@cyanheads/protein-mcp-server 0.4.1 → 0.5.0

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 (45) hide show
  1. package/AGENTS.md +1 -1
  2. package/CLAUDE.md +1 -1
  3. package/README.md +5 -4
  4. package/changelog/0.4.x/0.4.2.md +16 -0
  5. package/changelog/0.5.x/0.5.0.md +19 -0
  6. package/dist/mcp-server/resources/definitions/af-summary.resource.d.ts.map +1 -1
  7. package/dist/mcp-server/resources/definitions/af-summary.resource.js +8 -1
  8. package/dist/mcp-server/resources/definitions/af-summary.resource.js.map +1 -1
  9. package/dist/mcp-server/tools/definitions/_schemas.d.ts +25 -7
  10. package/dist/mcp-server/tools/definitions/_schemas.d.ts.map +1 -1
  11. package/dist/mcp-server/tools/definitions/_schemas.js +42 -40
  12. package/dist/mcp-server/tools/definitions/_schemas.js.map +1 -1
  13. package/dist/mcp-server/tools/definitions/analyze-collection.tool.d.ts +9 -4
  14. package/dist/mcp-server/tools/definitions/analyze-collection.tool.d.ts.map +1 -1
  15. package/dist/mcp-server/tools/definitions/analyze-collection.tool.js +15 -5
  16. package/dist/mcp-server/tools/definitions/analyze-collection.tool.js.map +1 -1
  17. package/dist/mcp-server/tools/definitions/compare-structures.tool.d.ts +7 -0
  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 +76 -13
  20. package/dist/mcp-server/tools/definitions/compare-structures.tool.js.map +1 -1
  21. package/dist/mcp-server/tools/definitions/get-structure.tool.js +18 -3
  22. package/dist/mcp-server/tools/definitions/get-structure.tool.js.map +1 -1
  23. package/dist/mcp-server/tools/definitions/search-structures.tool.d.ts +5 -11
  24. package/dist/mcp-server/tools/definitions/search-structures.tool.d.ts.map +1 -1
  25. package/dist/mcp-server/tools/definitions/search-structures.tool.js +16 -4
  26. package/dist/mcp-server/tools/definitions/search-structures.tool.js.map +1 -1
  27. package/dist/services/alignment/alignment-service.d.ts +7 -0
  28. package/dist/services/alignment/alignment-service.d.ts.map +1 -1
  29. package/dist/services/alignment/alignment-service.js +22 -3
  30. package/dist/services/alignment/alignment-service.js.map +1 -1
  31. package/dist/services/foldseek/foldseek-service.d.ts +1 -1
  32. package/dist/services/foldseek/foldseek-service.d.ts.map +1 -1
  33. package/dist/services/foldseek/foldseek-service.js +5 -1
  34. package/dist/services/foldseek/foldseek-service.js.map +1 -1
  35. package/dist/services/rcsb/rcsb-service.d.ts.map +1 -1
  36. package/dist/services/rcsb/rcsb-service.js +12 -8
  37. package/dist/services/rcsb/rcsb-service.js.map +1 -1
  38. package/dist/services/rcsb/types.d.ts +10 -3
  39. package/dist/services/rcsb/types.d.ts.map +1 -1
  40. package/dist/services/shared/identifiers.d.ts +7 -0
  41. package/dist/services/shared/identifiers.d.ts.map +1 -1
  42. package/dist/services/shared/identifiers.js +14 -1
  43. package/dist/services/shared/identifiers.js.map +1 -1
  44. package/package.json +1 -1
  45. package/server.json +3 -3
package/dist/services/foldseek/foldseek-service.js CHANGED
@@ -127,8 +127,12 @@ export class FoldseekService {
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  function normalizeHit(aln, database) {
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  const target = aln.target;
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  const hit = { target, database, ...parseTarget(target) };
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+ // Upstream (MMseqs2-App, which serves search.foldseek.com) emits `seqId` on a
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+ // 0–100 percentage scale for structure search, while this server declares
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+ // sequence identity as a 0–1 fraction (matching the `min_identity` inputs on
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+ // the RCSB paths), so convert once at the service boundary.
