@cyanheads/pubchem-mcp-server 0.1.23 → 0.2.0

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 (65) hide show
  1. package/README.md +43 -8
  2. package/dist/index.js +3 -1
  3. package/dist/index.js.map +1 -1
  4. package/dist/mcp-server/resources/definitions/assay.resource.d.ts +9 -0
  5. package/dist/mcp-server/resources/definitions/assay.resource.d.ts.map +1 -0
  6. package/dist/mcp-server/resources/definitions/assay.resource.js +24 -0
  7. package/dist/mcp-server/resources/definitions/assay.resource.js.map +1 -0
  8. package/dist/mcp-server/resources/definitions/compound-bioactivity.resource.d.ts +9 -0
  9. package/dist/mcp-server/resources/definitions/compound-bioactivity.resource.d.ts.map +1 -0
  10. package/dist/mcp-server/resources/definitions/compound-bioactivity.resource.js +28 -0
  11. package/dist/mcp-server/resources/definitions/compound-bioactivity.resource.js.map +1 -0
  12. package/dist/mcp-server/resources/definitions/compound-image.resource.d.ts +11 -0
  13. package/dist/mcp-server/resources/definitions/compound-image.resource.d.ts.map +1 -0
  14. package/dist/mcp-server/resources/definitions/compound-image.resource.js +28 -0
  15. package/dist/mcp-server/resources/definitions/compound-image.resource.js.map +1 -0
  16. package/dist/mcp-server/resources/definitions/compound-safety.resource.d.ts +9 -0
  17. package/dist/mcp-server/resources/definitions/compound-safety.resource.d.ts.map +1 -0
  18. package/dist/mcp-server/resources/definitions/compound-safety.resource.js +32 -0
  19. package/dist/mcp-server/resources/definitions/compound-safety.resource.js.map +1 -0
  20. package/dist/mcp-server/resources/definitions/compound-xrefs.resource.d.ts +9 -0
  21. package/dist/mcp-server/resources/definitions/compound-xrefs.resource.d.ts.map +1 -0
  22. package/dist/mcp-server/resources/definitions/compound-xrefs.resource.js +29 -0
  23. package/dist/mcp-server/resources/definitions/compound-xrefs.resource.js.map +1 -0
  24. package/dist/mcp-server/resources/definitions/compound.resource.d.ts +9 -0
  25. package/dist/mcp-server/resources/definitions/compound.resource.d.ts.map +1 -0
  26. package/dist/mcp-server/resources/definitions/compound.resource.js +28 -0
  27. package/dist/mcp-server/resources/definitions/compound.resource.js.map +1 -0
  28. package/dist/mcp-server/resources/definitions/index.d.ts +14 -0
  29. package/dist/mcp-server/resources/definitions/index.d.ts.map +1 -0
  30. package/dist/mcp-server/resources/definitions/index.js +19 -0
  31. package/dist/mcp-server/resources/definitions/index.js.map +1 -0
  32. package/dist/mcp-server/tools/definitions/get-bioactivity.tool.d.ts +3 -0
  33. package/dist/mcp-server/tools/definitions/get-bioactivity.tool.d.ts.map +1 -1
  34. package/dist/mcp-server/tools/definitions/get-bioactivity.tool.js +38 -6
  35. package/dist/mcp-server/tools/definitions/get-bioactivity.tool.js.map +1 -1
  36. package/dist/mcp-server/tools/definitions/get-compound-3d-structure.tool.d.ts +38 -0
  37. package/dist/mcp-server/tools/definitions/get-compound-3d-structure.tool.d.ts.map +1 -0
  38. package/dist/mcp-server/tools/definitions/get-compound-3d-structure.tool.js +133 -0
  39. package/dist/mcp-server/tools/definitions/get-compound-3d-structure.tool.js.map +1 -0
  40. package/dist/mcp-server/tools/definitions/get-compound-interactions.tool.d.ts +32 -0
  41. package/dist/mcp-server/tools/definitions/get-compound-interactions.tool.d.ts.map +1 -0
  42. package/dist/mcp-server/tools/definitions/get-compound-interactions.tool.js +92 -0
  43. package/dist/mcp-server/tools/definitions/get-compound-interactions.tool.js.map +1 -0
  44. package/dist/mcp-server/tools/definitions/get-compound-safety.tool.d.ts +19 -15
  45. package/dist/mcp-server/tools/definitions/get-compound-safety.tool.d.ts.map +1 -1
  46. package/dist/mcp-server/tools/definitions/get-compound-safety.tool.js +106 -73
