Alphafold update

package.json

@@ -37,7 +37,7 @@
     "@nightingale-elements/nightingale-navigation": "5.6.0",
     "@nightingale-elements/nightingale-sequence": "5.6.0",
     "@nightingale-elements/nightingale-sequence-heatmap": "5.6.2",
-    "@nightingale-elements/nightingale-structure": "5.7.0",
+    "@nightingale-elements/nightingale-structure": "5.8.0",
     "@nightingale-elements/nightingale-track-canvas": "5.6.0",
     "@nightingale-elements/nightingale-variation": "5.6.0",
     "color-hash": "2.0.2",

src/adapters/alphafold-confidence-adapter.ts

@@ -1,12 +1,12 @@
-import { AlphafoldPayload } from './types/alphafold';
+import { AlphaFoldPayload } from '@nightingale-elements/nightingale-structure';
 
 type AlphafoldConfidencePayload = {
   residueNumber: Array<number>;
   confidenceScore: Array<number>;
   confidenceCategory: Array<string>;
 };
 
-const getConfidenceURLFromPayload = (data: AlphafoldPayload) => {
+const getConfidenceURLFromPayload = (data: AlphaFoldPayload) => {
   const cifURL = data?.[0]?.cifUrl;
   return cifURL?.length
     ? cifURL.replace('-model', '-confidence').replace('.cif', '.json')
@@ -31,12 +31,17 @@ type PartialProtein = {
 };
 
 const transformData = async (
-  data: AlphafoldPayload,
+  data: AlphaFoldPayload,
   protein: PartialProtein
 ) => {
   const confidenceUrl = getConfidenceURLFromPayload(data);
-  const { uniprotSequence } = data?.[0] || {};
-  if (confidenceUrl && uniprotSequence === protein.sequence.sequence) {
+  if (!confidenceUrl) {
+    return;
+  }
+  const alphaFoldSequenceMatch = data?.filter(
+    ({ sequence }) => protein.sequence.sequence === sequence
+  );
+  if (alphaFoldSequenceMatch.length) {
     const confidenceData = await loadConfidence(confidenceUrl);
     return confidenceData?.confidenceCategory.join('');
   }

src/adapters/alphamissense-heatmap-adapter.ts

@@ -1,8 +1,9 @@
+import { AlphaFoldPayload } from '@nightingale-elements/nightingale-structure';
+
 import {
   cellSplitter,
   rowSplitter,
 } from './alphamissense-pathogenicity-adapter';
-import { AlphafoldPayload } from './types/alphafold';
 
 const parseCSV = (rawText: string): Array<Record<string, string>> => {
   const data = [];
@@ -43,13 +44,22 @@ type PartialProtein = {
 };
 
 const transformData = async (
-  data: AlphafoldPayload,
+  data: AlphaFoldPayload,
   protein: PartialProtein
 ) => {
-  const { amAnnotationsUrl, uniprotSequence } = data?.[0] || {};
-  if (amAnnotationsUrl && uniprotSequence === protein.sequence.sequence) {
-    const heatmapData = await loadAndParseAnnotations(amAnnotationsUrl);
+  const alphaFoldSequenceMatch = data?.filter(
+    ({ sequence, amAnnotationsUrl }) =>
+      protein.sequence.sequence === sequence && amAnnotationsUrl
+  );
+  if (alphaFoldSequenceMatch.length === 1) {
+    const heatmapData = await loadAndParseAnnotations(
+      alphaFoldSequenceMatch[0].amAnnotationsUrl
+    );
     return heatmapData;
+  } else if (alphaFoldSequenceMatch.length > 1) {
+    console.warn(
+      `Found more than one matches (${alphaFoldSequenceMatch.length}) for AlphaMissense pathogenicity against protein sequence: ${protein.sequence}`
+    );
   }
 };
 

src/adapters/alphamissense-pathogenicity-adapter.ts

@@ -1,4 +1,4 @@
-import { AlphafoldPayload } from './types/alphafold';
+import { AlphaFoldPayload } from '@nightingale-elements/nightingale-structure';
 
