SBStructuralModel

SBStructuralModel#

See also

SAMSON SDK: SBMStructuralModel

class samson.SBStructuralModel(self: samson.SBStructuralModel)#

Bases: SBModel

This class describes a structural model.

Constructs a structural model.

Examples

Add a structural model to the active document and make this operation undoable.

>>> structural_model = SBStructuralModel()
>>> structural_model.name = 'Structural model'
>>> SAMSON.beginHolding('Add structural model')
>>> SAMSON.hold(structural_model)
>>> structural_model.create()
>>> SAMSON.getActiveDocument().addChild(structural_model)
True
>>> SAMSON.endHolding()

static bondExists(atom1: SBMStructuralModelNodeAtom, atom2: SBMStructuralModelNodeAtom) → bool#

Checks whether the bond between atoms atom1 and atom2 exists.

Parameters:

atom1 (samson.SBAtom) – A first atom.
atom2 (samson.SBAtom) – A second atom.

Returns:

True if the bond exists, else False.

Return type:

bool

centerTransform(self: samson.SBStructuralModel) → None#: Centers the pivot of the transform on the center of mass of the particles contained in the structural model

clearConnectivityAnnotationInformation(self: samson.SBStructuralModel) → None#: Clears the model’s connectivity annotation information

clearCrystallographicAndTransformationInformation(self: samson.SBStructuralModel) → None#: Clears the model’s transformation information

clearHeterogenInformation(self: samson.SBStructuralModel) → None#: Clears the model’s heterogen information

clearMiscellaneousInformation(self: samson.SBStructuralModel) → None#: Clears the model’s miscellaneous information

clearPrimaryStructureInformation(self: samson.SBStructuralModel) → None#: Clears the model’s primary structure information

clearSecondaryStructureInformation(self: samson.SBStructuralModel) → None#: Clears the model’s secondary structure information

clearTitleInformation(self: samson.SBStructuralModel) → None#: Clears the model’s title information

static computeDomain(nodeIndexer: samson.SBNodeIndexer) → samson.SBSpatialDomain#: Computes the domain containing the atoms and bond atoms in the node indexer

computeSecondaryStructure(self: samson.SBStructuralModel, forceUpdate: bool = False) → tuple[bool, bool]#

Computes the secondary structure for all residues in the structural model.

Parameters:: forceUpdate (bool, default=False) – Whether to force the update of the secondary structure or not.
Returns:: 1st element - True if everything went well; 2nd element - True if and only if the secondary structure was changed compared to the previous call.
Return type:: Tuple(bool, bool)

static createBond(atom1: SBMStructuralModelNodeAtom, atom2: SBMStructuralModelNodeAtom, bondOrder: float, bondType: SBMStructuralModelNodeBond::BondType) → bool#

Creates a bond between atom1 and atom2 if there is none; sets the bond order to bondOrder and the bond type to bondType.

Parameters:

atom1 (samson.SBAtom) – A first atom.
atom2 (samson.SBAtom) – A second atom.
bondOrder (float, default=1.0) – The bond order.
bondType (samson.SBBond.BondType, default=samson.SBBond.BondType.Undefined) – The bond type.

Returns:

Whether the bond has been created or not.

Return type:

bool

createCovalentBonds(*args, **kwargs)#

Overloaded function.

createCovalentBonds(self: samson.SBStructuralModel) -> None

Creates covalent bonds for the atoms belonging to the structural model according to the inter-atomic distances

createCovalentBonds(self: samson.SBStructuralModel, additionalMargin: samson.SBQuantity.unitsSI) -> None

Creates covalent bonds for the atoms belonging to the structural model according to the inter-atomic distances and the given additional margin.

Parameters:: additionalMargin (samson.SBQuantity) – A margin additional to the sum of covalent radii of atoms when checking for the covalent bond creation.

createCovalentBondsByResidueType(*args, **kwargs)#

Overloaded function.

createCovalentBondsByResidueType(self: samson.SBStructuralModel) -> int

Creates covalent bonds for the atoms belonging to the structural model according to the residue types, regardless of inter-atomic distances. If the bonds are already present, it sets the order of covalent bonds for the atoms belonging to the structural model according to the residue types.

createCovalentBondsByResidueType(self: samson.SBStructuralModel, residueIndexer: samson.SBNodeIndexer) -> int

Creates covalent bonds for the atoms belonging to the given residues of the structural model according to the residue types, regardless of inter-atomic distances. If the bonds are already present, it sets the order of covalent bonds for the atoms belonging to the structural model according to the residue types.

