MoleculeRenderer

megane-viewer

---

megane-viewer / MoleculeRenderer

Class: MoleculeRenderer

Defined in: renderer/MoleculeRenderer.ts:62

Constructors

Constructor

new MoleculeRenderer(): MoleculeRenderer

Returns

MoleculeRenderer

Methods

alignCameraToAxis()

alignCameraToAxis(axis): void

Defined in: renderer/MoleculeRenderer.ts:1589

Turn the camera to look along a crystallographic (±a, ±b, ±c) or Cartesian (±x, ±y, ±z) axis, keeping the current target, distance and zoom. The crystal axes come from the loaded snapshot's cell; without one they coincide with x/y/z. See cameraOrientation.ts for the sign and up-vector conventions.

Parameters

axis

"+a" | "+b" | "+c" | "+x" | "+y" | "+z" | "-a" | "-b" | "-c" | "-x" | "-y" | "-z"

Returns

void

---

applyAtomColorOverrides()

applyAtomColorOverrides(overrides): void

Defined in: renderer/MoleculeRenderer.ts:847

Apply per-atom RGB overrides for the primary structure. Null reverts to the default CPK palette for every atom. Identity comparison short-circuits the GPU upload when the same buffer reference is supplied repeatedly.

Parameters

overrides

Float32Array<ArrayBufferLike> | null

Returns

void

---

applyCameraState()

applyCameraState(state): void

Defined in: renderer/MoleculeRenderer.ts:1604

Restore camera to a previously saved state.

Parameters

state

MeganeCameraState

Returns

void

---

clearAtomOverrides()

clearAtomOverrides(): void

Defined in: renderer/MoleculeRenderer.ts:824

Clear all per-atom overrides, reverting to global uniforms.

Returns

void

---

clearBondOpacityOverrides()

clearBondOpacityOverrides(): void

Defined in: renderer/MoleculeRenderer.ts:913

Clear per-bond opacity overrides, reverting to global opacity.

Returns

void

---

clearPolyhedra()

clearPolyhedra(): void

Defined in: renderer/MoleculeRenderer.ts:738

Clear all polyhedra from the scene.

Returns

void

---

clearSelection()

clearSelection(): void

Defined in: renderer/MoleculeRenderer.ts:1395

Clear all selected atoms.

Returns

void

---

dispose()

dispose(): void

Defined in: renderer/MoleculeRenderer.ts:1530

Clean up all resources.

Returns

void

---

dragDeltaForAtom()

dragDeltaForAtom(atomIndex, fromX, fromY, toX, toY): [number, number, number] | null

Defined in: renderer/MoleculeRenderer.ts:1359

World displacement of a screen drag in the camera-facing plane through atom atomIndex (at its current position). Null when nothing is loaded.

Parameters

atomIndex

number

fromX

number

fromY

number

toX

number

toY

number

Returns

[number, number, number] | null

---

dragGesture()

dragGesture(atomIndex, fromX, fromY, toX, toY): ViewDragGesture | null

Defined in: renderer/MoleculeRenderer.ts:1370

A drag grabbed at atom atomIndex, for an editor (see SelectionController.dragGesture).

Parameters

atomIndex

number

fromX

number

fromY

number

toX

number

toY

number

Returns

ViewDragGesture | null

---

endAxesDrag()

endAxesDrag(): void

Defined in: renderer/MoleculeRenderer.ts:1100

End the axes-inset drag.

Returns

void

---

fitToViewAll()

fitToViewAll(): void

Defined in: renderer/MoleculeRenderer.ts:789

Fit camera to show all structures (from all layers + primary snapshot). Call after loading snapshots into layers.

Returns

void

---

getCamera()

getCamera(): OrthographicCamera | PerspectiveCamera

Defined in: renderer/MoleculeRenderer.ts:1206

Get the active camera.

Returns

OrthographicCamera | PerspectiveCamera

---

getCameraState()

getCameraState(): MeganeCameraState | null

Defined in: renderer/MoleculeRenderer.ts:1599

Read current camera state. Returns null before mount.

Returns

MeganeCameraState | null

---

getCanvas()

getCanvas(): HTMLCanvasElement | null

Defined in: renderer/MoleculeRenderer.ts:1196

Get the canvas element for event listener attachment.

