Residue

See also

SAMSON API: SBMStructuralModelNodeResidue

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

Bases: samson.Modeling.StructuralModel.Group

This class describes a residue in a structural model.

Overloaded function.

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

Builds a residue

2. __init__(self: samson.Modeling.StructuralModel.Residue, arg0: str) -> None

Builds a residue

class HydrophobicityScale(self: samson.Modeling.StructuralModel.Residue.HydrophobicityScale, value: int) → None

Bases: pybind11_builtins.pybind11_object

Members:

KyteDoolittle1982 : A hydrophobicity scale of Kyte J, Doolittle RF, A simple method for displaying the hydropathic character of a protein, J Mol Biol. 1982.

SeredaEtAl1994

MoneraEtAl1995

WimleyWhite1996

HessaEtAl2005

ZhaoLondon2006

MoonFleming2011

HessaEtAl2005 = <HydrophobicityScale.HessaEtAl2005: 4>

KyteDoolittle1982 = <HydrophobicityScale.KyteDoolittle1982: 0>

MoneraEtAl1995 = <HydrophobicityScale.MoneraEtAl1995: 2>

MoonFleming2011 = <HydrophobicityScale.MoonFleming2011: 6>

SeredaEtAl1994 = <HydrophobicityScale.SeredaEtAl1994: 1>

WimleyWhite1996 = <HydrophobicityScale.WimleyWhite1996: 3>

ZhaoLondon2006 = <HydrophobicityScale.ZhaoLondon2006: 5>

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

class ResidueType(self: samson.Modeling.StructuralModel.Residue.ResidueType, value: int) → None

Bases: pybind11_builtins.pybind11_object

Members:

Undefined : Undefined residue type

ALA : Alanine

ARG : Arginine

ASP : Aspartic acid

ASN : Asparagine

VAL : Valine

HIS : Histidine

GLY : Glycine

GLU : Glutamic acid

GLN : Glutamine

ILE : Isoleucine

LEU : Leucine

LYS : Lysine

MET : Methionine

PRO : Proline

SER : Serine

TYR : Tyrosine

THR : Threonine

TRP : Tryptophan

PHE : Phenylalanine

CYS : Cysteine

ASX : ASN or ASP (Asparagine or Aspartic acid)

GLX : GLN or GLU (Glutamine or Glutamic acid)

XLE : LEU or ILE (Leucine or Isoleucine)

XAA : Unknown residue type

SEC : Selenocysteine

PYL : Pyrrolysine

A : Adenosine-5’-monophosphate

C : Cytidine-5’-monophosphate

G : Guanosine-5’-monophosphate

U : Uridine-5’-monophosphate

I : Inosinic acid

DA : 2’-deoxyadenosine-5’-monophosphate

DC : 2’-deoxycytidine-5’-monophosphate

DG : 2’-deoxyguanosine-5’-monophosphate

DT : Thymidine-5’-monophosphate

DI : 2’-deoxyinosine-5’-monophosphate

A = <ResidueType.A: 27>

ALA = <ResidueType.ALA: 1>

ARG = <ResidueType.ARG: 2>

ASN = <ResidueType.ASN: 4>

ASP = <ResidueType.ASP: 3>

ASX = <ResidueType.ASX: 21>

C = <ResidueType.C: 28>

CYS = <ResidueType.CYS: 20>

DA = <ResidueType.DA: 32>

DC = <ResidueType.DC: 33>

DG = <ResidueType.DG: 34>

DI = <ResidueType.DI: 36>

DT = <ResidueType.DT: 35>

G = <ResidueType.G: 29>

GLN = <ResidueType.GLN: 9>

GLU = <ResidueType.GLU: 8>

GLX = <ResidueType.GLX: 22>

GLY = <ResidueType.GLY: 7>

HIS = <ResidueType.HIS: 6>

I = <ResidueType.I: 31>

ILE = <ResidueType.ILE: 10>

LEU = <ResidueType.LEU: 11>

LYS = <ResidueType.LYS: 12>

MET = <ResidueType.MET: 13>

PHE = <ResidueType.PHE: 19>

PRO = <ResidueType.PRO: 14>

PYL = <ResidueType.PYL: 26>

SEC = <ResidueType.SEC: 25>

SER = <ResidueType.SER: 15>

THR = <ResidueType.THR: 17>

TRP = <ResidueType.TRP: 18>

TYR = <ResidueType.TYR: 16>

U = <ResidueType.U: 30>

Undefined = <ResidueType.Undefined: 0>

VAL = <ResidueType.VAL: 5>

XAA = <ResidueType.XAA: 24>

XLE = <ResidueType.XLE: 23>

property name

property value

class SecondaryStructureType(self: samson.Modeling.StructuralModel.Residue.SecondaryStructureType, value: int) → None