Parameters:: residueIndexer (samson.SBNodeIndexer) – An indexer with residues.

static findAtom(*args, **kwargs)#

Overloaded function.

findAtom(nodeIndexer: samson.SBNodeIndexer, elementType: samson.SBElement.ElementType, name: str) -> SBMStructuralModelNodeAtom

Returns, if found, an atom from a node indexer nodeIndexer with the element type elementType and name name; else returns None.

findAtom(nodeIndexer: samson.SBNodeIndexer, elementType: samson.SBElement.ElementType, name: str, altLoc: str) -> SBMStructuralModelNodeAtom

Returns, if found, an atom from a node indexer nodeIndexer with the element type elementType and name name, and an alternate location altLoc (if the atom has an alternate location); else returns None.

static getAsphericity(nodeIndexer: samson.SBNodeIndexer) → float#: Returns True if all atoms in nodeIndexer are in the same plane

static getCenterOfFormalCharge(nodeIndexer: samson.SBNodeIndexer) → samson.SBPhysicalVector3#: Returns the center of formal charge of atoms in the nodeIndexer

static getCenterOfMass(nodeIndexer: samson.SBNodeIndexer) → samson.SBPhysicalVector3#: Returns the center of mass of atoms in the nodeIndexer

static getCenterOfPartialCharge(nodeIndexer: samson.SBNodeIndexer) → samson.SBPhysicalVector3#: Returns the center of partial charge of atoms in the nodeIndexer

static getCentroid(nodeIndexer: samson.SBNodeIndexer) → samson.SBPhysicalVector3#: Returns the centroid (the geometric center) of atoms in the nodeIndexer

getChildren(self: samson.SBStructuralModel) → samson.SBNodeIndexer#: Returns the children of the structural model

static getDipoleMomentAtCenterOfCharge(nodeIndexer: samson.SBNodeIndexer) → samson.SBQuantity.unitsSI#: Returns the dipole moment of atoms in nodeIndexer at their center of charge (based on partial charge)

static getDipoleMomentAtCenterOfMass(nodeIndexer: samson.SBNodeIndexer) → samson.SBQuantity.unitsSI#: Returns the dipole moment of atoms in nodeIndexer at their center of mass

static getDipoleVectorAtCenterOfCharge(nodeIndexer: samson.SBNodeIndexer) → samson.SBPhysicalVector3#: Returns the dipole vector of atoms in nodeIndexer at their center of charge (based on partial charge)

static getDipoleVectorAtCenterOfMass(nodeIndexer: samson.SBNodeIndexer) → samson.SBPhysicalVector3#: Returns the dipole vector of atoms in nodeIndexer at their center of mass

static getInertiaTensor(nodeIndexer: samson.SBNodeIndexer) → samson.SBPhysicalMatrix33#: Returns the inertia tensor of the system of atoms (based on their positions and masses) in the nodeIndexer

static getMolecularWeightForNodeIndexer(nodeIndexer: samson.SBNodeIndexer) → samson.SBQuantity.unitsSI#: Returns the cumulative molecular weight of atoms in the nodeIndexer

getOrientation(self: samson.SBStructuralModel) → samson.SBPhysicalMatrix33#: Returns the orientation of the structural model

getPosition(self: samson.SBStructuralModel) → samson.SBPhysicalVector3#: Returns the position of the structural model

static getPrincipalAxes(nodeIndexer: samson.SBNodeIndexer) → samson.SBPhysicalMatrix33#: Returns the principal axes of the inertia tensor of the system of atoms (based on their positions and masses) in the nodeIndexer

static getRadiusOfGyration(nodeIndexer: samson.SBNodeIndexer) → samson.SBQuantity.unitsSI#: Returns the radius of gyration based on atoms in the nodeIndexer

static getShapeParameter(nodeIndexer: samson.SBNodeIndexer) → float#: Returns the shape parameter of the system of atoms (based on their positions and masses) in nodeIndexer. The shape parameter, S, changes in the [-0.25, 2] interval, where 0 corresponds to a sphere, negative values correspond to oblate ellipsoid, positive values correspond to prolate ellipsoid.

static getSolventAccessibleSurfaceArea(nodeIndexer: samson.SBNodeIndexer, probeRadius: samson.SBQuantity.unitsSI, numberOfPointsOnSphere: int) → samson.SBQuantity.unitsSI#

Returns the Solvent-Accessible Surface Area (SASA) based on atoms in nodeIndexer with the probe radius probeRadius, and the number of points on a sphere numberOfPointsOnSphere.

Parameters:

nodeIndexer (samson.SBNodeIndexer) – A node indexer with atoms
probeRadius (samson.SBQuantity.unitsSI) – The probe radius
numberOfPointsOnSphere (int) – The number of points on a sphere. Governs the accuracy.