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  if (typeof aln.seqId === 'number')
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- hit.sequenceIdentity = aln.seqId;
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+ hit.sequenceIdentity = aln.seqId / 100;
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  if (typeof aln.alnLength === 'number')
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  hit.alignmentLength = aln.alnLength;
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  if (typeof aln.prob === 'number')
package/dist/services/foldseek/foldseek-service.js.map CHANGED
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package/dist/services/rcsb/rcsb-service.js CHANGED
@@ -386,14 +386,18 @@ function normalizeBuckets(raw, spec) {
386
386
  bucket.rangeTo = from + interval;
387
387
  }
388
388
  }
389
- if (child && b.facets) {
390
- bucket.children = [
391
- {
392
- dimension: child.dimension,
393
- attribute: child.attribute,
394
- buckets: normalizeBuckets(b.facets[0]?.buckets, child),
395
- },
396
- ];
389
+ // Keyed on the SPEC, not the response: RCSB omits the nested facet key
390
+ // outright when nothing in the parent bucket carries a value for the child
391
+ // attribute (computed models have no experimental method). Emitting the child
392
+ // with an empty bucket list keeps a two-dimension request two-dimensional, so
393
+ // a present child means "a cross-tab was requested" and empty buckets mean
394
+ // "it aggregated to nothing" — conditions an absent child conflated.
395
+ if (child) {
396
+ bucket.child = {
397
+ dimension: child.dimension,
398
+ attribute: child.attribute,
399
+ buckets: normalizeBuckets(b.facets?.[0]?.buckets, child),
400
+ };
397
401
  }
398
402
  return bucket;
399
403
  });
package/dist/services/rcsb/rcsb-service.js.map CHANGED
@@ -1 +1 @@
1
- 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package/dist/services/rcsb/types.d.ts CHANGED
@@ -11,10 +11,17 @@ export interface SearchHit {
11
11
  /** RCSB relevance score. */
12
12
  score: number;
13
13
  }
14
- /** One facet bucket; `children` present only for multidimensional (nested) facets. */
14
+ /** One facet bucket; `child` present only for multidimensional (nested) facets. */
15
15
  export interface FacetBucket {
16
- /** Nested sub-facets for multidimensional cross-tabs. */
17
- children?: FacetDimension[];
16
+ /**
17
+ * The single nested sub-facet for a multidimensional cross-tab. A facet spec
18
+ * carries at most one child and the request builder sends exactly one nested
19
+ * facet, so a bucket is never cross-tabbed by more than one dimension. Present
20
+ * whenever a child dimension was requested — with an empty bucket list when the
21
+ * scope carries no value for it (computed models have no experimental method),
22
+ * so the shape reflects what was asked for rather than dropping the dimension.
23
+ */
24
+ child?: FacetDimension;
18
25
  /** Count of entries in the bucket. */
19
26
  count: number;
20
27
  /** Bucket label (category value, numeric bin start, or period). */
package/dist/services/rcsb/types.d.ts.map CHANGED
@@ -1 +1 @@
1
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1
