Atom¶

This class describes an atom in a structural model.

You can get a number of atom’s parameters on its topology (bonds), identity (type, lement name, atomic weight, etc), and other properties (chain, occupancy, serial number, formal charge, temperature factor, etc), for example:

# get the bond list of an atom
atom.getBondList

# atom's element name
atom.elementName

# atom's atomic weight
atom.atomicWeight

# atom's occupancy
atom.occupancy

# atom's temperature factor
if atom.hasTemperatureFactor:
        atom.temperatureFactor

# atom's water flag
if atom.hasWaterFlag:
        atom.waterFlag

# the name of a residue to which atom belongs
if atom.isInResidue:
        atom.residueName

Note

Parameters which are owned by an atom are accesible as properties (e.g. atom.partialCharge), but due to some limitations some parameters which are owned by atom’s parent nodes are accessible via getter and setter functions (if setter functions are available for a parameter).

There is a number of constructors for an atom node, for example:

from samson.Modeling.StructuralModel import Atom
from samson.Modeling.Element import Element

# construct a Carbon atom at (0, 0, 0) position
atom1 = Atom(Element.Carbon)
atom1.setPosition(Type.position3(Quantity.nm(1), Quantity.nm(-1.5), Quantity.nm(0)))
print(atom1)

# construct a Carbon atom at (0, 0, 0) position
atom2 = Atom(Element.Carbon, Type.position3(Quantity.nm(1), Quantity.nm(-1.5), Quantity.nm(0)))
print(atom2)

You can further add an atom to e.g. a structural model, chain, backbone, or sidechain:

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

# create the atom
atom.create()

# add the atom to a chain
chain.addChild(atom)

# turn the undo system off
SAMSON.endHolding()

See also

SAMSON API: SBMStructuralModelNodeAtom

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

Bases: samson.Modeling.StructuralModel.Particle

This class describes an atom in a structural model.

Overloaded function.

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

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

__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))

__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)

__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

__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 Geometry(self: samson.Modeling.StructuralModel.Atom.Geometry, value: int) → None¶

Bases: pybind11_builtins.pybind11_object

Members:

Undefined

Linear

Bent

TrigonalPlanar

TrigonalPyramidal

TShaped

Tetrahedral

SquarePlanar

Seesaw

TrigonalBipyramidal

SquarePyramidal

PentagonalPlanar

Octahedral

TrigonalPrismatic

PentagonalPyramidal

PentagonalBipyramidal

CappedOctahedral

CappedTrigonalPrismatic

SquareAntiprismatic

Dodecahedral

BicappedTrigonalPrismatic

TricappedTrigonalPrismatic

CappedSquareAntiprismatic

Bent = <Geometry.Bent: 22>¶

BicappedTrigonalPrismatic = <Geometry.BicappedTrigonalPrismatic: 83>¶

CappedOctahedral = <Geometry.CappedOctahedral: 72>¶

CappedSquareAntiprismatic = <Geometry.CappedSquareAntiprismatic: 92>¶

CappedTrigonalPrismatic = <Geometry.CappedTrigonalPrismatic: 73>¶

Dodecahedral = <Geometry.Dodecahedral: 82>¶

Linear = <Geometry.Linear: 21>¶

Octahedral = <Geometry.Octahedral: 61>¶

PentagonalBipyramidal = <Geometry.PentagonalBipyramidal: 71>¶

PentagonalPlanar = <Geometry.PentagonalPlanar: 53>¶

PentagonalPyramidal = <Geometry.PentagonalPyramidal: 63>¶

Seesaw = <Geometry.Seesaw: 43>¶

SquareAntiprismatic = <Geometry.SquareAntiprismatic: 81>¶

SquarePlanar = <Geometry.SquarePlanar: 42>¶

SquarePyramidal = <Geometry.SquarePyramidal: 52>¶

TShaped = <Geometry.TShaped: 33>¶

Tetrahedral = <Geometry.Tetrahedral: 41>¶

TricappedTrigonalPrismatic = <Geometry.TricappedTrigonalPrismatic: 91>¶

TrigonalBipyramidal = <Geometry.TrigonalBipyramidal: 51>¶

TrigonalPlanar = <Geometry.TrigonalPlanar: 31>¶

TrigonalPrismatic = <Geometry.TrigonalPrismatic: 62>¶

TrigonalPyramidal = <Geometry.TrigonalPyramidal: 32>¶

Undefined = <Geometry.Undefined: 0>¶

property name¶

property value¶

class Hybridization(self: samson.Modeling.StructuralModel.Atom.Hybridization, value: int) → None¶

