1.3.2

- workaround for FF <85
- needed for `texture-mesh` geometry

package-lock.json

@@ -1,6 +1,6 @@
 {
   "name": "molstar",
-  "version": "1.3.0",
+  "version": "1.3.2",
   "lockfileVersion": 2,
   "requires": true,
   "packages": {

package.json

@@ -1,6 +1,6 @@
 {
   "name": "molstar",
-  "version": "1.3.0",
+  "version": "1.3.2",
   "description": "A comprehensive macromolecular library.",
   "homepage": "https://github.com/molstar/molstar#readme",
   "repository": {

src/mol-canvas3d/passes/postprocessing.ts

@@ -237,10 +237,10 @@ function getPostprocessingRenderable(ctx: WebGLContext, colorTexture: Texture, d
 export const PostprocessingParams = {
     occlusion: PD.MappedStatic('on', {
         on: PD.Group({
-            samples: PD.Numeric(64, {min: 1, max: 256, step: 1}),
+            samples: PD.Numeric(32, {min: 1, max: 256, step: 1}),
             radius: PD.Numeric(5, { min: 0, max: 10, step: 0.1 }, { description: 'Final radius is 2^x.' }),
             bias: PD.Numeric(0.8, { min: 0, max: 3, step: 0.1 }),
-            blurKernelSize: PD.Numeric(20, { min: 1, max: 25, step: 2 }),
+            blurKernelSize: PD.Numeric(15, { min: 1, max: 25, step: 2 }),
         }),
         off: PD.Group({})
     }, { cycle: true, description: 'Darken occluded crevices with the ambient occlusion effect' }),

src/mol-canvas3d/util.ts

@@ -12,13 +12,13 @@ export function setCanvasSize(canvas: HTMLCanvasElement, width: number, height:
 }
 
 /** Resize canvas to container element taking `devicePixelRatio` into account */
-export function resizeCanvas (canvas: HTMLCanvasElement, container: Element, scale = 1) {
+export function resizeCanvas (canvas: HTMLCanvasElement, container: HTMLElement, scale = 1) {
     let width = window.innerWidth;
     let height = window.innerHeight;
     if (container !== document.body) {
-        let bounds = container.getBoundingClientRect();
-        width = bounds.right - bounds.left;
-        height = bounds.bottom - bounds.top;
+        // fixes issue #molstar/molstar#147, offsetWidth/offsetHeight is correct size when css transform:scale is used
+        width = container.offsetWidth;
+        height = container.offsetHeight;
     }
     setCanvasSize(canvas, width, height, scale);
 }

src/mol-gl/compute/marching-cubes/isosurface.ts

@@ -195,17 +195,17 @@ export function createIsosurfaceBuffers(ctx: WebGLContext, activeVoxelsBase: Tex
 export function extractIsosurface(ctx: WebGLContext, volumeData: Texture, gridDim: Vec3, gridTexDim: Vec3, gridTexScale: Vec2, transform: Mat4, isoValue: number, packedGroup: boolean, vertexTexture?: Texture, groupTexture?: Texture, normalTexture?: Texture) {
     // console.time('calcActiveVoxels');
     const activeVoxelsTex = calcActiveVoxels(ctx, volumeData, gridDim, gridTexDim, isoValue, gridTexScale);
-    // ctx.webgl.waitForGpuCommandsCompleteSync();
+    // ctx.waitForGpuCommandsCompleteSync();
     // console.timeEnd('calcActiveVoxels');
 
     // console.time('createHistogramPyramid');
     const compacted = createHistogramPyramid(ctx, activeVoxelsTex, gridTexScale, gridTexDim);
-    // ctx.webgl.waitForGpuCommandsCompleteSync();
+    // ctx.waitForGpuCommandsCompleteSync();
     // console.timeEnd('createHistogramPyramid');
 
