entities.OXDNA

entities.OXDNA(
    universe,
    name='NewOXDNAObject',
    world_scale=0.01,
    create_object=True,
)

A class to handle oxDNA trajectory data.

Parameters

Name	Type	Description	Default
universe	MDAnalysis.Universe	The MDAnalysis Universe object containing the trajectory data	required
world_scale	float	Scaling factor for the world coordinates, by default 0.01	0.01

Attributes

Name	Type	Description
_entity_type	EntityType	Type of the molecular entity
_att_names	tuple	Names of the attributes to track

Methods

Name	Description
add_style	Add a visual style to the trajectory.
create_object	Create and initialize Blender object for trajectory.
get_view	Get the 3D bounding box of a selection within the trajectory
reset_playback	Set the playback settings to their default values

add_style

entities.OXDNA.add_style(
    style='spheres',
    color='common',
    selection=None,
    material=None,
    name=None,
)

Add a visual style to the trajectory.

Parameters

Name	Type	Description	Default
style	bpy.types.GeometryNodeTree | str	The style to apply to the trajectory. Can be a GeometryNodeTree or a string identifying a predefined style (e.g., “spheres”, “sticks”, “ball_stick”). Default is “spheres”.	'spheres'
color	str | None	The coloring scheme to apply. Can be “common” (element-based coloring), “chain”, “residue”, or other supported schemes. If None, no coloring is applied. Default is “common”.	'common'
selection	str | AtomGroup | None	Apply the style only to atoms matching this selection. Can be: - A string referring to an existing boolean attribute on the trajectory - A AtomGroup object defining a selection criteria - None to apply to all atoms (default)	None
material	bpy.types.Material | str | None	The material to apply to the styled atoms. Can be a Blender Material object, a string with a material name, or None to use default materials. Default is None.	None
name	str | None	The label for this style	None

Returns

Name	Type	Description
	Trajectory	Returns self for method chaining.

Raises

Name	Type	Description
	ValueError	If an unsupported style string is passed

Notes

If a selection is provided, it will be evaluated and stored as a new named attribute on the trajectory with an automatically generated name (sel_N).

create_object

entities.OXDNA.create_object(name='NewUniverseObject')

Create and initialize Blender object for trajectory.

Creates mesh, computes attributes, sets up modifiers, registers with MolecularNodes.

Parameters

Name	Type	Description	Default
name	str	Name for the Blender object	"NewUniverseObject"

Returns

Name	Type	Description
	bpy.types.Object	Created Blender object

get_view

entities.OXDNA.get_view(selection=None, frame=None)

Get the 3D bounding box of a selection within the trajectory

Parameters

Name	Type	Description	Default
selection	str | AtomGroup	A selection phrase or AtomGroup When not specified, the whole entity is considered	None
frame	int | None	Frame number of trajectory to use for calculating bounds. When not specified, current trajectory frame is used	None

reset_playback

entities.OXDNA.reset_playback()

Set the playback settings to their default values