# PubChem Scraper — Compounds, Properties & SMILES (`logiover/pubchem-scraper`) Actor Scrape PubChem by name, CID, or formula search. Extract molecular formula, weight, SMILES, InChIKey, IUPAC name, XLogP, and synonyms for drug discovery, cheminformatics, and research. No API key needed. - **URL**: https://apify.com/logiover/pubchem-scraper.md - **Developed by:** [Logiover](https://apify.com/logiover) (community) - **Categories:** Other - **Stats:** 2 total users, 1 monthly users, 100.0% runs succeeded, 0 bookmarks - **User rating**: No ratings yet ## Pricing from $1.50 / 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. Since this Actor supports Apify Store discounts, the price gets lower the higher subscription plan you have. Learn more: https://docs.apify.com/platform/actors/running/actors-in-store#pay-per-event ## What's an Apify Actor? Actors are a software tools running on the Apify platform, for all kinds of web data extraction and automation use cases. 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. In JavaScript/TypeScript projects, use official [JavaScript/TypeScript client](https://docs.apify.com/api/client/js.md): ```bash npm install apify-client ``` In Python projects, use official [Python client library](https://docs.apify.com/api/client/python.md): ```bash pip install apify-client ``` In shell scripts, use [Apify CLI](https://docs.apify.com/cli/docs.md): ````bash # MacOS / Linux curl -fsSL https://apify.com/install-cli.sh | bash # Windows irm https://apify.com/install-cli.ps1 | iex ```bash In AI frameworks, you might use the [Apify MCP server](https://docs.apify.com/platform/integrations/mcp.md). If your project is in a different language, use 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 — Compounds, Properties & SMILES Extract chemical compound data from PubChem in bulk — molecular formula, weight, SMILES, InChIKey, IUPAC name, XLogP, and synonyms. No API key or login required. ### What does PubChem Scraper do? PubChem Scraper connects to the official NCBI PubChem PUG REST API (`pubchem.ncbi.nlm.nih.gov/rest/pug`) — a free, keyless government endpoint — and retrieves structured chemical compound records in bulk. You can look up compounds by common name (e.g., "aspirin"), by PubChem CID (numeric identifier), or by keyword search that returns all matching compounds. For each compound, the actor fetches properties from the `/compound/.../property/` endpoint and synonyms from the `/compound/.../synonyms/` endpoint. Requests are throttled to ≤5 concurrent calls to respect NCBI's politeness policy. Results are streamed to an Apify dataset as they arrive, so you can start using data while the run continues. Runs of 1,000+ compounds are fully supported. ### Who is it for? - **Cheminformatics researchers** who need to build local compound databases from CID lists or drug name lists. - **Drug discovery teams** looking for bulk property data (logP, formula, SMILES) without manually browsing PubChem's UI. - **Chemistry educators and students** who want to programmatically retrieve compound data for reports, visualisations, or lab prep. - **Regulatory and compliance analysts** who cross-reference ingredient lists against PubChem identifiers and InChIKeys. - **Data engineers and scientists** building chemical knowledge graphs, ML training sets, or similarity pipelines that need SMILES strings at scale. ### Use cases - **Drug pipeline screening**: upload 500 candidate CIDs and extract SMILES + XLogP in one run for Lipinski rule-of-five filtering. - **Ingredient label auditing**: input a list of ingredient names from a cosmetics or food product and retrieve canonical identifiers (InChIKey) for regulatory cross-referencing. - **Chemistry homework / teaching**: fetch molecular formulas and IUPAC names for an entire curriculum compound list with a single API input. - **Chemical similarity search prep**: extract CanonicalSMILES for a set of scaffolds to feed into RDKit or other cheminformatics pipelines. - **Synonym enrichment**: look up trade names, CAS numbers, and other synonyms for compounds in your product catalogue. ### Why use PubChem Scraper? - **100% keyless** — uses the public NCBI PubChem PUG REST API; no account or API key needed. - **10 fields per compound** — CID, name, IUPAC name, molecular formula, molecular weight, SMILES, InChIKey, XLogP, synonyms, PubChem URL. - **Bulk-ready** — process thousands of names or CIDs in a single run; search mode auto-expands to up to 10,000 results. - **Three lookup modes** — byName, byCid, and keyword search for maximum