@cyanheads/pubchem-mcp-server 0.4.0 → 0.4.2

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 (34) hide show
  1. package/Dockerfile +11 -7
  2. package/LICENSE +1 -1
  3. package/README.md +1 -1
  4. package/dist/mcp-server/resources/definitions/compound-safety.resource.d.ts.map +1 -1
  5. package/dist/mcp-server/resources/definitions/compound-safety.resource.js +12 -8
  6. package/dist/mcp-server/resources/definitions/compound-safety.resource.js.map +1 -1
  7. package/dist/mcp-server/resources/definitions/index.d.ts +3 -3
  8. package/dist/mcp-server/resources/definitions/index.d.ts.map +1 -1
  9. package/dist/mcp-server/tools/definitions/get-bioactivity.tool.d.ts +1 -1
  10. package/dist/mcp-server/tools/definitions/get-compound-3d-structure.tool.d.ts +1 -1
  11. package/dist/mcp-server/tools/definitions/get-compound-image.tool.d.ts +1 -1
  12. package/dist/mcp-server/tools/definitions/get-compound-interactions.tool.d.ts +0 -1
  13. package/dist/mcp-server/tools/definitions/get-compound-interactions.tool.d.ts.map +1 -1
  14. package/dist/mcp-server/tools/definitions/get-compound-interactions.tool.js +1 -6
  15. package/dist/mcp-server/tools/definitions/get-compound-interactions.tool.js.map +1 -1
  16. package/dist/mcp-server/tools/definitions/get-compound-safety.tool.d.ts +6 -0
  17. package/dist/mcp-server/tools/definitions/get-compound-safety.tool.d.ts.map +1 -1
  18. package/dist/mcp-server/tools/definitions/get-compound-safety.tool.js +51 -22
  19. package/dist/mcp-server/tools/definitions/get-compound-safety.tool.js.map +1 -1
  20. package/dist/mcp-server/tools/definitions/index.d.ts +200 -195
  21. package/dist/mcp-server/tools/definitions/index.d.ts.map +1 -1
  22. package/dist/mcp-server/tools/definitions/search-assays.tool.d.ts +2 -2
  23. package/dist/mcp-server/tools/definitions/search-compounds.tool.d.ts +6 -6
  24. package/dist/mcp-server/tools/definitions/search-compounds.tool.js.map +1 -1
  25. package/dist/services/pubchem/pubchem-client.d.ts +8 -2
  26. package/dist/services/pubchem/pubchem-client.d.ts.map +1 -1
  27. package/dist/services/pubchem/pubchem-client.js +215 -21
  28. package/dist/services/pubchem/pubchem-client.js.map +1 -1
  29. package/dist/services/pubchem/types.d.ts +24 -6
  30. package/dist/services/pubchem/types.d.ts.map +1 -1
  31. package/dist/services/pubchem/types.js.map +1 -1
  32. package/manifest.json +1 -1
  33. package/package.json +11 -10
  34. package/server.json +3 -3
package/dist/mcp-server/tools/definitions/index.d.ts CHANGED
@@ -3,83 +3,6 @@
3
3
  * @module mcp-server/tools/definitions
4
4
  */
5
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  export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
6
- cid: import("zod").ZodNumber;
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- outcomeFilter: import("zod").ZodDefault<import("zod").ZodEnum<{
8
- active: "active";
9
- inactive: "inactive";
10
- all: "all";
11
- }>>;
12
- targetGeneId: import("zod").ZodOptional<import("zod").ZodNumber>;
13
- targetAccession: import("zod").ZodOptional<import("zod").ZodString>;
14
- maxResults: import("zod").ZodDefault<import("zod").ZodNumber>;
15
- }, import("zod/v4/core").$strip>, import("zod").ZodObject<{
16
- cid: import("zod").ZodNumber;
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- totalAssays: import("zod").ZodNumber;
18
- activeCount: import("zod").ZodNumber;
19
- inactiveCount: import("zod").ZodNumber;
20
- results: import("zod").ZodArray<import("zod").ZodObject<{
21
- aid: import("zod").ZodNumber;
22
- assayName: import("zod").ZodString;
23
- outcome: import("zod").ZodString;
24
- targetAccession: import("zod").ZodOptional<import("zod").ZodString>;
25
- targetGeneId: import("zod").ZodOptional<import("zod").ZodNumber>;
26
- activityValues: import("zod").ZodArray<import("zod").ZodObject<{
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- name: import("zod").ZodOptional<import("zod").ZodString>;
28
- value: import("zod").ZodNumber;
29
- unit: import("zod").ZodOptional<import("zod").ZodString>;
30
- }, import("zod/v4/core").$strip>>;
31
- }, import("zod/v4/core").$strip>>;
32
- }, import("zod/v4/core").$strip>, undefined, {
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- readonly outcomeFilter: import("zod").ZodString;
34
- readonly targetFilter: import("zod").ZodOptional<import("zod").ZodString>;
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- readonly filteredCount: import("zod").ZodNumber;
36
- readonly returnedCount: import("zod").ZodNumber;
37
- readonly truncated: import("zod").ZodOptional<import("zod").ZodBoolean>;
38
- readonly shown: import("zod").ZodOptional<import("zod").ZodNumber>;
39
- readonly cap: import("zod").ZodOptional<import("zod").ZodNumber>;
