.StructuralModel.Atom, segment: str, size: int) → None

Set the atom’s segment

setStatusBit(self: samson.Modeling.StructuralModel.Atom, statusBit: str, size: int) → None

Set the atom’s statusBit

setSubstructureName(self: samson.Modeling.StructuralModel.Atom, substructureName: str, size: int) → None

Set the atom’s substructureName

setX(self: samson.Modeling.StructuralModel.Particle, arg0: samson.DataModel.Quantity.unitsSI) → None

setY(self: samson.Modeling.StructuralModel.Particle, arg0: samson.DataModel.Quantity.unitsSI) → None

setZ(self: samson.Modeling.StructuralModel.Particle, arg0: samson.DataModel.Quantity.unitsSI) → None

sprint(self: samson.Modeling.StructuralModel.Particle, offset: int=0) → None

Prints some debugging information

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

Converts to a string

ArticulatedBody = NodeType.DynamicalModelNodeArticulatedBody

ArticulatedBodySystem = NodeType.DynamicalModelArticulatedBodySystem

Atom = NodeType.Atom

Backbone = NodeType.StructuralModelNodeBackbone

Bond = NodeType.StructuralModelNodeBond

Camera = NodeType.Camera

Chain = NodeType.StructuralModelNodeChain

Conformation = NodeType.StructuralModelConformation

Controller = NodeType.Controller

ControllerNode = NodeType.ControllerNode

DataGraphNodeGroup = NodeType.DataGraphNodeGroup

Document = NodeType.Document

DocumentManager = NodeType.DocumentManager

DynamicalGroup = NodeType.DynamicalModelNodeGroup

DynamicalModel = NodeType.DynamicalModel

DynamicalModelArticulatedBodySystem = NodeType.DynamicalModelArticulatedBodySystem

DynamicalModelNode = NodeType.DynamicalModelNode

DynamicalModelNodeArticulatedBody = NodeType.DynamicalModelNodeArticulatedBody

DynamicalModelNodeGroup = NodeType.DynamicalModelNodeGroup

DynamicalModelNodeParticle = NodeType.DynamicalModelNodeParticle

DynamicalModelNodeRigidBody = NodeType.DynamicalModelNodeRigidBody

DynamicalModelNodeRoot = NodeType.DynamicalModelNodeRoot

DynamicalModelParticleSystem = NodeType.DynamicalModelParticleSystem

DynamicalModelRigidBodySystem = NodeType.DynamicalModelRigidBodySystem

DynamicalNode = NodeType.DynamicalModelNode

DynamicalParticle = NodeType.DynamicalModelNodeParticle

DynamicalRoot = NodeType.DynamicalModelNodeRoot

Folder = NodeType.Folder

InteractionModel = NodeType.InteractionModel

InteractionModelArticulatedBodySystem = NodeType.InteractionModelArticulatedBodySystem

