@cyanheads/protein-mcp-server 0.4.0 → 0.4.2
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/AGENTS.md +32 -25
- package/CLAUDE.md +32 -25
- package/Dockerfile +16 -7
- package/LICENSE +1 -1
- package/README.md +8 -6
- package/changelog/0.4.x/0.4.1.md +32 -0
- package/changelog/0.4.x/0.4.2.md +16 -0
- package/changelog/template.md +60 -19
- package/dist/mcp-server/resources/definitions/af-summary.resource.d.ts.map +1 -1
- package/dist/mcp-server/resources/definitions/af-summary.resource.js +8 -1
- package/dist/mcp-server/resources/definitions/af-summary.resource.js.map +1 -1
- package/dist/mcp-server/tools/definitions/_schemas.d.ts +34 -6
- package/dist/mcp-server/tools/definitions/_schemas.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/_schemas.js +149 -9
- package/dist/mcp-server/tools/definitions/_schemas.js.map +1 -1
- package/dist/mcp-server/tools/definitions/analyze-collection.tool.d.ts +9 -4
- package/dist/mcp-server/tools/definitions/analyze-collection.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/analyze-collection.tool.js +42 -13
- package/dist/mcp-server/tools/definitions/analyze-collection.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/compare-structures.tool.d.ts +6 -4
- package/dist/mcp-server/tools/definitions/compare-structures.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/compare-structures.tool.js +24 -7
- package/dist/mcp-server/tools/definitions/compare-structures.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/get-annotations.tool.d.ts +1 -1
- package/dist/mcp-server/tools/definitions/get-structure.tool.d.ts +2 -2
- package/dist/mcp-server/tools/definitions/get-structure.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/get-structure.tool.js +30 -7
- package/dist/mcp-server/tools/definitions/get-structure.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/search-structures.tool.d.ts +5 -3
- package/dist/mcp-server/tools/definitions/search-structures.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/search-structures.tool.js +22 -15
- package/dist/mcp-server/tools/definitions/search-structures.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/track-ligands.tool.d.ts +2 -2
- package/dist/services/alignment/alignment-service.d.ts +7 -0
- package/dist/services/alignment/alignment-service.d.ts.map +1 -1
- package/dist/services/alignment/alignment-service.js +22 -3
- package/dist/services/alignment/alignment-service.js.map +1 -1
- package/dist/services/alphafold/alphafold-service.d.ts.map +1 -1
- package/dist/services/alphafold/alphafold-service.js +1 -0
- package/dist/services/alphafold/alphafold-service.js.map +1 -1
- package/dist/services/beacons/beacons-service.d.ts.map +1 -1
- package/dist/services/foldseek/foldseek-service.d.ts +1 -1
- package/dist/services/foldseek/foldseek-service.d.ts.map +1 -1
- package/dist/services/foldseek/foldseek-service.js +5 -1
- package/dist/services/foldseek/foldseek-service.js.map +1 -1
- package/dist/services/rcsb/facets.d.ts +19 -19
- package/dist/services/rcsb/facets.d.ts.map +1 -1
- package/dist/services/rcsb/rcsb-service.d.ts +2 -2
- package/dist/services/rcsb/rcsb-service.d.ts.map +1 -1
- package/dist/services/rcsb/rcsb-service.js +24 -4
- package/dist/services/rcsb/rcsb-service.js.map +1 -1
- package/dist/services/rcsb/types.d.ts +14 -3
- package/dist/services/rcsb/types.d.ts.map +1 -1
- package/dist/services/shared/attribution.d.ts +6 -3
- package/dist/services/shared/attribution.d.ts.map +1 -1
- package/dist/services/shared/attribution.js +12 -2
- package/dist/services/shared/attribution.js.map +1 -1
- package/dist/services/shared/http.d.ts +7 -2
- package/dist/services/shared/http.d.ts.map +1 -1
- package/dist/services/shared/http.js +8 -18
- package/dist/services/shared/http.js.map +1 -1
- package/dist/services/shared/identifiers.d.ts +7 -0
- package/dist/services/shared/identifiers.d.ts.map +1 -1
- package/dist/services/shared/identifiers.js +14 -1
- package/dist/services/shared/identifiers.js.map +1 -1
- package/dist/services/uniprot/uniprot-service.d.ts.map +1 -1
- package/dist/services/uniprot/uniprot-service.js +1 -0
- package/dist/services/uniprot/uniprot-service.js.map +1 -1
- package/package.json +11 -10
- package/server.json +3 -3
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@@ -26,7 +26,7 @@ export interface FoldseekHit {
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probability?: number;
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/** Alignment bit score. */
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score?: number;
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/** Sequence identity (0–1) over the alignment
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/** Sequence identity (0–1) over the alignment, normalized from upstream's 0–100 `seqId`. */
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sequenceIdentity?: number;
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/** Raw target identifier as returned by Foldseek. */
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target: string;
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@@ -1 +1 @@
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-
{"version":3,"file":"foldseek-service.d.ts","sourceRoot":"","sources":["../../../src/services/foldseek/foldseek-service.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,wBAAwB,CAAC;AACtD,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,+BAA+B,CAAC;AAE/D,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,gCAAgC,CAAC;AACrE,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,2BAA2B,CAAC;AAI9D,oCAAoC;AACpC,MAAM,WAAW,WAAW;IAC1B,sBAAsB;IACtB,eAAe,CAAC,EAAE,MAAM,CAAC;IACzB,8BAA8B;IAC9B,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,yCAAyC;IACzC,QAAQ,EAAE,MAAM,CAAC;IACjB,yBAAyB;IACzB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,kCAAkC;IAClC,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,+BAA+B;IAC/B,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,2BAA2B;IAC3B,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,
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{"version":3,"file":"foldseek-service.d.ts","sourceRoot":"","sources":["../../../src/services/foldseek/foldseek-service.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,wBAAwB,CAAC;AACtD,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,+BAA+B,CAAC;AAE/D,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,gCAAgC,CAAC;AACrE,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,2BAA2B,CAAC;AAI9D,oCAAoC;AACpC,MAAM,WAAW,WAAW;IAC1B,sBAAsB;IACtB,eAAe,CAAC,EAAE,MAAM,CAAC;IACzB,8BAA8B;IAC9B,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,yCAAyC;IACzC,QAAQ,EAAE,MAAM,CAAC;IACjB,yBAAyB;IACzB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,kCAAkC;IAClC,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,+BAA+B;IAC/B,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,2BAA2B;IAC3B,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,4FAA4F;IAC5F,gBAAgB,CAAC,EAAE,MAAM,CAAC;IAC1B,qDAAqD;IACrD,MAAM,EAAE,MAAM,CAAC;IACf,4BAA4B;IAC5B,UAAU,EAAE,KAAK,GAAG,WAAW,GAAG,OAAO,CAAC;IAC1C,6CAA6C;IAC7C,gBAAgB,CAAC,EAAE,MAAM,CAAC;CAC3B;AAED,uDAAuD;AACvD,MAAM,MAAM,eAAe,GACvB;IAAE,MAAM,EAAE,UAAU,CAAC;IAAC,QAAQ,EAAE,MAAM,CAAC;IAAC,IAAI,EAAE,WAAW,EAAE,CAAA;CAAE,GAC7D;IAAE,MAAM,EAAE,WAAW,CAAC;IAAC,QAAQ,EAAE,MAAM,CAAA;CAAE,GACzC;IAAE,MAAM,EAAE,WAAW,CAAC;IAAC,QAAQ,EAAE,MAAM,CAAA;CAAE,GACzC;IAAE,MAAM,EAAE,QAAQ,CAAC;IAAC,KAAK,EAAE,MAAM,CAAA;CAAE,CAAC;AAExC,qBAAa,eAAe;IAC1B,OAAO,CAAC,QAAQ,CAAC,OAAO,CAAS;IAEjC,YAAY,OAAO,EAAE,SAAS,EAAE,QAAQ,EAAE,cAAc,EAAE,YAAY,EAAE,YAAY,EAEnF;IAED;;;OAGG;IACG,MAAM,CACV,MAAM,EAAE;QACN,WAAW,EAAE,MAAM,CAAC;QACpB,QAAQ,EAAE,MAAM,CAAC;QACjB,SAAS,EAAE,MAAM,EAAE,CAAC;QACpB,IAAI,EAAE,MAAM,CAAC;QACb,KAAK,EAAE,MAAM,CAAC;QACd,SAAS,EAAE,MAAM,CAAC;KACnB,EACD,GAAG,EAAE,OAAO,GACX,OAAO,CAAC,eAAe,CAAC,CA4B1B;IAED;;;;;OAKG;IACG,MAAM,CACV,MAAM,EAAE;QAAE,QAAQ,EAAE,MAAM,CAAC;QAAC,KAAK,EAAE,MAAM,CAAC;QAAC,SAAS,EAAE,MAAM,CAAA;KAAE,EAC9D,GAAG,EAAE,OAAO,GACX,OAAO,CAAC,eAAe,CAAC,CAqB1B;YAEa,MAAM;YA4BN,UAAU;YAsBV,YAAY;CAuB3B;AA+CD,wBAAgB,mBAAmB,CACjC,MAAM,EAAE,SAAS,EACjB,OAAO,EAAE,cAAc,EACvB,YAAY,EAAE,YAAY,GACzB,IAAI,CAEN;AAED,wBAAgB,kBAAkB,IAAI,eAAe,CAIpD"}
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@@ -127,8 +127,12 @@ export class FoldseekService {
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function normalizeHit(aln, database) {
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const target = aln.target;
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const hit = { target, database, ...parseTarget(target) };
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// Upstream (MMseqs2-App, which serves search.foldseek.com) emits `seqId` on a
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// 0–100 percentage scale for structure search, while this server declares
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// sequence identity as a 0–1 fraction (matching the `min_identity` inputs on
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// the RCSB paths), so convert once at the service boundary.