flexibility. - **Polite & reliable** — respects NCBI's rate limits, retries transient errors, and handles 404 (not found) gracefully per compound. - **Export to CSV / JSON / Excel / JSONL** — Apify dataset supports all formats out of the box; results are available via API or the Apify console. ### What data can you extract? #### Output fields | Field | Type | Description | |---|---|---| | `cid` | string | PubChem Compound ID (e.g., "2244") | | `name` | string | Input name or CID used to look up this compound | | `iupacName` | string | Official IUPAC name (e.g., "2-acetyloxybenzoic acid") | | `molecularFormula` | string | Hill notation formula (e.g., "C9H8O4") | | `molecularWeight` | string | Monoisotopic molecular weight in g/mol | | `canonicalSMILES` | string | Canonical SMILES string for structure representation | | `inchiKey` | string | IUPAC InChIKey hash for exact compound identification | | `xlogp` | string | Computed XLogP (octanol-water partition coefficient) | | `synonyms` | string | Semicolon-separated list of up to 10 synonyms / trade names | | `pubchemUrl` | string | Direct PubChem compound page URL | #### JSON output example ```json { "cid": "2244", "name": "aspirin", "iupacName": "2-acetyloxybenzoic acid", "molecularFormula": "C9H8O4", "molecularWeight": "180.2", "canonicalSMILES": "CC(=O)Oc1ccccc1C(=O)O", "inchiKey": "BSYNRYMUTXBXSQ-UHFFFAOYSA-N", "xlogp": "1.2", "synonyms": "Aspirin; acetylsalicylic acid; Ecotrin; Bayer Aspirin; Disprin; 2-acetoxybenzoic acid; ASA; Aspro; Anacin; Entrophen", "pubchemUrl": "https://pubchem.ncbi.nlm.nih.gov/compound/2244" } ```` ### How to use #### Option A — Look up by name (byName) Provide a list of chemical names. The actor resolves each name to a PubChem CID and fetches full properties. **Steps:** 1. Set `mode` to `byName`. 2. Add one or more chemical names to the `names` array. 3. Click **Start** and wait for results in the **Dataset** tab. **Input example:** ```json { "mode": "byName", "names": ["aspirin", "caffeine", "ibuprofen", "glucose", "paracetamol"], "proxyConfiguration": { "useApifyProxy": true } } ``` #### Option B — Look up by CID (byCid) Use this when you already have PubChem Compound IDs from another pipeline. **Steps:** 1. Set `mode` to `byCid`. 2. Provide one or more numeric CIDs in the `cids` array. **Input example:** ```json { "mode": "byCid", "cids": ["2244", "2519", "3672", "5793", "1983"] } ``` #### Option C — Keyword search (search) Search PubChem for all compounds matching a keyword. Great for exploring a chemical family (e.g., "penicillin", "vitamin"). **Steps:** 1. Set `mode` to `search`. 2. Set `searchQuery` to your keyword. 3. Optionally set `maxResults` to limit how many matching CIDs to process. **Input example:** ```json { "mode": "search", "searchQuery": "penicillin", "maxResults": 50, "proxyConfiguration": { "useApifyProxy": true } } ``` ### Input parameters | Parameter | Type | Default | Description | |---|---|---|---| | `mode` | string | `byName` | Lookup mode: `byName`, `byCid`, or `search` | | `names` | array | `[]` | List of chemical names (byName mode) | | `cids` | array | `[]` | List of PubChem CIDs as strings (byCid mode) | | `searchQuery` | string | — | Keyword for compound search (search mode) | | `maxResults` | integer | 100 | Max compounds to return (search mode) | | `proxyConfiguration` | object | — | Apify proxy config (optional; datacenter is sufficient) | **Full input JSON:** ```json { "mode": "byName", "names": ["aspirin", "caffeine"], "cids": [], "searchQuery": "", "maxResults": 100, "proxyConfiguration": { "useApifyProxy": true } } ``` ### Output example ```json { "cid": "2519", "name": "caffeine", "iupacName": "1,3,7-trimethylpurine-2,6-dione", "molecularFormula": "C8H10N4O2", "molecularWeight": "194.2", "canonicalSMILES": "Cn1cnc2c1c(=O)n(c(=O)n2C)C", "inchiKey": "RYYVLZVUVIJVGH-UHFFFAOYSA-N", "xlogp": "-0.1", "synonyms": "Caffeine; 1,3,7-trimethylxanthine; Guaranine; Mateina; Methyltheobromine; Theine; Coffeine; Koffein; Cafeina; No-Doz", "pubchemUrl": "https://pubchem.ncbi.nlm.nih.gov/compound/2519" } ``` ### Tips for best results - **Use official names or common drug names** in byName mode — PubChem resolves synonyms, trade names, and CAS numbers automatically. - **Prefer byCid when you have CID lists** — it skips the name-resolution step and is faster. - **For broad families** (e.g., "steroid", "antibiotic"), use search mode with `maxResults` ≤ 500 to keep run time manageable. - **Datacenter proxy is sufficient** — PubChem is an open government API and does not block datacenter IPs; residential proxy