Bases: pybind11_builtins.pybind11_object

Members:

None : No hybridization

SP : Hybridization of an s-orbital and one p-orbital

SP2 : Hybridization of an s-orbital and two p-orbitals

SP3 : Hybridization of an s-orbital and three p-orbitals

SP3D : Hybridization of an s-orbital, three p-orbitals, and a d-orbital

SP3D2 : Hybridization of an s-orbital, three p-orbitals, and two d-orbital

Unknown : Hybridization is unknown

None = <Hybridization.None: 0>¶

SP = <Hybridization.SP: 1>¶

SP2 = <Hybridization.SP2: 2>¶

SP3 = <Hybridization.SP3: 3>¶

SP3D = <Hybridization.SP3D: 4>¶

SP3D2 = <Hybridization.SP3D2: 5>¶

Unknown = <Hybridization.Unknown: 6>¶

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

addHydrogens(self: samson.Modeling.StructuralModel.Atom) → int¶: Adds hydrogens and returns the number of added hydrogens

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

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

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

clearGeometry(self: samson.Modeling.StructuralModel.Atom) → None¶: Clears the atom’s geometry

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

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

clearOxidationState(self: samson.Modeling.StructuralModel.Atom) → None¶: Clears the atom’s OxidationState

clearPartialCharge(self: samson.Modeling.StructuralModel.Atom) → None¶: Clears the atom’s PartialCharge

clearRecordType(self: samson.Modeling.StructuralModel.Atom) → None¶: Clears the atom’s RecordType

clearResonance(self: samson.Modeling.StructuralModel.Atom) → None¶: Clears the atom’s Resonance

clearSYBYLType(self: samson.Modeling.StructuralModel.Atom) → None¶: Clears the atom’s SYBYLType

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

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.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

getBackbone(self: samson.Modeling.StructuralModel.Atom) → SBMStructuralModelNodeBackbone¶: Returns a pointer to the backbone

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

getBondedAtoms(*args, **kwargs)¶

Overloaded function.

getBondedAtoms(self: samson.Modeling.StructuralModel.Atom) -> samson.DataModel.DataGraph.NodeIndexer

Returns an indexer with all bonded atoms

getBondedAtoms(self: samson.Modeling.StructuralModel.Atom, element: samson.Modeling.Element.Element.ElementType) -> samson.DataModel.DataGraph.NodeIndexer

Returns an indexer with all bonded atoms of type element

getBondedHeavyAtoms(self: samson.Modeling.StructuralModel.Atom) → samson.DataModel.DataGraph.NodeIndexer¶: Returns an indexer with all bonded heavy atoms (non-Hydrogens)

getChain(self: samson.Modeling.StructuralModel.Atom) → SBMStructuralModelNodeChain¶: Returns the atom’s chain

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

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

static getGeometryString(geometry: SBMStructuralModelNodeAtom::Geometry) → str¶: Returns the geometry as a string

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 getHybridizationString(hybridization: SBMStructuralModelNodeAtom::Hybridization) → str¶: Returns the hybridization as a string

getHydrogens(self: samson.Modeling.StructuralModel.Atom) → samson.DataModel.DataGraph.NodeIndexer¶: Returns an indexer with all bonded hydrogens

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¶

getMolecule(self: samson.Modeling.StructuralModel.Atom) → SBMStructuralModelNodeMolecule¶: Returns a molecule in which the atom is

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

getNumberOfBondedAtoms(*args, **kwargs)¶

Overloaded function.

getNumberOfBondedAtoms(self: samson.Modeling.StructuralModel.Atom) -> int

Returns the number of bonded atoms

getNumberOfBondedAtoms(self: samson.Modeling.StructuralModel.Atom, element: samson.Modeling.Element.Element.ElementType) -> int

