Function reference
Molecule
The unified Molecule entity and its facets. A Molecule represents any structure — static or trajectory — backed by an MDAnalysis.Universe.
| Molecule | Universe-backed molecular entity for Blender visualization. |
| entities.molecule.SelectionManager | Manages atom selections for a trajectory. |
| entities.molecule.DSSPManager | DSSP Manager for trajectories |
| entities.StreamingTrajectory | Molecule subclass for IMD streaming connections. |
Other Entities
Additional molecular entities for ensembles and coarse-grained models
| entities.Ensemble | |
| entities.OXDNA | A class to handle oxDNA trajectory data. |
Materials
The pre-built materials and their tweakable parameters
| material.Default | The default MolecularNodes material. |
| material.AmbientOcclusion | Colors shaded only by ambient occlusion. |
| material.Flat | Flat cartoon-like shading with an optional dark outline. |
| material.Squishy | A soft, subsurface-scattering material that makes molecules look jelly-like. |
| material.TransparentOutline | A partially transparent material with an optional solid outline. |
| material.PresetMaterial | Base class for the pre-built MolecularNodes materials. |
| material.append_material | Append a material from the MN_DATA_FILE. |
| material.add_all_materials | Append all pre-defined materials from the MN_DATA_FILE. |
Session
Session object to control molecular entities
| session.MNSession |
Annotations
Annotations for molecular entitites
| annotations.base | |
| annotations.interface | |
| annotations.manager | |
| entities.molecule.annotations | |
| entities.density.annotations |
Scene
Control settings for the Blender scene through the Canvas object.
| Canvas | High-level render controller for Blender scenes. |
| scene.camera | |
| scene.compositor.CompositorTree | Builder for the scene’s compositor node tree. |
| scene.recorder.FrameRecorder | Collect manually rendered frames into an animation. |
| scene.world.WorldTree | Builder for the scene world’s shader node tree (lighting & background). |
Nodes
The node groups included with Molecular Nodes, grouped by the same categories as the add menu inside of Geometry Nodes. Each node group is also available as a typed Python class for scripting.
| Materials | Shader node groups for the pre-built materials |
| General | |
| Animate | Animate values and geometry over frames |
| Attributes | Read attributes from structures |
| Color | Set and manipulate the colors of atoms |
| Curves | Create and manipulate curves |
| DNA | Nodes for working with oxDNA and other DNA models |
| Density | Work with volumetric density data |
| Ensemble | Instance and manipulate ensembles and assemblies |
| Geometry | General geometry processing utilities |
| Select | Create boolean selections based on the atomic attributes |
| Style | Generate geometry for the different molecular styles |
| Topology | Work with the bond and residue topology of structures |
| Utilities | Small helper node groups used throughout Molecular Nodes |
| Utilities / Attribute | |
| Utilities / Boolean | |
| Utilities / Color | |
| Utilities / Fields |