Merge branch 'master' into dpoit

CHANGELOG.md

@@ -6,6 +6,8 @@ Note that since we don't clearly distinguish between a public and private interf
 
 ## [Unreleased]
 
+- Support ``globalColorParams`` and ``globalSymmetryParams`` in common representation params
+- Support ``label`` parameter in ``Viewer.loadStructureFromUrl``
 - Integration of Dual depth peeling - OIT method
 
 ## [v3.15.0] - 2022-08-23

src/apps/viewer/app.ts

@@ -201,7 +201,7 @@ export class Viewer {
         return PluginCommands.State.Snapshots.OpenUrl(this.plugin, { url, type });
     }
 
-    loadStructureFromUrl(url: string, format: BuiltInTrajectoryFormat = 'mmcif', isBinary = false, options?: LoadStructureOptions) {
+    loadStructureFromUrl(url: string, format: BuiltInTrajectoryFormat = 'mmcif', isBinary = false, options?: LoadStructureOptions & { label?: string }) {
         const params = DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj!, this.plugin);
         return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadStructure, {
             source: {
@@ -210,6 +210,7 @@ export class Viewer {
                     url: Asset.Url(url),
                     format: format as any,
                     isBinary,
+                    label: options?.label,
                     options: { ...params.source.params.options, representationParams: options?.representationParams as any },
                 }
             }

src/apps/viewer/embedded.html

@@ -38,6 +38,15 @@
                 viewer.loadPdb('7bv2');
                 viewer.loadEmdb('EMD-30210', { detail: 6 });
                 // viewer.loadAllModelsOrAssemblyFromUrl('https://cs.litemol.org/5ire/full', 'mmcif', false, { representationParams: { theme: { globalName: 'operator-name' } } })
+                // viewer.loadStructureFromUrl('my url', 'pdb', false, {
+                //     representationParams: {
+                //         theme: {
+                //             globalName: 'uniform',
+                //             globalColorParams: { value: 0xff0000 }
+                //         }
+                //     },
+                //     label: 'my structure'
+                // });
             });
         </script>
     </body>

src/mol-plugin-state/actions/structure.ts

@@ -90,6 +90,7 @@ const DownloadStructure = StateAction.build({
                     url: PD.Url(''),
                     format: PD.Select<BuiltInTrajectoryFormat>('mmcif', PD.arrayToOptions(BuiltInTrajectoryFormats.map(f => f[0]), f => f)),
                     isBinary: PD.Boolean(false),
+                    label: PD.Optional(PD.Text('')),
                     options
                 }, { isFlat: true, label: 'URL' })
             })
@@ -104,7 +105,7 @@ const DownloadStructure = StateAction.build({
 
     switch (src.name) {
         case 'url':
-            downloadParams = [{ url: src.params.url, isBinary: src.params.isBinary }];
+            downloadParams = [{ url: src.params.url, isBinary: src.params.isBinary, label: src.params.label || undefined }];
             format = src.params.format;
             break;
         case 'pdb':

src/mol-plugin-state/builder/structure/representation-preset.ts

@@ -41,8 +41,10 @@ export namespace StructureRepresentationPresetProvider {
         quality: PD.Optional(PD.Select<VisualQuality>('auto', VisualQualityOptions)),
         theme: PD.Optional(PD.Group({
             globalName: PD.Optional(PD.Text<ColorTheme.BuiltIn>('')),
+            globalColorParams: PD.Optional(PD.Value<any>({}, { isHidden: true })),
             carbonColor: PD.Optional(PD.Select('chain-id', PD.arrayToOptions(['chain-id', 'operator-name', 'element-symbol'] as const))),
             symmetryColor: PD.Optional(PD.Text<ColorTheme.BuiltIn>('')),
+            symmetryColorParams: PD.Optional(PD.Value<any>({}, { isHidden: true })),
             focus: PD.Optional(PD.Group({
                 name: PD.Optional(PD.Text<ColorTheme.BuiltIn>('')),
                 params: PD.Optional(PD.Value<ColorTheme.BuiltInParams<ColorTheme.BuiltIn>>({} as any))
@@ -76,13 +78,15 @@ export namespace StructureRepresentationPresetProvider {
         if (params.ignoreLight !== void 0) typeParams.ignoreLight = !!params.ignoreLight;
         const color: ColorTheme.BuiltIn | undefined = params.theme?.globalName ? params.theme?.globalName : void 0;
         const ballAndStickColor: ColorTheme.BuiltInParams<'element-symbol'> = params.theme?.carbonColor !== undefined
-            ? { carbonColor: getCarbonColorParams(params.theme?.carbonColor) }
-            : { };
+            ? { carbonColor: getCarbonColorParams(params.theme?.carbonColor), ...params.theme?.globalColorParams }
+            : { ...params.theme?.globalColorParams };
         const symmetryColor: ColorTheme.BuiltIn | undefined = structure && params.theme?.symmetryColor
             ? isSymmetry(structure) ? params.theme?.symmetryColor : color
             : color;
+        const symmetryColorParams = params.theme?.symmetryColorParams ? { ...params.theme?.globalColorParams, ...params.theme?.symmetryColorParams } : { ...params.theme?.globalColorParams };
+        const globalColorParams = params.theme?.globalColorParams ? { ...params.theme?.globalColorParams } : undefined;
 
-        return { update, builder, color, symmetryColor, typeParams, ballAndStickColor };
+        return { update, builder, color, symmetryColor, symmetryColorParams, globalColorParams, typeParams, ballAndStickColor };
     }
 
     export function updateFocusRepr<T extends ColorTheme.BuiltIn>(plugin: PluginContext, structure: Structure, themeName: T | undefined, themeParams: ColorTheme.BuiltInParams<T> | undefined) {
@@ -177,18 +181,18 @@ const polymerAndLigand = StructureRepresentationPresetProvider({
         const waterType = (components.water?.obj?.data?.elementCount || 0) > 50_000 ? 'line' : 'ball-and-stick';
         const lipidType = (components.lipid?.obj?.data?.elementCount || 0) > 20_000 ? 'line' : 'ball-and-stick';
 
-        const { update, builder, typeParams, color, symmetryColor, ballAndStickColor } = reprBuilder(plugin, params, structure);
+        const { update, builder, typeParams, color, symmetryColor, symmetryColorParams, globalColorParams, ballAndStickColor } = reprBuilder(plugin, params, structure);
 
         const representations = {
-            polymer: builder.buildRepresentation(update, components.polymer, { type: 'cartoon', typeParams: { ...typeParams, ...cartoonProps }, color: symmetryColor }, { tag: 'polymer' }),
+            polymer: builder.buildRepresentation(update, components.polymer, { type: 'cartoon', typeParams: { ...typeParams, ...cartoonProps }, color: symmetryColor, colorParams: symmetryColorParams }, { tag: 'polymer' }),
             ligand: builder.buildRepresentation(update, components.ligand, { type: 'ball-and-stick', typeParams, color, colorParams: ballAndStickColor }, { tag: 'ligand' }),
             nonStandard: builder.buildRepresentation(update, components.nonStandard, { type: 'ball-and-stick', typeParams, color, colorParams: ballAndStickColor }, { tag: 'non-standard' }),
             branchedBallAndStick: builder.buildRepresentation(update, components.branched, { type: 'ball-and-stick', typeParams: { ...typeParams, alpha: 0.3 }, color, colorParams: ballAndStickColor }, { tag: 'branched-ball-and-stick' }),
-            branchedSnfg3d: builder.buildRepresentation(update, components.branched, { type: 'carbohydrate', typeParams, color }, { tag: 'branched-snfg-3d' }),
-            water: builder.buildRepresentation(update, components.water, { type: waterType, typeParams: { ...typeParams, alpha: 0.6, visuals: waterType === 'line' ? ['intra-bond', 'element-point'] : undefined }, color, colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'water' }),
-            ion: builder.buildRepresentation(update, components.ion, { type: 'ball-and-stick', typeParams, color, colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'ion' }),
-            lipid: builder.buildRepresentation(update, components.lipid, { type: lipidType, typeParams: { ...typeParams, alpha: 0.6, visuals: lipidType === 'line' ? ['intra-bond'] : undefined }, color, colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'lipid' }),
-            coarse: builder.buildRepresentation(update, components.coarse, { type: 'spacefill', typeParams, color: color || 'chain-id' }, { tag: 'coarse' })
+            branchedSnfg3d: builder.buildRepresentation(update, components.branched, { type: 'carbohydrate', typeParams, color, colorParams: globalColorParams }, { tag: 'branched-snfg-3d' }),
+            water: builder.buildRepresentation(update, components.water, { type: waterType, typeParams: { ...typeParams, alpha: 0.6, visuals: waterType === 'line' ? ['intra-bond', 'element-point'] : undefined }, color, colorParams: { carbonColor: { name: 'element-symbol', params: {} }, ...globalColorParams } }, { tag: 'water' }),
+            ion: builder.buildRepresentation(update, components.ion, { type: 'ball-and-stick', typeParams, color, colorParams: { carbonColor: { name: 'element-symbol', params: {} }, ...globalColorParams } }, { tag: 'ion' }),
+            lipid: builder.buildRepresentation(update, components.lipid, { type: lipidType, typeParams: { ...typeParams, alpha: 0.6, visuals: lipidType === 'line' ? ['intra-bond'] : undefined }, color, colorParams: { carbonColor: { name: 'element-symbol', params: {} }, ...globalColorParams } }, { tag: 'lipid' }),
+            coarse: builder.buildRepresentation(update, components.coarse, { type: 'spacefill', typeParams, color: color || 'chain-id', colorParams: globalColorParams }, { tag: 'coarse' })
         };
 
         await update.commit({ revertOnError: false });
@@ -223,11 +227,11 @@ const proteinAndNucleic = StructureRepresentationPresetProvider({
             smoothness: structure.isCoarseGrained ? 1.0 : 1.5,
         };
 
