Merge branch 'master' into backbone

CHANGELOG.md

@@ -7,6 +7,7 @@ Note that since we don't clearly distinguish between a public and private interf
 ## [Unreleased]
 
 - Add backbone representation
+- Fix outline in orthographic mode and set default scale to 2.
 
 ## [v2.0.7] - 2021-06-23
 

src/mol-canvas3d/camera.ts

@@ -364,8 +364,9 @@ function updateClip(camera: Camera) {
         near = Math.max(Math.min(radiusMax, 5), near);
         far = Math.max(5, far);
     } else {
-        near = Math.max(0, near);
-        far = Math.max(0, far);
+        // not too close to 0 as it causes issues with outline rendering
+        near = Math.max(Math.min(radiusMax, 5), near);
+        far = Math.max(5, far);
     }
 
     if (near === far) {

src/mol-canvas3d/passes/postprocessing.ts

@@ -250,7 +250,7 @@ export const PostprocessingParams = {
     }, { cycle: true, description: 'Darken occluded crevices with the ambient occlusion effect' }),
     outline: PD.MappedStatic('off', {
         on: PD.Group({
-            scale: PD.Numeric(1, { min: 1, max: 5, step: 1 }),
+            scale: PD.Numeric(2, { min: 1, max: 5, step: 1 }),
             threshold: PD.Numeric(0.33, { min: 0.01, max: 1, step: 0.01 }),
         }),
         off: PD.Group({})
@@ -434,8 +434,12 @@ export class PostprocessingPass {
         }
 
         if (props.outline.name === 'on') {
-            const factor = Math.pow(1000, props.outline.params.threshold) / 1000;
-            const maxPossibleViewZDiff = factor * (camera.far - camera.near);
+            let { threshold } = props.outline.params;
+            // orthographic needs lower threshold
+            if (camera.state.mode === 'orthographic') threshold /= 5;
+            const factor = Math.pow(1000, threshold) / 1000;
+            // use radiusMax for stable outlines when zooming
+            const maxPossibleViewZDiff = factor * camera.state.radiusMax;
             const outlineScale = props.outline.params.scale - 1;
 
             ValueCell.updateIfChanged(this.outlinesRenderable.values.uNear, camera.near);
@@ -443,7 +447,6 @@ export class PostprocessingPass {
             ValueCell.updateIfChanged(this.outlinesRenderable.values.uMaxPossibleViewZDiff, maxPossibleViewZDiff);
 
             ValueCell.updateIfChanged(this.renderable.values.uMaxPossibleViewZDiff, maxPossibleViewZDiff);
-            ValueCell.updateIfChanged(this.renderable.values.uOutlineThreshold, props.outline.params.threshold);
             if (this.renderable.values.dOutlineScale.ref.value !== outlineScale) { needsUpdateMain = true; }
             ValueCell.updateIfChanged(this.renderable.values.dOutlineScale, outlineScale);
         }

src/mol-gl/shader/postprocessing.frag.ts

@@ -26,9 +26,6 @@ uniform bool uTransparentBackground;
 uniform float uOcclusionBias;
 uniform float uOcclusionRadius;
 
-uniform float uOutlineScale;
-uniform float uOutlineThreshold;
-
 uniform float uMaxPossibleViewZDiff;
 
 const vec3 occlusionColor = vec3(0.0);

src/mol-repr/structure/visual/bond-intra-unit-line.ts

@@ -10,7 +10,7 @@ import { Unit, Structure, StructureElement } from '../../../mol-model/structure'
 import { Theme } from '../../../mol-theme/theme';
 import { Vec3 } from '../../../mol-math/linear-algebra';
 import { arrayEqual } from '../../../mol-util';
-import { LinkStyle, createLinkLines, LinkBuilderProps } from './util/link';
+import { LinkStyle, createLinkLines } from './util/link';
 import { UnitsVisual, UnitsLinesParams, UnitsLinesVisual, StructureGroup } from '../units-visual';
 import { VisualUpdateState } from '../../util';
 import { BondType } from '../../../mol-model/structure/model/types';

src/mol-repr/structure/visual/util/element.ts

@@ -46,7 +46,7 @@ export function makeElementIgnoreTest(structure: Structure, unit: Unit, props: E
     const childUnit = child?.unitMap.get(unit.id);
     if (child && !childUnit) throw new Error('expected childUnit to exist if child exists');
 
-    if (!child && ((!ignoreHydrogens && !traceOnly) || traceOnly)) return;
+    if (!child && !ignoreHydrogens && !traceOnly) return;
 
     return (element: ElementIndex) => {
         return (