rename NodeWithPy3DMol to NodeWithMolecule

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

@@ -35,8 +35,8 @@ 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 NodeWithPy3Dmol from "./nodes/NodeWithPy3DMol.tsx";
 import NodeWithTableView from "./nodes/NodeWithTableView.tsx";
 import NodeWithVisualization from "./nodes/NodeWithVisualization.tsx";
 
@@ -174,7 +174,7 @@ function LynxKiteFlow() {
       image: NodeWithImage,
       table_view: NodeWithTableView,
       graph_creation_view: NodeWithGraphCreationView,
-      py3dmol: NodeWithPy3Dmol,
+      molecule: NodeWithMolecule,
     }),
     [],
   );

lynxkite-app/web/src/workspace/nodes/{NodeWithPy3DMol.tsx → NodeWithMolecule.tsx}

@@ -1,8 +1,8 @@
-import React, { useEffect } from "react";
+import React, { useEffect, type CSSProperties } from "react";
 import NodeWithParams from "./NodeWithParams";
 const $3Dmol = await import("3dmol");
 
-const NodeWithPy3Dmol = (props: any) => {
+const NodeWithMolecule = (props: any) => {
   const containerRef = React.useRef<HTMLDivElement>(null);
   const viewerRef = React.useRef<any>(null);
 
@@ -47,8 +47,13 @@ const NodeWithPy3Dmol = (props: any) => {
     };
   }, [props.data?.display?.value]);
 
-  const nodeStyle = { display: "flex", flexDirection: "column", height: "100%" };
-  const vizStyle = {
+  const nodeStyle: CSSProperties = {
+    display: "flex",
+    flexDirection: "column",
+    height: "100%",
+  };
+
+  const vizStyle: CSSProperties = {
     flex: 1,
     minHeight: "300px",
     border: "1px solid #ddd",
@@ -64,4 +69,4 @@ const NodeWithPy3Dmol = (props: any) => {
   );
 };
 
-export default NodeWithPy3Dmol;
+export default NodeWithMolecule;

lynxkite-bio/src/lynxkite_bio/nims.py

@@ -115,7 +115,7 @@ async def query_openfold2(
     return bundle
 
 
-@op("View molecule", view="py3dmol")
+@op("View molecule", view="molecule")
 def view_molecule(
     bundle: Bundle,
     *,

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

@@ -180,7 +180,7 @@ class Op(BaseConfig):
                 "table_view",
                 "graph_creation_view",
                 "image",
-                "py3dmol",
+                "molecule",
             ]:
                 # If the operation is some kind of visualization, we use the output as the
                 # value to display by default.