@molstudio/core 0.1.0 → 0.1.2

package/dist/MolStudio.d.ts

@@ -51,6 +51,11 @@ export declare class MolStudio {
     loadVolume({ data, label, format }: LoadDataOptions<VolumeFormat>): Promise<void>;
     loadVolumeFromUrl(url: string, label: string, format: VolumeFormat, isBinary: boolean): Promise<void>;
     private applyStructurePreset;
+    /**
+     * Mol*'s default preset colors ligand carbons by chain, the same color as the protein around them;
+     * element colors keep a ligand distinct from its binding pocket.
+     */
+    private colorLigandCarbonsByElement;
     private applyVolumeVisuals;
     setVisible(id: string, visible: boolean): void;
     /**
@@ -113,6 +118,10 @@ export declare class MolStudio {
     private transparencyLayers;
     private partLoci;
     private residueRef;
+    /**
+     * Fits the visible structures, or everything when none is shown. A map's box is usually much larger
+     * than its density, so fitting it would leave a fitted model small in the middle of the view.
+     */
     resetCamera(): void;
     setSpinning(spinning: boolean): void;
     setBackground(hex: string): void;

package/dist/MolStudio.js

@@ -1,9 +1,11 @@
 import { PLDDTConfidenceColorThemeProvider } from "molstar/lib/extensions/model-archive/quality-assessment/color/plddt";
+import { QualityAssessment } from "molstar/lib/extensions/model-archive/quality-assessment/prop";
+import { MmcifFormat } from "molstar/lib/mol-model-formats/structure/mmcif";
 import { DownloadDensity } from "molstar/lib/mol-plugin-state/actions/volume";
 import { PluginConfig } from "molstar/lib/mol-plugin/config";
 import { Volume } from "molstar/lib/mol-model/volume";
 import { Loci } from "molstar/lib/mol-model/loci";
-import { Structure, StructureElement } from "molstar/lib/mol-model/structure";
+import { Model, Structure, StructureElement } from "molstar/lib/mol-model/structure";
 import { createStructureColorThemeParams, createStructureRepresentationParams, } from "molstar/lib/mol-plugin-state/helpers/structure-representation-params";
 import { clearStructureTransparency, setStructureTransparency } from "molstar/lib/mol-plugin-state/helpers/structure-transparency";
 import { createVolumeColorThemeParams } from "molstar/lib/mol-plugin-state/helpers/volume-representation-params";
@@ -70,7 +72,10 @@ export class MolStudio {
         }));
     }
     static async create(target) {
-        const plugin = new PluginContext(DefaultPluginSpec());
+        const spec = DefaultPluginSpec();
+        // Mol*'s "auto" mode renders at 1x on mobile browsers, which blurs structures on high-DPI phones.
+        spec.config = [...(spec.config ?? []), [PluginConfig.General.ResolutionMode, "native"]];
+        const plugin = new PluginContext(spec);
         await plugin.init();
         // Only the pLDDT theme is needed; Mol*'s quality-assessment behaviour also pulls in its React UI.
         plugin.representation.structure.themes.colorThemeRegistry.add(PLDDTConfidenceColorThemeProvider);
@@ -219,7 +224,27 @@ export class MolStudio {
     }
     async applyStructurePreset(raw, format) {
         const trajectory = await this.plugin.builders.structure.parseTrajectory(raw, format);
-        await this.plugin.builders.structure.hierarchy.applyPreset(trajectory, "default");
+        const result = await this.plugin.builders.structure.hierarchy.applyPreset(trajectory, "default");
+        // Mol* parses some malformed input (e.g. text that is not SDF) into an empty structure without failing.
+        if (!result?.structure.data?.elementCount) {
+            throw new Error(`The ${format} data contains no atoms.`);
+        }
+        await this.colorLigandCarbonsByElement(result.structure.ref);
+    }
+    /**
+     * Mol*'s default preset colors ligand carbons by chain, the same color as the protein around them;
+     * element colors keep a ligand distinct from its binding pocket.
+     */
+    async colorLigandCarbonsByElement(structureRef) {
+        const structure = this.requireStructure(structureRef);
+        const reprs = structure.components
+            .filter((component) => staticComponentType(component) === "ligand")
+            .flatMap((component) => component.representations)
+            .filter((repr) => repr.cell.transform.params?.colorTheme.name === "element-symbol");