Returns the number of bonded atoms with element type element

getNumberOfBondedCarbons(self: samson.Modeling.StructuralModel.Atom) → int¶: Returns the number of bonded carbons

getNumberOfBondedHeavyAtoms(self: samson.Modeling.StructuralModel.Atom) → int¶: Returns the number of bonded heavy atoms

getNumberOfBondedHydrogens(self: samson.Modeling.StructuralModel.Atom) → int¶: Returns the number of bonded hydrogens

getNumberOfBondedNitrogens(self: samson.Modeling.StructuralModel.Atom) → int¶: Returns the number of bonded nitrogens

getNumberOfBondedOxygens(self: samson.Modeling.StructuralModel.Atom) → int¶: Returns the number of bonded oxygens

getNumberOfBondedSulfurs(self: samson.Modeling.StructuralModel.Atom) → int¶: Returns the number of bonded sulfurs

getNumberOfBonds(self: samson.Modeling.StructuralModel.Atom) → int¶: The number of bonds without taking into account the bond order (NB: a double bond is considered as one bond)

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¶: Get the position

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¶

getRecordType(self: samson.Modeling.StructuralModel.Atom) → str¶: Returns the atom’s recordType

getResidue(self: samson.Modeling.StructuralModel.Atom) → SBMStructuralModelNodeResidue¶: Returns a residue in which the atom is

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) → SBMStructuralModelNodeSegment¶: Returns the segment in which the atom is

getSideChain(self: samson.Modeling.StructuralModel.Atom) → SBMStructuralModelNodeSideChain¶: Returns a pointer to the side chain

getStatusBit(self: samson.Modeling.StructuralModel.Atom) → str¶: Returns the atom’s statusBit

getSubstructure(self: samson.Modeling.StructuralModel.Atom) → samson.Modeling.StructuralModel.Group¶: Returns a substructure in which the atom is

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

getX(self: samson.Modeling.StructuralModel.Particle) → samson.DataModel.Quantity.unitsSI¶: Get the x-coordinate

getY(self: samson.Modeling.StructuralModel.Particle) → samson.DataModel.Quantity.unitsSI¶: Get the y-coordinate

getZ(self: samson.Modeling.StructuralModel.Particle) → samson.DataModel.Quantity.unitsSI¶: Get the z-coordinate

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

isAttachedToHydrogenBondDonor(self: samson.Modeling.StructuralModel.Atom) → bool¶: Returns true if the atom is connected to an H-Bond donor

isCarboxylOxygen(self: samson.Modeling.StructuralModel.Atom) → bool¶: Returns true for an Oxygen atom in a carboxyl group (C(=O)OH)

isDonorborneHydrogen(self: samson.Modeling.StructuralModel.Atom) → bool¶: Returns true if the atom is a hydrogen connected to an H-Bond donor

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

isHydrogenBondAcceptor(self: samson.Modeling.StructuralModel.Atom) → bool¶: Returns true if the atom is an H-Bond acceptor (N, O, S, F)

isHydrogenBondDonor(self: samson.Modeling.StructuralModel.Atom) → bool¶: Returns true if the atom is an H-Bond donor (N, O, S, F)

isIn(*args, **kwargs)¶

Overloaded function.

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

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

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

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

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

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

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

isNitroOxygen(self: samson.Modeling.StructuralModel.Atom) → bool¶: Returns true for an Oxygen atom in a nitro group (-NO2)

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

isPlanar(self: samson.Modeling.StructuralModel.Atom) → bool¶: Returns true if the atom with atoms bonded to it 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)

isSulfoneOxygen(self: samson.Modeling.StructuralModel.Atom) → bool¶: Returns true for an Oxygen atom in a sulfone (R1-SO2-R2)

isThiocarboxylOxygen(self: samson.Modeling.StructuralModel.Atom) → bool¶: Returns true for an Oxygen atom in a thiocarboxyl group (C(=S)OH or C(=O)SH)

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

removeHydrogens(self: samson.Modeling.StructuralModel.Atom) → int¶: Removes the hydrogens bonded to the atom and returns the number of removed hydrogens

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

setComment(self: samson.Modeling.StructuralModel.Atom, comment: str, size: int) → None¶: Set the atom’s comment

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

Sets the material for the node.

