MoleculeRenderer

megane-viewer

---

megane-viewer / MoleculeRenderer

Class: MoleculeRenderer

Defined in: renderer/MoleculeRenderer.ts:284

Constructors

Constructor

new MoleculeRenderer(): MoleculeRenderer

Returns

MoleculeRenderer

Methods

alignCameraToAxis()

alignCameraToAxis(axis): void

Defined in: renderer/MoleculeRenderer.ts:2249

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:1160

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:2282

Restore camera to a previously saved state.

Parameters

state

MeganeCameraState

Returns

void

---

clearAtomOverrides()

clearAtomOverrides(): void

Defined in: renderer/MoleculeRenderer.ts:1133

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

Returns

void

---

clearBondOpacityOverrides()

clearBondOpacityOverrides(): void

Defined in: renderer/MoleculeRenderer.ts:1226

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

Returns

void

---

clearPolyhedra()

clearPolyhedra(): void

Defined in: renderer/MoleculeRenderer.ts:1033

Clear all polyhedra from the scene.

Returns

void

---

clearSelection()

clearSelection(): void

Defined in: renderer/MoleculeRenderer.ts:1975

Clear all selected atoms.

Returns

void

---

dispose()

dispose(): void

Defined in: renderer/MoleculeRenderer.ts:2169

Clean up all resources.

Returns

void

---

endAxesDrag()

endAxesDrag(): void

Defined in: renderer/MoleculeRenderer.ts:1435

End the axes-inset drag.

Returns

void

---

fitToViewAll()

fitToViewAll(): void

Defined in: renderer/MoleculeRenderer.ts:1084

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:1777

Get the active camera.

Returns

OrthographicCamera | PerspectiveCamera

---

getCameraState()

getCameraState(): MeganeCameraState | null

Defined in: renderer/MoleculeRenderer.ts:2267

Read current camera state. Returns null before mount.

Returns

MeganeCameraState | null

---

getCanvas()

getCanvas(): HTMLCanvasElement | null

Defined in: renderer/MoleculeRenderer.ts:1767

Get the canvas element for event listener attachment.

Returns

HTMLCanvasElement | null

---

getCurrentPositionsCopy()

getCurrentPositionsCopy(): Float32Array<ArrayBufferLike> | null

Defined in: renderer/MoleculeRenderer.ts:1883

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

Returns

Float32Array<ArrayBufferLike> | null

---

getLabelOverlay()

getLabelOverlay(): LabelOverlay | null

Defined in: renderer/MoleculeRenderer.ts:1800

Get the label overlay canvas.

Returns

LabelOverlay | null

---

getLayer()

getLayer(layerId): StructureLayer | undefined

Defined in: renderer/MoleculeRenderer.ts:1052

Get an existing structure layer (or undefined).

Parameters

layerId

string

Returns

StructureLayer | undefined

---

getLayerIds()

getLayerIds(): string[]

Defined in: renderer/MoleculeRenderer.ts:1066

Get all current layer IDs.

Returns

string[]

---

getMeasurement()

getMeasurement(): Measurement | null

Defined in: renderer/MoleculeRenderer.ts:1981

Compute the current geometric measurement based on selected atoms.

Returns

Measurement | null

---

getOrCreateLayer()

getOrCreateLayer(layerId): StructureLayer

Defined in: renderer/MoleculeRenderer.ts:1042

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

Parameters

layerId

string

Returns

StructureLayer

---

getRenderer()

getRenderer(): WebGLRenderer

Defined in: renderer/MoleculeRenderer.ts:1782

Get the WebGL renderer.

Returns

WebGLRenderer

---

getScene()

getScene(): Scene

Defined in: renderer/MoleculeRenderer.ts:1772

Get the Three.js scene.

Returns

Scene

---

getStats()

getStats(): object

Defined in: renderer/MoleculeRenderer.ts:1792

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:1390

Check if cell data exists.

Returns

boolean

---

hasCellAxes()

hasCellAxes(): boolean

Defined in: renderer/MoleculeRenderer.ts:1447

Check if cell axes data exists.

Returns

boolean

---

hitTestAxesInset()

hitTestAxesInset(cssX, cssY): boolean

Defined in: renderer/MoleculeRenderer.ts:1409

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:1442

Whether an axes drag is in progress.

Returns

boolean

---

loadPolyhedra()

loadPolyhedra(data): void

Defined in: renderer/MoleculeRenderer.ts:1024

Load polyhedra mesh data for rendering.

Parameters

data

MeshData

Returns

void

---

loadSnapshot()

loadSnapshot(snapshot, opts?): void

Defined in: renderer/MoleculeRenderer.ts:534

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:416

Mount the viewer into a DOM element.

Parameters

container

HTMLElement

Returns

void

---

moveAxesDrag()

moveAxesDrag(cssX, cssY): boolean

Defined in: renderer/MoleculeRenderer.ts:1424

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:1896

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:1071

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:1057

Remove a structure layer and dispose its resources.

Parameters

layerId

string

Returns

void

---

renderSingleFrame()

renderSingleFrame(): void

Defined in: renderer/MoleculeRenderer.ts:1808

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:2224

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

Returns

void

---

resetView()

resetView(): void

Defined in: renderer/MoleculeRenderer.ts:1500

Reset view to fit all atoms.

Returns

void

---

resizeForCapture()

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

Defined in: renderer/MoleculeRenderer.ts:1842

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

---

selectAtomsInRect()

selectAtomsInRect(rect): number[]

Defined in: renderer/MoleculeRenderer.ts:1956

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:1109

Set atom opacity (independent of bonds).

