Merge pull request #49 from UCLOrengoGroup/48-get-protein-length-from…

…-alphafold-api

48 get protein length from alphafold api

frontend/src/components/AlphaFoldService/service.test.A0A6P4PER7.json

@@ -0,0 +1,50 @@
+{
+  "uniprot_entry": {
+    "ac": "A0A6P4PER7",
+    "id": "A0A6P4PER7_GOSAR",
+    "uniprot_checksum": "E5BF4AF471D8B238",
+    "sequence_length": 960,
+    "segment_start": 1,
+    "segment_end": 960
+  },
+  "structures": [
+    {
+      "summary": {
+        "model_identifier": "AF-A0A6P4PER7-F1",
+        "model_category": "AB-INITIO",
+        "model_url": "https://alphafold.ebi.ac.uk/files/AF-A0A6P4PER7-F1-model_v4.cif",
+        "model_format": "MMCIF",
+        "model_type": null,
+        "model_page_url": "https://alphafold.ebi.ac.uk/entry/A0A6P4PER7",
+        "provider": "AlphaFold DB",
+        "number_of_conformers": null,
+        "ensemble_sample_url": null,
+        "ensemble_sample_format": null,
+        "created": "2022-06-01",
+        "sequence_identity": 1,
+        "uniprot_start": 1,
+        "uniprot_end": 960,
+        "coverage": 1,
+        "experimental_method": null,
+        "resolution": null,
+        "confidence_type": "pLDDT",
+        "confidence_version": null,
+        "confidence_avg_local_score": 79.38,
+        "oligomeric_state": null,
+        "preferred_assembly_id": null,
+        "entities": [
+          {
+            "entity_type": "POLYMER",
+            "entity_poly_type": "POLYPEPTIDE(L)",
+            "identifier": "A0A6P4PER7",
+            "identifier_category": "UNIPROT",
+            "description": "probable disease resistance protein At1g58602",
+            "chain_ids": [
+              "A"
+            ]
+          }
+        ]
+      }
+    }
+  ]
+}

frontend/src/components/AlphaFoldService/service.test.ts

@@ -0,0 +1,16 @@
+import { expect, test } from 'vitest'
+
+import { convertWebToModel } from './service'
+
+import data_A0A6P4PER7 from './service.test.A0A6P4PER7.json'
+
+test('gets correct UniProt data from A0A6P4PER7', () => {
+    expect(data_A0A6P4PER7.uniprot_entry.ac).toBe('A0A6P4PER7')
+
+    const up_data = convertWebToModel(data_A0A6P4PER7)
+    expect(up_data.ac).toBe('A0A6P4PER7')
+    expect(up_data.id).toBe('A0A6P4PER7_GOSAR')
+    expect(up_data.uniprot_checksum).toBe('E5BF4AF471D8B238')
+    expect(up_data.sequence_length).toBe(960)
+})
+

frontend/src/components/AlphaFoldService/service.ts

@@ -0,0 +1,28 @@
+import axios from "axios";
+
+import { UniprotEntry } from "../../client/models/UniprotEntry"
+
+const http = axios.create({
+  baseURL: "https://alphafold.ebi.ac.uk/api/uniprot/summary/",
+  headers: {
+    "Content-type": "application/json"
+  }
+});
+
+export const convertWebToModel = (data: any): UniprotEntry => {
+  return data.uniprot_entry;
+}
+
+const get = (id: any): Promise<UniprotEntry> => {
+  return http.get(`/${id}.json`)
+    .then((response) => {
+      // console.log("AlphaFold.API.response.data: ", response.data)
+      return convertWebToModel(response.data);
+    });
+};
+
+const AlphaFoldUniprotEntryDataService = {
+  get,
+};
+
+export default AlphaFoldUniprotEntryDataService;

frontend/src/components/Utils/uniprotAccUtils.test.tsx

@@ -38,7 +38,7 @@ test('render_cath_label_single_label', () => {
   const cath_label = '1.10.8.10,2.40.60.10'
   const expected = render(
   <>
-    { cath_label.split(",").map((cath_id) => {
+    { [cath_label.split(",")[0]].map((cath_id) => {
       return <Link href={`${CATH_BASE_URL}/version/latest/cathnode/${cath_id}`} isExternal>
         {cath_id} <ExternalLinkIcon mx={"2px"}/>
       </Link>

