@cyanheads/protein-mcp-server 0.3.1 → 0.3.3
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 +1 -1
- package/CLAUDE.md +1 -1
- package/README.md +1 -1
- package/changelog/0.3.x/0.3.2.md +18 -0
- package/changelog/0.3.x/0.3.3.md +20 -0
- package/dist/mcp-server/tools/definitions/_schemas.d.ts +4 -0
- package/dist/mcp-server/tools/definitions/_schemas.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/_schemas.js +37 -3
- package/dist/mcp-server/tools/definitions/_schemas.js.map +1 -1
- package/dist/mcp-server/tools/definitions/analyze-collection.tool.d.ts +7 -3
- package/dist/mcp-server/tools/definitions/analyze-collection.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/analyze-collection.tool.js +6 -3
- package/dist/mcp-server/tools/definitions/analyze-collection.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/find-similar.tool.d.ts +1 -0
- package/dist/mcp-server/tools/definitions/find-similar.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/find-similar.tool.js +15 -3
- package/dist/mcp-server/tools/definitions/find-similar.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/search-structures.tool.d.ts +4 -0
- package/dist/mcp-server/tools/definitions/search-structures.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/search-structures.tool.js +5 -1
- 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 -1
- package/dist/mcp-server/tools/definitions/track-ligands.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/track-ligands.tool.js +54 -15
- package/dist/mcp-server/tools/definitions/track-ligands.tool.js.map +1 -1
- package/dist/services/rcsb/rcsb-service.d.ts +13 -1
- package/dist/services/rcsb/rcsb-service.d.ts.map +1 -1
- package/dist/services/rcsb/rcsb-service.js +69 -21
- package/dist/services/rcsb/rcsb-service.js.map +1 -1
- package/dist/services/rcsb/types.d.ts +12 -0
- package/dist/services/rcsb/types.d.ts.map +1 -1
- package/package.json +1 -1
- package/server.json +3 -3
package/AGENTS.md
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@@ -1,7 +1,7 @@
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# Developer Protocol
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**Server:** protein-mcp-server
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**Version:** 0.3.
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**Version:** 0.3.3
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**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.10.10`
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**Engines:** Bun ≥1.3.0, Node ≥24.0.0
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**MCP SDK:** `@modelcontextprotocol/sdk` ^1.29.0
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package/CLAUDE.md
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# Developer Protocol
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**Server:** protein-mcp-server
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**Version:** 0.3.
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**Version:** 0.3.3
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**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.10.10`
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**Engines:** Bun ≥1.3.0, Node ≥24.0.0
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**MCP SDK:** `@modelcontextprotocol/sdk` ^1.29.0
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package/README.md
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<div align="center">
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[](./CHANGELOG.md) [](./LICENSE) [](https://github.com/users/cyanheads/packages/container/package/protein-mcp-server) [](https://modelcontextprotocol.io/) [](https://www.npmjs.com/package/@cyanheads/protein-mcp-server) [](https://www.typescriptlang.org/) [](https://bun.sh/)
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</div>
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---
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summary: "protein_track_ligands find_ligand now ranks by deposition frequency instead of name order; structures_with_ligand sorts by resolution instead of a constant score; protein_find_similar sequence hits emit a chainable entry id with the entity id preserved separately."
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breaking: false
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security: false
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---
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# 0.3.2 — 2026-07-03
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## Added
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- **`protein_track_ligands` `find_ligand`** — ligand objects carry a new `depositionCount` field (PDB entries containing the component); candidates are sorted by it, most-deposited first. ([#17](https://github.com/cyanheads/protein-mcp-server/issues/17))
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- **`protein_find_similar` `by:"sequence"`** — hits carry a new optional `entityId` field with the raw matched polymer-entity ID (e.g. `1A00_1`). ([#18](https://github.com/cyanheads/protein-mcp-server/issues/18))
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## Changed
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- **`protein_track_ligands` `find_ligand`** — candidate ranking is deposition-frequency order instead of RCSB's name-string match order, so the canonical component (e.g. `HEM` for "heme") surfaces first instead of a near-namesake. ([#17](https://github.com/cyanheads/protein-mcp-server/issues/17))
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- **`protein_find_similar` `by:"sequence"`** — `id` is now the bare, chainable PDB entry ID (e.g. `1A00`) instead of the raw polymer-entity ID (`1A00_1`); the entity ID moved to the new `entityId` field. ([#18](https://github.com/cyanheads/protein-mcp-server/issues/18))
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- **`protein_track_ligands` `structures_with_ligand`** — entries drop the constant, meaningless `score` field in favor of `resolution` (Å) and sort best-resolution-first, instead of the undocumented PDB-ID-ascending order. ([#19](https://github.com/cyanheads/protein-mcp-server/issues/19))
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---
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summary: "protein_analyze_collection accepts stringified numeric inputs, protein_track_ligands find_ligand decouples its ranking pool from the display limit, and numeric facet histogram buckets carry explicit rangeFrom/rangeTo bounds."
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breaking: false
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security: false
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---
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# 0.3.3 — 2026-07-03
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## Added
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- **`protein_search_structures` / `protein_analyze_collection`** — numeric histogram facet buckets (resolution, molecular_weight) carry new `rangeFrom`/`rangeTo` fields describing the bucket's half-open `[rangeFrom, rangeTo)` interval, computed from the facet's fixed bin width. Resolves ambiguity in bare boundary labels like `1.0`. ([#21](https://github.com/cyanheads/protein-mcp-server/issues/21))
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## Changed
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- **`protein_search_structures`** — description now documents that a facet on an actively-filtered dimension (e.g. the organism facet while `organism` is set) shows unfiltered sibling values by design, matching RCSB's standard drill-down behavior. ([#21](https://github.com/cyanheads/protein-mcp-server/issues/21))
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## Fixed
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- **`protein_analyze_collection`** — `interval`, `max_resolution`, and `bucket_limit` now coerce stringified numeric input (`"0.5"` → `0.5`), so clients that serialize tool arguments as strings can reach the numeric-histogram path. `interval: "year"/"month"/"quarter"` still resolve to the date-period arm. ([#15](https://github.com/cyanheads/protein-mcp-server/issues/15))
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- **`protein_track_ligands` `find_ligand`** — the candidate pool is no longer capped by the display `limit` before re-ranking by deposition frequency, so a low-name-ranked canonical component (e.g. `HEM` for "heme") surfaces even at a small `limit`. ([#17](https://github.com/cyanheads/protein-mcp-server/issues/17))
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@@ -13,11 +13,15 @@ export declare const facetDimensionSchema: z.ZodObject<{
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buckets: z.ZodArray<z.ZodObject<{
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label: z.ZodString;
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count: z.ZodNumber;
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rangeFrom: z.ZodOptional<z.ZodNumber>;
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rangeTo: z.ZodOptional<z.ZodNumber>;
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children: z.ZodOptional<z.ZodArray<z.ZodObject<{
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dimension: z.ZodString;
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buckets: z.ZodArray<z.ZodObject<{
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label: z.ZodString;
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count: z.ZodNumber;
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rangeFrom: z.ZodOptional<z.ZodNumber>;
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rangeTo: z.ZodOptional<z.ZodNumber>;
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}, z.core.$strip>>;
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truncated: z.ZodOptional<z.ZodBoolean>;
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}, z.core.$strip>>>;
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{"version":3,"file":"_schemas.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/_schemas.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC3C,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,0BAA0B,CAAC;
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{"version":3,"file":"_schemas.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/_schemas.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC3C,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,0BAA0B,CAAC;AA4D/D,yCAAyC;AACzC,eAAO,MAAM,oBAAoB;;;;;;;;;;;;;;;;;;;iBAW4B,CAAC;AAE9D,MAAM,MAAM,oBAAoB,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,oBAAoB,CAAC,CAAC;AAWxE,oFAAoF;AACpF,wBAAgB,aAAa,CAAC,KAAK,EAAE,cAAc,EAAE,GAAG,EAAE,MAAM,GAAG,oBAAoB,CAsBtF;AAkBD,iFAAiF;AACjF,wBAAgB,YAAY,CAAC,MAAM,EAAE,oBAAoB,EAAE,GAAG,MAAM,EAAE,CAarE;AAED,sFAAsF;AACtF,eAAO,MAAM,iBAAiB;;;;;iBAWmD,CAAC;AAElF,MAAM,MAAM,iBAAiB,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,iBAAiB,CAAC,CAAC;AAElE,gGAAgG;AAChG,wBAAgB,iBAAiB,CAAC,YAAY,EAAE,iBAAiB,EAAE,GAAG,MAAM,EAAE,CAM7E"}
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.object({
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label: z.string().describe('Bucket value — category, numeric bin start, or period.'),
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count: z.number().describe('Number of entries in the bucket.'),
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rangeFrom: z
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.number()
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.optional()
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.describe('Inclusive lower bound of a numeric histogram bin (= label). Present only for numeric facets (resolution, molecular_weight); absent for term/period facets.'),
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rangeTo: z
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.number()
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.optional()
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.describe('Exclusive upper bound of a numeric histogram bin (rangeFrom + bin interval), so the bin covers [rangeFrom, rangeTo). Present only for numeric facets.'),
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})
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.describe('A leaf aggregation bucket: a value and its entry count.');
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/** A child (nested) facet dimension within a cross-tab bucket. */
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.object({
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label: z.string().describe('Bucket value — category, numeric bin start, or period.'),
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count: z.number().describe('Number of entries in the bucket.'),
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rangeFrom: z
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.number()
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.optional()
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.describe('Inclusive lower bound of a numeric histogram bin (= label). Present only for numeric facets (resolution, molecular_weight); absent for term/period facets.'),
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rangeTo: z
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.number()
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.optional()
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.describe('Exclusive upper bound of a numeric histogram bin (rangeFrom + bin interval), so the bin covers [rangeFrom, rangeTo). Present only for numeric facets.'),
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children: z
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.describe('True when buckets were capped by the per-dimension bucket limit.'),
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})
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.describe('A facet dimension and its aggregation buckets.');
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/** Copy the numeric-histogram range onto an output bucket when present. */
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function withRange(b) {
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return b.rangeFrom !== undefined && b.rangeTo !== undefined
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? { rangeFrom: b.rangeFrom, rangeTo: b.rangeTo }
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: {};
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}
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/** Project a domain {@link FacetDimension} to the output shape, capping buckets. */
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export function toFacetOutput(facet, cap) {
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label: b.label,
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count: b.count,
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...withRange(b),
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...(b.children
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? {
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dimension: c.dimension,
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buckets: c.buckets
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buckets: c.buckets
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.slice(0, cap)
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.map((cb) => ({ label: cb.label, count: cb.count, ...withRange(cb) })),
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...(c.buckets.length > cap ? { truncated: true } : {}),
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})),
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}
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};
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}
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/**
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* Render one bucket's `label: count` line, annotating numeric histogram buckets
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* with their explicit half-open `[rangeFrom, rangeTo)` bin so the bare boundary
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* label isn't ambiguous (does `1.0` count `[0.5, 1.0)` or `[1.0, 1.5)`?).