Return type:

samson.SBQuantity.unitsSI

static getSpatialTransform(nodeIndexer: samson.SBNodeIndexer) → samson.SBSpatialTransform#: Returns the spatial transform based on the inertia tensor of the system of atoms (based on their positions and masses) in the nodeIndexer

getStructuralRoot(self: samson.SBStructuralModel) → SBMStructuralModelNodeRoot#: Returns the root

static getSumOfFormalCharges(nodeIndexer: samson.SBNodeIndexer) → int#: Returns the sum of formal charges of nodes in nodeIndexer

static getSumOfPartialCharges(nodeIndexer: samson.SBNodeIndexer) → float#: Returns the sum of partial charges of nodes in nodeIndexer

getTransform(self: samson.SBStructuralModel) → samson.SBSpatialTransform#: Returns the spatial transform of the structural model

getWater(self: samson.SBStructuralModel) → samson.SBNodeIndexer#: Finds water nodes in the structural model

static getWaterFromNodeIndexer(nodeIndexer: samson.SBNodeIndexer) → samson.SBNodeIndexer#: Finds water nodes in the nodeIndexer

static isPlanar(nodeIndexer: samson.SBNodeIndexer) → bool#: Returns True if all atoms in nodeIndexer are in the same plane.

populateChainIDs(self: samson.SBStructuralModel, forceRenumbering: bool = False) → bool#: Populates the chain IDs for all chains in the structural model

static replaceAtom(oldAtom: SBMStructuralModelNodeAtom, newAtom: SBMStructuralModelNodeAtom, preserveOldAtomPosition: bool = False) → None#: Replaces atom oldAtom with atom newAtom. All bonds from the old atom are transferred to the new atom.

static replaceBond(oldBond: SBMStructuralModelNodeBond, newBond: SBMStructuralModelNodeBond, flipBond: bool = False, preserveOldBondPosition: bool = False) → None#: Replaces bond oldBond with bond newBond. All neighboring bonds from the old bond are transferred to the new bond

rotate(self: samson.SBStructuralModel, axis: samson.SBPhysicalVector3, angle: samson.SBQuantity.unitsSI) → None#: Rotates the structural model

setOrientation(*args, **kwargs)#

Overloaded function.

setOrientation(self: samson.SBStructuralModel, orientation: samson.SBPhysicalMatrix33) -> None

Sets the orientation of the structural model

setOrientation(self: samson.SBStructuralModel, orientation: samson.SBPhysicalMatrix33, transformParticles: bool) -> None

Sets the orientation of the structural model

setPosition(*args, **kwargs)#

Overloaded function.

setPosition(self: samson.SBStructuralModel, position: samson.SBPhysicalVector3) -> None

Sets the position of the structural model

setPosition(self: samson.SBStructuralModel, position: samson.SBPhysicalVector3, transformParticles: bool) -> None

Sets the position of the structural model

setTransform(*args, **kwargs)#

Overloaded function.

setTransform(self: samson.SBStructuralModel, transform: samson.SBSpatialTransform) -> None

Sets the spatial transform of the structural model

setTransform(self: samson.SBStructuralModel, transform: samson.SBSpatialTransform, transformParticles: bool) -> None

Sets the spatial transform of the structural model

transform(self: samson.SBStructuralModel, transform: samson.SBSpatialTransform) → None#: Applies a spatial transform to the structural model

translate(self: samson.SBStructuralModel, translation: samson.SBPhysicalVector3) → None#: Translates the structural model

property connectivityAnnotationInformation#: The model’s connectivity annotation information

property crystallographicAndTransformationInformation#: The model’s transformation information

property hasConnectivityAnnotationInformation#: Returns True when the model’s connectivity annotation information is set. A read-only property.

property hasCrystallographicAndTransformationInformation#: Returns True when the model’s transformation information is set. A read-only property.

property hasHeterogenInformation#: Returns True when the model’s heterogen information is set. A read-only property.

property hasMiscellaneousInformation#: Returns True when the model’s miscellaneous information is set. A read-only property.

property hasPrimaryStructureInformation#: Returns True when the model’s primary structure information is set. A read-only property.

property hasSecondaryStructureInformation#: Returns True when the model’s secondary structure information is set. A read-only property.

property hasTitleInformation#: Returns True when the model’s title information is set. A read-only property.

property heterogenInformation#: The model’s heterogen information

property miscellaneousInformation#: The model’s miscellaneous information

property modelType#: Returns the model type. A read-only property.

property primaryStructureInformation#: The model’s primary structure information

property secondaryStructureInformation#: The model’s secondary structure information

property structuralSignalFlag#: A flag whether the model can send structural signals

property titleInformation#: The model’s title information

SBStructuralModel

Contents

SBStructuralModel#