Bases: pybind11_builtins.pybind11_object

Members:

Unstructured : Unstructured secondary structure element

Alpha : Alpha helix secondary structure element

Beta : Beta strand/sheet secondary structure element

Alpha = <SecondaryStructureType.Alpha: 1>

Beta = <SecondaryStructureType.Beta: 2>

Unstructured = <SecondaryStructureType.Unstructured: 0>

property name

property value

class SideChainCharge(self: samson.Modeling.StructuralModel.Residue.SideChainCharge, value: int) → None

Bases: pybind11_builtins.pybind11_object

Members:

UndefinedSideChainCharge : Undefined side chain charge

Negative : Residue has a side chain with negative charge

Neutral : Residue has a side chain with neutral charge

Positive : Residue has a side chain with positive charge

Negative = <SideChainCharge.Negative: 1>

Neutral = <SideChainCharge.Neutral: 2>

Positive = <SideChainCharge.Positive: 3>

UndefinedSideChainCharge = <SideChainCharge.UndefinedSideChainCharge: 0>

property name

property value

class SideChainPolarity(self: samson.Modeling.StructuralModel.Residue.SideChainPolarity, value: int) → None

Bases: pybind11_builtins.pybind11_object

Members:

UndefinedSideChainPolarity : Undefined side chain polarity

Nonpolar : Residue has a nonpolar side chain

Polar : Residue has a polar side chain with

AcidicPolar : Residue has a side chain with acidic polarity

BasicPolar : Residue has a side chain with basic polarity

AcidicPolar = <SideChainPolarity.AcidicPolar: 3>

BasicPolar = <SideChainPolarity.BasicPolar: 4>

Nonpolar = <SideChainPolarity.Nonpolar: 1>

Polar = <SideChainPolarity.Polar: 2>

UndefinedSideChainPolarity = <SideChainPolarity.UndefinedSideChainPolarity: 0>

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

addHydrogensByResidueType(self: samson.Modeling.StructuralModel.Residue) → int

Adds hydrogen atoms based on the residue type

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

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

Clears the group’s Comment

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

Clears the group’s status bit

clearStructuralID(self: samson.Modeling.StructuralModel.Group) → None

Clears the structural group’s id

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

Returns a copy of the node and its descendants

computeAminoAcidChi1Angle(self: samson.Modeling.StructuralModel.Residue) → samson.DataModel.Quantity.unitsSI

Computes the chi1 angle (in degrees) for the amino acid residue’s side chain

computeAminoAcidChi2Angle(self: samson.Modeling.StructuralModel.Residue) → samson.DataModel.Quantity.unitsSI

Computes the chi2 angle (in degrees) for the amino acid residue’s side chain

computeAminoAcidChi3Angle(self: samson.Modeling.StructuralModel.Residue) → samson.DataModel.Quantity.unitsSI

Computes the chi3 angle (in degrees) for the amino acid residue’s side chain

computeAminoAcidChi4Angle(self: samson.Modeling.StructuralModel.Residue) → samson.DataModel.Quantity.unitsSI

Computes the chi4 angle (in degrees) for the amino acid residue’s side chain

computeAminoAcidChi5Angle(self: samson.Modeling.StructuralModel.Residue) → samson.DataModel.Quantity.unitsSI

Computes the chi5 angle (in degrees) for the amino acid residue’s side chain

computeAminoAcidPhiAngle(self: samson.Modeling.StructuralModel.Residue) → samson.DataModel.Quantity.unitsSI

Computes the phi dihedral angle (in degrees) for the amino acid residue’s backbone

computeAminoAcidPsiAngle(self: samson.Modeling.StructuralModel.Residue) → samson.DataModel.Quantity.unitsSI

