@cyanheads/pubchem-mcp-server 0.6.2 → 0.6.4
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/AGENTS.md +371 -0
- package/CLAUDE.md +371 -0
- package/README.md +217 -87
- package/changelog/0.1.x/0.1.21.md +23 -0
- package/changelog/0.1.x/0.1.22.md +14 -0
- package/changelog/0.1.x/0.1.23.md +18 -0
- package/changelog/0.2.x/0.2.0.md +24 -0
- package/changelog/0.2.x/0.2.1.md +14 -0
- package/changelog/0.2.x/0.2.2.md +17 -0
- package/changelog/0.2.x/0.2.3.md +27 -0
- package/changelog/0.2.x/0.2.4.md +27 -0
- package/changelog/0.3.x/0.3.0.md +31 -0
- package/changelog/0.3.x/0.3.1.md +19 -0
- package/changelog/0.4.x/0.4.0.md +15 -0
- package/changelog/0.4.x/0.4.1.md +12 -0
- package/changelog/0.4.x/0.4.2.md +41 -0
- package/changelog/0.4.x/0.4.3.md +18 -0
- package/changelog/0.5.x/0.5.0.md +24 -0
- package/changelog/0.5.x/0.5.1.md +24 -0
- package/changelog/0.5.x/0.5.2.md +21 -0
- package/changelog/0.6.x/0.6.0.md +15 -0
- package/changelog/0.6.x/0.6.1.md +40 -0
- package/changelog/0.6.x/0.6.2.md +29 -0
- package/changelog/0.6.x/0.6.3.md +40 -0
- package/changelog/0.6.x/0.6.4.md +23 -0
- package/changelog/template.md +151 -0
- package/dist/index.js +4 -0
- package/dist/index.js.map +1 -1
- package/dist/mcp-server/resources/definitions/assay.resource.js +1 -1
- package/dist/mcp-server/resources/definitions/assay.resource.js.map +1 -1
- package/dist/mcp-server/resources/definitions/compound-bioactivity.resource.js +1 -1
- package/dist/mcp-server/resources/definitions/compound-bioactivity.resource.js.map +1 -1
- package/dist/mcp-server/resources/definitions/compound-image.resource.js +1 -1
- package/dist/mcp-server/resources/definitions/compound-image.resource.js.map +1 -1
- package/dist/mcp-server/resources/definitions/compound-safety.resource.js +1 -1
- package/dist/mcp-server/resources/definitions/compound-safety.resource.js.map +1 -1
- package/dist/mcp-server/resources/definitions/compound-xrefs.resource.js +1 -1
- package/dist/mcp-server/resources/definitions/compound-xrefs.resource.js.map +1 -1
- package/dist/mcp-server/resources/definitions/compound.resource.js +1 -1
- package/dist/mcp-server/resources/definitions/compound.resource.js.map +1 -1
- package/dist/mcp-server/tools/definitions/get-bioactivity.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/get-bioactivity.tool.js +6 -2
- package/dist/mcp-server/tools/definitions/get-bioactivity.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/get-compound-3d-structure.tool.d.ts +1 -0
- package/dist/mcp-server/tools/definitions/get-compound-3d-structure.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/get-compound-3d-structure.tool.js +6 -3
- package/dist/mcp-server/tools/definitions/get-compound-3d-structure.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/get-compound-details.tool.js +1 -1
- package/dist/mcp-server/tools/definitions/get-compound-details.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/get-compound-image.tool.d.ts +1 -0
- package/dist/mcp-server/tools/definitions/get-compound-image.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/get-compound-image.tool.js +4 -1
- package/dist/mcp-server/tools/definitions/get-compound-image.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/get-compound-interactions.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/get-compound-interactions.tool.js +4 -1
- package/dist/mcp-server/tools/definitions/get-compound-interactions.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/get-compound-safety.tool.js +1 -1
- package/dist/mcp-server/tools/definitions/get-compound-safety.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/get-compound-xrefs.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/get-compound-xrefs.tool.js +5 -1
- package/dist/mcp-server/tools/definitions/get-compound-xrefs.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/index.d.ts +4 -2
- package/dist/mcp-server/tools/definitions/index.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/search-assays.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/search-assays.tool.js +3 -0
- package/dist/mcp-server/tools/definitions/search-assays.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/search-compounds.tool.d.ts +2 -2
- package/dist/mcp-server/tools/definitions/search-compounds.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/search-compounds.tool.js +8 -5
- package/dist/mcp-server/tools/definitions/search-compounds.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/untrusted-text.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/untrusted-text.js +8 -1
- package/dist/mcp-server/tools/definitions/untrusted-text.js.map +1 -1
- package/dist/services/pubchem/pubchem-client.d.ts.map +1 -1
- package/dist/services/pubchem/pubchem-client.js +51 -11
- package/dist/services/pubchem/pubchem-client.js.map +1 -1
- package/manifest.json +1 -1
- package/package.json +19 -9
- package/server.json +3 -3
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@@ -9,7 +9,7 @@ export const compoundSafetyResource = resource('pubchem://compound/{cid}/safety'
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description: 'GHS hazard classification for a PubChem compound by CID — signal word, pictograms, hazard (H) and precautionary (P) statements. Not every compound carries a deposited classification.',
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mimeType: 'application/json',
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params: z.object({
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cid: z.coerce.number().int().
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cid: z.coerce.number().int().min(1).describe('PubChem Compound ID.'),
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}),
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async handler(params) {
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const client = getPubChemClient();
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@@ -1 +1 @@
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-
{"version":3,"file":"compound-safety.resource.js","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/compound-safety.resource.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,QAAQ,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,gBAAgB,EAAE,MAAM,sCAAsC,CAAC;AAExE,MAAM,CAAC,MAAM,sBAAsB,GAAG,QAAQ,CAAC,iCAAiC,EAAE;IAChF,IAAI,EAAE,yBAAyB;IAC/B,WAAW,EACT,wLAAwL;IAC1L,QAAQ,EAAE,kBAAkB;IAC5B,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,GAAG,EAAE,CAAC,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,CAAC,
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{"version":3,"file":"compound-safety.resource.js","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/compound-safety.resource.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,QAAQ,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,gBAAgB,EAAE,MAAM,sCAAsC,CAAC;AAExE,MAAM,CAAC,MAAM,sBAAsB,GAAG,QAAQ,CAAC,iCAAiC,EAAE;IAChF,IAAI,EAAE,yBAAyB;IAC/B,WAAW,EACT,wLAAwL;IAC1L,QAAQ,EAAE,kBAAkB;IAC5B,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,GAAG,EAAE,CAAC,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,sBAAsB,CAAC;KACrE,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,MAAM;QAClB,MAAM,MAAM,GAAG,gBAAgB,EAAE,CAAC;QAClC,MAAM,MAAM,GAAG,MAAM,MAAM,CAAC,aAAa,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;QACtD,2FAA2F;QAC3F,wFAAwF;QACxF,IAAI,MAAM,CAAC,MAAM,KAAK,IAAI,EAAE,CAAC;YAC3B,OAAO,EAAE,GAAG,EAAE,MAAM,CAAC,GAAG,EAAE,OAAO,EAAE,KAAK,EAAE,MAAM,EAAE,MAAM,CAAC,MAAM,EAAE,CAAC;QACpE,CAAC;QACD,OAAO;YACL,GAAG,EAAE,MAAM,CAAC,GAAG;YACf,OAAO,EAAE,IAAI;YACb,MAAM,EAAE,MAAM,CAAC,MAAM;YACrB,GAAG,EAAE;gBACH,UAAU,EAAE,MAAM,CAAC,GAAG,CAAC,UAAU;gBACjC,UAAU,EAAE,MAAM,CAAC,GAAG,CAAC,UAAU;gBACjC,gBAAgB,EAAE,MAAM,CAAC,GAAG,CAAC,gBAAgB;gBAC7C,uBAAuB,EAAE,MAAM,CAAC,GAAG,CAAC,uBAAuB;aAC5D;YACD,MAAM,EAAE,MAAM,CAAC,GAAG,CAAC,MAAM;SAC1B,CAAC;IACJ,CAAC;CACF,CAAC,CAAC"}
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@@ -12,7 +12,7 @@ export const compoundXrefsResource = resource('pubchem://compound/{cid}/xrefs',
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description: 'External cross-references (CAS RN, registry IDs, PubMed) for a PubChem compound by CID, up to 25 per type. Use pubchem_get_compound_xrefs for the full set of xref types, a higher per-type cap, and to page through the rest with offset.',
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mimeType: 'application/json',
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params: z.object({
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cid: z.coerce.number().int().