-        const { update, builder, typeParams, symmetryColor } = reprBuilder(plugin, params, structure);
+        const { update, builder, typeParams, symmetryColor, symmetryColorParams } = reprBuilder(plugin, params, structure);
 
         const representations = {
-            protein: builder.buildRepresentation(update, components.protein, { type: 'cartoon', typeParams: { ...typeParams, ...cartoonProps }, color: symmetryColor }, { tag: 'protein' }),
-            nucleic: builder.buildRepresentation(update, components.nucleic, { type: 'gaussian-surface', typeParams: { ...typeParams, ...gaussianProps }, color: symmetryColor }, { tag: 'nucleic' })
+            protein: builder.buildRepresentation(update, components.protein, { type: 'cartoon', typeParams: { ...typeParams, ...cartoonProps }, color: symmetryColor, colorParams: symmetryColorParams }, { tag: 'protein' }),
+            nucleic: builder.buildRepresentation(update, components.nucleic, { type: 'gaussian-surface', typeParams: { ...typeParams, ...gaussianProps }, color: symmetryColor, colorParams: symmetryColorParams }, { tag: 'nucleic' })
         };
 
         await update.commit({ revertOnError: true });
@@ -275,11 +279,11 @@ const coarseSurface = StructureRepresentationPresetProvider({
             });
         }
 
-        const { update, builder, typeParams, symmetryColor } = reprBuilder(plugin, params, structure);
+        const { update, builder, typeParams, symmetryColor, symmetryColorParams } = reprBuilder(plugin, params, structure);
 
         const representations = {
-            polymer: builder.buildRepresentation(update, components.polymer, { type: 'gaussian-surface', typeParams: { ...typeParams, ...gaussianProps }, color: symmetryColor }, { tag: 'polymer' }),
-            lipid: builder.buildRepresentation(update, components.lipid, { type: 'gaussian-surface', typeParams: { ...typeParams, ...gaussianProps }, color: symmetryColor }, { tag: 'lipid' })
+            polymer: builder.buildRepresentation(update, components.polymer, { type: 'gaussian-surface', typeParams: { ...typeParams, ...gaussianProps }, color: symmetryColor, colorParams: symmetryColorParams }, { tag: 'polymer' }),
+            lipid: builder.buildRepresentation(update, components.lipid, { type: 'gaussian-surface', typeParams: { ...typeParams, ...gaussianProps }, color: symmetryColor, colorParams: symmetryColorParams }, { tag: 'lipid' })
         };
 
         await update.commit({ revertOnError: true });
@@ -309,10 +313,10 @@ const polymerCartoon = StructureRepresentationPresetProvider({
             sizeFactor: structure.isCoarseGrained ? 0.8 : 0.2
         };
 
-        const { update, builder, typeParams, symmetryColor } = reprBuilder(plugin, params, structure);
+        const { update, builder, typeParams, symmetryColor, symmetryColorParams } = reprBuilder(plugin, params, structure);
 
         const representations = {
-            polymer: builder.buildRepresentation(update, components.polymer, { type: 'cartoon', typeParams: { ...typeParams, ...cartoonProps }, color: symmetryColor }, { tag: 'polymer' })
+            polymer: builder.buildRepresentation(update, components.polymer, { type: 'cartoon', typeParams: { ...typeParams, ...cartoonProps }, color: symmetryColor, colorParams: symmetryColorParams }, { tag: 'polymer' })
         };
 
         await update.commit({ revertOnError: true });
@@ -367,9 +371,9 @@ const atomicDetail = StructureRepresentationPresetProvider({
             });
         }
 
-        const { update, builder, typeParams, color, ballAndStickColor } = reprBuilder(plugin, params, structure);
+        const { update, builder, typeParams, color, ballAndStickColor, globalColorParams } = reprBuilder(plugin, params, structure);
         const colorParams = lowResidueElementRatio && !bondsGiven
-            ? { carbonColor: { name: 'element-symbol', params: {} } }
+            ? { carbonColor: { name: 'element-symbol', params: {} }, ...globalColorParams }
             : ballAndStickColor;
 
         const representations = {
@@ -377,7 +381,7 @@ const atomicDetail = StructureRepresentationPresetProvider({
         };
         if (showCarbohydrateSymbol) {
             Object.assign(representations, {
-                snfg3d: builder.buildRepresentation(update, components.branched, { type: 'carbohydrate', typeParams: { ...typeParams, alpha: 0.4, visuals: ['carbohydrate-symbol'] }, color }, { tag: 'snfg-3d' }),
+                snfg3d: builder.buildRepresentation(update, components.branched, { type: 'carbohydrate', typeParams: { ...typeParams, alpha: 0.4, visuals: ['carbohydrate-symbol'] }, color, colorParams: globalColorParams }, { tag: 'snfg-3d' }),
             });
         }