 // from color scale B:0,H:0.1132,V:0.2264,L:0.3395,A:0.4527,l:0.5895,h:0.7264,p:0.8632,P:1
 const certainlyBenign = 0;
@@ -95,7 +95,7 @@ const loadAndParseAnnotations = async (url: string): Promise<string> => {
     const rawCSV = await payload.text();
     return parseCSV(rawCSV);
   } catch (e) {
-    console.error('Could not load AlphaMissense pathogenicity', e);
+    console.error('Could not load AlphaMissense pathogenicity score', e);
   }
 };
 
@@ -106,14 +106,22 @@ type PartialProtein = {
 };
 
 const transformData = async (
-  data: AlphafoldPayload,
+  data: AlphaFoldPayload,
   protein: PartialProtein
 ) => {
-  const { amAnnotationsUrl, uniprotSequence } = data?.[0] || {};
-  if (amAnnotationsUrl && uniprotSequence === protein.sequence.sequence) {
-    const variationData = await loadAndParseAnnotations(amAnnotationsUrl);
-    // return confidenceData?.confidenceCategory.join('');
-    return variationData;
+  const alphaFoldSequenceMatch = data?.filter(
+    ({ sequence, amAnnotationsUrl }) =>
+      protein.sequence.sequence === sequence && amAnnotationsUrl
+  );
+  if (alphaFoldSequenceMatch.length === 1) {
+    const heatmapData = await loadAndParseAnnotations(
+      alphaFoldSequenceMatch[0].amAnnotationsUrl
+    );
+    return heatmapData;
+  } else if (alphaFoldSequenceMatch.length > 1) {
+    console.warn(
+      `Found more than one matches (${alphaFoldSequenceMatch.length}) for AlphaMissense pathogenicity score against protein sequence: ${protein.sequence}`
+    );
   }
 };
 

src/config.ts

@@ -815,8 +815,10 @@ const config: ProtvistaConfig = {
       name: 'ALPHAMISSENSE_PATHOGENICITY',
       label: 'AlphaMissense',
       trackType: 'nightingale-colored-sequence',
-      scale: 'B:0,H:0.1132,V:0.2264,L:0.3395,A:0.4527,l:0.5895,h:0.7264,p:0.8632,P:1',
-      'color-range': '#2166ac:0,#4290bf:0.1132,#8cbcd4:0.2264,#c3d6e0:0.3395,#e2e2e2:0.4527,#edcdba:0.5895,#e99e7c:0.7264,#d15e4b:0.8632,#b2182b:1',
+      scale:
+        'B:0,H:0.1132,V:0.2264,L:0.3395,A:0.4527,l:0.5895,h:0.7264,p:0.8632,P:1',
+      'color-range':
+        '#2166ac:0,#4290bf:0.1132,#8cbcd4:0.2264,#c3d6e0:0.3395,#e2e2e2:0.4527,#edcdba:0.5895,#e99e7c:0.7264,#d15e4b:0.8632,#b2182b:1',
       tracks: [
         {
           name: 'alphamissense_pathogenicity',
@@ -836,13 +838,13 @@ const config: ProtvistaConfig = {
         {
           name: 'alphamissense_pathogenicity_heatmap',
           label: 'AlphaMissense Pathogenicity',
-          labelUrl: 'https://alphafold.ebi.ac.uk/entry/{accession}',
+          labelUrl: `${alphafoldEntry}{accession}`,
           trackType: 'nightingale-sequence-heatmap',
           data: [
             {
               adapter: 'alphamissense-heatmap-adapter',
               url: [
-                'https://alphafold.ebi.ac.uk/api/prediction/{accession}',
+                `${alphafoldApi}prediction/{accession}`,
                 `${proteinsApiServices.proteins}{accession}`,
               ],
             },

