Merge pull request #121 from biggraph/feat/bionemo-nims

lynxkite-app/web/package-lock.json

@@ -18,11 +18,13 @@
         "@syncedstore/react": "^0.6.0",
         "@types/node": "^22.10.1",
         "@xyflow/react": "^12.3.5",
+        "3dmol": "^2.4.2",
         "axios": "^1.8.2",
         "daisyui": "^4.12.20",
         "echarts": "^5.5.1",
         "fuse.js": "^7.0.0",
         "json-schema-to-typescript": "^15.0.3",
+        "monaco-editor": "^0.52.2",
         "react": "^18.3.1",
         "react-dom": "^18.3.1",
         "react-markdown": "^9.0.1",
@@ -2366,6 +2368,22 @@
         "d3-zoom": "^3.0.0"
       }
     },
+    "node_modules/3dmol": {
+      "version": "2.4.2",
+      "resolved": "https://registry.npmjs.org/3dmol/-/3dmol-2.4.2.tgz",
+      "integrity": "sha512-7R6uFaF5++s9EpO+R0a3bs6igi5idI+sgrVhtozaZlOGHg6oourYkAlAwYxWRaeBGlNcAd+oEIhbhJYhNxGyZA==",
+      "license": "BSD-3-Clause",
+      "dependencies": {
+        "iobuffer": "^5.3.1",
+        "netcdfjs": "^3.0.0",
+        "pako": "^2.1.0",
+        "upng-js": "^2.1.0"
+      },
+      "engines": {
+        "node": ">=16.16.0",
+        "npm": ">=8.11"
+      }
+    },
     "node_modules/abstract-leveldown": {
       "version": "6.2.3",
       "resolved": "https://registry.npmjs.org/abstract-leveldown/-/abstract-leveldown-6.2.3.tgz",
@@ -4187,6 +4205,12 @@
       "integrity": "sha512-0aO8FkhNZlj/ZIbNi7Lxxr12obT7cL1moPfE4tg1LkX7LlLfC6DeX4l2ZEud1ukP9jNQyNnfzQVqwbwmAATY4Q==",
       "license": "MIT"
     },
+    "node_modules/iobuffer": {
+      "version": "5.4.0",
+      "resolved": "https://registry.npmjs.org/iobuffer/-/iobuffer-5.4.0.tgz",
+      "integrity": "sha512-DRebOWuqDvxunfkNJAlc3IzWIPD5xVxwUNbHr7xKB8E6aLJxIPfNX3CoMJghcFjpv6RWQsrcJbghtEwSPoJqMA==",
+      "license": "MIT"
+    },
     "node_modules/is-alphabetical": {
       "version": "2.0.1",
       "resolved": "https://registry.npmjs.org/is-alphabetical/-/is-alphabetical-2.0.1.tgz",
@@ -5465,8 +5489,7 @@
       "version": "0.52.2",
       "resolved": "https://registry.npmjs.org/monaco-editor/-/monaco-editor-0.52.2.tgz",
       "integrity": "sha512-GEQWEZmfkOGLdd3XK8ryrfWz3AIP8YymVXiPHEdewrUq7mh0qrKrfHLNCXcbB6sTnMLnOZ3ztSiKcciFUkIJwQ==",
-      "license": "MIT",
-      "peer": true
+      "license": "MIT"
     },
     "node_modules/ms": {
       "version": "2.1.3",
@@ -5518,6 +5541,15 @@
       "dev": true,
       "license": "MIT"
     },
+    "node_modules/netcdfjs": {
+      "version": "3.0.0",
+      "resolved": "https://registry.npmjs.org/netcdfjs/-/netcdfjs-3.0.0.tgz",
+      "integrity": "sha512-LOvT8KkC308qtpUkcBPiCMBtii7ZQCN6LxcVheWgyUeZ6DQWcpSRFV9dcVXLj/2eHZ/bre9tV5HTH4Sf93vrFw==",
+      "license": "MIT",
+      "dependencies": {
+        "iobuffer": "^5.3.2"
+      }
+    },
     "node_modules/no-case": {
       "version": "3.0.4",
       "resolved": "https://registry.npmjs.org/no-case/-/no-case-3.0.4.tgz",
@@ -5649,6 +5681,12 @@
       "integrity": "sha512-g4+387DXDKlZzHkP+9FLt8yKj8+/3tOkPv7DVTJGGRm00RkEWgqbFstX1mXJ4M0VDYhUqsTOiISqNOJnhAu3PQ==",
       "license": "MIT"
     },
+    "node_modules/pako": {
+      "version": "2.1.0",
+      "resolved": "https://registry.npmjs.org/pako/-/pako-2.1.0.tgz",
+      "integrity": "sha512-w+eufiZ1WuJYgPXbV/PO3NCMEc3xqylkKHzp8bxp1uW4qaSNQUkwmLLEc3kKsfz8lpV1F8Ht3U1Cm+9Srog2ug==",
+      "license": "(MIT AND Zlib)"
+    },
     "node_modules/parent-module": {
       "version": "1.0.1",
       "resolved": "https://registry.npmjs.org/parent-module/-/parent-module-1.0.1.tgz",
@@ -7107,6 +7145,21 @@
         "browserslist": ">= 4.21.0"
       }
     },
+    "node_modules/upng-js": {
+      "version": "2.1.0",
+      "resolved": "https://registry.npmjs.org/upng-js/-/upng-js-2.1.0.tgz",
+      "integrity": "sha512-d3xzZzpMP64YkjP5pr8gNyvBt7dLk/uGI67EctzDuVp4lCZyVMo0aJO6l/VDlgbInJYDY6cnClLoBp29eKWI6g==",
+      "license": "MIT",
+      "dependencies": {
+        "pako": "^1.0.5"
+      }
+    },
+    "node_modules/upng-js/node_modules/pako": {
+      "version": "1.0.11",
+      "resolved": "https://registry.npmjs.org/pako/-/pako-1.0.11.tgz",
+      "integrity": "sha512-4hLB8Py4zZce5s4yd9XzopqwVv/yGNhV1Bl8NTmCq1763HeK2+EwVTv+leGeL13Dnh2wfbqowVPXCIO0z4taYw==",
+      "license": "(MIT AND Zlib)"
+    },
     "node_modules/uri-js": {
       "version": "4.4.1",
       "resolved": "https://registry.npmjs.org/uri-js/-/uri-js-4.4.1.tgz",