Returns

HTMLCanvasElement | null

---

getCurrentPositionsCopy()

getCurrentPositionsCopy(): Float32Array<ArrayBufferLike> | null

Defined in: renderer/MoleculeRenderer.ts:1302

Get a copy of current atom positions (public, for external use).

Returns

Float32Array<ArrayBufferLike> | null

---

getLabelOverlay()

getLabelOverlay(): LabelOverlay | null

Defined in: renderer/MoleculeRenderer.ts:1229

Get the label overlay canvas.

Returns

LabelOverlay | null

---

getLayer()

getLayer(layerId): StructureLayer | undefined

Defined in: renderer/MoleculeRenderer.ts:757

Get an existing structure layer (or undefined).

Parameters

layerId

string

Returns

StructureLayer | undefined

---

getLayerIds()

getLayerIds(): string[]

Defined in: renderer/MoleculeRenderer.ts:771

Get all current layer IDs.

Returns

string[]

---

getMeasurement()

getMeasurement(): Measurement | null

Defined in: renderer/MoleculeRenderer.ts:1400

Compute the current geometric measurement based on selected atoms.

Returns

Measurement | null

---

getOrCreateLayer()

getOrCreateLayer(layerId): StructureLayer

Defined in: renderer/MoleculeRenderer.ts:747

Get or create a structure layer for a given node ID.

Parameters

layerId

string

Returns

StructureLayer

---

getRenderer()

getRenderer(): WebGLRenderer

Defined in: renderer/MoleculeRenderer.ts:1211

Get the WebGL renderer.

Returns

WebGLRenderer

---

getScene()

getScene(): Scene

Defined in: renderer/MoleculeRenderer.ts:1201

Get the Three.js scene.

Returns

Scene

---

getStats()

getStats(): object

Defined in: renderer/MoleculeRenderer.ts:1221

Live rendering stats for the performance HUD: current FPS (updated by the rAF loop) and the draw-call count of the most recent frame. megane draws with instanced meshes, so draw calls — not a scene mesh-object count — are the meaningful GPU-load metric.

Returns

object

drawCalls

drawCalls: number

fps

fps: number

---

hasCell()

hasCell(): boolean

Defined in: renderer/MoleculeRenderer.ts:1055

Check if cell data exists.

Returns

boolean

---

hasCellAxes()

hasCellAxes(): boolean

Defined in: renderer/MoleculeRenderer.ts:1112

Check if cell axes data exists.

Returns

boolean

---

hitTestAxesInset()

hitTestAxesInset(cssX, cssY): boolean

Defined in: renderer/MoleculeRenderer.ts:1074

Returns true if the CSS-pixel coordinate hits the axes inset.

Parameters

cssX

number

cssY

number

Returns

boolean

---

isAxesDragging()

isAxesDragging(): boolean

Defined in: renderer/MoleculeRenderer.ts:1107

Whether an axes drag is in progress.

Returns

boolean

---

loadPolyhedra()

loadPolyhedra(data): void

Defined in: renderer/MoleculeRenderer.ts:729

Load polyhedra mesh data for rendering.

Parameters

data

MeshData

Returns

void

---

loadSnapshot()

loadSnapshot(snapshot, opts?): void

Defined in: renderer/MoleculeRenderer.ts:288

Load a molecular snapshot (topology + positions).

opts.fit (default true) controls the closing fitToView. Pass false when the snapshot is a re-mapping of the one already on screen (same topology, new positions — e.g. the wrap node toggling wrap/unwrap): the camera then keeps its current zoom/target instead of re-fitting to the new bounds.

Parameters

snapshot

Snapshot

opts?

fit?

boolean

Returns

void

---

mount()

mount(container): void

Defined in: renderer/MoleculeRenderer.ts:186

Mount the viewer into a DOM element.

Parameters

container

HTMLElement

Returns

void

---

moveAxesDrag()

moveAxesDrag(cssX, cssY): boolean

Defined in: renderer/MoleculeRenderer.ts:1089

Continue an axes-inset drag. Returns true if currently dragging.

Parameters

cssX

number

cssY

number

Returns

boolean

---

raycastAtPixel()

raycastAtPixel(clientX, clientY): HoverInfo

Defined in: renderer/MoleculeRenderer.ts:1315

Perform a pick at the given screen coordinates using CPU screen-space projection.

Parameters

clientX

number

clientY

number

Returns

HoverInfo

---

removeInactiveLayers()

removeInactiveLayers(activeIds): void

Defined in: renderer/MoleculeRenderer.ts:776

Remove layers not in the given set of active IDs.

