protvista-uniprot 4.4.7 → 4.5.0

package/dist/types/adapters/alphafold-confidence-adapter.d.ts

@@ -1,8 +1,8 @@
-import { AlphafoldPayload } from './types/alphafold';
+import { AlphaFoldPayload } from '@nightingale-elements/nightingale-structure';
 type PartialProtein = {
     sequence: {
         sequence: string;
     };
 };
-declare const transformData: (data: AlphafoldPayload, protein: PartialProtein) => Promise<string>;
+declare const transformData: (data: AlphaFoldPayload, protein: PartialProtein) => Promise<string>;
 export default transformData;

package/dist/types/adapters/alphamissense-heatmap-adapter.d.ts

@@ -1,8 +1,8 @@
-import { AlphafoldPayload } from './types/alphafold';
+import { AlphaFoldPayload } from '@nightingale-elements/nightingale-structure';
 type PartialProtein = {
     sequence: {
         sequence: string;
     };
 };
-declare const transformData: (data: AlphafoldPayload, protein: PartialProtein) => Promise<Record<string, string>[]>;
+declare const transformData: (data: AlphaFoldPayload, protein: PartialProtein) => Promise<Record<string, string>[]>;
 export default transformData;

package/dist/types/adapters/alphamissense-pathogenicity-adapter.d.ts

@@ -1,4 +1,4 @@
-import { AlphafoldPayload } from './types/alphafold';
+import { AlphaFoldPayload } from '@nightingale-elements/nightingale-structure';
 export declare const rowSplitter: RegExp;
 export declare const cellSplitter: RegExp;
 type PartialProtein = {
@@ -6,5 +6,5 @@ type PartialProtein = {
         sequence: string;
     };
 };
-declare const transformData: (data: AlphafoldPayload, protein: PartialProtein) => Promise<string>;
+declare const transformData: (data: AlphaFoldPayload, protein: PartialProtein) => Promise<string>;
 export default transformData;

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "protvista-uniprot",
   "description": "ProtVista tool for the UniProt website",
-  "version": "4.4.7",
+  "version": "4.5.0",
   "files": [
     "dist",
     "src"
@@ -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",

package/src/.vscode/settings.json

@@ -0,0 +1,3 @@
+{
+  "window.title": "${rootPath}${separator}[new-ptm-builds]"
+}

package/src/adapters/alphafold-confidence-adapter.ts

@@ -1,4 +1,4 @@
-import { AlphafoldPayload } from './types/alphafold';
+import { AlphaFoldPayload } from '@nightingale-elements/nightingale-structure';
 
 type AlphafoldConfidencePayload = {
   residueNumber: Array<number>;
@@ -6,7 +6,7 @@ type AlphafoldConfidencePayload = {
   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('');
   }

package/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}`
+    );
   }
 };
 

package/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}`
+    );
   }
 };
 

package/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}`,
               ],
             },

package/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,
   }));
 
@@ -178,16 +178,21 @@ const process3DBeaconsData = (data: BeaconsData): ProcessedStructureData[] => {
   const otherStructures = data?.structures?.filter(({ summary }) =>
     providersFrom3DBeacons.includes(summary.provider)
   );
-  return otherStructures?.map(({ summary }) => ({
-    id: summary['model_identifier'],
-    source: summary.provider,
-    method: sourceMethods.get(summary.provider),
-    positions: `${summary['uniprot_start']}-${summary['uniprot_end']}`,
-    protvistaFeatureId: summary['model_identifier'],
-    downloadLink: summary['model_url'],
-    // isoform.io does not have a model page url. Link to their homepage instead.
-    sourceDBLink: summary.provider === 'isoform.io' ? 'https://www.isoform.io/home' : summary['model_page_url'],
-  })) || [];
+  return (
+    otherStructures?.map(({ summary }) => ({
+      id: summary['model_identifier'],
+      source: summary.provider,
+      method: sourceMethods.get(summary.provider),
+      positions: `${summary['uniprot_start']}-${summary['uniprot_end']}`,
+      protvistaFeatureId: summary['model_identifier'],
+      downloadLink: summary['model_url'],
+      // isoform.io does not have a model page url. Link to their homepage instead.
+      sourceDBLink:
+        summary.provider === 'isoform.io'
+          ? 'https://www.isoform.io/home'
+          : summary['model_page_url'],
+    })) || []
+  );
 };
 
 const AFMetaInfo = html`
@@ -303,14 +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(
-      (data) => data.amAnnotationsUrl
+    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
@@ -370,8 +377,10 @@ class ProtvistaUniprotStructure extends LitElement {
   }) {
     if (providersFrom3DBeacons.includes(source)) {
       this.modelUrl = downloadLink;
+      // Reset the rest
       this.structureId = undefined;
       this.metaInfo = undefined;
+      this.colorTheme = 'alphafold';
     } else {
       this.structureId = id;
       this.modelUrl = undefined;
@@ -503,7 +512,6 @@ class ProtvistaUniprotStructure extends LitElement {
           ${this.modelUrl
             ? html`<nightingale-structure
                 model-url=${this.modelUrl}
-                color-theme=${this.colorTheme}
               ></nightingale-structure>`
             : html``}
         </div>

package/dist/types/adapters/types/alphafold.d.ts

@@ -1,25 +0,0 @@
-export type AlphafoldPayload = Array<{
-    entryId: string;
-    gene: string;
-    uniprotAccession: string;
-    uniprotId: string;
-    uniprotDescription: string;
-    taxId: number;
-    organismScientificName: string;
-    uniprotStart: number;
-    uniprotEnd: number;
-    uniprotSequence: string;
-    modelCreatedDate: string;
-    latestVersion: number;
-    allVersions: number[];
-    isReviewed: boolean;
-    isReferenceProteome: boolean;
-    cifUrl?: string;
-    bcifUrl?: string;
-    amAnnotationsUrl?: string;
-    amAnnotationsHg19Url?: string;
-    amAnnotationsHg38Url?: string;
-    pdbUrl: string;
-    paeImageUrl: string;
-    paeDocUrl: string;
-}>;

package/src/adapters/types/alphafold.ts

@@ -1,25 +0,0 @@
-export type AlphafoldPayload = Array<{
-  entryId: string;
-  gene: string;
-  uniprotAccession: string;
-  uniprotId: string;
-  uniprotDescription: string;
-  taxId: number;
-  organismScientificName: string;
-  uniprotStart: number;
-  uniprotEnd: number;
-  uniprotSequence: string;
-  modelCreatedDate: string;
-  latestVersion: number;
-  allVersions: number[];
-  isReviewed: boolean;
-  isReferenceProteome: boolean;
-  cifUrl?: string;
-  bcifUrl?: string;
-  amAnnotationsUrl?: string;
-  amAnnotationsHg19Url?: string;
-  amAnnotationsHg38Url?: string;
-  pdbUrl: string;
-  paeImageUrl: string;
-  paeDocUrl: string;
-}>;