From da5ee05c79e0ab09ab6b66e1a9307aab38fef93a Mon Sep 17 00:00:00 2001
From: ansengarvin <45224464+ansengarvin@users.noreply.github.com>
Date: Mon, 15 Apr 2024 13:11:55 -0700
Subject: [PATCH] Load Foldseek Data on TM Align Compare Page (#237)

* Changed directory name in delete_all py script from string to os.join so it works on windows, and hopefully universally.

* TM Align page now computes Foldseek data for compare protein

* Changed loading text

* Ruff reformat
---
 backend/src/api/search.py                     | 39 +++++++++++++++++
 backend/src/data/pdbAlphaFold/.gitignore      |  2 +-
 frontend/src/lib/openapi/core/ApiError.ts     |  2 +-
 .../src/lib/openapi/core/ApiRequestOptions.ts |  2 +-
 frontend/src/lib/openapi/core/ApiResult.ts    |  2 +-
 .../src/lib/openapi/core/CancelablePromise.ts |  8 ++--
 frontend/src/lib/openapi/core/OpenAPI.ts      |  2 +-
 frontend/src/lib/openapi/core/request.ts      |  4 +-
 frontend/src/lib/openapi/index.ts             |  2 +-
 frontend/src/lib/openapi/models/EditBody.ts   |  2 +-
 .../lib/openapi/models/HTTPValidationError.ts |  2 +-
 frontend/src/lib/openapi/models/LoginBody.ts  |  2 +-
 .../src/lib/openapi/models/LoginResponse.ts   |  2 +-
 .../lib/openapi/models/ProteinEditSuccess.ts  |  2 +-
 .../src/lib/openapi/models/ProteinEntry.ts    |  2 +-
 .../src/lib/openapi/models/RangeFilter.ts     |  2 +-
 .../lib/openapi/models/SearchProteinsBody.ts  |  2 +-
 .../openapi/models/SearchProteinsResults.ts   |  2 +-
 .../src/lib/openapi/models/SimilarProtein.ts  |  2 +-
 frontend/src/lib/openapi/models/Tutorial.ts   |  2 +-
 .../src/lib/openapi/models/TutorialEdit.ts    |  2 +-
 .../src/lib/openapi/models/TutorialUpload.ts  |  2 +-
 frontend/src/lib/openapi/models/UploadBody.ts |  2 +-
 .../src/lib/openapi/models/UploadError.ts     |  2 +-
 .../src/lib/openapi/models/UploadPNGBody.ts   |  2 +-
 .../src/lib/openapi/models/ValidationError.ts |  2 +-
 .../lib/openapi/services/DefaultService.ts    | 25 ++++++++++-
 frontend/src/routes/Align.svelte              | 43 ++++++++++++++++++-
 galaxy/delete_all.py                          |  2 +-
 29 files changed, 135 insertions(+), 32 deletions(-)

diff --git a/backend/src/api/search.py b/backend/src/api/search.py
index b634246a..7846fb30 100644
--- a/backend/src/api/search.py
+++ b/backend/src/api/search.py
@@ -229,3 +229,42 @@ def search_venome_similar(protein_name: str):
         raise HTTPException(500, "Error getting protein descriptions")
 
