Multimers, no BFVD

config/dev_config.yml

@@ -9,7 +9,6 @@ root:
   wikipedia: https://en.wikipedia.org/w/api.php
   readthedocs: https://interpro-documentation.readthedocs.io/en/latest/
   alphafold: https://alphafold.ebi.ac.uk/
-  bfvd: https://bfvd.foldseek.com/
   repeatsDB: https://repeatsdb.org/api/production/annotations/
   disprot: https://disprot.org/api/
   LLMFeedback: https://docs.google.com/forms/d/e/1FAIpQLSc9lPkgGOZBpnyLiHF87AbUYdAWyx_3YFTNNg4MGQEcqAK4jQ/viewform?usp=pp_url&entry.128814244=
@@ -52,7 +51,6 @@ pages:
       - proteome
       - model
       - alphafold
-      - bfvd
       - logo
       - entry_alignments
       - interactions
@@ -68,7 +66,6 @@ pages:
       - structure
       - sequence
       - alphafold
-      - bfvd
       - similar_proteins
   structure:
     subPages:

config/master_config.yml

@@ -9,7 +9,6 @@ root:
   readthedocs: https://interpro-documentation.readthedocs.io/en/latest/
   wikipedia: https://en.wikipedia.org/w/api.php
   alphafold: https://alphafold.ebi.ac.uk/
-  bfvd: https://bfvd.foldseek.com/
   repeatsDB: https://repeatsdb.org/api/production/annotations/
   disprot: https://disprot.org/api/
   LLMFeedback: https://docs.google.com/forms/d/e/1FAIpQLSc9lPkgGOZBpnyLiHF87AbUYdAWyx_3YFTNNg4MGQEcqAK4jQ/viewform?usp=pp_url&entry.128814244=
@@ -52,7 +51,6 @@ pages:
       - structure
       - logo
       - alphafold
-      - bfvd
       - entry_alignments
       - interactions
       - pathways
@@ -66,7 +64,6 @@ pages:
       - isoform
       - structure
       - alphafold
-      - bfvd
       - sequence
       - similar_proteins
   structure:

config/staging_config.yml

@@ -9,7 +9,6 @@ root:
   readthedocs: https://interpro-documentation.readthedocs.io/en/latest/
   wikipedia: https://en.wikipedia.org/w/api.php
   alphafold: https://alphafold.ebi.ac.uk/
-  bfvd: https://bfvd.foldseek.com/
   repeatsDB: https://repeatsdb.org/api/production/annotations/
   disprot: https://disprot.org/api/
   LLMFeedback: https://docs.google.com/forms/d/e/1FAIpQLSc9lPkgGOZBpnyLiHF87AbUYdAWyx_3YFTNNg4MGQEcqAK4jQ/viewform?usp=pp_url&entry.128814244=
@@ -53,7 +52,6 @@ pages:
       - model
       - logo
       - alphafold
-      - bfvd
       - entry_alignments
       - interactions
       - pathways
@@ -66,7 +64,6 @@ pages:
       - isoform
       - structure
       - alphafold
-      - bfvd
       - sequence
       - similar_proteins
   structure:

src/components/BreadCrumbs/index.tsx

@@ -197,7 +197,6 @@ const BreadCrumbForEntityDetail = ({
 
   if (detail) {
     if (detailToRender?.includes('alphafold')) detailToRender = 'AlphaFold';
-    else if (detailToRender?.includes('bfvd')) detailToRender = 'BFVD';
   }
 
   return (

src/components/EntryMenu/EntryMenuLink/index.tsx

@@ -88,13 +88,7 @@ export const EntryMenuLink = ({
       name.toLowerCase() === 'alphafold'
     ) {
       value = (payload.metadata as EntryMetadata).in_alphafold ? 1 : 0;
-    } else if (
-      mainKey?.toLowerCase() === 'protein' &&
-      name.toLowerCase() === 'bfvd'
-    ) {
-      value = (payload.metadata as EntryMetadata).in_bfvd ? 1 : 0;
     }
-
     /**
      * Enabling the menuitems that appear in the entry_annotations array,
      * i.e. only enable the menu item if there is info for it.

src/components/ExtLink/patternLinkWrapper/index.tsx

@@ -29,9 +29,4 @@ export const AlphafoldLink = patternLinkWrapper(
 );
 AlphafoldLink.displayName = 'AlphafoldLink';
 
-export const BFVDLink = patternLinkWrapper(
-  'https://bfvd.foldseek.com/cluster/{id}',
-);
-BFVDLink.displayName = 'BFVDLink';
-
 export default patternLinkWrapper;

src/components/Matches/index.tsx

@@ -553,11 +553,8 @@ const Matches = ({
       <Column
         dataKey="in_alphafold"
         displayIf={primary === 'protein'}
-        renderer={(
-          inAlphafold: boolean,
-          { accession, in_bfvd }: ProteinMetadata,
-        ) =>
-          inAlphafold ? (
+        renderer={(inAlphafold: boolean, { accession }: ProteinMetadata) =>
+          inAlphafold && (
             <Link
               to={{
                 description: {
@@ -568,22 +565,7 @@ const Matches = ({
             >
               AlphaFold
             </Link>
-          ) : in_bfvd ? (
-            <Link
-              to={{
-                description: {
-                  main: { key: 'protein' },
-                  protein: {
-                    db: 'uniprot',
-                    accession,
-                    detail: 'bfvd',
-                  },
-                },
-              }}
-            >
-              BFVD
-            </Link>
-          ) : null
+          )
         }
       >
         Predicted structure

src/components/Menu/SideMenu/ServerStatus/index.tsx

@@ -18,7 +18,6 @@ const mapEndpointToName = new Map([
   ['ipScan', 'InterProScan API'],
   ['wikipedia', 'Wikipedia API'],
   ['alphafold', 'AlphaFold API'],
-  ['bfvd', 'BFVD API'],
 ]);
 
