mol-plugin: Automatic default 3d representation

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

@@ -16,11 +16,14 @@ import { PresetStructureReprentations } from './structure/preset';
 import { StructureRepresentationProvider, RepresentationProviderTags } from './structure/provider';
 import { UniqueArray } from '../../../mol-data/generic';
 
+// TODO: support quality
+// TODO: support ignore hydrogens
+
 export class StructureRepresentationManager {
     private providers: StructureRepresentationProvider[] = [];
     private providerMap: Map<string, StructureRepresentationProvider> = new Map();
 
-    readonly defaultProvider = PresetStructureReprentations.default;
+    readonly defaultProvider = PresetStructureReprentations.auto;
 
     hasProvider(s: Structure) {
         for (const p of this.providers) {

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

@@ -13,85 +13,150 @@ import { StructureRepresentationProvider, RepresentationProviderTags } from './p
 import { StateBuilder } from '../../../../mol-state';
 import { PluginStateObject } from '../../objects';
 
-export const PresetStructureReprentations = {
-    default: StructureRepresentationProvider({
-        id: 'preset-structure-representation-default',
-        display: { name: 'Default', group: 'Preset' },
-        apply(state, structureCell, _, plugin) {
-            const root = state.build().to(structureCell.transform.ref);
-            const structure = structureCell.obj!.data;
-
-            const reprTags = [this.id, RepresentationProviderTags.Representation];
-
-            applyComplex(root, 'protein-or-nucleic')
-                .applyOrUpdateTagged(reprTags, StateTransforms.Representation.StructureRepresentation3D,
-                    StructureRepresentation3DHelpers.getDefaultParams(plugin, 'cartoon', structure));
-
-            applyComplex(root, 'ligand')
-                .applyOrUpdateTagged(reprTags, StateTransforms.Representation.StructureRepresentation3D,
-                    StructureRepresentation3DHelpers.getDefaultParams(plugin, 'ball-and-stick', structure));
-
-            applyComplex(root, 'modified')
-                .applyOrUpdateTagged(reprTags, StateTransforms.Representation.StructureRepresentation3D,
-                    StructureRepresentation3DHelpers.getDefaultParamsWithTheme(plugin, 'ball-and-stick', 'polymer-id', structure, void 0));
-
-            const branched = applyComplex(root, 'branched');
-
-            branched.applyOrUpdateTagged(reprTags, StateTransforms.Representation.StructureRepresentation3D,
-                StructureRepresentation3DHelpers.getDefaultParams(plugin, 'ball-and-stick', structure, { alpha: 0.15 }));
-            branched.applyOrUpdateTagged(reprTags, StateTransforms.Representation.StructureRepresentation3D,
-                StructureRepresentation3DHelpers.getDefaultParams(plugin, 'carbohydrate', structure));
-
-            applyComplex(root, 'water')
-                .applyOrUpdateTagged(reprTags, StateTransforms.Representation.StructureRepresentation3D,
-                    StructureRepresentation3DHelpers.getDefaultParams(plugin, 'ball-and-stick', structure, { alpha: 0.51 }));
-
-            applyComplex(root, 'coarse')
-                .applyOrUpdateTagged(reprTags, StateTransforms.Representation.StructureRepresentation3D,
-                    StructureRepresentation3DHelpers.getDefaultParamsWithTheme(plugin, 'spacefill', 'polymer-id', structure, {}));
-
-            return state.updateTree(root, { revertIfAborted: true });
+const auto = StructureRepresentationProvider({
+    id: 'preset-structure-representation-auto',
+    display: { name: 'Automaic', group: 'Preset' },
+    apply(state, structureCell, _, plugin) {
+        const s = structureCell.obj!.data;
+
+        // TODO: a way to improve this?
+
+        if (s.elementCount < 50000) {
+            return defaultPreset.apply(state, structureCell, void 0, plugin);
+        } else if (s.elementCount < 200000) {
+            return proteinAndNucleic.apply(state, structureCell, void 0, plugin);
+        } else {
+            if (s.unitSymmetryGroups[0].units.length > 10) {
+                return capsid.apply(state, structureCell, void 0, plugin);
+            } else {
+                return coarseCapsid.apply(state, structureCell, void 0, plugin);