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cid: z.coerce.number().int().min(1).describe('PubChem Compound ID.'),
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}),
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async handler(params) {
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const client = getPubChemClient();
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-
{"version":3,"file":"compound-xrefs.resource.js","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/compound-xrefs.resource.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,QAAQ,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,gBAAgB,EAAE,MAAM,sCAAsC,CAAC;AAExE,0FAA0F;AAC1F,MAAM,mBAAmB,GAAG,CAAC,IAAI,EAAE,YAAY,EAAE,UAAU,CAAU,CAAC;AACtE,MAAM,YAAY,GAAG,EAAE,CAAC;AAExB,MAAM,CAAC,MAAM,qBAAqB,GAAG,QAAQ,CAAC,gCAAgC,EAAE;IAC9E,IAAI,EAAE,wBAAwB;IAC9B,WAAW,EACT,4OAA4O;IAC9O,QAAQ,EAAE,kBAAkB;IAC5B,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,GAAG,EAAE,CAAC,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,CAAC,
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{"version":3,"file":"compound-xrefs.resource.js","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/compound-xrefs.resource.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,QAAQ,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,gBAAgB,EAAE,MAAM,sCAAsC,CAAC;AAExE,0FAA0F;AAC1F,MAAM,mBAAmB,GAAG,CAAC,IAAI,EAAE,YAAY,EAAE,UAAU,CAAU,CAAC;AACtE,MAAM,YAAY,GAAG,EAAE,CAAC;AAExB,MAAM,CAAC,MAAM,qBAAqB,GAAG,QAAQ,CAAC,gCAAgC,EAAE;IAC9E,IAAI,EAAE,wBAAwB;IAC9B,WAAW,EACT,4OAA4O;IAC9O,QAAQ,EAAE,kBAAkB;IAC5B,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,GAAG,EAAE,CAAC,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,sBAAsB,CAAC;KACrE,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,MAAM;QAClB,MAAM,MAAM,GAAG,gBAAgB,EAAE,CAAC;QAClC,MAAM,KAAK,GAA8E,EAAE,CAAC;QAC5F,KAAK,MAAM,IAAI,IAAI,mBAAmB,EAAE,CAAC;YACvC,MAAM,GAAG,GAAG,MAAM,MAAM,CAAC,QAAQ,CAAC,MAAM,CAAC,GAAG,EAAE,IAAI,CAAC,CAAC;YACpD,IAAI,GAAG,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;gBACnB,KAAK,CAAC,IAAI,CAAC,EAAE,IAAI,EAAE,GAAG,EAAE,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,YAAY,CAAC,EAAE,cAAc,EAAE,GAAG,CAAC,MAAM,EAAE,CAAC,CAAC;YACpF,CAAC;QACH,CAAC;QACD,OAAO,EAAE,GAAG,EAAE,MAAM,CAAC,GAAG,EAAE,KAAK,EAAE,CAAC;IACpC,CAAC;CACF,CAAC,CAAC"}
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@@ -11,7 +11,7 @@ export const compoundResource = resource('pubchem://compound/{cid}', {
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description: 'Core physicochemical properties for a PubChem compound by CID. Use pubchem_get_compound_details to select properties or add descriptions, synonyms, drug-likeness, and classification.',
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mimeType: 'application/json',
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params: z.object({
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cid: z.coerce.number().int().
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cid: z.coerce.number().int().min(1).describe('PubChem Compound ID.'),
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}),
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{"version":3,"file":"compound.resource.js","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/compound.resource.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,QAAQ,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,QAAQ,EAAE,MAAM,+BAA+B,CAAC;AACzD,OAAO,EAAE,gBAAgB,EAAE,MAAM,sCAAsC,CAAC;AACxE,OAAO,EAAE,kBAAkB,EAAE,MAAM,6BAA6B,CAAC;AAEjE,MAAM,CAAC,MAAM,gBAAgB,GAAG,QAAQ,CAAC,0BAA0B,EAAE;IACnE,IAAI,EAAE,kBAAkB;IACxB,WAAW,EACT,wLAAwL;IAC1L,QAAQ,EAAE,kBAAkB;IAC5B,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,GAAG,EAAE,CAAC,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,CAAC,
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{"version":3,"file":"compound.resource.js","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/compound.resource.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,QAAQ,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,QAAQ,EAAE,MAAM,+BAA+B,CAAC;AACzD,OAAO,EAAE,gBAAgB,EAAE,MAAM,sCAAsC,CAAC;AACxE,OAAO,EAAE,kBAAkB,EAAE,MAAM,6BAA6B,CAAC;AAEjE,MAAM,CAAC,MAAM,gBAAgB,GAAG,QAAQ,CAAC,0BAA0B,EAAE;IACnE,IAAI,EAAE,kBAAkB;IACxB,WAAW,EACT,wLAAwL;IAC1L,QAAQ,EAAE,kBAAkB;IAC5B,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,GAAG,EAAE,CAAC,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,sBAAsB,CAAC;KACrE,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,MAAM;QAClB,MAAM,MAAM,GAAG,gBAAgB,EAAE,CAAC;QAClC,MAAM,IAAI,GAAG,MAAM,MAAM,CAAC,aAAa,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,kBAAkB,CAAC,CAAC,CAAC;QAC/E,MAAM,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC;QACpB,6FAA6F;QAC7F,IAAI,CAAC,GAAG,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,KAAK,KAAK,CAAC,EAAE,CAAC;YACvD,MAAM,QAAQ,CAAC,qCAAqC,MAAM,CAAC,GAAG,GAAG,EAAE,EAAE,GAAG,EAAE,MAAM,CAAC,GAAG,EAAE,CAAC,CAAC;QAC1F,CAAC;QACD,MAAM,EAAE,GAAG,EAAE,IAAI,EAAE,GAAG,UAAU,EAAE,GAAG,GAAG,CAAC;QACzC,OAAO,EAAE,GAAG,EAAE,MAAM,CAAC,GAAG,EAAE,UAAU,EAAE,CAAC;IACzC,CAAC;CACF,CAAC,CAAC"}
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{"version":3,"file":"get-bioactivity.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-bioactivity.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAIjD,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
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{"version":3,"file":"get-bioactivity.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-bioactivity.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAIjD,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAyPzB,CAAC"}
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.describe('Max assay results to return per page (1-100). Well-studied compounds have thousands of records; use offset to reach the ones past this page. Default: 20.'),
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// The target filters are reached via pubchem_search_assays, whose targetType names
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// them `geneid` and `proteinaccession`; a caller carrying an identifier across sends
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-
{"version":3,"file":"get-bioactivity.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-bioactivity.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,sCAAsC,CAAC;AACxE,OAAO,EAAE,UAAU,EAAE,MAAM,qBAAqB,CAAC;AAEjD,MAAM,CAAC,MAAM,cAAc,GAAG,IAAI,CAAC,yBAAyB,EAAE;IAC5D,KAAK,EAAE,iBAAiB;IACxB,WAAW,EACT,kYAAkY;IACpY,WAAW,EAAE;QACX,YAAY,EAAE,IAAI;QAClB,cAAc,EAAE,IAAI;QACpB,aAAa,EAAE,IAAI;KACpB;IACD,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,GAAG,EAAE,CAAC;aACH,MAAM,EAAE;aACR,GAAG,EAAE;aACL,
|
|
1
|
+
{"version":3,"file":"get-bioactivity.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-bioactivity.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,sCAAsC,CAAC;AACxE,OAAO,EAAE,UAAU,EAAE,MAAM,qBAAqB,CAAC;AAEjD,MAAM,CAAC,MAAM,cAAc,GAAG,IAAI,CAAC,yBAAyB,EAAE;IAC5D,KAAK,EAAE,iBAAiB;IACxB,WAAW,EACT,kYAAkY;IACpY,WAAW,EAAE;QACX,YAAY,EAAE,IAAI;QAClB,cAAc,EAAE,IAAI;QACpB,aAAa,EAAE,IAAI;KACpB;IACD,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,GAAG,EAAE,CAAC;aACH,MAAM,EAAE;aACR,GAAG,EAAE;aACL,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,CAAC,8EAA8E,CAAC;QAC3F,aAAa,EAAE,CAAC;aACb,IAAI,CAAC,CAAC,QAAQ,EAAE,UAAU,EAAE,KAAK,CAAC,CAAC;aACnC,OAAO,CAAC,KAAK,CAAC;aACd,QAAQ,CACP,+JAA+J,CAChK;QACH,YAAY,EAAE,CAAC;aACZ,MAAM,EAAE;aACR,GAAG,EAAE;aACL,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,EAAE;aACV,QAAQ,CACP,2OAA2O,CAC5O;QACH,eAAe,EAAE,CAAC;aACf,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,kMAAkM,CACnM;QACH,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,GAAG,EAAE;aACL,GAAG,CAAC,CAAC,CAAC;aACN,OAAO,CAAC,CAAC,CAAC;aACV,QAAQ,CACP,+KAA+K,CAChL;QACH,UAAU,EAAE,CAAC;aACV,MAAM,EAAE;aACR,GAAG,EAAE;aACL,GAAG,CAAC,CAAC,CAAC;aACN,GAAG,CAAC,GAAG,CAAC;aACR,OAAO,CAAC,EAAE,CAAC;aACX,QAAQ,CACP,2JAA2J,CAC5J;KACJ,CAAC;IACF,mFAAmF;IACnF,qFAAqF;IACrF,2DAA2D;IAC3D,YAAY,EAAE,EAAE,MAAM,EAAE,cAAc,EAAE,SAAS,EAAE,iBAAiB,EAAE;IACtE,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,sBAAsB,CAAC;QAChD,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,wCAAwC,CAAC;QAC1E,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,+BAA+B,CAAC;QACjE,aAAa,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,iCAAiC,CAAC;QACrE,OAAO,EAAE,CAAC;aACP,KAAK,CACJ,CAAC;aACE,MAAM,CAAC;YACN,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,mBAAmB,CAAC;YAC7C,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,mBAAmB,CAAC;YACnD,OAAO,EAAE,CAAC;iBACP,MAAM,EAAE;iBACR,QAAQ,CAAC,gEAAgE,CAAC;YAC7E,eAAe,EAAE,CAAC;iBACf,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CAAC,6CAA6C,CAAC;YAC1D,YAAY,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,sBAAsB,CAAC;YACpE,cAAc,EAAE,CAAC;iBACd,KAAK,CACJ,CAAC;iBACE,MAAM,CAAC;gBACN,IAAI,EAAE,CAAC;qBACJ,MAAM,EAAE;qBACR,QAAQ,EAAE;qBACV,QAAQ,CACP,oEAAoE,CACrE;gBACH,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,iBAAiB,CAAC;gBAC7C,IAAI,EAAE,CAAC;qBACJ,MAAM,EAAE;qBACR,QAAQ,EAAE;qBACV,QAAQ,CAAC,+DAA+D,CAAC;aAC7E,CAAC;iBACD,QAAQ,CAAC,0CAA0C,CAAC,CACxD;iBACA,QAAQ,CAAC,qCAAqC,CAAC;SACnD,CAAC;aACD,QAAQ,CAAC,qBAAqB,CAAC,CACnC;aACA,QAAQ,CAAC,oCAAoC,CAAC;KAClD,CAAC;IACF,qFAAqF;IACrF,wFAAwF;IACxF,0DAA0D;IAC1D,EAAE;IACF,kFAAkF;IAClF,oFAAoF;IACpF,oFAAoF;IACpF,8EAA8E;IAC9E,UAAU,EAAE;QACV,aAAa,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,mDAAmD,CAAC;QACvF,YAAY,EAAE,CAAC;aACZ,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CAAC,qEAAqE,CAAC;QAClF,aAAa,EAAE,CAAC;aACb,MAAM,EAAE;aACR,QAAQ,CACP,mFAAmF,CACpF;QACH,aAAa,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,+BAA+B,CAAC;QACnE,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,+CAA+C,CAAC;QAC5E,UAAU,EAAE,CAAC;aACV,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,mGAAmG,CACpG;QACH,SAAS,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,kDAAkD,CAAC;QAC9F,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,+BAA+B,CAAC;QACtE,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,sCAAsC,CAAC;QAC3E,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,8FAA8F,CAC/F;KACJ;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,MAAM,MAAM,GAAG,gBAAgB,EAAE,CAAC;QAClC,MAAM,OAAO,GAAG,MAAM,MAAM,CAAC,eAAe,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC;QAExD,MAAM,WAAW,GAAG,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,OAAO,KAAK,QAAQ,CAAC,CAAC,MAAM,CAAC;QACzE,MAAM,aAAa,GAAG,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,OAAO,KAAK,UAAU,CAAC,CAAC,MAAM,CAAC;QAE7E,2EAA2E;QAC3E,yFAAyF;QACzF,IAAI,QAAQ,GAAG,OAAO,CAAC;QACvB,IAAI,KAAK,CAAC,aAAa,KAAK,QAAQ,EAAE,CAAC;YACrC,QAAQ,GAAG,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,OAAO,KAAK,QAAQ,CAAC,CAAC;QAC5D,CAAC;aAAM,IAAI,KAAK,CAAC,aAAa,KAAK,UAAU,EAAE,CAAC;YAC9C,QAAQ,GAAG,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,OAAO,KAAK,UAAU,CAAC,CAAC;QAC9D,CAAC;QAED,MAAM,WAAW,GAAG;YAClB,KAAK,CAAC,YAAY,IAAI,IAAI,CAAC,CAAC,CAAC,UAAU,KAAK,CAAC,YAAY,EAAE,CAAC,CAAC,CAAC,SAAS;YACvE,KAAK,CAAC,eAAe,CAAC,CAAC,CAAC,aAAa,KAAK,CAAC,eAAe,EAAE,CAAC,CAAC,CAAC,SAAS;SACzE;aACE,MAAM,CAAC,OAAO,CAAC;aACf,IAAI,CAAC,GAAG,CAAC,CAAC;QACb,IAAI,KAAK,CAAC,YAAY,IAAI,IAAI,EAAE,CAAC;YAC/B,QAAQ,GAAG,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,YAAY,KAAK,KAAK,CAAC,YAAY,CAAC,CAAC;QAC3E,CAAC;QACD,IAAI,KAAK,CAAC,eAAe,EAAE,CAAC;YAC1B,QAAQ,GAAG,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,eAAe,KAAK,KAAK,CAAC,eAAe,CAAC,CAAC;QACjF,CAAC;QAED,6EAA6E;QAC7E,iFAAiF;QACjF,MAAM,OAAO,GAAG,QAAQ,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,EAAE,KAAK,CAAC,MAAM,GAAG,KAAK,CAAC,UAAU,CAAC,CAAC;QAC9E,MAAM,UAAU,GAAG,KAAK,CAAC,MAAM,GAAG,OAAO,CAAC,MAAM,CAAC;QACjD,MAAM,OAAO,GAAG,UAAU,GAAG,QAAQ,CAAC,MAAM,CAAC;QAE7C,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,qBAAqB,EAAE;YAClC,GAAG,EAAE,KAAK,CAAC,GAAG;YACd,KAAK,EAAE,OAAO,CAAC,MAAM;YACrB,MAAM,EAAE,WAAW;YACnB,QAAQ,EAAE,QAAQ,CAAC,MAAM;YACzB,MAAM,EAAE,KAAK,CAAC,MAAM;YACpB,QAAQ,EAAE,OAAO,CAAC,MAAM;SACzB,CAAC,CAAC;QAEH,GAAG,CAAC,MAAM,CAAC;YACT,aAAa,EAAE,KAAK,CAAC,aAAa;YAClC,aAAa,EAAE,QAAQ,CAAC,MAAM;YAC9B,aAAa,EAAE,OAAO,CAAC,MAAM;YAC7B,MAAM,EAAE,KAAK,CAAC,MAAM;SACrB,CAAC,CAAC;QACH,IAAI,WAAW;YAAE,GAAG,CAAC,MAAM,CAAC,EAAE,YAAY,EAAE,WAAW,EAAE,CAAC,CAAC;QAC3D,IAAI,OAAO;YAAE,GAAG,CAAC,MAAM,CAAC,EAAE,UAAU,EAAE,CAAC,CAAC;QACxC,IAAI,OAAO,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACzB,GAAG,CAAC,MAAM,CAAC,MAAM,CACf,qCAAqC,KAAK,CAAC,GAAG,yFAAyF,CACxI,CAAC;QACJ,CAAC;aAAM,IAAI,QAAQ,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACjC,GAAG,CAAC,MAAM,CAAC,MAAM,CACf,WAAW;gBACT,CAAC,CAAC,OAAO,KAAK,CAAC,GAAG,QAAQ,OAAO,CAAC,MAAM,+CAA+C,WAAW,IAAI,KAAK,CAAC,aAAa,KAAK,KAAK,CAAC,CAAC,CAAC,wBAAwB,KAAK,CAAC,aAAa,GAAG,CAAC,CAAC,CAAC,EAAE,wFAAwF;gBACjR,CAAC,CAAC,OAAO,KAAK,CAAC,GAAG,QAAQ,OAAO,CAAC,MAAM,2CAA2C,KAAK,CAAC,aAAa,yCAAyC,CAClJ,CAAC;QACJ,CAAC;aAAM,IAAI,OAAO,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAChC,GAAG,CAAC,MAAM,CAAC,MAAM,CACf,UAAU,KAAK,CAAC,MAAM,gBAAgB,QAAQ,CAAC,MAAM,uDAAuD,QAAQ,CAAC,MAAM,GAAG,CAC/H,CAAC;QACJ,CAAC;aAAM,IAAI,OAAO,EAAE,CAAC;YACnB,GAAG,CAAC,MAAM,CAAC,SAAS,CAAC;gBACnB,KAAK,EAAE,OAAO,CAAC,MAAM;gBACrB,GAAG,EAAE,KAAK,CAAC,UAAU;gBACrB,QAAQ,EAAE,kBAAkB,KAAK,CAAC,MAAM,GAAG,CAAC,IAAI,UAAU,OAAO,QAAQ,CAAC,MAAM,iBAAiB,UAAU,qBAAqB;aACjI,CAAC,CAAC;QACL,CAAC;QAED,OAAO;YACL,GAAG,EAAE,KAAK,CAAC,GAAG;YACd,WAAW,EAAE,OAAO,CAAC,MAAM;YAC3B,WAAW;YACX,aAAa;YACb,OAAO;SACR,CAAC;IACJ,CAAC;IAED,MAAM,CAAC,MAAM;QACX,MAAM,KAAK,GAAa;YACtB,wBAAwB,MAAM,CAAC,GAAG,EAAE;YACpC,iBAAiB,MAAM,CAAC,WAAW,cAAc,MAAM,CAAC,WAAW,gBAAgB,MAAM,CAAC,aAAa,EAAE;YACzG,EAAE;SACH,CAAC;QAEF,IAAI,MAAM,CAAC,OAAO,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAChC,KAAK,CAAC,IAAI,CAAC,4BAA4B,CAAC,CAAC;YACzC,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACpD,CAAC;QAED,KAAK,MAAM,CAAC,IAAI,MAAM,CAAC,OAAO,EAAE,CAAC;YAC/B,MAAM,MAAM,GAAG,CAAC,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC,YAAY,EAAE,CAAC,CAAC,CAAC,SAAS,EAAE,CAAC,CAAC,eAAe,CAAC;iBACxF,MAAM,CAAC,OAAO,CAAC;iBACf,IAAI,CAAC,KAAK,CAAC,CAAC;YACf,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,GAAG,QAAQ,UAAU,CAAC,CAAC,CAAC,SAAS,CAAC,KAAK,CAAC,CAAC,OAAO,GAAG,CAAC,CAAC;YAC3E,IAAI,MAAM;gBAAE,KAAK,CAAC,IAAI,CAAC,aAAa,MAAM,EAAE,CAAC,CAAC;YAC9C,KAAK,MAAM,EAAE,IAAI,CAAC,CAAC,cAAc,EAAE,CAAC;gBAClC,MAAM,KAAK,GAAG,EAAE,CAAC,IAAI,IAAI,OAAO,CAAC;gBACjC,MAAM,IAAI,GAAG,EAAE,CAAC,IAAI,IAAI,EAAE,CAAC;gBAC3B,KAAK,CAAC,IAAI,CAAC,KAAK,KAAK,KAAK,EAAE,CAAC,KAAK,GAAG,IAAI,CAAC,CAAC,CAAC,IAAI,IAAI,EAAE,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;YACjE,CAAC;YACD,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACjB,CAAC;QAED,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IACpD,CAAC;CACF,CAAC,CAAC"}
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@@ -35,6 +35,7 @@ export declare const getCompound3dStructure: import("@cyanheads/mcp-ts-core").To
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}, z.core.$strip>, readonly [{
|
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36
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|
readonly reason: "no_3d_structure";
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readonly code: JsonRpcErrorCode.NotFound;
|
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38
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+
readonly thrownBy: "service";
|
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readonly when: "PubChem has no computed 3D conformer for the requested CID";
|
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39
40
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readonly recovery: "Use pubchem_get_compound_image for the 2D structure, or verify the CID with pubchem_search_compounds.";
|
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40
41
|
}], {
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@@ -1 +1 @@
|
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1
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-
{"version":3,"file":"get-compound-3d-structure.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-3d-structure.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAcjE,eAAO,MAAM,sBAAsB
|
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1
|
+
{"version":3,"file":"get-compound-3d-structure.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-3d-structure.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAcjE,eAAO,MAAM,sBAAsB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAoRjC,CAAC"}
|
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@@ -27,7 +27,7 @@ export const getCompound3dStructure = tool('pubchem_get_compound_3d_structure',
|
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27
27
|
cid: z
|
|
28
28
|
.number()
|
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29
29
|
.int()
|
|
30
|
-
.