40
- readonly notice: import("zod").ZodOptional<import("zod").ZodString>;
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- }> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
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- cid: import("zod").ZodNumber;
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- format: import("zod").ZodDefault<import("zod").ZodEnum<{
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- sdf: "sdf";
45
- json: "json";
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- }>>;
47
- includeAlternateConformerIds: import("zod").ZodDefault<import("zod").ZodBoolean>;
48
- maxAtoms: import("zod").ZodOptional<import("zod").ZodNumber>;
49
- maxBonds: import("zod").ZodOptional<import("zod").ZodNumber>;
50
- includeRawSdf: import("zod").ZodDefault<import("zod").ZodBoolean>;
51
- }, import("zod/v4/core").$strip>, import("zod").ZodObject<{
52
- cid: import("zod").ZodNumber;
53
- conformerId: import("zod").ZodOptional<import("zod").ZodString>;
54
- atomCount: import("zod").ZodNumber;
55
- bondCount: import("zod").ZodNumber;
56
- atoms: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodObject<{
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- element: import("zod").ZodString;
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- x: import("zod").ZodNumber;
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- y: import("zod").ZodNumber;
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- z: import("zod").ZodNumber;
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- }, import("zod/v4/core").$strip>>>;
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- bonds: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodObject<{
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- a1: import("zod").ZodNumber;
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- a2: import("zod").ZodNumber;
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- order: import("zod").ZodNumber;
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- }, import("zod/v4/core").$strip>>>;
67
- sdf: import("zod").ZodOptional<import("zod").ZodString>;
68
- alternateConformerIds: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodString>>;
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- }, import("zod/v4/core").$strip>, readonly [{
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- readonly reason: "no_3d_structure";
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- readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;
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- readonly when: "PubChem has no computed 3D conformer for the requested CID";
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- readonly recovery: "Use pubchem_get_compound_image for the 2D structure, or verify the CID with pubchem_search_compounds.";
74
- }], {
75
- readonly truncated: import("zod").ZodOptional<import("zod").ZodBoolean>;
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- readonly shownAtoms: import("zod").ZodOptional<import("zod").ZodNumber>;
77
- readonly shownBonds: import("zod").ZodOptional<import("zod").ZodNumber>;
78
- readonly atomCap: import("zod").ZodOptional<import("zod").ZodNumber>;
79
- readonly bondCap: import("zod").ZodOptional<import("zod").ZodNumber>;
80
- readonly shownSdfLines: import("zod").ZodOptional<import("zod").ZodNumber>;
81
- readonly notice: import("zod").ZodOptional<import("zod").ZodString>;
82
- }> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
83
6
  cids: import("zod").ZodArray<import("zod").ZodNumber>;
84
7
  properties: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodEnum<{
85
8
  [x: string]: string;
@@ -152,10 +75,86 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
152
75
  }, import("zod/v4/core").$strip>>;
153
76
  }, import("zod/v4/core").$strip>>;
154
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  }, import("zod/v4/core").$strip>, undefined, undefined> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
78
+ cid: import("zod").ZodNumber;
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+ xrefTypes: import("zod").ZodArray<import("zod").ZodEnum<{
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+ [x: string]: string;
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+ }>>;
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+ maxPerType: import("zod").ZodDefault<import("zod").ZodNumber>;
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+ }, import("zod/v4/core").$strip>, import("zod").ZodObject<{
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+ cid: import("zod").ZodNumber;
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+ xrefs: import("zod").ZodArray<import("zod").ZodObject<{
