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, arg0: int) → None

Bases: pybind11_builtins.pybind11_object

Members:

KyteDoolittle1982

SeredaEtAl1994

MoneraEtAl1995

WimleyWhite1996

HessaEtAl2005

ZhaoLondon2006

MoonFleming2011

HessaEtAl2005 = HydrophobicityScale.HessaEtAl2005

KyteDoolittle1982 = HydrophobicityScale.KyteDoolittle1982

MoneraEtAl1995 = HydrophobicityScale.MoneraEtAl1995

MoonFleming2011 = HydrophobicityScale.MoonFleming2011

SeredaEtAl1994 = HydrophobicityScale.SeredaEtAl1994

WimleyWhite1996 = HydrophobicityScale.WimleyWhite1996

ZhaoLondon2006 = HydrophobicityScale.ZhaoLondon2006

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

class ResidueType(self: samson.Modeling.StructuralModel.Residue.ResidueType, arg0: int) → None

Bases: pybind11_builtins.pybind11_object

Members:

Undefined

ALA

ARG

ASP

ASN

VAL

HIS

GLY

GLU

GLN

ILE

LEU

LYS

MET

PRO

SER

TYR

THR

TRP

PHE

CYS

ASX

GLX

XLE

XAA

SEC

PYL

A

C

G

U

I

DA

DC

DG

DT

DI

A = ResidueType.A

ALA = ResidueType.ALA

ARG = ResidueType.ARG

ASN = ResidueType.ASN

ASP = ResidueType.ASP

ASX = ResidueType.ASX

C = ResidueType.C

CYS = ResidueType.CYS

DA = ResidueType.DA

DC = ResidueType.DC

DG = ResidueType.DG

DI = ResidueType.DI

DT = ResidueType.DT

G = ResidueType.G

GLN = ResidueType.GLN

GLU = ResidueType.GLU

GLX = ResidueType.GLX

GLY = ResidueType.GLY

HIS = ResidueType.HIS

I = ResidueType.I

ILE = ResidueType.ILE

LEU = ResidueType.LEU

LYS = ResidueType.LYS

MET = ResidueType.MET

PHE = ResidueType.PHE

PRO = ResidueType.PRO

PYL = ResidueType.PYL

SEC = ResidueType.SEC

SER = ResidueType.SER

THR = ResidueType.THR

TRP = ResidueType.TRP

TYR = ResidueType.TYR

U = ResidueType.U

Undefined = ResidueType.Undefined

VAL = ResidueType.VAL

XAA = ResidueType.XAA

XLE = ResidueType.XLE

name

(self – handle) -> str

class SecondaryStructureType(self: samson.Modeling.StructuralModel.Residue.SecondaryStructureType, arg0: int) → None

Bases: pybind11_builtins.pybind11_object

Members:

Unstructured

Alpha

Beta

Alpha = SecondaryStructureType.Alpha

Beta = SecondaryStructureType.Beta

Unstructured = SecondaryStructureType.Unstructured

name

(self – handle) -> str

class SideChainCharge(self: samson.Modeling.StructuralModel.Residue.SideChainCharge, arg0: int) → None

Bases: pybind11_builtins.pybind11_object

Members:

UndefinedSideChainCharge

Negative

Neutral

Positive

Negative = SideChainCharge.Negative

Neutral = SideChainCharge.Neutral

Positive = SideChainCharge.Positive

UndefinedSideChainCharge = SideChainCharge.UndefinedSideChainCharge

name

(self – handle) -> str

class SideChainPolarity(self: samson.Modeling.StructuralModel.Residue.SideChainPolarity, arg0: int) → None

Bases: pybind11_builtins.pybind11_object

Members:

UndefinedSideChainPolarity

Nonpolar

Polar

AcidicPolar

BasicPolar

AcidicPolar = SideChainPolarity.AcidicPolar

BasicPolar = SideChainPolarity.BasicPolar

Nonpolar = SideChainPolarity.Nonpolar

Polar = SideChainPolarity.Polar

UndefinedSideChainPolarity = SideChainPolarity.UndefinedSideChainPolarity

name

(self – handle) -> str

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

Adds a child to the node

canAddChild(self: samson.Modeling.StructuralModel.Residue, 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.Modeling.StructuralModel.Residue, nodeType: samson.DataModel.DataGraph.Node.NodeType) → 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

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.Modeling.StructuralModel.Residue) → samson.Modeling.StructuralModel.Residue

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

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

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

Erases the node

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

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

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(self: samson.DataModel.DataGraph.Node, selectionString: str = '*', visitString: str = '*', includeDependencies: bool = False) → samson.DataModel.DataGraph.NodeIndexer

Returns nodes (in a node indexer), based on a selectionString and a visitString, with our without dependencies).

For selectionString and visitString use Node Specification Language (SAMSON API: Node Specification Language

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

Returns the parent of the node

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 getResidueTypeString(residueType: SBMStructuralModelNodeResidue::ResidueType) → str

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

getTypeString(type: SBDDataGraphNode::Type) → str

Returns a string describing the type of the data graph node

static hasDissociationConstant(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 hasSideChainCharge(residueType: SBMStructuralModelNodeResidue::ResidueType) → bool

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

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

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

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.Residue, offset: int = 0) → None

Prints some debugging information in stdout

removeChild(self: samson.Modeling.StructuralModel.Residue, 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 accordingle names for its backbone and side chain.