|
|
30
|
+
.min(1)
|
|
31
31
|
.describe('PubChem Compound ID. Resolve from name/SMILES with pubchem_search_compounds.'),
|
|
32
32
|
format: z
|
|
33
33
|
.enum(['sdf', 'json'])
|
|
@@ -40,13 +40,13 @@ export const getCompound3dStructure = tool('pubchem_get_compound_3d_structure',
|
|
|
40
40
|
maxAtoms: z
|
|
41
41
|
.number()
|
|
42
42
|
.int()
|
|
43
|
-
.
|
|
43
|
+
.min(1)
|
|
44
44
|
.optional()
|
|
45
45
|
.describe('Cap the atoms returned in the format="json" preview. atomCount always reports the full total; omitted rows are disclosed via the truncated/shownAtoms enrichment. Defaults to the first 200 atoms.'),
|
|
46
46
|
maxBonds: z
|
|
47
47
|
.number()
|
|
48
48
|
.int()
|
|
49
|
-
.
|
|
49
|
+
.min(1)
|
|
50
50
|
.optional()
|
|
51
51
|
.describe('Cap the bonds returned in the format="json" preview. bondCount always reports the full total; omitted rows are disclosed via the truncated/shownBonds enrichment. Defaults to the first 200 bonds.'),
|
|
52
52
|
includeRawSdf: z
|
|
@@ -128,6 +128,9 @@ export const getCompound3dStructure = tool('pubchem_get_compound_3d_structure',
|
|
|
128
128
|
{
|
|
129
129
|
reason: 'no_3d_structure',
|
|
130
130
|
code: JsonRpcErrorCode.NotFound,
|
|
131
|
+
// Raised by PubChemClient.getSdf3d, which distinguishes "no 3D record" from a
|
|
132
|
+
// transport failure while reading the SDF body.
|
|
133
|
+
thrownBy: 'service',
|
|
131
134
|
when: 'PubChem has no computed 3D conformer for the requested CID',
|
|
132
135
|
recovery: 'Use pubchem_get_compound_image for the 2D structure, or verify the CID with pubchem_search_compounds.',
|
|
133
136
|
},
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"get-compound-3d-structure.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-3d-structure.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,gBAAgB,EAAE,MAAM,sCAAsC,CAAC;AACxE,OAAO,EAAE,aAAa,EAAE,MAAM,kCAAkC,CAAC;AACjE,OAAO,EAAE,UAAU,EAAE,MAAM,qBAAqB,CAAC;AAEjD;;;;GAIG;AACH,MAAM,gBAAgB,GAAG,GAAG,CAAC;AAC7B,MAAM,gBAAgB,GAAG,GAAG,CAAC;AAC7B,MAAM,oBAAoB,GAAG,GAAG,CAAC;AAEjC,MAAM,CAAC,MAAM,sBAAsB,GAAG,IAAI,CAAC,mCAAmC,EAAE;IAC9E,KAAK,EAAE,2BAA2B;IAClC,WAAW,EACT,yZAAyZ;IAC3Z,WAAW,EAAE;QACX,YAAY,EAAE,IAAI;QAClB,cAAc,EAAE,IAAI;QACpB,aAAa,EAAE,IAAI;KACpB;IACD,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,GAAG,EAAE,CAAC;aACH,MAAM,EAAE;aACR,GAAG,EAAE;aACL,
|
|
1
|
+
{"version":3,"file":"get-compound-3d-structure.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-3d-structure.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,gBAAgB,EAAE,MAAM,sCAAsC,CAAC;AACxE,OAAO,EAAE,aAAa,EAAE,MAAM,kCAAkC,CAAC;AACjE,OAAO,EAAE,UAAU,EAAE,MAAM,qBAAqB,CAAC;AAEjD;;;;GAIG;AACH,MAAM,gBAAgB,GAAG,GAAG,CAAC;AAC7B,MAAM,gBAAgB,GAAG,GAAG,CAAC;AAC7B,MAAM,oBAAoB,GAAG,GAAG,CAAC;AAEjC,MAAM,CAAC,MAAM,sBAAsB,GAAG,IAAI,CAAC,mCAAmC,EAAE;IAC9E,KAAK,EAAE,2BAA2B;IAClC,WAAW,EACT,yZAAyZ;IAC3Z,WAAW,EAAE;QACX,YAAY,EAAE,IAAI;QAClB,cAAc,EAAE,IAAI;QACpB,aAAa,EAAE,IAAI;KACpB;IACD,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,GAAG,EAAE,CAAC;aACH,MAAM,EAAE;aACR,GAAG,EAAE;aACL,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,CAAC,8EAA8E,CAAC;QAC3F,MAAM,EAAE,CAAC;aACN,IAAI,CAAC,CAAC,KAAK,EAAE,MAAM,CAAC,CAAC;aACrB,OAAO,CAAC,MAAM,CAAC;aACf,QAAQ,CACP,sIAAsI,CACvI;QACH,4BAA4B,EAAE,CAAC;aAC5B,OAAO,EAAE;aACT,OAAO,CAAC,KAAK,CAAC;aACd,QAAQ,CACP,sHAAsH,CACvH;QACH,QAAQ,EAAE,CAAC;aACR,MAAM,EAAE;aACR,GAAG,EAAE;aACL,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,EAAE;aACV,QAAQ,CACP,oMAAoM,CACrM;QACH,QAAQ,EAAE,CAAC;aACR,MAAM,EAAE;aACR,GAAG,EAAE;aACL,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,EAAE;aACV,QAAQ,CACP,oMAAoM,CACrM;QACH,aAAa,EAAE,CAAC;aACb,OAAO,EAAE;aACT,OAAO,CAAC,KAAK,CAAC;aACd,QAAQ,CACP,uMAAuM,CACxM;KACJ,CAAC;IACF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,sBAAsB,CAAC;QAChD,WAAW,EAAE,CAAC;aACX,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,mFAAmF,CACpF;QACH,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,mCAAmC,CAAC;QACnE,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,mCAAmC,CAAC;QACnE,KAAK,EAAE,CAAC;aACL,KAAK,CACJ,CAAC;aACE,MAAM,CAAC;YACN,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,sCAAsC,CAAC;YACpE,CAAC,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,2BAA2B,CAAC;YACnD,CAAC,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,2BAA2B,CAAC;YACnD,CAAC,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,2BAA2B,CAAC;SACpD,CAAC;aACD,QAAQ,CAAC,qCAAqC,CAAC,CACnD;aACA,QAAQ,EAAE;aACV,QAAQ,CAAC,6CAA6C,CAAC;QAC1D,KAAK,EAAE,CAAC;aACL,KAAK,CACJ,CAAC;aACE,MAAM,CAAC;YACN,EAAE,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,6BAA6B,CAAC;YACtD,EAAE,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,8BAA8B,CAAC;YACvD,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,wDAAwD,CAAC;SACrF,CAAC;aACD,QAAQ,CAAC,yBAAyB,CAAC,CACvC;aACA,QAAQ,EAAE;aACV,QAAQ,CAAC,6CAA6C,CAAC;QAC1D,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,kDAAkD,CAAC;QACvF,qBAAqB,EAAE,CAAC;aACrB,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC;aACjB,QAAQ,EAAE;aACV,QAAQ,CACP,0GAA0G,CAC3G;KACJ,CAAC;IACF,8EAA8E;IAC9E,gFAAgF;IAChF,2EAA2E;IAC3E,+EAA+E;IAC/E,6BAA6B;IAC7B,UAAU,EAAE;QACV,SAAS,EAAE,CAAC;aACT,OAAO,EAAE;aACT,QAAQ,EAAE;aACV,QAAQ,CACP,+HAA+H,CAChI;QACH,UAAU,EAAE,CAAC;aACV,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,mFAAmF,CACpF;QACH,UAAU,EAAE,CAAC;aACV,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,mFAAmF,CACpF;QACH,OAAO,EAAE,CAAC;aACP,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,8FAA8F,CAC/F;QACH,OAAO,EAAE,CAAC;aACP,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,8FAA8F,CAC/F;QACH,aAAa,EAAE,CAAC;aACb,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,+GAA+G,CAChH;QACH,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CAAC,gEAAgE,CAAC;KAC9E;IACD,MAAM,EAAE;QACN;YACE,MAAM,EAAE,iBAAiB;YACzB,IAAI,EAAE,gBAAgB,CAAC,QAAQ;YAC/B,8EAA8E;YAC9E,gDAAgD;YAChD,QAAQ,EAAE,SAAS;YACnB,IAAI,EAAE,4DAA4D;YAClE,QAAQ,EACN,uGAAuG;SAC1G;KACF;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,MAAM,MAAM,GAAG,gBAAgB,EAAE,CAAC;QAElC,mFAAmF;QACnF,MAAM,GAAG,GAAG,MAAM,MAAM,CAAC,QAAQ,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC;QAC7C,MAAM,MAAM,GAAG,aAAa,CAAC,GAAG,CAAC,CAAC;QAElC,MAAM,GAAG,GASL,EAAE,GAAG,EAAE,KAAK,CAAC,GAAG,EAAE,SAAS,EAAE,MAAM,CAAC,SAAS,EAAE,SAAS,EAAE,MAAM,CAAC,SAAS,EAAE,CAAC;QAEjF,MAAM,OAAO,GAAG,KAAK,CAAC,QAAQ,IAAI,gBAAgB,CAAC;QACnD,MAAM,OAAO,GAAG,KAAK,CAAC,QAAQ,IAAI,gBAAgB,CAAC;QAEnD,IAAI,YAAY,GAAG,KAAK,CAAC;QACzB,IAAI,aAAa,GAAG,CAAC,CAAC;QAEtB,IAAI,KAAK,CAAC,MAAM,KAAK,MAAM,EAAE,CAAC;YAC5B,GAAG,CAAC,KAAK,GAAG,MAAM,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,EAAE,OAAO,CAAC,CAAC;YAC3C,GAAG,CAAC,KAAK,GAAG,MAAM,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,EAAE,OAAO,CAAC,CAAC;QAC7C,CAAC;aAAM,CAAC;YACN,MAAM,QAAQ,GAAG,GAAG,CAAC,KAAK,CAAC,UAAU,CAAC,CAAC;YACvC,IAAI,KAAK,CAAC,aAAa,IAAI,QAAQ,CAAC,MAAM,IAAI,oBAAoB,EAAE,CAAC;gBACnE,GAAG,CAAC,GAAG,GAAG,GAAG,CAAC;YAChB,CAAC;iBAAM,CAAC;gBACN,GAAG,CAAC,GAAG,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAC,EAAE,oBAAoB,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;gBAC7D,YAAY,GAAG,IAAI,CAAC;gBACpB,aAAa,GAAG,oBAAoB,CAAC;YACvC,CAAC;QACH,CAAC;QAED,IAAI,KAAK,CAAC,4BAA4B,EAAE,CAAC;YACvC,MAAM,GAAG,GAAG,MAAM,MAAM,CAAC,eAAe,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC;YACpD,IAAI,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC;gBACX,GAAG,CAAC,WAAW,GAAG,GAAG,CAAC,CAAC,CAAC,CAAC;gBACzB,MAAM,UAAU,GAAG,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC;gBAChC,IAAI,UAAU,CAAC,MAAM,GAAG,CAAC;oBAAE,GAAG,CAAC,qBAAqB,GAAG,UAAU,CAAC;YACpE,CAAC;QACH,CAAC;QAED,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,sBAAsB,EAAE;YACnC,GAAG,EAAE,KAAK,CAAC,GAAG;YACd,MAAM,EAAE,KAAK,CAAC,MAAM;YACpB,KAAK,EAAE,MAA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@@ -110,7 +110,7 @@ export const getCompoundDetails = tool('pubchem_get_compound_details', {
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110
110
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},
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111
111
|
input: z.object({
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112
112
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cids: z
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113
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-
.array(z.number().int().
|
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113
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+
.array(z.number().int().min(1))
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114
114
|
.min(1)
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115
115
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.max(100)
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116
116
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.describe('PubChem Compound IDs to fetch (1-100). Resolve from names/SMILES with pubchem_search_compounds.'),
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@@ -1 +1 @@
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1
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-
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1
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@@ -19,6 +19,7 @@ export declare const getCompoundImage: import("@cyanheads/mcp-ts-core").ToolDefi
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19
19
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}, z.core.$strip>, readonly [{
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20
20
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readonly reason: "cid_not_found";
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21
21
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readonly code: JsonRpcErrorCode.NotFound;
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22
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+
readonly thrownBy: "service";
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22
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readonly when: "PubChem returned 404 for the requested CID";
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readonly recovery: "Verify the CID with pubchem_search_compounds before retrying.";
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}], undefined>;
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"get-compound-image.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-image.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAGjE,eAAO,MAAM,gBAAgB
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1
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+
{"version":3,"file":"get-compound-image.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-image.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAGjE,eAAO,MAAM,gBAAgB;;;;;;;;;;;;;;;;;;cA+D3B,CAAC"}
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@@ -17,7 +17,7 @@ export const getCompoundImage = tool('pubchem_get_compound_image', {
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cid: z
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18
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.number()
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|
.int()
|
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20
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-
.
|
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20
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+
.min(1)
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21
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.describe('PubChem Compound ID. Resolve from name/SMILES with pubchem_search_compounds.'),
|
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size: z
|
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23
23
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.enum(['small', 'large'])
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@@ -35,6 +35,9 @@ export const getCompoundImage = tool('pubchem_get_compound_image', {
|
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{
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reason: 'cid_not_found',
|
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code: JsonRpcErrorCode.NotFound,
|
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38
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+
// Raised by PubChemClient.getImage, which owns the 404 → typed not-found mapping
|
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39
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+
// because the image endpoint returns binary and cannot report absence in the body.
|
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40
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+
thrownBy: 'service',
|
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|
when: 'PubChem returned 404 for the requested CID',
|
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recovery: 'Verify the CID with pubchem_search_compounds before retrying.',
|
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40
43
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},
|
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@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"get-compound-image.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-image.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,gBAAgB,EAAE,MAAM,sCAAsC,CAAC;AAExE,MAAM,CAAC,MAAM,gBAAgB,GAAG,IAAI,CAAC,4BAA4B,EAAE;IACjE,KAAK,EAAE,oBAAoB;IAC3B,WAAW,EAAE,iEAAiE;IAC9E,WAAW,EAAE;QACX,YAAY,EAAE,IAAI;QAClB,cAAc,EAAE,IAAI;QACpB,aAAa,EAAE,IAAI;KACpB;IACD,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,GAAG,EAAE,CAAC;aACH,MAAM,EAAE;aACR,GAAG,EAAE;aACL,
|
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1
|
+
{"version":3,"file":"get-compound-image.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-image.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,gBAAgB,EAAE,MAAM,sCAAsC,CAAC;AAExE,MAAM,CAAC,MAAM,gBAAgB,GAAG,IAAI,CAAC,4BAA4B,EAAE;IACjE,KAAK,EAAE,oBAAoB;IAC3B,WAAW,EAAE,iEAAiE;IAC9E,WAAW,EAAE;QACX,YAAY,EAAE,IAAI;QAClB,cAAc,EAAE,IAAI;QACpB,aAAa,EAAE,IAAI;KACpB;IACD,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,GAAG,EAAE,CAAC;aACH,MAAM,EAAE;aACR,GAAG,EAAE;aACL,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,CAAC,8EAA8E,CAAC;QAC3F,IAAI,EAAE,CAAC;aACJ,IAAI,CAAC,CAAC,OAAO,EAAE,OAAO,CAAC,CAAC;aACxB,OAAO,CAAC,OAAO,CAAC;aAChB,QAAQ,CAAC,uEAAuE,CAAC;KACrF,CAAC;IACF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,sBAAsB,CAAC;QAChD,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,gCAAgC,CAAC;QAClE,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,iCAAiC,CAAC;QAChE,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,wBAAwB,CAAC;QACpD,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,yBAAyB,CAAC;KACvD,CAAC;IACF,MAAM,EAAE;QACN;YACE,MAAM,EAAE,eAAe;YACvB,IAAI,EAAE,gBAAgB,CAAC,QAAQ;YAC/B,iFAAiF;YACjF,mFAAmF;YACnF,QAAQ,EAAE,SAAS;YACnB,IAAI,EAAE,4CAA4C;YAClD,QAAQ,EAAE,+DAA+D;SAC1E;KACF;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,MAAM,MAAM,GAAG,gBAAgB,EAAE,CAAC;QAClC,MAAM,MAAM,GAAG,MAAM,MAAM,CAAC,QAAQ,CAAC,KAAK,CAAC,GAAG,EAAE,KAAK,CAAC,IAAI,CAAC,CAAC;QAC5D,MAAM,GAAG,GAAG,KAAK,CAAC,IAAI,KAAK,OAAO,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC;QAE/C,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,eAAe,EAAE,EAAE,GAAG,EAAE,KAAK,CAAC,GAAG,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,EAAE,KAAK,EAAE,MAAM,CAAC,UAAU,EAAE,CAAC,CAAC;QAE9F,OAAO;YACL,GAAG,EAAE,KAAK,CAAC,GAAG;YACd,WAAW,EAAE,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,QAAQ,CAAC,QAAQ,CAAC;YACnD,QAAQ,EAAE,WAAW;YACrB,KAAK,EAAE,GAAG;YACV,MAAM,EAAE,GAAG;SACZ,CAAC;IACJ,CAAC;IAED,MAAM,CAAC,MAAM;QACX,OAAO;YACL,EAAE,IAAI,EAAE,OAAO,EAAE,IAAI,EAAE,MAAM,CAAC,WAAW,EAAE,QAAQ,EAAE,MAAM,CAAC,QAAQ,EAAE;YACtE;gBACE,IAAI,EAAE,MAAM;gBACZ,IAAI,EAAE,wBAAwB,MAAM,CAAC,GAAG,KAAK,MAAM,CAAC,KAAK,IAAI,MAAM,CAAC,MAAM,GAAG;aAC9E;SACF,CAAC;IACJ,CAAC;CACF,CAAC,CAAC"}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"get-compound-interactions.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-interactions.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAIjD,eAAO,MAAM,uBAAuB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
|
|
1
|
+
{"version":3,"file":"get-compound-interactions.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-interactions.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAIjD,eAAO,MAAM,uBAAuB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAyPlC,CAAC"}
|
|
@@ -17,7 +17,7 @@ export const getCompoundInteractions = tool('pubchem_get_compound_interactions',
|
|
|
17
17
|
cid: z
|
|
18
18
|
.number()
|
|
19
19
|
.int()
|
|
20
|
-
.
|
|
20
|
+
.min(1)
|
|
21
21
|
.describe('PubChem Compound ID. Resolve from name/SMILES with pubchem_search_compounds.'),
|
|
22
22
|
kinds: z
|
|
23
23
|
.array(z.enum(['drug-drug', 'drug-food', 'target']))
|
|
@@ -42,6 +42,9 @@ export const getCompoundInteractions = tool('pubchem_get_compound_interactions',
|
|
|
42
42
|
.default(10)
|
|
43
43
|
.describe('Max entries per kind per page (1-50). Well-studied drugs have a long tail of interactions; use offset to reach the ones past this page. Default: 10.'),
|
|
44
44
|
}),
|
|
45
|
+
// `maxEntries` is this tool's page size; the sibling search tools call the same
|
|
46
|
+
// concept `maxResults`, and only one page-size input exists here.
|
|
47
|
+
inputAliases: { maxResults: 'maxEntries' },
|
|
45
48
|
output: z.object({
|
|
46
49
|
cid: z.number().describe('PubChem Compound ID.'),
|
|
47
50
|
entries: z
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"get-compound-interactions.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-interactions.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,sCAAsC,CAAC;AACxE,OAAO,EAAE,UAAU,EAAE,SAAS,EAAE,MAAM,qBAAqB,CAAC;AAE5D,MAAM,CAAC,MAAM,uBAAuB,GAAG,IAAI,CAAC,mCAAmC,EAAE;IAC/E,KAAK,EAAE,2BAA2B;IAClC,WAAW,EACT,oZAAoZ;IACtZ,WAAW,EAAE;QACX,YAAY,EAAE,IAAI;QAClB,cAAc,EAAE,IAAI;QACpB,aAAa,EAAE,IAAI;KACpB;IACD,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,GAAG,EAAE,CAAC;aACH,MAAM,EAAE;aACR,GAAG,EAAE;aACL,
|
|
1
|
+
{"version":3,"file":"get-compound-interactions.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-interactions.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,sCAAsC,CAAC;AACxE,OAAO,EAAE,UAAU,EAAE,SAAS,EAAE,MAAM,qBAAqB,CAAC;AAE5D,MAAM,CAAC,MAAM,uBAAuB,GAAG,IAAI,CAAC,mCAAmC,EAAE;IAC/E,KAAK,EAAE,2BAA2B;IAClC,WAAW,EACT,oZAAoZ;IACtZ,WAAW,EAAE;QACX,YAAY,EAAE,IAAI;QAClB,cAAc,EAAE,IAAI;QACpB,aAAa,EAAE,IAAI;KACpB;IACD,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,GAAG,EAAE,CAAC;aACH,MAAM,EAAE;aACR,GAAG,EAAE;aACL,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,CAAC,8EAA8E,CAAC;QAC3F,KAAK,EAAE,CAAC;aACL,KAAK,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,WAAW,EAAE,WAAW,EAAE,QAAQ,CAAC,CAAC,CAAC;aACnD,GAAG,CAAC,CAAC,CAAC;aACN,OAAO,CAAC,CAAC,WAAW,CAAC,CAAC;aACtB,QAAQ,CACP,6LAA6L,CAC9L;QACH,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,GAAG,EAAE;aACL,GAAG,CAAC,CAAC,CAAC;YACP,wFAAwF;YACxF,yFAAyF;YACzF,oDAAoD;aACnD,GAAG,CAAC,UAAU,CAAC;aACf,OAAO,CAAC,CAAC,CAAC;aACV,QAAQ,CACP,qTAAqT,CACtT;QACH,UAAU,EAAE,CAAC;aACV,MAAM,EAAE;aACR,GAAG,EAAE;aACL,GAAG,CAAC,CAAC,CAAC;aACN,GAAG,CAAC,EAAE,CAAC;aACP,OAAO,CAAC,EAAE,CAAC;aACX,QAAQ,CACP,sJAAsJ,CACvJ;KACJ,CAAC;IACF,gFAAgF;IAChF,kEAAkE;IAClE,YAAY,EAAE,EAAE,UAAU,EAAE,YAAY,EAAE;IAC1C,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,sBAAsB,CAAC;QAChD,OAAO,EAAE,CAAC;aACP,KAAK,CACJ,CAAC;aACE,MAAM,CAAC;YACN,IAAI,EAAE,CAAC,CAAC,IAAI,CAAC,CAAC,WAAW,EAAE,WAAW,EAAE,QAAQ,CAAC,CAAC,CAAC,QAAQ,CAAC,uBAAuB,CAAC;YACpF,OAAO,EAAE,CAAC;iBACP,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CAAC,sEAAsE,CAAC;YACnF,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,oDAAoD,CAAC;YACjF,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,4BAA4B,CAAC;SACxD,CAAC;aACD,QAAQ,CAAC,6BAA6B,CAAC,CAC3C;aACA,QAAQ,CAAC,iDAAiD,CAAC;QAC9D,MAAM,EAAE,CAAC;aACN,KAAK,CACJ,CAAC;aACE,MAAM,CAAC;YACN,IAAI,EAAE,CAAC;iBACJ,IAAI,CAAC,CAAC,WAAW,EAAE,WAAW,EAAE,QAAQ,CAAC,CAAC;iBAC1C,QAAQ,CAAC,wCAAwC,CAAC;YACrD,aAAa,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,6CAA6C,CAAC;YACjF,YAAY,EAAE,CAAC;iBACZ,MAAM,EAAE;iBACR,QAAQ,CACP,6XAA6X,CAC9X;YACH,UAAU,EAAE,CAAC;iBACV,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CACP,8GAA8G,CAC/G;YACH,SAAS,EAAE,CAAC;iBACT,OAAO,EAAE;iBACT,QAAQ,CAAC,sEAAsE,CAAC;SACpF,CAAC;aACD,QAAQ,CAAC,yCAAyC,CAAC,CACvD;aACA,QAAQ,CACP,2JAA2J,CAC5J;KACJ,CAAC;IACF,yFAAyF;IACzF,sFAAsF;IACtF,+BAA+B;IAC/B,UAAU,EAAE;QACV,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,gDAAgD,CAAC;QACrF,aAAa,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,sDAAsD,CAAC;QAC1F,SAAS,EAAE,CAAC;aACT,OAAO,EAAE;aACT,QAAQ,CACP,oLAAoL,CACrL;QACH,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,4DAA4D,CAAC;QACzF,UAAU,EAAE,CAAC;aACV,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,yNAAyN,CAC1N;QACH,WAAW,EAAE,CAAC;aACX,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,4JAA4J,CAC7J;QACH,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,2MAA2M,CAC5M;KACJ;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,MAAM,MAAM,GAAG,gBAAgB,EAAE,CAAC;QAClC,MAAM,EAAE,OAAO,EAAE,KAAK,EAAE,WAAW,EAAE,GAAG,MAAM,MAAM,CAAC,eAAe,CAClE,KAAK,CAAC,GAAG,EACT,KAAK,CAAC,KAAK,EACX,KAAK,CAAC,UAAU,EAChB,KAAK,CAAC,MAAM,CACb,CAAC;QAEF,KAAK,MAAM,CAAC,IAAI,WAAW,EAAE,CAAC;YAC5B,GAAG,CAAC,GAAG,CAAC,OAAO,CAAC,yBAAyB,EAAE;gBACzC,GAAG,EAAE,KAAK,CAAC,GAAG;gBACd,IAAI,EAAE,CAAC,CAAC,IAAI;gBACZ,KAAK,EAAE,CAAC,CAAC,OAAO;aACjB,CAAC,CAAC;QACL,CAAC;QACD,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,sBAAsB,EAAE;YACnC,GAAG,EAAE,KAAK,CAAC,GAAG;YACd,KAAK,EAAE,KAAK,CAAC,KAAK;YAClB,MAAM,EAAE,KAAK,CAAC,MAAM;YACpB,QAAQ,EAAE,OAAO,CAAC,MAAM;YACxB,MAAM,EAAE,WAAW,CAAC,MAAM;SAC3B,CAAC,CAAC;QAEH,wFAAwF;QACxF,0FAA0F;QAC1F,2EAA2E;QAC3E,MAAM,MAAM,GAAG,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE;YAC7B,MAAM,IAAI,GAAG,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,eAAe,CAAC;YAC9C,MAAM,SAAS,GAAG,IAAI,GAAG,CAAC,CAAC,YAAY,CAAC;YACxC,OAAO;gBACL,IAAI,EAAE,CAAC,CAAC,IAAI;gBACZ,aAAa,EAAE,CAAC,CAAC,aAAa;gBAC9B,YAAY,EAAE,CAAC,CAAC,YAAY;gBAC5B,SAAS;gBACT,GAAG,CAAC,SAAS,CAAC,CAAC,CAAC,EAAE,UAAU,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;aAC3C,CAAC;QACJ,CAAC,CAAC,CAAC;QAEH,MAAM,SAAS,GAAG,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC;QAEpD,GAAG,CAAC,MAAM,CAAC;YACT,cAAc,EAAE,KAAK,CAAC,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC;YACtC,aAAa,EAAE,OAAO,CAAC,MAAM;YAC7B,SAAS,EAAE,SAAS,CAAC,MAAM,GAAG,CAAC;YAC/B,MAAM,EAAE,KAAK,CAAC,MAAM;SACrB,CAAC,CAAC;QAEH,yFAAyF;QACzF,mEAAmE;QACnE,MAAM,cAAc,GAAG,SAAS,CAAC,MAAM,KAAK,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,EAAE,UAAU,CAAC,CAAC,CAAC,SAAS,CAAC;QACrF,IAAI,cAAc,KAAK,SAAS;YAAE,GAAG,CAAC,MAAM,CAAC,EAAE,UAAU,EAAE,cAAc,EAAE,CAAC,CAAC;QAE7E,4EAA4E;QAC5E,MAAM,WAAW,GAAa,EAAE,CAAC;QAEjC,IAAI,WAAW,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;YAC3B,MAAM,KAAK,GAAG,WAAW,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;YACxD,MAAM,MAAM,GAAG,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC;YACtC,GAAG,CAAC,MAAM,CAAC,EAAE,WAAW,EAAE,KAAK,EAAE,CAAC,CAAC;YACnC,WAAW,CAAC,IAAI,CACd,sBAAsB,KAAK,eAAe,MAAM,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,YAAY,KAAK,CAAC,GAAG,IAC9E,OAAO,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,qCAAqC,CAAC,CAAC,CAA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@@ -44,7 +44,7 @@ export const getCompoundSafety = tool('pubchem_get_compound_safety', {
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44
44
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},
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45
45
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input: z.object({
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46
46
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cids: z
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47
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-
.array(z.number().int().