     // console.time('createIsosurfaceBuffers');
     const gv = createIsosurfaceBuffers(ctx, activeVoxelsTex, volumeData, compacted, gridDim, gridTexDim, transform, isoValue, packedGroup, vertexTexture, groupTexture, normalTexture);
-    // ctx.webgl.waitForGpuCommandsCompleteSync();
+    // ctx.waitForGpuCommandsCompleteSync();
     // console.timeEnd('createIsosurfaceBuffers');
 
     return gv;

src/mol-gl/shader/chunks/common-vert-params.glsl.ts

@@ -41,6 +41,12 @@ varying vec3 vViewPosition;
     attribute float aVertex;
     #define VertexID int(aVertex)
 #else
-    #define VertexID gl_VertexID
+    // not using gl_VertexID but aVertex to ensure there is an active attribute with divisor 0
+    // since FF 85 this is not needed anymore but lets keep it for backwards compatibility
+    // https://bugzilla.mozilla.org/show_bug.cgi?id=1679693
+    // see also note in src/mol-gl/webgl/render-item.ts
+    attribute float aVertex;
+    #define VertexID int(aVertex)
+    // #define VertexID gl_VertexID
 #endif
 `;

src/mol-gl/webgl/render-item.ts

@@ -112,7 +112,12 @@ export function createRenderItem<T extends string>(ctx: WebGLContext, drawMode:
     const { instancedArrays, vertexArrayObject } = ctx.extensions;
 
     // emulate gl_VertexID when needed
-    if (!ctx.isWebGL2 && values.uVertexCount) {
+    // if (!ctx.isWebGL2 && values.uVertexCount) {
+    // not using gl_VertexID in WebGL2 but aVertex to ensure there is an active attribute with divisor 0
+    // since FF 85 this is not needed anymore but lets keep it for backwards compatibility
+    // https://bugzilla.mozilla.org/show_bug.cgi?id=1679693
+    // see also note in src/mol-gl/shader/chunks/common-vert-params.glsl.ts
+    if (values.uVertexCount) {
         const vertexCount = values.uVertexCount.ref.value;
         (values as any).aVertex = ValueCell.create(fillSerial(new Float32Array(vertexCount)));
         (schema as any).aVertex = AttributeSpec('float32', 1, 0);

src/mol-math/geometry/spacegroup/construction.ts

@@ -111,33 +111,41 @@ namespace Spacegroup {
 
     const _translationRef = Vec3();
     const _translationRefSymop = Vec3();
+    const _translationRefOffset = Vec3();
     const _translationSymop = Vec3();
-    export function setOperatorMatrixRef(spacegroup: Spacegroup, index: number, i: number, j: number, k: number, ref: Vec3, target: Mat4) {
-        Vec3.set(_ijkVec, i, j, k);
-        Vec3.floor(_translationRef, ref);
-
-        Mat4.copy(target, spacegroup.operators[index]);
-
-        Vec3.floor(_translationRefSymop, Vec3.transformMat4(_translationRefSymop, ref, target));
-
-        Mat4.getTranslation(_translationSymop, target);
-        Vec3.sub(_translationSymop, _translationSymop, _translationRefSymop);
-        Vec3.add(_translationSymop, _translationSymop, _translationRef);
-        Vec3.add(_translationSymop, _translationSymop, _ijkVec);
-
-        Mat4.setTranslation(target, _translationSymop);
-        Mat4.mul(target, spacegroup.cell.fromFractional, target);
-        Mat4.mul(target, target, spacegroup.cell.toFractional);
-        return target;
-    }
 