  47. package/dist/mcp-server/tools/definitions/get-compound-safety.tool.js.map +1 -1
  48. package/dist/mcp-server/tools/definitions/index.d.ts +74 -12
  49. package/dist/mcp-server/tools/definitions/index.d.ts.map +1 -1
  50. package/dist/mcp-server/tools/definitions/index.js +4 -0
  51. package/dist/mcp-server/tools/definitions/index.js.map +1 -1
  52. package/dist/services/pubchem/pubchem-client.d.ts +20 -1
  53. package/dist/services/pubchem/pubchem-client.d.ts.map +1 -1
  54. package/dist/services/pubchem/pubchem-client.js +158 -0
  55. package/dist/services/pubchem/pubchem-client.js.map +1 -1
  56. package/dist/services/pubchem/sdf-parser.d.ts +20 -0
  57. package/dist/services/pubchem/sdf-parser.d.ts.map +1 -0
  58. package/dist/services/pubchem/sdf-parser.js +55 -0
  59. package/dist/services/pubchem/sdf-parser.js.map +1 -0
  60. package/dist/services/pubchem/types.d.ts +44 -0
  61. package/dist/services/pubchem/types.d.ts.map +1 -1
  62. package/dist/services/pubchem/types.js.map +1 -1
  63. package/manifest.json +1 -1
  64. package/package.json +1 -1
  65. package/server.json +3 -3
package/dist/mcp-server/tools/definitions/get-compound-safety.tool.js.map CHANGED
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AC,EAAE,EAAE,+BAA+B,CAAC,CAAC;gBAChD,KAAK,MAAM,CAAC,IAAI,CAAC,CAAC,uBAAuB;oBAAE,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,IAAI,KAAK,CAAC,CAAC,SAAS,EAAE,CAAC,CAAC;YACvF,CAAC;YAED,IAAI,CAAC,CAAC,MAAM;gBAAE,KAAK,CAAC,IAAI,CAAC,EAAE,EAAE,YAAY,CAAC,CAAC,MAAM,GAAG,CAAC,CAAC;YAEtD,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,EAAE,CAAC,CAAC;QACpC,CAAC;QAED,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IACrD,CAAC;CACF,CAAC,CAAC"}
package/dist/mcp-server/tools/definitions/index.d.ts CHANGED
@@ -9,6 +9,8 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
9
9
  inactive: "inactive";
10
10
  all: "all";
11
11
  }>>;
12
+ targetGeneId: import("zod").ZodOptional<import("zod").ZodNumber>;
13
+ targetAccession: import("zod").ZodOptional<import("zod").ZodString>;
12
14
  maxResults: import("zod").ZodDefault<import("zod").ZodNumber>;
13
15
  }, import("zod/v4/core").$strip>, import("zod").ZodObject<{
14
16
  cid: import("zod").ZodNumber;
@@ -29,10 +31,41 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
29
31
  }, import("zod/v4/core").$strip>>;
30
32
  }, import("zod/v4/core").$strip>, undefined, {
31
33
  readonly outcomeFilter: import("zod").ZodString;
34
+ readonly targetFilter: import("zod").ZodOptional<import("zod").ZodString>;
32
35
  readonly filteredCount: import("zod").ZodNumber;
33
36
  readonly returnedCount: import("zod").ZodNumber;
34
37
  readonly notice: import("zod").ZodOptional<import("zod").ZodString>;
35
38
  }> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
39
+ cid: import("zod").ZodNumber;
40
+ format: import("zod").ZodDefault<import("zod").ZodEnum<{
41
+ sdf: "sdf";
42
+ json: "json";
43
+ }>>;
44
+ includeAlternateConformerIds: import("zod").ZodDefault<import("zod").ZodBoolean>;
45
+ }, import("zod/v4/core").$strip>, import("zod").ZodObject<{
46
+ cid: import("zod").ZodNumber;
47
+ conformerId: import("zod").ZodOptional<import("zod").ZodString>;
48
+ atomCount: import("zod").ZodNumber;
49
+ bondCount: import("zod").ZodNumber;
50
+ atoms: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodObject<{
51
+ element: import("zod").ZodString;
52
+ x: import("zod").ZodNumber;
53
+ y: import("zod").ZodNumber;
54
+ z: import("zod").ZodNumber;
55
+ }, import("zod/v4/core").$strip>>>;
56
+ bonds: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodObject<{
57
+ a1: import("zod").ZodNumber;
58
+ a2: import("zod").ZodNumber;
59
+ order: import("zod").ZodNumber;
60
+ }, import("zod/v4/core").$strip>>>;
61
+ sdf: import("zod").ZodOptional<import("zod").ZodString>;
62
+ alternateConformerIds: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodString>>;