Parameters

opacity

number

Returns

void

---

setAtomOpacityOverrides()

setAtomOpacityOverrides(overrides): void

Defined in: renderer/MoleculeRenderer.ts:1125

Set per-atom opacity overrides from selection pipeline.

Parameters

overrides

Float32Array

Returns

void

---

setAtomScale()

setAtomScale(scale): void

Defined in: renderer/MoleculeRenderer.ts:1099

Set atom radius scale multiplier.

Parameters

scale

number

Returns

void

---

setAtomScaleOverrides()

setAtomScaleOverrides(overrides): void

Defined in: renderer/MoleculeRenderer.ts:1117

Set per-atom scale overrides from selection pipeline.

Parameters

overrides

Float32Array

Returns

void

---

setAtomsVisible()

setAtomsVisible(visible): void

Defined in: renderer/MoleculeRenderer.ts:1231

Toggle atom visibility.

Parameters

visible

boolean

Returns

void

---

setBackgroundColor()

setBackgroundColor(hexColor): void

Defined in: renderer/MoleculeRenderer.ts:1877

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:1150

Set bond opacity (independent of atoms).

Parameters

opacity

number

Returns

void

---

setBondOpacityOverrides()

setBondOpacityOverrides(overrides): void

Defined in: renderer/MoleculeRenderer.ts:1221

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

Parameters

overrides

Float32Array

Returns

void

---

setBondPeriodicImages()

setBondPeriodicImages(images): void

Defined in: renderer/MoleculeRenderer.ts:927

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:1142

Set bond radius scale multiplier.

Parameters

scale

number

Returns

void

---

setBondsVisible()

setBondsVisible(visible): void

Defined in: renderer/MoleculeRenderer.ts:1369

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:2262

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:2218

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

Parameters

mode

MeganeCameraMode

Returns

void

---

setCellAxesVisible()

setCellAxesVisible(visible): void

Defined in: renderer/MoleculeRenderer.ts:1395

Toggle cell axes indicator visibility.

Parameters

visible

boolean

Returns

void

---

setCellVisible()

setCellVisible(visible): void

Defined in: renderer/MoleculeRenderer.ts:1383

Toggle simulation cell visibility.

Parameters

visible

boolean

Returns

void

---

setControlsEnabled()

setControlsEnabled(enabled): void

Defined in: renderer/MoleculeRenderer.ts:1970

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:899

Apply the pipeline's Drawing Boundary atom collection.

Parameters

boundary

DrawingBoundaryData | null

Returns

void

---

setLabels()

setLabels(labels): void

Defined in: renderer/MoleculeRenderer.ts:893

Set per-atom labels for overlay display.

Parameters

labels

string[] | null

Returns

void

---

setPerspective()

setPerspective(enabled): void

Defined in: renderer/MoleculeRenderer.ts:1741

Switch between orthographic and perspective projection.

Parameters

enabled

boolean

Returns

void

---

setPivotMarkerVisible()

setPivotMarkerVisible(visible): void

Defined in: renderer/MoleculeRenderer.ts:1402

Toggle rotation-center marker visibility.

Parameters

visible

boolean

Returns

void

---

setPreviewSelection()

setPreviewSelection(atomIndices): void

Defined in: renderer/MoleculeRenderer.ts:1941

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:1323

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:1249

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:1511

Set the rotation center (controls target) to the given world coordinates.

Parameters

x

number

y

number

z

number

animate?

boolean = true

When true (default), smoothly animates the transition over PIVOT_ANIM_DURATION_MS. Pass false to update synchronously (legacy behaviour). The clicked atom is animated to the screen center.

Returns

void

---

setSelection()

setSelection(atomIndices): SelectionState

Defined in: renderer/MoleculeRenderer.ts:1930

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:1014

Set per-atom vector data for arrow display.

Parameters

vectors

Float32Array<ArrayBufferLike> | null

Returns

void

---

setVectorScale()

setVectorScale(scale): void

Defined in: renderer/MoleculeRenderer.ts:1019

Set arrow scale multiplier.

Parameters

scale

number

Returns

void

---

setViewInsets()

setViewInsets(left, right): void

Defined in: renderer/MoleculeRenderer.ts:1712

Set pixel insets for overlay panels that occlude viewport edges.

Parameters

left

number

right

number

Returns

void

---

startAxesDrag()

startAxesDrag(cssX, cssY): void

Defined in: renderer/MoleculeRenderer.ts:1415

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:2298

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

Returns

MeganeCameraState | null

---

testGetProjectedAtomPositions()

testGetProjectedAtomPositions(): MeganeProjectedAtom[]

Defined in: renderer/MoleculeRenderer.ts:2320

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

Returns

MeganeProjectedAtom[]

---

testGetVisibleSubsystems()

testGetVisibleSubsystems(): MeganeSubsystemVisibility

Defined in: renderer/MoleculeRenderer.ts:2303

Aggregate visibility booleans for each renderer subsystem.

Returns

MeganeSubsystemVisibility

---

toggleAtomSelection()

toggleAtomSelection(atomIndex): SelectionState

Defined in: renderer/MoleculeRenderer.ts:1915

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

Parameters

atomIndex

number

Returns

SelectionState

---

updateBonds()

updateBonds(bonds, bondOrders): void

Defined in: renderer/MoleculeRenderer.ts:822

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:844

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:699

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