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Merge branch 'master' of https://github.com/molstar/molstar into cam-anim-params

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Alexander Rose
2026-05-30 21:27:45 -07:00
parent 905eb3ec2f 055dfd4946
commit b94073b96f
9 changed files with 59 additions and 31 deletions
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4
CHANGELOG.md
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@@ -4,6 +4,8 @@ All notable changes to this project will be documented in this file, following t
Note that since we don't clearly distinguish between a public and private interfaces there will be changes in non-major versions that are potentially breaking. If we make breaking changes to less used interfaces we will highlight it in here.
## [Unreleased]
- Fix exported image artifacts on transparent background with emissive, bloom, or antialiasing
- Fix cel-shaded ambient color being stripped to luminance (now uses full RGB, matching the classic lighting path)
- Fix empty transforms default in `ShapeFromPly`
- Use morton order for spheres in dot visual with lod-levels
- Add `Camera.changed` event and rotation/translation setter/getter
@@ -12,8 +14,10 @@ Note that since we don't clearly distinguish between a public and private interf
- Add mesoscale representation preset
- Add presets option to `ObjectList` param definition
- Fix memory leak in `State.dispose()` not invoking transformer `dispose` callbacks for live cells
- Fix bugs in ModelServer surroundingLigands endpoint, resulting in omitWater not honored
- Fix `Volume` and `Isosurface` getBoundingSphere ignoring instances
- Add axis param to camera spin/rock animation
- Fix SSAO half/quarter resolution textures for multi-scale
## [v5.9.0] - 2026-05-03
- Fix edge case when `PluginSpec.animations` is empty

9
src/mol-canvas3d/canvas3d.ts
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@@ -98,7 +98,6 @@ export const Canvas3DParams = {
transparentBackground: PD.Boolean(false),
checkeredTransparentBackground: PD.Boolean(false),
dpoitIterations: PD.Numeric(2, { min: 1, max: 10, step: 1 }),
enableAnimation: PD.Boolean(true, { description: 'Enable GPU time-based animations (wiggle/tumble).' }),
pickPadding: PD.Numeric(3, { min: 0, max: 10, step: 1 }, { description: 'Extra pixels to around target to check in case target is empty.' }),
userInteractionReleaseMs: PD.Numeric(250, { min: 0, max: 1000, step: 1 }, { description: 'The time before the user is not considered interacting anymore.' }),
@@ -480,7 +479,6 @@ namespace Canvas3D {
const hiZ = new HiZPass(webgl, passes.draw, canvas, p.hiZ);
const renderer = Renderer.create(webgl, p.renderer);
renderer.setProps({ enableAnimation: p.enableAnimation });
renderer.setOcclusionTest(hiZ.isOccluded);
const shaderManager = new ShaderManager(webgl, scene);
@@ -677,7 +675,7 @@ namespace Canvas3D {
const xrChanged = xrManager.update(xrFrame);
if (!xrChanged && xrFrame) return false;
const activeAnimation = p.enableAnimation && scene.hasAnimation;
const activeAnimation = renderer.props.enableAnimation && scene.hasAnimation;
const shouldRender = force || cameraChanged || resized || forceNextRender || xrChanged || activeAnimation;
forceNextRender = false;
@@ -1071,7 +1069,6 @@ namespace Canvas3D {
transparentBackground: p.transparentBackground,
checkeredTransparentBackground: p.checkeredTransparentBackground,
dpoitIterations: p.dpoitIterations,
enableAnimation: p.enableAnimation,
pickPadding: p.pickPadding,
userInteractionReleaseMs: p.userInteractionReleaseMs,
viewport: p.viewport,
@@ -1317,10 +1314,6 @@ namespace Canvas3D {
if (props.transparentBackground !== undefined) p.transparentBackground = props.transparentBackground;
if (props.checkeredTransparentBackground !== undefined) p.checkeredTransparentBackground = props.checkeredTransparentBackground;
if (props.dpoitIterations !== undefined) p.dpoitIterations = props.dpoitIterations;
if (props.enableAnimation !== undefined) {
p.enableAnimation = props.enableAnimation;
renderer.setProps({ enableAnimation: p.enableAnimation });
}
if (props.pickPadding !== undefined) {
p.pickPadding = props.pickPadding;
pickHelper.setPickPadding(p.pickPadding);