63
+ }, import("zod/v4/core").$strip>, readonly [{
64
+ readonly reason: "no_3d_structure";
65
+ readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;
66
+ readonly when: "PubChem has no computed 3D conformer for the requested CID";
67
+ readonly recovery: "Use pubchem_get_compound_image for the 2D structure, or verify the CID with pubchem_search_compounds.";
68
+ }], undefined> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
36
69
  cids: import("zod").ZodArray<import("zod").ZodNumber>;
37
70
  properties: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodEnum<{
38
71
  [x: string]: string;
@@ -121,23 +154,52 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
121
154
  readonly recovery: "Verify the CID with pubchem_search_compounds before retrying.";
122
155
  }], undefined> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
123
156
  cid: import("zod").ZodNumber;
157
+ kinds: import("zod").ZodDefault<import("zod").ZodArray<import("zod").ZodEnum<{
158
+ "drug-drug": "drug-drug";
159
+ "drug-food": "drug-food";
160
+ target: "target";
161
+ }>>>;
162
+ maxEntries: import("zod").ZodDefault<import("zod").ZodNumber>;
124
163
  }, import("zod/v4/core").$strip>, import("zod").ZodObject<{
125
164
  cid: import("zod").ZodNumber;
126
- hasData: import("zod").ZodBoolean;
127
- ghs: import("zod").ZodOptional<import("zod").ZodObject<{
128
- signalWord: import("zod").ZodOptional<import("zod").ZodString>;
129
- pictograms: import("zod").ZodArray<import("zod").ZodString>;
130
- hazardStatements: import("zod").ZodArray<import("zod").ZodObject<{
131
- code: import("zod").ZodString;
132
- statement: import("zod").ZodString;
133
- }, import("zod/v4/core").$strip>>;
134
- precautionaryStatements: import("zod").ZodArray<import("zod").ZodObject<{
135
- code: import("zod").ZodString;
136
- statement: import("zod").ZodString;
165
+ entries: import("zod").ZodArray<import("zod").ZodObject<{
166
+ kind: import("zod").ZodEnum<{
167
+ "drug-drug": "drug-drug";
168
+ "drug-food": "drug-food";
169
+ target: "target";
170
+ }>;
171
+ partner: import("zod").ZodOptional<import("zod").ZodString>;
172
+ source: import("zod").ZodString;
173
+ severity: import("zod").ZodOptional<import("zod").ZodString>;
174
+ text: import("zod").ZodString;
175
+ }, import("zod/v4/core").$strip>>;
176
+ }, import("zod/v4/core").$strip>, undefined, {
177
+ readonly requestedKinds: import("zod").ZodString;
178
+ readonly returnedCount: import("zod").ZodNumber;
179
+ readonly notice: import("zod").ZodOptional<import("zod").ZodString>;
180
+ }> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
181
+ cids: import("zod").ZodArray<import("zod").ZodNumber>;
182
+ }, import("zod/v4/core").$strip>, import("zod").ZodObject<{
183
+ results: import("zod").ZodArray<import("zod").ZodObject<{
184
+ cid: import("zod").ZodNumber;
185
+ hasData: import("zod").ZodBoolean;
186
+ ghs: import("zod").ZodOptional<import("zod").ZodObject<{
187
+ signalWord: import("zod").ZodOptional<import("zod").ZodString>;
188
+ pictograms: import("zod").ZodArray<import("zod").ZodString>;
189
+ hazardStatements: import("zod").ZodArray<import("zod").ZodObject<{
190
+ code: import("zod").ZodString;
191
+ statement: import("zod").ZodString;
192
+ }, import("zod/v4/core").$strip>>;
193
+ precautionaryStatements: import("zod").ZodArray<import("zod").ZodObject<{
194
+ code: import("zod").ZodString;
195
+ statement: import("zod").ZodString;
196
+ }, import("zod/v4/core").$strip>>;
137
197
  }, import("zod/v4/core").$strip>>;
198
+ source: import("zod").ZodOptional<import("zod").ZodString>;
138
199
  }, import("zod/v4/core").$strip>>;
139
- source: import("zod").ZodOptional<import("zod").ZodString>;
140
200
  }, import("zod/v4/core").$strip>, undefined, {
201
+ readonly requestedCount: import("zod").ZodNumber;
202
+ readonly withDataCount: import("zod").ZodNumber;
141
203
  readonly notice: import("zod").ZodOptional<import("zod").ZodString>;
142
204
  }> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
143
205
  cid: import("zod").ZodNumber;
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;AAWH,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;KAS9B,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/index.js CHANGED
@@ -3,8 +3,10 @@
3
3
  * @module mcp-server/tools/definitions
4
4
  */
5
5
  import { getBioactivity } from './get-bioactivity.tool.js';
6
+ import { getCompound3dStructure } from './get-compound-3d-structure.tool.js';
6
7
  import { getCompoundDetails } from './get-compound-details.tool.js';
7
8
  import { getCompoundImage } from './get-compound-image.tool.js';
9
+ import { getCompoundInteractions } from './get-compound-interactions.tool.js';
8
10
  import { getCompoundSafety } from './get-compound-safety.tool.js';
9
11
  import { getCompoundXrefs } from './get-compound-xrefs.tool.js';
10
12
  import { getSummary } from './get-summary.tool.js';
@@ -14,9 +16,11 @@ export const allToolDefinitions = [
14
16
  searchCompounds,
15
17
  getCompoundDetails,
16
18
  getCompoundImage,
19
+ getCompound3dStructure,
17
20
  getCompoundXrefs,
18
21
  getCompoundSafety,
19
22
  getBioactivity,
23
+ getCompoundInteractions,
20
24
  searchAssays,
21
25
  getSummary,
22
26
  ];
package/dist/mcp-server/tools/definitions/index.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"index.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/index.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,cAAc,EAAE,MAAM,2BAA2B,CAAC;AAC3D,OAAO,EAAE,kBAAkB,EAAE,MAAM,gCAAgC,CAAC;AACpE,OAAO,EAAE,gBAAgB,EAAE,MAAM,8BAA8B,CAAC;AAChE,OAAO,EAAE,iBAAiB,EAAE,MAAM,+BAA+B,CAAC;AAClE,OAAO,EAAE,gBAAgB,EAAE,MAAM,8BAA8B,CAAC;AAChE,OAAO,EAAE,UAAU,EAAE,MAAM,uBAAuB,CAAC;AACnD,OAAO,EAAE,YAAY,EAAE,MAAM,yBAAyB,CAAC;AACvD,OAAO,EAAE,eAAe,EAAE,MAAM,4BAA4B,CAAC;AAE7D,MAAM,CAAC,MAAM,kBAAkB,GAAG;IAChC,eAAe;IACf,kBAAkB;IAClB,gBAAgB;IAChB,gBAAgB;IAChB,iBAAiB;IACjB,cAAc;IACd,YAAY;IACZ,UAAU;CACX,CAAC"}
1
+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/index.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,cAAc,EAAE,MAAM,2BAA2B,CAAC;AAC3D,OAAO,EAAE,sBAAsB,EAAE,MAAM,qCAAqC,CAAC;AAC7E,OAAO,EAAE,kBAAkB,EAAE,MAAM,gCAAgC,CAAC;AACpE,OAAO,EAAE,gBAAgB,EAAE,MAAM,8BAA8B,CAAC;AAChE,OAAO,EAAE,uBAAuB,EAAE,MAAM,qCAAqC,CAAC;AAC9E,OAAO,EAAE,iBAAiB,EAAE,MAAM,+BAA+B,CAAC;AAClE,OAAO,EAAE,gBAAgB,EAAE,MAAM,8BAA8B,CAAC;AAChE,OAAO,EAAE,UAAU,EAAE,MAAM,uBAAuB,CAAC;AACnD,OAAO,EAAE,YAAY,EAAE,MAAM,yBAAyB,CAAC;AACvD,OAAO,EAAE,eAAe,EAAE,MAAM,4BAA4B,CAAC;AAE7D,MAAM,CAAC,MAAM,kBAAkB,GAAG;IAChC,eAAe;IACf,kBAAkB;IAClB,gBAAgB;IAChB,sBAAsB;IACtB,gBAAgB;IAChB,iBAAiB;IACjB,cAAc;IACd,uBAAuB;IACvB,YAAY;IACZ,UAAU;CACX,CAAC"}
package/dist/services/pubchem/pubchem-client.d.ts CHANGED
@@ -3,13 +3,16 @@
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 } from './types.js';
6
+ import type { BioactivityRow, CompoundClassification, GHSClassification, InteractionEntry } from './types.js';
7
7
  export declare class PubChemClient {
8
8
  private readonly pugBase;
9
9
  private readonly viewBase;
10
+ private readonly sdqBase;
10
11
  private readonly rateLimiter;
11
12
  private fetchJson;
12
13
  private fetchBinary;
14
+ /** Fetch a text/plain body (e.g. an SDF record). Non-2xx is classified and thrown. */
15
+ private fetchText;
13
16
  /** Fetch CID list, with automatic ListKey polling for async searches */
14
17
  private fetchCids;
15
18
  /** Poll a PubChem ListKey until results are ready */
@@ -35,6 +38,22 @@ export declare class PubChemClient {
35
38
  private parseAssayTable;
36
39
  searchAssaysByTarget(targetType: string, query: string): Promise<number[]>;
37
40
  getEntitySummary(entityType: string, identifier: string | number): Promise<Record<string, unknown> | null>;
41
+ /** Fetch drug-drug, drug-food, and/or chemical-target interactions for a compound.
42
+ * Drug-drug and target data live in PubChem SDQ external tables (drugbankddi,
43
+ * consolidatedcompoundtarget); drug-food is inline PUG View text. Each kind is capped
44
+ * at maxEntries; absent data for a kind contributes nothing rather than erroring. */
45
+ getInteractions(cid: number, kinds: Array<'drug-drug' | 'drug-food' | 'target'>, maxEntries: number): Promise<InteractionEntry[]>;
46
+ private getInteractionsForKind;
47
+ private getDrugDrugInteractions;
48
+ private getTargetInteractions;
49
+ private getDrugFoodInteractions;
50
+ /** Query a PubChem SDQ external table for a single CID. Returns [] on not-found. */
51
+ private fetchSdq;
52
+ /** Fetch the default 3D conformer as raw V2000 SDF text. Throws a typed not-found when
53
+ * PubChem has no computed 3D coordinates (large molecules, mixtures, undefined salts). */
54
+ getSdf3d(cid: number): Promise<string>;
55
+ /** List the conformer IDs PubChem has computed for a compound. Returns [] on not-found. */
56
+ getConformerIds(cid: number): Promise<string[]>;
38
57
  }
39
58
  export declare function initPubChemClient(): void;
40
59
  export declare function getPubChemClient(): PubChemClient;
package/dist/services/pubchem/pubchem-client.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"pubchem-client.d.ts","sourceRoot":"","sources":["../../../src/services/pubchem/pubchem-client.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAIH,OAAO,KAAK,EAGV,cAAc,EAEd,sBAAsB,EACtB,iBAAiB,EAQlB,MAAM,YAAY,CAAC;AA8MpB,qBAAa,aAAa;IACxB,OAAO,CAAC,QAAQ,CAAC,OAAO,CAA+C;IACvE,OAAO,CAAC,QAAQ,CAAC,QAAQ,CAAoD;IAC7E,OAAO,CAAC,QAAQ,CAAC,WAAW,CAAsB;YAIpC,SAAS;YAgDT,WAAW;IA2BzB,wEAAwE;YAC1D,SAAS;IAWvB,qDAAqD;YACvC,WAAW;IAgBzB,YAAY,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;IAI7C,cAAc,CAAC,MAAM,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;IAQjD,gBAAgB,CAAC,QAAQ,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;IAMrD,eAAe,CAAC,OAAO,EAAE,MAAM,EAAE,UAAU,UAAQ,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;IAOvE,iBAAiB,CACf,IAAI,EAAE,cAAc,GAAG,gBAAgB,GAAG,YAAY,EACtD,KAAK,EAAE,MAAM,EACb,SAAS,EAAE,QAAQ,GAAG,KAAK,EAC3B,SAAS,CAAC,EAAE,MAAM,GACjB,OAAO,CAAC,MAAM,EAAE,CAAC;IA2Bd,aAAa,CACjB,IAAI,EAAE,MAAM,EAAE,EACd,UAAU,EAAE,MAAM,EAAE,GACnB,OAAO,CAAC,KAAK,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG;QAAE,GAAG,EAAE,MAAM,CAAA;KAAE,CAAC,CAAC;IA0BtD,WAAW,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;IAY3C,QAAQ,CAAC,GAAG,EAAE,MAAM,EAAE,IAAI,GAAE,OAAO,GAAG,OAAiB,GAAG,OAAO,CAAC,WAAW,CAAC;IAkB9E,QAAQ,CAAC,GAAG,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,GAAG,OAAO,CAAC,CAAC,MAAM,GAAG,MAAM,CAAC,EAAE,CAAC;IAiBrE,cAAc,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAC,KAAK,CAAC;QAAE,MAAM,CAAC,EAAE,MAAM,CAAC;QAAC,IAAI,EAAE,MAAM,CAAA;KAAE,CAAC,CAAC;IA8B9E,aAAa,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAC,iBAAiB,GAAG,IAAI,CAAC;IAgE7D,iBAAiB,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAC,sBAAsB,GAAG,IAAI,CAAC;IAwEtE,eAAe,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAC,cAAc,EAAE,CAAC;IAY7D,OAAO,CAAC,eAAe;IA0EjB,oBAAoB,CAAC,UAAU,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;IAgB1E,gBAAgB,CACpB,UAAU,EAAE,MAAM,EAClB,UAAU,EAAE,MAAM,GAAG,MAAM,GAC1B,OAAO,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,IAAI,CAAC;CAiC3C;AAMD,wBAAgB,iBAAiB,IAAI,IAAI,CAExC;AAED,wBAAgB,gBAAgB,IAAI,aAAa,CAIhD"}
1
+ {"version":3,"file":"pubchem-client.d.ts","sourceRoot":"","sources":["../../../src/services/pubchem/pubchem-client.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAIH,OAAO,KAAK,EAGV,cAAc,EAEd,sBAAsB,EAEtB,iBAAiB,EACjB,gBAAgB,EAQjB,MAAM,YAAY,CAAC;AA8MpB,qBAAa,aAAa;IACxB,OAAO,CAAC,QAAQ,CAAC,OAAO,CAA+C;IACvE,OAAO,CAAC,QAAQ,CAAC,QAAQ,CAAoD;IAC7E,OAAO,CAAC,QAAQ,CAAC,OAAO,CAAuD;IAC/E,OAAO,CAAC,QAAQ,CAAC,WAAW,CAAsB;YAIpC,SAAS;YAgDT,WAAW;IAyBzB,sFAAsF;YACxE,SAAS;IA2BvB,wEAAwE;YAC1D,SAAS;IAWvB,qDAAqD;YACvC,WAAW;IAgBzB,YAAY,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;IAI7C,cAAc,CAAC,MAAM,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;IAQjD,gBAAgB,CAAC,QAAQ,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;IAMrD,eAAe,CAAC,OAAO,EAAE,MAAM,EAAE,UAAU,UAAQ,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;IAOvE,iBAAiB,CACf,IAAI,EAAE,cAAc,GAAG,gBAAgB,GAAG,YAAY,EACtD,KAAK,EAAE,MAAM,EACb,SAAS,EAAE,QAAQ,GAAG,KAAK,EAC3B,SAAS,CAAC,EAAE,MAAM,GACjB,OAAO,CAAC,MAAM,EAAE,CAAC;IA2Bd,aAAa,CACjB,IAAI,EAAE,MAAM,EAAE,EACd,UAAU,EAAE,MAAM,EAAE,GACnB,OAAO,CAAC,KAAK,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG;QAAE,GAAG,EAAE,MAAM,CAAA;KAAE,CAAC,CAAC;IA0BtD,WAAW,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;IAY3C,QAAQ,CAAC,GAAG,EAAE,MAAM,EAAE,IAAI,GAAE,OAAO,GAAG,OAAiB,GAAG,OAAO,CAAC,WAAW,CAAC;IAkB9E,QAAQ,CAAC,GAAG,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,GAAG,OAAO,CAAC,CAAC,MAAM,GAAG,MAAM,CAAC,EAAE,CAAC;IAiBrE,cAAc,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAC,KAAK,CAAC;QAAE,MAAM,CAAC,EAAE,MAAM,CAAC;QAAC,IAAI,EAAE,MAAM,CAAA;KAAE,CAAC,CAAC;IA8B9E,aAAa,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAC,iBAAiB,GAAG,IAAI,CAAC;IAgE7D,iBAAiB,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAC,sBAAsB,GAAG,IAAI,CAAC;IAwEtE,eAAe,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAC,cAAc,EAAE,CAAC;IAY7D,OAAO,CAAC,eAAe;IA0EjB,oBAAoB,CAAC,UAAU,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;IAgB1E,gBAAgB,CACpB,UAAU,EAAE,MAAM,EAClB,UAAU,EAAE,MAAM,GAAG,MAAM,GAC1B,OAAO,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,IAAI,CAAC;IAoC1C;;;yFAGqF;IAC/E,eAAe,CACnB,GAAG,EAAE,MAAM,EACX,KAAK,EAAE,KAAK,CAAC,WAAW,GAAG,WAAW,GAAG,QAAQ,CAAC,EAClD,UAAU,EAAE,MAAM,GACjB,OAAO,CAAC,gBAAgB,EAAE,CAAC;IAO9B,OAAO,CAAC,sBAAsB;YAehB,uBAAuB;YAgBvB,qBAAqB;YA4BrB,uBAAuB;IA6BrC,oFAAoF;YACtE,QAAQ;IAwBtB;8FAC0F;IACpF,QAAQ,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,CAAC;IAiB5C,2FAA2F;IACrF,eAAe,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;CAWtD;AAMD,wBAAgB,iBAAiB,IAAI,IAAI,CAExC;AAED,wBAAgB,gBAAgB,IAAI,aAAa,CAIhD"}
package/dist/services/pubchem/pubchem-client.js CHANGED
@@ -194,6 +194,7 @@ const activityKey = (v) => `${v.name ?? ''}|${v.value}|${v.unit ?? ''}`;
194
194
  export class PubChemClient {
195
195
  pugBase = 'https://pubchem.ncbi.nlm.nih.gov/rest/pug';
196
196
  viewBase = 'https://pubchem.ncbi.nlm.nih.gov/rest/pug_view';
197
+ sdqBase = 'https://pubchem.ncbi.nlm.nih.gov/sdq/sdqagent.cgi';
197
198
  rateLimiter = new RateLimiter(5);
198
199
  // ── Core HTTP ────────────────────────────────────────────────────
199
200
  async fetchJson(url, init) {
@@ -259,6 +260,28 @@ export class PubChemClient {
259
260
  clearTimeout(timeoutId);
260
261
  }
261
262
  }
263
+ /** Fetch a text/plain body (e.g. an SDF record). Non-2xx is classified and thrown. */
264
+ async fetchText(url) {
265
+ await this.rateLimiter.acquire();
266
+ const controller = new AbortController();
267
+ const timeoutId = setTimeout(() => controller.abort(), 30_000);
268
+ try {
269
+ const response = await fetch(url, { signal: controller.signal });
270
+ if (!response.ok) {
271
+ const text = await response.text();
272
+ const fault = parseFaultMessage(text) ?? text.slice(0, 300);
273
+ throw await httpErrorFromResponse(response, {
274
+ captureBody: false,
275
+ service: 'PubChem',
276
+ data: { fault, url },
277
+ });
278
+ }
279
+ return await response.text();
280
+ }
281
+ finally {
282
+ clearTimeout(timeoutId);
283
+ }
284
+ }
262
285
  // ── CID Resolution ──────────────────────────────────────────────
263
286
  /** Fetch CID list, with automatic ListKey polling for async searches */
264
287
  async fetchCids(url, init) {
@@ -672,6 +695,141 @@ export class PubChemClient {
672
695
  throw error;
673
696
  }
674
697
  }
698
+ // ── Interactions ────────────────────────────────────────────────
699
+ /** Fetch drug-drug, drug-food, and/or chemical-target interactions for a compound.
700
+ * Drug-drug and target data live in PubChem SDQ external tables (drugbankddi,
701
+ * consolidatedcompoundtarget); drug-food is inline PUG View text. Each kind is capped
702
+ * at maxEntries; absent data for a kind contributes nothing rather than erroring. */
703
+ async getInteractions(cid, kinds, maxEntries) {
704
+ const batches = await Promise.all(kinds.map((kind) => this.getInteractionsForKind(cid, kind, maxEntries)));
705
+ return batches.flat();
706
+ }
707
+ getInteractionsForKind(cid, kind, maxEntries) {
708
+ switch (kind) {
709
+ case 'drug-drug':
710
+ return this.getDrugDrugInteractions(cid, maxEntries);
711
+ case 'drug-food':
712
+ return this.getDrugFoodInteractions(cid, maxEntries);
713
+ case 'target':
714
+ return this.getTargetInteractions(cid, maxEntries);
715
+ }
716
+ }
717
+ async getDrugDrugInteractions(cid, maxEntries) {
718
+ const rows = await this.fetchSdq('drugbankddi', cid, maxEntries);
719
+ const entries = [];
720
+ for (const row of rows) {
721
+ const text = typeof row.descr === 'string' ? row.descr : '';
722
+ if (!text)
723
+ continue;
724
+ const entry = { kind: 'drug-drug', source: 'DrugBank', text };
725
+ if (typeof row.name2 === 'string' && row.name2)
726
+ entry.partner = row.name2;
727
+ entries.push(entry);
728
+ }
729
+ return entries;
730
+ }
731
+ async getTargetInteractions(cid, maxEntries) {
732
+ const rows = await this.fetchSdq('consolidatedcompoundtarget', cid, maxEntries);
733
+ const entries = [];
734
+ for (const row of rows) {
735
+ const target = (typeof row.protname === 'string' && row.protname) ||
736
+ (typeof row.srctargetname === 'string' && row.srctargetname) ||
737
+ (typeof row.genename === 'string' && row.genename) ||
738
+ '';
739
+ const activity = [row.actname, row.actvalue]
740
+ .filter((v) => typeof v === 'string' && v.length > 0)
741
+ .join(': ');
742
+ const text = [target, activity].filter(Boolean).join(' — ');
743
+ if (!text)
744
+ continue;
745
+ const entry = {
746
+ kind: 'target',
747
+ source: typeof row.dsn === 'string' && row.dsn ? row.dsn : 'PubChem',
748
+ text,
749
+ };
750
+ if (target)
751
+ entry.partner = target;
752
+ entries.push(entry);
753
+ }
754
+ return entries;
755
+ }
756
+ async getDrugFoodInteractions(cid, maxEntries) {
757
+ try {
758
+ const data = await this.fetchJson(`${this.viewBase}/data/compound/${cid}/JSON?heading=Drug-Food+Interactions`);
759
+ const sections = data.Record.Section;
760
+ if (!sections)
761
+ return [];
762
+ const section = findSection(sections, 'Drug-Food Interactions');
763
+ if (!section)
764
+ return [];
765
+ const refToSource = new Map();
766
+ for (const ref of data.Record.Reference ?? []) {
767
+ refToSource.set(ref.ReferenceNumber, ref.SourceName);
768
+ }
769
+ const items = dedupByKey(extractDescriptionItems(section), descriptionKey);
770
+ return items.slice(0, maxEntries).map((item) => {
771
+ const source = item.refNum != null ? refToSource.get(item.refNum) : undefined;
772