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if (typeof aln.seqId === 'number')
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hit.sequenceIdentity = aln.seqId;
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hit.sequenceIdentity = aln.seqId / 100;
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if (typeof aln.alnLength === 'number')
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hit.alignmentLength = aln.alnLength;
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if (typeof aln.prob === 'number')
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-
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{"version":3,"file":"foldseek-service.js","sourceRoot":"","sources":["../../../src/services/foldseek/foldseek-service.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAIH,OAAO,EAAE,gBAAgB,EAAE,QAAQ,EAAE,MAAM,+BAA+B,CAAC;AAG3E,OAAO,EAAiB,aAAa,EAAE,MAAM,oBAAoB,CAAC;AAClE,OAAO,EAAE,SAAS,EAAE,MAAM,mBAAmB,CAAC;AAmC9C,MAAM,OAAO,eAAe;IACT,OAAO,CAAS;IAEjC,YAAY,OAAkB,EAAE,QAAwB,EAAE,YAA0B;QAClF,IAAI,CAAC,OAAO,GAAG,YAAY,CAAC,eAAe,CAAC;IAC9C,CAAC;IAED;;;OAGG;IACH,KAAK,CAAC,MAAM,CACV,MAOC,EACD,GAAY;QAEZ,IAAI,QAAgB,CAAC;QACrB,IAAI,CAAC;YACH,QAAQ,GAAG,MAAM,IAAI,CAAC,MAAM,CAC1B,MAAM,CAAC,WAAW,EAClB,MAAM,CAAC,QAAQ,EACf,MAAM,CAAC,SAAS,EAChB,MAAM,CAAC,IAAI,EACX,GAAG,CACJ,CAAC;QACJ,CAAC;QAAC,OAAO,GAAG,EAAE,CAAC;YACb,OAAO,EAAE,MAAM,EAAE,QAAQ,EAAE,KAAK,EAAE,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC;QACvF,CAAC;QAED,IAAI,CAAC;YACH,MAAM,OAAO,GAAG,MAAM,aAAa,CAAgB;gBACjD,IAAI,EAAE,GAAG,EAAE,CAAC,IAAI,CAAC,UAAU,CAAC,QAAQ,EAAE,MAAM,CAAC,KAAK,EAAE,GAAG,CAAC;gBACxD,SAAS,EAAE,MAAM,CAAC,SAAS;gBAC3B,GAAG;gBACH,UAAU,EAAE,IAAI;gBAChB,aAAa,EAAE,IAAI;aACpB,CAAC,CAAC;YACH,OAAO,OAAO,CAAC,MAAM,KAAK,UAAU;gBAClC,CAAC,CAAC,EAAE,MAAM,EAAE,UAAU,EAAE,QAAQ,EAAE,IAAI,EAAE,OAAO,CAAC,KAAK,EAAE;gBACvD,CAAC,CAAC,EAAE,MAAM,EAAE,WAAW,EAAE,QAAQ,EAAE,CAAC;QACxC,CAAC;QAAC,OAAO,GAAG,EAAE,CAAC;YACb,OAAO,EAAE,MAAM,EAAE,QAAQ,EAAE,KAAK,EAAE,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC;QACvF,CAAC;IACH,CAAC;IAED;;;;;OAKG;IACH,KAAK,CAAC,MAAM,CACV,MAA8D,EAC9D,GAAY;QAEZ,IAAI,CAAC;YACH,MAAM,OAAO,GAAG,MAAM,aAAa,CAAgB;gBACjD,IAAI,EAAE,GAAG,EAAE,CAAC,IAAI,CAAC,UAAU,CAAC,MAAM,CAAC,QAAQ,EAAE,MAAM,CAAC,KAAK,EAAE,GAAG,CAAC;gBAC/D,SAAS,EAAE,MAAM,CAAC,SAAS;gBAC3B,GAAG;gBACH,UAAU,EAAE,IAAI;gBAChB,aAAa,EAAE,IAAI;aACpB,CAAC,CAAC;YACH,OAAO,OAAO,CAAC,MAAM,KAAK,UAAU;gBAClC,CAAC,CAAC,EAAE,MAAM,EAAE,UAAU,EAAE,QAAQ,EAAE,MAAM,CAAC,QAAQ,EAAE,IAAI,EAAE,OAAO,CAAC,KAAK,EAAE;gBACxE,CAAC,CAAC,EAAE,MAAM,EAAE,WAAW,EAAE,QAAQ,EAAE,MAAM,CAAC,QAAQ,EAAE,CAAC;QACzD,CAAC;QAAC,OAAO,GAAG,EAAE,CAAC;YACb,yEAAyE;YACzE,qEAAqE;YACrE,4DAA4D;YAC5D,IAAI,GAAG,YAAY,QAAQ,IAAI,GAAG,CAAC,IAAI,KAAK,gBAAgB,CAAC,aAAa,EAAE,CAAC;gBAC3E,OAAO,EAAE,MAAM,EAAE,WAAW,EAAE,QAAQ,EAAE,MAAM,CAAC,QAAQ,EAAE,CAAC;YAC5D,CAAC;YACD,OAAO,EAAE,MAAM,EAAE,QAAQ,EAAE,KAAK,EAAE,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC;QACvF,CAAC;IACH,CAAC;IAEO,KAAK,CAAC,MAAM,CAClB,WAAmB,EACnB,QAAgB,EAChB,SAAmB,EACnB,IAAY,EACZ,GAAY;QAEZ,MAAM,IAAI,GAAG,IAAI,QAAQ,EAAE,CAAC;QAC5B,IAAI,CAAC,MAAM,CAAC,GAAG,EAAE,IAAI,IAAI,CAAC,CAAC,WAAW,CAAC,EAAE,EAAE,IAAI,EAAE,gBAAgB,EAAE,CAAC,EAAE,QAAQ,CAAC,CAAC;QAChF,KAAK,MAAM,EAAE,IAAI,SAAS;YAAE,IAAI,CAAC,MAAM,CAAC,YAAY,EAAE,EAAE,CAAC,CAAC;QAC1D,IAAI,CAAC,MAAM,CAAC,MAAM,EAAE,IAAI,CAAC,CAAC;QAC1B,8EAA8E;QAC9E,MAAM,GAAG,GAAG,MAAM,SAAS,CACzB,GAAG,IAAI,CAAC,OAAO,aAAa,EAC5B,GAAG,EACH;YACE,MAAM,EAAE,MAAM;YACd,IAAI,EAAE,IAAI;YACV,SAAS,EAAE,wBAAwB;YACnC,KAAK,EAAE,UAAU;YACjB,WAAW,EAAE,IAAI;YACjB,UAAU,EAAE,CAAC;SACd,CACF,CAAC;QACF,IAAI,CAAC,GAAG,CAAC,EAAE;YAAE,MAAM,IAAI,KAAK,CAAC,qCAAqC,CAAC,CAAC;QACpE,OAAO,GAAG,CAAC,EAAE,CAAC;IAChB,CAAC;IAEO,KAAK,CAAC,UAAU,CACtB,QAAgB,EAChB,KAAa,EACb,GAAY;QAEZ,MAAM,MAAM,GAAG,MAAM,SAAS,CAC5B,GAAG,IAAI,CAAC,OAAO,eAAe,kBAAkB,CAAC,QAAQ,CAAC,EAAE,EAC5D,GAAG,EACH;YACE,SAAS,EAAE,4BAA4B;YACvC,KAAK,EAAE,UAAU;YACjB,SAAS,EAAE,MAAM;YACjB,WAAW,EAAE,GAAG;SACjB,CACF,CAAC;QACF,MAAM,MAAM,GAAG,CAAC,MAAM,CAAC,MAAM,IAAI,EAAE,CAAC,CAAC,WAAW,EAAE,CAAC;QACnD,IAAI,MAAM,KAAK,OAAO;YAAE,MAAM,IAAI,KAAK,CAAC,qDAAqD,CAAC,CAAC;QAC/F,IAAI,MAAM,KAAK,UAAU;YAAE,OAAO,EAAE,KAAK,EAAE,KAAK,EAAE,CAAC;QACnD,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,YAAY,CAAC,QAAQ,EAAE,KAAK,EAAE,GAAG,CAAC,CAAC;QAC3D,OAAO,EAAE,KAAK,EAAE,IAAI,EAAE,KAAK,EAAE,IAAI,EAAE,CAAC;IACtC,CAAC;IAEO,KAAK,CAAC,YAAY,CACxB,QAAgB,EAChB,KAAa,EACb,GAAY;QAEZ,MAAM,GAAG,GAAG,MAAM,SAAS,CACzB,GAAG,IAAI,CAAC,OAAO,eAAe,kBAAkB,CAAC,QAAQ,CAAC,IAAI,EAC9D,GAAG,EACH,EAAE,SAAS,EAAE,8BAA8B,EAAE,KAAK,EAAE,UAAU,EAAE,WAAW,EAAE,GAAG,EAAE,CACnF,CAAC;QACF,MAAM,IAAI,GAAkB,EAAE,CAAC;QAC/B,KAAK,MAAM,QAAQ,IAAI,GAAG,CAAC,OAAO,IAAI,EAAE,EAAE,CAAC;YACzC,MAAM,EAAE,GAAG,QAAQ,CAAC,EAAE,IAAI,SAAS,CAAC;YACpC,KAAK,MAAM,KAAK,IAAI,QAAQ,CAAC,UAAU,IAAI,EAAE,EAAE,CAAC;gBAC9C,KAAK,MAAM,GAAG,IAAI,KAAK,IAAI,EAAE,EAAE,CAAC;oBAC9B,IAAI,CAAC,GAAG,CAAC,MAAM;wBAAE,SAAS;oBAC1B,IAAI,CAAC,IAAI,CAAC,YAAY,CAAC,GAAG,EAAE,EAAE,CAAC,CAAC,CAAC;oBACjC,IAAI,IAAI,CAAC,MAAM,IAAI,KAAK;wBAAE,OAAO,IAAI,CAAC;gBACxC,CAAC;YACH,CAAC;QACH,CAAC;QACD,OAAO,IAAI,CAAC;IACd,CAAC;CACF;AAED,iFAAiF;AAEjF,SAAS,YAAY,CAAC,GAAiB,EAAE,QAAgB;IACvD,MAAM,MAAM,GAAG,GAAG,CAAC,MAAgB,CAAC;IACpC,MAAM,GAAG,GAAgB,EAAE,MAAM,EAAE,QAAQ,EAAE,GAAG,WAAW,CAAC,MAAM,CAAC,EAAE,CAAC;IACtE,8EAA8E;IAC9E,0EAA0E;IAC1E,6EAA6E;IAC7E,4DAA4D;IAC5D,IAAI,OAAO,GAAG,CAAC,KAAK,KAAK,QAAQ;QAAE,GAAG,CAAC,gBAAgB,GAAG,GAAG,CAAC,KAAK,GAAG,GAAG,CAAC;IAC1E,IAAI,OAAO,GAAG,CAAC,SAAS,KAAK,QAAQ;QAAE,GAAG,CAAC,eAAe,GAAG,GAAG,CAAC,SAAS,CAAC;IAC3E,IAAI,OAAO,GAAG,CAAC,IAAI,KAAK,QAAQ;QAAE,GAAG,CAAC,WAAW,GAAG,GAAG,CAAC,IAAI,CAAC;IAC7D,IAAI,OAAO,GAAG,CAAC,IAAI,KAAK,QAAQ;QAAE,GAAG,CAAC,MAAM,GAAG,GAAG,CAAC,IAAI,CAAC;IACxD,IAAI,OAAO,GAAG,CAAC,KAAK,KAAK,QAAQ;QAAE,GAAG,CAAC,KAAK,GAAG,GAAG,CAAC,KAAK,CAAC;IACzD,OAAO,GAAG,CAAC;AACb,CAAC;AAED,qEAAqE;AACrE,SAAS,WAAW,CAClB,MAAc;IAEd,MAAM,EAAE,GAAG,yBAAyB,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;IAClD,IAAI,EAAE;QAAE,OAAO,EAAE,UAAU,EAAE,WAAW,EAAE,gBAAgB,EAAE,EAAE,CAAC,CAAC,CAAW,EAAE,CAAC;IAC9E,MAAM,GAAG,GAAG,uCAAuC,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;IACjE,IAAI,GAAG;QACL,OAAO,EAAE,UAAU,EAAE,KAAK,EAAE,KAAK,EAAG,GAAG,CAAC,CAAC,CAAY,CAAC,WAAW,EAAE,EAAE,KAAK,EAAE,GAAG,CAAC,CAAC,CAAW,EAAE,CAAC;IACjG,OAAO,EAAE,UAAU,EAAE,OAAO,EAAE,CAAC;AACjC,CAAC;AAgBD,IAAI,QAAqC,CAAC;AAE1C,MAAM,UAAU,mBAAmB,CACjC,MAAiB,EACjB,OAAuB,EACvB,YAA0B;IAE1B,QAAQ,GAAG,IAAI,eAAe,CAAC,MAAM,EAAE,OAAO,EAAE,YAAY,CAAC,CAAC;AAChE,CAAC;AAED,MAAM,UAAU,kBAAkB;IAChC,IAAI,CAAC,QAAQ;QACX,MAAM,IAAI,KAAK,CAAC,yEAAyE,CAAC,CAAC;IAC7F,OAAO,QAAQ,CAAC;AAClB,CAAC"}
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@@ -8,37 +8,37 @@ import type { FacetSpec } from './rcsb-service.js';
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8
8
|
/** The supported `group_by` / facet dimensions and how RCSB aggregates each. */
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9
9
|
export declare const FACET_DIMENSIONS: {
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readonly method: {
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-
readonly attribute:
|
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12
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-
readonly aggregation:
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13
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-
readonly label:
|
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11
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+
readonly attribute: 'exptl.method';
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12
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+
readonly aggregation: 'terms';
|
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13
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+
readonly label: 'Experimental method';
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14
14
|
};
|
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15
15
|
readonly organism: {
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-
readonly attribute:
|
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17
|
-
readonly aggregation:
|
|
18
|
-
readonly label:
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16
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+
readonly attribute: 'rcsb_entity_source_organism.ncbi_scientific_name';
|
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17
|
+
readonly aggregation: 'terms';
|
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18
|
+
readonly label: 'Source organism';
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19
|
};
|
|
20
20
|
readonly polymer_type: {
|
|
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|
-
readonly attribute:
|
|
22
|
-
readonly aggregation:
|
|
23
|
-
readonly label:
|
|
21
|
+
readonly attribute: 'rcsb_entry_info.polymer_composition';
|
|
22
|
+
readonly aggregation: 'terms';
|
|
23
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+
readonly label: 'Polymer composition';
|
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24
24
|
};
|
|
25
25
|
readonly resolution: {
|
|
26
|
-
readonly attribute:
|
|
27
|
-
readonly aggregation:
|
|
26
|
+
readonly attribute: 'rcsb_entry_info.resolution_combined';
|
|
27
|
+
readonly aggregation: 'histogram';
|
|
28
28
|
readonly defaultInterval: 0.5;
|
|
29
|
-
readonly label:
|
|
29
|
+
readonly label: 'Resolution (Å)';
|
|
30
30
|
};
|
|
31
31
|
readonly release_year: {
|
|
32
|
-
readonly attribute:
|
|
33
|
-
readonly aggregation:
|
|
34
|
-
readonly defaultInterval:
|
|
35
|
-
readonly label:
|
|
32
|
+
readonly attribute: 'rcsb_accession_info.initial_release_date';
|
|
33
|
+
readonly aggregation: 'date_histogram';
|
|
34
|
+
readonly defaultInterval: 'year';
|
|
35
|
+
readonly label: 'Release year';
|
|
36
36
|
};
|
|
37
37
|
readonly molecular_weight: {
|
|
38
|
-
readonly attribute:
|
|
39
|
-
readonly aggregation:
|
|
38
|
+
readonly attribute: 'rcsb_entry_info.molecular_weight';
|
|
39
|
+
readonly aggregation: 'histogram';
|
|
40
40
|
readonly defaultInterval: 50;
|
|
41
|
-
readonly label:
|
|
41
|
+
readonly label: 'Molecular weight (kDa)';
|
|
42
42
|
};
|
|
43
43
|
};
|
|
44
44
|
/** A supported facet dimension name. */
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"facets.d.ts","sourceRoot":"","sources":["../../../src/services/rcsb/facets.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,mBAAmB,CAAC;AAWnD,gFAAgF;AAChF,eAAO,MAAM,gBAAgB
|
|
1
|
+
{"version":3,"file":"facets.d.ts","sourceRoot":"","sources":["../../../src/services/rcsb/facets.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,mBAAmB,CAAC;AAWnD,gFAAgF;AAChF,eAAO,MAAM,gBAAgB;;iBAEzB,SAAS,EAAE,cAAc;iBACzB,WAAW,EAAE,OAAO;iBACpB,KAAK,EAAE,qBAAqB;;;iBAG5B,SAAS,EAAE,kDAAkD;iBAC7D,WAAW,EAAE,OAAO;iBACpB,KAAK,EAAE,iBAAiB;;;iBAGxB,SAAS,EAAE,qCAAqC;iBAChD,WAAW,EAAE,OAAO;iBACpB,KAAK,EAAE,qBAAqB;;;iBAG5B,SAAS,EAAE,qCAAqC;iBAChD,WAAW,EAAE,WAAW;iBACxB,eAAe,EAAE,GAAG;iBACpB,KAAK,EAAE,gBAAgB;;;iBAGvB,SAAS,EAAE,0CAA0C;iBACrD,WAAW,EAAE,gBAAgB;iBAC7B,eAAe,EAAE,MAAM;iBACvB,KAAK,EAAE,cAAc;;;iBAGrB,SAAS,EAAE,kCAAkC;iBAC7C,WAAW,EAAE,WAAW;iBACxB,eAAe,EAAE,EAAE;iBACnB,KAAK,EAAE,wBAAwB;;CAEc,CAAC;AAElD,wCAAwC;AACxC,MAAM,MAAM,kBAAkB,GAAG,MAAM,OAAO,gBAAgB,CAAC;AAE/D,qDAAqD;AACrD,eAAO,MAAM,qBAAqB,EAAoC,CACpE,kBAAkB,EAClB,GAAG,kBAAkB,EAAE,CACxB,CAAC;AAEF,sGAAsG;AACtG,wBAAgB,cAAc,CAC5B,SAAS,EAAE,kBAAkB,EAC7B,QAAQ,CAAC,EAAE,MAAM,GAAG,MAAM,EAC1B,KAAK,CAAC,EAAE,kBAAkB,GACzB,SAAS,CAYX"}
|
|
@@ -40,7 +40,7 @@ export declare class RcsbService {
|
|
|
40
40
|
maxEvalue?: number;
|
|
41
41
|
minIdentity?: number;
|
|
42
42
|
limit?: number;
|
|
43
|
-
contentType?: ContentType;
|
|
43
|
+
contentType?: ContentType[];
|
|
44
44
|
}, ctx: Context): Promise<SearchResult>;
|
|
45
45
|
/**
|
|
46
46
|
* Find entries containing a given ligand (exact chemical component ID),
|
|
@@ -51,7 +51,7 @@ export declare class RcsbService {
|
|
|
51
51
|
*/
|
|
52
52
|
searchByLigand(compId: string, opts: {
|
|
53
53
|
limit?: number;
|
|
54
|
-
contentType?: ContentType;
|
|
54
|
+
contentType?: ContentType[];
|
|
55
55
|
}, ctx: Context): Promise<SearchResult>;
|
|
56
56
|
/**
|
|
57
57
|
* Count PDB entries containing a given ligand (its deposition frequency). Used
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"rcsb-service.d.ts","sourceRoot":"","sources":["../../../src/services/rcsb/rcsb-service.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,wBAAwB,CAAC;AACtD,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,+BAA+B,CAAC;AAE/D,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,gCAAgC,CAAC;AACrE,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,2BAA2B,CAAC;AAE9D,OAAO,KAAK,EAEV,WAAW,EACX,QAAQ,EACR,WAAW,EACX,SAAS,EAET,cAAc,EAId,YAAY,EACZ,qBAAqB,EACrB,WAAW,EACZ,MAAM,YAAY,CAAC;AAEpB,iDAAiD;AACjD,MAAM,MAAM,UAAU,GAAG,OAAO,GAAG,gBAAgB,GAAG,gBAAgB,CAAC;AAEvE,+EAA+E;AAC/E,MAAM,WAAW,SAAS;IACxB,wBAAwB;IACxB,WAAW,EAAE,OAAO,GAAG,WAAW,GAAG,gBAAgB,CAAC;IACtD,mCAAmC;IACnC,SAAS,EAAE,MAAM,CAAC;IAClB,iDAAiD;IACjD,KAAK,CAAC,EAAE,SAAS,CAAC;IAClB,qDAAqD;IACrD,SAAS,EAAE,MAAM,CAAC;IAClB,gGAAgG;IAChG,QAAQ,CAAC,EAAE,MAAM,GAAG,MAAM,CAAC;CAC5B;AA6BD,qBAAa,WAAW;IACtB,OAAO,CAAC,QAAQ,CAAC,SAAS,CAAS;IACnC,OAAO,CAAC,QAAQ,CAAC,UAAU,CAAS;IACpC,OAAO,CAAC,QAAQ,CAAC,YAAY,CAAS;IACtC,OAAO,CAAC,QAAQ,CAAC,SAAS,CAAS;
|
|
1
|
+
{"version":3,"file":"rcsb-service.d.ts","sourceRoot":"","sources":["../../../src/services/rcsb/rcsb-service.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,wBAAwB,CAAC;AACtD,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,+BAA+B,CAAC;AAE/D,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,gCAAgC,CAAC;AACrE,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,2BAA2B,CAAC;AAE9D,OAAO,KAAK,EAEV,WAAW,EACX,QAAQ,EACR,WAAW,EACX,SAAS,EAET,cAAc,EAId,YAAY,EACZ,qBAAqB,EACrB,WAAW,EACZ,MAAM,YAAY,CAAC;AAEpB,iDAAiD;AACjD,MAAM,MAAM,UAAU,GAAG,OAAO,GAAG,gBAAgB,GAAG,gBAAgB,CAAC;AAEvE,+EAA+E;AAC/E,MAAM,WAAW,SAAS;IACxB,wBAAwB;IACxB,WAAW,EAAE,OAAO,GAAG,WAAW,GAAG,gBAAgB,CAAC;IACtD,mCAAmC;IACnC,SAAS,EAAE,MAAM,CAAC;IAClB,iDAAiD;IACjD,KAAK,CAAC,EAAE,SAAS,CAAC;IAClB,qDAAqD;IACrD,SAAS,EAAE,MAAM,CAAC;IAClB,gGAAgG;IAChG,QAAQ,CAAC,EAAE,MAAM,GAAG,MAAM,CAAC;CAC5B;AA6BD,qBAAa,WAAW;IACtB,OAAO,CAAC,QAAQ,CAAC,SAAS,CAAS;IACnC,OAAO,CAAC,QAAQ,CAAC,UAAU,CAAS;IACpC,OAAO,CAAC,QAAQ,CAAC,YAAY,CAAS;IACtC,OAAO,CAAC,QAAQ,CAAC,SAAS,CAAS;IAEnC,YAAY,OAAO,EAAE,SAAS,EAAE,QAAQ,EAAE,cAAc,EAAE,YAAY,EAAE,YAAY,EAKnF;IAID,gFAAgF;IAC1E,MAAM,CACV,MAAM,EAAE,qBAAqB,EAC7B,GAAG,EAAE,OAAO,EACZ,MAAM,CAAC,EAAE,SAAS,EAAE,GACnB,OAAO,CAAC,YAAY,CAAC,CAmBvB;IAED,uEAAuE;IACjE,cAAc,CAClB,QAAQ,EAAE,MAAM,EAChB,IAAI,EAAE;QAAE,SAAS,CAAC,EAAE,MAAM,CAAC;QAAC,WAAW,CAAC,EAAE,MAAM,CAAC;QAAC,KAAK,CAAC,EAAE,MAAM,CAAC;QAAC,WAAW,CAAC,EAAE,WAAW,EAAE,CAAA;KAAE,EAC/F,GAAG,EAAE,OAAO,GACX,OAAO,CAAC,YAAY,CAAC,CAqBvB;IAED;;;;;;OAMG;IACG,cAAc,CAClB,MAAM,EAAE,MAAM,EACd,IAAI,EAAE;QAAE,KAAK,CAAC,EAAE,MAAM,CAAC;QAAC,WAAW,CAAC,EAAE,WAAW,EAAE,CAAA;KAAE,EACrD,GAAG,EAAE,OAAO,GACX,OAAO,CAAC,YAAY,CAAC,CAOvB;IAED;;;;OAIG;IACG,sBAAsB,CAAC,MAAM,EAAE,MAAM,EAAE,GAAG,EAAE,OAAO,GAAG,OAAO,CAAC,MAAM,CAAC,CAO1E;IAED,yEAAyE;IACnE,aAAa,CAAC,KAAK,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,EAAE,GAAG,EAAE,OAAO,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC,CAqBjF;IAED,2EAA2E;IACrE,aAAa,CACjB,MAAM,EAAE,qBAAqB,EAC7B,MAAM,EAAE,SAAS,EAAE,EACnB,GAAG,EAAE,OAAO,GACX,OAAO,CAAC;QAAE,KAAK,EAAE,MAAM,CAAC;QAAC,MAAM,EAAE,cAAc,EAAE,CAAA;KAAE,CAAC,CAYtD;IAID,sEAAsE;IAChE,UAAU,CAAC,GAAG,EAAE,MAAM,EAAE,EAAE,GAAG,EAAE,OAAO,GAAG,OAAO,CAAC,SAAS,EAAE,CAAC,CASlE;IAED;;;;;;OAMG;IACG,sBAAsB,CAAC,KAAK,EAAE,MAAM,EAAE,GAAG,EAAE,OAAO,GAAG,OAAO,CAAC,WAAW,EAAE,CAAC,CAuBhF;IAED,kEAAkE;IAC5D,WAAW,CACf,KAAK,EAAE,MAAM,EACb,GAAG,EAAE,OAAO,GACX,OAAO,CAAC;QAAE,QAAQ,EAAE,MAAM,CAAC;QAAC,QAAQ,EAAE,MAAM,CAAA;KAAE,GAAG,IAAI,CAAC,CAaxD;IAED,oFAAoF;IAC9E,eAAe,CACnB,KAAK,EAAE,MAAM,EACb,MAAM,EAAE,MAAM,GAAG,SAAS,EAC1B,GAAG,EAAE,OAAO,GACX,OAAO,CAAC,WAAW,EAAE,CAAC,CA+BxB;IAID,uEAAuE;IACjE,WAAW,CAAC,MAAM,EAAE,MAAM,EAAE,GAAG,EAAE,OAAO,GAAG,OAAO,CAAC,QAAQ,GAAG,IAAI,CAAC,CAmBxE;IAID,gEAAgE;IAChE,iBAAiB,CAAC,KAAK,EAAE,MAAM,EAAE,MAAM,EAAE,KAAK,GAAG,KAAK,GAAG,MAAM,GAAG,MAAM,CAEvE;IAID,OAAO,CAAC,UAAU;YAeJ,OAAO;CAwBtB;AAID,yFAAyF;AACzF,wBAAgB,UAAU,CAAC,MAAM,EAAE,qBAAqB,GAAG,OAAO,CAqCjE;AAiDD,sFAAsF;AACtF,wBAAgB,WAAW,CAAC,IAAI,EAAE,SAAS,GAAG,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAUpE;AAuSD,wBAAgB,eAAe,CAC7B,MAAM,EAAE,SAAS,EACjB,OAAO,EAAE,cAAc,EACvB,YAAY,EAAE,YAAY,GACzB,IAAI,CAEN;AAED,wBAAgB,cAAc,IAAI,WAAW,CAG5C"}
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@@ -209,6 +209,7 @@ export class RcsbService {
|
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209
|
operation: 'RcsbService.getChemComp',
|
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|
label: 'RCSB Data API',
|
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211
|
baseDelayMs: 400,
|
|
212
|
+
expectedStatuses: [404],
|
|
212
213
|
});
|
|
213
214
|
}
|
|
214
215
|
catch (err) {
|
|
@@ -292,10 +293,15 @@ export function buildQuery(params) {
|
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|
292
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|
function textNode(attribute, operator, value) {
|
|
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|
return { type: 'terminal', service: 'text', parameters: { attribute, operator, value } };
|
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294
295
|
}
|
|
295
|
-
|
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|
-
|
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296
|
+
/**
|
|
297
|
+
* Emit the `results_content_type` request option for a content scope. Omitting
|
|
298
|
+
* the option is not a union — RCSB defaults to experimental only — so a caller
|
|
299
|
+
* wanting both universes must list both members explicitly.
|
|
300
|
+
*/
|
|
301
|
+
function contentTypeOption(contentTypes) {
|
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302
|
+
if (!contentTypes || contentTypes.length === 0)
|
|
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303
|
return {};
|
|
298
|
-
return { results_content_type:
|
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|
+
return { results_content_type: contentTypes };
|
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305
|
}
|
|
300
306
|
/**
|
|
301
307
|
* Ligand-containment search body (exact chemical-component ID), shared by
|
|
@@ -316,7 +322,7 @@ function ligandContainmentQuery(compId, contentType, rows, sortByResolution) {
|
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316
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|
},
|
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|
return_type: 'entry',
|
|
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|
request_options: {
|
|
319
|
-
...contentTypeOption(contentType ?? 'experimental'),
|
|
325
|
+
...contentTypeOption(contentType ?? ['experimental']),
|
|
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326
|
paginate: { start: 0, rows },
|
|
321
327
|
...(sortByResolution
|
|
322
328
|
? { sort: [{ sort_by: 'rcsb_entry_info.resolution_combined', direction: 'asc' }] }
|
|
@@ -392,7 +398,19 @@ function normalizeBuckets(raw, spec) {
|
|
|
392
398
|
return bucket;
|
|
393
399
|
});
|
|
394
400
|
}
|
|
401
|
+
/**
|
|
402
|
+
* RCSB's `source_db` spelling for a computed structure model → the attribution
|
|
403
|
+
* display name for that provider. An unrecognized value passes through verbatim
|
|
404
|
+
* rather than being dropped: crediting an unknown modelling provider by its own
|
|
405
|
+
* name beats silently attributing its model to the PDB.
|
|
406
|
+
*/
|
|
407
|
+
const CSM_PROVIDER_NAMES = {
|
|
408
|
+
AlphaFoldDB: 'AlphaFold DB',
|
|
409
|
+
ModelArchive: 'ModelArchive',
|
|
410
|
+
};
|
|
395
411
|
function normalizeEntry(raw) {
|
|
412
|
+
const sourceDb = raw.rcsb_comp_model_provenance?.source_db;
|
|
413
|
+
const computedModelProvider = sourceDb ? (CSM_PROVIDER_NAMES[sourceDb] ?? sourceDb) : undefined;
|
|
396
414
|
const polymerEntities = (raw.polymer_entities ?? []).map(normalizePolymerEntity);
|
|
397
415
|
const organisms = [
|
|
398
416
|
...new Set(polymerEntities.map((e) => e.organism).filter((o) => !!o)),
|
|
@@ -404,6 +422,7 @@ function normalizeEntry(raw) {
|
|
|
404
422
|
const resolution = raw.rcsb_entry_info?.resolution_combined?.[0];
|
|
405
423
|
return {
|
|
406
424
|
id: raw.rcsb_id,
|
|
425
|
+
...(computedModelProvider ? { computedModelProvider } : {}),
|
|
407
426
|
...(raw.struct?.title ? { title: raw.struct.title } : {}),
|
|
408
427
|
...(methods.length > 0 ? { methods } : {}),
|
|
409
428
|
...(typeof resolution === 'number' ? { resolution } : {}),
|
|
@@ -480,6 +499,7 @@ const ENTRIES_QUERY = `query Entries($ids: [String!]!) {
|
|
|
480
499
|
rcsb_id
|
|
481
500
|
struct { title }
|
|
482
501
|
exptl { method }
|
|
502
|
+
rcsb_comp_model_provenance { source_db }
|
|
483
503
|
rcsb_entry_info { resolution_combined molecular_weight }
|
|
484
504
|
rcsb_accession_info { initial_release_date }
|
|
485
505
|
polymer_entities {
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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+
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@@ -87,6 +87,13 @@ export interface LigandMeta {
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87
87
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}
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88
88
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/** Normalized entry-level metadata from the GraphQL batch. */
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89
89
|
export interface EntryMeta {
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90
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+
/**
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91
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+
* Modelling provider display name when this ID is a computed structure model
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|
92
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+
* (`AF_*` / `MA_*`) rather than an experimental entry — e.g. "AlphaFold DB",
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93
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+
* "ModelArchive". Absent for experimental entries. RCSB serves both universes
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94
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+
* through the same entry endpoint, so this is what separates them.
|
|
95
|
+
*/
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|
96
|
+
computedModelProvider?: string;
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|
90
97
|
/** PDB entry ID. */
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|
91
98
|
id: string;
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92
99
|
/** Bound ligands (non-polymer entities). */
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@@ -143,12 +150,16 @@ export interface ChemComp {
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143
150
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/** Component type (e.g. "non-polymer"). */
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144
151
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type?: string;
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145
152
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}
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|
146
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-
/**
|
|
153
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+
/** One structure universe RCSB can scope results to. */
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|
147
154
|
export type ContentType = 'experimental' | 'computational';
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|
148
155
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/** Inputs to a structure search (shared by search + analyze tools). */
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|
149
156
|
export interface StructureSearchParams {
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150
|
-
/**
|
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151
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-
|
|
157
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+
/**
|
|
158
|
+
* Result content universes, sent as `results_content_type`. Pass both members
|
|
159
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+
* for a union — omitting the field is NOT a union upstream, it is RCSB's
|
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160
|
+
* experimental-only default, which drops every computed model.
|
|
161
|
+
*/
|
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162
|
+
contentType?: ContentType[];
|
|
152
163
|
/** Page size. */
|
|
153
164
|
limit?: number;
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|
154
165
|
/** Max E-value for a sequence query. */
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|
@@ -1 +1 @@
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|
|
1
|
-
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|
|
1
|
+
{"version":3,"file":"types.d.ts","sourceRoot":"","sources":["../../../src/services/rcsb/types.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,sDAAsD;AACtD,MAAM,WAAW,SAAS;IACxB,qFAAqF;IACrF,EAAE,EAAE,MAAM,CAAC;IACX,4BAA4B;IAC5B,KAAK,EAAE,MAAM,CAAC;CACf;AAED,sFAAsF;AACtF,MAAM,WAAW,WAAW;IAC1B,yDAAyD;IACzD,QAAQ,CAAC,EAAE,cAAc,EAAE,CAAC;IAC5B,sCAAsC;IACtC,KAAK,EAAE,MAAM,CAAC;IACd,mEAAmE;IACnE,KAAK,EAAE,MAAM,CAAC;IACd;;;;OAIG;IACH,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB;;;;OAIG;IACH,OAAO,CAAC,EAAE,MAAM,CAAC;CAClB;AAED,yCAAyC;AACzC,MAAM,WAAW,cAAc;IAC7B,uDAAuD;IACvD,SAAS,EAAE,MAAM,CAAC;IAClB,yFAAyF;IACzF,OAAO,EAAE,WAAW,EAAE,CAAC;IACvB,2EAA2E;IAC3E,SAAS,EAAE,MAAM,CAAC;IAClB,gEAAgE;IAChE,SAAS,CAAC,EAAE,OAAO,CAAC;CACrB;AAED,oCAAoC;AACpC,MAAM,WAAW,YAAY;IAC3B,+CAA+C;IAC/C,MAAM,CAAC,EAAE,cAAc,EAAE,CAAC;IAC1B,gCAAgC;IAChC,IAAI,EAAE,SAAS,EAAE,CAAC;IAClB,kDAAkD;IAClD,KAAK,EAAE,MAAM,CAAC;CACf;AAED,kEAAkE;AAClE,MAAM,WAAW,iBAAiB;IAChC,iDAAiD;IACjD,MAAM,CAAC,EAAE,MAAM,EAAE,CAAC;IAClB,+DAA+D;IAC/D,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,yCAAyC;IACzC,QAAQ,EAAE,MAAM,CAAC;IACjB,uCAAuC;IACvC,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,8EAA8E;IAC9E,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,4CAA4C;IAC5C,cAAc,CAAC,EAAE,MAAM,CAAC;CACzB;AAED,mGAAmG;AACnG,MAAM,WAAW,WAAW;IAC1B,6CAA6C;IAC7C,SAAS,EAAE,MAAM,CAAC;IAClB,4EAA4E;IAC5E,MAAM,EAAE,MAAM,EAAE,CAAC;IACjB,oEAAoE;IACpE,WAAW,CAAC,EAAE,MAAM,CAAC;CACtB;AAED,8DAA8D;AAC9D,MAAM,WAAW,UAAU;IACzB,iDAAiD;IACjD,MAAM,EAAE,MAAM,CAAC;IACf,wCAAwC;IACxC,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,oCAAoC;IACpC,IAAI,CAAC,EAAE,MAAM,CAAC;CACf;AAED,8DAA8D;AAC9D,MAAM,WAAW,SAAS;IACxB;;;;;OAKG;IACH,qBAAqB,CAAC,EAAE,MAAM,CAAC;IAC/B,oBAAoB;IACpB,EAAE,EAAE,MAAM,CAAC;IACX,4CAA4C;IAC5C,OAAO,EAAE,UAAU,EAAE,CAAC;IACtB,2DAA2D;IAC3D,OAAO,CAAC,EAAE,MAAM,EAAE,CAAC;IACnB,kDAAkD;IAClD,eAAe,CAAC,EAAE,MAAM,CAAC;IACzB,yDAAyD;IACzD,SAAS,EAAE,MAAM,EAAE,CAAC;IACpB,gCAAgC;IAChC,eAAe,EAAE,iBAAiB,EAAE,CAAC;IACrC,uCAAuC;IACvC,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,4CAA4C;IAC5C,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,uBAAuB;IACvB,KAAK,CAAC,EAAE,MAAM,CAAC;CAChB;AAED,4DAA4D;AAC5D,MAAM,WAAW,cAAc;IAC7B,mDAAmD;IACnD,MAAM,EAAE,MAAM,CAAC;IACf,2CAA2C;IAC3C,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,kDAAkD;IAClD,aAAa,EAAE,MAAM,CAAC;IACtB,wCAAwC;IACxC,KAAK,CAAC,EAAE,MAAM,CAAC;CAChB;AAED,4DAA4D;AAC5D,MAAM,WAAW,WAAW;IAC1B,uCAAuC;IACvC,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,oCAAoC;IACpC,YAAY,EAAE,MAAM,CAAC;IACrB,mDAAmD;IACnD,QAAQ,EAAE,cAAc,EAAE,CAAC;CAC5B;AAED,gDAAgD;AAChD,MAAM,WAAW,QAAQ;IACvB,iCAAiC;IACjC,MAAM,EAAE,MAAM,CAAC;IACf,yBAAyB;IACzB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,2BAA2B;IAC3B,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,+BAA+B;IAC/B,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,qBAAqB;IACrB,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,sCAAsC;IACtC,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,2CAA2C;IAC3C,IAAI,CAAC,EAAE,MAAM,CAAC;CACf;AAED,wDAAwD;AACxD,MAAM,MAAM,WAAW,GAAG,cAAc,GAAG,eAAe,CAAC;AAE3D,uEAAuE;AACvE,MAAM,WAAW,qBAAqB;IACpC;;;;OAIG;IACH,WAAW,CAAC,EAAE,WAAW,EAAE,CAAC;IAC5B,iBAAiB;IACjB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,wCAAwC;IACxC,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,+BAA+B;IAC/B,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,6DAA6D;IAC7D,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,4DAA4D;IAC5D,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,gDAAgD;IAChD,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,2DAA2D;IAC3D,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,mBAAmB;IACnB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,uBAAuB;IACvB,IAAI,CAAC,EAAE,MAAM,CAAC;CACf"}
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@@ -8,8 +8,11 @@
|
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8
8
|
* `best_available` structures are federated through 3D-Beacons, an open set of
|
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9
9
|
* model providers (AlphaFold DB, SWISS-MODEL, BFVD, AlphaFill, …), so an uncurated
|
|
10
10
|
* provider gets an honest fallback entry that asserts no license rather than a
|
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11
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-
* fabricated one.
|
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12
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-
*
|
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11
|
+
* fabricated one. Computed structure models fetched by RCSB ID (`AF_*` / `MA_*`)
|
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12
|
+
* credit their modelling provider (AlphaFold DB, ModelArchive) rather than the
|
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13
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+
* PDB — the RCSB entry endpoint serves them, but the license is the provider's.
|
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14
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+
* Pure data + a projection helper; the Zod output schema and renderer live in
|
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15
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+
* the tools' shared `_schemas.ts`.
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13
16
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* @module services/shared/attribution
|
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14
17
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*/
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18
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/**
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@@ -17,7 +20,7 @@
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* render order. The structure sources come first (RCSB PDB, then the federated
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21
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* predicted providers), followed by the annotation trio.
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19
22
|
*/
|
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20
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-
export declare const CURATED_SOURCES: readonly [
|
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+
export declare const CURATED_SOURCES: readonly ['RCSB PDB', 'AlphaFold DB', 'SWISS-MODEL', 'BFVD', 'ModelArchive', 'UniProt', 'InterPro', 'GO'];
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24
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/** A curated data-source display name with a verified license + citation. */
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export type CuratedSource = (typeof CURATED_SOURCES)[number];
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/** License, citation, and homepage for one contributing data source. */
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"attribution.d.ts","sourceRoot":"","sources":["../../../src/services/shared/attribution.ts"],"names":[],"mappings":"AAAA
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1
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+
{"version":3,"file":"attribution.d.ts","sourceRoot":"","sources":["../../../src/services/shared/attribution.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;GAgBG;AAEH;;;;GAIG;AACH,eAAO,MAAM,eAAe,YAC1B,UAAU,EACV,cAAc,EACd,aAAa,EACb,MAAM,EACN,cAAc,EACd,SAAS,EACT,UAAU,EACV,IAAI,CACI,CAAC;AAEX,6EAA6E;AAC7E,MAAM,MAAM,aAAa,GAAG,CAAC,OAAO,eAAe,CAAC,CAAC,MAAM,CAAC,CAAC;AAE7D,wEAAwE;AACxE,MAAM,WAAW,WAAW;IAC1B,qEAAqE;IACrE,QAAQ,EAAE,MAAM,CAAC;IACjB,uBAAuB;IACvB,QAAQ,EAAE,MAAM,CAAC;IACjB,sEAAsE;IACtE,OAAO,EAAE,MAAM,CAAC;IAChB,iFAAiF;IACjF,MAAM,EAAE,MAAM,CAAC;CAChB;AAqFD;;;;;;GAMG;AACH,wBAAgB,eAAe,CAAC,OAAO,EAAE,QAAQ,CAAC,MAAM,CAAC,GAAG,WAAW,EAAE,CAQxE"}
|
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@@ -8,8 +8,11 @@
|
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8
8
|
* `best_available` structures are federated through 3D-Beacons, an open set of
|
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9
9
|
* model providers (AlphaFold DB, SWISS-MODEL, BFVD, AlphaFill, …), so an uncurated
|
|
10
10
|
* provider gets an honest fallback entry that asserts no license rather than a
|
|
11
|
-
* fabricated one.
|
|
12
|
-
*
|
|
11
|
+
* fabricated one. Computed structure models fetched by RCSB ID (`AF_*` / `MA_*`)
|
|
12
|
+
* credit their modelling provider (AlphaFold DB, ModelArchive) rather than the
|
|
13
|
+
* PDB — the RCSB entry endpoint serves them, but the license is the provider's.
|
|
14
|
+
* Pure data + a projection helper; the Zod output schema and renderer live in
|
|
15
|
+
* the tools' shared `_schemas.ts`.
|
|
13
16
|
* @module services/shared/attribution
|
|
14
17
|
*/
|
|
15
18
|
/**
|
|
@@ -22,6 +25,7 @@ export const CURATED_SOURCES = [
|
|
|
22
25
|
'AlphaFold DB',
|
|
23
26
|
'SWISS-MODEL',
|
|
24
27
|
'BFVD',
|
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28
|
+
'ModelArchive',
|
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25
29
|
'UniProt',
|
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26
30
|
'InterPro',
|
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27
31
|
'GO',
|
|
@@ -59,6 +63,12 @@ const ATTRIBUTIONS = {
|
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59
63
|
citation: 'Kim et al., "BFVD—a large repository of predicted viral protein structures," Nucleic Acids Research 53(D1):D340–D347 (2025). DOI: 10.1093/nar/gkae1119',
|
|
60
64
|
homepage: 'https://bfvd.steineggerlab.workers.dev/',
|
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61
65
|
},
|
|
66
|
+
ModelArchive: {
|
|
67
|
+
source: 'ModelArchive',
|
|
68
|
+
license: 'CC BY 4.0',
|
|
69
|
+
citation: 'ModelArchive (SIB Swiss Institute of Bioinformatics / Biozentrum, University of Basel). Each deposited model carries its own DOI — cite the model accession alongside its depositors.',
|
|
70
|
+
homepage: 'https://www.modelarchive.org/',
|
|
71
|
+
},
|
|
62
72
|
UniProt: {
|
|
63
73
|
source: 'UniProt',
|
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64
74
|
license: 'CC BY 4.0',
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"attribution.js","sourceRoot":"","sources":["../../../src/services/shared/attribution.ts"],"names":[],"mappings":"AAAA
|
|
1
|
+
{"version":3,"file":"attribution.js","sourceRoot":"","sources":["../../../src/services/shared/attribution.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;GAgBG;AAEH;;;;GAIG;AACH,MAAM,CAAC,MAAM,eAAe,GAAG;IAC7B,UAAU;IACV,cAAc;IACd,aAAa;IACb,MAAM;IACN,cAAc;IACd,SAAS;IACT,UAAU;IACV,IAAI;CACI,CAAC;AAiBX;;;;;;;GAOG;AACH,MAAM,YAAY,GAAuC;IACvD,UAAU,EAAE;QACV,MAAM,EAAE,UAAU;QAClB,OAAO,EAAE,mBAAmB;QAC5B,QAAQ,EACN,kHAAkH;QACpH,QAAQ,EAAE,uBAAuB;KAClC;IACD,cAAc,EAAE;QACd,MAAM,EAAE,cAAc;QACtB,OAAO,EAAE,WAAW;QACpB,QAAQ,EACN,0UAA0U;QAC5U,QAAQ,EAAE,8BAA8B;KACzC;IACD,aAAa,EAAE;QACb,MAAM,EAAE,aAAa;QACrB,OAAO,EAAE,cAAc;QACvB,QAAQ,EACN,0TAA0T;QAC5T,QAAQ,EAAE,gCAAgC;KAC3C;IACD,IAAI,EAAE;QACJ,MAAM,EAAE,MAAM;QACd,OAAO,EAAE,WAAW;QACpB,QAAQ,EACN,wJAAwJ;QAC1J,QAAQ,EAAE,yCAAyC;KACpD;IACD,YAAY,EAAE;QACZ,MAAM,EAAE,cAAc;QACtB,OAAO,EAAE,WAAW;QACpB,QAAQ,EACN,uLAAuL;QACzL,QAAQ,EAAE,+BAA+B;KAC1C;IACD,OAAO,EAAE;QACP,MAAM,EAAE,SAAS;QACjB,OAAO,EAAE,WAAW;QACpB,QAAQ,EACN,2JAA2J;QAC7J,QAAQ,EAAE,0BAA0B;KACrC;IACD,QAAQ,EAAE;QACR,MAAM,EAAE,UAAU;QAClB,OAAO,EAAE,mBAAmB;QAC5B,QAAQ,EACN,0JAA0J;QAC5J,QAAQ,EAAE,iCAAiC;KAC5C;IACD,EAAE,EAAE;QACF,MAAM,EAAE,IAAI;QACZ,OAAO,EAAE,WAAW;QACpB,QAAQ,EACN,+QAA+Q;QACjR,QAAQ,EAAE,2BAA2B;KACtC;CACF,CAAC;AAEF,MAAM,aAAa,GAAG,IAAI,GAAG,CAAS,eAAe,CAAC,CAAC;AAEvD;;;;GAIG;AACH,SAAS,mBAAmB,CAAC,MAAc;IACzC,OAAO;QACL,MAAM;QACN,OAAO,EAAE,oBAAoB;QAC7B,QAAQ,EAAE,iFAAiF;QAC3F,QAAQ,EAAE,yBAAyB;KACpC,CAAC;AACJ,CAAC;AAED;;;;;;GAMG;AACH,MAAM,UAAU,eAAe,CAAC,OAAyB;IACvD,MAAM,MAAM,GAAG,IAAI,GAAG,CAAC,OAAO,CAAC,CAAC;IAChC,MAAM,OAAO,GAAG,eAAe,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,YAAY,CAAC,CAAC,CAAC,CAAC,CAAC;IACzF,MAAM,SAAS,GAAG,CAAC,GAAG,MAAM,CAAC;SAC1B,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,aAAa,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC;SACpC,IAAI,EAAE;SACN,GAAG,CAAC,mBAAmB,CAAC,CAAC;IAC5B,OAAO,CAAC,GAAG,OAAO,EAAE,GAAG,SAAS,CAAC,CAAC;AACpC,CAAC"}
|
|
@@ -2,8 +2,7 @@
|
|
|
2
2
|
* @fileoverview Shared HTTP layer for the protein data providers. Wraps the
|
|
3
3
|
* framework's `fetchWithTimeout` + `withRetry` (retry covers the full fetch +
|
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4
4
|
* parse pipeline) and centralizes HTML-error-page / empty-body detection so each
|
|
5
|
-
* service stays thin.
|
|
6
|
-
* utilities expect is isolated here.
|
|
5
|
+
* service stays thin.
|
|
7
6
|
* @module services/shared/http
|
|
8
7
|
*/
|
|
9
8
|
import type { Context } from '@cyanheads/mcp-ts-core';
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@@ -13,6 +12,12 @@ export interface FetchOptions {
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13
12
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baseDelayMs?: number;
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14
13
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/** Request body (pre-serialized JSON string, FormData, etc.). */
|
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15
14
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body?: RequestInit['body'];
|
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15
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+
/**
|
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16
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+
* Non-2xx statuses this caller treats as an outcome rather than a failure
|
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17
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+
* (e.g. 404 → "no such record"). They still throw a status-mapped `McpError`
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18
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+
* for the caller to branch on, but log at `debug` instead of `error`.
|
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+
*/
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20
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+
expectedStatuses?: number[];
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16
21
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/** Request headers. */
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17
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|
headers?: Record<string, string>;
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18
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/** Human-readable provider label used in error messages. */
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@@ -1 +1 @@
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1
|
-
{"version":3,"file":"http.d.ts","sourceRoot":"","sources":["../../../src/services/shared/http.ts"],"names":[],"mappings":"AAAA
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1
|
+
{"version":3,"file":"http.d.ts","sourceRoot":"","sources":["../../../src/services/shared/http.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,wBAAwB,CAAC;AAmBtD,qDAAqD;AACrD,MAAM,WAAW,YAAY;IAC3B,yCAAyC;IACzC,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,iEAAiE;IACjE,IAAI,CAAC,EAAE,WAAW,CAAC,MAAM,CAAC,CAAC;IAC3B;;;;OAIG;IACH,gBAAgB,CAAC,EAAE,MAAM,EAAE,CAAC;IAC5B,uBAAuB;IACvB,OAAO,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IACjC,4DAA4D;IAC5D,KAAK,EAAE,MAAM,CAAC;IACd,wDAAwD;IACxD,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,kCAAkC;IAClC,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,oDAAoD;IACpD,SAAS,EAAE,MAAM,CAAC;IAClB,wCAAwC;IACxC,SAAS,CAAC,EAAE,MAAM,CAAC;CACpB;AAED;;;;GAIG;AACH,wBAAgB,SAAS,CAAC,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,GAAG,CAAC,CAgB3D;AAED;;;;;;GAMG;AACH,wBAAgB,SAAS,CAAC,CAAC,EACzB,GAAG,EAAE,MAAM,EACX,GAAG,EAAE,OAAO,EACZ,IAAI,EAAE,YAAY,GAAG;IAAE,WAAW,CAAC,EAAE,MAAM,CAAC,CAAA;CAAE,GAC7C,OAAO,CAAC,CAAC,CAAC,CAyBZ;AAED,wGAAwG;AACxG,wBAAgB,SAAS,CAAC,GAAG,EAAE,MAAM,EAAE,GAAG,EAAE,OAAO,EAAE,IAAI,EAAE,YAAY,GAAG,OAAO,CAAC,MAAM,CAAC,CAqBxF;AAED;;;;;GAKG;AACH,wBAAgB,aAAa,CAC3B,GAAG,EAAE,MAAM,EACX,GAAG,EAAE,OAAO,EACZ,IAAI,EAAE;IACJ,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,IAAI,CAAC,EAAE,WAAW,CAAC,MAAM,CAAC,CAAC;IAC3B,OAAO,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IACjC,SAAS,EAAE,MAAM,CAAC;IAClB,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,UAAU,CAAC,EAAE,MAAM,CAAC;CACrB,GACA,OAAO,CAAC,QAAQ,CAAC,CAoBnB"}
|
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@@ -2,8 +2,7 @@
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2
2
|
* @fileoverview Shared HTTP layer for the protein data providers. Wraps the
|
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3
3
|
* framework's `fetchWithTimeout` + `withRetry` (retry covers the full fetch +
|
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4
4
|
* parse pipeline) and centralizes HTML-error-page / empty-body detection so each
|
|
5
|
-
* service stays thin.
|
|
6
|
-
* utilities expect is isolated here.
|
|
5
|
+
* service stays thin.
|
|
7
6
|
* @module services/shared/http
|
|
8
7
|
*/
|
|
9
8
|
import { serializationError, serviceUnavailable } from '@cyanheads/mcp-ts-core/errors';
|
|
@@ -20,14 +19,6 @@ const USER_AGENT = 'protein-mcp-server (+https://github.com/cyanheads/protein-mc
|
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|
20
19
|
function withDefaultHeaders(headers) {
|
|
21
20
|
return { 'User-Agent': USER_AGENT, ...headers };
|
|
22
21
|
}
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|
23
|
-
/**
|
|
24
|
-
* The framework HTTP utilities type their context parameter as `RequestContext`;
|
|
25
|
-
* the handler `Context` is runtime-compatible (the logger strips non-serializable
|
|
26
|
-
* fields). Cast once here so callers pass `ctx` unchanged.
|
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27
|
-
*/
|
|
28
|
-
function asRequestContext(ctx) {
|
|
29
|
-
return ctx;
|
|
30
|
-
}
|
|
31
22
|
/**
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|
32
23
|
* Parse a JSON body, first rejecting HTML error pages and empty responses as
|
|
33
24
|
* transient `ServiceUnavailable` (so `withRetry` retries them rather than feeding
|
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@@ -55,12 +46,12 @@ export function parseJson(text, label) {
|
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|
55
46
|
* Content` rather than an empty hit list.
|
|
56
47
|
*/
|
|
57
48
|
export function fetchJson(url, ctx, opts) {
|
|
58
|
-
const rctx = asRequestContext(ctx);
|
|
59
49
|
const timeoutMs = opts.timeoutMs ?? DEFAULT_TIMEOUT_MS;
|
|
60
50
|
return withRetry(async () => {
|
|
61
|
-
const res = await fetchWithTimeout(url, timeoutMs,
|
|
51
|
+
const res = await fetchWithTimeout(url, timeoutMs, ctx, {
|
|
62
52
|
method: opts.method ?? 'GET',
|
|
63
53
|
...(opts.body !== undefined && { body: opts.body }),
|
|
54
|
+
...(opts.expectedStatuses && { expectedStatuses: opts.expectedStatuses }),
|
|
64
55
|
headers: withDefaultHeaders(opts.headers),
|
|
65
56
|
signal: ctx.signal,
|
|
66
57
|
});
|
|
@@ -71,7 +62,7 @@ export function fetchJson(url, ctx, opts) {
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|
71
62
|
return parseJson(text, opts.label);
|
|
72
63
|
}, {
|
|
73
64
|
operation: opts.operation,
|
|
74
|
-
context:
|
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65
|
+
context: ctx,
|
|
75
66
|
baseDelayMs: opts.baseDelayMs ?? 400,
|
|
76
67
|
...(opts.maxRetries !== undefined && { maxRetries: opts.maxRetries }),
|
|
77
68
|
signal: ctx.signal,
|
|
@@ -79,19 +70,19 @@ export function fetchJson(url, ctx, opts) {
|
|
|
79
70
|
}
|
|
80
71
|
/** Fetch raw text (coordinate files, etc.) with retry. Throws a status-mapped `McpError` on non-2xx. */
|
|
81
72
|
export function fetchText(url, ctx, opts) {
|
|
82
|
-
const rctx = asRequestContext(ctx);
|
|
83
73
|
const timeoutMs = opts.timeoutMs ?? DEFAULT_TIMEOUT_MS;
|
|
84
74
|
return withRetry(async () => {
|
|
85
|
-
const res = await fetchWithTimeout(url, timeoutMs,
|
|
75
|
+
const res = await fetchWithTimeout(url, timeoutMs, ctx, {
|
|
86
76
|
method: opts.method ?? 'GET',
|
|
87
77
|
...(opts.body !== undefined && { body: opts.body }),
|
|
78
|
+
...(opts.expectedStatuses && { expectedStatuses: opts.expectedStatuses }),
|
|
88
79
|
headers: withDefaultHeaders(opts.headers),
|
|
89
80
|
signal: ctx.signal,
|
|
90
81
|
});
|
|
91
82
|
return res.text();
|
|
92
83
|
}, {
|
|
93
84
|
operation: opts.operation,
|
|
94
|
-
context:
|
|
85
|
+
context: ctx,
|
|
95
86
|
baseDelayMs: opts.baseDelayMs ?? 400,
|
|
96
87
|
...(opts.maxRetries !== undefined && { maxRetries: opts.maxRetries }),
|
|
97
88
|
signal: ctx.signal,
|
|
@@ -104,7 +95,6 @@ export function fetchText(url, ctx, opts) {
|
|
|
104
95
|
* through. Combines `ctx.signal` with a per-attempt timeout.
