molstar · Simard302 · Jun 11, 2024 · Jun 11, 2024 · Jun 11, 2024 · Jun 12, 2024
diff --git a/inspect/list_entities/index.html b/inspect/list_entities/index.html
@@ -0,0 +1,14 @@
+<html>
+  <head>
+    <title>Mol* Gallery</title>
+    <meta charset="UTF-8" />
+  </head>
+
+  <body style="font-family: sans-serif; height: 100%; width: 100%; margin: 0;">
+    <div id="app" style="height: 100%;width: 100%;">
+      <canvas id="canvas" style="height: 100%;width: 100%;"></canvas>
+    </div>
+
+    <script src="src/index.ts"></script>
+  </body>
+</html>
diff --git a/inspect/list_entities/package.json b/inspect/list_entities/package.json
@@ -0,0 +1,24 @@
+{
+    "name": "molstar-typescript-example",
+    "version": "1.0.0",
+    "description": "Molstar and TypeScript example starter project",
+    "main": "index.html",
+    "scripts": {
+      "start": "parcel index.html",
+      "build": "parcel build index.html"
+    },
+    "dependencies": {
+      "parcel-bundler": "1.12.5",
+      "molstar": "4.3.0"
+    },
+    "devDependencies": {
+      "typescript": "4.4.4"
+    },
+    "resolutions": {
+      "@babel/preset-env": "7.13.8"
+    },
+    "keywords": [
+      "typescript",
+      "molstar"
+    ]
+  }
diff --git a/inspect/list_entities/src/common/init.ts b/inspect/list_entities/src/common/init.ts
@@ -0,0 +1,19 @@
+import { PluginContext } from "molstar/lib/mol-plugin/context";
+import { DefaultPluginSpec } from "molstar/lib/mol-plugin/spec";
+
+export async function createRootViewer() {
+  const viewport = document.getElementById("app") as HTMLDivElement;
+  const canvas = document.getElementById("canvas") as HTMLCanvasElement;
+
+  const plugin = new PluginContext(DefaultPluginSpec());
+  await plugin.init();
+
+  if (!plugin.initViewer(canvas, viewport)) {
+    viewport.innerHTML = "Failed to init Mol*";
+    throw new Error("init failed");
+  }
+  //@ts-ignore
+  window["molstar"] = plugin;
+
+  return plugin;
+}
diff --git a/inspect/list_entities/src/index.ts b/inspect/list_entities/src/index.ts
@@ -0,0 +1,120 @@
+import { Queries, QueryContext, StructureProperties, StructureSelection } from "molstar/lib/mol-model/structure";
+import { createRootViewer } from "./common/init";
+import { StructureSelectionQueries, StructureSelectionQuery } from "molstar/lib/mol-plugin-state/helpers/structure-selection-query";
+import { MolScriptBuilder as MS } from 'molstar/lib/mol-script/language/builder';
+import { Location } from "molstar/lib/mol-model/structure/structure/element/location";
+
+
+async function init() {
+    // Create viewer
+    const plugin = await createRootViewer();
+
+    // Download PDB
+    const fileData = await plugin.builders.data.download(
+        { url: "https://models.rcsb.org/1PTH.bcif", isBinary: true }
+    );
+
+    // Load PDB and create representation
+    const trajectory = await plugin.builders.structure.parseTrajectory(fileData, "mmcif");
+    const presetStateObjects = await plugin.builders.structure.hierarchy.applyPreset(trajectory, "default");
+
+    if (!presetStateObjects) {
+        throw new Error("Structure not loaded");
+    }
+
+    // Get Structure object from the structure stateObject selector.
+    // The Structure object contains properties and accessors to the underlying molecular data such as chains, residues, atoms, etc.
+    const struct = presetStateObjects.structure.data!;
+
+    // Create a QueryContext to be reused for all queries
+    // Limits the queries to only look at the structure
+    const ctx = new QueryContext(struct)
+
+
+    // ==== Number of Waters ====
+    // Created a query to select all residues that are water
+    // but only select 1 atom per water (ensuring a Singleton selection)
+    const waterQuery = Queries.generators.atoms({
+        'entityTest': ctx => StructureProperties.entity.type(ctx.element) === 'water'
+    })
+    // Since we used Queries.generators.atoms, our selection will by grouped by Atom and is therefore Singletons
+    const waterSelection = waterQuery(ctx) as StructureSelection.Singletons;
+    const numWaters = waterSelection.structure.atomicResidueCount;
+
+
+    // ==== Covalent ligand names and residue code ====
+    // Create a query expression for all ligands connected to the protein
+    const covalentLigandExp = MS.struct.filter.isConnectedTo({
+        0: StructureSelectionQueries.ligand.expression,         // All ligands
+        target: StructureSelectionQueries.protein.expression,   // All protein atoms
+        'bond-test': true  // Only atoms covalently bound to the protein
+    })
+    // Query the atoms with the context to get a StructureSelection
+    const covLigQuery = StructureSelectionQuery('only-covalent-ligands', covalentLigandExp).query;
+    const covLigSelection = covLigQuery(ctx);
+    // Assume ligands in structure have >1 atoms.
