SBConformation

SBConformation#

This class describes a structural conformation, i.e. a set of positions of atoms (samson.SBAtom).

You can get a node indexer of atoms in the conformation:

# get all conformation in the active document
conformationIndexer = SAMSON.getNodes('node.type conformation')

if len(conformationIndexer):
        # get the first conformation
        conformation = conformationIndexer[0]

        # get an indexer of atoms in the conformation
        atomIndexer = conformation.getAtomIndexer()

You can restore a conformation:

Restoring a conformation#

# make the operation undoable
SAMSON.beginHolding("Restore conformation")

    conformation.restore()

# stop holding the undoable operation
SAMSON.endHolding()

You can add, insert, and remove atoms using samson.SBConformation.addAtom(), samson.SBConformation.insertAtom(), and samson.SBConformation.removeAtom() functions respectively.

You can also get and set positions, velocities, and forces for all atoms in a conformation or for a particular atom.

class samson.SBConformation(*args, **kwargs)#

Bases: SBNode

This class describes a structural conformation.

Overloaded function.

__init__(self: samson.SBConformation) -> None

Constructs a structural conformation

__init__(self: samson.SBConformation, name: str, nodeIndexer: samson.SBNodeIndexer) -> None

Constructs a structural conformation with the given name from the nodes in nodeIndexer.

Parameters:

name (str) – A name of the conformation
nodeIndexer (samson.SBNodeIndexer) – An indexer with structural nodes.

addAtom(self: samson.SBConformation, atom: SBMStructuralModelNodeAtom, atomPosition: samson.SBPhysicalVector3) → bool#: Adds a atom with position atomPosition

createStructuralModels(self: samson.SBConformation) → samson.SBNodeIndexer#: Create structural models corresponding to all steps

getAtomIndexer(self: samson.SBConformation) → samson.SBNodeIndexer#

Returns the indexer of atoms for which a position is saved.

Returns:: A node indexer with the associated atoms.
Return type:: samson.SBNodeIndexer

getEnergy(self: samson.SBConformation) → samson.SBQuantity.unitsSI#: Returns the energy data

getForce(*args, **kwargs)#

Overloaded function.

getForce(self: samson.SBConformation, atomIndex: int) -> samson.SBPhysicalVector3

Retrieves the force of atom with atomIndex

getForce(self: samson.SBConformation, atom: SBMStructuralModelNodeAtom) -> samson.SBPhysicalVector3

Retrieves the force of atom

getForceData(self: samson.SBConformation) → list[samson.SBPhysicalVector3]#: Returns the force data

getNextConformation(self: samson.SBConformation) → samson.SBConformation#: Returns the next conformation in the document

getPosition(*args, **kwargs)#

Overloaded function.

getPosition(self: samson.SBConformation, atomIndex: int) -> samson.SBPhysicalVector3

Retrieves the position of atom with atomIndex

getPosition(self: samson.SBConformation, atom: SBMStructuralModelNodeAtom) -> samson.SBPhysicalVector3

Retrieves the position of atom

getPositionData(self: samson.SBConformation) → list[samson.SBPhysicalVector3]#: Returns the position data

getPreviousConformation(self: samson.SBConformation) → samson.SBConformation#: Returns the previous conformation in the document

getTime(self: samson.SBConformation) → samson.SBQuantity.unitsSI#: Returns the time data

getVelocity(*args, **kwargs)#

Overloaded function.

getVelocity(self: samson.SBConformation, atomIndex: int) -> samson.SBPhysicalVector3

Retrieves the velocity of atom with atomIndex

getVelocity(self: samson.SBConformation, atom: SBMStructuralModelNodeAtom) -> samson.SBPhysicalVector3

Retrieves the velocity of atom

getVelocityData(self: samson.SBConformation) → list[samson.SBPhysicalVector3]#: Returns the velocity data

insertAtom(self: samson.SBConformation, atomIndex: int, atom: SBMStructuralModelNodeAtom, atomPosition: samson.SBPhysicalVector3) → bool#: Inserts an atom with position atomPosition at index atomIndex

removeAtom(self: samson.SBConformation, atom: SBMStructuralModelNodeAtom) → bool#: Removes an atom from the conformation

restore(self: samson.SBConformation) → None#: Restores the conformation

setEnergy(self: samson.SBConformation, energy: samson.SBQuantity.unitsSI) → None#: Sets the energy data

setForce(*args, **kwargs)#

Overloaded function.

setForce(self: samson.SBConformation, atomIndex: int, atomForce: samson.SBPhysicalVector3) -> None

Sets the force of atom with atomIndex

setForce(self: samson.SBConformation, atom: SBMStructuralModelNodeAtom, atomForce: samson.SBPhysicalVector3) -> None

Sets the force of atom

setForceData(self: samson.SBConformation, forceData: list[samson.SBPhysicalVector3]) → None#: Sets the force data; forceData is a vector of forces

setPosition(*args, **kwargs)#

Overloaded function.

setPosition(self: samson.SBConformation, atomIndex: int, atomPosition: samson.SBPhysicalVector3) -> None

Sets the position of atom with atomIndex

setPosition(self: samson.SBConformation, atom: SBMStructuralModelNodeAtom, atomPosition: samson.SBPhysicalVector3) -> None

Sets the position of atom

setPositionData(self: samson.SBConformation, positionData: list[samson.SBPhysicalVector3]) → None#: Sets the position data; positionData is a vector of positions

setTime(self: samson.SBConformation, time: samson.SBQuantity.unitsSI) → None#: Sets the time data

setVelocity(*args, **kwargs)#

Overloaded function.

setVelocity(self: samson.SBConformation, atomIndex: int, atomVelocity: samson.SBPhysicalVector3) -> None

Sets the velocity of atom with atomIndex

setVelocity(self: samson.SBConformation, atom: SBMStructuralModelNodeAtom, atomVelocity: samson.SBPhysicalVector3) -> None

Sets the velocity of atom

setVelocityData(self: samson.SBConformation, velocityData: list[samson.SBPhysicalVector3]) → None#: Sets the velocity data; velocityData is a vector of velocities

property numberOfStructuralParticles#: Returns the number of atoms for which a position is saved

SBConformation

Contents

SBConformation#