Parameters

activeIds

Set<string>

Returns

void

---

removeLayer()

removeLayer(layerId): void

Defined in: renderer/MoleculeRenderer.ts:762

Remove a structure layer and dispose its resources.

Parameters

layerId

string

Returns

void

---

renderSingleFrame()

renderSingleFrame(): void

Defined in: renderer/MoleculeRenderer.ts:1237

Render a single frame synchronously at the current (or custom) size. Used for image/video capture outside the rAF loop.

Returns

void

---

resetCamera()

resetCamera(): void

Defined in: renderer/MoleculeRenderer.ts:1578

Re-fit the camera to the current snapshot's bounding box.

Returns

void

---

resetRotationCenter()

resetRotationCenter(): void

Defined in: renderer/MoleculeRenderer.ts:1181

Reset the rotation center to the model center — the point a fresh fit orbits around (cell center, or the atoms' centroid without a cell) — keeping the view as setRotationCenter does.

Returns

void

---

resetView()

resetView(): void

Defined in: renderer/MoleculeRenderer.ts:1159

Reset view to fit all atoms.

Returns

void

---

resizeForCapture()

resizeForCapture(width, height): () => void

Defined in: renderer/MoleculeRenderer.ts:1271

Temporarily resize the renderer for capture, suppressing auto-resize. Returns a restore function to call after capture is complete.

Parameters

width

number

height

number

Returns

() => void

---

screenToWorldAtPivot()

screenToWorldAtPivot(clientX, clientY): [number, number, number] | null

Defined in: renderer/MoleculeRenderer.ts:1385

World point under a client pixel on the camera-facing plane through the current rotation pivot (the structure's center by default). Used to place a new atom on empty space. Null when nothing is mounted.

Parameters

clientX

number

clientY

number

Returns

[number, number, number] | null

---

selectAtomsInRect()

selectAtomsInRect(rect): number[]

Defined in: renderer/MoleculeRenderer.ts:1351

Return the indices of atoms whose centers fall inside a screen rectangle.

Parameters

rect

ClientRect

Returns

number[]

---

setAtomOpacity()

setAtomOpacity(opacity): void

Defined in: renderer/MoleculeRenderer.ts:809

Set atom opacity (independent of bonds).

Parameters

opacity

number

Returns

void

---

setAtomOpacityOverrides()

setAtomOpacityOverrides(overrides): void

Defined in: renderer/MoleculeRenderer.ts:819

Set per-atom opacity overrides from selection pipeline.

Parameters

overrides

Float32Array

Returns

void

---

setAtomScale()

setAtomScale(scale): void

Defined in: renderer/MoleculeRenderer.ts:804

Set atom radius scale multiplier.

Parameters

scale

number

Returns

void

---

setAtomScaleOverrides()

setAtomScaleOverrides(overrides): void

Defined in: renderer/MoleculeRenderer.ts:814

Set per-atom scale overrides from selection pipeline.

Parameters

overrides

Float32Array

Returns

void

---

setAtomsVisible()

setAtomsVisible(visible): void

Defined in: renderer/MoleculeRenderer.ts:918

Toggle atom visibility.

Parameters

visible

boolean

Returns

void

---

setBackgroundColor()

setBackgroundColor(hexColor): void

Defined in: renderer/MoleculeRenderer.ts:1296

Update the Three.js scene and canvas background color (e.g. when theme changes).

Parameters

hexColor

number

Returns

void

---

setBondOpacity()

setBondOpacity(opacity): void

Defined in: renderer/MoleculeRenderer.ts:837

Set bond opacity (independent of atoms).

Parameters

opacity

number

Returns

void

---

setBondOpacityOverrides()

setBondOpacityOverrides(overrides): void

Defined in: renderer/MoleculeRenderer.ts:908

Apply per-bond opacity overrides (one value per logical bond).

Parameters

overrides

Float32Array

Returns

void

---

setBondPeriodicImages()

setBondPeriodicImages(images): void

Defined in: renderer/MoleculeRenderer.ts:648

Apply outside-boundary neighbor images emitted by a coordination/bond stream.

Parameters

images

PeriodicAtomImageData | null

Returns

void

---

setBondScale()

setBondScale(scale): void

Defined in: renderer/MoleculeRenderer.ts:829

Set bond radius scale multiplier.