     return formatted
+
+
+@router.get(
+    "/search/venome/similar/{protein_name:str}/{protein_compare:str}",
+    response_model=SimilarProtein,
+)
+def search_venome_similar_compare(protein_name: str, protein_compare: str):
+    target = stored_pdb_file_name(protein_compare)
+    # ignore the first since it's itself as the most similar
+    try:
+        similar = easy_search(
+            stored_pdb_file_name(protein_name),
+            target,
+            out_format="target,prob,evalue,qstart,qend",
+        )  # qend,qstart refer to alignment
+        formatted = [
+            SimilarProtein(
+                name=name.rstrip(".pdb"),
+                prob=prob,
+                evalue=evalue,
+                qstart=qstart,
+                qend=qend,
+                alntmscore=0,
+            )
+            for [name, prob, evalue, qstart, qend] in similar
+        ]
+    except Exception:
+        raise HTTPException(404, "Error in 'foldseek easy-search' command")
+
+    try:
+        # populate protein descriptions for the similar proteins
+        descriptions = get_descriptions([s.name for s in formatted])
+        if descriptions is not None:
+            for f, d in zip(formatted, descriptions):
+                f.description = d
+    except Exception:
+        raise HTTPException(500, "Error getting protein descriptions")
+
+    return formatted[0]
diff --git a/backend/src/data/pdbAlphaFold/.gitignore b/backend/src/data/pdbAlphaFold/.gitignore
index eadd157d..2da6d9aa 100644
--- a/backend/src/data/pdbAlphaFold/.gitignore
+++ b/backend/src/data/pdbAlphaFold/.gitignore
@@ -1 +1 @@
-*.pdb
+*.pdb 
diff --git a/frontend/src/lib/openapi/core/ApiError.ts b/frontend/src/lib/openapi/core/ApiError.ts
index d6b8fcc3..ec7b16af 100644
--- a/frontend/src/lib/openapi/core/ApiError.ts
+++ b/frontend/src/lib/openapi/core/ApiError.ts
@@ -1,4 +1,4 @@
-/* generated using openapi-typescript-codegen -- do no edit */
+/* generated using openapi-typescript-codegen -- do not edit */
 /* istanbul ignore file */
 /* tslint:disable */
 /* eslint-disable */
diff --git a/frontend/src/lib/openapi/core/ApiRequestOptions.ts b/frontend/src/lib/openapi/core/ApiRequestOptions.ts
index c19adcc9..93143c3c 100644
--- a/frontend/src/lib/openapi/core/ApiRequestOptions.ts
+++ b/frontend/src/lib/openapi/core/ApiRequestOptions.ts
@@ -1,4 +1,4 @@
-/* generated using openapi-typescript-codegen -- do no edit */
+/* generated using openapi-typescript-codegen -- do not edit */
 /* istanbul ignore file */
 /* tslint:disable */
 /* eslint-disable */
diff --git a/frontend/src/lib/openapi/core/ApiResult.ts b/frontend/src/lib/openapi/core/ApiResult.ts
index ad8fef2b..ee1126e2 100644
--- a/frontend/src/lib/openapi/core/ApiResult.ts
+++ b/frontend/src/lib/openapi/core/ApiResult.ts
@@ -1,4 +1,4 @@
-/* generated using openapi-typescript-codegen -- do no edit */
+/* generated using openapi-typescript-codegen -- do not edit */
 /* istanbul ignore file */
 /* tslint:disable */
 /* eslint-disable */
diff --git a/frontend/src/lib/openapi/core/CancelablePromise.ts b/frontend/src/lib/openapi/core/CancelablePromise.ts
index eb02246c..d70de929 100644
--- a/frontend/src/lib/openapi/core/CancelablePromise.ts
+++ b/frontend/src/lib/openapi/core/CancelablePromise.ts
@@ -1,4 +1,4 @@
-/* generated using openapi-typescript-codegen -- do no edit */
+/* generated using openapi-typescript-codegen -- do not edit */
 /* istanbul ignore file */
 /* tslint:disable */
 /* eslint-disable */
@@ -85,9 +85,9 @@ export class CancelablePromise<T> implements Promise<T> {
         });
     }
 
-     get [Symbol.toStringTag]() {
-            return "Cancellable Promise";
-     }
+    get [Symbol.toStringTag]() {
+        return "Cancellable Promise";
+    }
 
     public then<TResult1 = T, TResult2 = never>(
         onFulfilled?: ((value: T) => TResult1 | PromiseLike<TResult1>) | null,
diff --git a/frontend/src/lib/openapi/core/OpenAPI.ts b/frontend/src/lib/openapi/core/OpenAPI.ts
index e357bb22..0cfae5db 100644
--- a/frontend/src/lib/openapi/core/OpenAPI.ts
+++ b/frontend/src/lib/openapi/core/OpenAPI.ts
@@ -1,4 +1,4 @@
-/* generated using openapi-typescript-codegen -- do no edit */
+/* generated using openapi-typescript-codegen -- do not edit */
 /* istanbul ignore file */
 /* tslint:disable */
 /* eslint-disable */
diff --git a/frontend/src/lib/openapi/core/request.ts b/frontend/src/lib/openapi/core/request.ts
index 2201a0e6..f83d7119 100644
--- a/frontend/src/lib/openapi/core/request.ts
+++ b/frontend/src/lib/openapi/core/request.ts
@@ -1,4 +1,4 @@
-/* generated using openapi-typescript-codegen -- do no edit */
+/* generated using openapi-typescript-codegen -- do not edit */
 /* istanbul ignore file */
 /* tslint:disable */
 /* eslint-disable */
@@ -164,7 +164,7 @@ export const getHeaders = async (config: OpenAPIConfig, options: ApiRequestOptio
         headers['Authorization'] = `Basic ${credentials}`;
     }
 