+            }
         }
-    }),
-    capsid: StructureRepresentationProvider({
-        id: 'preset-structure-representation-capsid',
-        display: { name: 'Capsid', group: 'Preset' },
-        apply(state, structureCell, _, plugin) {
-            const root = plugin.state.dataState.build().to(structureCell.transform.ref);
-            const structure = structureCell.obj!.data;
-
-            const params = StructureRepresentation3DHelpers.createParams(plugin, structure, {
-                repr: [BuiltInStructureRepresentations['gaussian-surface'], () => ({ smoothness: 1 })]
-            });
-
-            const reprTags = [this.id, RepresentationProviderTags.Representation];
-
-            applySelection(root, 'polymer')
-                .applyOrUpdateTagged(reprTags, StateTransforms.Representation.StructureRepresentation3D, params);
-
-            return state.updateTree(root, { revertIfAborted: true });
-        }
-    }),
-    cartoon: StructureRepresentationProvider({
-        id: 'preset-structure-representation-cartoon',
-        display: { name: 'Cartoon', group: 'Preset' },
-        apply(state, structureCell, _, plugin) {
-            const root = plugin.state.dataState.build().to(structureCell.transform.ref);
-            const structure = structureCell.obj!.data;
-
-            const params = StructureRepresentation3DHelpers.createParams(plugin, structure, {
-                repr: BuiltInStructureRepresentations['cartoon']
-            });
-
-            const reprTags = [this.id, RepresentationProviderTags.Representation];
-
-            applySelection(root, 'polymer')
-                .applyOrUpdateTagged(reprTags, StateTransforms.Representation.StructureRepresentation3D, params);
-
-            return state.updateTree(root, { revertIfAborted: true });
-        }
-    })
-};
+    }
+});
+
+const defaultPreset = StructureRepresentationProvider({
+    id: 'preset-structure-representation-default',
+    display: { name: 'Default', group: 'Preset' },
+    apply(state, structureCell, _, plugin) {
+        const root = state.build().to(structureCell.transform.ref);
+        const structure = structureCell.obj!.data;
+
+        const reprTags = [this.id, RepresentationProviderTags.Representation];
+
+        applyComplex(root, 'protein-or-nucleic')
+            .applyOrUpdateTagged(reprTags, StateTransforms.Representation.StructureRepresentation3D,
+                StructureRepresentation3DHelpers.getDefaultParams(plugin, 'cartoon', structure));
+
+        applyComplex(root, 'ligand')
+            .applyOrUpdateTagged(reprTags, StateTransforms.Representation.StructureRepresentation3D,
+                StructureRepresentation3DHelpers.getDefaultParams(plugin, 'ball-and-stick', structure));
+
+        applyComplex(root, 'modified')
+            .applyOrUpdateTagged(reprTags, StateTransforms.Representation.StructureRepresentation3D,
+                StructureRepresentation3DHelpers.getDefaultParamsWithTheme(plugin, 'ball-and-stick', 'polymer-id', structure, void 0));
+
+        const branched = applyComplex(root, 'branched');
+
+        branched.applyOrUpdateTagged(reprTags, StateTransforms.Representation.StructureRepresentation3D,
+            StructureRepresentation3DHelpers.getDefaultParams(plugin, 'ball-and-stick', structure, { alpha: 0.15 }));
+        branched.applyOrUpdateTagged(reprTags, StateTransforms.Representation.StructureRepresentation3D,
+            StructureRepresentation3DHelpers.getDefaultParams(plugin, 'carbohydrate', structure));
+
+        applyComplex(root, 'water')
+            .applyOrUpdateTagged(reprTags, StateTransforms.Representation.StructureRepresentation3D,
+                StructureRepresentation3DHelpers.getDefaultParams(plugin, 'ball-and-stick', structure, { alpha: 0.51 }));
+
+        applyComplex(root, 'coarse')
+            .applyOrUpdateTagged(reprTags, StateTransforms.Representation.StructureRepresentation3D,
+                StructureRepresentation3DHelpers.getDefaultParamsWithTheme(plugin, 'spacefill', 'polymer-id', structure, {}));
+
+        return state.updateTree(root, { revertIfAborted: true });
+    }
+});
+
+const proteinAndNucleic = StructureRepresentationProvider({
+    id: 'preset-structure-representation-protein-and-nucleic',
+    display: { name: 'Protein & Nucleic', group: 'Preset' },
