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
with SAMSON.holding("Restore conformation"):
            conformation.restore()

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

property sourceFileName#: The source file name

SBConformation

Contents

SBConformation#