-    if (options.body) {
+    if (options.body !== undefined) {
         if (options.mediaType) {
             headers['Content-Type'] = options.mediaType;
         } else if (isBlob(options.body)) {
diff --git a/frontend/src/lib/openapi/index.ts b/frontend/src/lib/openapi/index.ts
index 8852fd30..44a2b797 100644
--- a/frontend/src/lib/openapi/index.ts
+++ b/frontend/src/lib/openapi/index.ts
@@ -1,4 +1,4 @@
-/* generated using openapi-typescript-codegen -- do no edit */
+/* generated using openapi-typescript-codegen -- do not edit */
 /* istanbul ignore file */
 /* tslint:disable */
 /* eslint-disable */
diff --git a/frontend/src/lib/openapi/models/EditBody.ts b/frontend/src/lib/openapi/models/EditBody.ts
index d7c56b56..68f8ef07 100644
--- a/frontend/src/lib/openapi/models/EditBody.ts
+++ b/frontend/src/lib/openapi/models/EditBody.ts
@@ -1,4 +1,4 @@
-/* generated using openapi-typescript-codegen -- do no edit */
+/* generated using openapi-typescript-codegen -- do not edit */
 /* istanbul ignore file */
 /* tslint:disable */
 /* eslint-disable */
diff --git a/frontend/src/lib/openapi/models/HTTPValidationError.ts b/frontend/src/lib/openapi/models/HTTPValidationError.ts
index 892e4257..f9b1a79e 100644
--- a/frontend/src/lib/openapi/models/HTTPValidationError.ts
+++ b/frontend/src/lib/openapi/models/HTTPValidationError.ts
@@ -1,4 +1,4 @@
-/* generated using openapi-typescript-codegen -- do no edit */
+/* generated using openapi-typescript-codegen -- do not edit */
 /* istanbul ignore file */
 /* tslint:disable */
 /* eslint-disable */
diff --git a/frontend/src/lib/openapi/models/LoginBody.ts b/frontend/src/lib/openapi/models/LoginBody.ts
index 5dc8041c..ff5c4ff6 100644
--- a/frontend/src/lib/openapi/models/LoginBody.ts
+++ b/frontend/src/lib/openapi/models/LoginBody.ts
@@ -1,4 +1,4 @@
-/* generated using openapi-typescript-codegen -- do no edit */
+/* generated using openapi-typescript-codegen -- do not edit */
 /* istanbul ignore file */
 /* tslint:disable */
 /* eslint-disable */
diff --git a/frontend/src/lib/openapi/models/LoginResponse.ts b/frontend/src/lib/openapi/models/LoginResponse.ts
index 2f1faac8..1b25684a 100644
--- a/frontend/src/lib/openapi/models/LoginResponse.ts
+++ b/frontend/src/lib/openapi/models/LoginResponse.ts
@@ -1,4 +1,4 @@
-/* generated using openapi-typescript-codegen -- do no edit */
+/* generated using openapi-typescript-codegen -- do not edit */
 /* istanbul ignore file */
 /* tslint:disable */
 /* eslint-disable */
diff --git a/frontend/src/lib/openapi/models/ProteinEditSuccess.ts b/frontend/src/lib/openapi/models/ProteinEditSuccess.ts
index e1a4aee7..da3d0969 100644
--- a/frontend/src/lib/openapi/models/ProteinEditSuccess.ts
+++ b/frontend/src/lib/openapi/models/ProteinEditSuccess.ts
@@ -1,4 +1,4 @@
-/* generated using openapi-typescript-codegen -- do no edit */
+/* generated using openapi-typescript-codegen -- do not edit */
 /* istanbul ignore file */
 /* tslint:disable */
 /* eslint-disable */
diff --git a/frontend/src/lib/openapi/models/ProteinEntry.ts b/frontend/src/lib/openapi/models/ProteinEntry.ts
index 02779401..6c12f6df 100644
--- a/frontend/src/lib/openapi/models/ProteinEntry.ts
+++ b/frontend/src/lib/openapi/models/ProteinEntry.ts
@@ -1,4 +1,4 @@
-/* generated using openapi-typescript-codegen -- do no edit */
+/* generated using openapi-typescript-codegen -- do not edit */
 /* istanbul ignore file */
 /* tslint:disable */
