npm - @cyanheads/pubchem-mcp-server - Versions diffs - 0.5.1 → 0.6.0 - Mend

@cyanheads/pubchem-mcp-server 0.5.1 → 0.6.0

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Files changed (30) hide show

package/dist/mcp-server/tools/definitions/search-compounds.tool.js CHANGED Viewed

@@ -19,7 +19,7 @@ const queryTypeEnum = z.enum(['smiles', 'cid']);
 const propertyEnum = z.enum(COMPOUND_PROPERTIES);
 export const searchCompounds = tool('pubchem_search_compounds', {
     title: 'Search Compounds',
-    description: 'Search PubChem for chemical compounds by identifier (name, SMILES, or InChIKey, batched up to 25), molecular formula in Hill notation, substructure or superstructure containment, or 2D Tanimoto similarity. Optionally hydrate results with properties to avoid a follow-up pubchem_get_compound_details call.',
+    description: 'Search PubChem for chemical compounds by identifier (name, SMILES, or InChIKey, batched up to 25), molecular formula in Hill notation, substructure or superstructure containment, or 2D Tanimoto similarity. Returns a page of CIDs — reach matches past maxResults with offset. Optionally hydrate results with properties to avoid a follow-up pubchem_get_compound_details call.',
     annotations: {
         readOnlyHint: true,
         idempotentHint: true,
@@ -60,12 +60,20 @@ export const searchCompounds = tool('pubchem_search_compounds', {
             .max(100)
             .default(90)
             .describe('Similarity search only. Minimum Tanimoto similarity (70-100). 90+ for close analogs, 70-80 for scaffold hops. Default: 90.'),
+        offset: z
+            .number()
+            .int()
+            .min(0)
+            .max(10000)
+            .default(0)
+            .describe('Zero-based index of the first CID to return. Pass the nextOffset from a previous call to read the following page. Identifier lookups resolve every match up front, so paging them is free; formula, substructure, superstructure, and similarity searches have to ask PubChem for offset + maxResults records to reach a page, so deep pages cost progressively more upstream — hence the 10000 ceiling. Default: 0.'),
         maxResults: z
             .number()
+            .int()
             .min(1)
             .max(200)
             .default(20)
-            .describe('Maximum CIDs to return (1-200). Default: 20.'),
+            .describe('Maximum CIDs to return per page (1-200). Use offset to reach matches past this page. Default: 20.'),
         properties: z
             .array(propertyEnum)
             .optional()
@@ -92,8 +100,9 @@ export const searchCompounds = tool('pubchem_search_compounds', {
             .optional()
             .describe('Identifier-mode only: input identifiers that resolved to no CID. Omitted when every identifier resolved and for non-identifier searches.'),
     }),
-    // Agent-facing context — search strategy echo, total before cap, and an empty-result
-    // notice. Reaches structuredContent and content[] automatically; not in the domain return.
+    // Agent-facing context — search strategy echo, total, the page boundary, and a notice
+    // covering unresolved identifiers, an empty page, and further pages. Reaches
+    // structuredContent and content[] automatically; not in the domain return.