+ {"version":3,"file":"types.d.ts","sourceRoot":"","sources":["../../../src/services/rcsb/types.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,sDAAsD;AACtD,MAAM,WAAW,SAAS;IACxB,qFAAqF;IACrF,EAAE,EAAE,MAAM,CAAC;IACX,4BAA4B;IAC5B,KAAK,EAAE,MAAM,CAAC;CACf;AAED,mFAAmF;AACnF,MAAM,WAAW,WAAW;IAC1B;;;;;;;OAOG;IACH,KAAK,CAAC,EAAE,cAAc,CAAC;IACvB,sCAAsC;IACtC,KAAK,EAAE,MAAM,CAAC;IACd,mEAAmE;IACnE,KAAK,EAAE,MAAM,CAAC;IACd;;;;OAIG;IACH,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB;;;;OAIG;IACH,OAAO,CAAC,EAAE,MAAM,CAAC;CAClB;AAED,yCAAyC;AACzC,MAAM,WAAW,cAAc;IAC7B,uDAAuD;IACvD,SAAS,EAAE,MAAM,CAAC;IAClB,yFAAyF;IACzF,OAAO,EAAE,WAAW,EAAE,CAAC;IACvB,2EAA2E;IAC3E,SAAS,EAAE,MAAM,CAAC;IAClB,gEAAgE;IAChE,SAAS,CAAC,EAAE,OAAO,CAAC;CACrB;AAED,oCAAoC;AACpC,MAAM,WAAW,YAAY;IAC3B,+CAA+C;IAC/C,MAAM,CAAC,EAAE,cAAc,EAAE,CAAC;IAC1B,gCAAgC;IAChC,IAAI,EAAE,SAAS,EAAE,CAAC;IAClB,kDAAkD;IAClD,KAAK,EAAE,MAAM,CAAC;CACf;AAED,kEAAkE;AAClE,MAAM,WAAW,iBAAiB;IAChC,iDAAiD;IACjD,MAAM,CAAC,EAAE,MAAM,EAAE,CAAC;IAClB,+DAA+D;IAC/D,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,yCAAyC;IACzC,QAAQ,EAAE,MAAM,CAAC;IACjB,uCAAuC;IACvC,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,8EAA8E;IAC9E,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,4CAA4C;IAC5C,cAAc,CAAC,EAAE,MAAM,CAAC;CACzB;AAED,mGAAmG;AACnG,MAAM,WAAW,WAAW;IAC1B,6CAA6C;IAC7C,SAAS,EAAE,MAAM,CAAC;IAClB,4EAA4E;IAC5E,MAAM,EAAE,MAAM,EAAE,CAAC;IACjB,oEAAoE;IACpE,WAAW,CAAC,EAAE,MAAM,CAAC;CACtB;AAED,8DAA8D;AAC9D,MAAM,WAAW,UAAU;IACzB,iDAAiD;IACjD,MAAM,EAAE,MAAM,CAAC;IACf,wCAAwC;IACxC,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,oCAAoC;IACpC,IAAI,CAAC,EAAE,MAAM,CAAC;CACf;AAED,8DAA8D;AAC9D,MAAM,WAAW,SAAS;IACxB;;;;;OAKG;IACH,qBAAqB,CAAC,EAAE,MAAM,CAAC;IAC/B,oBAAoB;IACpB,EAAE,EAAE,MAAM,CAAC;IACX,4CAA4C;IAC5C,OAAO,EAAE,UAAU,EAAE,CAAC;IACtB,2DAA2D;IAC3D,OAAO,CAAC,EAAE,MAAM,EAAE,CAAC;IACnB,kDAAkD;IAClD,eAAe,CAAC,EAAE,MAAM,CAAC;IACzB,yDAAyD;IACzD,SAAS,EAAE,MAAM,EAAE,CAAC;IACpB,gCAAgC;IAChC,eAAe,EAAE,iBAAiB,EAAE,CAAC;IACrC,uCAAuC;IACvC,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,4CAA4C;IAC5C,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,uBAAuB;IACvB,KAAK,CAAC,EAAE,MAAM,CAAC;CAChB;AAED,4DAA4D;AAC5D,MAAM,WAAW,cAAc;IAC7B,mDAAmD;IACnD,MAAM,EAAE,MAAM,CAAC;IACf,2CAA2C;IAC3C,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,kDAAkD;IAClD,aAAa,EAAE,MAAM,CAAC;IACtB,wCAAwC;IACxC,KAAK,CAAC,EAAE,MAAM,CAAC;CAChB;AAED,4DAA4D;AAC5D,MAAM,WAAW,WAAW;IAC1B,uCAAuC;IACvC,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,oCAAoC;IACpC,YAAY,EAAE,MAAM,CAAC;IACrB,mDAAmD;IACnD,QAAQ,EAAE,cAAc,EAAE,CAAC;CAC5B;AAED,gDAAgD;AAChD,MAAM,WAAW,QAAQ;IACvB,iCAAiC;IACjC,MAAM,EAAE,MAAM,CAAC;IACf,yBAAyB;IACzB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,2BAA2B;IAC3B,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,+BAA+B;IAC/B,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,qBAAqB;IACrB,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,sCAAsC;IACtC,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,2CAA2C;IAC3C,IAAI,CAAC,EAAE,MAAM,CAAC;CACf;AAED,wDAAwD;AACxD,MAAM,MAAM,WAAW,GAAG,cAAc,GAAG,eAAe,CAAC;AAE3D,uEAAuE;AACvE,MAAM,WAAW,qBAAqB;IACpC;;;;OAIG;IACH,WAAW,CAAC,EAAE,WAAW,EAAE,CAAC;IAC5B,iBAAiB;IACjB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,wCAAwC;IACxC,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,+BAA+B;IAC/B,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,6DAA6D;IAC7D,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,4DAA4D;IAC5D,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,gDAAgD;IAChD,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,2DAA2D;IAC3D,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,mBAAmB;IACnB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,uBAAuB;IACvB,IAAI,CAAC,EAAE,MAAM,CAAC;CACf"}