Computes the psi dihedral angle (in degrees) for the amino acid residue’s backbone

computeNucleicAcidAlphaAngle(self: samson.Modeling.StructuralModel.Residue) → samson.DataModel.Quantity.unitsSI

Computes the alpha (O3’(i-1)-P-O5’-C5’) dihedral angle (in degrees) for the nucleic acid’s backbone

computeNucleicAcidBetaAngle(self: samson.Modeling.StructuralModel.Residue) → samson.DataModel.Quantity.unitsSI

Computes the beta (P-O5’-C5’-C4’) dihedral angle (in degrees) for the nucleic acid’s backbone

computeNucleicAcidChiAngle(self: samson.Modeling.StructuralModel.Residue) → samson.DataModel.Quantity.unitsSI

Computes the chi dihedral angle (in degrees) for the nucleic acid’s backbone

computeNucleicAcidDeltaAngle(self: samson.Modeling.StructuralModel.Residue) → samson.DataModel.Quantity.unitsSI

Computes the delta (C5’-C4’-C3’-O3’) dihedral angle (in degrees) for the nucleic acid’s backbone

computeNucleicAcidEpsilonAngle(self: samson.Modeling.StructuralModel.Residue) → samson.DataModel.Quantity.unitsSI

Computes the epsilon (C4’-C3’-O3’-P(i+1)) dihedral angle (in degrees) for the nucleic acid’s backbone

computeNucleicAcidGammaAngle(self: samson.Modeling.StructuralModel.Residue) → samson.DataModel.Quantity.unitsSI

Computes the gamma (O5’-C5’-C4’-C3’) dihedral angle (in degrees) for the nucleic acid’s backbone

computeNucleicAcidZetaAngle(self: samson.Modeling.StructuralModel.Residue) → samson.DataModel.Quantity.unitsSI

Computes the zeta (C3’-O3’-P(i+1)-O5’(i+1)) dihedral angle (in degrees) for the nucleic acid’s backbone

countNodes(*args, **kwargs)

Overloaded function.

1. 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

2. 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

createCovalentBondsByResidueType(self: samson.Modeling.StructuralModel.Residue) → int

Sets the order of covalent bonds for the atoms belonging to the residue according to the residue type, regardless of inter-atomic distances

descendsFrom(*args, **kwargs)

Overloaded function.

1. 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

2. 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

static getAminoAcidOneLetterCode(residueType: SBMStructuralModelNodeResidue::ResidueType) → str

Returns one letter code of the amino acid residue residueTypee

getBackbone(self: samson.Modeling.StructuralModel.Residue) → samson.Modeling.StructuralModel.Backbone

getChildren(self: samson.Modeling.StructuralModel.Group) → samson.DataModel.DataGraph.NodeIndexer

Returns the children of the group

static getDissociationConstant1(residueType: SBMStructuralModelNodeResidue::ResidueType) → float

Returns the pKa1 value (the negative of the logarithm of the dissociation constant for the carboxyl functional group, -COOH) for the residue residueType

static getDissociationConstant2(residueType: SBMStructuralModelNodeResidue::ResidueType) → float

Returns the pKa2 value (the negative of the logarithm of the dissociation constant for the amino functional group, -NH3) for the residue residueType

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

Returns the document the node belongs to

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

Returns the flags

getHierarchyString(self: samson.DataModel.DataGraph.Node, separator: str = ' / ', includeNodeType: bool = False) → str

Returns a string with hierarchical information on the node and its parents names

getHydrophobicity(*args, **kwargs)

Overloaded function.

1. getHydrophobicity(self: samson.Modeling.StructuralModel.Residue) -> float

Returns the residue’s hydrophobicity in the current hydrophobicity scale

2. getHydrophobicity(self: samson.Modeling.StructuralModel.Residue, hydrophobicityScale: samson.Modeling.StructuralModel.Residue.HydrophobicityScale) -> float

Returns the residue’s hydrophobicity in the given hydrophobicity scale hydrophobicityScale

static getHydrophobicityForResidueType(residueType: SBMStructuralModelNodeResidue::ResidueType, hydrophobicityScale: samson.Modeling.StructuralModel.Residue.HydrophobicityScale) → float