     //
     // Bounded-total convention: a reported total states only what the server actually
     // observed. `totalFound` carries a true count and appears only when the whole match set
@@ -108,21 +117,23 @@ export const searchCompounds = tool('pubchem_search_compounds', {
         totalFound: z
             .number()
             .optional()
-            .describe('Exact number of matching CIDs, before the maxResults cap. Omitted when a formula, substructure, superstructure, or similarity search filled its page — PubChem returns no match count for those, so totalFoundAtLeast reports a floor instead.'),
+            .describe('Exact number of matching CIDs across all pages. Omitted when a formula, substructure, superstructure, or similarity search saturated the records it requested — PubChem returns no match count for those, so totalFoundAtLeast reports a floor instead.'),
         totalFoundAtLeast: z
             .number()
             .optional()
-            .describe('Lower bound on matching CIDs, reported in place of totalFound when the exact count is unavailable. At least this many match, and the true total may be higher; raise maxResults to retrieve more.'),
-        truncated: z
-            .boolean()
+            .describe('Lower bound on matching CIDs, reported in place of totalFound when the exact count is unavailable. At least this many match, and the true total may be higher; page further with offset to observe more.'),
+        offset: z.number().describe('Zero-based index of the first CID returned.'),
+        nextOffset: z
+            .number()
             .optional()
-            .describe('True when CIDs were capped at maxResults — more matches exist than returned.'),
-        shown: z.number().optional().describe('CIDs returned after the maxResults cap.'),
+            .describe('Offset to pass on the next call to continue past this page. Omitted when no further matches remain.'),
+        truncated: z.boolean().optional().describe('True when matching CIDs remain past this page.'),
+        shown: z.number().optional().describe('CIDs returned on this page.'),
         cap: z.number().optional().describe('The maxResults cap that was applied.'),
         notice: z
             .string()
             .optional()
-            .describe('Recovery guidance when no compounds matched — echoes search strategy and suggests how to broaden. Absent when results were returned.'),
+            .describe('Recovery guidance when no compounds matched, when the offset runs past the matches observed, when identifiers failed to resolve, or when further pages remain. Absent when this page is complete and every identifier resolved.'),
     },
     errors: [
         {
@@ -153,10 +164,12 @@ export const searchCompounds = tool('pubchem_search_compounds', {
     async handler(input, ctx) {
         const client = getPubChemClient();
         let allCids = [];
-        // Formula and structure searches are bounded server-side. One record past the cap is
-        // enough to prove more matches exist without moving the rest of PubChem's match set,
-        // which for a common substructure runs to 16.3 MB of CIDs.
-        const recordCap = input.maxResults + 1;
+        // Formula and structure searches are bounded server-side. One record past the requested
+        // page is enough to prove more matches exist without moving the rest of PubChem's match
+        // set, which for a common substructure runs to 16.3 MB of CIDs. The window has to cover
+        // the offset too — these endpoints take a record count, not a start position, and their
+        // ordering is a stable prefix, so reaching page N means asking for everything up to it.
+        const recordCap = input.offset + input.maxResults + 1;
         let boundedSearch = false;
         const identifierMap = new Map();
         // Identifier-mode resolution tracking (#29): inputs that resolved to no CID, and
@@ -243,23 +256,33 @@ export const searchCompounds = tool('pubchem_search_compounds', {
                 break;
             }
         }
-        // Deduplicate and cap
+        // Deduplicate, then take the requested page.
         const uniqueCids = [...new Set(allCids)];
         const observedTotal = uniqueCids.length;
-        const cappedCids = uniqueCids.slice(0, input.maxResults);
+        const pagedCids = uniqueCids.slice(input.offset, input.offset + input.maxResults);
         // A bounded search that came back short of its cap returned everything PubChem had, so
         // the count is exact. A saturated one only proves a floor.
         const totalIsExact = !boundedSearch || allCids.length < recordCap;
+        // The stride comes from the page that was returned, never from maxResults — that input
+        // accepts a fractional value, which would emit a nextOffset this tool's own integer
+        // offset validator then rejects.
+        const nextOffset = input.offset + pagedCids.length;
+        // A saturated bounded search proved a record beyond the window it asked for, so more
+        // remain even though observedTotal cannot say how many.
+        const hasMore = !totalIsExact || nextOffset < observedTotal;
         ctx.log.info('Search completed', {
             searchType: input.searchType,
             observedTotal,
             totalIsExact,
-            returned: cappedCids.length,
+            offset: input.offset,
+            returned: pagedCids.length,
         });
-        // Agent-facing context: search strategy echo, total, and empty-result notice.