Args:
material (Material): material to set

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

setPositionOnTetrahedron(self: samson.Modeling.StructuralModel.Particle, center: samson.DataModel.Type.vector3, vertex1: samson.DataModel.Type.vector3, vertex2: samson.DataModel.Type.vector3, vertex3: samson.DataModel.Type.vector3, distanceFromCenter: samson.DataModel.Quantity.unitsSI) → None¶: Sets the particle’s position on a tetrahedron vertex based on the center position, the distance from the center distanceFromCenter, and positions of other 3 vertices vertex1, vertex2, and vertex3.

setSYBYLType(self: samson.Modeling.StructuralModel.Atom, SYBYLType: str, size: int) → None¶: Set the atom’s SYBYLType

setStatusBit(self: samson.Modeling.StructuralModel.Atom, statusBit: str, size: int) → None¶: Set the atom’s statusBit

setX(self: samson.Modeling.StructuralModel.Particle, arg0: samson.DataModel.Quantity.unitsSI) → None¶: Set the x-coordinate

setY(self: samson.Modeling.StructuralModel.Particle, arg0: samson.DataModel.Quantity.unitsSI) → None¶: Set the y-coordinate

setZ(self: samson.Modeling.StructuralModel.Particle, arg0: samson.DataModel.Quantity.unitsSI) → None¶: Set the z-coordinate

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

Animation = <NodeType.Animation: 26>¶

ArticulatedBody = <NodeType.ArticulatedBody: 603>¶

ArticulatedBodySystem = <NodeType.ArticulatedBodySystem: 502>¶

Asset = <NodeType.Asset: 50>¶

Atom = <NodeType.Atom: 20100>¶

Backbone = <NodeType.Backbone: 209>¶

Bent = <Geometry.Bent: 22>¶

BicappedTrigonalPrismatic = <Geometry.BicappedTrigonalPrismatic: 83>¶

Bond = <NodeType.Bond: 202>¶

Camera = <NodeType.Camera: 23>¶

CappedOctahedral = <Geometry.CappedOctahedral: 72>¶

CappedSquareAntiprismatic = <Geometry.CappedSquareAntiprismatic: 92>¶

CappedTrigonalPrismatic = <Geometry.CappedTrigonalPrismatic: 73>¶

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>¶

Dodecahedral = <Geometry.Dodecahedral: 82>¶

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>¶

Linear = <Geometry.Linear: 21>¶

Mesh = <NodeType.Mesh: 300>¶

Molecule = <NodeType.Molecule: 208>¶

NodeGroup = <NodeType.DataGraphNodeGroup: 30>¶

None = <Hybridization.None: 0>¶

Note = <NodeType.Note: 25>¶

Octahedral = <Geometry.Octahedral: 61>¶

ParticleSystem = <NodeType.ParticleSystem: 500>¶

Path = <NodeType.Path: 29>¶

PentagonalBipyramidal = <Geometry.PentagonalBipyramidal: 71>¶

PentagonalPlanar = <Geometry.PentagonalPlanar: 53>¶

PentagonalPyramidal = <Geometry.PentagonalPyramidal: 63>¶

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>¶

SP = <Hybridization.SP: 1>¶

SP2 = <Hybridization.SP2: 2>¶

SP3 = <Hybridization.SP3: 3>¶

SP3D = <Hybridization.SP3D: 4>¶

SP3D2 = <Hybridization.SP3D2: 5>¶

property SYBYLTypeSize¶: The atom’s SYBYLType size

Seesaw = <Geometry.Seesaw: 43>¶

Segment = <NodeType.Segment: 205>¶

SideChain = <NodeType.SideChain: 210>¶

Simulator = <NodeType.Simulator: 11>¶

SimulatorArticulatedBodySystem = <NodeType.SimulatorArticulatedBodySystem: 1102>¶

