Merge branch 'master' of https://github.com/molstar/molstar

src/extensions/dnatco/confal-pyramids/color.ts

@@ -181,6 +181,6 @@ export const ConfalPyramidsColorThemeProvider: ColorTheme.Provider<ConfalPyramid
     isApplicable: (ctx: ThemeDataContext) => !!ctx.structure && ctx.structure.models.some(m => ConfalPyramids.isApplicable(m)),
     ensureCustomProperties: {
         attach: (ctx: CustomProperty.Context, data: ThemeDataContext) => data.structure ? ConfalPyramidsProvider.attach(ctx, data.structure.models[0], void 0, true) : Promise.resolve(),
-        detach: (data) => data.structure && data.structure.models[0].customProperties.reference(ConfalPyramidsProvider.descriptor, false)
+        detach: (data) => data.structure && ConfalPyramidsProvider.ref(data.structure.models[0], false)
     }
 };

src/extensions/pdbe/structure-quality-report/color.ts

@@ -115,6 +115,6 @@ export const StructureQualityReportColorThemeProvider: ColorTheme.Provider<Param
     isApplicable: (ctx: ThemeDataContext) => StructureQualityReport.isApplicable(ctx.structure?.models[0]),
     ensureCustomProperties: {
         attach: (ctx: CustomProperty.Context, data: ThemeDataContext) => data.structure ? StructureQualityReportProvider.attach(ctx, data.structure.models[0], void 0, true) : Promise.resolve(),
-        detach: (data) => data.structure && data.structure.models[0].customProperties.reference(StructureQualityReportProvider.descriptor, false)
+        detach: (data) => data.structure && StructureQualityReportProvider.ref(data.structure.models[0], false)
     }
 };

src/extensions/rcsb/assembly-symmetry/color.ts

@@ -109,6 +109,6 @@ export const AssemblySymmetryClusterColorThemeProvider: ColorTheme.Provider<Asse
     isApplicable: (ctx: ThemeDataContext) => AssemblySymmetry.isApplicable(ctx.structure),
     ensureCustomProperties: {
         attach: (ctx: CustomProperty.Context, data: ThemeDataContext) => data.structure ? AssemblySymmetryProvider.attach(ctx, data.structure, void 0, true) : Promise.resolve(),
-        detach: (data) => data.structure && data.structure.customPropertyDescriptors.reference(AssemblySymmetryProvider.descriptor, false)
+        detach: (data) => data.structure && AssemblySymmetryProvider.ref(data.structure, false)
     }
 };

src/extensions/rcsb/validation-report/color/density-fit.ts

@@ -77,6 +77,6 @@ export const DensityFitColorThemeProvider: ColorTheme.Provider<{}, ValidationRep
     isApplicable: (ctx: ThemeDataContext) => !!ctx.structure && ValidationReport.isApplicable(ctx.structure.models[0]) && Model.isFromXray(ctx.structure.models[0]) && Model.probablyHasDensityMap(ctx.structure.models[0]),
     ensureCustomProperties: {
         attach: (ctx: CustomProperty.Context, data: ThemeDataContext) => data.structure ? ValidationReportProvider.attach(ctx, data.structure.models[0], void 0, true) : Promise.resolve(),
-        detach: (data) => data.structure && data.structure.models[0].customProperties.reference(ValidationReportProvider.descriptor, false)
+        detach: (data) => data.structure && ValidationReportProvider.ref(data.structure.models[0], false)
     }
 };

src/extensions/rcsb/validation-report/color/geometry-quality.ts

@@ -115,6 +115,6 @@ export const GeometryQualityColorThemeProvider: ColorTheme.Provider<GeometricQua
     isApplicable: (ctx: ThemeDataContext) => ValidationReport.isApplicable(ctx.structure?.models[0]),
     ensureCustomProperties: {
         attach: (ctx: CustomProperty.Context, data: ThemeDataContext) => data.structure ? ValidationReportProvider.attach(ctx, data.structure.models[0], void 0, true) : Promise.resolve(),
-        detach: (data) => data.structure && data.structure.models[0].customProperties.reference(ValidationReportProvider.descriptor, false)
+        detach: (data) => data.structure && ValidationReportProvider.ref(data.structure.models[0], false)
     }
 };