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*/
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function renderBucket(b) {
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const range = b.rangeFrom !== undefined && b.rangeTo !== undefined ? ` [${b.rangeFrom}–${b.rangeTo})` : '';
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return `${b.label}${range}: ${b.count}`;
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}
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/** Render a list of facet dimensions to markdown lines for `format()` parity. */
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export function renderFacets(facets) {
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const lines = [];
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for (const f of facets) {
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lines.push(`\n**${f.dimension}**${f.truncated ? ' (truncated)' : ''}`);
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for (const b of f.buckets) {
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lines.push(`- ${b
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lines.push(`- ${renderBucket(b)}`);
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for (const c of b.children ?? []) {
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const inner = c.buckets.map(
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const inner = c.buckets.map(renderBucket).join(', ');
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lines.push(` - ${c.dimension} → ${inner}${c.truncated ? ' (truncated)' : ''}`);
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}
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}
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{"version":3,"file":"_schemas.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/_schemas.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAG3C,kCAAkC;AAClC,MAAM,gBAAgB,GAAG,CAAC;KACvB,MAAM,CAAC;IACN,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,wDAAwD,CAAC;IACpF,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,kCAAkC,CAAC;
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{"version":3,"file":"_schemas.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/_schemas.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAG3C,kCAAkC;AAClC,MAAM,gBAAgB,GAAG,CAAC;KACvB,MAAM,CAAC;IACN,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,wDAAwD,CAAC;IACpF,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,kCAAkC,CAAC;IAC9D,SAAS,EAAE,CAAC;SACT,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,4JAA4J,CAC7J;IACH,OAAO,EAAE,CAAC;SACP,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,uJAAuJ,CACxJ;CACJ,CAAC;KACD,QAAQ,CAAC,yDAAyD,CAAC,CAAC;AAEvE,kEAAkE;AAClE,MAAM,oBAAoB,GAAG,CAAC;KAC3B,MAAM,CAAC;IACN,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,wBAAwB,CAAC;IACxD,OAAO,EAAE,CAAC,CAAC,KAAK,CAAC,gBAAgB,CAAC,CAAC,QAAQ,CAAC,0CAA0C,CAAC;IACvF,SAAS,EAAE,CAAC;SACT,OAAO,EAAE;SACT,QAAQ,EAAE;SACV,QAAQ,CAAC,iFAAiF,CAAC;CAC/F,CAAC;KACD,QAAQ,CAAC,sDAAsD,CAAC,CAAC;AAEpE,kFAAkF;AAClF,MAAM,YAAY,GAAG,CAAC;KACnB,MAAM,CAAC;IACN,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,wDAAwD,CAAC;IACpF,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,kCAAkC,CAAC;IAC9D,SAAS,EAAE,CAAC;SACT,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,4JAA4J,CAC7J;IACH,OAAO,EAAE,CAAC;SACP,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,uJAAuJ,CACxJ;IACH,QAAQ,EAAE,CAAC;SACR,KAAK,CAAC,oBAAoB,CAAC;SAC3B,QAAQ,EAAE;SACV,QAAQ,CACP,uFAAuF,CACxF;CACJ,CAAC;KACD,QAAQ,CAAC,gFAAgF,CAAC,CAAC;AAE9F,yCAAyC;AACzC,MAAM,CAAC,MAAM,oBAAoB,GAAG,CAAC;KAClC,MAAM,CAAC;IACN,SAAS,EAAE,CAAC;SACT,MAAM,EAAE;SACR,QAAQ,CAAC,gEAAgE,CAAC;IAC7E,OAAO,EAAE,CAAC,CAAC,KAAK,CAAC,YAAY,CAAC,CAAC,QAAQ,CAAC,kDAAkD,CAAC;IAC3F,SAAS,EAAE,CAAC;SACT,OAAO,EAAE;SACT,QAAQ,EAAE;SACV,QAAQ,CAAC,kEAAkE,CAAC;CAChF,CAAC;KACD,QAAQ,CAAC,gDAAgD,CAAC,CAAC;AAI9D,2EAA2E;AAC3E,SAAS,SAAS,CAChB,CAAI;IAEJ,OAAO,CAAC,CAAC,SAAS,KAAK,SAAS,IAAI,CAAC,CAAC,OAAO,KAAK,SAAS;QACzD,CAAC,CAAC,EAAE,SAAS,EAAE,CAAC,CAAC,SAAS,EAAE,OAAO,EAAE,CAAC,CAAC,OAAO,EAAE;QAChD,CAAC,CAAC,EAAE,CAAC;AACT,CAAC;AAED,oFAAoF;AACpF,MAAM,UAAU,aAAa,CAAC,KAAqB,EAAE,GAAW;IAC9D,MAAM,SAAS,GAAG,KAAK,CAAC,OAAO,CAAC,MAAM,GAAG,GAAG,CAAC;IAC7C,OAAO;QACL,SAAS,EAAE,KAAK,CAAC,SAAS;QAC1B,OAAO,EAAE,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,EAAE,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;YAC/C,KAAK,EAAE,CAAC,CAAC,KAAK;YACd,KAAK,EAAE,CAAC,CAAC,KAAK;YACd,GAAG,SAAS,CAAC,CAAC,CAAC;YACf,GAAG,CAAC,CAAC,CAAC,QAAQ;gBACZ,CAAC,CAAC;oBACE,QAAQ,EAAE,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;wBAC/B,SAAS,EAAE,CAAC,CAAC,SAAS;wBACtB,OAAO,EAAE,CAAC,CAAC,OAAO;6BACf,KAAK,CAAC,CAAC,EAAE,GAAG,CAAC;6BACb,GAAG,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC,EAAE,KAAK,EAAE,EAAE,CAAC,KAAK,EAAE,KAAK,EAAE,EAAE,CAAC,KAAK,EAAE,GAAG,SAAS,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC;wBACxE,GAAG,CAAC,CAAC,CAAC,OAAO,CAAC,MAAM,GAAG,GAAG,CAAC,CAAC,CAAC,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;qBACvD,CAAC,CAAC;iBACJ;gBACH,CAAC,CAAC,EAAE,CAAC;SACR,CAAC,CAAC;QACH,GAAG,CAAC,SAAS,CAAC,CAAC,CAAC,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;KAC1C,CAAC;AACJ,CAAC;AAED;;;;GAIG;AACH,SAAS,YAAY,CAAC,CAKrB;IACC,MAAM,KAAK,GACT,CAAC,CAAC,SAAS,KAAK,SAAS,IAAI,CAAC,CAAC,OAAO,KAAK,SAAS,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,SAAS,IAAI,CAAC,CAAC,OAAO,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC;IAC/F,OAAO,GAAG,CAAC,CAAC,KAAK,GAAG,KAAK,KAAK,CAAC,CAAC,KAAK,EAAE,CAAC;AAC1C,CAAC;AAED,iFAAiF;AACjF,MAAM,UAAU,YAAY,CAAC,MAA8B;IACzD,MAAM,KAAK,GAAa,EAAE,CAAC;IAC3B,KAAK,MAAM,CAAC,IAAI,MAAM,EAAE,CAAC;QACvB,KAAK,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,SAAS,KAAK,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,cAAc,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;QACvE,KAAK,MAAM,CAAC,IAAI,CAAC,CAAC,OAAO,EAAE,CAAC;YAC1B,KAAK,CAAC,IAAI,CAAC,KAAK,YAAY,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC;YACnC,KAAK,MAAM,CAAC,IAAI,CAAC,CAAC,QAAQ,IAAI,EAAE,EAAE,CAAC;gBACjC,MAAM,KAAK,GAAG,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,YAAY,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;gBACrD,KAAK,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,SAAS,MAAM,KAAK,GAAG,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,cAAc,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;YAClF,CAAC;QACH,CAAC;IACH,CAAC;IACD,OAAO,KAAK,CAAC;AACf,CAAC;AAED,sFAAsF;AACtF,MAAM,CAAC,MAAM,iBAAiB,GAAG,CAAC;KAC/B,MAAM,CAAC;IACN,MAAM,EAAE,CAAC;SACN,MAAM,EAAE;SACR,QAAQ,CACP,uLAAuL,CACxL;IACH,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,+DAA+D,CAAC;IAC7F,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,mDAAmD,CAAC;IAClF,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,iCAAiC,CAAC;CACjE,CAAC;KACD,QAAQ,CAAC,oEAAoE,CAAC,CAAC;AAIlF,gGAAgG;AAChG,MAAM,UAAU,iBAAiB,CAAC,YAAiC;IACjE,MAAM,KAAK,GAAa,EAAE,CAAC;IAC3B,KAAK,MAAM,CAAC,IAAI,YAAY,EAAE,CAAC;QAC7B,KAAK,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,MAAM,OAAO,CAAC,CAAC,OAAO,OAAO,CAAC,CAAC,QAAQ,MAAM,CAAC,CAAC,QAAQ,EAAE,CAAC,CAAC;IACjF,CAAC;IACD,OAAO,KAAK,CAAC;AACf,CAAC"}
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@@ -20,18 +20,18 @@ export declare const analyzeCollection: import("@cyanheads/mcp-ts-core").ToolDef
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20
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query: z.ZodOptional<z.ZodString>;
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21
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organism: z.ZodOptional<z.ZodString>;
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method: z.ZodOptional<z.ZodString>;
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-
max_resolution: z.ZodOptional<z.
