3.31.4

* Fixed degenerate case (1-point) in PCA - now correctly returns identity matrix

* Changelog

CHANGELOG.md

@@ -6,6 +6,18 @@ Note that since we don't clearly distinguish between a public and private interf
 
 ## [Unreleased]
 
+## [v3.31.4] - 2023-02-24
+
+- Allow link cylinder/line `dashCount` set to '0'
+- Stop animation loop when disposing `PluginContext` (thanks @gfrn for identifying the issue)
+
+## [v3.31.3] - 2023-02-22
+
+- Fix impostor bond visuals not correctly updating on `sizeFactor` changes
+- Fix degenerate case in PCA
+- Fix near clipping avoidance in impostor shaders
+- Update `fs` import in `data-source.ts`
+
 ## [v3.31.2] - 2023-02-12
 
 - Fix exit code of volume pack executable (pack.ts). Now exits with non-0 status when an error happens

package-lock.json

@@ -1,12 +1,12 @@
 {
   "name": "molstar",
-  "version": "3.31.2",
+  "version": "3.31.4",
   "lockfileVersion": 2,
   "requires": true,
   "packages": {
     "": {
       "name": "molstar",
-      "version": "3.31.2",
+      "version": "3.31.4",
       "license": "MIT",
       "dependencies": {
         "@types/argparse": "^2.0.10",

package.json

@@ -1,6 +1,6 @@
 {
   "name": "molstar",
-  "version": "3.31.2",
+  "version": "3.31.4",
   "description": "A comprehensive macromolecular library.",
   "homepage": "https://github.com/molstar/molstar#readme",
   "repository": {
@@ -95,7 +95,8 @@
     "Gianluca Tomasello <giagitom@gmail.com>",
     "Ke Ma <mark.ma@rcsb.org>",
     "Jason Pattle <jpattle@exscientia.co.uk>",
-    "David Williams <dwilliams@nobiastx.com>"
+    "David Williams <dwilliams@nobiastx.com>",
+    "Zhenyu Zhang <jump2cn@gmail.com>"
   ],
   "license": "MIT",
   "devDependencies": {

src/mol-canvas3d/canvas3d.ts

@@ -65,7 +65,7 @@ export const Canvas3DParams = {
     cameraClipping: PD.Group({
         radius: PD.Numeric(100, { min: 0, max: 99, step: 1 }, { label: 'Clipping', description: 'How much of the scene to show.' }),
         far: PD.Boolean(true, { description: 'Hide scene in the distance' }),
-        minNear: PD.Numeric(5, { min: 0.1, max: 10, step: 0.1 }, { description: 'Note, may cause performance issues rendering impostors when set too small and cause issues with outline rendering when too close to 0.' }),
+        minNear: PD.Numeric(5, { min: 0.1, max: 100, step: 0.1 }, { description: 'Note, may cause performance issues rendering impostors when set too small and cause issues with outline rendering when too close to 0.' }),
     }, { pivot: 'radius' }),
     viewport: PD.MappedStatic('canvas', {
         canvas: PD.Group({}),
@@ -908,6 +908,7 @@ namespace Canvas3D {
             },
             dispose: () => {
                 contextRestoredSub.unsubscribe();
+                cancelAnimationFrame(animationFrameHandle);
 
                 markBuffer = [];
 

src/mol-gl/shader/cylinders.vert.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -71,8 +71,10 @@ void main() {
     vViewPosition = mvPosition.xyz;
     gl_Position = uProjection * mvPosition;
 
-    mvPosition.z -= 2.0 * (length(vEnd - vStart) + vSize); // avoid clipping
-    gl_Position.z = (uProjection * mvPosition).z;
+    if (gl_Position.z < -gl_Position.w) {
+        mvPosition.z -= 2.0 * (length(vEnd - vStart) + vSize); // avoid clipping
+        gl_Position.z = (uProjection * mvPosition).z;
+    }
 
     #include clip_instance
 }

src/mol-gl/shader/spheres.vert.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -96,8 +96,10 @@ void main(void){
 
     vModelPosition = (uModel * aTransform * position4).xyz; // for clipping in frag shader
 
-    mvPosition.z -= 2.0 * vRadius; // avoid clipping
-    gl_Position.z = (uProjection * vec4(mvPosition.xyz, 1.0)).z;
+    if (gl_Position.z < -gl_Position.w) {
+        mvPosition.z -= 2.0 * vRadius; // avoid clipping
+        gl_Position.z = (uProjection * vec4(mvPosition.xyz, 1.0)).z;
+    }
 
