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.

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 Geometry(self: samson.Modeling.StructuralModel.Atom.Geometry, arg0: 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

BicappedTrigonalPrismatic = Geometry.BicappedTrigonalPrismatic

CappedOctahedral = Geometry.CappedOctahedral

CappedSquareAntiprismatic = Geometry.CappedSquareAntiprismatic

CappedTrigonalPrismatic = Geometry.CappedTrigonalPrismatic

Dodecahedral = Geometry.Dodecahedral

Linear = Geometry.Linear

Octahedral = Geometry.Octahedral

PentagonalBipyramidal = Geometry.PentagonalBipyramidal

PentagonalPlanar = Geometry.PentagonalPlanar

PentagonalPyramidal = Geometry.PentagonalPyramidal

Seesaw = Geometry.Seesaw

SquareAntiprismatic = Geometry.SquareAntiprismatic

SquarePlanar = Geometry.SquarePlanar

SquarePyramidal = Geometry.SquarePyramidal

TShaped = Geometry.TShaped

Tetrahedral = Geometry.Tetrahedral

TricappedTrigonalPrismatic = Geometry.TricappedTrigonalPrismatic

TrigonalBipyramidal = Geometry.TrigonalBipyramidal

TrigonalPlanar = Geometry.TrigonalPlanar

TrigonalPrismatic = Geometry.TrigonalPrismatic

TrigonalPyramidal = Geometry.TrigonalPyramidal

Undefined = Geometry.Undefined

name

(self – handle) -> str

class Hybridization(self: samson.Modeling.StructuralModel.Atom.Hybridization, arg0: int) → None

Bases: pybind11_builtins.pybind11_object

Members:

None

SP

SP2

SP3

SP3D

SP3D2

Unknown

None = Hybridization.None

SP = Hybridization.SP

SP2 = Hybridization.SP2

SP3 = Hybridization.SP3

SP3D = Hybridization.SP3D

SP3D2 = Hybridization.SP3D2

Unknown = Hybridization.Unknown

name

(self – handle) -> str

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

Bases: pybind11_builtins.pybind11_object

Members:

Undefined

StructuralModel

StructuralModelNode

StructuralModelConformation

Conformation

StructuralModelPath

Path

StructuralModelNodeGroup

StructuralGroup

StructuralModelNodeRoot

Root

StructuralModelNodeParticle

StructuralParticle

StructuralModelNodeAtom

Atom

StructuralModelNodePseudoAtom

PseudoAtom

StructuralModelNodeBond

Bond

StructuralModelNodeResidue

Residue

StructuralModelNodeSegment

Segment

StructuralModelNodeProtein

Protein

StructuralModelNodeChain

Chain

StructuralModelNodeMolecule

Molecule

StructuralModelNodeBackbone

Backbone

StructuralModelNodeSideChain

SideChain

VisualModel

DynamicalModel

DynamicalModelParticleSystem

ParticleSystem

DynamicalModelRigidBodySystem

RigidBodySystem

DynamicalModelArticulatedBodySystem

ArticulatedBodySystem

DynamicalModelNode

DynamicalNode

DynamicalModelNodeGroup

DynamicalGroup

DynamicalModelNodeRoot

DynamicalRoot

DynamicalModelNodeParticle

DynamicalParticle

DynamicalModelNodeRigidBody

RigidBody

DynamicalModelNodeArticulatedBody

ArticulatedBody

InteractionModel

InteractionModelParticleSystem

InteractionModelRigidBodySystem

InteractionModelArticulatedBodySystem

PropertyModel

PropertyModelFunction

Simulator

SimulatorParticleSystem

SimulatorRigidBodySystem

SimulatorArticulatedBodySystem

StateUpdater

StateUpdaterParticleSystem

StateUpdaterRigidBodySystem

StateUpdaterArticulatedBodySystem

DocumentManager

Document

Folder

Camera

Label

DataGraphNodeGroup

NodeGroup

Controller

ControllerNode

Asset

ArticulatedBody = NodeType.DynamicalModelNodeArticulatedBody

ArticulatedBodySystem = NodeType.DynamicalModelArticulatedBodySystem

Asset = NodeType.Asset

Atom = NodeType.StructuralModelNodeAtom

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.StructuralModelNodeAtom

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

name

(self – handle) -> str

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

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

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.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) → 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(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

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

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.