48
src/mol-canvas3d/passes/ssao.ts
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@@ -1,5 +1,5 @@
/**
* Copyright (c) 2019-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
* Copyright (c) 2019-2026 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
* @author Áron Samuel Kovács <aron.kovacs@mail.muni.cz>
@@ -484,27 +484,45 @@ export class SsaoPass {
if (isTimingMode) this.webgl.timer.markEnd('SSAO.downsample');
}
if (isTimingMode) this.webgl.timer.mark('SSAO.half');
if (multiScale) {
// half-resolution viewport (matches dimensions of depthHalfTarget*)
const hsx = Math.floor(sx * 0.5);
const hsy = Math.floor(sy * 0.5);
const hsw = Math.ceil(sw * 0.5);
const hsh = Math.ceil(sh * 0.5);
state.viewport(hsx, hsy, hsw, hsh);
state.scissor(hsx, hsy, hsw, hsh);
if (isTimingMode) this.webgl.timer.mark('SSAO.half');
this.depthHalfTargetOpaque.bind();
this.depthHalfRenderableOpaque.render();
}
if (multiScale && includeTransparent) {
this.depthHalfTargetTransparent.bind();
this.depthHalfRenderableTransparent.render();
}
if (isTimingMode) this.webgl.timer.markEnd('SSAO.half');
if (includeTransparent) {
this.depthHalfTargetTransparent.bind();
this.depthHalfRenderableTransparent.render();
}
if (isTimingMode) this.webgl.timer.markEnd('SSAO.half');
if (isTimingMode) this.webgl.timer.mark('SSAO.quarter');
if (multiScale) {
// quarter-resolution viewport (matches dimensions of depthQuarterTarget*)
const qsx = Math.floor(sx * 0.25);
const qsy = Math.floor(sy * 0.25);
const qsw = Math.ceil(sw * 0.25);
const qsh = Math.ceil(sh * 0.25);
state.viewport(qsx, qsy, qsw, qsh);
state.scissor(qsx, qsy, qsw, qsh);
if (isTimingMode) this.webgl.timer.mark('SSAO.quarter');
this.depthQuarterTargetOpaque.bind();
this.depthQuarterRenderableOpaque.render();
if (includeTransparent) {
this.depthQuarterTargetTransparent.bind();
this.depthQuarterRenderableTransparent.render();
}
if (isTimingMode) this.webgl.timer.markEnd('SSAO.quarter');
// restore full-scale viewport for SSAO + blur passes
state.viewport(sx, sy, sw, sh);
state.scissor(sx, sy, sw, sh);
}
if (multiScale && includeTransparent) {
this.depthQuarterTargetTransparent.bind();
this.depthQuarterRenderableTransparent.render();
}
if (isTimingMode) this.webgl.timer.markEnd('SSAO.quarter');
if (isTimingMode) this.webgl.timer.mark('SSAO.opaque');
this.ssaoDepthTexture.attachFramebuffer(this.framebuffer, 'color0');

2
src/mol-gl/shader/chunks/apply-light-color.glsl.ts
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@@ -78,7 +78,7 @@ export const apply_light_color = `
}
#pragma unroll_loop_end
outgoingLight += physicalMaterial.diffuseColor * luminance(uAmbientColor);
outgoingLight += physicalMaterial.diffuseColor * uAmbientColor;
#else
ReflectedLight reflectedLight = ReflectedLight(vec3(0.0), vec3(0.0), vec3(0.0), vec3(0.0));

6
src/mol-model/structure/query/queries/modifiers.ts
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@@ -545,6 +545,12 @@ export function surroundingLigands({ query, radius, includeWater }: SurroundingL
continue;
}
// Water is handled exclusively by the `includeWater` 3D-lookup branch below.
// A single water pulled in via a struct_conn metalc/covale edge would
// otherwise match every other water in the chain (all share label_seq_id
// and label_comp_id) and leak the entire chain.
if (StructureProperties.entity.type(l) === 'water') continue;
residuesIt.setSegment(chainSegment);
while (residuesIt.hasNext) {
const residueSegment = residuesIt.move();

13
src/mol-util/image.ts
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@@ -2,6 +2,7 @@
* Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
* @author Gianluca Tomasello <giagitom@gmail.com>
*/
export { PixelData };
@@ -37,12 +38,14 @@ namespace PixelData {
/** to undo pre-multiplied alpha */
export function divideByAlpha(pixelData: PixelData): PixelData {
const { array } = pixelData;
const factor = (array instanceof Uint8Array) ? 255 : 1;
// clamp: emissive, bloom and antialiasing can lift premul RGB above alpha; without it Uint8Array silently wraps.
const max = (array instanceof Uint8Array) ? 255 : 1;
for (let i = 0, il = array.length; i < il; i += 4) {
const a = array[i + 3] / factor;
array[i] /= a;
array[i + 1] /= a;
array[i + 2] /= a;
const a = array[i + 3] / max;
if (a === 0) continue;
array[i] = Math.min(max, array[i] / a);
array[i + 1] = Math.min(max, array[i + 1] / a);
array[i + 2] = Math.min(max, array[i + 2] / a);
}
return pixelData;
}

4
src/servers/model/CHANGELOG.md
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@@ -1,3 +1,7 @@
# 0.9.13
* /surroundingLigands: honor `omit_water=true|false` for REST GET requests (boolean parser previously coerced both to `false`)
* /surroundingLigands: stop leaking the asymmetric unit's water chain into the result when `omit_water=true` (water residues pulled in via struct_conn covale/metalc edges no longer match every other water in the chain)
# 0.9.12
* add `health-check` endpoint + `healthCheckPath` config prop to report service health

2
src/servers/model/server/api.ts
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@@ -295,7 +295,7 @@ function _normalizeQueryParams(params: { [p: string]: string }, paramList: Query
case QueryParamType.String: el = value; break;
case QueryParamType.Integer: el = parseInt(value); break;
case QueryParamType.Float: el = parseFloat(value); break;
case QueryParamType.Boolean: el = Boolean(+value); break;
case QueryParamType.Boolean: el = isTrue(value); break;
}
if (p.validation) p.validation(el);

2
src/servers/model/version.ts
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@@ -4,4 +4,4 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
export const VERSION = '0.9.12';
export const VERSION = '0.9.13';