Returns the hydrophobicity value for the residue residueType in the hydrophobicity scale hydrophobicityScale

static getHydrophobicityScaleString(hydrophobicityScale: samson.Modeling.StructuralModel.Residue.HydrophobicityScale) → str

Returns the hydrophobicity scale hydrophobicityScale as a string

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

Returns the inherited flags

static getIsoelectricPointPH(residueType: SBMStructuralModelNodeResidue::ResidueType) → float

Returns the pI value (the pH at the isoelectric point) for the residue residueType

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

getMolecularWeight(self: samson.Modeling.StructuralModel.Group) → samson.DataModel.Quantity.unitsSI

Returns the cumulative molecular weight of atoms in the structural group

getNextAminoAcid(self: samson.Modeling.StructuralModel.Residue) → samson.Modeling.StructuralModel.Residue

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

getNextNucleicAcid(self: samson.Modeling.StructuralModel.Residue) → samson.Modeling.StructuralModel.Residue

getNextResidue(self: samson.Modeling.StructuralModel.Residue) → samson.Modeling.StructuralModel.Residue

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.

1. 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

2. 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

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

Returns the parent of the node

getPreviousAminoAcid(self: samson.Modeling.StructuralModel.Residue) → samson.Modeling.StructuralModel.Residue

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

getPreviousNucleicAcid(self: samson.Modeling.StructuralModel.Residue) → samson.Modeling.StructuralModel.Residue

getPreviousResidue(self: samson.Modeling.StructuralModel.Residue) → samson.Modeling.StructuralModel.Residue

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

static getResidueTypeFromString(residueTypeString: str) → SBMStructuralModelNodeResidue::ResidueType

Returns the residue’s type based on the given string

static getResidueTypeFullName(residueType: SBMStructuralModelNodeResidue::ResidueType) → str

Returns the full name of the residue type residueType

static getResidueTypeString(residueType: SBMStructuralModelNodeResidue::ResidueType) → str

Returns the string representation of the residue type residueType

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

Returns the root of the hierarchy the node belongs to

getSecondaryStructureTypeString(self: samson.Modeling.StructuralModel.Residue, secondaryStructureType: SBMStructuralModelNodeResidue::SecondaryStructureType) → str

Returns the secondary structure type secondaryStructureType as a string

getSideChain(self: samson.Modeling.StructuralModel.Residue) → SBMStructuralModelNodeSideChain

static getSideChainCharge(residueType: SBMStructuralModelNodeResidue::ResidueType) → samson.Modeling.StructuralModel.Residue.SideChainCharge

Returns the residue’s side chain charge for the residue residueType

static getSideChainChargeString(sideChainCharge: samson.Modeling.StructuralModel.Residue.SideChainCharge) → str

Returns a side chain charge sideChainCharge as a string

static getSideChainPolarity(residueType: SBMStructuralModelNodeResidue::ResidueType) → samson.Modeling.StructuralModel.Residue.SideChainPolarity

Returns the residue’s side chain polarity for the residue residueType

static getSideChainPolarityString(sideChainPolarity: samson.Modeling.StructuralModel.Residue.SideChainPolarity) → str

Returns a side chain polarity sideChainPolarity as a string

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

hasAminoAcidChi1Angle(self: samson.Modeling.StructuralModel.Residue) → bool

Returns true if it is an amino acid and has chi1 angle

static hasAminoAcidChi1AngleForResidueType(residueType: SBMStructuralModelNodeResidue::ResidueType) → bool

Returns true if the residue type residueType is an amino acid and has chi1 angle

hasAminoAcidChi2Angle(self: samson.Modeling.StructuralModel.Residue) → bool

Returns true if it is an amino acid and has chi2 angle

static hasAminoAcidChi2AngleForResidueType(residueType: SBMStructuralModelNodeResidue::ResidueType) → bool

Returns true if the residue type residueType is an amino acid and has chi2 angle

hasAminoAcidChi3Angle(self: samson.Modeling.StructuralModel.Residue) → bool

Returns true if it is an amino acid and has chi3 angle

static hasAminoAcidChi3AngleForResidueType(residueType: SBMStructuralModelNodeResidue::ResidueType) → bool

