@cyanheads/protein-mcp-server 0.3.3 → 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/0.4.x/0.4.0.md +15 -0
- 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/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_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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{"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;
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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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a: z.string().describe('First structure of the pair (entry[.chain]).'),
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b: z.string().describe('Second structure of the pair (entry[.chain]).'),
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status: z.enum(['complete', 'computing', 'failed']).describe('Outcome for this pair.'),
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tmScore: z
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tmScore: z
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.number()
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.optional()
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.describe('TM-score (0–1; higher is more similar). Length-normalized, so it can be sensitive to ' +
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'terminal length differences between the two structures — a one-residue overhang can flip ' +
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'the greedy superposition into a worse local optimum, dropping the score sharply. Cross-check ' +
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'rmsd and alignedResidues to spot such cases.'),
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rmsd: z.number().optional().describe('RMSD in Å over aligned residues.'),
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alignedResidues: z.number().optional().describe('Number of aligned residue pairs.'),
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uuid: z
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'job, fanned out with a concurrency cap and per-pair partial success — a pair still computing when the ' +
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'budget elapses returns status "computing" with its job UUID, and a failed pair degrades its row without ' +
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"sinking the others. Re-call with a matching entry in resume[] to poll a computing pair's UUID instead " +
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'of resubmitting. Returns TM-score, RMSD, and aligned-residue count per pair.'
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'of resubmitting. Returns TM-score, RMSD, and aligned-residue count per pair. TM-score is ' +
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'length-normalized and can shift sharply between structures that differ only by a terminal residue or ' +
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'two — the greedy superposition can settle into a worse local optimum — so read tmScore alongside rmsd ' +
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'and alignedResidues, the columns that make such cases diagnosable.',
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annotations: { readOnlyHint: true, openWorldHint: true },
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errors: [
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{
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+
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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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|
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",
|