src/extensions/rcsb/validation-report/color/random-coil-index.ts

@@ -68,6 +68,6 @@ export const RandomCoilIndexColorThemeProvider: ColorTheme.Provider<{}, Validati
     isApplicable: (ctx: ThemeDataContext) => !!ctx.structure && ValidationReport.isApplicable(ctx.structure.models[0]) && Model.isFromNmr(ctx.structure.models[0]),
     ensureCustomProperties: {
         attach: (ctx: CustomProperty.Context, data: ThemeDataContext) => data.structure ? ValidationReportProvider.attach(ctx, data.structure.models[0], void 0, true) : Promise.resolve(),
-        detach: (data) => data.structure && data.structure.models[0].customProperties.reference(ValidationReportProvider.descriptor, false)
+        detach: (data) => data.structure && ValidationReportProvider.ref(data.structure.models[0], false)
     }
 };

src/mol-canvas3d/passes/draw.ts

@@ -290,7 +290,7 @@ export class DrawPass {
         renderer.setViewport(x, y, width, height);
         renderer.update(camera);
 
-        if (transparentBackground) {
+        if (transparentBackground && !antialiasingEnabled && toDrawingBuffer) {
             this.drawTarget.bind();
             renderer.clear(false);
         }

src/mol-canvas3d/passes/image.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -103,7 +103,9 @@ export class ImagePass {
         } else {
             this.webgl.readPixels(viewport.x, height - viewport.y - viewport.height, w, h, array);
         }
-        PixelData.flipY({ array, width: w, height: h });
+        const pixelData = PixelData.create(array, w, h);
+        PixelData.flipY(pixelData);
+        PixelData.divideByAlpha(pixelData);
         return new ImageData(new Uint8ClampedArray(array), w, h);
     }
 }

src/mol-model-props/computed/themes/accessible-surface-area.ts

@@ -83,6 +83,6 @@ export const AccessibleSurfaceAreaColorThemeProvider: ColorTheme.Provider<Access
     isApplicable: (ctx: ThemeDataContext) => !!ctx.structure,
     ensureCustomProperties: {
         attach: (ctx: CustomProperty.Context, data: ThemeDataContext) => data.structure ? AccessibleSurfaceAreaProvider.attach(ctx, data.structure, void 0, true) : Promise.resolve(),
-        detach: (data) => data.structure && data.structure.customPropertyDescriptors.reference(AccessibleSurfaceAreaProvider.descriptor, false)
+        detach: (data) => data.structure && AccessibleSurfaceAreaProvider.ref(data.structure, false)
     }
 };

src/mol-model-props/computed/themes/interaction-type.ts

@@ -117,6 +117,6 @@ export const InteractionTypeColorThemeProvider: ColorTheme.Provider<InteractionT
     isApplicable: (ctx: ThemeDataContext) => !!ctx.structure,
     ensureCustomProperties: {
         attach: (ctx: CustomProperty.Context, data: ThemeDataContext) => data.structure ? InteractionsProvider.attach(ctx, data.structure, void 0, true) : Promise.resolve(),
-        detach: (data) => data.structure && data.structure.customPropertyDescriptors.reference(InteractionsProvider.descriptor, false)
+        detach: (data) => data.structure && InteractionsProvider.ref(data.structure, false)
     }
 };

src/mol-model-props/integrative/cross-link-restraint/color.ts

@@ -70,6 +70,6 @@ export const CrossLinkColorThemeProvider: ColorTheme.Provider<CrossLinkColorThem
     isApplicable: (ctx: ThemeDataContext) => !!ctx.structure && CrossLinkRestraint.isApplicable(ctx.structure),
     ensureCustomProperties: {
         attach: (ctx: CustomProperty.Context, data: ThemeDataContext) => data.structure ? CrossLinkRestraintProvider.attach(ctx, data.structure, void 0, true) : Promise.resolve(),
-        detach: (data) => data.structure && data.structure.customPropertyDescriptors.reference(CrossLinkRestraintProvider.descriptor, false)
+        detach: (data) => data.structure && CrossLinkRestraintProvider.ref(data.structure, false)
     }
 };