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+
max_resolution: z.ZodOptional<z.ZodCoercedNumber<unknown>>;
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content_type: z.ZodDefault<z.ZodEnum<{
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experimental: "experimental";
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predicted: "predicted";
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all: "all";
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}>>;
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-
interval: z.ZodOptional<z.ZodUnion<readonly [z.
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+
interval: z.ZodOptional<z.ZodUnion<readonly [z.ZodCoercedNumber<unknown>, z.ZodEnum<{
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year: "year";
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31
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month: "month";
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quarter: "quarter";
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}>]>>;
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-
bucket_limit: z.ZodOptional<z.
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+
bucket_limit: z.ZodOptional<z.ZodCoercedNumber<unknown>>;
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}, z.core.$strip>, z.ZodObject<{
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total: z.ZodNumber;
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facets: z.ZodArray<z.ZodObject<{
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@@ -39,11 +39,15 @@ export declare const analyzeCollection: import("@cyanheads/mcp-ts-core").ToolDef
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buckets: z.ZodArray<z.ZodObject<{
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label: z.ZodString;
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count: z.ZodNumber;
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+
rangeFrom: z.ZodOptional<z.ZodNumber>;
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+
rangeTo: z.ZodOptional<z.ZodNumber>;
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children: z.ZodOptional<z.ZodArray<z.ZodObject<{
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dimension: z.ZodString;
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buckets: z.ZodArray<z.ZodObject<{
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label: z.ZodString;
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count: z.ZodNumber;
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49
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+
rangeFrom: z.ZodOptional<z.ZodNumber>;
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+
rangeTo: z.ZodOptional<z.ZodNumber>;
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47
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}, z.core.$strip>>;
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truncated: z.ZodOptional<z.ZodBoolean>;
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49
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}, z.core.$strip>>>;
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"analyze-collection.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/analyze-collection.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAOjE,eAAO,MAAM,iBAAiB
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1
|
+
{"version":3,"file":"analyze-collection.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/analyze-collection.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAOjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA4H5B,CAAC"}
|
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@@ -40,7 +40,7 @@ export const analyzeCollection = tool('protein_analyze_collection', {
|
|
|
40
40
|
.describe('Optional free-text scope (e.g. "kinase"); omit to profile the whole PDB.'),
|
|
41
41
|
organism: z.string().optional().describe('Optional source-organism scope.'),
|
|
42
42
|
method: z.string().optional().describe('Optional experimental-method scope.'),
|
|
43
|
-
max_resolution: z
|
|
43
|
+
max_resolution: z.coerce
|
|
44
44
|
.number()
|
|
45
45
|
.positive()
|
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46
46
|
.optional()
|
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@@ -51,7 +51,10 @@ export const analyzeCollection = tool('protein_analyze_collection', {
|
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|
51
51
|
.describe('Which structure universe to profile. Default experimental.'),
|
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52
52
|
interval: z
|
|
53
53
|
.union([
|
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54
|
-
|
|
54
|
+
// Coerce the numeric arm: many clients stringify tool args, and "0.5" must
|
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55
|
+
// still reach the histogram path. z.coerce.number() on "year" yields NaN,
|
|
56
|
+
// which .positive() rejects, so period strings still fall through to the enum.
|
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+
z.coerce
|
|
55
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|
.number()
|
|
56
59
|
.positive()
|
|
57
60
|
.describe('Numeric bin width for a value histogram (e.g. resolution Å).'),
|
|
@@ -59,7 +62,7 @@ export const analyzeCollection = tool('protein_analyze_collection', {
|
|
|
59
62
|
])
|
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60
63
|
.optional()
|
|
61
64
|
.describe('Bin width for a histogram dimension (number) or period for a date histogram (year/month/quarter).'),
|
|
62
|
-
bucket_limit: z
|
|
65
|
+
bucket_limit: z.coerce
|
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63
66
|
.number()
|
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64
67
|
.int()
|
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65
68
|
.min(1)
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"analyze-collection.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/analyze-collection.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,eAAe,EAAE,MAAM,2BAA2B,CAAC;AAC5D,OAAO,EAAE,cAAc,EAAE,qBAAqB,EAAE,MAAM,2BAA2B,CAAC;AAClF,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AAEjE,OAAO,EAAE,oBAAoB,EAAE,YAAY,EAAE,aAAa,EAAE,MAAM,eAAe,CAAC;AAElF,MAAM,CAAC,MAAM,iBAAiB,GAAG,IAAI,CAAC,4BAA4B,EAAE;IAClE,KAAK,EAAE,wCAAwC;IAC/C,WAAW,EACT,kGAAkG;QAClG,wGAAwG;QACxG,uGAAuG;QACvG,wGAAwG;QACxG,mDAAmD;IACrD,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IAExD,MAAM,EAAE;QACN;YACE,MAAM,EAAE,mBAAmB;YAC3B,IAAI,EAAE,gBAAgB,CAAC,aAAa;YACpC,IAAI,EAAE,0DAA0D;YAChE,QAAQ,EACN,2GAA2G;SAC9G;KACF;IAED,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,QAAQ,EAAE,CAAC;aACR,KAAK,CAAC,CAAC,CAAC,IAAI,CAAC,qBAAqB,CAAC,CAAC;aACpC,GAAG,CAAC,CAAC,CAAC;aACN,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,CAAC,iFAAiF,CAAC;QAC9F,KAAK,EAAE,CAAC;aACL,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CAAC,0EAA0E,CAAC;QACvF,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,iCAAiC,CAAC;QAC3E,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,qCAAqC,CAAC;QAC7E,cAAc,EAAE,CAAC;
|
|
1
|
+
{"version":3,"file":"analyze-collection.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/analyze-collection.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,eAAe,EAAE,MAAM,2BAA2B,CAAC;AAC5D,OAAO,EAAE,cAAc,EAAE,qBAAqB,EAAE,MAAM,2BAA2B,CAAC;AAClF,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AAEjE,OAAO,EAAE,oBAAoB,EAAE,YAAY,EAAE,aAAa,EAAE,MAAM,eAAe,CAAC;AAElF,MAAM,CAAC,MAAM,iBAAiB,GAAG,IAAI,CAAC,4BAA4B,EAAE;IAClE,KAAK,EAAE,wCAAwC;IAC/C,WAAW,EACT,kGAAkG;QAClG,wGAAwG;QACxG,uGAAuG;QACvG,wGAAwG;QACxG,mDAAmD;IACrD,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IAExD,MAAM,EAAE;QACN;YACE,MAAM,EAAE,mBAAmB;YAC3B,IAAI,EAAE,gBAAgB,CAAC,aAAa;YACpC,IAAI,EAAE,0DAA0D;YAChE,QAAQ,EACN,2GAA2G;SAC9G;KACF;IAED,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,QAAQ,EAAE,CAAC;aACR,KAAK,CAAC,CAAC,CAAC,IAAI,CAAC,qBAAqB,CAAC,CAAC;aACpC,GAAG,CAAC,CAAC,CAAC;aACN,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,CAAC,iFAAiF,CAAC;QAC9F,KAAK,EAAE,CAAC;aACL,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CAAC,0EAA0E,CAAC;QACvF,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,iCAAiC,CAAC;QAC3E,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,qCAAqC,CAAC;QAC7E,cAAc,EAAE,CAAC,CAAC,MAAM;aACrB,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,EAAE;aACV,QAAQ,CAAC,wCAAwC,CAAC;QACrD,YAAY,EAAE,CAAC;aACZ,IAAI,CAAC,CAAC,cAAc,EAAE,WAAW,EAAE,KAAK,CAAC,CAAC;aAC1C,OAAO,CAAC,cAAc,CAAC;aACvB,QAAQ,CAAC,4DAA4D,CAAC;QACzE,QAAQ,EAAE,CAAC;aACR,KAAK,CAAC;YACL,2EAA2E;YAC3E,0EAA0E;YAC1E,+EAA+E;YAC/E,CAAC,CAAC,MAAM;iBACL,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CAAC,8DAA8D,CAAC;YAC3E,CAAC,CAAC,IAAI,CAAC,CAAC,MAAM,EAAE,OAAO,EAAE,SAAS,CAAC,CAAC,CAAC,QAAQ,CAAC,0CAA0C,CAAC;SAC1F,CAAC;aACD,QAAQ,EAAE;aACV,QAAQ,CACP,mGAAmG,CACpG;QACH,YAAY,EAAE,CAAC,CAAC,MAAM;aACnB,MAAM,EAAE;aACR,GAAG,EAAE;aACL,GAAG,CAAC,CAAC,CAAC;aACN,GAAG,CAAC,GAAG,CAAC;aACR,QAAQ,EAAE;aACV,QAAQ,CAAC,6EAA6E,CAAC;KAC3F,CAAC;IAEF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,yCAAyC,CAAC;QACrE,MAAM,EAAE,CAAC,CAAC,KAAK,CAAC,oBAAoB,CAAC,CAAC,QAAQ,CAAC,6BAA6B,CAAC;KAC9E,CAAC;IAEF,UAAU,EAAE;QACV,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,+CAA+C,CAAC;QACtF,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,sDAAsD,CAAC;KAC/F;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,MAAM,GAAG,GAAG,eAAe,EAAE,CAAC;QAC9B,MAAM,IAAI,GAAG,cAAc,EAAE,CAAC;QAC9B,MAAM,GAAG,GAAG,KAAK,CAAC,YAAY,IAAI,GAAG,CAAC,cAAc,CAAC;QACrD,MAAM,WAAW,GACf,KAAK,CAAC,YAAY,KAAK,KAAK;YAC1B,CAAC,CAAC,SAAS;YACX,CAAC,CAAC,KAAK,CAAC,YAAY,KAAK,WAAW;gBAClC,CAAC,CAAC,eAAe;gBACjB,CAAC,CAAC,cAAc,CAAC;QAEvB,MAAM,CAAC,OAAO,EAAE,SAAS,CAAC,GAAG,KAAK,CAAC,QAAQ,CAAC;QAC5C,IAAI,CAAC,OAAO;YACV,MAAM,GAAG,CAAC,IAAI,CAAC,mBAAmB,EAAE,2CAA2C,EAAE;gBAC/E,GAAG,GAAG,CAAC,WAAW,CAAC,mBAAmB,CAAC;aACxC,CAAC,CAAC;QACL,MAAM,IAAI,GAAG,cAAc,CAAC,OAAO,EAAE,KAAK,CAAC,QAAQ,EAAE,SAAS,CAAC,CAAC;QAEhE,MAAM,EAAE,KAAK,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,aAAa,CAChD;YACE,GAAG,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,IAAI,EAAE,KAAK,CAAC,KAAK,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;YAC7C,GAAG,CAAC,KAAK,CAAC,QAAQ,CAAC,CAAC,CAAC,EAAE,QAAQ,EAAE,KAAK,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;YACvD,GAAG,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,MAAM,EAAE,KAAK,CAAC,MAAM,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;YACjD,GAAG,CAAC,OAAO,KAAK,CAAC,cAAc,KAAK,QAAQ;gBAC1C,CAAC,CAAC,EAAE,aAAa,EAAE,KAAK,CAAC,cAAc,EAAE;gBACzC,CAAC,CAAC,EAAE,CAAC;YACP,GAAG,CAAC,WAAW,CAAC,CAAC,CAAC,EAAE,WAAW,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;SACxC,EACD,CAAC,IAAI,CAAC,EACN,GAAG,CACJ,CAAC;QAEF,MAAM,GAAG,GAAG,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,aAAa,CAAC,CAAC,EAAE,GAAG,CAAC,CAAC,CAAC;QACrD,IAAI,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,SAAS,CAAC,EAAE,CAAC;YACjC,GAAG,CAAC,MAAM,CAAC,MAAM,CACf,mCAAmC,GAAG,sEAAsE,CAC7G,CAAC;QACJ,CAAC;QACD,MAAM,SAAS,GAAG,CAAC,KAAK,CAAC,KAAK,EAAE,KAAK,CAAC,QAAQ,EAAE,KAAK,CAAC,MAAM,CAAC,CAAC,MAAM,CAAC,OAAO,CAAC,CAAC;QAC9E,IAAI,SAAS,CAAC,MAAM,GAAG,CAAC;YAAE,GAAG,CAAC,MAAM,CAAC,EAAE,KAAK,EAAE,SAAS,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;QAEvE,OAAO,EAAE,KAAK,EAAE,MAAM,EAAE,GAAG,EAAE,CAAC;IAChC,CAAC;IAED,MAAM,EAAE,CAAC,MAAM,EAAE,EAAE;QACjB,MAAM,KAAK,GAAa,CAAC,2BAA2B,MAAM,CAAC,KAAK,UAAU,CAAC,CAAC;QAC5E,KAAK,CAAC,IAAI,CAAC,GAAG,YAAY,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC;QAC3C,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IACpD,CAAC;CACF,CAAC,CAAC"}
|
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@@ -33,6 +33,7 @@ export declare const findSimilar: import("@cyanheads/mcp-ts-core").ToolDefinitio
|
|
|
33
33
|
ticketId: z.ZodOptional<z.ZodString>;
|
|
34
34
|
hits: z.ZodArray<z.ZodObject<{
|
|
35
35
|
id: z.ZodString;
|
|
36
|
+
entityId: z.ZodOptional<z.ZodString>;
|
|
36
37
|
source: z.ZodEnum<{
|
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37
38
|
experimental: "experimental";
|
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38
39
|
predicted: "predicted";
|
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@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"find-similar.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/find-similar.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAA6B,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACtE,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;
|
|
1
|
+
{"version":3,"file":"find-similar.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/find-similar.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAA6B,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACtE,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAkHjE,eAAO,MAAM,WAAW;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAwEtB,CAAC"}
|
|
@@ -60,7 +60,13 @@ const outputSchema = z.object({
|
|
|
60
60
|
hits: z
|
|
61
61
|
.array(z
|
|
62
62
|
.object({
|
|
63
|
-
id: z
|
|
63
|
+
id: z
|
|
64
|
+
.string()
|
|
65
|
+
.describe('Hit identifier that chains directly into protein_get_structure: a bare PDB entry ID (e.g. 1A00), or a UniProt accession for predicted hits.'),
|
|
66
|
+
entityId: z
|
|
67
|
+
.string()
|
|
68
|
+
.optional()
|
|
69
|
+
.describe('Matched polymer-entity ID (e.g. 1A00_1) for sequence hits; the chainable entry ID is in `id`.'),
|
|
64
70
|
source: z
|
|
65
71
|
.enum(['experimental', 'predicted'])
|
|
66
72
|
.describe('Whether the hit is an experimental or predicted structure.'),
|
|
@@ -145,6 +151,7 @@ export const findSimilar = tool('protein_find_similar', {
|
|
|
145
151
|
if (h.title)
|
|
146
152
|
lines.push(h.title);
|
|
147
153
|
const parts = [
|
|
154
|
+
h.entityId ? `**Entity:** ${h.entityId}` : null,
|
|
148
155
|
typeof h.score === 'number' ? `**Score:** ${h.score}` : null,
|
|
149
156
|
typeof h.evalue === 'number' ? `**E-value:** ${h.evalue}` : null,
|
|
150
157
|
typeof h.identity === 'number' ? `**Identity:** ${h.identity}` : null,
|
|
@@ -180,9 +187,14 @@ async function runSequence(input, enrichLimit, ctx) {
|
|
|
180
187
|
engine: 'RCSB mmseqs2',
|
|
181
188
|
status: 'complete',
|
|
182
189
|
hits: result.hits.map((h) => {
|
|
183
|
-
|
|
190
|
+
// mmseqs2 emits polymer-entity IDs (1A00_1); expose the bare entry ID as
|
|
191
|
+
// `id` so it chains uniformly into protein_get_structure like the other
|
|
192
|
+
// tools, and keep the raw entity ID as `entityId` for the matched entity.
|
|
193
|
+
const entryId = entryIdOf(h.id);
|
|
194
|
+
const meta = metaById.get(entryId);
|
|
184
195
|
return {
|
|
185
|
-
id:
|
|
196
|
+
id: entryId,
|
|
197
|
+
entityId: h.id,
|
|
186
198
|
source: 'experimental',
|
|
187
199
|
score: h.score,
|
|
188
200
|
...(meta?.title ? { title: meta.title } : {}),
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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@@ -48,11 +48,15 @@ export declare const searchStructures: import("@cyanheads/mcp-ts-core").ToolDefi
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buckets: z.ZodArray<z.ZodObject<{
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label: z.ZodString;
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count: z.ZodNumber;
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rangeFrom: z.ZodOptional<z.ZodNumber>;
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rangeTo: z.ZodOptional<z.ZodNumber>;
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children: z.ZodOptional<z.ZodArray<z.ZodObject<{
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dimension: z.ZodString;
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buckets: z.ZodArray<z.ZodObject<{
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label: z.ZodString;
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count: z.ZodNumber;
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rangeFrom: z.ZodOptional<z.ZodNumber>;
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rangeTo: z.ZodOptional<z.ZodNumber>;
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}, z.core.$strip>>;
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truncated: z.ZodOptional<z.ZodBoolean>;
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}, z.core.$strip>>>;
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"search-structures.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/search-structures.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAwBjE,eAAO,MAAM,gBAAgB
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1
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+
{"version":3,"file":"search-structures.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/search-structures.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAwBjE,eAAO,MAAM,gBAAgB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAgM3B,CAAC"}
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@@ -31,7 +31,11 @@ export const searchStructures = tool('protein_search_structures', {
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'protein sequence (triggers an mmseqs2 similarity search), and/or organism, method, and ' +
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'resolution filters. Returns ranked hits; the experimental page is enriched with title, method, ' +
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'resolution, and organism. Chain hit IDs into protein_get_structure. Optionally returns a facet ' +
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'breakdown (counts by method / organism / release year / …) alongside the hits at no extra call.'
