npm - @cyanheads/pubchem-mcp-server - Versions diffs - 0.1.22 → 0.2.0 - Mend

@cyanheads/pubchem-mcp-server 0.1.22 → 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 (73) hide show

package/dist/services/pubchem/pubchem-client.js CHANGED Viewed

@@ -3,7 +3,7 @@
  * Wraps both PUG REST and PUG View APIs behind a shared rate limiter.
  * @module services/pubchem/pubchem-client
  */
-import { JsonRpcErrorCode, McpError } from '@cyanheads/mcp-ts-core/errors';
+import { JsonRpcErrorCode, McpError, notFound } from '@cyanheads/mcp-ts-core/errors';
 import { httpErrorFromResponse } from '@cyanheads/mcp-ts-core/utils';
 const isNotFound = (error) => error instanceof McpError && error.code === JsonRpcErrorCode.NotFound;
 // ── Rate Limiter ─────────────────────────────────────────────────────
@@ -194,6 +194,7 @@ const activityKey = (v) => `${v.name ?? ''}|${v.value}|${v.unit ?? ''}`;
 export class PubChemClient {
     pugBase = 'https://pubchem.ncbi.nlm.nih.gov/rest/pug';
     viewBase = 'https://pubchem.ncbi.nlm.nih.gov/rest/pug_view';
+    sdqBase = 'https://pubchem.ncbi.nlm.nih.gov/sdq/sdqagent.cgi';
     rateLimiter = new RateLimiter(5);
     // ── Core HTTP ────────────────────────────────────────────────────
     async fetchJson(url, init) {
@@ -259,6 +260,28 @@ export class PubChemClient {
             clearTimeout(timeoutId);
         }
     }
+    /** Fetch a text/plain body (e.g. an SDF record). Non-2xx is classified and thrown. */
+    async fetchText(url) {
+        await this.rateLimiter.acquire();
+        const controller = new AbortController();
+        const timeoutId = setTimeout(() => controller.abort(), 30_000);
+        try {
+            const response = await fetch(url, { signal: controller.signal });
+            if (!response.ok) {
+                const text = await response.text();
+                const fault = parseFaultMessage(text) ?? text.slice(0, 300);
+                throw await httpErrorFromResponse(response, {
+                    captureBody: false,
+                    service: 'PubChem',
+                    data: { fault, url },
+                });
+            }
+            return await response.text();
+        }
+        finally {
+            clearTimeout(timeoutId);
+        }
+    }
     // ── CID Resolution ──────────────────────────────────────────────
     /** Fetch CID list, with automatic ListKey polling for async searches */
     async fetchCids(url, init) {
@@ -357,9 +380,23 @@ export class PubChemClient {
             throw error;
         }
     }
-    getImage(cid, size = 'large') {
+    async getImage(cid, size = 'large') {
         const sizeParam = size === 'small' ? '?image_size=small' : '?image_size=large';
-        return this.fetchBinary(`${this.pugBase}/compound/cid/${cid}/PNG${sizeParam}`);
+        try {
+            return await this.fetchBinary(`${this.pugBase}/compound/cid/${cid}/PNG${sizeParam}`);
+        }
+        catch (error) {
+            // The image endpoint returns binary, so absence can't be a structured success like
+            // the other per-CID tools — surface a typed not-found with a recovery hint instead.
+            if (isNotFound(error)) {
+                throw notFound(`No PubChem compound found for CID ${cid}.`, {
+                    cid,
+                    reason: 'cid_not_found',
+                    recovery: { hint: 'Verify the CID with pubchem_search_compounds before retrying.' },
+                });
+            }
+            throw error;
+        }
     }
     async getXrefs(cid, xrefType) {
         try {
@@ -658,6 +695,141 @@ export class PubChemClient {
             throw error;
         }
     }
+    // ── Interactions ────────────────────────────────────────────────
+    /** Fetch drug-drug, drug-food, and/or chemical-target interactions for a compound.
+     * Drug-drug and target data live in PubChem SDQ external tables (drugbankddi,
+     * consolidatedcompoundtarget); drug-food is inline PUG View text. Each kind is capped
+     * at maxEntries; absent data for a kind contributes nothing rather than erroring. */
+    async getInteractions(cid, kinds, maxEntries) {
+        const batches = await Promise.all(kinds.map((kind) => this.getInteractionsForKind(cid, kind, maxEntries)));
+        return batches.flat();
+    }
+    getInteractionsForKind(cid, kind, maxEntries) {
+        switch (kind) {
+            case 'drug-drug':
+                return this.getDrugDrugInteractions(cid, maxEntries);
+            case 'drug-food':
+                return this.getDrugFoodInteractions(cid, maxEntries);
+            case 'target':
+                return this.getTargetInteractions(cid, maxEntries);
+        }
+    }
+    async getDrugDrugInteractions(cid, maxEntries) {
+        const rows = await this.fetchSdq('drugbankddi', cid, maxEntries);
+        const entries = [];
+        for (const row of rows) {
+            const text = typeof row.descr === 'string' ? row.descr : '';