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

A string representation

A = ResidueType.A

ALA = ResidueType.ALA

ARG = ResidueType.ARG

ASN = ResidueType.ASN

ASP = ResidueType.ASP

ASX = ResidueType.ASX

AcidicPolar = SideChainPolarity.AcidicPolar

Alpha = SecondaryStructureType.Alpha

ArticulatedBody = NodeType.DynamicalModelNodeArticulatedBody

ArticulatedBodySystem = NodeType.DynamicalModelArticulatedBodySystem

Asset = NodeType.Asset

Atom = NodeType.StructuralModelNodeAtom

Backbone = NodeType.StructuralModelNodeBackbone

BasicPolar = SideChainPolarity.BasicPolar

Beta = SecondaryStructureType.Beta

Bond = NodeType.StructuralModelNodeBond

C = ResidueType.C

CYS = ResidueType.CYS

Camera = NodeType.Camera

Chain = NodeType.StructuralModelNodeChain

Conformation = NodeType.StructuralModelConformation

Controller = NodeType.Controller

ControllerNode = NodeType.ControllerNode

DA = ResidueType.DA

DC = ResidueType.DC

DG = ResidueType.DG

DI = ResidueType.DI

DT = ResidueType.DT

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

G = ResidueType.G

GLN = ResidueType.GLN

GLU = ResidueType.GLU

GLX = ResidueType.GLX

GLY = ResidueType.GLY

HIS = ResidueType.HIS

HessaEtAl2005 = HydrophobicityScale.HessaEtAl2005

I = ResidueType.I

ILE = ResidueType.ILE

InteractionModel = NodeType.InteractionModel

InteractionModelArticulatedBodySystem = NodeType.InteractionModelArticulatedBodySystem

InteractionModelParticleSystem = NodeType.InteractionModelParticleSystem

InteractionModelRigidBodySystem = NodeType.InteractionModelRigidBodySystem

KyteDoolittle1982 = HydrophobicityScale.KyteDoolittle1982

LEU = ResidueType.LEU

LYS = ResidueType.LYS

Label = NodeType.Label

MET = ResidueType.MET

Molecule = NodeType.StructuralModelNodeMolecule

MoneraEtAl1995 = HydrophobicityScale.MoneraEtAl1995

MoonFleming2011 = HydrophobicityScale.MoonFleming2011

Negative = SideChainCharge.Negative

Neutral = SideChainCharge.Neutral

NodeGroup = NodeType.DataGraphNodeGroup

Nonpolar = SideChainPolarity.Nonpolar

PHE = ResidueType.PHE

PRO = ResidueType.PRO

PYL = ResidueType.PYL

ParticleSystem = NodeType.DynamicalModelParticleSystem

Path = NodeType.StructuralModelPath

Polar = SideChainPolarity.Polar

Positive = SideChainCharge.Positive

PropertyModel = NodeType.PropertyModel

PropertyModelFunction = NodeType.PropertyModelFunction

Protein = NodeType.StructuralModelNodeProtein

PseudoAtom = NodeType.StructuralModelNodePseudoAtom

Residue = NodeType.StructuralModelNodeResidue

RigidBody = NodeType.DynamicalModelNodeRigidBody

RigidBodySystem = NodeType.DynamicalModelRigidBodySystem

Root = NodeType.StructuralModelNodeRoot

SEC = ResidueType.SEC

SER = ResidueType.SER

Segment = NodeType.StructuralModelNodeSegment

SeredaEtAl1994 = HydrophobicityScale.SeredaEtAl1994

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

THR = ResidueType.THR

TRP = ResidueType.TRP

TYR = ResidueType.TYR

U = ResidueType.U

Undefined = ResidueType.Undefined

UndefinedSideChainCharge = SideChainCharge.UndefinedSideChainCharge

UndefinedSideChainPolarity = SideChainPolarity.UndefinedSideChainPolarity

Unstructured = SecondaryStructureType.Unstructured

VAL = ResidueType.VAL

VisualModel = NodeType.VisualModel

WimleyWhite1996 = HydrophobicityScale.WimleyWhite1996

XAA = ResidueType.XAA

XLE = ResidueType.XLE

ZhaoLondon2006 = HydrophobicityScale.ZhaoLondon2006

comment

The group’s comment

dissociationConstant

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

dissociationConstant1

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

dissociationConstant2

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

hasComment

Returns true when the group’s Comment is set

hasCompleteAminoAcidBackbone

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

hasHydrophobicity

Returns true if the residue’s hydrophobicity is defined

hasStatusBit

Returns true when the group’s status bit is set

hasStructuralID

Returns true when the structural group’s id is set

highlightingFlag

hydrophobicityScale

The current residue’s hydrophobicity scale

hydrophobicityScaleString

Returns the current hydrophobicity scale as a string

isAminoAcid

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

isCreated

Returns true if and only if the node is created

isErased

Returns true if and only if the node is erased

isHighlighted

Returns whether the node is highlighted

isNucleicAcid

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

isSelected

Returns whether the node is selected

isSerializable

Returns true when the class is serializable

isTerminal

Returns true if and only if the residue is terminal

isVisible

Returns whether the node is visible

isoelectricPointPH

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

mobilityFlag

The node’s mobility flag

name

The name of the group

nodeIndex

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

residueType

residueTypeString

secondaryStructureType

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

secondaryStructureTypeString

The secondary structure type as a string

selectionFlag

sideChainCharge

Returns the residue’s side chain charge

sideChainChargeString

Returns the residue’s side chain charge as a string

sideChainPolarity

Returns the residue’s side chain polarity

sideChainPolarityString

Returns the residue’s side chain polarity as a string

statusBit

The group’s status bit

structuralID

The structural group’s id

type

The type of the data graph node

typeString

Returns a string describing the type of this data graph node

visibilityFlag