|
|
105
96
|
*/
|
|
106
97
|
export function fetchResponse(url, ctx, opts) {
|
|
107
|
-
const rctx = asRequestContext(ctx);
|
|
108
98
|
const timeoutMs = opts.timeoutMs ?? DEFAULT_TIMEOUT_MS;
|
|
109
99
|
return withRetry(() => {
|
|
110
100
|
const signal = AbortSignal.any([ctx.signal, AbortSignal.timeout(timeoutMs)]);
|
|
@@ -116,7 +106,7 @@ export function fetchResponse(url, ctx, opts) {
|
|
|
116
106
|
});
|
|
117
107
|
}, {
|
|
118
108
|
operation: opts.operation,
|
|
119
|
-
context:
|
|
109
|
+
context: ctx,
|
|
120
110
|
baseDelayMs: opts.baseDelayMs ?? 400,
|
|
121
111
|
maxRetries: opts.maxRetries ?? 2,
|
|
122
112
|
signal: ctx.signal,
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"http.js","sourceRoot":"","sources":["../../../src/services/shared/http.ts"],"names":[],"mappings":"AAAA
|
|
1
|
+
{"version":3,"file":"http.js","sourceRoot":"","sources":["../../../src/services/shared/http.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAGH,OAAO,EAAE,kBAAkB,EAAE,kBAAkB,EAAE,MAAM,+BAA+B,CAAC;AACvF,OAAO,EAAE,gBAAgB,EAAE,SAAS,EAAE,MAAM,8BAA8B,CAAC;AAE3E,MAAM,kBAAkB,GAAG,MAAM,CAAC;AAElC;;;;;GAKG;AACH,MAAM,UAAU,GAAG,uEAAuE,CAAC;AAE3F,wEAAwE;AACxE,SAAS,kBAAkB,CAAC,OAAgC;IAC1D,OAAO,EAAE,YAAY,EAAE,UAAU,EAAE,GAAG,OAAO,EAAE,CAAC;AAClD,CAAC;AA4BD;;;;GAIG;AACH,MAAM,UAAU,SAAS,CAAI,IAAY,EAAE,KAAa;IACtD,IAAI,mCAAmC,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;QACnD,MAAM,kBAAkB,CACtB,GAAG,KAAK,sEAAsE,CAC/E,CAAC;IACJ,CAAC;IACD,IAAI,IAAI,CAAC,IAAI,EAAE,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QAC7B,MAAM,kBAAkB,CACtB,GAAG,KAAK,wEAAwE,CACjF,CAAC;IACJ,CAAC;IACD,IAAI,CAAC;QACH,OAAO,IAAI,CAAC,KAAK,CAAC,IAAI,CAAM,CAAC;IAC/B,CAAC;IAAC,MAAM,CAAC;QACP,MAAM,kBAAkB,CAAC,GAAG,KAAK,+BAA+B,IAAI,CAAC,KAAK,CAAC,CAAC,EAAE,GAAG,CAAC,EAAE,CAAC,CAAC;IACxF,CAAC;AACH,CAAC;AAED;;;;;;GAMG;AACH,MAAM,UAAU,SAAS,CACvB,GAAW,EACX,GAAY,EACZ,IAA8C;IAE9C,MAAM,SAAS,GAAG,IAAI,CAAC,SAAS,IAAI,kBAAkB,CAAC;IACvD,OAAO,SAAS,CACd,KAAK,IAAI,EAAE;QACT,MAAM,GAAG,GAAG,MAAM,gBAAgB,CAAC,GAAG,EAAE,SAAS,EAAE,GAAG,EAAE;YACtD,MAAM,EAAE,IAAI,CAAC,MAAM,IAAI,KAAK;YAC5B,GAAG,CAAC,IAAI,CAAC,IAAI,KAAK,SAAS,IAAI,EAAE,IAAI,EAAE,IAAI,CAAC,IAAI,EAAE,CAAC;YACnD,GAAG,CAAC,IAAI,CAAC,gBAAgB,IAAI,EAAE,gBAAgB,EAAE,IAAI,CAAC,gBAAgB,EAAE,CAAC;YACzE,OAAO,EAAE,kBAAkB,CAAC,IAAI,CAAC,OAAO,CAAC;YACzC,MAAM,EAAE,GAAG,CAAC,MAAM;SACnB,CAAC,CAAC;QACH,MAAM,IAAI,GAAG,MAAM,GAAG,CAAC,IAAI,EAAE,CAAC;QAC9B,IAAI,IAAI,CAAC,WAAW,IAAI,CAAC,GAAG,CAAC,MAAM,KAAK,GAAG,IAAI,IAAI,CAAC,IAAI,EAAE,CAAC,MAAM,KAAK,CAAC,CAAC,EAAE,CAAC;YACzE,OAAO,IAAI,CAAC,WAAW,EAAE,CAAC;QAC5B,CAAC;QACD,OAAO,SAAS,CAAI,IAAI,EAAE,IAAI,CAAC,KAAK,CAAC,CAAC;IACxC,CAAC,EACD;QACE,SAAS,EAAE,IAAI,CAAC,SAAS;QACzB,OAAO,EAAE,GAAG;QACZ,WAAW,EAAE,IAAI,CAAC,WAAW,IAAI,GAAG;QACpC,GAAG,CAAC,IAAI,CAAC,UAAU,KAAK,SAAS,IAAI,EAAE,UAAU,EAAE,IAAI,CAAC,UAAU,EAAE,CAAC;QACrE,MAAM,EAAE,GAAG,CAAC,MAAM;KACnB,CACF,CAAC;AACJ,CAAC;AAED,wGAAwG;AACxG,MAAM,UAAU,SAAS,CAAC,GAAW,EAAE,GAAY,EAAE,IAAkB;IACrE,MAAM,SAAS,GAAG,IAAI,CAAC,SAAS,IAAI,kBAAkB,CAAC;IACvD,OAAO,SAAS,CACd,KAAK,IAAI,EAAE;QACT,MAAM,GAAG,GAAG,MAAM,gBAAgB,CAAC,GAAG,EAAE,SAAS,EAAE,GAAG,EAAE;YACtD,MAAM,EAAE,IAAI,CAAC,MAAM,IAAI,KAAK;YAC5B,GAAG,CAAC,IAAI,CAAC,IAAI,KAAK,SAAS,IAAI,EAAE,IAAI,EAAE,IAAI,CAAC,IAAI,EAAE,CAAC;YACnD,GAAG,CAAC,IAAI,CAAC,gBAAgB,IAAI,EAAE,gBAAgB,EAAE,IAAI,CAAC,gBAAgB,EAAE,CAAC;YACzE,OAAO,EAAE,kBAAkB,CAAC,IAAI,CAAC,OAAO,CAAC;YACzC,MAAM,EAAE,GAAG,CAAC,MAAM;SACnB,CAAC,CAAC;QACH,OAAO,GAAG,CAAC,IAAI,EAAE,CAAC;IACpB,CAAC,EACD;QACE,SAAS,EAAE,IAAI,CAAC,SAAS;QACzB,OAAO,EAAE,GAAG;QACZ,WAAW,EAAE,IAAI,CAAC,WAAW,IAAI,GAAG;QACpC,GAAG,CAAC,IAAI,CAAC,UAAU,KAAK,SAAS,IAAI,EAAE,UAAU,EAAE,IAAI,CAAC,UAAU,EAAE,CAAC;QACrE,MAAM,EAAE,GAAG,CAAC,MAAM;KACnB,CACF,CAAC;AACJ,CAAC;AAED;;;;;GAKG;AACH,MAAM,UAAU,aAAa,CAC3B,GAAW,EACX,GAAY,EACZ,IAQC;IAED,MAAM,SAAS,GAAG,IAAI,CAAC,SAAS,IAAI,kBAAkB,CAAC;IACvD,OAAO,SAAS,CACd,GAAG,EAAE;QACH,MAAM,MAAM,GAAG,WAAW,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,MAAM,EAAE,WAAW,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC;QAC7E,OAAO,KAAK,CAAC,GAAG,EAAE;YAChB,MAAM,EAAE,IAAI,CAAC,MAAM,IAAI,KAAK;YAC5B,GAAG,CAAC,IAAI,CAAC,IAAI,KAAK,SAAS,IAAI,EAAE,IAAI,EAAE,IAAI,CAAC,IAAI,EAAE,CAAC;YACnD,OAAO,EAAE,kBAAkB,CAAC,IAAI,CAAC,OAAO,CAAC;YACzC,MAAM;SACP,CAAC,CAAC;IACL,CAAC,EACD;QACE,SAAS,EAAE,IAAI,CAAC,SAAS;QACzB,OAAO,EAAE,GAAG;QACZ,WAAW,EAAE,IAAI,CAAC,WAAW,IAAI,GAAG;QACpC,UAAU,EAAE,IAAI,CAAC,UAAU,IAAI,CAAC;QAChC,MAAM,EAAE,GAAG,CAAC,MAAM;KACnB,CACF,CAAC;AACJ,CAAC"}
|
|
@@ -5,6 +5,13 @@
|
|
|
5
5
|
*/
|
|
6
6
|
/** True when `value` is a syntactically valid UniProt accession. */
|
|
7
7
|
export declare function isUniProtAccession(value: string): boolean;
|
|
8
|
+
/**
|
|
9
|
+
* True when `value` is an AlphaFold DB entry ID (`AF-P69905-F1`). Both AlphaFold's
|
|
10
|
+
* prediction endpoint and 3D-Beacons accept this form alongside the bare accession,
|
|
11
|
+
* and the `af://` resource emits it as `entryId`, so a caller can hand it straight
|
|
12
|
+
* back to a predicted-source lookup.
|
|
13
|
+
*/
|
|
14
|
+
export declare function isAlphaFoldEntryId(value: string): boolean;
|
|
8
15
|
/** True when `value` is a syntactically valid PDB entry ID. */
|
|
9
16
|
export declare function isPdbId(value: string): boolean;
|
|
10
17
|
/** Extract the PDB entry ID from a polymer-entity ID (`4HHB_1` → `4HHB`). */
|