npm - @cyanheads/pubchem-mcp-server - Versions diffs - 0.1.23 → 0.2.1 - Mend

@cyanheads/pubchem-mcp-server 0.1.23 → 0.2.1

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

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

@@ -194,18 +194,23 @@ 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) {
+    /** Shared HTTP core: rate-limit, 30s timeout, retry once on 5xx and once on a transient
+     * network error, and surface a clean timeout message. Returns the ok Response; callers
+     * extract the body (JSON, bytes, or text). Centralizing this keeps every fetch variant on
+     * one resilience contract — the divergence that left fetchBinary without retry or a clean
+     * timeout message (#16) cannot recur. */
+    async fetchResponse(url, init) {
         for (let attempt = 0;; attempt++) {
             await this.rateLimiter.acquire();
             const controller = new AbortController();
             const timeoutId = setTimeout(() => controller.abort(), 30_000);
             try {
                 const response = await fetch(url, { ...init, signal: controller.signal });
-                if (response.ok) {
-                    return (await response.json());
-                }
+                if (response.ok)
+                    return response;
                 const text = await response.text();
                 const fault = parseFaultMessage(text) ?? text.slice(0, 300);
                 // Retry once on 5xx
@@ -238,26 +243,18 @@ export class PubChemClient {
             }
         }
     }
+    async fetchJson(url, init) {
+        const response = await this.fetchResponse(url, init);
+        return (await response.json());
+    }
     async fetchBinary(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.arrayBuffer();
-        }
-        finally {
-            clearTimeout(timeoutId);
-        }
+        const response = await this.fetchResponse(url);
+        return response.arrayBuffer();
+    }
+    /** Fetch a text/plain body (e.g. an SDF record). Non-2xx is classified and thrown. */
+    async fetchText(url) {
+        const response = await this.fetchResponse(url);
+        return response.text();
     }
     // ── CID Resolution ──────────────────────────────────────────────
     /** Fetch CID list, with automatic ListKey polling for async searches */
@@ -672,6 +669,177 @@ 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) {
+        // Per-kind isolation: a failure in one source (upstream parse error, timeout, network)
+        // must not discard the kinds that succeeded. Failures are reported, not thrown (#21).
+        const settled = await Promise.allSettled(kinds.map((kind) => this.getInteractionsForKind(cid, kind, maxEntries)));
+        const entries = [];
+        const failedKinds = [];
+        kinds.forEach((kind, i) => {
+            const result = settled[i];
+            if (result?.status === 'fulfilled') {
+                entries.push(...result.value);
+            }
+            else if (result?.status === 'rejected') {
+                const reason = result.reason;
+                failedKinds.push({
+                    kind,
+                    message: reason instanceof Error ? reason.message : String(reason),
+                });
+            }
+        });
+        return { entries, failedKinds };
+    }
+    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, ['cid', 'name2', 'descr'], 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;
+    }
+    /** Chemical-target binding/activity from PubChem's `bioactivity` SDQ collection (BindingDB,
+     * ChEMBL, and others). That collection is cid-keyed and scopes correctly to the requested
+     * compound; the `consolidatedcompoundtarget` collection used previously is gene-indexed, so
+     * its `cid` filter was silently ignored — every CID returned the same default compound (#20).
+     * Only rows naming a molecular target are returned; untargeted assay outcomes are the domain
+     * of pubchem_get_bioactivity. */
+    async getTargetInteractions(cid, maxEntries) {
+        // `targetname` is sparse (most rows are untargeted assay outcomes), so oversample and keep
+        // the target-bearing rows, most-potent-first.
+        const window = Math.min(Math.max(maxEntries * 4, 20), 100);
+        const rows = await this.fetchSdq('bioactivity', cid, ['cid', 'targetname', 'acname', 'acqualifier', 'acvalue', 'aidsrcname'], window, ['acvalue,asc']);
+        const entries = [];
+        for (const row of rows) {
+            const target = typeof row.targetname === 'string' ? row.targetname.trim() : '';
+            if (!target)
+                continue;
+            const acname = typeof row.acname === 'string' ? row.acname : '';
+            const qualifier = typeof row.acqualifier === 'string' ? row.acqualifier : '';
+            const acvalue = row.acvalue == null ? '' : String(row.acvalue).trim();
+            // Faithful to the source: the bioactivity collection carries no unit column, so the raw
+            // activity value is surfaced without an asserted unit.
+            const activity = acname && acvalue ? `${acname} ${qualifier} ${acvalue}`.replace(/\s+/g, ' ').trim() : '';
+            entries.push({
+                kind: 'target',
+                source: typeof row.aidsrcname === 'string' && row.aidsrcname ? row.aidsrcname : 'PubChem',
+                partner: target,
+                text: activity || 'Activity reported',
+            });
+        }
+        // Collapse duplicate measurements of the same target/value reported across assays.
+        return dedupByKey(entries, (e) => `${e.partner ?? ''}|${e.text}`).slice(0, maxEntries);
+    }
+    async getDrugFoodInteractions(cid, maxEntries) {
+        try {
+            const data = await this.fetchJson(`${this.viewBase}/data/compound/${cid}/JSON?heading=Drug-Food+Interactions`);
+            const sections = data.Record.Section;
+            if (!sections)
+                return [];
+            const section = findSection(sections, 'Drug-Food Interactions');
+            if (!section)
+                return [];
+            const refToSource = new Map();
+            for (const ref of data.Record.Reference ?? []) {
+                refToSource.set(ref.ReferenceNumber, ref.SourceName);
+            }
+            const items = dedupByKey(extractDescriptionItems(section), descriptionKey);
+            return items.slice(0, maxEntries).map((item) => {
+                const source = item.refNum != null ? refToSource.get(item.refNum) : undefined;
+                return { kind: 'drug-food', source: source ?? 'PubChem', text: item.text };
+            });
+        }
+        catch (error) {
+            if (isNotFound(error))
+                return [];
+            throw error;
+        }
+    }
+    /** Query a PubChem SDQ external table for a single CID, projecting only the columns the
+     * caller maps. Projection keeps payloads small and excludes the free-text `citations` column
+     * whose unescaped quotes make PubChem emit invalid JSON (#20). Returns [] on not-found; on an
+     * unparseable body throws a contextful error rather than the bare `Failed to parse JSON`, so
+     * the caller and per-kind isolation can report it cleanly. */
+    async fetchSdq(collection, cid, columns, limit, order) {
+        const query = JSON.stringify({
+            download: columns,
+            collection,
+            where: { ands: [{ cid: String(cid) }] },
+            ...(order ? { order } : {}),
+            start: 1,
+            limit,
+        });
+        const url = `${this.sdqBase}?infmt=json&outfmt=json&query=${encodeURIComponent(query)}`;
+        let body;
+        try {
+            body = await this.fetchText(url);
+        }
+        catch (error) {
+            if (isNotFound(error))
+                return [];
+            throw error;
+        }
+        try {
+            const data = JSON.parse(body);
+            return Array.isArray(data) ? data : [];
+        }
+        catch {
+            throw new McpError(JsonRpcErrorCode.ServiceUnavailable, `PubChem SDQ returned unparseable JSON for collection "${collection}"`, { collection, cid, snippet: body.slice(0, 200) });
+        }
+    }
+    // ── 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

