ensure SecondaryStructure is available

src/mol-plugin/state/transforms/helpers.ts

@@ -11,6 +11,7 @@ import { parseMolScript } from 'mol-script/language/parser';
 import { transpileMolScript } from 'mol-script/script/mol-script/symbols';
 import { compile } from 'mol-script/runtime/query/compiler';
 import { Transparency } from 'mol-theme/transparency';
+import { ComputedSecondaryStructure } from 'mol-model-props/computed/secondary-structure';
 
 type Script = { language: string, expression: string }
 
@@ -35,4 +36,15 @@ export function getStructureOverpaint(structure: Structure, scriptLayers: { scri
 
 export function getStructureTransparency(structure: Structure, script: Script, value: number, variant: Transparency.Variant): Transparency {
     return { loci: scriptToLoci(structure, script), value, variant }
+}
+
+/**
+ * Attaches ComputedSecondaryStructure property when unavailable in sourceData
+ */
+export async function ensureSecondaryStructure(s: Structure) {
+    if (s.model.sourceData.kind === 'mmCIF') {
+        if (!s.model.sourceData.data.struct_conf.id.isDefined && !s.model.sourceData.data.struct_sheet_range.id.isDefined) {
+            await ComputedSecondaryStructure.attachFromCifOrCompute(s)
+        }
+    }
 }

src/mol-plugin/state/transforms/model.ts

@@ -26,6 +26,7 @@ import { parseMolScript } from 'mol-script/language/parser';
 import { transpileMolScript } from 'mol-script/script/mol-script/symbols';
 import { shapeFromPly } from 'mol-model-formats/shape/ply';
 import { SymmetryOperator } from 'mol-math/geometry';
+import { ensureSecondaryStructure } from './helpers';
 
 export { TrajectoryFromBlob };
 export { TrajectoryFromMmCif };
@@ -167,9 +168,12 @@ const StructureFromModel = PluginStateTransform.BuiltIn({
     to: SO.Molecule.Structure
 })({
     apply({ a }) {
-        let s = Structure.ofModel(a.data);
-        const props = { label: a.data.label, description: s.elementCount === 1 ? '1 element' : `${s.elementCount} elements` };
-        return new SO.Molecule.Structure(s, props);
+        return Task.create('Build Structure', async ctx => {
+            const s = Structure.ofModel(a.data);
+            await ensureSecondaryStructure(s)
+            const props = { label: a.data.label, description: s.elementCount === 1 ? '1 element' : `${s.elementCount} elements` };
+            return new SO.Molecule.Structure(s, props);
+        })
     }
 });
 
@@ -218,12 +222,14 @@ const StructureAssemblyFromModel = PluginStateTransform.BuiltIn({
 
             const base = Structure.ofModel(model);
             if (!asm) {
+                await ensureSecondaryStructure(base)
                 const label = { label: a.data.label, description: structureDesc(base) };
                 return new SO.Molecule.Structure(base, label);
             }
 
             id = asm.id;
             const s = await StructureSymmetry.buildAssembly(base, id!).runInContext(ctx);
+            await ensureSecondaryStructure(s)
             const props = { label: `Assembly ${id}`, description: structureDesc(s) };
             return new SO.Molecule.Structure(s, props);
         })
@@ -249,6 +255,7 @@ const StructureSymmetryFromModel = PluginStateTransform.BuiltIn({
             const model = a.data;
             const base = Structure.ofModel(model);
             const s = await StructureSymmetry.buildSymmetryRange(base, ijkMin, ijkMax).runInContext(ctx);
+            await ensureSecondaryStructure(s)
             const props = { label: `Symmetry [${ijkMin}] to [${ijkMax}]`, description: structureDesc(s) };
             return new SO.Molecule.Structure(s, props);
         })