Ensemble

Instance and manipulate ensembles and assemblies

Assembly Instance

nodes.geometry.AssemblyInstance(
    geometry=None,
    selection=True,
    data_object=None,
    assembly_id=1,
    realize_all=False,
    position=1.0,
    rotation=1.0,
)

GUI reference: Assembly Instance.

Parameters

Name	Type	Description	Default
geometry	`InputGeometry`	Geometry that is instanced on the points	`None`
selection	`InputBoolean`	Selection	`True`
data_object	`InputObject`	Data Object	`None`
assembly_id	`InputInteger`	Assembly ID	`1`
realize_all	`InputBoolean`	Realize all levels of nested instances for a top-level instances. Overrides the value of the Depth input	`False`
position	`InputFloat`	Amount of mixing between the A and B inputs	`1.0`
rotation	`InputFloat`	Amount of mixing between the A and B inputs	`1.0`

Inputs

Name	Type	Description
i.geometry	`GeometrySocket`	Geometry that is instanced on the points
i.selection	`BooleanSocket`	Selection
i.data_object	`ObjectSocket`	Data Object
i.assembly_id	`IntegerSocket`	Assembly ID
i.realize_all	`BooleanSocket`	Realize all levels of nested instances for a top-level instances. Overrides the value of the Depth input
i.position	`FloatSocket`	Amount of mixing between the A and B inputs
i.rotation	`FloatSocket`	Amount of mixing between the A and B inputs

Outputs

Name	Type	Description
o.instances	`GeometrySocket`	Instances
o.chain_id	`IntegerSocket`	chain_id

Ensemble Instance

nodes.geometry.EnsembleInstance(
    points=None,
    selection=True,
    selection_type='Simple',
    instances=None,
    fraction=1.0,
    as_points=True,
    point_radius=0.1,
    point_material=None,
)

GUI reference: Ensemble Instance.

Parameters

Name	Type	Description	Default
points	`InputGeometry`	Points	`None`
selection	`InputBoolean`	Selection of atoms to apply this node to	`True`
selection_type	`InputMenu` \| Literal['Simple', 'Precise']	Selection Type	`'Simple'`
instances	`InputCollection`	Instances	`None`
fraction	`InputFloat`	Fraction	`1.0`
as_points	`InputBoolean`	As Points	`True`
point_radius	`InputFloat`	Point Radius	`0.1`
point_material	`InputMaterial`	Point Material	`None`

Inputs

Name	Type	Description
i.points	`GeometrySocket`	Points
i.selection	`BooleanSocket`	Selection of atoms to apply this node to
i.selection_type	`MenuSocket`	Selection Type
i.instances	`CollectionSocket`	Instances
i.fraction	`FloatSocket`	Fraction
i.as_points	`BooleanSocket`	As Points
i.point_radius	`FloatSocket`	Point Radius
i.point_material	`MaterialSocket`	Point Material

Outputs

Name	Type	Description
o.instances	`GeometrySocket`	Instances

Lattice Grid

nodes.geometry.LatticeGrid(a=None, b=None, c=None, x=3, y=3, z=3)

GUI reference: Lattice Grid.

Parameters

Name	Type	Description	Default
a	`InputVector`	A	`None`
b	`InputVector`	B	`None`
c	`InputVector`	C	`None`
x	`InputInteger`	Number of images along the a vector	`3`
y	`InputInteger`	Number of images along the b vector	`3`
z	`InputInteger`	Number of images along the c vector	`3`

Inputs

Name	Type	Description
i.a	`VectorSocket`	A
i.b	`VectorSocket`	B
i.c	`VectorSocket`	C
i.x	`IntegerSocket`	Number of images along the a vector
i.y	`IntegerSocket`	Number of images along the b vector
i.z	`IntegerSocket`	Number of images along the c vector

Outputs

Name	Type	Description
o.grid	`GeometrySocket`	Grid

Periodic Array

nodes.geometry.PeriodicArray(
    geometry=None,
    update=True,
    a=0.0,
    b=0.0,
    c=0.0,
    alpha=0.0,
    beta=0.0,
    gamma=0.0,
    x=3,
    y=3,
    z=3,
)

GUI reference: Periodic Array.