Returns true if the residue type residueType is an amino acid and has chi3 angle

hasAminoAcidChi4Angle(self: samson.Modeling.StructuralModel.Residue) → bool

Returns true if it is an amino acid and has chi4 angle

static hasAminoAcidChi4AngleForResidueType(residueType: SBMStructuralModelNodeResidue::ResidueType) → bool

Returns true if the residue type residueType is an amino acid and has chi4 angle

hasAminoAcidChi5Angle(self: samson.Modeling.StructuralModel.Residue) → bool

Returns true if it is an amino acid and has chi5 angle

static hasAminoAcidChi5AngleForResidueType(residueType: SBMStructuralModelNodeResidue::ResidueType) → bool

Returns true if the residue type residueType is an amino acid and has chi5 angle

static hasDissociationConstantForResidueType(residueType: SBMStructuralModelNodeResidue::ResidueType) → bool

Returns true if the dissociation constants (pKa1, pKa2) and isoelectric point are defined for the residue residueType

static hasHydrophobicityForResidueType(residueType: SBMStructuralModelNodeResidue::ResidueType) → bool

Returns true if for the residue type residueType the hydrophobicity is defined

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

static hasSideChainChargeForResidueType(residueType: SBMStructuralModelNodeResidue::ResidueType) → bool

Returns true if for the residue type residueType the side chain charge is defined

static hasSideChainPolarityForResidueType(residueType: SBMStructuralModelNodeResidue::ResidueType) → bool

Returns true if for the residue type residueType the side chain polarity is defined

static isAminoAcidResidueType(residueType: SBMStructuralModelNodeResidue::ResidueType) → bool

Returns true if and only if the given residue type is of amino acid

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, or belongs to a group stored in node

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, 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

static isNucleicAcidResidueType(residueType: SBMStructuralModelNodeResidue::ResidueType) → bool

Returns true if and only if the given residue type is of nucleic acid

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

isWater(self: samson.Modeling.StructuralModel.Group) → bool

Returns true if the structural group is a water molecule

orientAminoAcidSideChain(self: samson.Modeling.StructuralModel.Residue, chi1: samson.DataModel.Quantity.unitsSI, chi2: samson.DataModel.Quantity.unitsSI = 0, 000000 (dimensionless), chi3: samson.DataModel.Quantity.unitsSI = 0, 000000 (dimensionless), chi4: samson.DataModel.Quantity.unitsSI = 0, 000000 (dimensionless), chi5: samson.DataModel.Quantity.unitsSI = 0, 000000 (dimensionless)) → bool

Rotates the amino acid’s side chain to orient it according to given digedral angles chi1, chi2, chi3, chi4, chi5. Returns true if at least chi1 rotation was performed.

printDebugInfo(self: samson.DataModel.DataGraph.Node, offset: int = 0) → None

Prints some debugging information in stdout

removeChild(self: samson.DataModel.DataGraph.Node, node: samson.DataModel.DataGraph.Node) → bool

Removes a child from the node

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

Removes material from the node

setColor(self: samson.DataModel.DataGraph.Node, color: SBDTypeColor) → bool

Sets the color for the node (modifies an existing material of the node or adds a material with a given color)

Args:

color (Color): color to set

setColorScheme(self: samson.DataModel.DataGraph.Node, colorScheme: SBDDataGraphNodeColorScheme) → bool

Sets the color scheme for the node (modifies an existing material of the node or adds a material with a given color scheme)

Args: colorScheme (ColorScheme): color scheme to set

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

Sets the material for the node.

Args:

material (Material): material to set

setName(self: samson.Modeling.StructuralModel.Residue, arg0: str) → None

Sets the name of the residue, and updates accordingly names for its backbone and side chain.

