pubchem-cli 0.1.0

package/README.md

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+# PubChem CLI
+
+PubChem in your terminal.
+
+`pubchem` is a JSON-first, agent-friendly CLI for compounds, substances, assays, references, PUG View browsing, raw PubChem/NCBI endpoints, resolution workflows, exports, and batch automation.
+
+The npm package ships prebuilt binaries for Linux, macOS, and Windows on `amd64` and `arm64`, so `npx pubchem-cli` works directly on common platforms.
+
+## Install
+
+Run without installing:
+
+```bash
+npx pubchem-cli --help
+```
+
+Global install:
+
+```bash
+npm install -g pubchem-cli
+```
+
+For local development in this repo:
+
+```bash
+go build -o ./pubchem ./cmd/pubchem
+./pubchem --help
+```
+
+## Usage
+
+```bash
+pubchem <command> [flags]
+```
+
+Root flags:
+
+- `--json`: Output JSON to stdout.
+- `--plain`: Output stable plain text to stdout.
+- `--results-only`: In JSON mode, emit only the primary result.
+- `--select`: In JSON mode, select comma-separated fields with dot-path support.
+- `--force`: Skip confirmations for future destructive commands.
+- `--no-input`: Never prompt; fail instead.
+- `--enable-commands`: Comma-separated list of enabled top-level commands.
+- `--version`: Print version and exit.
+- `--help`: Show context-sensitive help.
+
+Top-level command families:
+
+- `compound`
+- `substance`
+- `assay`
+- `entity`
+- `batch`
+- `refs`
+- `view`
+- `raw`
+- `resolve`
+- `identity`
+- `export`
+- `schema`
+- `agent`
+- `completion`
+
+## Examples
+
+Version:
+
+```bash
+$ pubchem --version
+pubchem dev
+```
+
+Compound search:
+
+```bash
+$ pubchem compound search aspirin --max 1
+{
+  "mode": "name",
+  "query": "aspirin",
+  "totalFound": 1,
+  "returned": 1,
+  "pageSize": 1,
+  "results": [
+    {
+      "cid": 2244,
+      "properties": {
+        "Charge": 0,
+        "Complexity": 212,
+        "ConnectivitySMILES": "CC(=O)OC1=CC=CC=C1C(=O)O",
+        "HBondAcceptorCount": 4,
+        "HBondDonorCount": 1,
+        "HeavyAtomCount": 13,
+        "IUPACName": "2-acetyloxybenzoic acid",
+        "InChIKey": "BSYNRYMUTXBXSQ-UHFFFAOYSA-N",
+        "MolecularFormula": "C9H8O4",
+        "MolecularWeight": "180.16",
+        "RotatableBondCount": 3,
+        "SMILES": "CC(=O)OC1=CC=CC=C1C(=O)O",
+        "TPSA": 63.6,
+        "XLogP": 1.2
+      }
+    }
+  ]
+}
+```
+
+3D structure metadata:
+
+```bash
+$ pubchem compound structure 2244 --record-type 3d --format json
+{
+  "recordType": "3d",
+  "downloadUrl": "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/2244/SDF?record_type=3d",
+  "results": [
+    {
+      "cid": 2244,
+      "structure": {
+        "title": "Aspirin",
+        "molecularFormula": "C9H8O4",
+        "molecularWeight": 180.16,
+        "inchiKey": "BSYNRYMUTXBXSQ-UHFFFAOYSA-N",
+        "has3d": true
+      }
+    }
+  ]
+}
+```
+
+For the full command tree and machine-readable schema, use:
+
+```bash
+pubchem --help
+pubchem schema
+```
+
+If you want the exact command and flag surface for automation, prefer `pubchem schema <command>` and `pubchem --help` over guessing from memory.

package/bin/pubchem.js

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+#!/usr/bin/env node
+
+const { spawn } = require("node:child_process");
+const { existsSync } = require("node:fs");
+const path = require("node:path");
+
+const TARGETS = {
+  linux: {
+    x64: "linux-amd64",
+    arm64: "linux-arm64",
+  },
+  darwin: {
+    x64: "darwin-amd64",
+    arm64: "darwin-arm64",
+  },
+  win32: {
+    x64: "windows-amd64",
+    arm64: "windows-arm64",
+  },
+};
+
+const platformTargets = TARGETS[process.platform];
+if (!platformTargets) {
+  throw new Error(`Unsupported platform: ${process.platform} (${process.arch})`);
+}
+
+const target = platformTargets[process.arch];
+if (!target) {
+  throw new Error(`Unsupported platform: ${process.platform} (${process.arch})`);
+}
+
+const binaryName = process.platform === "win32" ? "pubchem.exe" : "pubchem";
+const binaryPath = path.join(__dirname, "..", "vendor", target, "pubchem", binaryName);
+
+if (!existsSync(binaryPath)) {
+  throw new Error(
+    `Missing PubChem binary at ${binaryPath}.\n` +
+      "Reinstall with: npm install -g pubchem-cli",
+  );
+}
+
+const child = spawn(binaryPath, process.argv.slice(2), {
+  stdio: "inherit",
+});
+
+child.on("error", (err) => {
+  console.error(err);
+  process.exit(1);
+});
+
+const forwardSignal = (signal) => {
+  if (child.killed) {
+    return;
+  }
+
+  try {
+    child.kill(signal);
+  } catch {
+    // Ignore forwarding failures; the child exit handler will still finish cleanly.
+  }
+};
+
+["SIGINT", "SIGTERM", "SIGHUP"].forEach((signal) => {
+  process.on(signal, () => forwardSignal(signal));
+});
+
+child.on("exit", (code, signal) => {
+  if (signal) {
+    process.kill(process.pid, signal);
+    return;
+  }
+
+  process.exit(code ?? 1);
+});

package/package.json

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+{
+  "name": "pubchem-cli",
+  "version": "0.1.0",
+  "description": "PubChem in your terminal.",
+  "repository": {
+    "type": "git",
+    "url": "git+https://github.com/siddheshkothadi/pubchem-cli.git"
+  },
+  "bin": {
+    "pubchem": "bin/pubchem.js"
+  },
+  "files": [
+    "bin",
+    "vendor"
+  ],
+  "engines": {
+    "node": ">=16"
+  },
+  "publishConfig": {
+    "access": "public"
+  }
+}