+            if (!text)
+                continue;
+            const entry = { kind: 'drug-drug', source: 'DrugBank', text };
+            if (typeof row.name2 === 'string' && row.name2)
+                entry.partner = row.name2;
+            entries.push(entry);
+        }
+        return entries;
+    }
+    async getTargetInteractions(cid, maxEntries) {
+        const rows = await this.fetchSdq('consolidatedcompoundtarget', cid, maxEntries);
+        const entries = [];
+        for (const row of rows) {
+            const target = (typeof row.protname === 'string' && row.protname) ||
+                (typeof row.srctargetname === 'string' && row.srctargetname) ||
+                (typeof row.genename === 'string' && row.genename) ||
+                '';
+            const activity = [row.actname, row.actvalue]
+                .filter((v) => typeof v === 'string' && v.length > 0)
+                .join(': ');
+            const text = [target, activity].filter(Boolean).join(' — ');
+            if (!text)
+                continue;
+            const entry = {
+                kind: 'target',
+                source: typeof row.dsn === 'string' && row.dsn ? row.dsn : 'PubChem',
+                text,
+            };
+            if (target)
+                entry.partner = target;
+            entries.push(entry);
+        }
+        return entries;
+    }
+    async getDrugFoodInteractions(cid, maxEntries) {
+        try {
+            const data = await this.fetchJson(`${this.viewBase}/data/compound/${cid}/JSON?heading=Drug-Food+Interactions`);
+            const sections = data.Record.Section;
+            if (!sections)
+                return [];
+            const section = findSection(sections, 'Drug-Food Interactions');
+            if (!section)
+                return [];
+            const refToSource = new Map();
+            for (const ref of data.Record.Reference ?? []) {
+                refToSource.set(ref.ReferenceNumber, ref.SourceName);
+            }
+            const items = dedupByKey(extractDescriptionItems(section), descriptionKey);
+            return items.slice(0, maxEntries).map((item) => {
+                const source = item.refNum != null ? refToSource.get(item.refNum) : undefined;
+                return { kind: 'drug-food', source: source ?? 'PubChem', text: item.text };
+            });
+        }
+        catch (error) {
+            if (isNotFound(error))
+                return [];
+            throw error;
+        }
+    }
+    /** Query a PubChem SDQ external table for a single CID. Returns [] on not-found. */
+    async fetchSdq(collection, cid, limit) {
+        const query = JSON.stringify({
+            download: '*',
+            collection,
+            where: { ands: [{ cid: String(cid) }] },
+            start: 1,
+            limit,
+        });
+        const url = `${this.sdqBase}?infmt=json&outfmt=json&query=${encodeURIComponent(query)}`;
+        try {
+            const data = await this.fetchJson(url);
+            return Array.isArray(data) ? data : [];
+        }
+        catch (error) {
+            if (isNotFound(error))
+                return [];
+            throw error;
+        }
+    }
+    // ── 3D Structure ────────────────────────────────────────────────
+    /** Fetch the default 3D conformer as raw V2000 SDF text. Throws a typed not-found when
+     * PubChem has no computed 3D coordinates (large molecules, mixtures, undefined salts). */
+    async getSdf3d(cid) {
+        try {
+            return await this.fetchText(`${this.pugBase}/compound/cid/${cid}/record/SDF?record_type=3d`);
+        }
+        catch (error) {
+            if (isNotFound(error)) {
+                throw notFound(`No 3D conformer available for CID ${cid}.`, {
+                    cid,
+                    reason: 'no_3d_structure',
+                    recovery: {
+                        hint: 'PubChem has no computed 3D coordinates for this compound (common for very large molecules, mixtures, and undefined salts). Use pubchem_get_compound_image for the 2D structure.',
+                    },
+                });
+            }
+            throw error;
+        }
+    }
+    /** List the conformer IDs PubChem has computed for a compound. Returns [] on not-found. */
+    async getConformerIds(cid) {
+        try {
+            const data = await this.fetchJson(`${this.pugBase}/compound/cid/${cid}/conformers/JSON`);
+            return data.InformationList.Information[0]?.ConformerID ?? [];
+        }
+        catch (error) {
+            if (isNotFound(error))
+                return [];
+            throw error;
+        }
+    }
 }
 // ── Init/Accessor ────────────────────────────────────────────────────
 let _client;

package/dist/services/pubchem/pubchem-client.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/services/pubchem/sdf-parser.d.ts ADDED Viewed