 /* eslint-disable */
diff --git a/frontend/src/lib/openapi/models/RangeFilter.ts b/frontend/src/lib/openapi/models/RangeFilter.ts
index 13a16880..f7cab08b 100644
--- a/frontend/src/lib/openapi/models/RangeFilter.ts
+++ b/frontend/src/lib/openapi/models/RangeFilter.ts
@@ -1,4 +1,4 @@
-/* generated using openapi-typescript-codegen -- do no edit */
+/* generated using openapi-typescript-codegen -- do not edit */
 /* istanbul ignore file */
 /* tslint:disable */
 /* eslint-disable */
diff --git a/frontend/src/lib/openapi/models/SearchProteinsBody.ts b/frontend/src/lib/openapi/models/SearchProteinsBody.ts
index d739124f..1e6dc7a1 100644
--- a/frontend/src/lib/openapi/models/SearchProteinsBody.ts
+++ b/frontend/src/lib/openapi/models/SearchProteinsBody.ts
@@ -1,4 +1,4 @@
-/* generated using openapi-typescript-codegen -- do no edit */
+/* generated using openapi-typescript-codegen -- do not edit */
 /* istanbul ignore file */
 /* tslint:disable */
 /* eslint-disable */
diff --git a/frontend/src/lib/openapi/models/SearchProteinsResults.ts b/frontend/src/lib/openapi/models/SearchProteinsResults.ts
index 76e1e22c..3ab92cf9 100644
--- a/frontend/src/lib/openapi/models/SearchProteinsResults.ts
+++ b/frontend/src/lib/openapi/models/SearchProteinsResults.ts
@@ -1,4 +1,4 @@
-/* generated using openapi-typescript-codegen -- do no edit */
+/* generated using openapi-typescript-codegen -- do not edit */
 /* istanbul ignore file */
 /* tslint:disable */
 /* eslint-disable */
diff --git a/frontend/src/lib/openapi/models/SimilarProtein.ts b/frontend/src/lib/openapi/models/SimilarProtein.ts
index 16113600..340f9abc 100644
--- a/frontend/src/lib/openapi/models/SimilarProtein.ts
+++ b/frontend/src/lib/openapi/models/SimilarProtein.ts
@@ -1,4 +1,4 @@
-/* generated using openapi-typescript-codegen -- do no edit */
+/* generated using openapi-typescript-codegen -- do not edit */
 /* istanbul ignore file */
 /* tslint:disable */
 /* eslint-disable */
diff --git a/frontend/src/lib/openapi/models/Tutorial.ts b/frontend/src/lib/openapi/models/Tutorial.ts
index 12717ea8..e93bb9fd 100644
--- a/frontend/src/lib/openapi/models/Tutorial.ts
+++ b/frontend/src/lib/openapi/models/Tutorial.ts
@@ -1,4 +1,4 @@
-/* generated using openapi-typescript-codegen -- do no edit */
+/* generated using openapi-typescript-codegen -- do not edit */
 /* istanbul ignore file */
 /* tslint:disable */
 /* eslint-disable */
diff --git a/frontend/src/lib/openapi/models/TutorialEdit.ts b/frontend/src/lib/openapi/models/TutorialEdit.ts
index b180c057..b92d939e 100644
--- a/frontend/src/lib/openapi/models/TutorialEdit.ts
+++ b/frontend/src/lib/openapi/models/TutorialEdit.ts
@@ -1,4 +1,4 @@
-/* generated using openapi-typescript-codegen -- do no edit */
+/* generated using openapi-typescript-codegen -- do not edit */
 /* istanbul ignore file */
 /* tslint:disable */
 /* eslint-disable */
diff --git a/frontend/src/lib/openapi/models/TutorialUpload.ts b/frontend/src/lib/openapi/models/TutorialUpload.ts
index 74bdcacd..87497606 100644
--- a/frontend/src/lib/openapi/models/TutorialUpload.ts
+++ b/frontend/src/lib/openapi/models/TutorialUpload.ts
@@ -1,4 +1,4 @@
-/* generated using openapi-typescript-codegen -- do no edit */
+/* generated using openapi-typescript-codegen -- do not edit */
 /* istanbul ignore file */
 /* tslint:disable */
 /* eslint-disable */
diff --git a/frontend/src/lib/openapi/models/UploadBody.ts b/frontend/src/lib/openapi/models/UploadBody.ts
