Ensemble
Instance and manipulate ensembles and assemblies
Assembly Instance
Inputs
| Name | Type | Description |
|---|---|---|
| Geometry | Geometry |
Geometry that is instanced on the points |
| Selection | Bool |
|
| Data Object | Object |
|
| Assembly ID | Int |
|
| Realize All | Bool |
Realize all levels of nested instances for a top-level instances. Overrides the value of the Depth input |
| Position | Float |
Amount of mixing between the A and B inputs |
| Rotation | Float |
Amount of mixing between the A and B inputs |
Outputs
| Name | Type | Description |
|---|---|---|
| Instances | Geometry |
|
| chain_id | Int |
API Reference: nodes.geometry.AssemblyInstance
Ensemble Instance
Instance the items of an ensemble onto the given points
Inputs
| Name | Type | Description |
|---|---|---|
| Points | Geometry |
|
| Selection | Bool |
Selection of atoms to apply this node to |
| Selection Type | Menu |
|
| Instances | Collection |
|
| Fraction | Float |
|
| As Points | Bool |
|
| Point Radius | Float |
|
| Point Material | Material |
Outputs
| Name | Type | Description |
|---|---|---|
| Instances | Geometry |
API Reference: nodes.geometry.EnsembleInstance
Lattice Grid
Create a grid of lattice points based on the periodic box vectors.
Inputs
| Name | Type | Description |
|---|---|---|
| A | Vector |
|
| B | Vector |
|
| C | Vector |
|
| X | Int |
Number of images along the a vector |
| Y | Int |
Number of images along the b vector |
| Z | Int |
Number of images along the c vector |
Outputs
| Name | Type | Description |
|---|---|---|
| Grid | Geometry |
API Reference: nodes.geometry.LatticeGrid
Periodic Array
Replicate the trajectory across periodic boundaries.
Inputs
| Name | Type | Description |
|---|---|---|
| Geometry | Geometry |
|
| Update | Bool |
Update the box lengths and angles with the simulation |
| a | Float |
|
| b | Float |
|
| c | Float |
|
| alpha | Float |
|
| beta | Float |
|
| gamma | Float |
|
| X | Int |
Number of images along the a vector |
| Y | Int |
Number of images along the b vector |
| Z | Int |
Number of images along the c vector |
Outputs
| Name | Type | Description |
|---|---|---|
| Instances | Geometry |
API Reference: nodes.geometry.PeriodicArray
Periodic Box
Get the box vectors for a trajectory’s periodic simulation box. These vectors can be used to create periodic images of the trajectory
Inputs
| Name | Type | Description |
|---|---|---|
| Update | Bool |
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. |
| a | Float |
|
| b | Float |
|
| c | Float |
|
| alpha | Float |
|
| beta | Float |
|
| gamma | Float |
Outputs
| Name | Type | Description |
|---|---|---|
| A | Vector |
|
| B | Vector |
|
| C | Vector |
API Reference: nodes.geometry.PeriodicBox
Periodic Image
Get the location of a single lattice point of the trajectory, based on the box vectors and the chosen lattice indices.
Inputs
| Name | Type | Description |
|---|---|---|
| A | Vector |
|
| B | Vector |
|
| C | Vector |
|
| Image A | Int |
|
| Image B | Int |
|
| Image C | Int |
Outputs
| Name | Type | Description |
|---|---|---|
| Points | Geometry |
API Reference: nodes.geometry.PeriodicImage
Rotation cisTEM
A rotation calculated from relevant columns of a cisTEM .star file
Outputs
| Name | Type | Description |
|---|---|---|
| Rotation | Rotation |
|
| Is Valid | Bool |
API Reference: nodes.geometry.RotationCisTEM
Rotation RELION
A rotation calculated from relevant columns of a RELION .star file
Outputs
| Name | Type | Description |
|---|---|---|
| Rotation | Rotation |
|
| Is Valid | Bool |
API Reference: nodes.geometry.RotationRELION
TEM Rotation
Inputs
| Name | Type | Description |
|---|---|---|
| Phi | String |
|
| Theta | String |
|
| Psi | String |
Outputs
| Name | Type | Description |
|---|---|---|
| Rotation | Rotation |
The combined Rotation |
| Boolean | Bool |
API Reference: nodes.geometry.TEMRotation