+    // Therefore, the StructureSelection must be a Sequence
+    // If the selection is empty, set the ligand structures to an empty array
+    const covLigStructures = StructureSelection.isEmpty(covLigSelection) ? [] : (covLigSelection as StructureSelection.Sequence).structures;
+    // Retrieve each ligand name and residue code
+    const covLigNames: string[] = [];
+    const covLigRes: string[] = [];
+    const auxCovLigLocation = Location.create();  // Create a Location object to retrieve properties
+    covLigStructures.forEach(s => {
+        auxCovLigLocation.structure = s;  // Set the structure for the location
+        s.units.map(u => {
+            // Set the Location to the first element of the ligand
+            auxCovLigLocation.unit = u;
+            auxCovLigLocation.element = u.elements[0];
+            // Use the Location to query the ligand name property of the ligand
+            const name = StructureProperties.entity.pdbx_description(auxCovLigLocation).join('|')
+            covLigNames.push(name);
+            s// Use the Location to query the reidue code for the ligand
+            const res = StructureProperties.atom.label_comp_id(auxCovLigLocation)
+            covLigRes.push(res);
+        })
+    })
+
+
+    // ==== Number of AltLoc positions ====
+    const altLocQuery = Queries.generators.atoms({
+        // Any atom with a non '' alt_id
+        'atomTest': ctx => !!StructureProperties.atom.label_alt_id(ctx.element),
+    });
+    // Since we used Queries.generators.atoms, our selection will by grouped by Atom and is therefore Singletons
+    const altLocSelection = altLocQuery(ctx) as StructureSelection.Singletons;
+    const numAltLocs = altLocSelection.structure.elementCount;
+
+
+    // ==== Polymer ASYM Unit name and chain ====
+    const polymerSelection = StructureSelectionQueries.polymer.query(ctx)
+    // Polymer query groups selected atoms by entity. Assume it creates a Sequence StructureSelection
+    const polymerStructues = (polymerSelection as StructureSelection.Sequence).structures;
+    // Iterate over each polymer unit in each structure and get the name and chain
+    const namePolymers: string[] = [];
+    const chainPolymers: string[] = [];
+    const auxPolymerLocation = Location.create();  // Create a Location object to retrieve properties
+    polymerStructues.forEach(s => {
+        auxPolymerLocation.structure = s;   // Set the structure for the location
+        s.units.map(u => {
+            // Set the Location to the first element of the polymer
+            auxPolymerLocation.unit = u;
+            auxPolymerLocation.element = u.elements[0];
+            // Use the Location to query the polymer name and chain
+            const name = StructureProperties.entity.pdbx_description(auxPolymerLocation).join('|')
+            namePolymers.push(name);
+            const chain = StructureProperties.chain.auth_asym_id(auxPolymerLocation);
+            chainPolymers.push(chain);
+        })
+    })
+
+    console.table([
+        {title: 'Water count', value: numWaters},
+        {title: 'Covalent Ligand name', value: covLigNames.join(', ')},
+        {title: 'Covalent Ligand residue', value: covLigRes.join(', ')},
+        {title: 'Alt Loc Count', value: numAltLocs},
+        {title: 'Poly ASYM Unit name', value: namePolymers.join(', ')},
+        {title: 'Poly ASYM Unit chain', value: chainPolymers.join(', ')}
+    ])
+}
+init();
diff --git a/inspect/list_entities/tsconfig.json b/inspect/list_entities/tsconfig.json
@@ -0,0 +1,16 @@
+{
+    "compilerOptions": {
+      "strict": true,
+      "module": "commonjs",
+      "jsx": "preserve",
+      "esModuleInterop": true,
+      "sourceMap": true,
+      "allowJs": true,
+      "lib": [
+        "es6",
+        "dom"
+      ],
+      "rootDir": "src",
+      "moduleResolution": "node"
+    }
+  }
diff --git a/readme.md b/readme.md
@@ -55,6 +55,8 @@ npm run watch
   - [Move camera](https://codesandbox.io/p/sandbox/github/molstar/example-gallery/master/camera/move_camera)
 - Coloring
   - [Color a selection](https://codesandbox.io/p/sandbox/github/molstar/example-gallery/master/coloring/color_a_selection)
+- Inspect
+  - [List entities](https://codesandbox.io/p/sandbox/github/molstar/example-gallery/master/inspect/list_entities)
 - IO
   - [Load file](https://codesandbox.io/p/sandbox/github/molstar/example-gallery/master/io/load_file)
   - [Save session](https://codesandbox.io/p/sandbox/github/molstar/example-gallery/master/io/save_session)