Add ModelWithCoordinates transform (#1378)

* Add ModelWithCoordinates transform

* PR feedback

docs/docs/plugin/transforms/custom-conformation.md

@@ -0,0 +1,45 @@
+# Assign custom conformation to a Model
+
+This document shows how to update model conformation dynamically using the `ModelWithCoordinates` transforms. If this does not work well with your particular use case, it is suggested to write a custom version of `ModelWithCoordinates` with similar usage as outlined in this document.
+
+```ts
+async function animateFirstXCoordinateExample(plugin: PluginContext, url: string, format: BuiltInTrajectoryFormat) {
+    // Load data
+    const _data = await plugin.builders.data.download({ url });
+    const trajectory = await plugin.builders.structure.parseTrajectory(_data, format);
+    const hierarchy = await this.plugin.builders.structure.hierarchy.applyPreset(trajectory, 'default');
+    if (!hierarchy) return;
+
+    // Insert ModelWithCoordinates cell to be updated in the loop bellow
+    const coordinatesNode = await plugin.build().to(hierarchy!.model).insert(ModelWithCoordinates).commit();
+
+    const x0 = hierarchy!.model.data!.atomicConformation.x[0];
+    let xOffset = 0;
+    async function animateFirstXCoord() {
+        // Normally, the whole conformation would come from an API/library call, but here we fake it:
+        const { x, y, z } = hierarchy!.model.data!.atomicConformation;
+        const nextX = [...(x as number[])];
+        nextX[0] = x0 + xOffset;
+        xOffset += 0.05;
+        if (xOffset > 1) xOffset = 0;
+
+        // Construct new coodinate frame from the data and commit the update.
+        // Rest of the state tree will reconcile automatically.
+        await plugin.build().to(coordinatesNode).update({
+            atomicCoordinateFrame: {
+                elementCount: x.length,
+                time: { value: 0, unit: 'step' },
+                xyzOrdering: { isIdentity: true },
+                x: nextX,
+                y,
+                z,
+            }
+        }).commit();
+
+        requestAnimationFrame(animateFirstXCoord);
+    }
+    animateFirstXCoord();
+}
+
+// animateFirstXCoordinateExample('https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/CID/2244/record/SDF/?record_type=3d', 'sdf');
+```

docs/mkdocs.yml

@@ -40,6 +40,7 @@ nav:
     - CIF Schemas: 'plugin/cif-schemas.md'
     - State Transforms:
       - Custom Trajectory: 'plugin/transforms/custom-trajectory.md'
+      - Custom Conformation: 'plugin/transforms/custom-conformation.md'
   - Data Access Tools:
     - 'data-access-tools/model-server.md'
     - Volume Server: