@cyanheads/protein-mcp-server 0.3.2 → 0.4.0
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/0.3.3.md +20 -0
- package/changelog/0.4.x/0.4.0.md +15 -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/compare-structures.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/compare-structures.tool.js +11 -2
- package/dist/mcp-server/tools/definitions/compare-structures.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/get-annotations.tool.d.ts +2 -0
- package/dist/mcp-server/tools/definitions/get-annotations.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/get-annotations.tool.js +49 -4
- package/dist/mcp-server/tools/definitions/get-annotations.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.map +1 -1
- package/dist/mcp-server/tools/definitions/track-ligands.tool.js +10 -7
- package/dist/mcp-server/tools/definitions/track-ligands.tool.js.map +1 -1
- package/dist/services/rcsb/rcsb-service.d.ts.map +1 -1
- package/dist/services/rcsb/rcsb-service.js +25 -3
- 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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# Developer Protocol
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**Server:** protein-mcp-server
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**Version:** 0.
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**Version:** 0.4.0
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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.
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**Version:** 0.4.0
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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_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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---
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summary: "protein_get_annotations gains a per-class limit to cap features/variants/domains independently, and protein_compare_structures documents TM-score's length-normalization sensitivity to terminal length differences."
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breaking: false
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security: false
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---
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# 0.4.0 — 2026-07-03
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## Added
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- **`protein_get_annotations`** — new `limit` input (1–200, default 50) caps features, natural variants, and InterPro domains independently, so a densely-annotated protein (a well-studied protein can carry 150+ natural variants) no longer returns an unbounded payload dominated by one class. A capped class is disclosed in the response `notice` ("Showing N of M \<class\>"), an empty requested class gets a "No \<class\> present" note, and `truncated: true` is set when any class was capped. ([#20](https://github.com/cyanheads/protein-mcp-server/issues/20))
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## Changed
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- **`protein_compare_structures`** — tool description and the `tmScore` output field now document that TM-score is length-normalized and can shift sharply between structures that differ only by a terminal residue or two, since the greedy superposition can settle into a worse local optimum; cross-check `rmsd` and `alignedResidues` to spot such cases. ([#22](https://github.com/cyanheads/protein-mcp-server/issues/22))
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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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.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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.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 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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...withRange(b),
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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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* 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}: ${b.count}`;
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}
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/** Render a list of facet dimensions to markdown lines for `format()` parity. */
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export function renderFacets(facets) {
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for (const f of facets) {
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lines.push(`\n**${f.dimension}**${f.truncated ? ' (truncated)' : ''}`);
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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
|
+
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@@ -1 +1 @@
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1
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-
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1
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+
{"version":3,"file":"compare-structures.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/compare-structures.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAwGjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAmI5B,CAAC"}
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@@ -68,7 +68,13 @@ const outputSchema = z.object({
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68
68
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a: z.string().describe('First structure of the pair (entry[.chain]).'),
|
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69
69
|
b: z.string().describe('Second structure of the pair (entry[.chain]).'),
|
|
70
70
|
status: z.enum(['complete', 'computing', 'failed']).describe('Outcome for this pair.'),
|
|
71
|
-
tmScore: z
|
|
71
|
+
tmScore: z
|
|
72
|
+
.number()
|
|
73
|
+
.optional()
|
|
74
|
+
.describe('TM-score (0–1; higher is more similar). Length-normalized, so it can be sensitive to ' +
|
|
75
|
+
'terminal length differences between the two structures — a one-residue overhang can flip ' +
|
|
76
|
+
'the greedy superposition into a worse local optimum, dropping the score sharply. Cross-check ' +
|
|
77
|
+
'rmsd and alignedResidues to spot such cases.'),
|
|
72
78
|
rmsd: z.number().optional().describe('RMSD in Å over aligned residues.'),
|
|
73
79
|
alignedResidues: z.number().optional().describe('Number of aligned residue pairs.'),
|
|
74
80
|
uuid: z
|
|
@@ -88,7 +94,10 @@ export const compareStructures = tool('protein_compare_structures', {
|
|
|
88
94
|
'job, fanned out with a concurrency cap and per-pair partial success — a pair still computing when the ' +
|
|
89
95
|
'budget elapses returns status "computing" with its job UUID, and a failed pair degrades its row without ' +
|
|
90
96
|
"sinking the others. Re-call with a matching entry in resume[] to poll a computing pair's UUID instead " +
|
|
91
|
-
'of resubmitting. Returns TM-score, RMSD, and aligned-residue count per pair.'