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+ type: import("zod").ZodString;
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+ ids: import("zod").ZodArray<import("zod").ZodUnion<readonly [import("zod").ZodString, import("zod").ZodNumber]>>;
88
+ totalAvailable: import("zod").ZodNumber;
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+ truncated: import("zod").ZodBoolean;
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+ }, import("zod/v4/core").$strip>>;
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+ }, import("zod/v4/core").$strip>, undefined, {
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+ readonly notice: import("zod").ZodOptional<import("zod").ZodString>;
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+ }> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
94
+ searchType: import("zod").ZodEnum<{
95
+ formula: "formula";
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+ identifier: "identifier";
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+ similarity: "similarity";
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+ substructure: "substructure";
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+ superstructure: "superstructure";
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+ }>;
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+ identifierType: import("zod").ZodOptional<import("zod").ZodEnum<{
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+ inchikey: "inchikey";
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+ name: "name";
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+ smiles: "smiles";
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+ }>>;
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+ identifiers: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodString>>;
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+ formula: import("zod").ZodOptional<import("zod").ZodString>;
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+ allowOtherElements: import("zod").ZodDefault<import("zod").ZodBoolean>;
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+ query: import("zod").ZodOptional<import("zod").ZodString>;
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+ queryType: import("zod").ZodOptional<import("zod").ZodEnum<{
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+ cid: "cid";
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+ smiles: "smiles";
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+ }>>;
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+ threshold: import("zod").ZodDefault<import("zod").ZodNumber>;
115
+ maxResults: import("zod").ZodDefault<import("zod").ZodNumber>;
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+ properties: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodEnum<{
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+ [x: string]: string;
118
+ }>>>;
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+ }, import("zod/v4/core").$strip>, import("zod").ZodObject<{
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+ results: import("zod").ZodArray<import("zod").ZodObject<{
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+ cid: import("zod").ZodNumber;
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+ identifier: import("zod").ZodOptional<import("zod").ZodString>;
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+ properties: import("zod").ZodOptional<import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodUnknown>>;
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+ }, import("zod/v4/core").$strip>>;
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+ unresolvedIdentifiers: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodString>>;
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+ }, import("zod/v4/core").$strip>, readonly [{
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+ readonly reason: "missing_identifier_args";
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+ readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
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+ readonly when: "searchType is \"identifier\" but identifierType or identifiers were omitted";
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+ readonly recovery: "Set identifierType (name/smiles/inchikey) and pass a non-empty identifiers array (1-25 entries).";
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+ }, {
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+ readonly reason: "missing_formula";
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+ readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
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+ readonly when: "searchType is \"formula\" but the formula field was omitted";
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+ readonly recovery: "Pass formula in Hill notation, for example \"C6H12O6\" or \"CaH2O2\".";
136
+ }, {
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+ readonly reason: "missing_structure_args";
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+ readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
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+ readonly when: "substructure/superstructure/similarity search missing query or queryType";
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+ readonly recovery: "Provide both query (SMILES string or CID as string) and queryType (\"smiles\" or \"cid\").";
141
+ }, {
142
+ readonly reason: "invalid_cid_query";
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+ readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
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+ readonly when: "structure/similarity search with queryType \"cid\" but query is not a positive integer CID";
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+ readonly recovery: "Pass a positive integer CID string (e.g. \"2244\"), or set queryType \"smiles\" with a SMILES query.";
146
+ }], {
147
+ readonly searchType: import("zod").ZodString;
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+ readonly totalFound: import("zod").ZodNumber;
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+ readonly truncated: import("zod").ZodOptional<import("zod").ZodBoolean>;
150
+ readonly shown: import("zod").ZodOptional<import("zod").ZodNumber>;
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+ readonly cap: import("zod").ZodOptional<import("zod").ZodNumber>;
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+ readonly notice: import("zod").ZodOptional<import("zod").ZodString>;
153
+ }> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
155
154
  cid: import("zod").ZodNumber;
156
155
  size: import("zod").ZodDefault<import("zod").ZodEnum<{
157
- small: "small";
158
156
  large: "large";
157
+ small: "small";
159
158
  }>>;
160
159
  }, import("zod/v4/core").$strip>, import("zod").ZodObject<{
161
160
  cid: import("zod").ZodNumber;
@@ -170,29 +169,44 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
170
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  readonly recovery: "Verify the CID with pubchem_search_compounds before retrying.";
171
170
  }], undefined> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
172
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  cid: import("zod").ZodNumber;
173
- kinds: import("zod").ZodDefault<import("zod").ZodArray<import("zod").ZodEnum<{
174
- "drug-drug": "drug-drug";
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- "drug-food": "drug-food";
176
- target: "target";
177
- }>>>;
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- maxEntries: import("zod").ZodDefault<import("zod").ZodNumber>;
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+ format: import("zod").ZodDefault<import("zod").ZodEnum<{
173
+ json: "json";
174
+ sdf: "sdf";
175
+ }>>;
176
+ includeAlternateConformerIds: import("zod").ZodDefault<import("zod").ZodBoolean>;
177
+ maxAtoms: import("zod").ZodOptional<import("zod").ZodNumber>;
178
+ maxBonds: import("zod").ZodOptional<import("zod").ZodNumber>;
179
+ includeRawSdf: import("zod").ZodDefault<import("zod").ZodBoolean>;
179
180
  }, import("zod/v4/core").$strip>, import("zod").ZodObject<{
180
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  cid: import("zod").ZodNumber;
181
- entries: import("zod").ZodArray<import("zod").ZodObject<{
182
- kind: import("zod").ZodEnum<{
183
- "drug-drug": "drug-drug";
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- "drug-food": "drug-food";
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- target: "target";
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- }>;
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- partner: import("zod").ZodOptional<import("zod").ZodString>;
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- source: import("zod").ZodString;
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- severity: import("zod").ZodOptional<import("zod").ZodString>;
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- text: import("zod").ZodString;
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- }, import("zod/v4/core").$strip>>;
192
- }, import("zod/v4/core").$strip>, undefined, {
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- readonly requestedKinds: import("zod").ZodString;
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- readonly returnedCount: import("zod").ZodNumber;
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- readonly failedKinds: import("zod").ZodOptional<import("zod").ZodString>;
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+ conformerId: import("zod").ZodOptional<import("zod").ZodString>;
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+ atomCount: import("zod").ZodNumber;
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+ bondCount: import("zod").ZodNumber;
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+ atoms: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodObject<{
186
+ element: import("zod").ZodString;
187
+ x: import("zod").ZodNumber;
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+ y: import("zod").ZodNumber;
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+ z: import("zod").ZodNumber;
190
+ }, import("zod/v4/core").$strip>>>;
191
+ bonds: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodObject<{
192
+ a1: import("zod").ZodNumber;
193
+ a2: import("zod").ZodNumber;
194
+ order: import("zod").ZodNumber;
195
+ }, import("zod/v4/core").$strip>>>;
196
+ sdf: import("zod").ZodOptional<import("zod").ZodString>;
197
+ alternateConformerIds: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodString>>;
198
+ }, import("zod/v4/core").$strip>, readonly [{
199
+ readonly reason: "no_3d_structure";
200
+ readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;
201
+ readonly when: "PubChem has no computed 3D conformer for the requested CID";
202
+ readonly recovery: "Use pubchem_get_compound_image for the 2D structure, or verify the CID with pubchem_search_compounds.";
203
+ }], {
204
+ readonly truncated: import("zod").ZodOptional<import("zod").ZodBoolean>;
205
+ readonly shownAtoms: import("zod").ZodOptional<import("zod").ZodNumber>;
206
+ readonly shownBonds: import("zod").ZodOptional<import("zod").ZodNumber>;
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+ readonly atomCap: import("zod").ZodOptional<import("zod").ZodNumber>;
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+ readonly bondCap: import("zod").ZodOptional<import("zod").ZodNumber>;
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+ readonly shownSdfLines: import("zod").ZodOptional<import("zod").ZodNumber>;
196
210
  readonly notice: import("zod").ZodOptional<import("zod").ZodString>;
197
211
  }> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
198
212
  cids: import("zod").ZodArray<import("zod").ZodNumber>;
@@ -200,6 +214,11 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
200
214
  results: import("zod").ZodArray<import("zod").ZodObject<{
201
215
  cid: import("zod").ZodNumber;
202
216
  hasData: import("zod").ZodBoolean;
217
+ status: import("zod").ZodEnum<{
218
+ cid_not_found: "cid_not_found";
219
+ no_ghs_data: "no_ghs_data";
220
+ ok: "ok";
221
+ }>;
203
222
  ghs: import("zod").ZodOptional<import("zod").ZodObject<{
204
223
  signalWord: import("zod").ZodOptional<import("zod").ZodString>;
205
224
  pictograms: import("zod").ZodArray<import("zod").ZodString>;
@@ -210,6 +229,7 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
210
229
  precautionaryStatements: import("zod").ZodArray<import("zod").ZodObject<{
211
230
  code: import("zod").ZodString;
212
231
  statement: import("zod").ZodString;
232
+ decoded: import("zod").ZodBoolean;
213
233
  }, import("zod/v4/core").$strip>>;
214
234
  }, import("zod/v4/core").$strip>>;
215
235
  source: import("zod").ZodOptional<import("zod").ZodString>;
@@ -220,62 +240,71 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
220
240
  readonly notice: import("zod").ZodOptional<import("zod").ZodString>;
221
241
  }> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
222
242
  cid: import("zod").ZodNumber;
223
- xrefTypes: import("zod").ZodArray<import("zod").ZodEnum<{
224
- [x: string]: string;
243
+ outcomeFilter: import("zod").ZodDefault<import("zod").ZodEnum<{
244
+ active: "active";
245
+ all: "all";
246
+ inactive: "inactive";
225
247
  }>>;
226
- maxPerType: import("zod").ZodDefault<import("zod").ZodNumber>;
248
+ targetGeneId: import("zod").ZodOptional<import("zod").ZodNumber>;
249
+ targetAccession: import("zod").ZodOptional<import("zod").ZodString>;
250
+ maxResults: import("zod").ZodDefault<import("zod").ZodNumber>;
227
251
  }, import("zod/v4/core").$strip>, import("zod").ZodObject<{
228
252
  cid: import("zod").ZodNumber;
229
- xrefs: import("zod").ZodArray<import("zod").ZodObject<{
230
- type: import("zod").ZodString;
231
- ids: import("zod").ZodArray<import("zod").ZodUnion<readonly [import("zod").ZodString, import("zod").ZodNumber]>>;
232
- totalAvailable: import("zod").ZodNumber;
233
- truncated: import("zod").ZodBoolean;
253
+ totalAssays: import("zod").ZodNumber;
254
+ activeCount: import("zod").ZodNumber;
255
+ inactiveCount: import("zod").ZodNumber;
256
+ results: import("zod").ZodArray<import("zod").ZodObject<{
257
+ aid: import("zod").ZodNumber;
258
+ assayName: import("zod").ZodString;
259
+ outcome: import("zod").ZodString;
260
+ targetAccession: import("zod").ZodOptional<import("zod").ZodString>;
261
+ targetGeneId: import("zod").ZodOptional<import("zod").ZodNumber>;
262
+ activityValues: import("zod").ZodArray<import("zod").ZodObject<{
263
+ name: import("zod").ZodOptional<import("zod").ZodString>;
264
+ value: import("zod").ZodNumber;
265
+ unit: import("zod").ZodOptional<import("zod").ZodString>;
266
+ }, import("zod/v4/core").$strip>>;
234
267
  }, import("zod/v4/core").$strip>>;
235
268
  }, import("zod/v4/core").$strip>, undefined, {
269
+ readonly outcomeFilter: import("zod").ZodString;
270
+ readonly targetFilter: import("zod").ZodOptional<import("zod").ZodString>;
271
+ readonly filteredCount: import("zod").ZodNumber;
272
+ readonly returnedCount: import("zod").ZodNumber;
273
+ readonly truncated: import("zod").ZodOptional<import("zod").ZodBoolean>;
274
+ readonly shown: import("zod").ZodOptional<import("zod").ZodNumber>;
275
+ readonly cap: import("zod").ZodOptional<import("zod").ZodNumber>;
236
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  readonly notice: import("zod").ZodOptional<import("zod").ZodString>;
237
277
  }> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
238
- entityType: import("zod").ZodEnum<{
239
- assay: "assay";
240
- gene: "gene";
241
- protein: "protein";
242
- taxonomy: "taxonomy";
243
- }>;
244
- identifiers: import("zod").ZodArray<import("zod").ZodUnion<readonly [import("zod").ZodString, import("zod").ZodNumber]>>;
278
+ cid: import("zod").ZodNumber;
279
+ kinds: import("zod").ZodDefault<import("zod").ZodArray<import("zod").ZodEnum<{
280
+ "drug-drug": "drug-drug";
281
+ "drug-food": "drug-food";
282
+ target: "target";
283
+ }>>>;
284
+ maxEntries: import("zod").ZodDefault<import("zod").ZodNumber>;
245
285
  }, import("zod/v4/core").$strip>, import("zod").ZodObject<{
246
- entityType: import("zod").ZodString;
247
- summaries: import("zod").ZodArray<import("zod").ZodObject<{
248
- identifier: import("zod").ZodUnion<readonly [import("zod").ZodString, import("zod").ZodNumber]>;
249
- found: import("zod").ZodBoolean;
250
- data: import("zod").ZodOptional<import("zod").ZodObject<{
251
- aid: import("zod").ZodOptional<import("zod").ZodNumber>;
252
- name: import("zod").ZodOptional<import("zod").ZodString>;
253
- description: import("zod").ZodOptional<import("zod").ZodString>;
254
- sourceName: import("zod").ZodOptional<import("zod").ZodString>;
255
- numSubstances: import("zod").ZodOptional<import("zod").ZodNumber>;
256
- numActive: import("zod").ZodOptional<import("zod").ZodNumber>;
257
- geneId: import("zod").ZodOptional<import("zod").ZodNumber>;
258
- symbol: import("zod").ZodOptional<import("zod").ZodString>;
259
- taxonomyId: import("zod").ZodOptional<import("zod").ZodNumber>;
260
- taxonomy: import("zod").ZodOptional<import("zod").ZodString>;
261
- synonyms: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodString>>;
262
- proteinAccession: import("zod").ZodOptional<import("zod").ZodString>;
263
- scientificName: import("zod").ZodOptional<import("zod").ZodString>;
264
- commonName: import("zod").ZodOptional<import("zod").ZodString>;
265
- rank: import("zod").ZodOptional<import("zod").ZodString>;
266
- lineage: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodString>>;
267
- }, import("zod/v4/core").$strip>>;
286
+ cid: import("zod").ZodNumber;
287
+ entries: import("zod").ZodArray<import("zod").ZodObject<{
288
+ kind: import("zod").ZodEnum<{
289
+ "drug-drug": "drug-drug";
290
+ "drug-food": "drug-food";
291
+ target: "target";
292
+ }>;
293
+ partner: import("zod").ZodOptional<import("zod").ZodString>;
294
+ source: import("zod").ZodString;
295
+ text: import("zod").ZodString;
268
296
  }, import("zod/v4/core").$strip>>;
269
297
  }, import("zod/v4/core").$strip>, undefined, {
270
- readonly requestedCount: import("zod").ZodNumber;
271
- readonly foundCount: import("zod").ZodNumber;
298
+ readonly requestedKinds: import("zod").ZodString;
299
+ readonly returnedCount: import("zod").ZodNumber;
300
+ readonly failedKinds: import("zod").ZodOptional<import("zod").ZodString>;
272
301
  readonly notice: import("zod").ZodOptional<import("zod").ZodString>;
273
302
  }> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
274
303
  targetType: import("zod").ZodEnum<{
275
- proteinaccession: "proteinaccession";
304
+ geneid: "geneid";
276
305
  genesymbol: "genesymbol";
306
+ proteinaccession: "proteinaccession";
277
307
  proteinname: "proteinname";
278
- geneid: "geneid";
279
308
  }>;
280
309
  targetQuery: import("zod").ZodString;
281
310
  maxResults: import("zod").ZodDefault<import("zod").ZodNumber>;
@@ -300,64 +329,40 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
300
329
  readonly cap: import("zod").ZodOptional<import("zod").ZodNumber>;
301
330
  readonly notice: import("zod").ZodOptional<import("zod").ZodString>;
302
331
  }> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
303
- searchType: import("zod").ZodEnum<{
304
- substructure: "substructure";
305
- superstructure: "superstructure";
306
- similarity: "similarity";
307
- identifier: "identifier";
308
- formula: "formula";
332
+ entityType: import("zod").ZodEnum<{
333
+ assay: "assay";
334
+ gene: "gene";
335
+ protein: "protein";
336
+ taxonomy: "taxonomy";
309
337
  }>;
310
- identifierType: import("zod").ZodOptional<import("zod").ZodEnum<{
311
- smiles: "smiles";
312
- name: "name";
313
- inchikey: "inchikey";
314
- }>>;
315
- identifiers: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodString>>;
316
- formula: import("zod").ZodOptional<import("zod").ZodString>;
317
- allowOtherElements: import("zod").ZodDefault<import("zod").ZodBoolean>;
318
- query: import("zod").ZodOptional<import("zod").ZodString>;
319
- queryType: import("zod").ZodOptional<import("zod").ZodEnum<{
320
- smiles: "smiles";
321
- cid: "cid";
322
- }>>;
323
- threshold: import("zod").ZodDefault<import("zod").ZodNumber>;
324
- maxResults: import("zod").ZodDefault<import("zod").ZodNumber>;
325
- properties: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodEnum<{
326
- [x: string]: string;
327
- }>>>;
338
+ identifiers: import("zod").ZodArray<import("zod").ZodUnion<readonly [import("zod").ZodString, import("zod").ZodNumber]>>;
328
339
  }, import("zod/v4/core").$strip>, import("zod").ZodObject<{
329
- results: import("zod").ZodArray<import("zod").ZodObject<{
330
- cid: import("zod").ZodNumber;
331
- identifier: import("zod").ZodOptional<import("zod").ZodString>;
332
- properties: import("zod").ZodOptional<import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodUnknown>>;
340
+ entityType: import("zod").ZodString;
341
+ summaries: import("zod").ZodArray<import("zod").ZodObject<{
342
+ identifier: import("zod").ZodUnion<readonly [import("zod").ZodString, import("zod").ZodNumber]>;
343
+ found: import("zod").ZodBoolean;
344
+ data: import("zod").ZodOptional<import("zod").ZodObject<{
345
+ aid: import("zod").ZodOptional<import("zod").ZodNumber>;
346
+ name: import("zod").ZodOptional<import("zod").ZodString>;
347
+ description: import("zod").ZodOptional<import("zod").ZodString>;
348
+ sourceName: import("zod").ZodOptional<import("zod").ZodString>;
349
+ numSubstances: import("zod").ZodOptional<import("zod").ZodNumber>;
350
+ numActive: import("zod").ZodOptional<import("zod").ZodNumber>;
351
+ geneId: import("zod").ZodOptional<import("zod").ZodNumber>;
352
+ symbol: import("zod").ZodOptional<import("zod").ZodString>;
353
+ taxonomyId: import("zod").ZodOptional<import("zod").ZodNumber>;
354
+ taxonomy: import("zod").ZodOptional<import("zod").ZodString>;
355
+ synonyms: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodString>>;
356
+ proteinAccession: import("zod").ZodOptional<import("zod").ZodString>;
357
+ scientificName: import("zod").ZodOptional<import("zod").ZodString>;
358
+ commonName: import("zod").ZodOptional<import("zod").ZodString>;
359
+ rank: import("zod").ZodOptional<import("zod").ZodString>;
360
+ lineage: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodString>>;
361
+ }, import("zod/v4/core").$strip>>;
333
362
  }, import("zod/v4/core").$strip>>;
334
- unresolvedIdentifiers: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodString>>;
335
- }, import("zod/v4/core").$strip>, readonly [{
336
- readonly reason: "missing_identifier_args";
337
- readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
338
- readonly when: "searchType is \"identifier\" but identifierType or identifiers were omitted";
339
- readonly recovery: "Set identifierType (name/smiles/inchikey) and pass a non-empty identifiers array (1-25 entries).";
340
- }, {
341
- readonly reason: "missing_formula";
342
- readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
343
- readonly when: "searchType is \"formula\" but the formula field was omitted";
344
- readonly recovery: "Pass formula in Hill notation, for example \"C6H12O6\" or \"CaH2O2\".";
345
- }, {
346
- readonly reason: "missing_structure_args";
347
- readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
348
- readonly when: "substructure/superstructure/similarity search missing query or queryType";
349
- readonly recovery: "Provide both query (SMILES string or CID as string) and queryType (\"smiles\" or \"cid\").";
350
- }, {
351
- readonly reason: "invalid_cid_query";
352
- readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
353
- readonly when: "structure/similarity search with queryType \"cid\" but query is not a positive integer CID";
354
- readonly recovery: "Pass a positive integer CID string (e.g. \"2244\"), or set queryType \"smiles\" with a SMILES query.";
355
- }], {
356
- readonly searchType: import("zod").ZodString;
357
- readonly totalFound: import("zod").ZodNumber;
358
- readonly truncated: import("zod").ZodOptional<import("zod").ZodBoolean>;
359
- readonly shown: import("zod").ZodOptional<import("zod").ZodNumber>;
360
- readonly cap: import("zod").ZodOptional<import("zod").ZodNumber>;
363
+ }, import("zod/v4/core").$strip>, undefined, {
364
+ readonly requestedCount: import("zod").ZodNumber;
365
+ readonly foundCount: import("zod").ZodNumber;
361
366
  readonly notice: import("zod").ZodOptional<import("zod").ZodString>;
362
367
  }>)[];
363
368
  //# sourceMappingURL=index.d.ts.map
package/dist/mcp-server/tools/definitions/index.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/index.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAaH,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;KAW9B,CAAC"}
1
+ {"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/index.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAaH,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;KAW9B,CAAC"}
package/dist/mcp-server/tools/definitions/search-assays.tool.d.ts CHANGED
@@ -7,10 +7,10 @@ import { z } from '@cyanheads/mcp-ts-core';
7
7
  import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
8
8
  export declare const searchAssays: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
9
9
  targetType: z.ZodEnum<{
10
- proteinaccession: "proteinaccession";
10
+ geneid: "geneid";
11
11
  genesymbol: "genesymbol";
12
+ proteinaccession: "proteinaccession";
12
13
  proteinname: "proteinname";
13
- geneid: "geneid";
14
14
  }>;
15
15
  targetQuery: z.ZodString;
16
16
  maxResults: z.ZodDefault<z.ZodNumber>;
package/dist/mcp-server/tools/definitions/search-compounds.tool.d.ts CHANGED
@@ -7,24 +7,24 @@ import { z } from '@cyanheads/mcp-ts-core';
7
7
  import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
8
8
  export declare const searchCompounds: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
9
9
  searchType: z.ZodEnum<{
10
+ formula: "formula";
11
+ identifier: "identifier";
12
+ similarity: "similarity";
10
13
  substructure: "substructure";
11
14
  superstructure: "superstructure";
12
- similarity: "similarity";
13
- identifier: "identifier";
14
- formula: "formula";
15
15
  }>;
16
16
  identifierType: z.ZodOptional<z.ZodEnum<{
17
- smiles: "smiles";
18
- name: "name";
19
17
  inchikey: "inchikey";
18
+ name: "name";
19
+ smiles: "smiles";
20
20
  }>>;
21
21
  identifiers: z.ZodOptional<z.ZodArray<z.ZodString>>;
22
22
  formula: z.ZodOptional<z.ZodString>;
23
23
  allowOtherElements: z.ZodDefault<z.ZodBoolean>;
24
24
  query: z.ZodOptional<z.ZodString>;
25
25
  queryType: z.ZodOptional<z.ZodEnum<{
26
- smiles: "smiles";
27
26
  cid: "cid";
27
+ smiles: "smiles";
28
28
  }>>;
29
29
  threshold: z.ZodDefault<z.ZodNumber>;
30
30
  maxResults: z.ZodDefault<z.ZodNumber>;
package/dist/mcp-server/tools/definitions/search-compounds.tool.js.map CHANGED
@@ -1 +1 @@
1
- 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package/dist/services/pubchem/pubchem-client.d.ts CHANGED
@@ -3,7 +3,7 @@
3
3
  * Wraps both PUG REST and PUG View APIs behind a shared rate limiter.
4
4
  * @module services/pubchem/pubchem-client
5
5
  */
6
- import type { BioactivityRow, CompoundClassification, GHSClassification, InteractionsResult } from './types.js';
6
+ import type { BioactivityRow, CompoundClassification, InteractionsResult, SafetyLookup } from './types.js';
7
7
  export declare class PubChemClient {
8
8
  private readonly pugBase;
9
9
  private readonly viewBase;
@@ -38,7 +38,13 @@ export declare class PubChemClient {
38
38
  source?: string;
39
39
  text: string;
40
40
  }>>;
41
- getSafetyData(cid: number): Promise<GHSClassification | null>;
41
+ /** Fetch a compound's GHS classification.
42
+ *
43
+ * Reports "this CID has no PubChem record" separately from "this compound has no deposited
44
+ * GHS classification" — a nonexistent CID and a real compound without safety data are
45
+ * different answers that call for different follow-up, and both used to surface as an
46
+ * absent result. */
47
+ getSafetyData(cid: number): Promise<SafetyLookup>;
42
48
  getClassification(cid: number): Promise<CompoundClassification | null>;
43
49
  getAssaySummary(cid: number): Promise<BioactivityRow[]>;
44
50
  private parseAssayTable;
package/dist/services/pubchem/pubchem-client.d.ts.map CHANGED
@@ -1 +1 @@
1
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