src/protvista-uniprot-structure.ts

@@ -2,7 +2,7 @@ import { LitElement, html, svg, TemplateResult, css, nothing } from 'lit';
 import { customElement, state } from 'lit/decorators.js';
 import { unsafeHTML } from 'lit/directives/unsafe-html.js';
 import NightingaleStructure, {
-  PredictionData,
+  AlphaFoldPayload,
 } from '@nightingale-elements/nightingale-structure';
 import ProtvistaDatatable from 'protvista-datatable';
 import { fetchAll, loadComponent } from './utils';
@@ -164,13 +164,13 @@ const processPDBData = (data: UniProtKBData): ProcessedStructureData[] =>
         transformedItem !== undefined
     );
 
-const processAFData = (data: PredictionData[]): ProcessedStructureData[] =>
+const processAFData = (data: AlphaFoldPayload): ProcessedStructureData[] =>
   data.map((d) => ({
-    id: d.entryId,
+    id: d.modelEntityId,
     source: 'AlphaFold',
     method: 'Predicted',
-    positions: `${d.uniprotStart}-${d.uniprotEnd}`,
-    protvistaFeatureId: d.entryId,
+    positions: `${d.sequenceStart}-${d.sequenceEnd}`,
+    protvistaFeatureId: d.modelEntityId,
     downloadLink: d.pdbUrl,
   }));
 
@@ -308,14 +308,16 @@ class ProtvistaUniprotStructure extends LitElement {
     const pdbData = processPDBData(rawData[pdbUrl] || []);
     let afData = [];
     // Check if AF sequence matches UniProt sequence
-    if (
-      rawData[pdbUrl].sequence?.value === rawData[alphaFoldUrl]?.[0]?.sequence
-    ) {
-      afData = processAFData(rawData[alphaFoldUrl] || []);
-      this.alphamissenseAvailable = rawData[alphaFoldUrl].some(
+    const alphaFoldSequenceMatch = rawData[alphaFoldUrl]?.filter(
+      ({ sequence }) => rawData[pdbUrl].sequence?.value === sequence
+    );
+    if (alphaFoldSequenceMatch.length) {
+      afData = processAFData(alphaFoldSequenceMatch);
+      this.alphamissenseAvailable = alphaFoldSequenceMatch.some(
         (data) => data.amAnnotationsUrl
       );
     }
+
     const beaconsData = process3DBeaconsData(rawData[beaconsUrl] || []);
 
     // TODO: return if no data at all

yarn.lock

@@ -1841,10 +1841,10 @@
     "@nightingale-elements/nightingale-new-core" "^5.6.0"
     d3 "7.9.0"
 
-"@nightingale-elements/nightingale-structure@5.7.0":
-  version "5.7.0"
-  resolved "https://registry.yarnpkg.com/@nightingale-elements/nightingale-structure/-/nightingale-structure-5.7.0.tgz#dcfb75b3d73332c01abc0e34090bec173f211bf6"
-  integrity sha512-sP554EZqt1gJcZTok5qVa4kdBC7pM1OSTbqnx15LYqThqHiUJ0RwiJoCVyPD6RcjlKUZEM4l60e7kISnaKGNbA==
+"@nightingale-elements/nightingale-structure@5.8.0":
+  version "5.8.0"
+  resolved "https://registry.yarnpkg.com/@nightingale-elements/nightingale-structure/-/nightingale-structure-5.8.0.tgz#55e69196a05206fa6cb8507a7e97836f2c3765b9"
+  integrity sha512-HdInDB0hh7d7LSyAOUJwEYgoBNffR/kvOU1p8I9ezMccpQ4YYf6E/Fj3xUd9NxWfULNfGk9AF/Fsg43qC6HzHw==
   dependencies:
     "@nightingale-elements/nightingale-new-core" "^5.6.0"
     d3 "7.9.0"