     #include clip_instance
 }

src/mol-math/linear-algebra/matrix/principal-axes.ts

@@ -27,7 +27,7 @@ namespace PrincipalAxes {
 
     export function calculateMomentsAxes(positions: NumberArray): Axes3D {
         if (positions.length === 3) {
-            return Axes3D.create(Vec3.fromArray(Vec3(), positions, 0), Vec3.create(1, 0, 0), Vec3.create(0, 1, 0), Vec3.create(0, 1, 0));
+            return Axes3D.create(Vec3.fromArray(Vec3(), positions, 0), Vec3.create(1, 0, 0), Vec3.create(0, 1, 0), Vec3.create(0, 0, 1));
         }
 
         const points = Matrix.fromArray(positions, 3, positions.length / 3);
@@ -143,4 +143,4 @@ namespace PrincipalAxes {
 
         return Axes3D.create(origin, dirA, dirB, dirC);
     }
-}
+}

src/mol-plugin/context.ts

@@ -362,6 +362,7 @@ export class PluginContext {
         }
         this.subs = [];
 
+        this.animationLoop.stop();
         this.commands.dispose();
         this.canvas3d?.dispose();
         this.canvas3dContext?.dispose(options);

src/mol-repr/structure/visual/bond-inter-unit-cylinder.ts

@@ -218,6 +218,7 @@ export function InterUnitBondCylinderImpostorVisual(materialId: number): Complex
         eachLocation: eachInterBond,
         setUpdateState: (state: VisualUpdateState, newProps: PD.Values<InterUnitBondCylinderParams>, currentProps: PD.Values<InterUnitBondCylinderParams>, newTheme: Theme, currentTheme: Theme, newStructure: Structure, currentStructure: Structure) => {
             state.createGeometry = (
+                newProps.sizeFactor !== currentProps.sizeFactor ||
                 newProps.sizeAspectRatio !== currentProps.sizeAspectRatio ||
                 newProps.linkScale !== currentProps.linkScale ||
                 newProps.linkSpacing !== currentProps.linkSpacing ||

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

@@ -235,6 +235,7 @@ export function IntraUnitBondCylinderImpostorVisual(materialId: number): UnitsVi
         eachLocation: eachIntraBond,
         setUpdateState: (state: VisualUpdateState, newProps: PD.Values<IntraUnitBondCylinderParams>, currentProps: PD.Values<IntraUnitBondCylinderParams>, newTheme: Theme, currentTheme: Theme, newStructureGroup: StructureGroup, currentStructureGroup: StructureGroup) => {
             state.createGeometry = (
+                newProps.sizeFactor !== currentProps.sizeFactor ||
                 newProps.sizeAspectRatio !== currentProps.sizeAspectRatio ||
                 newProps.linkScale !== currentProps.linkScale ||
                 newProps.linkSpacing !== currentProps.linkSpacing ||

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

@@ -2,6 +2,7 @@
  * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Zhenyu Zhang <jump2cn@gmail.com>
  */
 
 import { Vec3 } from '../../../../mol-math/linear-algebra';
@@ -25,7 +26,7 @@ export const LinkCylinderParams = {
     aromaticScale: PD.Numeric(0.3, { min: 0, max: 1, step: 0.01 }),
     aromaticSpacing: PD.Numeric(1.5, { min: 0, max: 3, step: 0.01 }),
     aromaticDashCount: PD.Numeric(2, { min: 2, max: 6, step: 2 }),
-    dashCount: PD.Numeric(4, { min: 2, max: 10, step: 2 }),
+    dashCount: PD.Numeric(4, { min: 0, max: 10, step: 2 }),
     dashScale: PD.Numeric(0.8, { min: 0, max: 2, step: 0.1 }),
     dashCap: PD.Boolean(true),
     stubCap: PD.Boolean(true),
@@ -38,7 +39,7 @@ export const LinkLineParams = {
     linkScale: PD.Numeric(0.5, { min: 0, max: 1, step: 0.1 }),
     linkSpacing: PD.Numeric(0.1, { min: 0, max: 2, step: 0.01 }),
     aromaticDashCount: PD.Numeric(2, { min: 2, max: 6, step: 2 }),
-    dashCount: PD.Numeric(4, { min: 2, max: 10, step: 2 }),
+    dashCount: PD.Numeric(4, { min: 0, max: 10, step: 2 }),
 };
 export const DefaultLinkLineProps = PD.getDefaultValues(LinkLineParams);
 export type LinkLineProps = typeof DefaultLinkLineProps
@@ -164,7 +165,11 @@ export function createLinkCylinderMesh(ctx: VisualContext, linkBuilder: LinkBuil
             cylinderProps.radiusTop = cylinderProps.radiusBottom = linkRadius * dashScale;
             cylinderProps.topCap = cylinderProps.bottomCap = dashCap;
 