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

A string representation

A = <ResidueType.A: 27>

ALA = <ResidueType.ALA: 1>

ARG = <ResidueType.ARG: 2>

ASN = <ResidueType.ASN: 4>

ASP = <ResidueType.ASP: 3>

ASX = <ResidueType.ASX: 21>

AcidicPolar = <SideChainPolarity.AcidicPolar: 3>

Alpha = <SecondaryStructureType.Alpha: 1>

Animation = <NodeType.Animation: 26>

ArticulatedBody = <NodeType.ArticulatedBody: 603>

ArticulatedBodySystem = <NodeType.ArticulatedBodySystem: 502>

Asset = <NodeType.Asset: 50>

Atom = <NodeType.Atom: 20100>

Backbone = <NodeType.Backbone: 209>

BasicPolar = <SideChainPolarity.BasicPolar: 4>

Beta = <SecondaryStructureType.Beta: 2>

Bond = <NodeType.Bond: 202>

C = <ResidueType.C: 28>

CYS = <ResidueType.CYS: 20>

Camera = <NodeType.Camera: 23>

Chain = <NodeType.Chain: 207>

Conformation = <NodeType.Conformation: 28>

Controller = <NodeType.Controller: 40>

ControllerNode = <NodeType.ControllerNode: 41>

DA = <ResidueType.DA: 32>

DC = <ResidueType.DC: 33>

DG = <ResidueType.DG: 34>

DI = <ResidueType.DI: 36>

DT = <ResidueType.DT: 35>

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>

G = <ResidueType.G: 29>

GLN = <ResidueType.GLN: 9>

GLU = <ResidueType.GLU: 8>

GLX = <ResidueType.GLX: 22>

GLY = <ResidueType.GLY: 7>

HIS = <ResidueType.HIS: 6>

HessaEtAl2005 = <HydrophobicityScale.HessaEtAl2005: 4>

HydrogenBond = <NodeType.HydrogenBond: 20202>

HydrogenBondGroup = <NodeType.HydrogenBondGroup: 20203>

I = <ResidueType.I: 31>

ILE = <ResidueType.ILE: 10>

InteractionModel = <NodeType.InteractionModel: 7>

InteractionModelArticulatedBodySystem = <NodeType.InteractionModelArticulatedBodySystem: 702>

InteractionModelParticleSystem = <NodeType.InteractionModelParticleSystem: 700>

InteractionModelRigidBodySystem = <NodeType.InteractionModelRigidBodySystem: 701>

KyteDoolittle1982 = <HydrophobicityScale.KyteDoolittle1982: 0>

LEU = <ResidueType.LEU: 11>

LYS = <ResidueType.LYS: 12>

Label = <NodeType.Label: 24>

MET = <ResidueType.MET: 13>

Mesh = <NodeType.Mesh: 300>

Molecule = <NodeType.Molecule: 208>

MoneraEtAl1995 = <HydrophobicityScale.MoneraEtAl1995: 2>

MoonFleming2011 = <HydrophobicityScale.MoonFleming2011: 6>

Negative = <SideChainCharge.Negative: 1>

Neutral = <SideChainCharge.Neutral: 2>

NodeGroup = <NodeType.DataGraphNodeGroup: 30>

Nonpolar = <SideChainPolarity.Nonpolar: 1>

Note = <NodeType.Note: 25>

PHE = <ResidueType.PHE: 19>

PRO = <ResidueType.PRO: 14>

PYL = <ResidueType.PYL: 26>

ParticleSystem = <NodeType.ParticleSystem: 500>

Path = <NodeType.Path: 29>

Polar = <SideChainPolarity.Polar: 2>

Positive = <SideChainCharge.Positive: 3>

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>

SEC = <ResidueType.SEC: 25>

SER = <ResidueType.SER: 15>

Segment = <NodeType.Segment: 205>

SeredaEtAl1994 = <HydrophobicityScale.SeredaEtAl1994: 1>

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>

THR = <ResidueType.THR: 17>

TRP = <ResidueType.TRP: 18>

TYR = <ResidueType.TYR: 16>

U = <ResidueType.U: 30>

Undefined = <ResidueType.Undefined: 0>

UndefinedSideChainCharge = <SideChainCharge.UndefinedSideChainCharge: 0>

UndefinedSideChainPolarity = <SideChainPolarity.UndefinedSideChainPolarity: 0>

Unstructured = <SecondaryStructureType.Unstructured: 0>

VAL = <ResidueType.VAL: 5>

VisualModel = <NodeType.VisualModel: 3>

VisualModelMesh = <NodeType.Mesh: 300>

WimleyWhite1996 = <HydrophobicityScale.WimleyWhite1996: 3>

XAA = <ResidueType.XAA: 24>

XLE = <ResidueType.XLE: 23>

ZhaoLondon2006 = <HydrophobicityScale.ZhaoLondon2006: 5>

property aminoAcidOneLetterCode

Returns one letter code of the amino acid residue

property comment

The group’s comment

property defaultOpacity

Returns the default opacity

property defaultTransparency

Returns the default transparency

property dissociationConstant1

Returns the pKa1 value (the negative of the logarithm of the dissociation constant for the carboxyl functional group, -COOH) for this residue

