@cyanheads/protein-mcp-server 0.5.3 → 0.7.0

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.
Files changed (42) hide show
  1. package/AGENTS.md +5 -5
  2. package/CLAUDE.md +5 -5
  3. package/README.md +8 -6
  4. package/changelog/0.6.x/0.6.0.md +34 -0
  5. package/changelog/0.7.x/0.7.0.md +25 -0
  6. package/dist/mcp-server/resources/definitions/pdb-summary.resource.d.ts +5 -3
  7. package/dist/mcp-server/resources/definitions/pdb-summary.resource.d.ts.map +1 -1
  8. package/dist/mcp-server/resources/definitions/pdb-summary.resource.js +8 -22
  9. package/dist/mcp-server/resources/definitions/pdb-summary.resource.js.map +1 -1
  10. package/dist/mcp-server/tools/definitions/_schemas.d.ts +40 -1
  11. package/dist/mcp-server/tools/definitions/_schemas.d.ts.map +1 -1
  12. package/dist/mcp-server/tools/definitions/_schemas.js +81 -3
  13. package/dist/mcp-server/tools/definitions/_schemas.js.map +1 -1
  14. package/dist/mcp-server/tools/definitions/analyze-collection.tool.d.ts +3 -7
  15. package/dist/mcp-server/tools/definitions/analyze-collection.tool.d.ts.map +1 -1
  16. package/dist/mcp-server/tools/definitions/analyze-collection.tool.js +43 -21
  17. package/dist/mcp-server/tools/definitions/analyze-collection.tool.js.map +1 -1
  18. package/dist/mcp-server/tools/definitions/compare-structures.tool.d.ts.map +1 -1
  19. package/dist/mcp-server/tools/definitions/compare-structures.tool.js +1 -1
  20. package/dist/mcp-server/tools/definitions/compare-structures.tool.js.map +1 -1
  21. package/dist/mcp-server/tools/definitions/get-annotations.tool.d.ts +1 -1
  22. package/dist/mcp-server/tools/definitions/get-annotations.tool.js +2 -2
  23. package/dist/mcp-server/tools/definitions/get-annotations.tool.js.map +1 -1
  24. package/dist/mcp-server/tools/definitions/get-structure.tool.d.ts +22 -3
  25. package/dist/mcp-server/tools/definitions/get-structure.tool.d.ts.map +1 -1
  26. package/dist/mcp-server/tools/definitions/get-structure.tool.js +115 -36
  27. package/dist/mcp-server/tools/definitions/get-structure.tool.js.map +1 -1
  28. package/dist/mcp-server/tools/definitions/search-structures.tool.d.ts +5 -0
  29. package/dist/mcp-server/tools/definitions/search-structures.tool.d.ts.map +1 -1
  30. package/dist/mcp-server/tools/definitions/search-structures.tool.js +45 -5
  31. package/dist/mcp-server/tools/definitions/search-structures.tool.js.map +1 -1
  32. package/dist/services/rcsb/facets.d.ts +20 -1
  33. package/dist/services/rcsb/facets.d.ts.map +1 -1
  34. package/dist/services/rcsb/facets.js +36 -3
  35. package/dist/services/rcsb/facets.js.map +1 -1
  36. package/dist/services/rcsb/rcsb-service.d.ts.map +1 -1
  37. package/dist/services/rcsb/rcsb-service.js +10 -3
  38. package/dist/services/rcsb/rcsb-service.js.map +1 -1
  39. package/dist/services/rcsb/types.d.ts +11 -2
  40. package/dist/services/rcsb/types.d.ts.map +1 -1
  41. package/package.json +8 -8
  42. package/server.json +3 -3
package/dist/services/rcsb/facets.js CHANGED
@@ -42,8 +42,25 @@ export const FACET_DIMENSIONS = {
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  };
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  /** All supported dimension names (for Zod enums). */
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  export const FACET_DIMENSION_NAMES = Object.keys(FACET_DIMENSIONS);
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- /** Build a {@link FacetSpec} for a dimension, with an optional interval override and nested child. */
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- export function buildFacetSpec(dimension, interval, child) {
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+ /** The histogram / date-histogram dimensions, in enum order — the set an `interval` can reach. */
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+ export const INTERVAL_DIMENSION_NAMES = FACET_DIMENSION_NAMES.filter((d) => FACET_DIMENSIONS[d].aggregation !== 'terms');
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+ /**
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+ * Which requested dimension can consume an `interval` override, or `undefined`
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+ * when neither can. Compatibility is by value type rather than merely "not
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+ * terms": a numeric bin width belongs to a `histogram` dimension, the `year`
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+ * period to a `date_histogram` one. The primary position wins when both could
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+ * take it, so an ambiguous override lands where the caller can predict.