     /**
      * Get Symmetry operator for transformation around the given
      * reference point `ref` in fractional coordinates
      */
     export function getSymmetryOperatorRef(spacegroup: Spacegroup, spgrOp: number, i: number, j: number, k: number, ref: Vec3) {
-        const operator = setOperatorMatrixRef(spacegroup, spgrOp, i, j, k, ref, Mat4.zero());
-        return SymmetryOperator.create(`${spgrOp + 1}_${5 + i}${5 + j}${5 + k}`, operator, { hkl: Vec3.create(i, j, k), spgrOp });
+
+        const operator =  Mat4.zero();
+
+        Vec3.set(_ijkVec, i, j, k);
+        Vec3.floor(_translationRef, ref);
+
+        Mat4.copy(operator, spacegroup.operators[spgrOp]);
+
+        Vec3.floor(_translationRefSymop, Vec3.transformMat4(_translationRefSymop, ref, operator));
+
+        Mat4.getTranslation(_translationSymop, operator);
+        Vec3.sub(_translationSymop, _translationSymop, _translationRefSymop);
+        Vec3.add(_translationSymop, _translationSymop, _translationRef);
+        Vec3.add(_translationSymop, _translationSymop, _ijkVec);
+
+        Mat4.setTranslation(operator, _translationSymop);
+        Mat4.mul(operator, spacegroup.cell.fromFractional, operator);
+        Mat4.mul(operator, operator, spacegroup.cell.toFractional);
+
+        Vec3.sub(_translationRefOffset, _translationRefSymop, _translationRef);
+
+        const _i = i - _translationRefOffset[0];
+        const _j = j - _translationRefOffset[1];
+        const _k = k - _translationRefOffset[2];
+
+        // const operator = setOperatorMatrixRef(spacegroup, spgrOp, i, j, k, ref, Mat4.zero());
+        return SymmetryOperator.create(`${spgrOp + 1}_${5 + _i}${5 + _j}${5 + _k}`, operator, { hkl: Vec3.create(_i, _j, _k), spgrOp });
     }
 
     function getOperatorMatrix(ids: number[]) {

src/mol-model-formats/structure/common/component.ts

@@ -50,6 +50,7 @@ const StandardComponents = (function() {
         { id: 'ASP', name: 'ASPARTIC ACID', type: 'L-peptide linking' },
         { id: 'GLU', name: 'GLUTAMIC ACID', type: 'L-peptide linking' },
         { id: 'THR', name: 'THREONINE', type: 'L-peptide linking' },
+        { id: 'PRO', name: 'PROLINE', type: 'L-peptide linking' },
         { id: 'SEC', name: 'SELENOCYSTEINE', type: 'L-peptide linking' },
         { id: 'PYL', name: 'PYRROLYSINE', type: 'L-peptide linking' },
 

src/mol-model-props/common/custom-element-property.ts

@@ -61,7 +61,7 @@ namespace CustomElementProperty {
             type: builder.type || 'dynamic',
             defaultParams: {},
             getParams: (data: Model) => ({}),
-            isApplicable: (data: Model) => !!builder.isApplicable?.(data),
+            isApplicable: (data: Model) => !builder.isApplicable || !!builder.isApplicable(data),
             obtain: async (ctx: CustomProperty.Context, data: Model) => {
                 return await builder.getData(data, ctx);
             }

src/mol-plugin/behavior/static/representation.ts

@@ -76,11 +76,18 @@ export function UpdateRepresentationVisibility(ctx: PluginContext) {
     ctx.state.data.events.cell.stateUpdated.subscribe(e => {
         const cell = e.state.cells.get(e.ref)!;
         if (!SO.isRepresentation3D(cell.obj)) return;
-        updateVisibility(cell, cell.obj.data.repr);
-        ctx.canvas3d?.syncVisibility();
+
+        if (updateVisibility(cell, cell.obj.data.repr)) {
+            ctx.canvas3d?.syncVisibility();
+        }
     });
 }
 
 function updateVisibility(cell: StateObjectCell, r: Representation<any>) {
-    r.setState({ visible: !cell.state.isHidden });
+    if (r.state.visible === cell.state.isHidden) {
+        r.setState({ visible: !cell.state.isHidden });
+        return true;
+    } else {
+        return false;
+    }
 }