+ return { kind: 'drug-food', source: source ?? 'PubChem', text: item.text };
773
+ });
774
+ }
775
+ catch (error) {
776
+ if (isNotFound(error))
777
+ return [];
778
+ throw error;
779
+ }
780
+ }
781
+ /** Query a PubChem SDQ external table for a single CID. Returns [] on not-found. */
782
+ async fetchSdq(collection, cid, limit) {
783
+ const query = JSON.stringify({
784
+ download: '*',
785
+ collection,
786
+ where: { ands: [{ cid: String(cid) }] },
787
+ start: 1,
788
+ limit,
789
+ });
790
+ const url = `${this.sdqBase}?infmt=json&outfmt=json&query=${encodeURIComponent(query)}`;
791
+ try {
792
+ const data = await this.fetchJson(url);
793
+ return Array.isArray(data) ? data : [];
794
+ }
795
+ catch (error) {
796
+ if (isNotFound(error))
797
+ return [];
798
+ throw error;
799
+ }
800
+ }
801
+ // ── 3D Structure ────────────────────────────────────────────────
802
+ /** Fetch the default 3D conformer as raw V2000 SDF text. Throws a typed not-found when
803
+ * PubChem has no computed 3D coordinates (large molecules, mixtures, undefined salts). */
804
+ async getSdf3d(cid) {
805
+ try {
806
+ return await this.fetchText(`${this.pugBase}/compound/cid/${cid}/record/SDF?record_type=3d`);
807
+ }
808
+ catch (error) {
809
+ if (isNotFound(error)) {
810
+ throw notFound(`No 3D conformer available for CID ${cid}.`, {
811
+ cid,
812
+ reason: 'no_3d_structure',
813
+ recovery: {
814
+ hint: 'PubChem has no computed 3D coordinates for this compound (common for very large molecules, mixtures, and undefined salts). Use pubchem_get_compound_image for the 2D structure.',
815
+ },
816
+ });
817
+ }
818
+ throw error;
819
+ }
820
+ }
821
+ /** List the conformer IDs PubChem has computed for a compound. Returns [] on not-found. */
822
+ async getConformerIds(cid) {
823
+ try {
824
+ const data = await this.fetchJson(`${this.pugBase}/compound/cid/${cid}/conformers/JSON`);
825
+ return data.InformationList.Information[0]?.ConformerID ?? [];
826
+ }
827
+ catch (error) {
828
+ if (isNotFound(error))
829
+ return [];
830
+ throw error;
831
+ }
832
+ }
675
833
  }
676
834
  // ── Init/Accessor ────────────────────────────────────────────────────
677
835
  let _client;
package/dist/services/pubchem/pubchem-client.js.map CHANGED
@@ -1 +1 @@
1
- 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package/dist/services/pubchem/sdf-parser.d.ts ADDED
@@ -0,0 +1,20 @@
1
+ /**
2
+ * @fileoverview Minimal parser for the V2000 SDF connection table (atom + bond blocks).
3
+ * PubChem emits V2000 for 3D conformer records; the format is fixed-column and has been
4
+ * stable since 1991, so a focused slice-based parser is more robust than a dependency.
5
+ * @module services/pubchem/sdf-parser
6
+ */
7
+ import type { Sdf3DStructure } from './types.js';
8
+ /**
9
+ * Parse the first molecule's atom and bond blocks from a V2000 SDF record.
10
+ *
11
+ * Layout: three header lines, then a counts line (atom count at columns 0–3, bond count at
12
+ * columns 3–6), then one fixed-column line per atom (x/y/z as `F10.4` at columns 0–10/10–20/
13
+ * 20–30, element symbol at columns 31–34), then one line per bond (atom1/atom2/order as
14
+ * three-column integers). The block is terminated by `M END`.
15
+ *
16
+ * Throws when the counts line is missing or unparseable — a malformed record is a hard
17
+ * failure, not a silently-empty success.
18
+ */
19
+ export declare function parseSdfV2000(sdf: string): Sdf3DStructure;
20
+ //# sourceMappingURL=sdf-parser.d.ts.map
package/dist/services/pubchem/sdf-parser.d.ts.map ADDED
@@ -0,0 +1 @@
1
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