+        await this.updateEach(reprs, (old) => ({
+            ...old,
+            colorTheme: { ...old.colorTheme, params: { ...old.colorTheme.params, carbonColor: { name: "element-symbol", params: {} } } },
+        }));
     }
     async applyVolumeVisuals(raw, format) {
         const provider = this.plugin.dataFormats.get(format);
@@ -373,7 +398,7 @@ export class MolStudio {
             ? structure.components.flatMap((component) => component.representations)
             : (volume?.representations ?? this.requireComponent(target).representations);
         const renderObjects = reprs.flatMap((repr) => repr.cell.obj?.data.repr.renderObjects ?? []);
-        this.plugin.managers.camera.focusRenderObjects(renderObjects);
+        this.plugin.managers.camera.focusRenderObjects(renderObjects, FOCUS_OPTIONS);
     }
     async remove(id) {
         await PluginCommands.State.RemoveObject(this.plugin, {
@@ -401,7 +426,7 @@ export class MolStudio {
         const loci = this.partLoci(part);
         if (part.scope === "residue")
             this.plugin.managers.structure.focus.setFromLoci(loci);
-        this.plugin.managers.camera.focusLoci(loci);
+        this.plugin.managers.camera.focusLoci(loci, FOCUS_OPTIONS);
     }
     /** Leaves Mol*'s focus view, removing its target and surroundings components, and returns to the earlier view. */
     clearFocus() {
@@ -555,8 +580,21 @@ export class MolStudio {
         return owner ? { objectId: owner.cell.transform.ref, residueIndex } : null;
     }
     // ---- viewport ----
+    /**
+     * Fits the visible structures, or everything when none is shown. A map's box is usually much larger
+     * than its density, so fitting it would leave a fitted model small in the middle of the view.
+     */
     resetCamera() {
-        PluginCommands.Camera.Reset(this.plugin, {});
+        const renderObjects = this.plugin.managers.structure.hierarchy.current.structures
+            .flatMap((structure) => structure.components)
+            .flatMap((component) => component.representations)
+            .flatMap((repr) => repr.cell.obj?.data.repr.renderObjects ?? [])
+            .filter((renderObject) => renderObject.state.visible);
+        if (renderObjects.length === 0) {
+            PluginCommands.Camera.Reset(this.plugin, {});
+            return;
+        }
+        this.plugin.managers.camera.focusRenderObjects(renderObjects, { extraRadius: 0 });
     }
     setSpinning(spinning) {
         const canvas3d = this.requireCanvas();
@@ -720,8 +758,7 @@ export class MolStudio {
     }
     applicableSchemes(ref) {
         const structure = ref.cell.obj?.data;
-        const plddt = this.plugin.representation.structure.themes.colorThemeRegistry.get("plddt-confidence");
-        const hasPlddt = !!structure && !!plddt?.isApplicable({ structure });
+        const hasPlddt = !!structure && structure.models.some(isPredictedModel);
         return hasPlddt ? ["plddt-confidence", ...BASE_SCHEMES] : [...BASE_SCHEMES];
     }
     // ---- lookup helpers ----
@@ -834,6 +871,21 @@ const AXES = {
 };
 /** Matches Mol*'s default camera focus animation. */
 const CAMERA_TRANSITION_MS = 250;
+/** Keeps the surroundings of small targets (a ligand, a residue) in view instead of filling the screen with them. */
+const FOCUS_OPTIONS = { minRadius: 14 };
+/**
+ * Whether B-factors hold pLDDT scores. Mol* assumes so for any model not marked experimental, but most
+ * PDB entries lack that mark, so an entry with experimental methods recorded does not count.
+ */
+function isPredictedModel(model) {
+    if (QualityAssessment.isApplicable(model, "pLDDT"))
+        return true;
+    if (!MmcifFormat.is(model.sourceData) || !model.atomicConformation.B_iso_or_equiv.isDefined)
+        return false;
+    if (Model.isExperimental(model))
+        return false;
+    return model.sourceData.data.db.exptl.method.rowCount === 0;
+}
 const FOCUS_TAGS = {
     [StructureFocusRepresentationTags.TargetSel]: "target",
     [StructureFocusRepresentationTags.SurrSel]: "surroundings",

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@molstudio/core",
-  "version": "0.1.0",
+  "version": "0.1.2",
   "description": "UI-less Mol* controller that exposes the viewer as objects and display operations.",
   "license": "MIT",
   "keywords": [