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, 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
VisualModelMesh
Mesh
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
Note
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¶
-
Mesh
= NodeType.VisualModelMesh¶
-
Molecule
= NodeType.StructuralModelNodeMolecule¶
-
NodeGroup
= NodeType.DataGraphNodeGroup¶
-
Note
= NodeType.Note¶
-
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¶
-
VisualModelMesh
= NodeType.VisualModelMesh¶
-
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
-
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.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: pagenodespecificationlanguage
-
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
(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
-
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
(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: pagenodespecificationlanguage
-
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.
- 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
-
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.
- 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
-
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
-
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
-
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¶
-
Mesh
= NodeType.VisualModelMesh¶
-
Molecule
= NodeType.StructuralModelNodeMolecule¶
-
NodeGroup
= NodeType.DataGraphNodeGroup¶
-
None
= Hybridization.None¶
-
Note
= NodeType.Note¶
-
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¶
-
VisualModelMesh
= NodeType.VisualModelMesh¶
-
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
-
hasAminoAcidBackboneAtomName
¶ Returns true when the atom’s name corresponds to one of the amino-acid backbone atoms
-
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
-
hasNucleicAcidBackboneAtomName
¶ Returns true when the atom’s name corresponds to one of the nucleic acid backbone atoms
-
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
-
isDonorborneHydrogen
¶ Returns true if the atom is a hydrogen connected to an H-Bond donor
-
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 (N, O, S, F)
-
isHydrogenBondDonor
¶ Returns true if the atom is an H-Bond donor (N, O, S, F)
-
isInBackbone
¶ Returns true when the atom is in a backbone
-
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