Parameters

scale

number

Returns

void

---

setBondsVisible()

setBondsVisible(visible): void

Defined in: renderer/MoleculeRenderer.ts:1037

Set whether the active pipeline emits bonds for the primary structure. The bond mesh is only shown when this AND the current representation (atoms/both) both call for bonds — otherwise switching templates would resurface stale bond geometry once the representation toggles back to atoms.

Parameters

visible

boolean

Returns

void

---

setCameraChangeCallback()

setCameraChangeCallback(cb): void

Defined in: renderer/MoleculeRenderer.ts:1594

Register a callback invoked after each user camera interaction ends.

Parameters

cb

(() => void) | null

Returns

void

---

setCameraMode()

setCameraMode(mode): void

Defined in: renderer/MoleculeRenderer.ts:1573

Switch projection mode by name (wraps setPerspective for symmetry).

Parameters

mode

MeganeCameraMode

Returns

void

---

setCellAxesVisible()

setCellAxesVisible(visible): void

Defined in: renderer/MoleculeRenderer.ts:1060

Toggle cell axes indicator visibility.

Parameters

visible

boolean

Returns

void

---

setCellVisible()

setCellVisible(visible): void

Defined in: renderer/MoleculeRenderer.ts:1048

Toggle simulation cell visibility.

Parameters

visible

boolean

Returns

void

---

setControlsEnabled()

setControlsEnabled(enabled): void

Defined in: renderer/MoleculeRenderer.ts:1390

Enable/disable camera controls (used to suspend camera rotation during a box drag).

Parameters

enabled

boolean

Returns

void

---

setDrawingBoundary()

setDrawingBoundary(boundary): void

Defined in: renderer/MoleculeRenderer.ts:629

Apply the pipeline's Drawing Boundary atom collection.

Parameters

boundary

DrawingBoundaryData | null

Returns

void

---

setHoverHighlight()

setHoverHighlight(atomIndices, color?): void

Defined in: renderer/MoleculeRenderer.ts:1341

Builder: mark the atoms a click would act on (null clears).

Parameters

atomIndices

number[] | null

color?

number

Returns

void

---

setLabels()

setLabels(labels): void

Defined in: renderer/MoleculeRenderer.ts:623

Set per-atom labels for overlay display.

Parameters

labels

string[] | null

Returns

void

---

setPerspective()

setPerspective(enabled): void

Defined in: renderer/MoleculeRenderer.ts:1191

Switch between orthographic and perspective projection.

Parameters

enabled

boolean

Returns

void

---

setPivotMarkerVisible()

setPivotMarkerVisible(visible): void

Defined in: renderer/MoleculeRenderer.ts:1067

Toggle rotation-center marker visibility.

Parameters

visible

boolean

Returns

void

---

setPreviewSelection()

setPreviewSelection(atomIndices): void

Defined in: renderer/MoleculeRenderer.ts:1336

Highlight an arbitrary set of atoms as a live "preview" of the Selection Inspector's current selection (green, translucent). Independent of the measurement selection. Pass null or [] to clear.

Parameters

atomIndices

number[] | null

Returns

void

---

setRepresentationByAtom()

setRepresentationByAtom(modes): void

Defined in: renderer/MoleculeRenderer.ts:989

Apply a per-atom representation: atoms flagged "line" are drawn by the line renderer while every other atom keeps the global mesh representation (setRepresentationType). This enables mixed views such as "show the water as lines while the rest stays ball-and-stick". Pass null to revert to the uniform global representation.

Must run after setRepresentationType, which establishes the base mesh mode and reloads the line geometry; this overlays the per-atom split on top.

Parameters

modes

RepresentationType[] | null

Returns

void

---

setRepresentationType()

setRepresentationType(type): void

Defined in: renderer/MoleculeRenderer.ts:932

Switch between atom/bond and cartoon representation modes. "atoms" – classic ball-and-stick (default) "cartoon" – Cα backbone only; atoms/bonds hidden "both" – cartoon overlaid on atoms/bonds "surface" – solvent-accessible surface only "line" – VMD/PyMOL-style thin wireframe lines; atoms/bonds meshes hidden "illustrative" – Mol*-style spacefill spheres at full vdW radius with flat, unlit shading and a silhouette outline; bonds hidden

Parameters

type

RepresentationType

Returns

void

---

setRotationCenter()

setRotationCenter(x, y, z, animate?): void

Defined in: renderer/MoleculeRenderer.ts:1172

Set the rotation center (controls target) to the given world point. Orthographic cameras keep the image and start orbiting around the point where it is on screen (OVITO); perspective cameras pan it to the screen center, smoothly when animate is true (default). See CameraController.setRotationCenter.