index 9d05cbcd..6b0884f3 100644
--- a/frontend/src/lib/openapi/models/UploadBody.ts
+++ b/frontend/src/lib/openapi/models/UploadBody.ts
@@ -1,4 +1,4 @@
-/* generated using openapi-typescript-codegen -- do no edit */
+/* generated using openapi-typescript-codegen -- do not edit */
 /* istanbul ignore file */
 /* tslint:disable */
 /* eslint-disable */
diff --git a/frontend/src/lib/openapi/models/UploadError.ts b/frontend/src/lib/openapi/models/UploadError.ts
index 5240304b..9a91db09 100644
--- a/frontend/src/lib/openapi/models/UploadError.ts
+++ b/frontend/src/lib/openapi/models/UploadError.ts
@@ -1,4 +1,4 @@
-/* generated using openapi-typescript-codegen -- do no edit */
+/* generated using openapi-typescript-codegen -- do not edit */
 /* istanbul ignore file */
 /* tslint:disable */
 /* eslint-disable */
diff --git a/frontend/src/lib/openapi/models/UploadPNGBody.ts b/frontend/src/lib/openapi/models/UploadPNGBody.ts
index c9e295c5..44dcfa5c 100644
--- a/frontend/src/lib/openapi/models/UploadPNGBody.ts
+++ b/frontend/src/lib/openapi/models/UploadPNGBody.ts
@@ -1,4 +1,4 @@
-/* generated using openapi-typescript-codegen -- do no edit */
+/* generated using openapi-typescript-codegen -- do not edit */
 /* istanbul ignore file */
 /* tslint:disable */
 /* eslint-disable */
diff --git a/frontend/src/lib/openapi/models/ValidationError.ts b/frontend/src/lib/openapi/models/ValidationError.ts
index f2ff49a2..aaf1c921 100644
--- a/frontend/src/lib/openapi/models/ValidationError.ts
+++ b/frontend/src/lib/openapi/models/ValidationError.ts
@@ -1,4 +1,4 @@
-/* generated using openapi-typescript-codegen -- do no edit */
+/* generated using openapi-typescript-codegen -- do not edit */
 /* istanbul ignore file */
 /* tslint:disable */
 /* eslint-disable */
diff --git a/frontend/src/lib/openapi/services/DefaultService.ts b/frontend/src/lib/openapi/services/DefaultService.ts
index f6a6e18b..1114558e 100644
--- a/frontend/src/lib/openapi/services/DefaultService.ts
+++ b/frontend/src/lib/openapi/services/DefaultService.ts
@@ -1,4 +1,4 @@
-/* generated using openapi-typescript-codegen -- do no edit */
+/* generated using openapi-typescript-codegen -- do not edit */
 /* istanbul ignore file */
 /* tslint:disable */
 /* eslint-disable */
@@ -112,6 +112,29 @@ export class DefaultService {
             },
         });
     }
+    /**
+     * Search Venome Similar Compare
+     * @param proteinName
+     * @param proteinCompare
+     * @returns SimilarProtein Successful Response
+     * @throws ApiError
+     */
+    public static searchVenomeSimilarCompare(
+        proteinName: string,
+        proteinCompare: string,
+    ): CancelablePromise<SimilarProtein> {
+        return __request(OpenAPI, {
+            method: 'GET',
+            url: '/search/venome/similar/{protein_name}/{protein_compare}',
+            path: {
+                'protein_name': proteinName,
+                'protein_compare': proteinCompare,
+            },
+            errors: {
+                422: `Validation Error`,
+            },
+        });
+    }
     /**
      * Get Pdb File
      * @param proteinName
diff --git a/frontend/src/routes/Align.svelte b/frontend/src/routes/Align.svelte
index ecc246a3..2d9ae838 100644
--- a/frontend/src/routes/Align.svelte
+++ b/frontend/src/routes/Align.svelte
@@ -2,19 +2,22 @@
 	import TMAlignEntry from "./TMAlignEntry.svelte";
 