InteractionModelParticleSystem = NodeType.InteractionModelParticleSystem

InteractionModelRigidBodySystem = NodeType.InteractionModelRigidBodySystem

Label = NodeType.Label

Molecule = NodeType.StructuralModelNodeMolecule

NodeGroup = NodeType.DataGraphNodeGroup

ParticleSystem = NodeType.DynamicalModelParticleSystem

Path = NodeType.StructuralModelPath

PropertyModel = NodeType.PropertyModel

PropertyModelFunction = NodeType.PropertyModelFunction

Protein = NodeType.StructuralModelNodeProtein

PseudoAtom = NodeType.StructuralModelNodePseudoAtom

Residue = NodeType.StructuralModelNodeResidue

RigidBody = NodeType.DynamicalModelNodeRigidBody

RigidBodySystem = NodeType.DynamicalModelRigidBodySystem

Root = NodeType.StructuralModelNodeRoot

SYBYLTypeSize

atom’s SYBYLType size

Segment = NodeType.StructuralModelNodeSegment

SideChain = NodeType.StructuralModelNodeSideChain

Simulator = NodeType.Simulator

SimulatorArticulatedBodySystem = NodeType.SimulatorArticulatedBodySystem

SimulatorParticleSystem = NodeType.SimulatorParticleSystem

SimulatorRigidBodySystem = NodeType.SimulatorRigidBodySystem

StateUpdater = NodeType.StateUpdater

StateUpdaterArticulatedBodySystem = NodeType.StateUpdaterArticulatedBodySystem

StateUpdaterParticleSystem = NodeType.StateUpdaterParticleSystem

StateUpdaterRigidBodySystem = NodeType.StateUpdaterRigidBodySystem

StructuralGroup = NodeType.StructuralModelNodeGroup

StructuralModel = NodeType.StructuralModel

StructuralModelConformation = NodeType.StructuralModelConformation

StructuralModelNode = NodeType.StructuralModelNode

StructuralModelNodeAtom = NodeType.Atom

StructuralModelNodeBackbone = NodeType.StructuralModelNodeBackbone

StructuralModelNodeBond = NodeType.StructuralModelNodeBond

StructuralModelNodeChain = NodeType.StructuralModelNodeChain

StructuralModelNodeGroup = NodeType.StructuralModelNodeGroup

StructuralModelNodeMolecule = NodeType.StructuralModelNodeMolecule

StructuralModelNodeParticle = NodeType.StructuralModelNodeParticle

StructuralModelNodeProtein = NodeType.StructuralModelNodeProtein

StructuralModelNodePseudoAtom = NodeType.StructuralModelNodePseudoAtom

StructuralModelNodeResidue = NodeType.StructuralModelNodeResidue

StructuralModelNodeRoot = NodeType.StructuralModelNodeRoot

StructuralModelNodeSegment = NodeType.StructuralModelNodeSegment

StructuralModelNodeSideChain = NodeType.StructuralModelNodeSideChain

StructuralModelPath = NodeType.StructuralModelPath

StructuralParticle = NodeType.StructuralModelNodeParticle

Undefined = NodeType.Undefined

VisualModel = NodeType.VisualModel

alternateLocation

atom’s alternate location

anisotropicTFactors

atom’s AnisotropicTFactors

aromaticity

atom’s Aromaticity

atomicWeight

block

chainID

atom’s ChainID

chainSize

atom’s chain size

commentSize

atom’s comment size

covalentRadius

customType

atom’s CustomType

electronegativity

elementName

elementSymbol

elementType

formalCharge

atom’s FormalCharge

group

hasAltLocation

Returns true when the atom’s alternate location is set

hasAnisotropicTFactors

Returns true when the atom’s AnisotropicTFactors is set

hasAromaticity

Returns true when the atom’s Aromaticity is set

hasChain

Returns true when the atom’s chain is set

hasChainID

Returns true when the atom’s ChainID is set

hasComment

Returns true when the atom’s Comment is set

hasCustomType

Returns true when the atom’s CustomType is set

hasFormalCharge

Returns true when the atom’s FormalCharge is set

hasHybridization

Returns true when the atom’s Hybridization is set

hasInsertionCode

Returns true when the atom’s insertion code is set

hasMoleculeName

Returns true when the atom’s MoleculeName is set

hasName

Returns true when the atom’s name is set

hasOccupancy

Returns true when the atom’s occupancy is set

hasOxydationState

Returns true when the atom’s OxydationState is set

hasPartialCharge

Returns true when the atom’s PartialCharge is set

hasRecordType

Returns true when the atom’s RecordType is set

hasResidueName

Returns true when the atom’s ResidueName is set

hasResidueSequenceNumber

Returns true when the atom’s ResidueSequenceNumber is set

hasResonance

Returns true when the atom’s Resonance is set

hasSYBYLType

Returns true when the atom’s SYBYLType is set

hasSegment

Returns true when the atom’s Segment is set

hasSerialNumber

Returns true when the atom’s serial number is set

hasStatusBit

Returns true when the atom’s statusBit is set

hasSubstructureName

Returns true when the atom’s SubstructureName is set

hasSubstructureSequenceNumber

Returns true when the atom’s SubstructureSequenceNumber is set

hasTemperatureFactor

Returns true when the atom’s TemperatureFactor is set

hasWaterFlag

Returns true when the atom’s WaterFlag is set

highlightingFlag

hybridization

atom’s Hybridization

insertionCode

atom’s insertion code

isCreated

Returns true if and only if the node is created

isErased

Returns true if and only if the node is erased

isFromAminoAcidBackbone

Returns true when the atom is from an amino-acid backbone

isFromNucleicAcidBackbone

Returns true when the atom is from a nucleic acid backbone

isHighlighted

Returns whether the node is highlighted

isSelected

Returns whether the node is selected

isSerializable

Returns true when the class is serializable

isVisible

Returns whether the node is visible

mobilityFlag

moleculeNameSize

atom’s moleculeName size

name

atom’s full name

nodeIndex

Returns the node index (unique in the whole data graph, but non-persistent)

occupancy

atom’s occupancy

oxydationState

atom’s OxydationState

partialCharge

atom’s PartialCharge

period

recordTypeSize

atom’s RecordType size

residueNameSize

atom’s residue name size

residueSequenceNumber

atom’s ResidueSequenceNumber

resonance

atom’s Resonance

segmentSize

atom’s segment size

selectionFlag

serialNumber

atom’s serial number

statusBitSize

atom’s statusBit size

substructureNameSize

atom’s substructureName size

substructureSequenceNumber

atom’s SubstructureSequenceNumber

temperatureFactor

atom’s TemperatureFactor

type

typeString

Returns a string describing the type of this data graph node

vanDerWaalsRadius

visibilityFlag

waterFlag

atom’s WaterFlag