Skip to content

Change AlphaFoldPayload variable name and update type. #326

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
dlrice merged 2 commits into from
Oct 14, 2025
Merged

Change AlphaFoldPayload variable name and update type. #326

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
6d76486
Change AlphaFoldPayload variable name and update type.
dlrice Oct 13, 2025
4ba7347
Remove obsolete properties from AlphaFold.
dlrice Oct 14, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
46 changes: 32 additions & 14 deletions packages/nightingale-structure/src/nightingale-structure.ts
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -48,26 +48,44 @@ export type PDBData = Record<
}
>;

export type PredictionData = {
entryId: string;
export type AlphaFoldPayload = Array<{
modelEntityId: string;
toolUsed?: string;
providerId?: string;
entityType?: string;
isUniProt?: boolean;
modelCreatedDate?: Date;
sequenceVersionDate?: Date;
globalMetricValue?: number;
fractionPlddtVeryLow?: number;
fractionPlddtLow?: number;
fractionPlddtConfident?: number;
fractionPlddtVeryHigh?: number;
latestVersion?: number;
allVersions?: number[];
sequence?: string;
sequenceStart?: number;
sequenceEnd?: number;
sequenceChecksum?: string;
isUniProtReviewed?: boolean;
gene?: string;
uniprotAccession?: string;
uniprotId?: string;
uniprotDescription?: string;
taxId?: number;
organismScientificName?: string;
uniprotStart?: number;
uniprotEnd?: number;
uniprotSequence?: string;
modelCreatedDate?: string;
latestVersion?: number;
allVersions?: number[];
isUniProtReferenceProteome?: boolean;
bcifUrl?: string;
cifUrl?: string;
pdbUrl?: string;
distogramUrl?: string;
paeImageUrl?: string;
msaUrl?: string;
plddtDocUrl?: string;
paeDocUrl?: string;
amAnnotationsUrl?: string;
};
amAnnotationsHg19Url?: string;
amAnnotationsHg38Url?: string;
}>;

const uniProtMappingUrl = "https://www.ebi.ac.uk/pdbe/api/mappings/uniprot/";

Expand Down Expand Up @@ -248,7 +266,7 @@ class NightingaleStructure extends withManager(
}
}

async loadAFEntry(id: string): Promise<PredictionData[]> {
async loadAFEntry(id: string): Promise<AlphaFoldPayload> {
this.#structureViewer?.plugin.clear();
this.showMessage("Loading", id);
try {
Expand Down Expand Up @@ -282,7 +300,7 @@ class NightingaleStructure extends withManager(
if (this.isAF()) {
const afPredictions = await this.loadAFEntry(this["protein-accession"]);
const afInfo = afPredictions.find(
(prediction) => prediction.entryId === this["structure-id"]
(prediction) => prediction.modelEntityId === this["structure-id"]
);
// Note: maybe use bcif instead of cif, but I have issues loading it atm
if (afInfo?.cifUrl) {
Expand Down Expand Up @@ -346,8 +364,8 @@ class NightingaleStructure extends withManager(
): void {
// sequencePositions assumed to be in PDB coordinate space
if (
(!sequencePositions?.length ||
sequencePositions.some((pos) => !Number.isInteger(pos.position)))
!sequencePositions?.length ||
sequencePositions.some((pos) => !Number.isInteger(pos.position))
) {
return;
}
Expand Down