package/dist/services/shared/identifiers.d.ts CHANGED
@@ -5,6 +5,13 @@
5
5
  */
6
6
  /** True when `value` is a syntactically valid UniProt accession. */
7
7
  export declare function isUniProtAccession(value: string): boolean;
8
+ /**
9
+ * True when `value` is an AlphaFold DB entry ID (`AF-P69905-F1`). Both AlphaFold's
10
+ * prediction endpoint and 3D-Beacons accept this form alongside the bare accession,
11
+ * and the `af://` resource emits it as `entryId`, so a caller can hand it straight
12
+ * back to a predicted-source lookup.
13
+ */
14
+ export declare function isAlphaFoldEntryId(value: string): boolean;
8
15
  /** True when `value` is a syntactically valid PDB entry ID. */
9
16
  export declare function isPdbId(value: string): boolean;
10
17
  /** Extract the PDB entry ID from a polymer-entity ID (`4HHB_1` → `4HHB`). */
package/dist/services/shared/identifiers.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"identifiers.d.ts","sourceRoot":"","sources":["../../../src/services/shared/identifiers.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAQH,oEAAoE;AACpE,wBAAgB,kBAAkB,CAAC,KAAK,EAAE,MAAM,GAAG,OAAO,CAEzD;AAED,+DAA+D;AAC/D,wBAAgB,OAAO,CAAC,KAAK,EAAE,MAAM,GAAG,OAAO,CAE9C;AAED,6EAA6E;AAC7E,wBAAgB,SAAS,CAAC,UAAU,EAAE,MAAM,GAAG,MAAM,CAGpD"}
1
+ {"version":3,"file":"identifiers.d.ts","sourceRoot":"","sources":["../../../src/services/shared/identifiers.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAcH,oEAAoE;AACpE,wBAAgB,kBAAkB,CAAC,KAAK,EAAE,MAAM,GAAG,OAAO,CAEzD;AAED;;;;;GAKG;AACH,wBAAgB,kBAAkB,CAAC,KAAK,EAAE,MAAM,GAAG,OAAO,CAEzD;AAED,+DAA+D;AAC/D,wBAAgB,OAAO,CAAC,KAAK,EAAE,MAAM,GAAG,OAAO,CAE9C;AAED,6EAA6E;AAC7E,wBAAgB,SAAS,CAAC,UAAU,EAAE,MAAM,GAAG,MAAM,CAGpD"}
package/dist/services/shared/identifiers.js CHANGED
@@ -3,14 +3,27 @@
3
3
  * (PDB) and predicted (UniProt-keyed) halves of the federation. Pure, no I/O.
4
4
  * @module services/shared/identifiers
5
5
  */
6
+ /** UniProt accession body (6- or 10-character forms), unanchored. */
7
+ const UNIPROT_BODY = '(?:[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9](?:[A-Z][A-Z0-9]{2}[0-9]){1,2})';
6
8
  /** UniProt accession pattern (6- or 10-character forms). */
7
- const UNIPROT_RE = /^(?:[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9](?:[A-Z][A-Z0-9]{2}[0-9]){1,2})$/i;
9
+ const UNIPROT_RE = new RegExp(`^${UNIPROT_BODY}$`, 'i');
10
+ /** AlphaFold DB entry ID pattern: `AF-<accession>-F<fragment>` (e.g. AF-P69905-F1). */
11
+ const AF_ENTRY_RE = new RegExp(`^AF-${UNIPROT_BODY}-F\\d+$`, 'i');
8
12
  /** PDB entry ID pattern: 4 alphanumerics, first character a digit (e.g. 4HHB, 1IEP). */
9
13
  const PDB_RE = /^[0-9][A-Za-z0-9]{3}$/;
10
14
  /** True when `value` is a syntactically valid UniProt accession. */
11
15
  export function isUniProtAccession(value) {
12
16
  return UNIPROT_RE.test(value.trim());
13
17
  }
18
+ /**
19
+ * True when `value` is an AlphaFold DB entry ID (`AF-P69905-F1`). Both AlphaFold's
20
+ * prediction endpoint and 3D-Beacons accept this form alongside the bare accession,
21
+ * and the `af://` resource emits it as `entryId`, so a caller can hand it straight
22
+ * back to a predicted-source lookup.
23
+ */
24
+ export function isAlphaFoldEntryId(value) {
25
+ return AF_ENTRY_RE.test(value.trim());
26
+ }
14
27
  /** True when `value` is a syntactically valid PDB entry ID. */
15
28
  export function isPdbId(value) {
16
29
  return PDB_RE.test(value.trim());
package/dist/services/shared/identifiers.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"identifiers.js","sourceRoot":"","sources":["../../../src/services/shared/identifiers.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,4DAA4D;AAC5D,MAAM,UAAU,GAAG,+EAA+E,CAAC;AAEnG,wFAAwF;AACxF,MAAM,MAAM,GAAG,uBAAuB,CAAC;AAEvC,oEAAoE;AACpE,MAAM,UAAU,kBAAkB,CAAC,KAAa;IAC9C,OAAO,UAAU,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC,CAAC;AACvC,CAAC;AAED,+DAA+D;AAC/D,MAAM,UAAU,OAAO,CAAC,KAAa;IACnC,OAAO,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC,CAAC;AACnC,CAAC;AAED,6EAA6E;AAC7E,MAAM,UAAU,SAAS,CAAC,UAAkB;IAC1C,MAAM,IAAI,GAAG,UAAU,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,IAAI,UAAU,CAAC;IACvD,OAAO,IAAI,CAAC,WAAW,EAAE,CAAC;AAC5B,CAAC"}
1
+ {"version":3,"file":"identifiers.js","sourceRoot":"","sources":["../../../src/services/shared/identifiers.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,qEAAqE;AACrE,MAAM,YAAY,GAAG,4EAA4E,CAAC;AAElG,4DAA4D;AAC5D,MAAM,UAAU,GAAG,IAAI,MAAM,CAAC,IAAI,YAAY,GAAG,EAAE,GAAG,CAAC,CAAC;AAExD,uFAAuF;AACvF,MAAM,WAAW,GAAG,IAAI,MAAM,CAAC,OAAO,YAAY,SAAS,EAAE,GAAG,CAAC,CAAC;AAElE,wFAAwF;AACxF,MAAM,MAAM,GAAG,uBAAuB,CAAC;AAEvC,oEAAoE;AACpE,MAAM,UAAU,kBAAkB,CAAC,KAAa;IAC9C,OAAO,UAAU,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC,CAAC;AACvC,CAAC;AAED;;;;;GAKG;AACH,MAAM,UAAU,kBAAkB,CAAC,KAAa;IAC9C,OAAO,WAAW,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC,CAAC;AACxC,CAAC;AAED,+DAA+D;AAC/D,MAAM,UAAU,OAAO,CAAC,KAAa;IACnC,OAAO,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC,CAAC;AACnC,CAAC;AAED,6EAA6E;AAC7E,MAAM,UAAU,SAAS,CAAC,UAAkB;IAC1C,MAAM,IAAI,GAAG,UAAU,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,IAAI,UAAU,CAAC;IACvD,OAAO,IAAI,CAAC,WAAW,EAAE,CAAC;AAC5B,CAAC"}
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@cyanheads/protein-mcp-server",
3
- "version": "0.4.1",
3
+ "version": "0.5.0",
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": "0.4.1",
9
+ "version": "0.5.0",
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": "0.4.1",
22
+ "version": "0.5.0",
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": "0.4.1",
51
+ "version": "0.5.0",
52
52
  "packageArguments": [
53
53
  {
54
54
  "type": "positional",