is unnecessary. - **XLogP may be null** for inorganic compounds or salts — this is expected and not an error. - **Synonyms list is capped at 10 entries** — full synonym lists can have hundreds of entries; the top 10 are the most useful. - **IUPAC name may be long** — for polymers and complex molecules, the IUPAC name can exceed 200 characters; store in a text column. - **Respect NCBI's fair-use policy** — this actor throttles to ≤5 concurrent requests and 200 ms delay between calls. - **Export to Google Sheets** using the integration below for collaborative review of compound libraries. - **Combine with Apify schedules** to refresh compound databases automatically (e.g., weekly NDA ingredient cross-check). ### Integrations - **Google Sheets** — connect via Apify's Google Sheets integration; each run appends new compound rows automatically. - **Slack** — configure a Webhook to notify your team when a bulk compound run completes. - **Zapier / Make** — trigger downstream workflows (e.g., send a CSV to Dropbox, create a Jira ticket) when new compounds are scraped. - **Webhooks** — Apify supports run-completion webhooks; POST results to your own endpoint in real time. - **Schedule** — run the actor on a cron schedule (daily, weekly) to keep your chemical database fresh. ### API usage #### cURL ```bash curl -X POST \ "https://api.apify.com/v2/acts/logiover~pubchem-scraper/runs?token=YOUR_TOKEN" \ -H "Content-Type: application/json" \ -d '{"mode":"byName","names":["aspirin","caffeine"]}' ``` #### Node.js ```js import { ApifyClient } from 'apify-client'; const client = new ApifyClient({ token: 'YOUR_TOKEN' }); const run = await client.actor('logiover/pubchem-scraper').call({ mode: 'byName', names: ['aspirin', 'caffeine', 'ibuprofen'], }); const { items } = await client.dataset(run.defaultDatasetId).listItems(); console.log(items); ``` #### Python ```python from apify_client import ApifyClient client = ApifyClient("YOUR_TOKEN") run = client.actor("logiover/pubchem-scraper").call(run_input={ "mode": "byName", "names": ["aspirin", "caffeine", "ibuprofen"], }) for item in client.dataset(run["defaultDatasetId"]).iterate_items(): print(item["molecularFormula"], item["canonicalSMILES"]) ``` ### Use with AI agents (MCP) PubChem Scraper is compatible with Apify's MCP (Model Context Protocol) server, allowing AI agents to retrieve chemical data on demand. Connect Claude, GPT, or any MCP-compatible agent to Apify and use a prompt like: *"Use the PubChem scraper to look up the molecular formula, SMILES, and XLogP for aspirin, ibuprofen, and paracetamol, then export the results to a CSV."* The agent handles input construction, run polling, and dataset retrieval automatically. ### FAQ #### Is an API key required? No. PubChem Scraper uses the official NCBI PubChem PUG REST API (`pubchem.ncbi.nlm.nih.gov/rest/pug`), which is fully public and keyless. No account registration is needed. #### How many compounds can I scrape in one run? Practically unlimited for byName and byCid modes — just provide your full list. For search mode, set `maxResults` up to 10,000. Large runs of 1,000+ compounds typically complete within 10–20 minutes. #### What are the rate limits? NCBI requests a maximum of 5 requests per second from any single source. This actor throttles to ≤5 concurrent requests with a 200 ms inter-request delay to stay within limits. Transient errors are retried up to 3 times with exponential back-off. #### What if a compound returns zero results? If a name is misspelled or not indexed in PubChem, the actor logs a warning and continues with the next compound. The missing compound will not appear in the dataset. Check the actor logs for "No CIDs found for name:" messages. #### Why are some fields null? Some properties (especially `xlogp` and `iupacName`) may be absent for inorganic compounds, salts, or newly added compounds without full computational data. Null fields are expected and not errors. #### Can I export results to Excel? Yes. Open your dataset in the Apify console and click **Export** → **Excel (XLSX)**. You can also export to CSV, JSON, JSONL, or XML. #### How fast is the scraper? With concurrency ≤5 and NCBI's politeness delay, expect roughly 10–15 compounds per minute. A 1,000-compound run takes approximately 70–100 minutes. byCid mode is faster than byName because it skips the name-resolution step. #### Is the data up to date? PubChem is updated continuously. This actor fetches live data from the API on every run, so results reflect the current state of the PubChem database. #### Is scraping PubChem