+    apply(state, structureCell, _, plugin) {
+        const root = plugin.state.dataState.build().to(structureCell.transform.ref);
+        const structure = structureCell.obj!.data;
+        const reprTags = [this.id, RepresentationProviderTags.Representation];
+
+        applySelection(root, 'protein')
+            .applyOrUpdateTagged(reprTags, StateTransforms.Representation.StructureRepresentation3D,
+                StructureRepresentation3DHelpers.getDefaultParams(plugin, 'cartoon', structure));
+
+        applySelection(root, 'nucleic')
+            .applyOrUpdateTagged(reprTags, StateTransforms.Representation.StructureRepresentation3D,
+                StructureRepresentation3DHelpers.getDefaultParams(plugin, 'gaussian-surface', structure));
+
+        return state.updateTree(root, { revertIfAborted: true });
+    }
+});
+
+const capsid = StructureRepresentationProvider({
+    id: 'preset-structure-representation-capsid',
+    display: { name: 'Capsid', group: 'Preset' },
+    apply(state, structureCell, _, plugin) {
+        const root = plugin.state.dataState.build().to(structureCell.transform.ref);
+        const structure = structureCell.obj!.data;
+
+        const params = StructureRepresentation3DHelpers.createParams(plugin, structure, {
+            repr: [BuiltInStructureRepresentations['gaussian-surface'], () => ({ smoothness: 1 })]
+        });
+
+        const reprTags = [this.id, RepresentationProviderTags.Representation];
+
+        applySelection(root, 'polymer')
+            .applyOrUpdateTagged(reprTags, StateTransforms.Representation.StructureRepresentation3D, params);
+
+        return state.updateTree(root, { revertIfAborted: true });
+    }
+});
+
+const coarseCapsid = StructureRepresentationProvider({
+    id: 'preset-structure-representation-coarse-capsid',
+    display: { name: 'Coarse Capsid', group: 'Preset' },
+    apply(state, structureCell, _, plugin) {
+        const root = plugin.state.dataState.build().to(structureCell.transform.ref);
+        const structure = structureCell.obj!.data;
+
+        const params = StructureRepresentation3DHelpers.createParams(plugin, structure, {
+            repr: [
+                BuiltInStructureRepresentations['gaussian-surface'],
+                () => ({ smoothness: 0.5, radiusOffset: 1, /*visuals: ['gaussian-surface-mesh']*/ })
+            ]
+        });
+
+        const reprTags = [this.id, RepresentationProviderTags.Representation];
+
+        applySelection(root, 'trace')
+            .applyOrUpdateTagged(reprTags, StateTransforms.Representation.StructureRepresentation3D, params);
+
+        return state.updateTree(root, { revertIfAborted: true });
+    }
+});
+
+const cartoon = StructureRepresentationProvider({
+    id: 'preset-structure-representation-cartoon',
+    display: { name: 'Cartoon', group: 'Preset' },
+    apply(state, structureCell, _, plugin) {
+        const root = plugin.state.dataState.build().to(structureCell.transform.ref);
+        const structure = structureCell.obj!.data;
+
+        const params = StructureRepresentation3DHelpers.createParams(plugin, structure, {
+            repr: BuiltInStructureRepresentations['cartoon']
+        });
+
+        const reprTags = [this.id, RepresentationProviderTags.Representation];
+
+        applySelection(root, 'polymer')
+            .applyOrUpdateTagged(reprTags, StateTransforms.Representation.StructureRepresentation3D, params);
+
+        return state.updateTree(root, { revertIfAborted: true });
+    }
+});
 
 function applyComplex(to: StateBuilder.To<PluginStateObject.Molecule.Structure>, type: keyof typeof StructureComplexElementTypes) {
     return to.applyOrUpdateTagged(type, StateTransforms.Model.StructureComplexElement, { type }, { tags: RepresentationProviderTags.Selection });
@@ -101,4 +166,13 @@ function applySelection(to: StateBuilder.To<PluginStateObject.Molecule.Structure
     return to.applyOrUpdateTagged(query, StateTransforms.Model.StructureSelectionFromExpression,
         { expression: Q[query].expression, label: Q[query].label },
         { tags: RepresentationProviderTags.Selection });
-}
+}
+
+export const PresetStructureReprentations = {
+    auto,
+    default: defaultPreset,
+    proteinAndNucleic,
+    capsid,
+    coarseCapsid,
+    cartoon
+};