|
|
97
|
+
'of resubmitting. Returns TM-score, RMSD, and aligned-residue count per pair. TM-score is ' +
|
|
98
|
+
'length-normalized and can shift sharply between structures that differ only by a terminal residue or ' +
|
|
99
|
+
'two — the greedy superposition can settle into a worse local optimum — so read tmScore alongside rmsd ' +
|
|
100
|
+
'and alignedResidues, the columns that make such cases diagnosable.',
|
|
92
101
|
annotations: { readOnlyHint: true, openWorldHint: true },
|
|
93
102
|
errors: [
|
|
94
103
|
{
|
|
@@ -1 +1 @@
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|
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1
|
-
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1
|
+
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|
|
@@ -18,6 +18,7 @@ export declare const getAnnotations: import("@cyanheads/mcp-ts-core").ToolDefini
|
|
|
18
18
|
domains: "domains";
|
|
19
19
|
variants: "variants";
|
|
20
20
|
}>>;
|
|
21
|
+
limit: z.ZodDefault<z.ZodNumber>;
|
|
21
22
|
}, z.core.$strip>, z.ZodObject<{
|
|
22
23
|
accession: z.ZodString;
|
|
23
24
|
proteinName: z.ZodOptional<z.ZodString>;
|
|
@@ -74,6 +75,7 @@ export declare const getAnnotations: import("@cyanheads/mcp-ts-core").ToolDefini
|
|
|
74
75
|
readonly recovery: "Omit chain for the deterministic default mapping, or pass an author chain ID the entry exposes (see polymerEntities[].chains in the pdb://{entry_id} resource).";
|
|
75
76
|
}], {
|
|
76
77
|
readonly resolvedFrom: z.ZodOptional<z.ZodString>;
|
|
78
|
+
readonly truncated: z.ZodOptional<z.ZodBoolean>;
|
|
77
79
|
readonly notice: z.ZodOptional<z.ZodString>;
|
|
78
80
|
}>;
|
|
79
81
|
//# sourceMappingURL=get-annotations.tool.d.ts.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"get-annotations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-annotations.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAwEjE,eAAO,MAAM,cAAc
|
|
1
|
+
{"version":3,"file":"get-annotations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-annotations.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAwEjE,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA6QzB,CAAC"}
|
|
@@ -102,6 +102,16 @@ export const getAnnotations = tool('protein_get_annotations', {
|
|
|
102
102
|
.enum(['features', 'domains', 'variants', 'all'])
|
|
103
103
|
.default('all')
|
|
104
104
|
.describe('Which annotation classes to fetch: features, domains (InterPro), variants, or all.'),
|
|
105
|
+
limit: z
|
|
106
|
+
.number()
|
|
107
|
+
.int()
|
|
108
|
+
.min(1)
|
|
109
|
+
.max(200)
|
|
110
|
+
.default(50)
|
|
111
|
+
.describe('Per-class cap (1–200): features, natural variants, and InterPro domains are each independently ' +
|
|
112
|
+
'truncated to at most this many records. The default keeps a typical annotation set intact while ' +
|
|
113
|
+
'bounding a densely-annotated protein (a well-studied protein can carry 150+ natural variants); a ' +
|
|
114
|
+
'truncated class is disclosed in the response notice — raise it to retrieve more.'),
|
|
105
115
|
}),
|
|
106
116
|
output: z.object({
|
|
107
117
|
accession: z.string().describe('UniProt accession the annotations describe.'),
|
|
@@ -125,7 +135,14 @@ export const getAnnotations = tool('protein_get_annotations', {
|
|
|
125
135
|
.string()
|
|
126
136
|
.optional()
|
|
127
137
|
.describe('PDB ID the accession was resolved from, when applicable.'),
|
|
128
|
-
|
|
138
|
+
truncated: z
|
|
139
|
+
.boolean()
|
|
140
|
+
.optional()
|
|
141
|
+
.describe('True when at least one annotation class hit the per-class limit and was capped; the notice names each capped class with its pre-cap count.'),
|
|
142
|
+
notice: z
|
|
143
|
+
.string()
|
|
144
|
+
.optional()
|
|
145
|
+
.describe('Advisory note: a per-class "showing N of M" line for each capped class and a no-data note for any requested-but-empty class.'),
|
|
129
146
|
},
|
|
130
147
|
async handler(input, ctx) {
|
|
131
148
|
const uniprot = getUniProtService();
|
|
@@ -182,6 +199,30 @@ export const getAnnotations = tool('protein_get_annotations', {
|
|
|
182
199
|
const variants = entry.features.filter((f) => f.category === 'variant');
|
|
183
200
|
const wantFeatures = include === 'features' || include === 'all';
|
|
184
201
|
const wantVariants = include === 'variants' || include === 'all';
|
|
202
|
+
// Cap each annotation class independently to the per-class limit, so one dense
|
|
203
|
+
// class (e.g. a protein's 150+ natural variants) can't dominate the payload.
|
|
204
|
+
// Collect every advisory fragment — a "showing N of M" line per truncated class
|
|
205
|
+
// plus a "no <class> present" note per requested-but-empty class — and emit them
|
|
206
|
+
// as ONE notice: ctx.enrich.notice is last-wins, so a second call would silently
|
|
207
|
+
// drop the first fragment.
|
|
208
|
+
const { limit } = input;
|
|
209
|
+
const notices = [];
|
|
210
|
+
let truncated = false;
|
|
211
|
+
for (const cls of [
|
|
212
|
+
{ want: wantFeatures, count: features.length, label: 'features' },
|
|
213
|
+
{ want: wantVariants, count: variants.length, label: 'variants' },
|
|
214
|
+
{ want: wantInterPro, count: interpro.length, label: 'domains' },
|
|
215
|
+
]) {
|
|
216
|
+
if (!cls.want)
|
|
217
|
+
continue;
|
|
218
|
+
if (cls.count > limit) {
|
|
219
|
+
truncated = true;
|
|
220
|
+
notices.push(`Showing ${limit} of ${cls.count} ${cls.label}; raise limit to see more.`);
|
|
221
|
+
}
|
|
222
|
+
else if (cls.count === 0) {
|
|
223
|
+
notices.push(`No ${cls.label} present.`);
|
|
224
|
+
}
|
|
225
|
+
}
|
|
185
226
|
// Attribution rides with the data. UniProt always contributes on success;
|
|
186
227
|
// InterPro only when it returned entries; GO only when a returned entry carries
|
|
187
228
|
// GO terms. InterPro (CC0) and GO (CC BY 4.0) are gated independently — an
|
|
@@ -193,6 +234,10 @@ export const getAnnotations = tool('protein_get_annotations', {
|
|
|
193
234
|
sources.add('GO');
|
|
194
235
|
if (resolvedFrom)
|
|
195
236
|
ctx.enrich({ resolvedFrom });
|
|
237
|
+
if (truncated)
|
|
238
|
+
ctx.enrich({ truncated: true });
|
|
239
|
+
if (notices.length > 0)
|
|
240
|
+
ctx.enrich.notice(notices.join(' '));
|
|
196
241
|
return {
|
|
197
242
|
accession: entry.accession,
|
|
198
243
|
...(entry.proteinName ? { proteinName: entry.proteinName } : {}),
|
|
@@ -200,9 +245,9 @@ export const getAnnotations = tool('protein_get_annotations', {
|
|
|
200
245
|
...(entry.organism ? { organism: entry.organism } : {}),
|
|
201
246
|
...(entry.function ? { function: entry.function } : {}),
|
|
202
247
|
...(typeof entry.sequenceLength === 'number' ? { sequenceLength: entry.sequenceLength } : {}),
|
|
203
|
-
...(wantFeatures ? { features: toFeatureOutput(features) } : {}),
|
|
204
|
-
...(wantVariants ? { variants: toFeatureOutput(variants) } : {}),
|
|
205
|
-
...(wantInterPro ? { domains: interpro } : {}),
|
|
248
|
+
...(wantFeatures ? { features: toFeatureOutput(features.slice(0, limit)) } : {}),
|
|
249
|
+
...(wantVariants ? { variants: toFeatureOutput(variants.slice(0, limit)) } : {}),
|
|
250
|
+
...(wantInterPro ? { domains: interpro.slice(0, limit) } : {}),
|
|
206
251
|
...(ambiguity ? { ambiguity } : {}),
|
|
207
252
|
attribution: attributionsFor(sources),
|
|
208
253
|
};
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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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
|
+
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|
@@ -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;AA0CjE,eAAO,MAAM,YAAY;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
|
|
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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@@ -127,12 +127,14 @@ export const trackLigands = tool('protein_track_ligands', {
|
|
|
127
127
|
throw ctx.fail('missing_param', 'mode find_ligand requires a name or formula in "query".', {
|
|
128
128
|
...ctx.recoveryFor('missing_param'),
|
|
129
129
|
});
|
|
130
|
-
|
|
131
|
-
//
|
|
132
|
-
//
|
|
133
|
-
//
|
|
134
|
-
//
|
|
135
|
-
//
|
|
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);
|
|
136
138
|
const resolved = await mapWithConcurrency(ids, cfg.fanoutConcurrency, async (id) => {
|
|
137
139
|
const [chem, depositionCount] = await Promise.all([
|
|
138
140
|
rcsb.getChemComp(id, ctx),
|
|
@@ -142,7 +144,8 @@ export const trackLigands = tool('protein_track_ligands', {
|
|
|
142
144
|
});
|
|
143
145
|
const ligands = resolved