legal? PubChem is a public database operated by the US National Institutes of Health (NIH). Its data is freely available under a public-domain licence. The PUG REST API is designed for programmatic access. This actor respects NCBI's fair-use policy and does not scrape HTML pages or circumvent any access controls. Always review NCBI's usage policies for your specific use case. #### How often should I run it? For drug pipeline monitoring or ingredient database maintenance, a weekly schedule is typically sufficient. PubChem's chemical properties rarely change; new compounds and updated records are added continuously. Use Apify Schedules to automate this. #### What is XLogP? XLogP is a computed estimate of the octanol-water partition coefficient (log P), a key parameter in drug-likeness assessment (Lipinski's rule of five). Higher values indicate more lipophilic (fat-soluble) compounds; lower values indicate more hydrophilic compounds. Oral drugs typically have XLogP between −2 and 5. #### Can I use this with a Jupyter notebook? Yes. Use the Apify Python client (`pip install apify-client`) to start a run and fetch results directly into a pandas DataFrame for cheminformatics analysis. ### Is it legal? PubChem is a free, public database provided by the US National Center for Biotechnology Information (NCBI), part of the National Institutes of Health. All data is in the public domain and explicitly designed for bulk programmatic access via the PUG REST API. This actor does not bypass any authentication, does not scrape private data, and respects NCBI's rate-limit guidelines. No personal data is collected or processed. Use of this actor is your responsibility — verify compliance with your institution's data policies and any downstream regulatory requirements for the chemical data you collect. ### Related scrapers - **[LinkedIn Company Scraper](https://apify.com/logiover/linkedin-company-scraper)** — extract company profiles for drug company intelligence. - **[B2B Lead Scraper](https://apify.com/logiover/b2b-lead-scraper)** — find pharma and biotech companies by country and sector. - **[GitHub Activity Scraper](https://apify.com/logiover/github-activity-scraper)** — monitor cheminformatics and bioinformatics open-source repositories. - **[CVE Advisory Scraper](https://apify.com/logiover/cve-advisory-scraper)** — track security advisories for chemical data management software. # Actor input Schema ## `mode` (type: `string`): How to look up compounds: By Name (list of chemical names), By CID (list of PubChem CIDs), or Search / Keyword (name keyword returning multiple CIDs). ## `names` (type: `array`): List of chemical names to look up (used when mode = By Name). Leave empty to browse popular compounds. Example: \["aspirin", "caffeine"]. ## `cids` (type: `array`): List of numeric PubChem Compound IDs to look up (used when mode = By CID). Example: \[2244, 2519]. ## `searchQuery` (type: `string`): Keyword or partial name for compound search (used when mode = Search / Keyword). Example: "acetaminophen" or "vitamin". ## `maxResults` (type: `integer`): Maximum number of compounds to return. Applies to search mode (name list / CID list are processed in full unless very large). ## `proxyConfiguration` (type: `object`): Proxy settings. PubChem is an open government API; Automatic Apify Proxy (AUTO) is recommended and a direct connection is used as a final fallback. ## Actor input object example ```json { "mode": "byName", "names": [ "aspirin", "caffeine", "glucose", "ibuprofen", "acetaminophen", "dopamine", "serotonin", "melatonin", "testosterone", "estradiol", "cortisol", "cholesterol", "adrenaline", "ascorbic acid", "penicillin", "morphine", "nicotine", "ethanol", "benzene", "acetone", "formaldehyde", "toluene", "chloroform", "methanol", "water" ], "maxResults": 200, "proxyConfiguration": { "useApifyProxy": true } } ``` # Actor output Schema ## `results` (type: `string`): All records extracted by this run. Open the Dataset tab to browse, filter, and export as CSV, JSON, or Excel. # 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 '' with your token const client = new ApifyClient({ token: '', }); // Prepare Actor input const input = { "names": [ "aspirin", "caffeine", "glucose", "ibuprofen", "acetaminophen", "dopamine", "serotonin", "melatonin", "testosterone", "estradiol", "cortisol", "cholesterol", "adrenaline", "ascorbic acid", "penicillin", "morphine", "nicotine", "ethanol", "benzene", "acetone", "formaldehyde", "toluene", "chloroform", "methanol", "water" ], "proxyConfiguration": { "useApifyProxy": true } }; // