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.
- __init__(self: samson.Modeling.StructuralModel.Residue) -> None
Builds a residue
- __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
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
-
-
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
-
addHydrogensByResidueType
(self: samson.Modeling.StructuralModel.Residue) → int¶ Adds hydrogen atoms based on the residue type
-
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
-
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.Modeling.StructuralModel.Residue) → samson.Modeling.StructuralModel.Residue¶ 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
-
computePhiAngle
(self: samson.Modeling.StructuralModel.Residue) → samson.DataModel.Quantity.unitsSI¶ Computes the phi dihedral angle (in degrees) for the residue’s backbone
-
computePsiAngle
(self: samson.Modeling.StructuralModel.Residue) → samson.DataModel.Quantity.unitsSI¶ Computes the psi dihedral angle (in degrees) for the residue’s backbone
-
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
-
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.
- 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
-
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.
- getHydrophobicity(self: samson.Modeling.StructuralModel.Residue) -> float
Returns the residue’s hydrophobicity in the current hydrophobicity scale
- 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.
- 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
-
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: pagenodespecificationlanguage
-
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.
- 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
-
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
-
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.
- 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
-
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
-
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.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 accordingly 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¶
-
Mesh
= NodeType.VisualModelMesh¶
-
Molecule
= NodeType.StructuralModelNodeMolecule¶
-
MoneraEtAl1995
= HydrophobicityScale.MoneraEtAl1995¶
-
MoonFleming2011
= HydrophobicityScale.MoonFleming2011¶
-
Negative
= SideChainCharge.Negative¶
-
Neutral
= SideChainCharge.Neutral¶
-
NodeGroup
= NodeType.DataGraphNodeGroup¶
-
Nonpolar
= SideChainPolarity.Nonpolar¶
-
Note
= NodeType.Note¶
-
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¶
-
VisualModelMesh
= NodeType.VisualModelMesh¶
-
WimleyWhite1996
= HydrophobicityScale.WimleyWhite1996¶
-
XAA
= ResidueType.XAA¶
-
XLE
= ResidueType.XLE¶
-
ZhaoLondon2006
= HydrophobicityScale.ZhaoLondon2006¶
-
aminoAcidOneLetterCode
¶ Returns one letter code of the amino acid residue
-
comment
¶ The group’s comment
-
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
-
hasDissociationConstant
¶ Returns true if the dissociation constants (pKa1, pKa2) and isoelectric point are defined for this residue
-
hasHydrophobicity
¶ Returns true if the residue’s hydrophobicity is defined
-
hasSideChainCharge
¶ Returns true if the residue’s side chain charge is defined
-
hasSideChainPolarity
¶ Returns true if the residue’s side chain polarity 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 node
-
nodeIndex
¶ Returns the node index (unique in the whole data graph, but non-persistent)
-
residueType
¶
-
residueTypeFullName
¶ Returns the full name of the residue’s type
-
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
¶