property dissociationConstant2

Returns the pKa2 value (the negative of the logarithm of the dissociation constant for the amino functional group, -NH3) for this residue

property hasComment

Returns true when the group’s Comment is set

property hasCompleteAminoAcidBackbone

Returns true if and only if the residue has a complete amino-acid backbone

property hasDissociationConstant

Returns true if the dissociation constants (pKa1, pKa2) and isoelectric point are defined for this residue

property hasHydrophobicity

Returns true if the residue’s hydrophobicity is defined

property hasMaterial

Returns whether the node has a material (by itself, or inherited)

property hasOpacityRange

Returns whether the node has opacity range

property hasSideChainCharge

Returns true if the residue’s side chain charge is defined

property hasSideChainPolarity

Returns true if the residue’s side chain polarity is defined

property hasStatusBit

Returns true when the group’s status bit is set

property hasStructuralID

Returns true when the structural group’s id is set

property hasTransparencyRange

Returns whether the node has transparency range

property highlightingFlag

Highlighting flag

property hydrophobicityScale

The current residue’s hydrophobicity scale

property hydrophobicityScaleString

Returns the current hydrophobicity scale as a string

property isAminoAcid

Returns true if and only if the residue is an amino acid

property isCreated

Returns true if and only if the node is created

property isErased

Returns true if and only if the node is erased

property isHighlighted

Returns whether the node is highlighted

property isLocked

Returns whether the node is locked

property isNucleicAcid

Returns true if and only if the residue is a nucleic acid

property isSelected

Returns whether the node is selected

property isSerializable

Returns true when the class is serializable

property isTerminal

Returns true if and only if the residue is terminal

property isVisible

Returns whether the node is visible

property isoelectricPointPH

Returns the pI value (the pH at the isoelectric point) for this residue

property lockedFlag

Locked flag

property maximumOpacity

Returns the maximum opacity

property maximumTransparency

Returns the maximum transparency

property minimumOpacity

Returns the minimum opacity

property minimumTransparency

Returns the minimum transparency

property mobilityFlag

The node’s mobility flag

property molecularWeight

Returns the molecular weight

property name

The name of the node

property nodeIndex

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

property numberOfAtoms

Returns the number of atoms

property numberOfCarbons

Returns the number of carbons

property numberOfChains

Returns the number of chains

property numberOfHydrogens

Returns the number of hydrogens

property numberOfMolecules

Returns the number of molecules

property numberOfNitrogens

Returns the number of nitrogens

property numberOfOtherAtoms

Returns the number of other atoms

property numberOfOxygens

Returns the number of oxygens

property numberOfResidues

Returns the number of residues

property numberOfSegments

Returns the number of segments

property numberOfStructuralGroups

Returns the number of structural groups

property numberOfStructuralModels

Returns the number of structural models

property numberOfSulfurs

Returns the number of sulfurs

property opacity

Opacity

property ownsMaterial

Returns whether the node owns a material

property residueType

property residueTypeFullName

Returns the full name of the residue’s type

property residueTypeString

property secondaryStructureType

Returns the most probable secondary structure based on bonds parameters and residue geometry

property secondaryStructureTypeString

The secondary structure type as a string

property selectionFlag

Selection flag

property sideChainCharge

Returns the residue’s side chain charge

property sideChainChargeString

Returns the residue’s side chain charge as a string

property sideChainPolarity

Returns the residue’s side chain polarity

property sideChainPolarityString

Returns the residue’s side chain polarity as a string

property statusBit

The group’s status bit

property structuralID

The structural group’s id

property sumOfFormalCharges

Returns the sum of formal charges

property sumOfPartialCharges

Returns the sum of partial charges

property transparency

Transparency

property type

Returns the type of the data graph node

property typeString

Returns a string describing the type of this data graph node

property visibilityFlag

Visibility flag