lynxkite-app/web/package.json

@@ -21,11 +21,13 @@
     "@syncedstore/react": "^0.6.0",
     "@types/node": "^22.10.1",
     "@xyflow/react": "^12.3.5",
+    "3dmol": "^2.4.2",
     "axios": "^1.8.2",
     "daisyui": "^4.12.20",
     "echarts": "^5.5.1",
     "fuse.js": "^7.0.0",
     "json-schema-to-typescript": "^15.0.3",
+    "monaco-editor": "^0.52.2",
     "react": "^18.3.1",
     "react-dom": "^18.3.1",
     "react-markdown": "^9.0.1",

lynxkite-app/web/src/workspace/Workspace.tsx

@@ -37,6 +37,7 @@ import { LynxKiteState } from "./LynxKiteState";
 import NodeSearch, { type OpsOp, type Catalog, type Catalogs } from "./NodeSearch.tsx";
 import NodeWithGraphCreationView from "./nodes/GraphCreationNode.tsx";
 import NodeWithImage from "./nodes/NodeWithImage.tsx";
+import NodeWithMolecule from "./nodes/NodeWithMolecule.tsx";
 import NodeWithParams from "./nodes/NodeWithParams";
 import NodeWithTableView from "./nodes/NodeWithTableView.tsx";
 import NodeWithVisualization from "./nodes/NodeWithVisualization.tsx";
@@ -175,6 +176,7 @@ function LynxKiteFlow() {
       image: NodeWithImage,
       table_view: NodeWithTableView,
       graph_creation_view: NodeWithGraphCreationView,
+      molecule: NodeWithMolecule,
     }),
     [],
   );

lynxkite-app/web/src/workspace/nodes/NodeWithMolecule.tsx

@@ -0,0 +1,73 @@
+import React, { useEffect, type CSSProperties } from "react";
+import NodeWithParams from "./NodeWithParams";
+
+const NodeWithMolecule = (props: any) => {
+  const containerRef = React.useRef<HTMLDivElement>(null);
+  const viewerRef = React.useRef<any>(null);
+
+  useEffect(() => {
+    const config = props.data?.display?.value;
+    if (!config || !containerRef.current) return;
+    async function run() {
+      const $3Dmol = await import("3dmol");
+
+      try {
+        // Initialize viewer only once
+        if (!viewerRef.current) {
+          viewerRef.current = $3Dmol.createViewer(containerRef.current, {
+            backgroundColor: "white",
+          });
+        }
+
+        const viewer = viewerRef.current;
+
+        // Clear previous models
+        viewer.clear();
+
+        // Add new model and style it
+        viewer.addModel(config.data, config.format);
+        viewer.setStyle({}, { stick: {} });
+        viewer.zoomTo();
+        viewer.render();
+      } catch (error) {
+        console.error("Error rendering 3D molecule:", error);
+      }
+    }
+    run();
+    const resizeObserver = new ResizeObserver(() => {
+      viewerRef.current?.resize();
+    });
+
+    const observed = containerRef.current;
+    resizeObserver.observe(observed);
+    return () => {
+      resizeObserver.unobserve(observed);
+      if (viewerRef.current) {
+        viewerRef.current.clear();
+      }
+    };
+  }, [props.data?.display?.value]);
+
+  const nodeStyle: CSSProperties = {
+    display: "flex",
+    flexDirection: "column",
+    height: "100%",
+  };
+
+  const vizStyle: CSSProperties = {
+    flex: 1,
+    minHeight: "300px",
+    border: "1px solid #ddd",
+    borderRadius: "4px",
+    overflow: "hidden",
+    position: "relative",
+  };
+
+  return (
+    <NodeWithParams nodeStyle={nodeStyle} collapsed {...props}>
+      <div style={vizStyle} ref={containerRef} />
+    </NodeWithParams>
+  );
+};
+
+export default NodeWithMolecule;

lynxkite-core/src/lynxkite/core/ops.py

@@ -180,6 +180,7 @@ class Op(BaseConfig):
                 "table_view",
                 "graph_creation_view",
                 "image",
+                "molecule",
             ]:
                 # If the operation is some kind of visualization, we use the output as the
                 # value to display by default.