Parameters

Name	Type	Description	Default
geometry	`InputGeometry`	Geometry	`None`
update	`InputBoolean`	Update the box lengths and angles with the simulation	`True`
a	`InputFloat`	a	`0.0`
b	`InputFloat`	b	`0.0`
c	`InputFloat`	c	`0.0`
alpha	`InputFloat`	alpha	`0.0`
beta	`InputFloat`	beta	`0.0`
gamma	`InputFloat`	gamma	`0.0`
x	`InputInteger`	Number of images along the a vector	`3`
y	`InputInteger`	Number of images along the b vector	`3`
z	`InputInteger`	Number of images along the c vector	`3`

Inputs

Name	Type	Description
i.geometry	`GeometrySocket`	Geometry
i.update	`BooleanSocket`	Update the box lengths and angles with the simulation
i.a	`FloatSocket`	a
i.b	`FloatSocket`	b
i.c	`FloatSocket`	c
i.alpha	`FloatSocket`	alpha
i.beta	`FloatSocket`	beta
i.gamma	`FloatSocket`	gamma
i.x	`IntegerSocket`	Number of images along the a vector
i.y	`IntegerSocket`	Number of images along the b vector
i.z	`IntegerSocket`	Number of images along the c vector

Outputs

Name	Type	Description
o.instances	`GeometrySocket`	Instances

Periodic Box

nodes.geometry.PeriodicBox(
    update=True,
    a=0.0,
    b=0.0,
    c=0.0,
    alpha=0.0,
    beta=0.0,
    gamma=0.0,
)

GUI reference: Periodic Box.

Parameters

Name	Type	Description	Default
update	`InputBoolean`	Update the box lengths and angles with the simulation. This does not change anything directly inside of the node tree, but the mda.Universe that updates the positions will also update this node.	`True`
a	`InputFloat`	a	`0.0`
b	`InputFloat`	b	`0.0`
c	`InputFloat`	c	`0.0`
alpha	`InputFloat`	alpha	`0.0`
beta	`InputFloat`	beta	`0.0`
gamma	`InputFloat`	gamma	`0.0`

Inputs

Name	Type	Description
i.update	`BooleanSocket`	Update the box lengths and angles with the simulation. This does not change anything directly inside of the node tree, but the mda.Universe that updates the positions will also update this node.
i.a	`FloatSocket`	a
i.b	`FloatSocket`	b
i.c	`FloatSocket`	c
i.alpha	`FloatSocket`	alpha
i.beta	`FloatSocket`	beta
i.gamma	`FloatSocket`	gamma

Outputs

Name	Type	Description
o.a	`VectorSocket`	A
o.b	`VectorSocket`	B
o.c	`VectorSocket`	C

Periodic Image

nodes.geometry.PeriodicImage(
    a=None,
    b=None,
    c=None,
    image_a=0,
    image_b=0,
    image_c=0,
)

GUI reference: Periodic Image.

Parameters

Name	Type	Description	Default
a	`InputVector`	A	`None`
b	`InputVector`	B	`None`
c	`InputVector`	C	`None`
image_a	`InputInteger`	Image A	`0`
image_b	`InputInteger`	Image B	`0`
image_c	`InputInteger`	Image C	`0`

Inputs

Name	Type	Description
i.a	`VectorSocket`	A
i.b	`VectorSocket`	B
i.c	`VectorSocket`	C
i.image_a	`IntegerSocket`	Image A
i.image_b	`IntegerSocket`	Image B
i.image_c	`IntegerSocket`	Image C

Outputs

Name	Type	Description
o.points	`GeometrySocket`	Points

Rotation cisTEM

nodes.geometry.RotationCisTEM()

GUI reference: Rotation cisTEM.

Outputs

Name	Type	Description
o.rotation	`RotationSocket`	Rotation
o.is_valid	`BooleanSocket`	Is Valid

Rotation RELION

nodes.geometry.RotationRELION()

GUI reference: Rotation RELION.

Outputs

Name	Type	Description
o.rotation	`RotationSocket`	Rotation
o.is_valid	`BooleanSocket`	Is Valid

TEM Rotation

nodes.geometry.TEMRotation(
    phi='rlnAngleRot',
    theta='rlnAngleTilt',
    psi='rlnAnglePsi',
)

GUI reference: TEM Rotation.

Parameters

Name	Type	Description	Default
phi	`InputString`	Phi	`'rlnAngleRot'`
theta	`InputString`	Theta	`'rlnAngleTilt'`
psi	`InputString`	Psi	`'rlnAnglePsi'`

Inputs

Name	Type	Description
i.phi	`StringSocket`	Phi
i.theta	`StringSocket`	Theta
i.psi	`StringSocket`	Psi

Outputs

Name	Type	Description
o.rotation	`RotationSocket`	The combined Rotation
o.boolean	`BooleanSocket`	Boolean