@cyanheads/pubchem-mcp-server 0.1.23 → 0.2.0

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

@@ -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

@@ -0,0 +1 @@
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package/dist/services/pubchem/types.d.ts

@@ -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 */

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

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

@@ -1 +1 @@
-{"version":3,"file":"types.js","sourceRoot":"","sources":["../../../src/services/pubchem/types.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAgJH,wEAAwE;AAExE,gDAAgD;AAChD,MAAM,CAAC,MAAM,mBAAmB,GAAG;IACjC,kBAAkB;IAClB,iBAAiB;IACjB,iBAAiB;IACjB,gBAAgB;IAChB,OAAO;IACP,UAAU;IACV,WAAW;IACX,OAAO;IACP,OAAO;IACP,WAAW;IACX,kBAAkB;IAClB,MAAM;IACN,YAAY;IACZ,QAAQ;IACR,iBAAiB;IACjB,oBAAoB;IACpB,oBAAoB;IACpB,gBAAgB;IAChB,kBAAkB;IAClB,iBAAiB;IACjB,wBAAwB;IACxB,0BAA0B;IAC1B,iBAAiB;IACjB,wBAAwB;IACxB,0BAA0B;IAC1B,mBAAmB;IACnB,UAAU;CACF,CAAC;AAEX,6CAA6C;AAC7C,MAAM,CAAC,MAAM,kBAAkB,GAAG;IAChC,kBAAkB;IAClB,iBAAiB;IACjB,WAAW;IACX,iBAAiB;IACjB,gBAAgB;IAChB,UAAU;IACV,OAAO;IACP,MAAM;IACN,iBAAiB;IACjB,oBAAoB;IACpB,oBAAoB;IACpB,gBAAgB;IAChB,QAAQ;IACR,YAAY;CACJ,CAAC;AAEX,sCAAsC;AACtC,MAAM,CAAC,MAAM,UAAU,GAAG;IACxB,YAAY;IACZ,IAAI;IACJ,UAAU;IACV,UAAU;IACV,QAAQ;IACR,WAAW;IACX,YAAY;CACJ,CAAC"}
+{"version":3,"file":"types.js","sourceRoot":"","sources":["../../../src/services/pubchem/types.ts"],"names":[],"mappings":"AAAA;;;GAGG;AA8LH,wEAAwE;AAExE,gDAAgD;AAChD,MAAM,CAAC,MAAM,mBAAmB,GAAG;IACjC,kBAAkB;IAClB,iBAAiB;IACjB,iBAAiB;IACjB,gBAAgB;IAChB,OAAO;IACP,UAAU;IACV,WAAW;IACX,OAAO;IACP,OAAO;IACP,WAAW;IACX,kBAAkB;IAClB,MAAM;IACN,YAAY;IACZ,QAAQ;IACR,iBAAiB;IACjB,oBAAoB;IACpB,oBAAoB;IACpB,gBAAgB;IAChB,kBAAkB;IAClB,iBAAiB;IACjB,wBAAwB;IACxB,0BAA0B;IAC1B,iBAAiB;IACjB,wBAAwB;IACxB,0BAA0B;IAC1B,mBAAmB;IACnB,UAAU;CACF,CAAC;AAEX,6CAA6C;AAC7C,MAAM,CAAC,MAAM,kBAAkB,GAAG;IAChC,kBAAkB;IAClB,iBAAiB;IACjB,WAAW;IACX,iBAAiB;IACjB,gBAAgB;IAChB,UAAU;IACV,OAAO;IACP,MAAM;IACN,iBAAiB;IACjB,oBAAoB;IACpB,oBAAoB;IACpB,gBAAgB;IAChB,QAAQ;IACR,YAAY;CACJ,CAAC;AAEX,sCAAsC;AACtC,MAAM,CAAC,MAAM,UAAU,GAAG;IACxB,YAAY;IACZ,IAAI;IACJ,UAAU;IACV,UAAU;IACV,QAAQ;IACR,WAAW;IACX,YAAY;CACJ,CAAC"}

package/manifest.json

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

@@ -1,6 +1,6 @@
 {
   "name": "@cyanheads/pubchem-mcp-server",
-  "version": "0.1.23",
+  "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",

package/server.json

@@ -6,7 +6,7 @@
     "url": "https://github.com/cyanheads/pubchem-mcp-server",
     "source": "github"
   },
-  "version": "0.1.23",
+  "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": "0.1.23",
+      "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": "0.1.23",
+      "version": "0.2.0",
       "packageArguments": [
         { "type": "positional", "value": "run" },
         { "type": "positional", "value": "start:http" }