Tweaks (#174)

* Dockerfile casing

* Dockerfile casing

* Dockerfile casing

* Add a button to enable download of docking configurations

* Add pocket center to the pocket properties

* Add residues to the pocket details

Author: luk27official

administration/Dockerfile

@@ -2,7 +2,7 @@
 # java-tools
 #
 
-FROM debian:bookworm-20231009 as java-tools
+FROM debian:bookworm-20231009 AS java-tools
 
 RUN apt-get update \
   && apt-get -y --no-install-recommends install openjdk-17-jdk

executor-docking/run_task.py

@@ -194,6 +194,9 @@ def execute_directory_task(docking_directory: str, taskId: int):
             stream.write(result_json)
         finally:
             stream.flush()
+
+    # copy the docking parameters file to the public directory
+    shutil.copy(os.path.join(docking_directory, str(taskId), "docking_parameters.json"), os.path.join(docking_directory, str(taskId), "public", "docking_parameters.json"))
 
     # update the status file, reload it first to make sure we don't overwrite any changes
     status = _load_json(status_file)

executor-p2rank/Dockerfile

@@ -2,7 +2,7 @@
 # java-tools
 #
 
-FROM debian:bookworm-20231009 as java-tools
+FROM debian:bookworm-20231009 AS java-tools
 
 RUN apt-get update \
   && apt-get -y --no-install-recommends install openjdk-17-jdk
@@ -21,7 +21,7 @@ RUN chmod +x ./gradlew && ./gradlew installDist \
 # * /opt/alignment-based-conservation-dependencies
 #
 
-FROM debian:bookworm-20231009 as alignment-based-conservation
+FROM debian:bookworm-20231009 AS alignment-based-conservation
 
 RUN apt-get update \
   && apt-get -y --no-install-recommends install \
@@ -67,7 +67,7 @@ RUN chmod a+x /opt/alignment-based-conservation/conservation_alignment_based.py
 # * /opt/hmm-based-conservation-dependencies
 #
 
-FROM debian:bookworm-20231009 as hmm-based-conservation
+FROM debian:bookworm-20231009 AS hmm-based-conservation
 
 RUN apt-get update \
   && apt-get -y --no-install-recommends install \

frontend/client/viewer/components/data-table-row-details.tsx

@@ -39,6 +39,14 @@ export default function DataTableRowDetails(props: { pocket: PocketData; setTab:
             name: "Number of residues",
             value: pocket.residues.length
         },
+        {
+            name: "Pocket center",
+            value: `(${pocket.center[0]}, ${pocket.center[1]}, ${pocket.center[2]})`
+        },
+        {
+            name: "Residues",
+            value: pocket.residues.join(", ")
+        },
     ];
 
     if (pocket.avgAlphaFold) shownProperties.push({

frontend/client/visualize/docking/main.tsx

@@ -218,10 +218,11 @@ async function createMolstarViewer() {
 export async function getDockingTaskContent(id: string, database: string, hash: string, structureName: string): Promise<DockingTaskProps> {
     const apiEndpoint = getApiEndpoint(database, id, "docking");
     const response = await fetch(`${apiEndpoint}/${hash}/public/out_vina.pdbqt`).then(res => res.text()).catch(err => console.log(err));
+    const dockingConfigurationURL = `${apiEndpoint}/${hash}/public/docking_parameters.json`;
 
     if (response === undefined) {
-        return { ligandPDBQT: "Error", hash: hash, id: id, database: database, structureName: structureName };
+        return { ligandPDBQT: "Error", hash: hash, id: id, database: database, structureName: structureName, dockingConfigurationURL: dockingConfigurationURL };
     }
 
-    return { ligandPDBQT: response, hash: hash, id: id, database: database, structureName: structureName };
+    return { ligandPDBQT: response, hash: hash, id: id, database: database, structureName: structureName, dockingConfigurationURL: dockingConfigurationURL };
 }

frontend/client/visualize/docking/right-panel.tsx

@@ -65,7 +65,7 @@ function Row(props: { row: Model; models: number[]; handleClick: (models: number
 }
 
 export function DockingTaskRightPanel({ pdbqtModels, dp, plugin, ligandRepresentations }: { pdbqtModels: Model[], dp: DockingTaskProps, plugin: PluginUIContext, ligandRepresentations: StateObjectSelector[]; }) {
-    const handleDownload = () => {
+    const handleResultDownload = () => {
         const element = document.createElement("a");
         const file = new Blob([dp.ligandPDBQT], { type: 'text/plain' });
         element.href = URL.createObjectURL(file);
@@ -74,6 +74,21 @@ export function DockingTaskRightPanel({ pdbqtModels, dp, plugin, ligandRepresent
         element.click();
     };
 
+    const handleConfigurationDownload = async () => {
+        await fetch(dp.dockingConfigurationURL)
+            .then(response => response.text())
+            .then(content => {
+                const element = document.createElement("a");
+                const file = new Blob([content], { type: 'text/plain' });
+                element.href = URL.createObjectURL(file);
+                element.download = `docking-configuration-${new Date().toISOString()}.json`;
+                document.body.appendChild(element);
+                element.click();
+                document.body.removeChild(element);
+            })
+            .catch(error => console.error("Error downloading docking configuration:", error));
+    };
+
     const [models, setModels] = React.useState<number[]>([1]);
 
     const handleClick = (model: number) => {
@@ -148,7 +163,9 @@ export function DockingTaskRightPanel({ pdbqtModels, dp, plugin, ligandRepresent
                     </TableBody>
                 </Table>
             </TableContainer>
-            <Button style={{ marginTop: "1em" }} variant="contained" onClick={handleDownload}>Download results</Button>
+            <Button style={{ marginTop: "1em" }} variant="contained" onClick={handleConfigurationDownload}>Download docking configuration</Button>
+            &nbsp;
+            <Button style={{ marginTop: "1em" }} variant="contained" onClick={handleResultDownload}>Download results</Button>
         </>
     );
 }

frontend/client/visualize/docking/types.ts

@@ -4,6 +4,7 @@ export interface DockingTaskProps {
     id: string;
     hash: string;
     structureName: string;
+    dockingConfigurationURL: string;
 }
 
 export type Hetatm = {

gateway/Dockerfile

@@ -25,7 +25,7 @@ RUN npm run build
 #
 # Prepare passwords.
 #
-FROM debian:bookworm-20231009 as htpasswd
+FROM debian:bookworm-20231009 AS htpasswd
 
 RUN apt-get update && apt-get -y install apache2-utils