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'breakdown (counts by method / organism / release year / …) alongside the hits at no extra call. ' +
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'A facet on a dimension you are already filtering (e.g. the organism facet while organism is set) ' +
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'lists unfiltered alternatives by design — it does not constrain by its own active filter, so you ' +
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'can see sibling values to pivot to. Numeric histogram buckets (resolution, molecular weight) carry ' +
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'explicit rangeFrom/rangeTo bounds so a boundary label is unambiguous.',
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annotations: { readOnlyHint: true, openWorldHint: true },
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errors: [
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{
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"search-structures.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/search-structures.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,eAAe,EAAE,MAAM,2BAA2B,CAAC;AAC5D,OAAO,EAAE,cAAc,EAAE,qBAAqB,EAAE,MAAM,2BAA2B,CAAC;AAClF,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AAEjE,OAAO,EAAE,SAAS,EAAE,MAAM,kCAAkC,CAAC;AAC7D,OAAO,EAAE,oBAAoB,EAAE,YAAY,EAAE,aAAa,EAAE,MAAM,eAAe,CAAC;AAElF,MAAM,gBAAgB,GAAG;IACvB,YAAY,EAAE,CAAC,cAAc,CAAC;IAC9B,SAAS,EAAE,CAAC,eAAe,CAAC;IAC5B,GAAG,EAAE,CAAC,cAAc,EAAE,eAAe,CAAC;CAC+B,CAAC;AAExE,2FAA2F;AAC3F,SAAS,aAAa,CAAC,EAAU;IAC/B,OAAO,YAAY,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;AAC/B,CAAC;AAED,6GAA6G;AAC7G,SAAS,gBAAgB,CAAC,EAAU;IAClC,OAAO,yBAAyB,CAAC,IAAI,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,WAAW,EAAE,CAAC;AAChE,CAAC;AAED,MAAM,CAAC,MAAM,gBAAgB,GAAG,IAAI,CAAC,2BAA2B,EAAE;IAChE,KAAK,EAAE,uCAAuC;IAC9C,WAAW,EACT,4FAA4F;QAC5F,yFAAyF;QACzF,iGAAiG;QACjG,iGAAiG;QACjG,
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1
|
+
{"version":3,"file":"search-structures.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/search-structures.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,eAAe,EAAE,MAAM,2BAA2B,CAAC;AAC5D,OAAO,EAAE,cAAc,EAAE,qBAAqB,EAAE,MAAM,2BAA2B,CAAC;AAClF,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AAEjE,OAAO,EAAE,SAAS,EAAE,MAAM,kCAAkC,CAAC;AAC7D,OAAO,EAAE,oBAAoB,EAAE,YAAY,EAAE,aAAa,EAAE,MAAM,eAAe,CAAC;AAElF,MAAM,gBAAgB,GAAG;IACvB,YAAY,EAAE,CAAC,cAAc,CAAC;IAC9B,SAAS,EAAE,CAAC,eAAe,CAAC;IAC5B,GAAG,EAAE,CAAC,cAAc,EAAE,eAAe,CAAC;CAC+B,CAAC;AAExE,2FAA2F;AAC3F,SAAS,aAAa,CAAC,EAAU;IAC/B,OAAO,YAAY,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;AAC/B,CAAC;AAED,6GAA6G;AAC7G,SAAS,gBAAgB,CAAC,EAAU;IAClC,OAAO,yBAAyB,CAAC,IAAI,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,WAAW,EAAE,CAAC;AAChE,CAAC;AAED,MAAM,CAAC,MAAM,gBAAgB,GAAG,IAAI,CAAC,2BAA2B,EAAE;IAChE,KAAK,EAAE,uCAAuC;IAC9C,WAAW,EACT,4FAA4F;QAC5F,yFAAyF;QACzF,iGAAiG;QACjG,iGAAiG;QACjG,kGAAkG;QAClG,mGAAmG;QACnG,mGAAmG;QACnG,qGAAqG;QACrG,uEAAuE;IACzE,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IAExD,MAAM,EAAE;QACN;YACE,MAAM,EAAE,aAAa;YACrB,IAAI,EAAE,gBAAgB,CAAC,aAAa;YACpC,IAAI,EAAE,sEAAsE;YAC5E,QAAQ,EACN,oGAAoG;SACvG;KACF;IAED,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,KAAK,EAAE,CAAC;aACL,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CAAC,iEAAiE,CAAC;QAC9E,QAAQ,EAAE,CAAC;aACR,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,sFAAsF,CACvF;QACH,QAAQ,EAAE,CAAC;aACR,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CAAC,kEAAkE,CAAC;QAC/E,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CAAC,kFAAkF,CAAC;QAC/F,cAAc,EAAE,CAAC;aACd,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,EAAE;aACV,QAAQ,CAAC,iFAAiF,CAAC;QAC9F,YAAY,EAAE,CAAC;aACZ,MAAM,EAAE;aACR,GAAG,CAAC,CAAC,CAAC;aACN,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,EAAE;aACV,QAAQ,CAAC,mEAAmE,CAAC;QAChF,UAAU,EAAE,CAAC;aACV,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,EAAE;aACV,QAAQ,CAAC,mDAAmD,CAAC;QAChE,YAAY,EAAE,CAAC;aACZ,IAAI,CAAC,CAAC,cAAc,EAAE,WAAW,EAAE,KAAK,CAAC,CAAC;aAC1C,OAAO,CAAC,KAAK,CAAC;aACd,QAAQ,CACP,8FAA8F,CAC/F;QACH,MAAM,EAAE,CAAC;aACN,KAAK,CAAC,CAAC,CAAC,IAAI,CAAC,qBAAqB,CAAC,CAAC;aACpC,QAAQ,EAAE;aACV,QAAQ,CAAC,2EAA2E,CAAC;QACxF,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC,QAAQ,CAAC,iCAAiC,CAAC;KAChG,CAAC;IAEF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,IAAI,EAAE,CAAC;aACJ,KAAK,CACJ,CAAC;aACE,MAAM,CAAC;YACN,EAAE,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,2DAA2D,CAAC;YACpF,MAAM,EAAE,CAAC;iBACN,IAAI,CAAC,CAAC,cAAc,EAAE,WAAW,CAAC,CAAC;iBACnC,QAAQ,CAAC,mCAAmC,CAAC;YAChD,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,uBAAuB,CAAC;YAC9D,gBAAgB,EAAE,CAAC;iBAChB,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CAAC,oEAAoE,CAAC;YACjF,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,+CAA+C,CAAC;YACtF,MAAM,EAAE,CAAC;iBACN,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CAAC,sDAAsD,CAAC;YACnE,UAAU,EAAE,CAAC;iBACV,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CAAC,+CAA+C,CAAC;YAC5D,QAAQ,EAAE,CAAC;iBACR,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CAAC,uDAAuD,CAAC;SACrE,CAAC;aACD,QAAQ,CAAC,2DAA2D,CAAC,CACzE;aACA,QAAQ,CAAC,wBAAwB,CAAC;QACrC,MAAM,EAAE,CAAC;aACN,KAAK,CAAC,oBAAoB,CAAC;aAC3B,QAAQ,EAAE;aACV,QAAQ,CAAC,0CAA0C,CAAC;KACxD,CAAC;IAEF,UAAU,EAAE;QACV,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,2CAA2C,CAAC;QAC5E,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,wCAAwC,CAAC;QACxF,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CAAC,sEAAsE,CAAC;KACpF;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,IAAI,CAAC,KAAK,CAAC,KAAK,IAAI,CAAC,KAAK,CAAC,QAAQ,IAAI,CAAC,KAAK,CAAC,QAAQ,EAAE,CAAC;YACvD,MAAM,GAAG,CAAC,IAAI,CAAC,aAAa,EAAE,sDAAsD,EAAE;gBACpF,GAAG,GAAG,CAAC,WAAW,CAAC,aAAa,CAAC;aAClC,CAAC,CAAC;QACL,CAAC;QACD,MAAM,GAAG,GAAG,eAAe,EAAE,CAAC;QAC9B,MAAM,IAAI,GAAG,cAAc,EAAE,CAAC;QAC9B,MAAM,YAAY,GAAG,gBAAgB,CAAC,KAAK,CAAC,YAAY,CAAC,CAAC;QAC1D,MAAM,UAAU,GAAG,KAAK,CAAC,MAAM,EAAE,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,cAAc,CAAC,CAAC,CAAC,CAAC,CAAC;QAE/D,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,MAAM,CAC9B;YACE,GAAG,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,IAAI,EAAE,KAAK,CAAC,KAAK,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;YAC7C,GAAG,CAAC,KAAK,CAAC,QAAQ,CAAC,CAAC,CAAC,EAAE,QAAQ,EAAE,KAAK,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;YACvD,GAAG,CAAC,KAAK,CAAC,QAAQ,CAAC,CAAC,CAAC,EAAE,QAAQ,EAAE,KAAK,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;YACvD,GAAG,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,MAAM,EAAE,KAAK,CAAC,MAAM,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;YACjD,GAAG,CAAC,OAAO,KAAK,CAAC,cAAc,KAAK,QAAQ;gBAC1C,CAAC,CAAC,EAAE,aAAa,EAAE,KAAK,CAAC,cAAc,EAAE;gBACzC,CAAC,CAAC,EAAE,CAAC;YACP,GAAG,CAAC,OAAO,KAAK,CAAC,YAAY,KAAK,QAAQ,CAAC,CAAC,CAAC,EAAE,WAAW,EAAE,KAAK,CAAC,YAAY,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;YACtF,GAAG,CAAC,OAAO,KAAK,CAAC,UAAU,KAAK,QAAQ,CAAC,CAAC,CAAC,EAAE,SAAS,EAAE,KAAK,CAAC,UAAU,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;YAChF,8EAA8E;YAC9E,GAAG,CAAC,YAAY,CAAC,MAAM,KAAK,CAAC,CAAC,CAAC,CAAC,EAAE,WAAW,EAAE,YAAY,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;YACtE,KAAK,EAAE,KAAK,CAAC,KAAK;SACnB,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@@ -31,10 +31,11 @@ export declare const trackLigands: import("@cyanheads/mcp-ts-core").ToolDefiniti
