mn-render

# Rendering with Molecular Nodes from a Python script ## 1. Mental model - **One `Canvas`, many entities.** `mn.Canvas` wraps the active Blender scene: engine, resolution, camera, world lighting, compositor and output. Molecules are `mn.Molecule` entities that you load, style and then frame with `canvas.look_at`. - **Create the Canvas before loading anything.** It loads the Molecular Nodes scene preset (camera, lights, world, compositor) into an empty scene. Calling `mn.Canvas()` again is safe: it binds to the existing scene and only reloads the preset when the scene holds no molecules. - **Styles are node trees.** `add_style` builds a small node branch per call; the render shows whatever the evaluated geometry is. `look_at` frames that evaluated geometry, so a molecule with one chain styled is framed on that chain. - **Units.** Positions are Å times `world_scale = 0.1`, so 1 Å is 0.1 Blender units. - There is no `mn.Trajectory` any more; MD topologies and trajectories load into `mn.Molecule` as well. ## 2. Environment for a script Always via `uv run` (never bare `python`). In a script that imports `bpy` directly: ```python import os, tempfile os.environ.setdefault( "BLENDER_USER_EXTENSIONS", tempfile.mkdtemp() ) # before import bpy import bpy # mathutils is importable only after this import molecularnodes as mn canvas = mn.Canvas(mn.scene.Cycles(samples=64, device="CPU"), resolution=(1200, 900)) canvas.compositor.device = ( "CPU" # Blender 5 defaults the compositor to GPU; aborts without one ) ``` Without the `BLENDER_USER_EXTENSIONS` line, an installed MN extension's bundled wheels shadow the venv. `tests/conftest.py` does the same thing. Keep scratch scripts outside the repo. **Inside Blender with the installed extension** (`blender -b --python script.py`), the package is `import bl_ext.blender_org.molecularnodes as mn`; `import molecularnodes` fails there. Install headless with `blender --online-mode --command extension install --enable molecularnodes` (without `--online-mode` Blender refuses to reach the platform). Do not call `bpy.ops.wm.read_factory_settings()` to reset between renders: it has been reported to strip the extension's bundled wheels mid-run, so the next `Molecule.load()` fails on a missing biotite file. Delete the default objects by hand, or use one Blender process per render. Don't name a scratch script after a standard-library module (`inspect.py`, `code.py`, `types.py`, ...). Importing `bpy` imports that module, finds the script instead, and Blender initialises twice and aborts with `Check failed: !IsGoogleLoggingInitialized()`. ## 3. Minimal still ```python mol = mn.Molecule.fetch("4ozs") # .bcif from RCSB, cached mol.add_style("cartoon", material=mn.material.AmbientOcclusion()) canvas.look_at(mol, viewpoint="front") canvas.snapshot("4ozs.png") # returns an IPython Image for PNG/JPEG ``` `snapshot(path=None, frame=None, file_format="PNG", render_scale=100)`. With no path it renders to a temp file and returns the image (notebooks display it). `frame=` renders one scene frame and restores the current frame afterwards. TIFF/EXR write the file but return `None`. The canonical docs versions are in `docs/api/index.qmd` and `docs/api/rendering.qmd`. ## 4. Canvas settings | member | meaning | | --- | --- | | `engine` | `mn.scene.EEVEE(samples=64, raytracing=True)` or `mn.scene.Cycles(samples=256, device="GPU", denoise=True, denoise_gpu=True)`; also accepts `"EEVEE"` / `"CYCLES"`. Constructor values are written to the scene on assignment. | | `resolution` | `(x, y)` pixels. `render_scale` is the percentage. | | `samples` | samples on the active engine. | | `transparent` | film transparency (alpha background). | | `background` | world background RGBA; shortcut into the `MN_world_shader` node. | | `world.hdri_strength` | lighting strength of the preset HDRI. | | `view_transform`, `exposure`, `gamma`, `look` | colour management. Blender defaults to AgX; use `"Standard"` when colours must come out as specified. `mn.Canvas(view_transform="Standard")` sets it on construction. | | `passes` | render passes: combined, z, mist, normal, position, vector, diffuse_color, emit, environment, ambient_occlusion. | | `frame`, `frame_start`, `frame_end`, `frame_range`, `fps` | timeline. Setting `frame` uses `frame_set`, so trajectories update. | | `camera` | `lens`, `clip_start`, `clip_end`, `rotation` (XYZ Euler in degrees), `basis`, `set_viewpoint(...)`, `frame_points(points, margin)`. | | `compositor` | `device`, `precision`, denoise settings, `reset()`, `clear()`, `add_annotations()`. | - `canvas.clear()` deletes every object except cameras and lights (including the preset backdrop), purges orphans recursively, and keeps engine, world, compositor and render settings. `canvas.load_preset()` reloads the whole preset. - `Cycles(device="GPU")` tries OPTIX, CUDA, METAL, HIP, ONEAPI and falls back to CPU with a warning. EEVEE needs a GPU; the GitHub runners do not have one, so CI-facing scripts use Cycles CPU. - `world.reset()` and `compositor.reset()` remove the preset nodes: after them `canvas.background` raises `ValueError` and the annotation overlay is gone (`compositor.add_annotations()` restores it). ## 5. Loading entities ```python mol = mn.Molecule.fetch("9MD2") # format=".bcif", database="rcsb" af = mn.Molecule.fetch("Q8W3K0", database="alphafold") pdb = mn.Molecule.load("path/protein.pdb", style="cartoon") # single structure traj = mn.Molecule.load("topol.tpr", "traj.xtc", name="md") # MD topology + coordinates u_mol = mn.Molecule(u) # from an MDAnalysis Universe ``` `fetch(code, format=".bcif", cache=download.CACHE_DIR, database="rcsb")`. `load` routes single files through biotite and topology plus coordinates through MDAnalysis; `style=` is optional and defaults to no style, leaving the tree empty. In tests use the `fetch` fixture instead, which loads from `tests/data` and never downloads. ## 6. Styles, materials, colour ```python mol.add_style( "surface", selection="protein", material=mn.material.Flat(), color="common" ) mol.add_style("ball_and_stick", selection="not protein", color=(1.0, 0.5, 0.0, 1.0)) mol.add_style( lambda: mg.StyleCartoon(quality=5, loop_radius=0.6), color=lambda: mg.ColorRainbow() ) ``` - **Style names:** `spheres`, `cartoon`, `ribbon`, `surface`, `sticks`, `ball_and_stick`. Extra kwargs go to the style node's inputs (`quality`, `scale`, `loop_radius`, `sphere`, ...); unknown names raise `TypeError`, unknown style strings `ValueError`. `add_style` returns the molecule, so calls chain. - **Callable style** (`lambda: mg.StyleX(...)`) builds the node itself, so it cannot be combined with `selection`, `material` or kwargs (`TypeError`); `color`, `assembly` and `name` are fine. - **Selection** is an existing boolean attribute name first, then an MDAnalysis phrase (stored as a managed `sel_N` attribute), an `AtomGroup`, or a callable returning a boolean socket (`lambda: mg.IsPeptide() & mg.IsSideChain()`). - **`assembly=True`** instances the style over the file's biological assembly. - **Materials.** Presets in `mn.material`: `Default(roughness, ao_distance, ao_exponent)`, `AmbientOcclusion(distance, exponent)`, `Flat(outline, threshold, thickness)` (no outline unless `outline=True`), `Squishy(subsurface_scale, roughness)`, `Transparent(transparency, fresnel, outline_color)`. Each instantiation builds an independent datablock (`"Flat.001"`), and its parameters are live: `mat.distance = 0.15` changes the next render. Passing the string `material="Flat"` reuses one shared datablock, so edits affect every style using it. `"Fresnel Outline"` exists only as `mn.material.append_material("Fresnel Outline")`. `Transparent` needs the blended surface method, which its recipe sets. To swap the material on an existing style: `style.i.material.default_value = mat.material`. - **Colour.** `color=` takes `"common"`/`"default"` (elements, carbons random per chain), `"plddt"`, the name of an existing *colour* attribute, an RGBA sequence, or a callable returning a colour socket. Any other string warns and applies nothing (this replaced a silent black render). Arrays go on directly with `mol["Color"] = rgba_array`. - **Colouring part of a representation.** Do not add the same style once per selection to colour regions (a cartoon per section, sticks per nucleotide): each style builds its own geometry, so a cartoon or ribbon is cut at every boundary (blocky helix ends, stubs at the cuts). Add each style once and colour it from a per-atom attribute: ```python mol["Color"][mol.universe.select_atoms("chainID A and resid 19-26").ix, :3] = ( 0.1, 0.7, 0.7, ) # color=None reads Color; or store under another name and pass color="name" mol.add_style("cartoon") mol.add_style("sticks", selection="chainID A and resid 19-26") ``` A new attribute needs `atype="FLOAT_COLOR"`: `mol["name"] = rgba` infers a `FLOAT4`, which `add_style` rejects (it warns and applies nothing). Cartoon colour follows the backbone atoms, so colouring only side-chain atoms leaves the cartoon unchanged. - **Spheres in EEVEE.** Point clouds are ray-traced only by Cycles; on other engines `add_style` switches `StyleSpheres` from `sphere="Point"` to `"Instance"` for you. If you build the tree by hand, set `sphere="Instance"` or `"Mesh"` yourself, and use instances whenever point clouds with different materials are joined. ## 7. Framing ```python canvas.look_at(mol) # keep current direction, fit the subject canvas.look_at( mol, viewpoint="top", margin=0.15 ) # front, back, top, bottom, left, right, default canvas.look_at(mol, viewpoint=(90, 0, 45)) # XYZ Euler degrees canvas.look_at(mol.get_view("chainID A and resid 1-40")) canvas.look_at(points_xyz) # any (N, 3) array in world units ``` - `look_at(target, viewpoint=None, margin=0.05)` fits the camera to the evaluated geometry without changing where it points; `margin=0` is exact, negative crops. - `camera.lens` changes after `look_at` invalidate the fit: set the lens first, or call `look_at` again. - **Stale camera basis.** `set_viewpoint` writes `rotation_euler`, but the fit reads `matrix_world`, which only updates with the depsgraph. `look_at(entity_or_object, viewpoint=...)` is safe because reading the evaluated geometry updates it first. `look_at(points_array, viewpoint=...)`, or `set_viewpoint(...)` followed by a separate `look_at`, fits against the previous orientation and renders empty or off-centre (measured 2026-09-18). Call `bpy.context.view_layer.update()` between the two until `look_at` does it itself. - `frame_points` extends `clip_end` when the subject would be clipped; if a hand-placed camera renders nothing, check `camera.clip_end` first. - Rotating the subject instead of the camera: leave the camera at `"default"` and rotate the object, or use the `viewpoint` tuple in a loop for orbits (section 9). ## 8. Trajectories Per-molecule playback properties, all stored on the Blender object: `frame`, `subframes`, `offset`, `average`, `correct_periodic`, `interpolate`. A trajectory with `n` universe frames and `subframes = s` spans `n * (s + 1) - 1` scene frames. ```python traj = mn.Molecule(u) # secondary structure per frame, if cartoon/ribbon needs it traj.calculations.dssp(updating=True) traj.subframes, traj.interpolate, traj.average = 1, True, 1 traj.add_style("cartoon", color="common") canvas.fps = 24 canvas.frame_range = (0, u.trajectory.n_frames * 2 - 1) canvas.frame = 0 canvas.look_at(traj, viewpoint="top", margin=0.35) ``` `Molecule.frames_to_collection(start=0, stop=None, step=1)` bakes frames into a collection for the *Animate Frames* node when the timeline route is not wanted. `set_frame` is what the frame-change handler calls; user code sets `canvas.frame`. ## 9. Animations and image sequences Three routes, pick by what changes between frames: 1. **Timeline only changes** (trajectory playback, keyframed values, `SceneTime` in a tree): `canvas.animation(path="out.mp4", frame_start=None, frame_end=None, render_scale=100, fps=None, format=None)`. Format is inferred from a `.gif` suffix; MP4 is H.264; GIF needs pillow. It locks the interface, renders to a temp directory and restores frame, fps, scale and output settings afterwards. 2. **Camera, style or colour change per frame:** ```python with canvas.record("orbit.mp4", fps=12) as movie: for i in range(36): canvas.look_at(mol, viewpoint=(90, 0, i * 10)) movie.render(render_scale=50) ``` `record(path=None, fps=None, render_scale=100, frames_dir=None, overwrite=True)` returns a `FrameRecorder`; `render()` writes `%05d.png`, `finalize(path, fps, format)` assembles them. The context manager finalises only on a clean exit and only when a path was given. `frames_dir=` plus `overwrite=False` resumes an interrupted run. All frames must share one resolution. 3. **A few stills at chosen frames:** `canvas.snapshot(path, frame=f)` in a loop. ## 10. Deterministic renders and tests - Same-seed Cycles CPU renders are pixel-identical on one platform. Recipe: ```python canvas.engine = mn.scene.Cycles(samples=32, device="CPU", denoise=False) canvas.compositor.device = "CPU" ``` Compare decoded pixels, not PNG bytes (metadata differs). Exactness does not hold across platforms or Blender versions.