# PubChem Scraper — Chemical Compound Data (`ponderable_hydrometer/pubchem-scraper`) Actor

Look up chemical compounds from PubChem by name or CID — formula, weight, SMILES, InChI, IUPAC name, logP, TPSA & synonyms. Free keyless API. For chem, pharma & research.

- **URL**: https://apify.com/ponderable\_hydrometer/pubchem-scraper.md
- **Developed by:** [Ponderable Hydrometer](https://apify.com/ponderable_hydrometer) (community)
- **Categories:** Developer tools, Automation, SEO tools
- **Stats:** 2 total users, 1 monthly users, 100.0% runs succeeded, 0 bookmarks
- **User rating**: No ratings yet

## Pricing

from $2.00 / 1,000 results

This Actor is paid per event. You are not charged for the Apify platform usage, but only a fixed price for specific events.

Learn more: https://docs.apify.com/platform/actors/running/actors-in-store#pay-per-event

## What's an Apify Actor?

Actors are web data automations that power AI and operations. They run on the Apify platform to scrape websites, process data, connect APIs, and automate workflows.
In Batch mode, an Actor accepts a well-defined JSON input, performs an action which can take anything from a few seconds to a few hours,
and optionally produces a well-defined JSON output, datasets with results, or files in key-value store.
In Standby mode, an Actor provides a web server which can be used as a website, API, or an MCP server.
Actors are written with capital "A".

## How to integrate an Actor?

If asked about integration, you help developers integrate Actors into their projects.
You adapt to their stack and deliver integrations that are safe, well-documented, and production-ready.
The best way to integrate Actors is as follows.

- **AI agents and MCP clients** — the [Apify MCP server](https://docs.apify.com/integrations/mcp.md) at `https://mcp.apify.com` (remote, streamable HTTP, OAuth on first use).
- **Agentic workflows and local Actor development** — [Agent Skills](https://apify.com/.well-known/agent-skills/index.json) with the [Apify CLI](https://docs.apify.com/cli/docs.md): `npm install -g apify-cli`, then `apify login`.
- **JavaScript/TypeScript projects** — the official [JS/TS client](https://docs.apify.com/api/client/js/docs.md): `npm install apify-client`.
- **Python projects** — the official [Python client](https://docs.apify.com/api/client/python/docs.md): `pip install apify-client`.
- **Any other language** — the [REST API](https://docs.apify.com/api/v2.md).

For usage examples, see the [API](#api) section below.

For more details, see Apify documentation as [Markdown index](https://docs.apify.com/llms.txt) and [Markdown full-text](https://docs.apify.com/llms-full.txt).

# README

## PubChem Scraper — Chemical Compound Data

**Structured chemical compound data from PubChem — molecular properties and standard identifiers — by name or CID, batched.** Formula, weight, SMILES, InChI/InChIKey, IUPAC name, XLogP, TPSA, H-bond counts and more. Free, keyless, no proxies.

Built on PubChem's official **PUG REST** API. Pass plain names (`"aspirin"`) and get the canonical property keys chemists expect (`SMILES`, `InChIKey`, `IUPACName`) verbatim, ready to join into any cheminformatics pipeline.

### What you get

One row per compound. Default property set:

- `cid` (PubChem Compound ID) and canonical `url`
- **Identity** — `Title`, `MolecularFormula`, `MolecularWeight`, `IUPACName`
- **Structure keys** — `SMILES`, `InChI`, `InChIKey`
- **Descriptors** — `XLogP`, `TPSA`, `Charge`, `HBondDonorCount`, `HBondAcceptorCount`, `RotatableBondCount`, `HeavyAtomCount`
- **Synonyms** (optional) — common names/aliases per compound
- Override the property list to request any PubChem property (e.g. `Complexity`)

### Output sample

```json
{
  "cid": 2244,
  "Title": "Aspirin",
  "MolecularFormula": "C9H8O4",
  "MolecularWeight": "180.16",
  "SMILES": "CC(=O)OC1=CC=CC=C1C(=O)O",
  "InChI": "InChI=1S/C9H8O4/c1-6(10)13-8-5-3-2-4-7(8)9(11)12/h2-5H,1H3,(H,11,12)",
  "InChIKey": "BSYNRYMUTXBXSQ-UHFFFAOYSA-N",
  "IUPACName": "2-acetyloxybenzoic acid",
  "XLogP": 1.2,
  "TPSA": 63.6,
  "Charge": 0,
  "HBondDonorCount": 1,
  "HBondAcceptorCount": 4,
  "RotatableBondCount": 3,
  "HeavyAtomCount": 13,
  "url": "https://pubchem.ncbi.nlm.nih.gov/compound/2244"
}
```

### Input

| Field | Type | Default | Description |
|-------|------|---------|-------------|
| `names` | array | `["aspirin","caffeine"]` | Chemical names to look up |
| `cids` | array | — | Specific PubChem Compound IDs |
| `properties` | array | (rich default) | Override which properties to return |
| `includeSynonyms` | boolean | `false` | Also fetch synonyms (extra request per compound) |
| `maxSynonyms` | integer | `20` | Cap synonyms per compound |
| `maxResultsPerName` | integer | `1` | How many matching CIDs to keep per name |

Provide `names` and/or `cids`.