@@ -0,0 +1,20 @@
+/**
+ * @fileoverview Minimal parser for the V2000 SDF connection table (atom + bond blocks).
+ * PubChem emits V2000 for 3D conformer records; the format is fixed-column and has been
+ * stable since 1991, so a focused slice-based parser is more robust than a dependency.
+ * @module services/pubchem/sdf-parser
+ */
+import type { Sdf3DStructure } from './types.js';
+/**
+ * Parse the first molecule's atom and bond blocks from a V2000 SDF record.
+ *
+ * Layout: three header lines, then a counts line (atom count at columns 0–3, bond count at
+ * columns 3–6), then one fixed-column line per atom (x/y/z as `F10.4` at columns 0–10/10–20/
+ * 20–30, element symbol at columns 31–34), then one line per bond (atom1/atom2/order as
+ * three-column integers). The block is terminated by `M  END`.
+ *
+ * Throws when the counts line is missing or unparseable — a malformed record is a hard
+ * failure, not a silently-empty success.
+ */
+export declare function parseSdfV2000(sdf: string): Sdf3DStructure;
+//# sourceMappingURL=sdf-parser.d.ts.map

package/dist/services/pubchem/sdf-parser.d.ts.map ADDED Viewed

	@@ -0,0 +1 @@
1	+ {"version":3,"file":"sdf-parser.d.ts","sourceRoot":"","sources":["../../../src/services/pubchem/sdf-parser.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,YAAY,CAAC;AAEjD;;;;;;;;;;GAUG;AACH,wBAAgB,aAAa,CAAC,GAAG,EAAE,MAAM,GAAG,cAAc,CAsCzD"}

package/dist/services/pubchem/sdf-parser.js ADDED Viewed

@@ -0,0 +1,55 @@
+/**
+ * @fileoverview Minimal parser for the V2000 SDF connection table (atom + bond blocks).
+ * PubChem emits V2000 for 3D conformer records; the format is fixed-column and has been
+ * stable since 1991, so a focused slice-based parser is more robust than a dependency.
+ * @module services/pubchem/sdf-parser
+ */
+/**
+ * Parse the first molecule's atom and bond blocks from a V2000 SDF record.
+ *
+ * Layout: three header lines, then a counts line (atom count at columns 0–3, bond count at
+ * columns 3–6), then one fixed-column line per atom (x/y/z as `F10.4` at columns 0–10/10–20/
+ * 20–30, element symbol at columns 31–34), then one line per bond (atom1/atom2/order as
+ * three-column integers). The block is terminated by `M  END`.
+ *
+ * Throws when the counts line is missing or unparseable — a malformed record is a hard
+ * failure, not a silently-empty success.
+ */
+export function parseSdfV2000(sdf) {
+    const lines = sdf.split('\n');
+    // Header is three lines (title, program/timestamp, comment); the counts line is index 3.
+    const countsLine = lines[3];
+    if (countsLine === undefined)
+        throw new Error('Malformed SDF: missing counts line');
+    const atomCount = Number.parseInt(countsLine.slice(0, 3), 10);
+    const bondCount = Number.parseInt(countsLine.slice(3, 6), 10);
+    if (!Number.isInteger(atomCount) || !Number.isInteger(bondCount)) {
+        throw new Error('Malformed SDF: unparseable atom/bond counts');
+    }
+    const atoms = [];
+    for (let i = 0; i < atomCount; i++) {
+        const line = lines[4 + i];
+        if (line === undefined)
+            break;
+        atoms.push({
+            x: Number.parseFloat(line.slice(0, 10)),
+            y: Number.parseFloat(line.slice(10, 20)),
+            z: Number.parseFloat(line.slice(20, 30)),
+            element: line.slice(31, 34).trim(),
+        });
+    }
+    const bonds = [];
+    const bondStart = 4 + atomCount;
+    for (let i = 0; i < bondCount; i++) {
+        const line = lines[bondStart + i];
+        if (line === undefined)
+            break;
+        bonds.push({
+            a1: Number.parseInt(line.slice(0, 3), 10),
+            a2: Number.parseInt(line.slice(3, 6), 10),
+            order: Number.parseInt(line.slice(6, 9), 10),
+        });
+    }
+    return { atomCount, bondCount, atoms, bonds };
+}
+//# sourceMappingURL=sdf-parser.js.map

package/dist/services/pubchem/sdf-parser.js.map ADDED Viewed

@@ -0,0 +1 @@

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package/dist/services/pubchem/types.d.ts CHANGED Viewed