SimulatorParticleSystem = <NodeType.SimulatorParticleSystem: 1100>¶

SimulatorRigidBodySystem = <NodeType.SimulatorRigidBodySystem: 1101>¶

SquareAntiprismatic = <Geometry.SquareAntiprismatic: 81>¶

SquarePlanar = <Geometry.SquarePlanar: 42>¶

SquarePyramidal = <Geometry.SquarePyramidal: 52>¶

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>¶

TShaped = <Geometry.TShaped: 33>¶

Tetrahedral = <Geometry.Tetrahedral: 41>¶

TricappedTrigonalPrismatic = <Geometry.TricappedTrigonalPrismatic: 91>¶

TrigonalBipyramidal = <Geometry.TrigonalBipyramidal: 51>¶

TrigonalPlanar = <Geometry.TrigonalPlanar: 31>¶

TrigonalPrismatic = <Geometry.TrigonalPrismatic: 62>¶

TrigonalPyramidal = <Geometry.TrigonalPyramidal: 32>¶

Undefined = <Geometry.Undefined: 0>¶

Unknown = <Hybridization.Unknown: 6>¶

VisualModel = <NodeType.VisualModel: 3>¶

VisualModelMesh = <NodeType.Mesh: 300>¶

property alternateLocation¶: The atom’s alternate location

property anisotropicTFactors¶: The atom’s AnisotropicTFactors

property aromaticity¶: The atom’s Aromaticity

property atomicWeight¶: The atom’s atomic weight

property block¶: The atom’s block

property chainID¶: Returns the ID of a chain in which the atom is

property chainIDString¶: Returns the ID (as a string) of a chain in which the atom is

property chainName¶: Returns the atom’s chain name

property commentSize¶: The atom’s comment size

property covalentRadius¶: The atom’s covalent radius

property currentValence¶: The current valence, i.e. the sum of the orders of the bonds connected to the atom

property customType¶: The atom’s CustomType

property defaultOpacity¶: Returns the default opacity

property defaultTransparency¶: Returns the default transparency

property electronegativity¶: The atom’s electronegativity

property elementName¶: The atom’s element name

property elementSymbol¶: The atom’s element symbol

property elementType¶: The atom’s element type

property expectedValence¶: The expected valence of the atom based on its formal charge and its number of bonds (based on the MDL valence model)

property formalCharge¶: The atom’s FormalCharge

property geometry¶: The atom’s geometry

property geometryString¶: Returns the geometry as a string

property group¶: The atom’s group

property hasAltLocation¶: Returns true when the atom’s alternate location is set

property hasAminoAcidBackboneAtomName¶: Returns true when the atom’s name corresponds to one of the amino-acid backbone atoms

property hasAnisotropicTFactors¶: Returns true when the atom’s AnisotropicTFactors is set

property hasAromaticity¶: Returns true when the atom’s Aromaticity is set

property hasChainID¶: Returns true when the atom is in a chain and the chain’s ID is set

property hasComment¶: Returns true when the atom’s Comment is set

property hasCustomType¶: Returns true when the atom’s CustomType is set

property hasFormalCharge¶: Returns true when the atom’s FormalCharge is set

property hasGeometry¶: Returns true when the atom’s geometry is set

property hasHybridization¶: Returns true when the atom’s hybridization is set

property hasInsertionCode¶: Returns true when the atom’s insertion code is set

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

property hasName¶: Returns true when the atom’s name is set

property hasNucleicAcidBackboneAtomName¶: Returns true when the atom’s name corresponds to one of the nucleic acid backbone atoms

property hasOccupancy¶: Returns true when the atom’s occupancy is set

property hasOpacityRange¶: Returns whether the node has opacity range

property hasOxidationState¶: Returns true when the atom’s OxidationState is set

property hasPartialCharge¶: Returns true when the atom’s PartialCharge is set

property hasRecordType¶: Returns true when the atom’s RecordType is set

property hasResidueSequenceNumber¶: Returns true when the atom is in a residue and the chain’s ID is set

property hasResonance¶: Returns true when the atom’s Resonance is set

property hasSYBYLType¶: Returns true when the atom’s SYBYLType is set

property hasSerialNumber¶: Returns true when the atom’s serial number is set

property hasStatusBit¶: Returns true when the atom’s statusBit is set

property hasSubstructureSequenceNumber¶: Returns true when the atom is in a substructure and the chain’s ID is set

property hasTemperatureFactor¶: Returns true when the atom’s TemperatureFactor is set

