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Merged
Swaathik merged 6 commits into from
Jul 10, 2026
Merged

Structure table #178

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616e0a3
Add/remove properties in structure table
Swaathik Jun 19, 2026
a6803a2
Use predictions API for fetching complexes
Swaathik Jun 19, 2026
fa6bf0f
Show chain ids only if the identifier_category is uniprot
Swaathik Jun 19, 2026
0ba9a16
Add chain information from AF payload
Swaathik Jun 23, 2026
c7a6caa
Update nightingale dependency
Swaathik Jul 9, 2026
7877911
Remove commented code
Swaathik Jul 10, 2026
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2 changes: 1 addition & 1 deletion package.json
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Original file line number Diff line number Diff line change
Expand Up @@ -44,7 +44,7 @@
"@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": "5.8.0",
"@nightingale-elements/nightingale-structure": "5.10.2",
"@nightingale-elements/nightingale-track-canvas": "5.6.0",
"@nightingale-elements/nightingale-variation-canvas": "^5.10.1",
"color-hash": "2.0.2",
Expand Down
70 changes: 31 additions & 39 deletions src/protvista-uniprot-structure.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -26,15 +26,13 @@ const PDBLinks = [
{ name: 'PDBe', link: 'https://www.ebi.ac.uk/pdbe-srv/view/entry/' },
{ name: 'RCSB-PDB', link: 'https://www.rcsb.org/structure/' },
{ name: 'PDBj', link: 'https://pdbj.org/mine/summary/' },
{ name: 'PDBsum', link: 'https://www.ebi.ac.uk/pdbsum/' },
];
const alphaFoldLinkUrl = 'https://alphafold.ebi.ac.uk/search/text/';
const foldseekUrl = `https://search.foldseek.com/search`;
const uniprotKBUrl = 'https://www.uniprot.org/uniprotkb/';

// Excluded source from 3d-beacons is PDBe as we fetch them separately from UniProt
const providersFrom3DBeacons = [
'AlphaFold DB',
'SWISS-MODEL',
'ModelArchive',
'PED',
Expand All @@ -45,18 +43,6 @@ const providersFrom3DBeacons = [
'levylab',
];

const sourceMethods = new Map([
['AlphaFold DB', 'Predicted'],
['SWISS-MODEL', 'Modeling'],
['ModelArchive', 'Modeling'],
['PED', 'Modeling'],
['SASBDB', 'SAS'],
['isoform.io', 'Predicted'],
['AlphaFill', 'Predicted'],
['HEGELAB', 'Modeling'],
['levylab', 'Modeling'],
]);

type UniProtKBData = {
uniProtKBCrossReferences: UniProtKBCrossReference[];
sequence: Sequence;
Expand Down Expand Up @@ -140,6 +126,7 @@ export type ProcessedStructureData = {
isoformId?: string;
isoformIsCanonical?: boolean;
afPrediction?: boolean; // Flag to differentiate the structure source as AlphaFold prediction API vs 3DBeacons AlphaFold
oligomericState?: string;
};

type IsoformIdSequence = Array<{
Expand Down Expand Up @@ -189,7 +176,7 @@ const processPDBData = (data: UniProtKBData): ProcessedStructureData[] =>
method,
resolution:
!resolution || resolution === '-' ? undefined : resolution,
downloadUrl: `https://www.ebi.ac.uk/pdbe/entry-files/download/pdb${id.toLowerCase()}.ent`,
downloadUrl: `https://www.ebi.ac.uk/pdbe/entry-files/download/${id.toLowerCase()}_updated.cif`,
chain,
positions,
protvistaFeatureId: id,
Expand All @@ -203,29 +190,48 @@ const processAFData = (
data: AlphaFoldPayload,
isoforms?: IsoformIdSequence,
canonicalSequence?: string
): ProcessedStructureData[] =>
data
): ProcessedStructureData[] => {
const uniqueData = [
...new Map(data.map((d) => [d.modelEntityId, d])).values(),
];

return uniqueData
.map((d) => {
const isoformMatch = isoforms?.find(
({ sequence }) => d.sequence === sequence
);

let chain = d.chainId;
const oligomericState = d.isComplex
? `${d.assemblyType}${d.oligomericState}`
: 'Monomer';

if (d.isComplex && oligomericState === 'Homodimer') {
chain = data.filter(({ modelEntityId }) => modelEntityId === d.modelEntityId).flatMap(({ chainId }) => chainId).sort().join(', ');
}
return {
id: d.modelEntityId,
source: 'AlphaFold DB',
method: 'Predicted',
positions: `${d.sequenceStart}-${d.sequenceEnd}`,
protvistaFeatureId: d.modelEntityId,
downloadUrl: d.pdbUrl,
amAnnotationsUrl: d.amAnnotationsUrl,
isoformId: isoformMatch?.isoformId,
isoformIsCanonical: isoformMatch
isoformId: !d.isComplex ? isoformMatch?.isoformId : undefined,
isoformIsCanonical: !d.isComplex && isoformMatch
? isoformMatch.sequence === canonicalSequence
: undefined,
afPrediction: true,
oligomericState,
chain
};
})
.sort((a, b) => getIsoformNum(a.id) - getIsoformNum(b.id));
.sort((a, b) => getIsoformNum(a.id) - getIsoformNum(b.id))
.sort((a, b) => {
const aMonomer = a.oligomericState === 'Monomer' ? 0 : 1;
const bMonomer = b.oligomericState === 'Monomer' ? 0 : 1;
return aMonomer - bMonomer;
});
};