@@ -56,6 +56,15 @@ export interface AssaySummaryTableResponse {
         }>;
     };
 }
+/** Conformer ID list for a compound */
+export interface ConformerListResponse {
+    InformationList: {
+        Information: Array<{
+            CID: number;
+            ConformerID: string[];
+        }>;
+    };
+}
 export interface PugViewResponse {
     Record: {
         RecordType: string;
@@ -120,6 +129,41 @@ export interface BioactivityRow {
     targetAccession?: string;
     targetGeneId?: number;
 }
+/** A single compound interaction entry (drug-drug, drug-food, or chemical-target). */
+export interface InteractionEntry {
+    /** Interaction category. */
+    kind: 'drug-drug' | 'drug-food' | 'target';
+    /** Interacting compound, food, or target name as the source reports it. Absent for food
+     * interactions and any entry where the source carries no distinct partner. */
+    partner?: string;
+    /** Raw severity as the source reports it. Not normalized across sources, and frequently
+     * unset — most sources embed severity in the statement text rather than a discrete field. */
+    severity?: string;
+    /** Originating source (e.g. "DrugBank", "BindingDB"). */
+    source: string;
+    /** The interaction statement. */
+    text: string;
+}
+/** A single atom in a 3D conformer (Cartesian coordinates, Angstroms). */
+export interface Sdf3DAtom {
+    element: string;
+    x: number;
+    y: number;
+    z: number;
+}
+/** A single bond in a 3D conformer (1-based atom indices). */
+export interface Sdf3DBond {
+    a1: number;
+    a2: number;
+    order: number;
+}
+/** Parsed atoms and bonds from a V2000 SDF connection table. */
+export interface Sdf3DStructure {
+    atomCount: number;
+    atoms: Sdf3DAtom[];
+    bondCount: number;
+    bonds: Sdf3DBond[];
+}
 /** Pharmacological classification from PUG View */
 export interface CompoundClassification {
     /** ATC codes with hierarchical descriptions */

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package/dist/services/pubchem/types.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/manifest.json CHANGED Viewed

@@ -1,7 +1,7 @@
 {
   "manifest_version": "0.3",
   "name": "pubchem-mcp-server",
-  "version": "0.1.22",
+  "version": "0.2.0",
   "description": "Search PubChem compounds, properties, safety data, bioactivity, cross-references, and entity summaries via MCP.",
   "author": {
     "name": "cyanheads"

package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "@cyanheads/pubchem-mcp-server",
-  "version": "0.1.22",
+  "version": "0.2.0",
   "description": "MCP server for the PubChem chemical database. Search compounds, fetch properties, safety data, bioactivity, cross-references, and entity summaries. STDIO & Streamable HTTP.",
   "mcpName": "io.github.cyanheads/pubchem-mcp-server",
   "type": "module",
@@ -83,6 +83,6 @@
     "ignore": "^7.0.5",
     "tsc-alias": "^1.8.17",
     "typescript": "^6.0.3",
-    "vitest": "^4.1.7"
+    "vitest": "^4.1.8"
   }
 }

package/server.json CHANGED Viewed

@@ -6,7 +6,7 @@
     "url": "https://github.com/cyanheads/pubchem-mcp-server",
     "source": "github"
   },
-  "version": "0.1.22",
+  "version": "0.2.0",
   "remotes": [
     {
       "type": "streamable-http",
@@ -19,7 +19,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubchem-mcp-server",
       "runtimeHint": "bun",
-      "version": "0.1.22",
+      "version": "0.2.0",
       "packageArguments": [
         { "type": "positional", "value": "run" },
         { "type": "positional", "value": "start:stdio" }
@@ -42,7 +42,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubchem-mcp-server",
       "runtimeHint": "bun",
-      "version": "0.1.22",
+      "version": "0.2.0",
       "packageArguments": [
         { "type": "positional", "value": "run" },
         { "type": "positional", "value": "start:http" }