 type BrowserProps = {

src/components/Protein/Isoforms/Viewer/index.tsx

@@ -160,7 +160,7 @@ const Viewer = ({ protein, isoform, data, dataConfidence }: LoadedProps) => {
       dataConfidence,
       accession,
       proteinDataRecord,
-      protein.in_bfvd ? 'bfvd' : 'alphafold',
+      'alphafold',
     );
   }
   proteinDataRecord = sectionsReorganization(proteinDataRecord);

src/components/Protein/Summary/index.tsx

@@ -233,34 +233,6 @@ export const SummaryProtein = ({ data, loading }: LoadedProps) => {
                     UniProt
                   </UniProtLink>
                 </li>
-                {metadata.in_bfvd ? (
-                  <>
-                    <li>
-                      {' '}
-                      <Link
-                        href={
-                          config.root.alphafold.href +
-                          'entry/' +
-                          metadata.accession
-                        }
-                        className={css('ext')}
-                        target="_blank"
-                      >
-                        Alphafold DB
-                      </Link>
-                    </li>
-                    <li>
-                      <BaseLink
-                        id={metadata.accession}
-                        target={'_blank'}
-                        pattern="https://search.foldseek.com/search?accession={id}&source=BFVD"
-                        className={css('ext')}
-                      >
-                        Foldseek
-                      </BaseLink>
-                    </li>
-                  </>
-                ) : null}
                 {metadata.in_alphafold ? (
                   <>
                     <li>

src/components/ProteinViewer/LabelsInTrack/ExceptionalLabels/index.tsx

@@ -3,11 +3,7 @@ import React from 'react';
 import { NOT_MEMBER_DBS } from 'menuConfig';
 import Link from 'components/generic/Link';
 
-import {
-  AlphafoldLink,
-  PTMLink,
-  BFVDLink,
-} from 'components/ExtLink/patternLinkWrapper';
+import { AlphafoldLink, PTMLink } from 'components/ExtLink/patternLinkWrapper';
 import Tooltip from 'components/SimpleCommonComponents/Tooltip';
 
 import { FunFamLink } from 'subPages/Subfamilies';
@@ -120,16 +116,6 @@ const ExceptionalLabels = ({ entry, isPrinting, databases }: PropsEL) => {
     );
   }
 
-  if (entry.source_database === 'bfvd') {
-    return isPrinting ? (
-      <span>pLDDT</span>
-    ) : (
-      <BFVDLink id={entry.protein || ''} className={css('ext')}>
-        pLDDT
-      </BFVDLink>
-    );
-  }
-
   if (entry.source_database === 'ptm') {
     return isPrinting ? (
       <span>UniProt</span>

src/components/ProteinViewer/index.tsx

@@ -149,7 +149,6 @@ export const ProteinViewer = ({
   const [isPrinting, setPrinting] = useState(false);
 
   const mainTracks = [
-    'bfvd confidence',
     'alphafold confidence',
     'domain',
     'family',

src/components/ProteinViewer/utils.ts

@@ -49,7 +49,6 @@ export type ExtendedFeature = Feature & {
 };
 
 export const typeNameToSectionName: Record<string, string> = {
-  'bfvd confidence': 'BFVD Confidence',
   'alphafold confidence': 'AlphaFold Confidence',
   family: 'Families',
   domain: 'Domains',

src/components/Related/DomainsOnProtein/DomainsOnProteinLoaded/index.tsx

@@ -225,7 +225,7 @@ const DomainsOnProteinLoaded = ({
       dataConfidence,
       protein.accession,
       processedDataMerged,
-      protein.in_bfvd ? 'bfvd' : 'alphafold',
+      'alphafold',
     );
 
   let interpro_NMatchesCount = 0;
@@ -240,7 +240,6 @@ const DomainsOnProteinLoaded = ({
     const interProNData = dataInterProNMatches.payload;
     const allTracks = Object.keys(processedDataMerged);
     const unaffectedTracks = [
-      'bfvd_confidence',
       'alphafold_confidence',
       'intrinsically_disordered_regions',
       'funfam',

src/components/Related/DomainsOnProtein/DomainsOnProteinLoaded/utils.ts

@@ -9,7 +9,6 @@ export const UNDERSCORE = /_/g;
 
 const FIRST_IN_ORDER = [
   'alphafold_confidence',
-  'bfvd_confidence',
   'secondary_structure',
   'family',
   'domain',

src/components/Structure/Viewer/index.tsx

@@ -23,7 +23,6 @@ import Labels from './Labels';
 import { Selection } from '../ViewerAndEntries';
 import { AfConfidenceProvider } from './af-confidence/prop';
 import { AfConfidenceColorThemeProvider } from './af-confidence/color';
-import { BFactorColorThemeProvider } from './bfvd-confidence/color';
 import { CustomThemeProvider } from './custom/color';
 
 import cssBinder from 'styles/cssBinder';
@@ -101,10 +100,6 @@ class StructureView extends PureComponent<Props> {
         this.viewer.representation.structure.themes.colorThemeRegistry.add(
           CustomThemeProvider,
         );
-
-        this.viewer.representation.structure.themes.colorThemeRegistry.add(
-          BFactorColorThemeProvider,
-        );
       }
       // mouseover ?????
       // window.viewer = this.viewer;
@@ -305,9 +300,6 @@ class StructureView extends PureComponent<Props> {
       case 'af':
         colouringTheme = AfConfidenceColorThemeProvider.name;
         break;
-      case 'bfvd':
-        colouringTheme = BFactorColorThemeProvider.name;
-        break;
       case 'ted':
         colouringTheme = CustomThemeProvider.name;
         break;