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+ */
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+ export function intervalTarget(interval, dimension, child) {
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+ const wanted = typeof interval === 'number' ? 'histogram' : 'date_histogram';
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+ if (FACET_DIMENSIONS[dimension].aggregation === wanted)
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+ return dimension;
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+ if (child && FACET_DIMENSIONS[child].aggregation === wanted)
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+ return child;
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+ return undefined;
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+ }
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+ /** Build one position's {@link FacetSpec}, falling back to its default bin width or period. */
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+ function specFor(dimension, interval) {
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  const def = FACET_DIMENSIONS[dimension];
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  const resolvedInterval = interval ?? def.defaultInterval;
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  return {
@@ -53,7 +70,23 @@ export function buildFacetSpec(dimension, interval, child) {
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  ...(def.aggregation !== 'terms' && resolvedInterval !== undefined
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  ? { interval: resolvedInterval }
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  : {}),
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- ...(child ? { child: buildFacetSpec(child) } : {}),
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+ };
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+ }
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+ /**
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+ * Build a {@link FacetSpec} for a dimension, with an optional interval override
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+ * and nested child. The override reaches whichever of the two positions can
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+ * consume it ({@link intervalTarget}) — RCSB honours a per-position `interval`
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+ * on a nested facet, so a histogram child is not stuck on its default just
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+ * because the parent aggregates by terms. The position that cannot consume it
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+ * keeps its own default, and an override no position accepts is dropped rather
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+ * than sent upstream; callers that must reject that case ask
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+ * {@link intervalTarget} first.
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+ */
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+ export function buildFacetSpec(dimension, interval, child) {
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+ const target = interval === undefined ? undefined : intervalTarget(interval, dimension, child);
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+ return {
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+ ...specFor(dimension, target === dimension ? interval : undefined),
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+ ...(child ? { child: specFor(child, target === child ? interval : undefined) } : {}),
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  };
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  }
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  //# sourceMappingURL=facets.js.map
package/dist/services/rcsb/facets.js.map CHANGED
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package/dist/services/rcsb/rcsb-service.d.ts.map CHANGED
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package/dist/services/rcsb/rcsb-service.js CHANGED
@@ -443,14 +443,21 @@ function normalizeEntry(raw) {
443
443
  }
444
444
  function normalizePolymerEntity(raw) {
445
445
  const organism = raw.rcsb_entity_source_organism?.find((o) => o.ncbi_scientific_name)?.ncbi_scientific_name;
446
- const chains = raw.rcsb_polymer_entity_container_identifiers?.auth_asym_ids;
446
+ // Two distinct chain namespaces, never interchangeable: `auth_asym_ids` are the
447
+ // depositor's labels (what protein_get_annotations.chain takes), `asym_ids` the
448
+ // mmCIF label_asym_ids (what protein_compare_structures.chain takes). For many
449
+ // entries they coincide; for 6QNR_9 they are ["82","8E"] vs ["I","OB"].
