entities.Molecule

entities.Molecule(self, file_path)

Abstract base class for representing a molecule.

It associates the atomic data (the array) with the created 3D model inside of Blender (the object). If multiple conformations are imported, then a frames collection is also instantiated.

The named_attribute() and store_named_attribute() methods access and set attributes on object that is in the Blender scene.

Attributes

Name	Type	Description
file_path	str	The file path to the file which stores the atomic coordinates.
file	Any	The opened file.
object	bpy.types.Object	The Blender object representing the molecule.
frames	bpy.types.Collection	The Blender collection which holds the objects making up the frames to animate.
array	np.ndarray:	The numpy array which stores the atomic coordinates and associated attributes.
entity_ids	np.ndarray	The entity IDs of the molecule.
chain_ids	np.ndarray	The chain IDs of the molecule.

Methods

Name	Description
assemblies	Get the biological assemblies of the molecule.
create_object	Create a 3D model of the molecule inside of Blender.

assemblies

entities.Molecule.assemblies(as_array=False)

Get the biological assemblies of the molecule.

Parameters

Name	Type	Description	Default
as_array	bool	Whether to return the assemblies as an array of quaternions. Default is False.	False

Returns

Name	Type	Description
	dict or None	The biological assemblies of the molecule, as a dictionary of transformation matrices, or None if no assemblies are available.

create_object

entities.Molecule.create_object(
    name='NewMolecule',
    style='spheres',
    selection=None,
    build_assembly=False,
    centre='',
    del_solvent=True,
    del_hydrogen=False,
    collection=None,
    verbose=False,
    color='common',
)

Create a 3D model of the molecule inside of Blender.

Creates a 3D model with one vertex per atom, and one edge per bond. Each vertex is given attributes which correspond to the atomic data such as atomic_number for the element and res_name for the residue name that the atom is associated with.

If multiple conformations of the structure are detected, the collection attribute is also created which will store an object for each conformation, so that the object can interpolate between those conformations.

Parameters

Name	Type	Description	Default
name	str	The name of the model. Default is ‘NewMolecule’.	'NewMolecule'
style	str	The style of the model. Default is ‘spheres’.	'spheres'
selection	np.ndarray	The selection of atoms to include in the model. Default is None.	None
build_assembly	bool	Whether to build the biological assembly. Default is False.	False
centre	str	Denote method used to determine center of structure. Default is ’’, resulting in no translational motion being removed. Accepted values are centroid or mass. Any other value will result in default behavior.	''
del_solvent	bool	Whether to delete solvent molecules. Default is True.	True
del_hydrogen	bool	Whether to delete hydrogen atoms. Default is False.	False
collection	str	The collection to add the model to. Default is None.	None
verbose	bool	Whether to print verbose output. Default is False.	False
color	Optional[str]	The color scheme to use for the model. Default is ‘common’.	'common'

Returns

Name	Type	Description
	bpy.types.Object	The created 3D model, as an object in the 3D scene.