### Example input

```json
{
  "names": ["aspirin", "ibuprofen", "paracetamol"],
  "includeSynonyms": true
}
```

Custom property set:

```json
{ "names": ["caffeine"], "properties": ["MolecularFormula", "MolecularWeight", "XLogP", "TPSA", "Complexity"] }
```

### Why this actor

- **Name-to-structure in one step** — resolves names to CIDs, then batches property lookups.
- **Standard identifiers** — SMILES / InChIKey / IUPACName kept verbatim for clean joins.
- **Keyless & rate-limit-aware** — PubChem's own API with throttling and backoff on 429/503.
- **Flexible** — pick your own property list or take the rich default.

### Pricing

Pay per result — **$2.00 per 1,000 results** (one compound = one result). No subscription or platform fees.

### Related actors

- **Food & Nutrition Scraper (Open Food Facts)** — ingredient and additive data for products.
- **USDA FoodData Scraper** — official nutrient database.
- **Semantic Scholar Scraper** — chemistry/pharma literature and citations.

### Notes

- Data is PubChem's official PUG REST API (NCBI); the actor throttles to stay under ~5 req/s and retries on 429/503.
- A name may map to several CIDs — use `maxResultsPerName` to control how many you keep.
- Not every property is populated for every compound (missing values are omitted/null).
- This actor is an independent tool, not affiliated with or endorsed by NCBI / PubChem.

# Actor input Schema

## `names` (type: `array`):

Chemical names to look up, e.g. \["aspirin","caffeine","glucose"].

## `cids` (type: `array`):

Specific PubChem Compound IDs, e.g. \["2244","2519"].

## `properties` (type: `array`):

PubChem property names to return. Leave empty for a rich default (formula, weight, SMILES, InChI, IUPACName, XLogP, TPSA, H-bond counts). Examples: MolecularFormula, MolecularWeight, SMILES, InChIKey, XLogP, TPSA, Complexity.

## `includeSynonyms` (type: `boolean`):

Also fetch common names/synonyms for each compound (extra request per compound).

## `maxSynonyms` (type: `integer`):

Cap on synonyms returned per compound.

## `maxResultsPerName` (type: `integer`):

How many matching compounds to keep per name (a name may map to several CIDs).

## Actor input object example

```json
{
  "names": [
    "aspirin",
    "caffeine"
  ],
  "includeSynonyms": false,
  "maxSynonyms": 20,
  "maxResultsPerName": 1
}
```

# API

You can run this Actor programmatically using our API. Below are code examples in JavaScript, Python, and CLI, as well as the OpenAPI specification and MCP server setup.

## JavaScript example

```javascript
import { ApifyClient } from 'apify-client';

// Initialize the ApifyClient with your Apify API token
// Replace the '<YOUR_API_TOKEN>' with your token
const client = new ApifyClient({
    token: '<YOUR_API_TOKEN>',
});

// Prepare Actor input
const input = {
    "names": [
        "aspirin",
        "caffeine"
    ]
};

// Run the Actor and wait for it to finish
const run = await client.actor("ponderable_hydrometer/pubchem-scraper").call(input);

// Fetch and print Actor results from the run's dataset (if any)
console.log('Results from dataset');
console.log(`💾 Check your data here: https://console.apify.com/storage/datasets/${run.defaultDatasetId}`);
const { items } = await client.dataset(run.defaultDatasetId).listItems();
items.forEach((item) => {
    console.dir(item);
});

// 📚 Want to learn more 📖? Go to → https://docs.apify.com/api/client/js/docs

```

## Python example

```python
from apify_client import ApifyClient

# Initialize the ApifyClient with your Apify API token
# Replace '<YOUR_API_TOKEN>' with your token.
client = ApifyClient("<YOUR_API_TOKEN>")

# Prepare the Actor input
run_input = { "names": [
        "aspirin",
        "caffeine",
    ] }

# Run the Actor and wait for it to finish
run = client.actor("ponderable_hydrometer/pubchem-scraper").call(run_input=run_input)

# Fetch and print Actor results from the run's dataset (if there are any)
print("💾 Check your data here: https://console.apify.com/storage/datasets/" + run["defaultDatasetId"])
for item in client.dataset(run["defaultDatasetId"]).iterate_items():
    print(item)

# 📚 Want to learn more 📖? Go to → https://docs.apify.com/api/client/python/docs/quick-start

```

## CLI example

```bash
echo '{
  "names": [
    "aspirin",
    "caffeine"
  ]
}' |
apify call ponderable_hydrometer/pubchem-scraper --silent --output-dataset

```

## MCP server setup

```json
{
    "mcpServers": {
        "apify": {
            "command": "npx",
            "args": [
                "mcp-remote",
                "https://mcp.apify.com/?tools=ponderable_hydrometer/pubchem-scraper",
                "--header",
                "Authorization: Bearer <YOUR_API_TOKEN>"
            ]
        }
    }
}

```

## OpenAPI specification

Download the OpenAPI definition: https://api.apify.com/v2/actors/48T5brNndz0F1UWdI/builds/Br550x4zfED906WE5/openapi.json