|
|
|
31
31
|
smiles: z.ZodOptional<z.ZodString>;
|
|
32
32
|
inchikey: z.ZodOptional<z.ZodString>;
|
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33
33
|
type: z.ZodOptional<z.ZodString>;
|
|
34
|
+
depositionCount: z.ZodNumber;
|
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34
35
|
}, z.core.$strip>>>;
|
|
35
36
|
structures: z.ZodOptional<z.ZodArray<z.ZodObject<{
|
|
36
37
|
id: z.ZodString;
|
|
37
|
-
|
|
38
|
+
resolution: z.ZodOptional<z.ZodNumber>;
|
|
38
39
|
}, z.core.$strip>>>;
|
|
39
40
|
bindingSites: z.ZodOptional<z.ZodArray<z.ZodObject<{
|
|
40
41
|
ligandCompId: z.ZodString;
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"track-ligands.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/track-ligands.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;
|
|
1
|
+
{"version":3,"file":"track-ligands.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/track-ligands.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA0CjE,eAAO,MAAM,YAAY;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAuOvB,CAAC"}
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@@ -19,6 +19,9 @@ const chemCompSchema = z
|
|
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19
19
|
smiles: z.string().optional().describe('Isomeric SMILES.'),
|
|
20
20
|
inchikey: z.string().optional().describe('InChIKey.'),
|
|
21
21
|
type: z.string().optional().describe('Component type (e.g. non-polymer).'),
|
|
22
|
+
depositionCount: z
|
|
23
|
+
.number()
|
|
24
|
+
.describe('Number of PDB entries containing this component (deposition frequency). Candidates are ranked by this value, most-deposited first.'),
|
|
22
25
|
})
|
|
23
26
|
.describe('A resolved chemical component (ligand) and its identifiers.');
|
|
24
27
|
const bindingSiteSchema = z
|
|
@@ -40,10 +43,12 @@ const bindingSiteSchema = z
|
|
|
40
43
|
export const trackLigands = tool('protein_track_ligands', {
|
|
41
44
|
title: 'protein-mcp-server: track ligands',
|
|
42
45
|
description: 'Ligand discovery and binding-site analysis across the PDB. mode "find_ligand" resolves a name or ' +
|
|
43
|
-
'formula to chemical component IDs with metadata (formula, weight, SMILES)
|
|
44
|
-
'
|
|
45
|
-
'
|
|
46
|
-
'
|
|
46
|
+
'formula to chemical component IDs with metadata (formula, weight, SMILES), ranked by deposition ' +
|
|
47
|
+
'frequency — most-deposited component first, so the top hit is the most common match for the name, ' +
|
|
48
|
+
'not necessarily an exact name-string match. mode "structures_with_ligand" returns PDB entries ' +
|
|
49
|
+
'containing a ligand (by exact component ID — get the ID from find_ligand first), highest-resolution ' +
|
|
50
|
+
'first, each with its resolution in Å. mode "binding_site" returns the protein residues lining a ' +
|
|
51
|
+
"ligand's pocket in a given structure, with contact distances. Binding sites are experimental-only " +
|
|
47
52
|
'(computed from deposited coordinates; predicted models carry no bound ligands).',
|
|
48
53
|
annotations: { readOnlyHint: true, openWorldHint: true },
|
|
49
54
|
errors: [
|
|
@@ -90,11 +95,14 @@ export const trackLigands = tool('protein_track_ligands', {
|
|
|
90
95
|
.array(z
|
|
91
96
|
.object({
|
|
92
97
|
id: z.string().describe('PDB entry ID containing the ligand.'),
|
|
93
|
-
|
|
98
|
+
resolution: z
|
|
99
|
+
.number()
|
|
100
|
+
.optional()
|
|
101
|
+
.describe('Best reported resolution in Å (absent for methods without one, e.g. NMR).'),
|
|
94
102
|
})
|
|
95
|
-
.describe('A PDB entry containing the ligand.'))
|
|
103
|
+
.describe('A PDB entry containing the ligand, with its resolution.'))
|
|
96
104
|
.optional()
|
|
97
|
-
.describe('PDB entries containing the ligand (structures_with_ligand).'),
|
|
105
|
+
.describe('PDB entries containing the ligand, highest-resolution first (structures_with_ligand).'),
|
|
98
106
|
bindingSites: z
|
|
99
107
|
.array(bindingSiteSchema)
|
|
100
108
|
.optional()
|
|
@@ -119,8 +127,25 @@ export const trackLigands = tool('protein_track_ligands', {
|
|
|
119
127
|
throw ctx.fail('missing_param', 'mode find_ligand requires a name or formula in "query".', {
|
|
120
128
|
...ctx.recoveryFor('missing_param'),
|
|
121
129
|
});
|
|
122
|
-
|
|
123
|
-
|
|
130
|
+
// Over-fetch a candidate pool larger than the display limit, then re-rank by
|
|
131
|
+
// deposition frequency and slice to the limit. The canonical component (e.g.
|
|
132
|
+
// HEM for "heme") is the most-deposited but RCSB name-ranks it low, so a small
|
|
133
|
+
// `limit` would never fetch it — the count re-rank can only reorder what it
|
|
134
|
+
// pulls. Re-rank, never filter. RCSB returns a bounded candidate set per name,
|
|
135
|
+
// so a pool of ~25 stays cheap while still covering low-name-ranked canonicals.
|
|
136
|
+
const candidatePool = Math.max(input.limit, 25);
|
|
137
|
+
const ids = await rcsb.findChemComps(input.query, candidatePool, ctx);
|
|
138
|
+
const resolved = await mapWithConcurrency(ids, cfg.fanoutConcurrency, async (id) => {
|
|
139
|
+
const [chem, depositionCount] = await Promise.all([
|
|
140
|
+
rcsb.getChemComp(id, ctx),
|
|
141
|
+
rcsb.countEntriesWithLigand(id, ctx),
|
|
142
|
+
]);
|
|
143
|
+
return chem ? { ...chem, depositionCount } : null;
|
|
144
|
+
});
|
|
145
|
+
const ligands = resolved
|
|
146
|
+
.filter((c) => c != null)
|
|
147
|
+
.sort((a, b) => b.depositionCount - a.depositionCount)
|
|
148
|
+
.slice(0, input.limit);
|
|
124
149
|
if (ligands.length === 0) {
|
|
125
150
|
throw ctx.fail('not_found', `No chemical component matched "${input.query}".`, {
|
|
126
151
|
recovery: {
|
|
@@ -144,10 +169,23 @@ export const trackLigands = tool('protein_track_ligands', {
|
|
|
144
169
|
if (result.hits.length === 0) {
|
|
145
170
|
ctx.enrich.notice(`No PDB entries contain ${compId}. Verify the component ID via mode find_ligand.`);
|
|
146
171
|
}
|
|
147
|
-
|
|
148
|
-
|
|
149
|
-
|
|
150
|
-
|
|
172
|
+
// Replace RCSB's uniform containment score (noise for a boolean filter) with
|
|
173
|
+
// each entry's resolution, enriched via the same batched entry-metadata path
|
|
174
|
+
// the other tools use. The search is resolution-sorted server-side; sort
|
|
175
|
+
// again by the enriched value since getEntries does not preserve input order.