src/mol-model-props/sequence/best-database-mapping.ts

@@ -29,7 +29,7 @@ namespace BestDatabaseSequenceMapping {
         type: 'static',
         defaultParams: {},
         getParams: () => ({}),
-        isApplicable: (data: Model) => MmcifFormat.is(data.sourceData) && data.sourceData.data.frame.categories?.atom_site.fieldNames.indexOf('db_name') >= 0,
+        isApplicable: (data: Model) => MmcifFormat.is(data.sourceData) && data.sourceData.data.frame.categories?.atom_site?.fieldNames.indexOf('db_name') >= 0,
         obtain: async (ctx, data) => {
             return { value: fromCif(data) };
         }
@@ -92,4 +92,4 @@ namespace BestDatabaseSequenceMapping {
 
         return { dbName, accession, num, residue };
     }
-}
+}

src/mol-model-props/sequence/themes/best-database-mapping.ts

@@ -98,7 +98,7 @@ export const BestDatabaseSequenceMappingColorThemeProvider: ColorTheme.Provider<
         detach: (data) => {
             if (!data.structure) return;
             for (const m of data.structure.models) {
-                m.customProperties.reference(BestDatabaseSequenceMapping.Provider.descriptor, false);
+                BestDatabaseSequenceMapping.Provider.ref(m, false);
             }
         }
     }

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

@@ -205,6 +205,7 @@ export function InterUnitBondCylinderImpostorVisual(materialId: number): Complex
         eachLocation: eachInterBond,
         setUpdateState: (state: VisualUpdateState, newProps: PD.Values<InterUnitBondCylinderParams>, currentProps: PD.Values<InterUnitBondCylinderParams>) => {
             state.createGeometry = (
+                newProps.sizeAspectRatio !== currentProps.sizeAspectRatio ||
                 newProps.linkScale !== currentProps.linkScale ||
                 newProps.linkSpacing !== currentProps.linkSpacing ||
                 newProps.ignoreHydrogens !== currentProps.ignoreHydrogens ||

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

@@ -187,6 +187,7 @@ 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.sizeAspectRatio !== currentProps.sizeAspectRatio ||
                 newProps.linkScale !== currentProps.linkScale ||
                 newProps.linkSpacing !== currentProps.linkSpacing ||
                 newProps.ignoreHydrogens !== currentProps.ignoreHydrogens ||

src/mol-theme/color/secondary-structure.ts

@@ -123,6 +123,6 @@ export const SecondaryStructureColorThemeProvider: ColorTheme.Provider<Secondary
     isApplicable: (ctx: ThemeDataContext) => !!ctx.structure,
     ensureCustomProperties: {
         attach: (ctx: CustomProperty.Context, data: ThemeDataContext) => data.structure ? SecondaryStructureProvider.attach(ctx, data.structure, void 0, true) : Promise.resolve(),
-        detach: (data) => data.structure && data.structure.customPropertyDescriptors.reference(SecondaryStructureProvider.descriptor, false)
+        detach: (data) => data.structure && SecondaryStructureProvider.ref(data.structure, false)
     }
 };

src/mol-util/image.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -32,4 +32,16 @@ namespace PixelData {
         }
         return pixelData;
     }
+
+    /** to undo pre-multiplied alpha */
+    export function divideByAlpha(pixelData: PixelData): PixelData {
+        const { array } = pixelData;
+        for (let i = 0, il = array.length; i < il; i += 4) {
+            const a = array[i + 3] / 255;
+            array[i] /= a;
+            array[i + 1] /= a;
+            array[i + 2] /= a;
+        }
+        return pixelData;
+    }
 }