450
+ const container = raw.rcsb_polymer_entity_container_identifiers;
451
+ const authAsymIds = container?.auth_asym_ids;
452
+ const labelAsymIds = container?.asym_ids;
447
453
  return {
448
454
  entityId: raw.rcsb_id ?? '',
455
+ ...(authAsymIds && authAsymIds.length > 0 ? { authAsymIds } : {}),
449
456
  ...(raw.rcsb_polymer_entity?.pdbx_description
450
457
  ? { description: raw.rcsb_polymer_entity.pdbx_description }
451
458
  : {}),
459
+ ...(labelAsymIds && labelAsymIds.length > 0 ? { labelAsymIds } : {}),
452
460
  ...(organism ? { organism } : {}),
453
- ...(chains && chains.length > 0 ? { chains } : {}),
454
461
  ...(typeof raw.entity_poly?.rcsb_sample_sequence_length === 'number'
455
462
  ? { sequenceLength: raw.entity_poly.rcsb_sample_sequence_length }
456
463
  : {}),
@@ -509,7 +516,7 @@ const ENTRIES_QUERY = `query Entries($ids: [String!]!) {
509
516
  polymer_entities {
510
517
  rcsb_id
511
518
  rcsb_polymer_entity { pdbx_description }
512
- rcsb_polymer_entity_container_identifiers { auth_asym_ids }
519
+ rcsb_polymer_entity_container_identifiers { auth_asym_ids asym_ids }
513
520
  entity_poly { rcsb_sample_sequence_length }
514
521
  rcsb_entity_source_organism { ncbi_scientific_name }
515
522
  }
package/dist/services/rcsb/rcsb-service.js.map CHANGED
@@ -1 +1 @@
1
- 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package/dist/services/rcsb/types.d.ts CHANGED
@@ -61,12 +61,21 @@ export interface SearchResult {
61
61
  }
62
62
  /** A modeled polymer (protein/nucleic) entity within an entry. */
63
63
  export interface PolymerEntityMeta {
64
- /** Author-assigned chain IDs for this entity. */
65
- chains?: string[];
64
+ /**
65
+ * Author-assigned chain IDs (`auth_asym_id`) for this entity — the namespace
66
+ * `protein_get_annotations.chain` consumes. Absent when upstream omits it.
67
+ */
68
+ authAsymIds?: string[];
66
69
  /** Free-text description (e.g. "Hemoglobin subunit alpha"). */
67
70
  description?: string;
68
71
  /** Entity identifier (e.g. `4HHB_1`). */
69
72
  entityId: string;
73
+ /**
74
+ * mmCIF `label_asym_id` chain IDs for this entity — the namespace
75
+ * `protein_compare_structures.chain` consumes. Unrelated to `authAsymIds` by any
76
+ * transformation, though the two coincide for many entries.
77
+ */
78
+ labelAsymIds?: string[];
70
79
  /** Source organism scientific name. */
71
80
  organism?: string;
72
81
  /** One-letter canonical sequence (present only when explicitly requested). */
package/dist/services/rcsb/types.d.ts.map CHANGED
@@ -1 +1 @@
1
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package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@cyanheads/protein-mcp-server",
3
- "version": "0.5.3",
3
+ "version": "0.7.0",
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",
@@ -91,18 +91,18 @@
91
91
  "access": "public"
92
92
  },
93
93
  "dependencies": {
94
- "@cyanheads/mcp-ts-core": "^0.12.3",
94
+ "@cyanheads/mcp-ts-core": "^0.12.7",
95
95
  "pino-pretty": "^13.1.3",
96
- "zod": "^4.4.3"
96
+ "zod": "^4.5.4"
97
97
  },
98
98
  "devDependencies": {
99
- "@biomejs/biome": "2.5.10",
99
+ "@biomejs/biome": "2.5.12",
100
100
  "@socketsecurity/bun-security-scanner": "^1.1.2",
101
- "@types/node": "26.2.0",
101
+ "@types/node": "26.4.1",
102
102
  "depcheck": "^1.4.7",
103
- "ignore": "^7.0.6",
104
- "tsc-alias": "^1.9.2",
103
+ "ignore": "^7.0.8",
104
+ "tsc-alias": "^1.9.4",
105
105
  "typescript": "^7.0.2",
106
- "vitest": "^4.1.11"
106
+ "vitest": "^5.0.0"
107
107
  }
108
108
  }
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": "0.5.3",
9
+ "version": "0.7.0",
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": "0.5.3",
22
+ "version": "0.7.0",
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": "0.5.3",
51
+ "version": "0.7.0",
52
52
  "packageArguments": [
53
53
  {
54
54
  "type": "positional",