|
|
176
|
+
const ids = result.hits.map((h) => h.id);
|
|
177
|
+
const metaById = new Map();
|
|
178
|
+
if (ids.length > 0) {
|
|
179
|
+
for (const meta of await rcsb.getEntries(ids, ctx))
|
|
180
|
+
metaById.set(meta.id, meta);
|
|
181
|
+
}
|
|
182
|
+
const structures = ids
|
|
183
|
+
.map((id) => {
|
|
184
|
+
const resolution = metaById.get(id.toUpperCase())?.resolution;
|
|
185
|
+
return { id, ...(typeof resolution === 'number' ? { resolution } : {}) };
|
|
186
|
+
})
|
|
187
|
+
.sort((a, b) => (a.resolution ?? Infinity) - (b.resolution ?? Infinity));
|
|
188
|
+
return { mode: input.mode, structures };
|
|
151
189
|
}
|
|
152
190
|
// binding_site
|
|
153
191
|
const compId = input.comp_id?.toUpperCase();
|
|
@@ -181,6 +219,7 @@ export const trackLigands = tool('protein_track_ligands', {
|
|
|
181
219
|
l.formula ? `**Formula:** ${l.formula}` : null,
|
|
182
220
|
typeof l.formulaWeight === 'number' ? `**Weight:** ${l.formulaWeight} Da` : null,
|
|
183
221
|
l.type ? `**Type:** ${l.type}` : null,
|
|
222
|
+
typeof l.depositionCount === 'number' ? `**PDB entries:** ${l.depositionCount}` : null,
|
|
184
223
|
].filter(Boolean);
|
|
185
224
|
if (parts.length > 0)
|
|
186
225
|
lines.push(parts.join(' | '));
|
|
@@ -193,8 +232,8 @@ export const trackLigands = tool('protein_track_ligands', {
|
|
|
193
232
|
lines.push(`\n**${result.structures.length} structures:**`);
|
|
194
233
|
lines.push(result.structures.map((s) => s.id).join(', '));
|
|
195
234
|
for (const s of result.structures) {
|
|
196
|
-
if (typeof s.
|
|
197
|
-
lines.push(`- ${s.id}
|
|
235
|
+
if (typeof s.resolution === 'number')
|
|
236
|
+
lines.push(`- ${s.id} — ${s.resolution.toFixed(2)} Å`);
|
|
198
237
|
}
|
|
199
238
|
}
|
|
200
239
|
for (const site of result.bindingSites ?? []) {
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"track-ligands.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/track-ligands.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,eAAe,EAAE,MAAM,2BAA2B,CAAC;AAC5D,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AAEjE,OAAO,EAAE,kBAAkB,EAAE,MAAM,4BAA4B,CAAC;AAEhE,MAAM,cAAc,GAAG,CAAC;KACrB,MAAM,CAAC;IACN,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,wCAAwC,CAAC;IACrE,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,gBAAgB,CAAC;IACtD,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,oBAAoB,CAAC;IAC7D,aAAa,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,uBAAuB,CAAC;IACtE,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,kBAAkB,CAAC;IAC1D,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,WAAW,CAAC;IACrD,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,oCAAoC,CAAC;
|
|
1
|
+
{"version":3,"file":"track-ligands.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/track-ligands.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,eAAe,EAAE,MAAM,2BAA2B,CAAC;AAC5D,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AAEjE,OAAO,EAAE,kBAAkB,EAAE,MAAM,4BAA4B,CAAC;AAEhE,MAAM,cAAc,GAAG,CAAC;KACrB,MAAM,CAAC;IACN,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,wCAAwC,CAAC;IACrE,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,gBAAgB,CAAC;IACtD,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,oBAAoB,CAAC;IAC7D,aAAa,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,uBAAuB,CAAC;IACtE,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,kBAAkB,CAAC;IAC1D,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,WAAW,CAAC;IACrD,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,oCAAoC,CAAC;IAC1E,eAAe,EAAE,CAAC;SACf,MAAM,EAAE;SACR,QAAQ,CACP,oIAAoI,CACrI;CACJ,CAAC;KACD,QAAQ,CAAC,6DAA6D,CAAC,CAAC;AAE3E,MAAM,iBAAiB,GAAG,CAAC;KACxB,MAAM,CAAC;IACN,YAAY,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,qCAAqC,CAAC;IACxE,YAAY,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,kCAAkC,CAAC;IAChF,QAAQ,EAAE,CAAC;SACR,KAAK,CACJ,CAAC;SACE,MAAM,CAAC;QACN,aAAa,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,sCAAsC,CAAC;QAC1E,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,kCAAkC,CAAC;QAC/D,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,4BAA4B,CAAC;QACnE,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,sCAAsC,CAAC;KACjF,CAAC;SACD,QAAQ,CAAC,8CAA8C,CAAC,CAC5D;SACA,QAAQ,CAAC,oDAAoD,CAAC;CAClE,CAAC;KACD,QAAQ,CAAC,+DAA+D,CAAC,CAAC;AAE7E,MAAM,CAAC,MAAM,YAAY,GAAG,IAAI,CAAC,uBAAuB,EAAE;IACxD,KAAK,EAAE,mCAAmC;IAC1C,WAAW,EACT,mGAAmG;QACnG,kGAAkG;QAClG,oGAAoG;QACpG,gGAAgG;QAChG,sGAAsG;QACtG,kGAAkG;QAClG,oGAAoG;QACpG,iFAAiF;IACnF,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IAExD,MAAM,EAAE;QACN;YACE,MAAM,EAAE,eAAe;YACvB,IAAI,EAAE,gBAAgB,CAAC,aAAa;YACpC,IAAI,EAAE,8HAA8H;YACpI,QAAQ,EACN,0IAA0I;SAC7I;QACD;YACE,MAAM,EAAE,WAAW;YACnB,IAAI,EAAE,gBAAgB,CAAC,QAAQ;YAC/B,IAAI,EAAE,iGAAiG;YACvG,QAAQ,EACN,kJAAkJ;SACrJ;KACF;IAED,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,IAAI,EAAE,CAAC;aACJ,IAAI,CAAC,CAAC,aAAa,EAAE,wBAAwB,EAAE,cAAc,CAAC,CAAC;aAC/D,QAAQ,CACP,0FAA0F,CAC3F;QACH,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,4CAA4C,CAAC;QACnF,OAAO,EAAE,CAAC;aACP,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CAAC,8EAA8E,CAAC;QAC3F,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,mCAAmC,CAAC;QAC3E,KAAK,EAAE,CAAC;aACL,MAAM,EAAE;aACR,GAAG,EAAE;aACL,GAAG,CAAC,CAAC,CAAC;aACN,GAAG,CAAC,GAAG,CAAC;aACR,OAAO,CAAC,EAAE,CAAC;aACX,QAAQ,CAAC,oCAAoC,CAAC;KAClD,CAAC;IAEF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,IAAI,EAAE,CAAC;aACJ,IAAI,CAAC,CAAC,aAAa,EAAE,wBAAwB,EAAE,cAAc,CAAC,CAAC;aAC/D,QAAQ,CAAC,cAAc,CAAC;QAC3B,OAAO,EAAE,CAAC;aACP,KAAK,CAAC,cAAc,CAAC;aACrB,QAAQ,EAAE;aACV,QAAQ,CAAC,6CAA6C,CAAC;QAC1D,UAAU,EAAE,CAAC;aACV,KAAK,CACJ,CAAC;aACE,MAAM,CAAC;YACN,EAAE,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,qCAAqC,CAAC;YAC9D,UAAU,EAAE,CAAC;iBACV,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CACP,2EAA2E,CAC5E;SACJ,CAAC;aACD,QAAQ,CAAC,yDAAyD,CAAC,CACvE;aACA,QAAQ,EAAE;aACV,QAAQ,CACP,uFAAuF,CACxF;QACH,YAAY,EAAE,CAAC;aACZ,KAAK,CAAC,iBAAiB,CAAC;aACxB,QAAQ,EAAE;aACV,QAAQ,CAAC,uCAAuC,CAAC;KACrD,CAAC;IAEF,UAAU,EAAE;QACV,UAAU,EAAE,CAAC;aACV,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CAAC,oEAAoE,CAAC;QACjF,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,0CAA0C,CAAC;QAC1F,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CAAC,gEAAgE,CAAC;KAC9E;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,MAAM,IAAI,GAAG,cAAc,EAAE,CAAC;QAC9B,MAAM,GAAG,GAAG,eAAe,EAAE,CAAC;QAE9B,IAAI,KAAK,CAAC,IAAI,KAAK,aAAa,EAAE,CAAC;YACjC,IAAI,CAAC,KAAK,CAAC,KAAK;gBACd,MAAM,GAAG,CAAC,IAAI,CAAC,eAAe,EAAE,yDAAyD,EAAE;oBACzF,GAAG,GAAG,CAAC,WAAW,CAAC,eAAe,CAAC;iBACpC,CAAC,CAAC;YACL,6EAA6E;YAC7E,6EAA6E;YAC7E,+EAA+E;YAC/E,4EAA4E;YAC5E,+EAA+E;YAC/E,gFAAgF;YAChF,MAAM,aAAa,GAAG,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,KAAK,EAAE,EAAE,CAAC,CAAC;YAChD,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,aAAa,CAAC,KAAK,CAAC,KAAK,EAAE,aAAa,EAAE,GAAG,CAAC,CAAC;YACtE,MAAM,QAAQ,GAAG,MAAM,kBAAkB,CAAC,GAAG,EAAE,GAAG,CAAC,iBAAiB,EAAE,KAAK,EAAE,EAAE,EAAE,EAAE;gBACjF,MAAM,CAAC,IAAI,EAAE,eAAe,CAAC,GAAG,MAAM,OAAO,CAAC,GAAG,CAAC;oBAChD,IAAI,CAAC,WAAW,CAAC,EAAE,EAAE,GAAG,CAAC;oBACzB,IAAI,CAAC,sBAAsB,CAAC,EAAE,EAAE,GAAG,CAAC;iBACrC,CAAC,CAAC;gBACH,OAAO,IAAI,CAAC,CAAC,CAAC,EAAE,GAAG,IAAI,EAAE,eAAe,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC;YACpD,CAAC,CAAC,CAAC;YACH,MAAM,OAAO,GAAG,QAAQ;iBACrB,MAAM,CAAC,CAAC,CAAC,EAA+C,EAAE,CAAC,CAAC,IAAI,IAAI,CAAC;iBACrE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,eAAe,GAAG,CAAC,CAAC,eAAe,CAAC;iBACrD,KAAK,CAAC,CAAC,EAAE,KAAK,CAAC,KAAK,CAAC,CAAC;YACzB,IAAI,OAAO,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;gBACzB,MAAM,GAAG,CAAC,IAAI,CAAC,WAAW,EAAE,kCAAkC,KAAK,CAAC,KAAK,IAAI,EAAE;oBAC7E,QAAQ,EAAE;wBACR,IAAI,EAAE,sBAAsB,KAAK,CAAC,KAAK,iDAAiD;qBACzF;iBACF,CAAC,CAAC;YACL,CAAC;YACD,OAAO,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@@ -42,11 +42,23 @@ export declare class RcsbService {
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42
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limit?: number;
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43
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contentType?: ContentType;
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44
44
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}, ctx: Context): Promise<SearchResult>;
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45
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-
/**
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45
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+
/**
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46
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+
* Find entries containing a given ligand (exact chemical component ID),
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47
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+
* highest-resolution first. Containment is boolean so RCSB's relevance score is
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48
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+
* uniform; a server-side resolution sort orders the page by a signal that
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49
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+
* actually discriminates (the returned page is the globally best-resolution
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50
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+
* entries, not an arbitrary PDB-ID-ascending slice).