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

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

The number of bonded atoms with element type element

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)

getNumberOfHydrogens(self: samson.Modeling.StructuralModel.Atom) → int

The number of all bonded hydrogens

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.

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

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

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

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

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

printDebugInfo(self: samson.Modeling.StructuralModel.Atom, 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

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

ArticulatedBody = NodeType.DynamicalModelNodeArticulatedBody

ArticulatedBodySystem = NodeType.DynamicalModelArticulatedBodySystem

Asset = NodeType.Asset

Atom = NodeType.StructuralModelNodeAtom

Backbone = NodeType.StructuralModelNodeBackbone

Bent = Geometry.Bent

BicappedTrigonalPrismatic = Geometry.BicappedTrigonalPrismatic

Bond = NodeType.StructuralModelNodeBond

Camera = NodeType.Camera

CappedOctahedral = Geometry.CappedOctahedral

CappedSquareAntiprismatic = Geometry.CappedSquareAntiprismatic

CappedTrigonalPrismatic = Geometry.CappedTrigonalPrismatic

Chain = NodeType.StructuralModelNodeChain

Conformation = NodeType.StructuralModelConformation

Controller = NodeType.Controller

ControllerNode = NodeType.ControllerNode

DataGraphNodeGroup = NodeType.DataGraphNodeGroup

Document = NodeType.Document

DocumentManager = NodeType.DocumentManager

Dodecahedral = Geometry.Dodecahedral

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

Linear = Geometry.Linear

Molecule = NodeType.StructuralModelNodeMolecule

NodeGroup = NodeType.DataGraphNodeGroup

None = Hybridization.None

Octahedral = Geometry.Octahedral

ParticleSystem = NodeType.DynamicalModelParticleSystem

Path = NodeType.StructuralModelPath

PentagonalBipyramidal = Geometry.PentagonalBipyramidal

PentagonalPlanar = Geometry.PentagonalPlanar

PentagonalPyramidal = Geometry.PentagonalPyramidal

PropertyModel = NodeType.PropertyModel

PropertyModelFunction = NodeType.PropertyModelFunction

Protein = NodeType.StructuralModelNodeProtein

PseudoAtom = NodeType.StructuralModelNodePseudoAtom

Residue = NodeType.StructuralModelNodeResidue

RigidBody = NodeType.DynamicalModelNodeRigidBody

RigidBodySystem = NodeType.DynamicalModelRigidBodySystem

Root = NodeType.StructuralModelNodeRoot

SP = Hybridization.SP

SP2 = Hybridization.SP2

SP3 = Hybridization.SP3

SP3D = Hybridization.SP3D

SP3D2 = Hybridization.SP3D2

SYBYLTypeSize

The atom’s SYBYLType size

Seesaw = Geometry.Seesaw

Segment = NodeType.StructuralModelNodeSegment

SideChain = NodeType.StructuralModelNodeSideChain

Simulator = NodeType.Simulator

SimulatorArticulatedBodySystem = NodeType.SimulatorArticulatedBodySystem

SimulatorParticleSystem = NodeType.SimulatorParticleSystem

SimulatorRigidBodySystem = NodeType.SimulatorRigidBodySystem

SquareAntiprismatic = Geometry.SquareAntiprismatic

SquarePlanar = Geometry.SquarePlanar

SquarePyramidal = Geometry.SquarePyramidal

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.StructuralModelNodeAtom

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

TShaped = Geometry.TShaped

Tetrahedral = Geometry.Tetrahedral

TricappedTrigonalPrismatic = Geometry.TricappedTrigonalPrismatic

TrigonalBipyramidal = Geometry.TrigonalBipyramidal

TrigonalPlanar = Geometry.TrigonalPlanar

TrigonalPrismatic = Geometry.TrigonalPrismatic

TrigonalPyramidal = Geometry.TrigonalPyramidal

Undefined = Geometry.Undefined

Unknown = Hybridization.Unknown

VisualModel = NodeType.VisualModel

alternateLocation

The atom’s alternate location

anisotropicTFactors

The atom’s AnisotropicTFactors

aromaticity

The atom’s Aromaticity

atomicWeight

The atom’s atomic weight

block

The atom’s block

chainID

Returns the ID of a chain in which the atom is

chainIDString

Returns the ID (as a string) of a chain in which the atom is

chainName

Returns the atom’s chain name

commentSize

The atom’s comment size

covalentRadius

The atom’s covalent radius

currentValence

The current valence, i.e. the sum of the orders of the bonds connected to the atom