|
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47
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+
.array(z.number().int().min(1))
|
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48
48
|
.min(1)
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49
49
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.max(25)
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50
50
|
.describe('PubChem Compound IDs to fetch safety data for (1-25). Resolve from names/SMILES with pubchem_search_compounds.'),
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"get-compound-safety.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-safety.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,sCAAsC,CAAC;AAExE,OAAO,EAAE,UAAU,EAAE,MAAM,qBAAqB,CAAC;AAEjD,MAAM,SAAS,GAAG,CAAC;KAChB,MAAM,CAAC;IACN,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,yCAAyC,CAAC;IACrF,UAAU,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,QAAQ,CAAC,mDAAmD,CAAC;IAC7F,gBAAgB,EAAE,CAAC;SAChB,KAAK,CACJ,CAAC;SACE,MAAM,CAAC;QACN,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,uBAAuB,CAAC;QAClD,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,wBAAwB,CAAC;KACzD,CAAC;SACD,QAAQ,CAAC,6BAA6B,CAAC,CAC3C;SACA,QAAQ,CAAC,wBAAwB,CAAC;IACrC,uBAAuB,EAAE,CAAC;SACvB,KAAK,CACJ,CAAC;SACE,MAAM,CAAC;QACN,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,uBAAuB,CAAC;QAClD,SAAS,EAAE,CAAC;aACT,MAAM,EAAE;aACR,QAAQ,CACP,8OAA8O,CAC/O;QACH,OAAO,EAAE,CAAC;aACP,OAAO,EAAE;aACT,QAAQ,CACP,uQAAuQ,CACxQ;KACJ,CAAC;SACD,QAAQ,CAAC,oCAAoC,CAAC,CAClD;SACA,QAAQ,CAAC,+BAA+B,CAAC;CAC7C,CAAC;KACD,QAAQ,CAAC,0BAA0B,CAAC,CAAC;AAExC,sGAAsG;AACtG,MAAM,aAAa,GAAG,EAAE,CAAC;AAEzB,MAAM,CAAC,MAAM,iBAAiB,GAAG,IAAI,CAAC,6BAA6B,EAAE;IACnE,KAAK,EAAE,qBAAqB;IAC5B,WAAW,EACT,qSAAqS;IACvS,WAAW,EAAE;QACX,YAAY,EAAE,IAAI;QAClB,cAAc,EAAE,IAAI;QACpB,aAAa,EAAE,IAAI;KACpB;IACD,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,IAAI,EAAE,CAAC;aACJ,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,CAAC,
|
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1
|
+
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"get-compound-xrefs.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-xrefs.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAMjD,eAAO,MAAM,gBAAgB;;;;;;;;;;;;;;;;;;;;
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1
|
+
{"version":3,"file":"get-compound-xrefs.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-xrefs.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAMjD,eAAO,MAAM,gBAAgB;;;;;;;;;;;;;;;;;;;;EAkM3B,CAAC"}
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@@ -18,7 +18,7 @@ export const getCompoundXrefs = tool('pubchem_get_compound_xrefs', {
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18
18
|
cid: z
|
|
19
19
|
.number()
|
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20
20
|
.int()
|
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21
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-
.
|
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21
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+
.min(1)
|
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22
22
|
.describe('PubChem Compound ID. Resolve from name/SMILES with pubchem_search_compounds.'),
|
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23
23
|
xrefTypes: z
|
|
24
24
|
.array(xrefTypeEnum)
|
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@@ -38,6 +38,10 @@ export const getCompoundXrefs = tool('pubchem_get_compound_xrefs', {
|
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38
38
|
.default(50)
|
|
39
39
|
.describe('Max IDs to return per xref type per page (1-500). A compound may have thousands of PubMed references; use offset to reach the ones past this page. Total count always reported. Default: 50.'),
|
|
40
40
|
}),
|
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41
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+
// Every other paging tool here names its page size `maxResults`; this one caps per
|
|
42
|
+
// xref type, so a caller arriving from pubchem_search_compounds reaches for the
|
|
43
|
+
// sibling spelling. One page-size input exists, so the mapping is unambiguous.
|
|
44
|
+
inputAliases: { maxResults: 'maxPerType' },
|
|
41
45
|
output: z.object({
|
|
42
46
|
cid: z.number().describe('PubChem Compound ID.'),
|
|
43
47
|
xrefs: z
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"get-compound-xrefs.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-xrefs.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,sCAAsC,CAAC;AACxE,OAAO,EAAE,UAAU,EAAE,MAAM,6BAA6B,CAAC;AAEzD,MAAM,YAAY,GAAG,CAAC,CAAC,IAAI,CAAC,UAA8C,CAAC,CAAC;AAE5E,MAAM,CAAC,MAAM,gBAAgB,GAAG,IAAI,CAAC,4BAA4B,EAAE;IACjE,KAAK,EAAE,+BAA+B;IACtC,WAAW,EACT,6QAA6Q;IAC/Q,WAAW,EAAE;QACX,YAAY,EAAE,IAAI;QAClB,cAAc,EAAE,IAAI;QACpB,aAAa,EAAE,IAAI;KACpB;IACD,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,GAAG,EAAE,CAAC;aACH,MAAM,EAAE;aACR,GAAG,EAAE;aACL,
|
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1
|
+
{"version":3,"file":"get-compound-xrefs.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-xrefs.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,sCAAsC,CAAC;AACxE,OAAO,EAAE,UAAU,EAAE,MAAM,6BAA6B,CAAC;AAEzD,MAAM,YAAY,GAAG,CAAC,CAAC,IAAI,CAAC,UAA8C,CAAC,CAAC;AAE5E,MAAM,CAAC,MAAM,gBAAgB,GAAG,IAAI,CAAC,4BAA4B,EAAE;IACjE,KAAK,EAAE,+BAA+B;IACtC,WAAW,EACT,6QAA6Q;IAC/Q,WAAW,EAAE;QACX,YAAY,EAAE,IAAI;QAClB,cAAc,EAAE,IAAI;QACpB,aAAa,EAAE,IAAI;KACpB;IACD,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,GAAG,EAAE,CAAC;aACH,MAAM,EAAE;aACR,GAAG,EAAE;aACL,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,CAAC,8EAA8E,CAAC;QAC3F,SAAS,EAAE,CAAC;aACT,KAAK,CAAC,YAAY,CAAC;aACnB,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,CACP,iNAAiN,CAClN;QACH,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,GAAG,EAAE;aACL,GAAG,CAAC,CAAC,CAAC;aACN,OAAO,CAAC,CAAC,CAAC;aACV,QAAQ,CACP,wMAAwM,CACzM;QACH,UAAU,EAAE,CAAC;aACV,MAAM,EAAE;aACR,GAAG,EAAE;aACL,GAAG,CAAC,CAAC,CAAC;aACN,GAAG,CAAC,GAAG,CAAC;aACR,OAAO,CAAC,EAAE,CAAC;aACX,QAAQ,CACP,8LAA8L,CAC/L;KACJ,CAAC;IACF,mFAAmF;IACnF,gFAAgF;IAChF,+EAA+E;IAC/E,YAAY,EAAE,EAAE,UAAU,EAAE,YAAY,EAAE;IAC1C,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,sBAAsB,CAAC;QAChD,KAAK,EAAE,CAAC;aACL,KAAK,CACJ,CAAC;aACE,MAAM,CAAC;YACN,IAAI,EAAE,CAAC;iBACJ,MAAM,EAAE;iBACR,QAAQ,CACP,6FAA6F,CAC9F;YACH,GAAG,EAAE,CAAC;iBACH,KAAK,CACJ,CAAC;iBACE,KAAK,CAAC;gBACL,CAAC;qBACE,MAAM,EAAE;qBACR,QAAQ,CAAC,2DAA2D,CAAC;gBACxE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,uDAAuD,CAAC;aAC7E,CAAC;iBACD,QAAQ,CAAC,kEAAkE,CAAC,CAChF;iBACA,QAAQ,CAAC,mEAAmE,CAAC;YAChF,cAAc,EAAE,CAAC;iBACd,MAAM,EAAE;iBACR,QAAQ,CAAC,sDAAsD,CAAC;YACnE,SAAS,EAAE,CAAC;iBACT,OAAO,EAAE;iBACT,QAAQ,CAAC,2DAA2D,CAAC;SACzE,CAAC;aACD,QAAQ,CAAC,qCAAqC,CAAC,CACnD;aACA,QAAQ,CAAC,mCAAmC,CAAC;KACjD,CAAC;IACF,yFAAyF;IACzF,oFAAoF;IACpF,2FAA2F;IAC3F,0BAA0B;IAC1B,UAAU,EAAE;QACV,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,6DAA6D,CAAC;QAC1F,SAAS,EAAE,CAAC;aACT,OAAO,EAAE;aACT,QAAQ,CACP,8KAA8K,CAC/K;QACH,UAAU,EAAE,CAAC;aACV,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,6GAA6G,CAC9G;QACH,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,0LAA0L,CAC3L;KACJ;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,MAAM,MAAM,GAAG,gBAAgB,EAAE,CAAC;QAElC,iDAAiD;QACjD,MAAM,KAAK,GAKN,EAAE,CAAC;QAER,KAAK,MAAM,QAAQ,IAAI,KAAK,CAAC,SAAS,EAAE,CAAC;YACvC,MAAM,MAAM,GAAG,MAAM,MAAM,CAAC,QAAQ,CAAC,KAAK,CAAC,GAAG,EAAE,QAAQ,CAAC,CAAC;YAC1D,MAAM,cAAc,GAAG,MAAM,CAAC,MAAM,CAAC;YACrC,sFAAsF;YACtF,4DAA4D;YAC5D,MAAM,GAAG,GAAG,MAAM,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,EAAE,KAAK,CAAC,MAAM,GAAG,KAAK,CAAC,UAAU,CAAC,CAAC;YAExE,KAAK,CAAC,IAAI,CAAC;gBACT,IAAI,EAAE,QAAQ;gBACd,GAAG;gBACH,cAAc;gBACd,SAAS,EAAE,KAAK,CAAC,MAAM,GAAG,GAAG,CAAC,MAAM,GAAG,cAAc;aACtD,CAAC,CAAC;QACL,CAAC;QAED,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,eAAe,EAAE;YAC5B,GAAG,EAAE,KAAK,CAAC,GAAG;YACd,KAAK,EAAE,KAAK,CAAC,SAAS;YACtB,MAAM,EAAE,KAAK,CAAC,MAAM;YACpB,QAAQ,EAAE,KAAK,CAAC,MAAM,CAAC,CAAC,GAAG,EAAE,CAAC,EAAE,EAAE,CAAC,GAAG,GAAG,CAAC,CAAC,GAAG,CAAC,MAAM,EAAE,CAAC,CAAC;SAC1D,CAAC,CAAC;QAEH,2FAA2F;QAC3F,4FAA4F;QAC5F,yFAAyF;QACzF,0EAA0E;QAC1E,MAAM,cAAc,GAAG,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC;QACxD,MAAM,OAAO,GAAG,cAAc,CAAC,MAAM,GAAG,CAAC,CAAC;QAC1C,MAAM,UAAU,GAAG,KAAK,CAAC,MAAM,GAAG,CAAC,cAAc,CAAC,CAAC,CAAC,EAAE,GAAG,CAAC,MAAM,IAAI,CAAC,CAAC,CAAC;QACvE,MAAM,YAAY,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,cAAc,CAAC,CAAC,CAAC;QAErE,GAAG,CAAC,MAAM,CAAC,EAAE,MAAM,EAAE,KAAK,CAAC,MAAM,EAAE,SAAS,EAAE,OAAO,EAAE,CAAC,CAAC;QACzD,IAAI,OAAO;YAAE,GAAG,CAAC,MAAM,CAAC,EAAE,UAAU,EAAE,CAAC,CAAC;QAExC,mFAAmF;QACnF,yFAAyF;QACzF,IAAI,YAAY,KAAK,CAAC,EAAE,CAAC;YACvB,GAAG,CAAC,MAAM,CAAC,MAAM,CACf,qCAAqC,KAAK,CAAC,GAAG,kCAAkC,KAAK,CAAC,SAAS,CAAC,IAAI,CAAC,IAAI,CAAC,oGAAoG,CAC/M,CAAC;QACJ,CAAC;aAAM,IAAI,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,MAAM,KAAK,CAAC,CAAC,EAAE,CAAC;YAClD,GAAG,CAAC,MAAM,CAAC,MAAM,CACf,UAAU,KAAK,CAAC,MAAM,mDAAmD,YAAY,gCAAgC,YAAY,GAAG,CACrI,CAAC;QACJ,CAAC;aAAM,IAAI,OAAO,EAAE,CAAC;YACnB,MAAM,SAAS,GAAG,cAAc;iBAC7B,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,GAAG,CAAC,CAAC,IAAI,KAAK,CAAC,CAAC,cAAc,SAAS,CAAC;iBACnD,IAAI,CAAC,IAAI,CAAC,CAAC;YACd,GAAG,CAAC,MAAM,CAAC,MAAM,CACf,wBAAwB,SAAS,iBAAiB,UAAU,qBAAqB,CAClF,CAAC;QACJ,CAAC;QAED,OAAO,EAAE,GAAG,EAAE,KAAK,CAAC,GAAG,EAAE,KAAK,EAAE,CAAC;IACnC,CAAC;IAED,MAAM,CAAC,MAAM;QACX,MAAM,KAAK,GAAa,CAAC,4BAA4B,MAAM,CAAC,GAAG,EAAE,EAAE,EAAE,CAAC,CAAC;QAEvE,KAAK,MAAM,IAAI,IAAI,MAAM,CAAC,KAAK,EAAE,CAAC;YAChC,mFAAmF;YACnF,6EAA6E;YAC7E,IAAI,SAAS,GAAG,GAAG,IAAI,CAAC,cAAc,QAAQ,CAAC;YAC/C,IAAI,IAAI,CAAC,GAAG,CAAC,MAAM,KAAK,IAAI,CAAC,cAAc,EAAE,CAAC;gBAC5C,SAAS,GAAG,GAAG,IAAI,CAAC,GAAG,CAAC,MAAM,OAAO,IAAI,CAAC,cAAc,QAAQ,CAAC;gBACjE,IAAI,IAAI,CAAC,SAAS;oBAAE,SAAS,IAAI,cAAc,CAAC;YAClD,CAAC;YACD,KAAK,CAAC,IAAI,CAAC,KAAK,IAAI,CAAC,IAAI,OAAO,SAAS,GAAG,CAAC,CAAC;YAE9C,IAAI,IAAI,CAAC,GAAG,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;gBACxB,gFAAgF;gBAChF,wFAAwF;gBACxF,KAAK,CAAC,IAAI,CAAC,KAAK,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;YACzC,CAAC;iBAAM,CAAC;gBACN,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,cAAc,GAAG,CAAC,CAAC,CAAC,CAAC,qBAAqB,CAAC,CAAC,CAAC,cAAc,CAAC,CAAC;YAC/E,CAAC;YACD,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACjB,CAAC;QAED,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IACpD,CAAC;CACF,CAAC,CAAC"}
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@@ -147,12 +147,12 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
|
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|
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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 when: "searchType is \"formula\" but the formula field was omitted or blank";
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|
readonly recovery: "Pass formula in Hill notation, for example \"C6H12O6\" or \"CaH2O2\".";
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}, {
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153
153
|
readonly reason: "missing_structure_args";
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154
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|
readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
|
|
155
|
-
readonly when: "substructure/superstructure/similarity search
|
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155
|
+
readonly when: "substructure/superstructure/similarity search with query or queryType omitted, or a blank query";
|
|
156
156
|
readonly recovery: "Provide both query (SMILES string or CID as string) and queryType (\"smiles\" or \"cid\").";
|
|
157
157
|
}, {
|
|
158
158
|
readonly reason: "invalid_cid_query";
|
|
@@ -184,6 +184,7 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
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|
184
184
|
}, import("zod/v4/core").$strip>, readonly [{
|
|
185
185
|
readonly reason: "cid_not_found";
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|
186
186
|
readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;
|
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187
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+
readonly thrownBy: "service";
|
|
187
188
|
readonly when: "PubChem returned 404 for the requested CID";
|
|
188
189
|
readonly recovery: "Verify the CID with pubchem_search_compounds before retrying.";
|
|
189
190
|
}], undefined> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
|
|
@@ -217,6 +218,7 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
|
|
|
217
218
|
}, import("zod/v4/core").$strip>, readonly [{
|
|
218
219
|
readonly reason: "no_3d_structure";
|
|
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|
readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;
|
|
221
|
+
readonly thrownBy: "service";
|
|
220
222
|
readonly when: "PubChem has no computed 3D conformer for the requested CID";
|
|
221
223
|
readonly recovery: "Use pubchem_get_compound_image for the 2D structure, or verify the CID with pubchem_search_compounds.";
|
|
222
224
|
}], {
|
|
@@ -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
|
|
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"}
|