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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 @@
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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 +129,52 @@ 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;
+}
+/** Result of a multi-kind interaction fetch. Kinds are fetched independently so a failure in
+ * one (upstream parse error, timeout, network) never discards the kinds that succeeded. */
+export interface InteractionsResult {
+    /** Interaction entries across the kinds that resolved successfully. */
+    entries: InteractionEntry[];
+    /** Kinds whose fetch failed, with the failure message. Empty when every kind resolved. */
+    failedKinds: Array<{
+        kind: string;
+        message: 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 */

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

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package/manifest.json CHANGED Viewed

@@ -1,7 +1,7 @@
 {
   "manifest_version": "0.3",
   "name": "pubchem-mcp-server",
-  "version": "0.1.23",
+  "version": "0.2.1",
   "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": "0.1.23",
+  "version": "0.2.1",
   "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",

package/server.json CHANGED Viewed

@@ -6,7 +6,7 @@
     "url": "https://github.com/cyanheads/pubchem-mcp-server",
     "source": "github"
   },
-  "version": "0.1.23",
+  "version": "0.2.1",
   "remotes": [
     {
       "type": "streamable-http",
@@ -19,7 +19,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubchem-mcp-server",
       "runtimeHint": "bun",
-      "version": "0.1.23",
+      "version": "0.2.1",
       "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": "0.1.23",
+      "version": "0.2.1",
       "packageArguments": [
         { "type": "positional", "value": "run" },
         { "type": "positional", "value": "start:http" }