-            addFixedCountDashedCylinder(builderState, va, vb, 0.5, segmentCount, cylinderProps);
+            if (segmentCount > 1) {
+                addFixedCountDashedCylinder(builderState, va, vb, 0.5, segmentCount, cylinderProps);
+            } else {
+                addCylinder(builderState, va, vb, 0.5, cylinderProps);
+            }
         } else if (linkStyle === LinkStyle.Double || linkStyle === LinkStyle.OffsetDouble || linkStyle === LinkStyle.Triple || linkStyle === LinkStyle.OffsetTriple || linkStyle === LinkStyle.Aromatic || linkStyle === LinkStyle.MirroredAromatic) {
             const order = (linkStyle === LinkStyle.Double || linkStyle === LinkStyle.OffsetDouble) ? 2 :
                 (linkStyle === LinkStyle.Triple || linkStyle === LinkStyle.OffsetTriple) ? 3 : 1.5;
@@ -303,9 +308,14 @@ export function createLinkCylinderImpostors(ctx: VisualContext, linkBuilder: Lin
             v3scale(vm, v3add(vm, va, vb), 0.5);
             builder.add(va[0], va[1], va[2], vm[0], vm[1], vm[2], 1, linkCap, linkStub, edgeIndex);
         } else if (linkStyle === LinkStyle.Dashed) {
-            v3scale(tmpV12, v3sub(tmpV12, vb, va), lengthScale);
-            v3sub(vb, vb, tmpV12);
-            builder.addFixedCountDashes(va, vb, segmentCount, dashScale, dashCap, dashCap, edgeIndex);
+            if (segmentCount > 1) {
+                v3scale(tmpV12, v3sub(tmpV12, vb, va), lengthScale);
+                v3sub(vb, vb, tmpV12);
+                builder.addFixedCountDashes(va, vb, segmentCount, dashScale, dashCap, dashCap, edgeIndex);
+            } else {
+                v3scale(vm, v3add(vm, va, vb), 0.5);
+                builder.add(va[0], va[1], va[2], vm[0], vm[1], vm[2], dashScale, dashCap, dashCap, edgeIndex);
+            }
         } else if (linkStyle === LinkStyle.Double || linkStyle === LinkStyle.OffsetDouble || linkStyle === LinkStyle.Triple || linkStyle === LinkStyle.OffsetTriple || linkStyle === LinkStyle.Aromatic || linkStyle === LinkStyle.MirroredAromatic) {
             const order = (linkStyle === LinkStyle.Double || linkStyle === LinkStyle.OffsetDouble) ? 2 :
                 (linkStyle === LinkStyle.Triple || linkStyle === LinkStyle.OffsetTriple) ? 3 : 1.5;
@@ -423,9 +433,14 @@ export function createLinkLines(ctx: VisualContext, linkBuilder: LinkBuilderProp
             v3scale(vm, v3add(vm, va, vb), 0.5);
             builder.add(va[0], va[1], va[2], vm[0], vm[1], vm[2], edgeIndex);
         } else if (linkStyle === LinkStyle.Dashed) {
-            v3scale(tmpV12, v3sub(tmpV12, vb, va), lengthScale);
-            v3sub(vb, vb, tmpV12);
-            builder.addFixedCountDashes(va, vb, segmentCount, edgeIndex);
+            if (segmentCount > 1) {
+                v3scale(tmpV12, v3sub(tmpV12, vb, va), lengthScale);
+                v3sub(vb, vb, tmpV12);
+                builder.addFixedCountDashes(va, vb, segmentCount, edgeIndex);
+            } else {
+                v3scale(vm, v3add(vm, va, vb), 0.5);
+                builder.add(va[0], va[1], va[2], vm[0], vm[1], vm[2], edgeIndex);
+            }
         } else if (linkStyle === LinkStyle.Double || linkStyle === LinkStyle.OffsetDouble || linkStyle === LinkStyle.Triple || linkStyle === LinkStyle.OffsetTriple || linkStyle === LinkStyle.Aromatic || linkStyle === LinkStyle.MirroredAromatic) {
             const order = linkStyle === LinkStyle.Double || linkStyle === LinkStyle.OffsetDouble ? 2 :
                 linkStyle === LinkStyle.Triple || linkStyle === LinkStyle.OffsetTriple ? 3 : 1.5;

src/mol-util/data-source.ts

@@ -305,7 +305,8 @@ function ajaxGetInternal<T extends DataType>(title: string | undefined, url: str
 let _fs: (typeof import ('fs')) | undefined = undefined;
 function getFS() {
     if (_fs) return _fs!;
-    _fs = require('fs');
+    const req = require; // To fool webpack
+    _fs = req('fs');
     return _fs!;
 }