Parameters

x

number

y

number

z

number

animate?

boolean = true

Returns

void

---

setSelection()

setSelection(atomIndices): SelectionState

Defined in: renderer/MoleculeRenderer.ts:1327

Set selected atoms directly (for external triggers). Returns new selection state.

Parameters

atomIndices

number[]

Returns

SelectionState

---

setVectors()

setVectors(vectors): void

Defined in: renderer/MoleculeRenderer.ts:719

Set per-atom vector data for arrow display.

Parameters

vectors

Float32Array<ArrayBufferLike> | null

Returns

void

---

setVectorScale()

setVectorScale(scale): void

Defined in: renderer/MoleculeRenderer.ts:724

Set arrow scale multiplier.

Parameters

scale

number

Returns

void

---

setViewInsets()

setViewInsets(left, right): void

Defined in: renderer/MoleculeRenderer.ts:1186

Set pixel insets for overlay panels that occlude viewport edges.

Parameters

left

number

right

number

Returns

void

---

setWarningHighlight()

setWarningHighlight(atomIndices): void

Defined in: renderer/MoleculeRenderer.ts:1346

Builder: mark atoms in a close contact in red (null clears).

Parameters

atomIndices

number[] | null

Returns

void

---

startAxesDrag()

startAxesDrag(cssX, cssY): void

Defined in: renderer/MoleculeRenderer.ts:1080

Begin an axes-inset drag at the given CSS coordinates.

Parameters

cssX

number

cssY

number

Returns

void

---

testGetCameraState()

testGetCameraState(): MeganeCameraState | null

Defined in: renderer/MoleculeRenderer.ts:1609

Read camera state for tests. Returns null before mount/snapshot.

Returns

MeganeCameraState | null

---

testGetProjectedAtomPositions()

testGetProjectedAtomPositions(): MeganeProjectedAtom[]

Defined in: renderer/MoleculeRenderer.ts:1631

Project every atom of the primary snapshot to viewer-space pixels.

Returns

MeganeProjectedAtom[]

---

testGetVisibleSubsystems()

testGetVisibleSubsystems(): MeganeSubsystemVisibility

Defined in: renderer/MoleculeRenderer.ts:1614

Aggregate visibility booleans for each renderer subsystem.

Returns

MeganeSubsystemVisibility

---

toggleAtomSelection()

toggleAtomSelection(atomIndex): SelectionState

Defined in: renderer/MoleculeRenderer.ts:1322

Toggle atom selection (right-click). Returns new selection state.

Parameters

atomIndex

number

Returns

SelectionState

---

updateBonds()

updateBonds(bonds, bondOrders): void

Defined in: renderer/MoleculeRenderer.ts:552

Replace bond data and re-render bonds without resetting the camera. Used for per-frame bond recalculation (e.g. distance-based bonds).

Parameters

bonds

Uint32Array

bondOrders

Uint8Array<ArrayBufferLike> | null

Returns

void

---

updateBondsExt()

updateBondsExt(bonds, bondOrders, positions, elements, nAtoms): void

Defined in: renderer/MoleculeRenderer.ts:574

Replace bond data with optional extended positions/elements (PBC ghost atoms). When positions/elements are provided, they include ghost atoms appended to the original arrays, and bond indices may reference those ghost atoms.

Parameters

bonds

Uint32Array

bondOrders

Uint8Array<ArrayBufferLike> | null

positions

Float32Array<ArrayBufferLike> | null

elements

Uint8Array<ArrayBufferLike> | null

nAtoms

number

Returns

void

---

updateFrame()

updateFrame(frame): void

Defined in: renderer/MoleculeRenderer.ts:427

Update positions from a trajectory frame.

Fast path (uniform trajectory): the frame carries only positions, so this is a positions-only update reusing the frame-0 snapshot's topology and cell — allocation-free, exactly as before.

Slow path (heterogeneous trajectory): the frame additionally carries elements/bonds/box, so the atom/bond meshes and unit cell are rebuilt to match this frame's differing atom count, elements, or cell.

Parameters

frame

Frame

Returns

void