const process3DBeaconsData = (
data: BeaconsData,
Expand Down Expand Up @@ -263,7 +269,6 @@ const process3DBeaconsData = (
structures?.map(({ summary }) => ({
id: summary.model_identifier,
source: summary.provider,
method: sourceMethods.get(summary.provider),
positions:
summary.uniprot_start && summary.uniprot_end
? `${summary.uniprot_start}-${summary.uniprot_end}`
Expand All @@ -275,8 +280,9 @@ const process3DBeaconsData = (
? 'https://www.isoform.io/home'
: summary.model_page_url,
chain:
summary.entities?.flatMap((entity) => entity.chain_ids).join(', ') ||
summary.entities?.flatMap((entity) => entity.identifier_category === 'UNIPROT' ? entity.chain_ids : []).join(', ') ||
undefined,
oligomericState: summary.oligomeric_state || undefined,
})) || []
);
};
Expand Down Expand Up @@ -514,7 +520,7 @@ class ProtvistaUniprotStructure extends LitElement {
// AlphaMissense predictions are only available in AF predictions endpoint
const alphaFoldUrl =
this.accession && !this.checksum
? `https://alphafold.ebi.ac.uk/api/prediction/${this.accession}`
? `https://alphafold.ebi.ac.uk/api/prediction/${this.accession}?include_complexes=true`
: '';
// exclude_provider accepts only value hence 'pdbe' as majority of the models are from there if querying by accession
const beaconsUrl =
Expand Down Expand Up @@ -566,21 +572,7 @@ class ProtvistaUniprotStructure extends LitElement {
// TODO: return if no data at all
// if (!payload) return;

const beaconsAFData = beaconsData.filter(
({ source }) => source === 'AlphaFold DB'
);
const beaconsNonAFData = beaconsData.filter(
({ source }) => source !== 'AlphaFold DB'
);

const uniqueAFData = [
...new Map(
// The order of the spread is important as we want to prioritise AF data from AF predictions API over 3DBeacons
[...beaconsAFData, ...afData].map((obj) => [obj.id, obj])
).values(),
];

const data = [...pdbData, ...uniqueAFData, ...beaconsNonAFData];
const data = [...pdbData, ...afData, ...beaconsData];

this.data = data;
this.columns = this.getColumns();
Expand Down
18 changes: 13 additions & 5 deletions yarn.lock
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Original file line number Diff line number Diff line change
Expand Up @@ -485,13 +485,14 @@
"@nightingale-elements/nightingale-new-core" "^5.6.0"
d3 "7.9.0"

"@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==
"@nightingale-elements/nightingale-structure@5.10.2":
version "5.10.2"
resolved "https://registry.yarnpkg.com/@nightingale-elements/nightingale-structure/-/nightingale-structure-5.10.2.tgz#84f019b51f856441efde742f6b961d5971e8492a"
integrity sha512-udJKAR6cDJHWpSlM8rnCcYojPxVJwtmmZ2d+qVGtidAdEiJ9WxqJkXmMtkUmn+zkFpKylHWoXlmzlPGHPK6XhQ==
dependencies:
"@nightingale-elements/nightingale-new-core" "^5.6.0"
d3 "7.9.0"
dompurify "^3.0.0"
molstar "3.44.0"

"@nightingale-elements/nightingale-track-canvas@5.6.0":
Expand Down Expand Up @@ -1066,7 +1067,7 @@
resolved "https://registry.yarnpkg.com/@types/swagger-ui-dist/-/swagger-ui-dist-3.30.4.tgz#2d74bc67bcae443d2daf912cb803b4c274d46514"
integrity sha512-FeOBc7uj4/lAIh4jkBzorvmNoUU9JgSccyDIRo0E9MJw9KQfSxlwpHCyKGnU9kfV5N5dEdfpY8wm7to3nSwTmA==

"@types/trusted-types@^2.0.2":
"@types/trusted-types@^2.0.2", "@types/trusted-types@^2.0.7":
version "2.0.7"
resolved "https://registry.yarnpkg.com/@types/trusted-types/-/trusted-types-2.0.7.tgz#baccb07a970b91707df3a3e8ba6896c57ead2d11"
integrity sha512-ScaPdn1dQczgbl0QFTeTOmVHFULt394XJgOQNoyVhZ6r2vLnMLJfBPd53SB52T/3G36VI1/g2MZaX0cwDuXsfw==
Expand Down Expand Up @@ -2781,6 +2782,13 @@ domhandler@^5.0.2, domhandler@^5.0.3:
dependencies:
domelementtype "^2.3.0"

dompurify@^3.0.0:
version "3.4.11"
resolved "https://registry.yarnpkg.com/dompurify/-/dompurify-3.4.11.tgz#29c8ba496475f279ef4015784068452fb14a0680"
integrity sha512-zhlUV12GsaRzMsf9q5M254YhA4+VuF0fG+QFqu6aYpoGlKtz+w8//jBcGVYBgQkR5GHjUomejY84AV+/uPbWdw==
optionalDependencies:
"@types/trusted-types" "^2.0.7"

domutils@^2.8.0:
version "2.8.0"
resolved "https://registry.yarnpkg.com/domutils/-/domutils-2.8.0.tgz#4437def5db6e2d1f5d6ee859bd95ca7d02048135"
Expand Down
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