frontend/src/routes/_layout/uniprot/$uniprotAcc.tsx

@@ -41,6 +41,7 @@ export const Route = createFileRoute("/_layout/uniprot/$uniprotAcc")({
 import { getQueryParamsFromChoppingString, getDomainAnnotationFromDomainSummary } from "../../../components/Utils/DomainSummary"
 import UniprotEntryDataService from "../../../components/UniprotService/service"
 import { UniprotData } from "../../../components/UniprotService/model"
+import { UniprotEntry } from "../../../client/models/UniprotEntry"
 import classes from './$uniprotAcc.module.css'
 import ProteinSummaryFigure, { ProteinSummaryFigureProps } from "../../../components/Common/ProteinSummaryFigure"
 
@@ -54,6 +55,7 @@ import {
   get_chainparse_data_link, 
   get_domainsummary_data_link 
 } from "../../../components/Utils/uniprotAccUtils"
+import AlphaFoldUniprotEntryDataService from "../../../components/AlphaFoldService/service"
 
 
 function UniprotAcc() {
@@ -64,6 +66,8 @@ function UniprotAcc() {
   const [ selectedDomainId, setSelectedDomainId ] = useState<string | null>(null)
   const [ uniprotEntry, setUniprotEntry ] = useState<UniprotData | null>(null)
   const [ uniprotDidLoad, setUniprotDidLoad ] = useState<boolean>(false)
+  const [ afUniProtEntry, setAFUniprotEntry ] = useState<UniprotEntry | null>(null)
+  const [ afDidLoad, setAFDidLoad ] = useState<boolean>(false)
   const domainSummaryResult = useQuery(["domainsummary", uniprotAcc], () => {
     return UniprotService.readUniprotSummary({
       uniprotAcc: uniprotAcc,
@@ -102,6 +106,16 @@ function UniprotAcc() {
       })
       setUniprotDidLoad(true)
     }
+    if (!afDidLoad) {
+      // console.log("useEffect.UPDATE: ", uniprotAcc)
+      AlphaFoldUniprotEntryDataService.get(uniprotAcc).then((up_entry: UniprotEntry) => {
+        // console.log("afuniprot.data: ", up_entry);
+        setAFUniprotEntry(up_entry);
+      }).catch((err) => {
+        console.error("Error fetching AF UniProt entry: ", err)
+      })
+      setAFDidLoad(true)
+    }
   }, [uniprotAcc])
 
   const selectChopping = (dom: DomainSummaryPublicWithInteractions) => {
@@ -143,11 +157,11 @@ function UniprotAcc() {
   let structureFigure = null
   if (domain_summary_entries) {
     const domain_annotations = domain_summary_entries.data.map((d) => getDomainAnnotationFromDomainSummary(d))
-    if (uniprotEntry) {
+    if (afUniProtEntry && afUniProtEntry.sequence_length) {
       const opts: ProteinSummaryFigureProps = {
         width: 500,
         height: 30,
-        totalResidues: uniprotEntry.sequence.length,
+        totalResidues: afUniProtEntry.sequence_length,
         domainAnnotations: domain_annotations,
       }
       if (highlightedDomainId) {
@@ -168,11 +182,13 @@ function UniprotAcc() {
       <dl>
         <dt>Accession</dt>
         <dd>{uniprotAcc}</dd>
+        {afUniProtEntry && (<>
+        <dt>Length</dt>
+        <dd>{afUniProtEntry.sequence_length} Residues</dd>
+        </>)}
         {uniprotEntry ? (<>
         <dt>Name</dt>
         <dd>{uniprotEntry.proteinDescription.fullName}</dd>
-        <dt>Length</dt>
-        <dd>{uniprotEntry.sequence.length} Residues</dd>
         <dt>Organism</dt>
         <dd>{uniprotEntry.organism.scientificName}</dd>
         <dt>Lineage</dt>