+        // Agent-facing context: search strategy echo, total, page boundary, and notices.
         ctx.enrich(totalIsExact
-            ? { searchType: input.searchType, totalFound: observedTotal }
-            : { searchType: input.searchType, totalFoundAtLeast: observedTotal });
+            ? { searchType: input.searchType, totalFound: observedTotal, offset: input.offset }
+            : { searchType: input.searchType, totalFoundAtLeast: observedTotal, offset: input.offset });
+        if (hasMore)
+            ctx.enrich({ nextOffset });
         // Identifier-mode signals (#29): name inputs that did not resolve and flag CID
         // collisions, so a partial miss is never silent. Empty for other search types.
         const noticeParts = [];
@@ -270,20 +293,30 @@ export const searchCompounds = tool('pubchem_search_compounds', {
         for (const c of collisions) {
             noticeParts.push(`Identifiers ${c.identifiers.join(', ')} all resolved to CID ${c.cid}; the result row echoes only "${identifierMap.get(c.cid)}" for it.`);
         }
-        if (cappedCids.length === 0) {
-            ctx.enrich.notice(noticeParts.length > 0
-                ? noticeParts.join(' ')
-                : `No compounds matched the ${input.searchType} search. Try a different identifier, broaden the formula, lower the similarity threshold, or verify the SMILES/CID.`);
+        if (pagedCids.length === 0) {
+            // An empty page is either "nothing matched" or "the offset ran past the matches" —
+            // say which, and name the bound the caller can page back inside.
+            if (observedTotal === 0) {
+                if (noticeParts.length === 0) {
+                    noticeParts.push(`No compounds matched the ${input.searchType} search. Try a different identifier, broaden the formula, lower the similarity threshold, or verify the SMILES/CID.`);
+                }
+            }
+            else {
+                // Reachable only with an exact total: a saturated bounded search observed
+                // offset + maxResults + 1 records, so its page is never empty.
+                noticeParts.push(`offset ${input.offset} is past the ${observedTotal} match(es) found. Pass an offset below ${observedTotal}.`);
+            }
+            ctx.enrich.notice(noticeParts.join(' '));
         }
-        else if (observedTotal > cappedCids.length) {
+        else if (hasMore) {
             // Truncated: fold any identifier notice into the truncation guidance (notice is
             // last-wins, so compose rather than emit two). Without an exact total there is no
-            // "of N" to quote — say more exist and stop.
+            // "of N" to quote — say more exist, and still hand over the next offset.
             const truncationGuidance = totalIsExact
-                ? `Showing ${cappedCids.length} of ${observedTotal} matches — raise maxResults (max 200) for more.`
-                : `Showing ${cappedCids.length} matches; more exist, but PubChem reports no match count for a ${input.searchType} search — raise maxResults (max 200) for more.`;
+                ? `Showing matches ${input.offset + 1}-${nextOffset} of ${observedTotal}. Pass offset=${nextOffset} for the next page.`
+                : `Showing matches ${input.offset + 1}-${nextOffset}; more exist, but PubChem reports no match count for a ${input.searchType} search. Pass offset=${nextOffset} for the next page.`;
             ctx.enrich.truncated({
-                shown: cappedCids.length,
+                shown: pagedCids.length,
                 cap: input.maxResults,
                 guidance: noticeParts.length > 0
                     ? `${noticeParts.join(' ')} ${truncationGuidance}`
@@ -295,11 +328,11 @@ export const searchCompounds = tool('pubchem_search_compounds', {
         }
         // Optionally hydrate with properties
         let propsMap;
-        if (input.properties && input.properties.length > 0 && cappedCids.length > 0) {
-            const rows = await client.getProperties(cappedCids, input.properties);
+        if (input.properties && input.properties.length > 0 && pagedCids.length > 0) {
+            const rows = await client.getProperties(pagedCids, input.properties);
             propsMap = new Map(rows.map((r) => [r.CID, r]));
         }
-        const results = cappedCids.map((cid) => {
+        const results = pagedCids.map((cid) => {
             const result = { cid };
             const identifier = identifierMap.get(cid);
             if (identifier)

package/dist/mcp-server/tools/definitions/search-compounds.tool.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/services/pubchem/pubchem-client.d.ts CHANGED Viewed

@@ -73,10 +73,11 @@ export declare class PubChemClient {
     searchAssaysByTarget(targetType: string, query: string): Promise<number[]>;
     getEntitySummary(entityType: string, identifier: string | number): Promise<Record<string, unknown> | null>;
     /** 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. */
-    getInteractions(cid: number, kinds: Array<'drug-drug' | 'drug-food' | 'target'>, maxEntries: number): Promise<InteractionsResult>;
+     * Drug-drug and target data live in PubChem SDQ external tables (drugbankddi, bioactivity);
+     * drug-food is inline PUG View text. Each kind reads a window of `maxEntries` entries
+     * starting at `offset` records into that kind's own stream; absent data for a kind
+     * contributes an empty page rather than erroring. */
+    getInteractions(cid: number, kinds: Array<'drug-drug' | 'drug-food' | 'target'>, maxEntries: number, offset: number): Promise<InteractionsResult>;
     private getInteractionsForKind;
     private getDrugDrugInteractions;
     /** Chemical-target binding/activity from PubChem's `bioactivity` SDQ collection (BindingDB,
@@ -84,15 +85,35 @@ export declare class PubChemClient {
      * 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. */
+     * of pubchem_get_bioactivity.
+     *
+     * Because most rows are dropped, the page position is an index into the activity records, not
+     * into the entries returned — the walk records exactly how many rows it read so the next page
+     * resumes at the first unread one. */
     private getTargetInteractions;
     private getDrugFoodInteractions;
     /** 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. */
+     * whose unescaped quotes make PubChem emit invalid JSON (#20).
+     *
+     * Uses SDQ's `select` projection rather than `download`: the `SDQOutputSet` envelope it
+     * answers with carries `totalCount` — the records matching the query across all pages —
+     * beside the requested window, which is the only way to tell a full page from the last one.
+     * `start` is 1-based upstream; `offset` here is zero-based like every other paging input.
+     *
+     * Returns an empty page on not-found. A rejected query is reported, never read as "no data":
+     * SDQ answers a malformed query with a 5xx that the shared HTTP core already classifies and
+     * throws, and the `status.error` check covers the same rejection arriving inside a 2xx body.
+     * An unparseable body throws with the collection and a body snippet attached, so per-kind
+     * isolation can name what failed. */
     private fetchSdq;
+    /** Resolve a kind's record total for the page just fetched.
+     *
+     * SDQ reports `totalCount` alongside every non-empty page, but a `start` past the last record
+     * answers `totalCount` 0 — so an offset that overshoots would otherwise report "no records"
+     * for a compound that has thousands. A one-row probe from the top recovers the real bound,
+     * and only runs on that case. */
+    private resolveSdqTotal;
     /** 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). */
     getSdf3d(cid: number): Promise<string>;

package/dist/services/pubchem/pubchem-client.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/services/pubchem/pubchem-client.js CHANGED Viewed

@@ -908,19 +908,25 @@ export class PubChemClient {
     }
     // ── 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) {
+     * Drug-drug and target data live in PubChem SDQ external tables (drugbankddi, bioactivity);
+     * drug-food is inline PUG View text. Each kind reads a window of `maxEntries` entries
+     * starting at `offset` records into that kind's own stream; absent data for a kind
+     * contributes an empty page rather than erroring. */
+    async getInteractions(cid, kinds, maxEntries, offset) {
         // 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)));
+        // Page state is recorded per kind from that kind's own result, so a failing kind leaves
+        // the others' continuation signals untouched rather than zeroing them.
+        const settled = await Promise.allSettled(kinds.map((kind) => this.getInteractionsForKind(cid, kind, maxEntries, offset)));
         const entries = [];
+        const pages = [];
         const failedKinds = [];
         kinds.forEach((kind, i) => {
             const result = settled[i];
             if (result?.status === 'fulfilled') {
-                entries.push(...result.value);
+                const { entries: kindEntries, totalRecords, recordsConsumed } = result.value;
+                entries.push(...kindEntries);
+                pages.push({ kind, returnedCount: kindEntries.length, totalRecords, recordsConsumed });
             }
             else if (result?.status === 'rejected') {
                 const reason = result.reason;
@@ -930,20 +936,20 @@ export class PubChemClient {
                 });
             }
         });
-        return { entries, failedKinds };
+        return { entries, pages, failedKinds };
     }
-    getInteractionsForKind(cid, kind, maxEntries) {
+    getInteractionsForKind(cid, kind, maxEntries, offset) {
         switch (kind) {
             case 'drug-drug':
-                return this.getDrugDrugInteractions(cid, maxEntries);
+                return this.getDrugDrugInteractions(cid, maxEntries, offset);
             case 'drug-food':
-                return this.getDrugFoodInteractions(cid, maxEntries);
+                return this.getDrugFoodInteractions(cid, maxEntries, offset);
             case 'target':
-                return this.getTargetInteractions(cid, maxEntries);
+                return this.getTargetInteractions(cid, maxEntries, offset);
         }
     }
-    async getDrugDrugInteractions(cid, maxEntries) {
-        const rows = await this.fetchSdq('drugbankddi', cid, ['cid', 'name2', 'descr'], maxEntries);
+    async getDrugDrugInteractions(cid, maxEntries, offset) {
+        const { rows, totalCount } = await this.fetchSdq('drugbankddi', cid, ['cid', 'name2', 'descr'], maxEntries, offset);
         const entries = [];
         for (const row of rows) {
             const text = typeof row.descr === 'string' ? row.descr : '';
@@ -954,21 +960,35 @@ export class PubChemClient {
                 entry.partner = row.name2;
             entries.push(entry);
         }
-        return entries;
+        return {
+            entries,
+            totalRecords: await this.resolveSdqTotal('drugbankddi', cid, rows.length, totalCount, offset),
+            recordsConsumed: rows.length,
+        };
     }
     /** 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) {
+     * of pubchem_get_bioactivity.
+     *
+     * Because most rows are dropped, the page position is an index into the activity records, not
+     * into the entries returned — the walk records exactly how many rows it read so the next page
+     * resumes at the first unread one. */
+    async getTargetInteractions(cid, maxEntries, offset) {
         // `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 { rows, totalCount } = await this.fetchSdq('bioactivity', cid, ['cid', 'targetname', 'acname', 'acqualifier', 'acvalue', 'aidsrcname'], window, offset, ['acvalue,asc']);
         const entries = [];
+        // Collapse duplicate measurements of the same target/value reported across assays.
+        const seen = new Set();
+        let recordsConsumed = 0;
         for (const row of rows) {
+            if (entries.length === maxEntries)
+                break;
+            recordsConsumed++;
             const target = typeof row.targetname === 'string' ? row.targetname.trim() : '';
             if (!target)
                 continue;
@@ -981,53 +1001,79 @@ export class PubChemClient {
             // assaysummary endpoint's "Activity Value [uM]" column. We assert that documented µM
             // convention here — it is not a per-row unit fetched from SDQ (none exists to fetch).
             const activity = acname && acvalue ? `${acname} ${qualifier} ${acvalue} uM`.replace(/\s+/g, ' ').trim() : '';
+            const text = activity || 'Activity reported';
+            const key = `${target}|${text}`;
+            if (seen.has(key))
+                continue;
+            seen.add(key);
             entries.push({
                 kind: 'target',
                 source: typeof row.aidsrcname === 'string' && row.aidsrcname ? row.aidsrcname : 'PubChem',
                 partner: target,
-                text: activity || 'Activity reported',
+                text,
             });
         }
-        // Collapse duplicate measurements of the same target/value reported across assays.
-        return dedupByKey(entries, (e) => `${e.partner ?? ''}|${e.text}`).slice(0, maxEntries);
+        return {
+            entries,
+            totalRecords: await this.resolveSdqTotal('bioactivity', cid, rows.length, totalCount, offset),
+            recordsConsumed,
+        };
     }
-    async getDrugFoodInteractions(cid, maxEntries) {
+    async getDrugFoodInteractions(cid, maxEntries, offset) {
+        const empty = { entries: [], totalRecords: 0, recordsConsumed: 0 };
         try {
             const data = await this.fetchJson(`${this.viewBase}/data/compound/${cid}/JSON?heading=Drug-Food+Interactions`);
             const sections = data.Record.Section;
             if (!sections)
-                return [];
+                return empty;
             const section = findSection(sections, 'Drug-Food Interactions');
             if (!section)
-                return [];
+                return empty;
             const refToSource = new Map();
             for (const ref of data.Record.Reference ?? []) {
                 refToSource.set(ref.ReferenceNumber, ref.SourceName);
             }
+            // PUG View returns the whole section inline, so the deduped item list is the complete
+            // record stream and the page is a plain slice of it.
             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 };
-            });
+            const page = items.slice(offset, offset + maxEntries);
+            return {
+                entries: page.map((item) => {
+                    const source = item.refNum != null ? refToSource.get(item.refNum) : undefined;
+                    return { kind: 'drug-food', source: source ?? 'PubChem', text: item.text };
+                }),
+                totalRecords: items.length,
+                recordsConsumed: page.length,
+            };
         }
         catch (error) {
             if (isNotFound(error))
-                return [];
+                return empty;
             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) {
+     * whose unescaped quotes make PubChem emit invalid JSON (#20).
+     *
+     * Uses SDQ's `select` projection rather than `download`: the `SDQOutputSet` envelope it
+     * answers with carries `totalCount` — the records matching the query across all pages —
+     * beside the requested window, which is the only way to tell a full page from the last one.
+     * `start` is 1-based upstream; `offset` here is zero-based like every other paging input.
+     *
+     * Returns an empty page on not-found. A rejected query is reported, never read as "no data":
+     * SDQ answers a malformed query with a 5xx that the shared HTTP core already classifies and
+     * throws, and the `status.error` check covers the same rejection arriving inside a 2xx body.
+     * An unparseable body throws with the collection and a body snippet attached, so per-kind
+     * isolation can name what failed. */
+    async fetchSdq(collection, cid, columns, limit, offset = 0, order) {
+        const empty = { rows: [], totalCount: 0 };
         const query = JSON.stringify({
-            download: columns,
+            select: columns,
             collection,
             where: { ands: [{ cid: String(cid) }] },
             ...(order ? { order } : {}),
-            start: 1,
+            start: offset + 1,
             limit,
         });
         const url = `${this.sdqBase}?infmt=json&outfmt=json&query=${encodeURIComponent(query)}`;
@@ -1037,16 +1083,35 @@ export class PubChemClient {
         }
         catch (error) {
             if (isNotFound(error))
-                return [];
+                return empty;
             throw error;
         }
+        let parsed;
         try {
-            const data = JSON.parse(body);
-            return Array.isArray(data) ? data : [];
+            parsed = JSON.parse(body);
         }
         catch {
             throw new McpError(JsonRpcErrorCode.ServiceUnavailable, `PubChem SDQ returned unparseable JSON for collection "${collection}"`, { collection, cid, snippet: body.slice(0, 200) });
         }
+        const set = parsed.SDQOutputSet?.[0];
+        if (!set)
+            return empty;
+        if (set.status?.error) {
+            throw new McpError(JsonRpcErrorCode.ServiceUnavailable, `PubChem SDQ rejected the query for collection "${collection}": ${set.status.error}`, { collection, cid, sdqError: set.status.error });
+        }
+        return { rows: set.rows ?? [], totalCount: set.totalCount ?? 0 };
+    }
+    /** Resolve a kind's record total for the page just fetched.
+     *
+     * SDQ reports `totalCount` alongside every non-empty page, but a `start` past the last record
+     * answers `totalCount` 0 — so an offset that overshoots would otherwise report "no records"
+     * for a compound that has thousands. A one-row probe from the top recovers the real bound,
+     * and only runs on that case. */
+    async resolveSdqTotal(collection, cid, rowsReturned, reportedTotal, offset) {
+        if (rowsReturned > 0 || offset === 0)
+            return reportedTotal;
+        const { totalCount } = await this.fetchSdq(collection, cid, ['cid'], 1);
+        return totalCount;
     }
     // ── 3D Structure ────────────────────────────────────────────────
     /** Fetch the default 3D conformer as raw V2000 SDF text. Throws a typed not-found when