customType

The atom’s CustomType

electronegativity

The atom’s electronegativity

elementName

The atom’s element name

elementSymbol

The atom’s element symbol

elementType

The atom’s element type

expectedValence

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

formalCharge

The atom’s FormalCharge

geometry

The atom’s geometry

geometryString

Returns the geometry as a string

group

The atom’s 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

hasChainID

Returns true when the atom is in a chain and the chain’s ID 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

hasGeometry

Returns true when the atom’s geometry is set

hasHybridization

Returns true when the atom’s hybridization is set

hasInsertionCode

Returns true when the atom’s insertion code is set

hasName

Returns true when the atom’s name is set

hasOccupancy

Returns true when the atom’s occupancy is set

hasOxidationState

Returns true when the atom’s OxidationState is set

hasPartialCharge

Returns true when the atom’s PartialCharge is set

hasRecordType

Returns true when the atom’s RecordType is set

hasResidueSequenceNumber

Returns true when the atom is in a residue and the chain’s ID is set

hasResonance

Returns true when the atom’s Resonance is set

hasSYBYLType

Returns true when the atom’s SYBYLType is set

hasSerialNumber

Returns true when the atom’s serial number is set

hasStatusBit

Returns true when the atom’s statusBit is set

hasSubstructureSequenceNumber

Returns true when the atom is in a substructure and the chain’s ID is set

hasTemperatureFactor

Returns true when the atom’s TemperatureFactor is set

hasWaterFlag

Returns true when the atom’s WaterFlag is set

highlightingFlag

hybridization

The atom’s hybridization

hybridizationString

Returns the hybridization as a string

insertionCode

The atom’s insertion code

isAttachedToHydrogenBondDonor

Returns true if the atom is connected to an H-Bond donor

isCarboxylOxygen

Returns true for an Oxygen atom in a carboxyl group (C(=O)OH)

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

isHydrogenBondAcceptor

Returns true if the atom is an H-Bond acceptor

isHydrogenBondDonor

Returns true if the atom is an H-Bond donor

isInChain

Returns true when the atom is in a chain

isInMolecule

Returns true when the atom is in a molecule

isInResidue

Returns true when the atom is in a residue group

isInSegment

Returns true when the atom is in segment

isInSubstructure

Returns true when the atom is in a substructure group

isMetal

Returns true if the atom is metal

isNitroOxygen

Returns true for an Oxygen atom in a nitro group (-NO2)

isSelected

Returns whether the node is selected

isSerializable

Returns true when the class is serializable

isSulfoneOxygen

Returns true for an Oxygen atom in a sulfone (R1-SO2-R2)

isThiocarboxylOxygen

Returns true for an Oxygen atom in a thiocarboxyl group (C(=S)OH or C(=O)SH)

isVisible

Returns whether the node is visible

metalSubcategory

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

metalSubcategoryString

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

mobilityFlag

The node’s mobility flag

moleculeName

Returns the name of a molecule in which the atom is

name

The atom’s full name

nodeIndex

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

occupancy

The atom’s occupancy

oxidationState

The atom’s OxidationState

partialCharge

The atom’s PartialCharge

period

The atom’s period

recordTypeSize

The atom’s RecordType size

residueName

Returns the name of a residue in which the atom is

residueSequenceNumber

Returns the sequence number of a residue in which the atom is

residueSequenceNumberString

Returns the sequence number (as a string) of a residue in which the atom is

residueTypeString

Returns the name of a residue in which the atom is

resonance

The atom’s Resonance

segmentName

Returns the name of a segment in which the atom is

selectionFlag

serialNumber

The atom’s serial number

statusBitSize

The atom’s statusBit size

substructureName

Returns the name of a substructure in which the atom is

substructureSequenceNumber

Returns the sequence number of a substructure in which the atom is

substructureSequenceNumberString

Returns the sequence number (as a string) of a substructure in which the atom is

temperatureFactor

The atom’s TemperatureFactor

type

The type of the data graph node

typeString

Returns a string describing the type of this data graph node

vanDerWaalsRadius

The atom’s van der Waals radius

visibilityFlag

waterFlag

The atom’s WaterFlag