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51
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+
*/
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46
52
|
searchByLigand(compId: string, opts: {
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limit?: number;
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contentType?: ContentType;
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49
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}, ctx: Context): Promise<SearchResult>;
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56
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+
/**
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57
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+
* Count PDB entries containing a given ligand (its deposition frequency). Used
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58
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+
* to re-rank name-search candidates so the canonical, most-deposited component
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59
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+
* surfaces first — a count-only query (rows 0), no rows or sort pulled.
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60
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+
*/
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61
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+
countEntriesWithLigand(compId: string, ctx: Context): Promise<number>;
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50
62
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/** Resolve a ligand name/synonym to candidate chemical component IDs. */
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51
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findChemComps(query: string, limit: number, ctx: Context): Promise<string[]>;
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52
64
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/** Facet-only aggregation over an optional scoping query (no row pull). */
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@@ -1 +1 @@
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1
|
-
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1
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/**
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* Count PDB entries containing a given ligand (its deposition frequency). Used
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* to re-rank name-search candidates so the canonical, most-deposited component
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* surfaces first — a count-only query (rows 0), no rows or sort pulled.
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}
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/** Resolve a ligand name/synonym to candidate chemical component IDs. */
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/**
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|
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*/
|
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|
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function ligandContainmentQuery(compId, contentType, rows, sortByResolution) {
|
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return {
|
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query: {
|
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service: 'text_chem',
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|
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return_type: 'entry',
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+
...contentTypeOption(contentType ?? 'experimental'),
|
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+
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|
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|
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|
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|
+
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: {}),
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};
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|
/** Translate a friendly FacetSpec into the RCSB facet request shape (recursively). */
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|
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@@ -323,21 +349,43 @@ function normalizeFacets(raw, specs) {
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|
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|
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|
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|
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|
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|
}
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|
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|
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/**
|
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+
* The fixed bin width for a numeric histogram facet, or `undefined` for term and
|
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|
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* date-period facets. Only numeric histograms carry an interpretable numeric
|
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|
+
* `[label, label + interval)` range; date_histogram intervals are period words
|
|
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|
+
* (`year`) and terms have no interval.
|
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|
+
*/
|
|
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|
+
function binInterval(spec) {
|
|
363
|
+
return spec.aggregation === 'histogram' && typeof spec.interval === 'number'
|
|
364
|
+
? spec.interval
|
|
365
|
+
: undefined;
|
|
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|
+
}
|
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|
+
function normalizeBuckets(raw, spec) {
|
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|
+
const interval = binInterval(spec);
|
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|
+
const child = spec.child;
|
|
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370
|
return (raw ?? []).map((b) => {
|
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|
const label = b.label ?? (b.value != null ? String(b.value) : '');
|
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|
const count = b.population ?? b.count ?? 0;
|
|
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373
|
const bucket = { label, count };
|
|
374
|
+
if (interval !== undefined) {
|
|
375
|
+
const from = Number(label);
|
|
376
|
+
// Range from the fixed bin width, not the next label — the histogram drops
|
|
377
|
+
// empty bins, so adjacent labels can be >1 interval apart at the sparse tail.
|
|
378
|
+
if (Number.isFinite(from)) {
|
|
379
|
+
bucket.rangeFrom = from;
|
|
380
|
+
bucket.rangeTo = from + interval;
|
|
381
|
+
}
|
|
382
|
+
}
|
|
335
383
|
if (child && b.facets) {
|
|
336
384
|
bucket.children = [
|
|
337
385
|
{
|
|
338
386
|
dimension: child.dimension,
|
|
339
387
|
attribute: child.attribute,
|
|
340
|
-
buckets: normalizeBuckets(b.facets[0]?.buckets, child
|
|
388
|
+
buckets: normalizeBuckets(b.facets[0]?.buckets, child),
|
|
341
389
|
},
|
|
342
390
|
];
|
|
343
391
|
}
|
|
@@ -1 +1 @@
|
|
|
1
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-
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1
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+
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@@ -19,6 +19,18 @@ export interface FacetBucket {
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19
19
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count: number;
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20
20
|
/** Bucket label (category value, numeric bin start, or period). */
|
|
21
21
|
label: string;
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|
22
|
+
/**
|
|
23
|
+
* Inclusive lower bound of a numeric histogram bin (= `Number(label)`). Present
|
|
24
|
+
* only for numeric histogram facets (resolution, molecular_weight); absent for
|
|
25
|
+
* term and date-period facets.
|
|
26
|
+
*/
|
|
27
|
+
rangeFrom?: number;
|
|
28
|
+
/**
|
|
29
|
+
* Exclusive upper bound of a numeric histogram bin (`rangeFrom + bin interval`).
|
|
30
|
+
* Uses the facet's fixed bin width, not the next bucket's label — the histogram
|
|
31
|
+
* omits empty bins, so consecutive labels are not necessarily one interval apart.
|
|
32
|
+
*/
|
|
33
|
+
rangeTo?: number;
|
|
22
34
|
}
|
|
23
35
|
/** A facet dimension and its buckets. */
|
|
24
36
|
export interface FacetDimension {
|
|
@@ -1 +1 @@
|
|
|
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;
|
|
1
|
+
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|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@cyanheads/protein-mcp-server",
|
|
3
|
-
"version": "0.3.
|
|
3
|
+
"version": "0.3.3",
|
|
4
4
|
"mcpName": "io.github.cyanheads/protein-mcp-server",
|
|
5
5
|
"description": "Federated protein structure & annotation across experimental (PDB) and predicted (AlphaFold) models via MCP. STDIO or Streamable HTTP.",
|
|
6
6
|
"type": "module",
|
package/server.json
CHANGED
|
@@ -6,7 +6,7 @@
|
|
|
6
6
|
"url": "https://github.com/cyanheads/protein-mcp-server",
|
|
7
7
|
"source": "github"
|
|
8
8
|
},
|
|
9
|
-
"version": "0.3.
|
|
9
|
+
"version": "0.3.3",
|
|
10
10
|
"remotes": [
|
|
11
11
|
{
|
|
12
12
|
"type": "streamable-http",
|
|
@@ -19,7 +19,7 @@
|
|
|
19
19
|
"registryBaseUrl": "https://registry.npmjs.org",
|
|
20
20
|
"identifier": "@cyanheads/protein-mcp-server",
|
|
21
21
|
"runtimeHint": "node",
|
|
22
|
-
"version": "0.3.
|
|
22
|
+
"version": "0.3.3",
|
|
23
23
|
"packageArguments": [
|
|
24
24
|
{
|
|
25
25
|
"type": "positional",
|
|
@@ -48,7 +48,7 @@
|
|
|
48
48
|
"registryBaseUrl": "https://registry.npmjs.org",
|
|
49
49
|
"identifier": "@cyanheads/protein-mcp-server",
|
|
50
50
|
"runtimeHint": "node",
|
|
51
|
-
"version": "0.3.
|
|
51
|
+
"version": "0.3.3",
|
|
52
52
|
"packageArguments": [
|
|
53
53
|
{
|
|
54
54
|
"type": "positional",
|