 	import { onMount } from "svelte";
-	import { Backend, BACKEND_URL, type ProteinEntry } from "../lib/backend";
+	import { Backend, BACKEND_URL, type SimilarProtein, type ProteinEntry } from "../lib/backend";
 	import Molstar from "../lib/Molstar.svelte";
 	import DelayedSpinner from "../lib/DelayedSpinner.svelte";
 	import { DownloadOutline } from "flowbite-svelte-icons";
 	import { Button } from "flowbite-svelte";
 	import * as d3 from "d3";
 	import { undoFormatProteinName } from "../lib/format";
+    import AlignBlock from "../lib/AlignBlock.svelte";
 
 	export let proteinA: string;
 	export let proteinB: string;
 	let combined = proteinA + "/" + proteinB;
 	let entryA: ProteinEntry | null = null;
 	let entryB: ProteinEntry | null = null;
+    let foldseekData: SimilarProtein;
+    let foldseekError = false;
 	let error = false;
 
 	const dark2green = d3.schemeDark2[0];
@@ -34,6 +37,17 @@
 		entryA = await Backend.getProteinEntry(proteinA);
 		entryB = await Backend.getProteinEntry(proteinB);
 
+        try {
+			foldseekData = await Backend.searchVenomeSimilarCompare(proteinA, proteinB)
+		} catch (e) {
+			console.error(e);
+			console.error(
+				"NEED TO DOWNLOAD FOLDSEEK IN THE SERVER. SEE THE SERVER ERROR MESSAGE."
+			);
+			foldseekError = true;
+		}
+        
+
 		// if we could not find the entry, the id is garbo
 		if (entryA == null || entryB == null) error = true;
 		console.log(entryA, entryB);
@@ -58,6 +72,33 @@
 				</div>
 				<TMAlignEntry entry={entryA} color={dark2green} />
 				<TMAlignEntry entry={entryB} color={dark2orange} />
+                <h1>
+                    Foldseek Data
+                </h1>
+                {#if foldseekData === undefined && !foldseekError}
+                    <DelayedSpinner
+                        text="Loading Foldseek..."
+                        textRight
+                        msDelay={0}
+                    />
+                {:else if foldseekData !== undefined}
+                    <div>
+                        <b>Prob. Match:</b> {foldseekData.prob}
+                    </div>
+                    <div>
+                        <b>E-Value:</b> {foldseekData.evalue}
+                    </div>
+                    <div>
+                        <b>Region of Similarity</b>
+                        <AlignBlock
+                            width={260}
+                            height={20}
+                            ogLength={entryA.length}
+                            qstart={foldseekData.qstart}
+                            qend={foldseekData.qend}
+                        />
+                    </div>
+                {/if}
 				<div style="width: 300px;" class="mt-3">
 					<Button href="{BACKEND_URL}/protein/pdb/{combined}"
 						>Download Aligned PDB File<DownloadOutline
diff --git a/galaxy/delete_all.py b/galaxy/delete_all.py
index 58a897e4..33e25949 100644
--- a/galaxy/delete_all.py
+++ b/galaxy/delete_all.py
@@ -1,7 +1,7 @@
 import requests
 import os
 
-DIR = "../backend/src/data/pdbAlphaFold"
+DIR = os.path.join('..', 'backend', 'src', 'data', 'pdbAlphaFold')
 
 
 def delete_protein_files():