property hasTransparencyRange¶: Returns whether the node has transparency range

property hasWaterFlag¶: Returns true when the atom’s WaterFlag is set

property highlightingFlag¶: Highlighting flag

property hybridization¶: The atom’s hybridization

property hybridizationString¶: Returns the hybridization as a string

property insertionCode¶: The atom’s insertion code

property isActinide¶: Returns true if the atom is actinide metal

property isAlkaliMetal¶: Returns true if the atom is alkali metal

property isAlkalineEarthMetal¶: Returns true if the atom is alkaline earth metal

property isCreated¶: Returns true if and only if the node is created

property isDiatomicNonmetal¶: Returns true if the atom is diatomic nonmetal

property isErased¶: Returns true if and only if the node is erased

property isFromAminoAcidBackbone¶: Returns true when the atom is from an amino-acid backbone

property isFromNucleicAcidBackbone¶: Returns true when the atom is from a nucleic acid backbone

property isHalogen¶: Returns true if the atom is halogen

property isHighlighted¶: Returns whether the node is highlighted

property isInAminoAcid¶: Returns true when the atom is in an amino acid residue

property isInBackbone¶: Returns true when the atom is in a backbone

property isInChain¶: Returns true when the atom is in a chain

property isInMolecule¶: Returns true when the atom is in a molecule

property isInNucleicAcid¶: Returns true when the atom is in a nucleic acid residue

property isInResidue¶: Returns true when the atom is in a residue group

property isInSegment¶: Returns true when the atom is in segment

property isInSideChain¶: Returns true when the atom is in a side chain

property isInSubstructure¶: Returns true when the atom is in a substructure group

property isLanthanide¶: Returns true if the atom is lanthanide metal

property isLocked¶: Returns whether the node is locked

property isMetal¶: Returns true if the atom is metal

property isMetalloid¶: Returns true if the atom is metalloid

property isNobleGas¶: Returns true if the atom is noble gas

property isPolyatomicNonmetal¶: Returns true if the atom is polyatomic nonmetal

property isPosttransitionMetal¶: Returns true if the atom is posttransition metal

property isReactiveNonmetal¶: Returns true if the atom is reactive nonmetal

property isSelected¶: Returns whether the node is selected

property isSerializable¶: Returns true when the class is serializable

property isTransitionMetal¶: Returns true if the atom is transition metal

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 metalSubcategory¶: Returns the atom’s subcategory type in the metal–metalloid–nonmetal trend

property metalSubcategoryString¶: Returns the string representation of the atom’s subcategory type in the metal–metalloid–nonmetal trend

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 moleculeName¶: Returns the name of a molecule in which the atom is

property name¶: The atom’s full name

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 occupancy¶: The atom’s occupancy

property opacity¶: Opacity

property ownsMaterial¶: Returns whether the node owns a material

property oxidationState¶: The atom’s OxidationState

property partialCharge¶: The atom’s PartialCharge

property period¶: The atom’s period

property recordTypeSize¶: The atom’s RecordType size

property residueName¶: Returns the name of a residue in which the atom is

property residueSequenceNumber¶: Returns the sequence number of a residue in which the atom is

property residueSequenceNumberString¶: Returns the sequence number (as a string) of a residue in which the atom is

property residueTypeString¶: Returns the name of a residue in which the atom is

property resonance¶: The atom’s Resonance

property segmentName¶: Returns the name of a segment in which the atom is

property selectionFlag¶: Selection flag

property serialNumber¶: The atom’s serial number

property statusBitSize¶: The atom’s statusBit size

property substructureName¶: Returns the name of a substructure in which the atom is

property substructureSequenceNumber¶: Returns the sequence number of a substructure in which the atom is

property substructureSequenceNumberString¶: Returns the sequence number (as a string) of a substructure in which the atom is

property sumOfFormalCharges¶: Returns the sum of formal charges

property sumOfPartialCharges¶: Returns the sum of partial charges

property temperatureFactor¶: The atom’s TemperatureFactor

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 vanDerWaalsRadius¶: The atom’s van der Waals radius

property visibilityFlag¶: Visibility flag

property waterFlag¶: The atom’s WaterFlag