|
|
144
146
|
.filter((c) => c != null)
|
|
145
|
-
.sort((a, b) => b.depositionCount - a.depositionCount)
|
|
147
|
+
.sort((a, b) => b.depositionCount - a.depositionCount)
|
|
148
|
+
.slice(0, input.limit);
|
|
146
149
|
if (ligands.length === 0) {
|
|
147
150
|
throw ctx.fail('not_found', `No chemical component matched "${input.query}".`, {
|
|
148
151
|
recovery: {
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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-
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1
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+
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@@ -349,21 +349,43 @@ function normalizeFacets(raw, specs) {
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return {
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dimension: spec.dimension,
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attribute: spec.attribute,
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352
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-
buckets: normalizeBuckets(match?.buckets, spec
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buckets: normalizeBuckets(match?.buckets, spec),
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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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* 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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361
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+
*/
|
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362
|
+
function binInterval(spec) {
|
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363
|
+
return spec.aggregation === 'histogram' && typeof spec.interval === 'number'
|
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364
|
+
? spec.interval
|
|
365
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+
: undefined;
|
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366
|
+
}
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367
|
+
function normalizeBuckets(raw, spec) {
|
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368
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+
const interval = binInterval(spec);
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369
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+
const child = spec.child;
|
|
357
370
|
return (raw ?? []).map((b) => {
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358
371
|
const label = b.label ?? (b.value != null ? String(b.value) : '');
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359
372
|
const count = b.population ?? b.count ?? 0;
|
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360
373
|
const bucket = { label, count };
|
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374
|
+
if (interval !== undefined) {
|
|
375
|
+
const from = Number(label);
|
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376
|
+
// Range from the fixed bin width, not the next label — the histogram drops
|
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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
|
+
}
|
|
361
383
|
if (child && b.facets) {
|
|
362
384
|
bucket.children = [
|
|
363
385
|
{
|
|
364
386
|
dimension: child.dimension,
|
|
365
387
|
attribute: child.attribute,
|
|
366
|
-
buckets: normalizeBuckets(b.facets[0]?.buckets, child
|
|
388
|
+
buckets: normalizeBuckets(b.facets[0]?.buckets, child),
|
|
367
389
|
},
|
|
368
390
|
];
|
|
369
391
|
}
|
|
@@ -1 +1 @@
|
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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
|
+
"version": "0.4.0",
|
|
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.
|
|
9
|
+
"version": "0.4.0",
|
|
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.
|
|
22
|
+
"version": "0.4.0",
|
|
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.
|
|
51
|
+
"version": "0.4.0",
|
|
52
52
|
"packageArguments": [
|
|
53
53
|
{
|
|
54
54
|
"type": "positional",
|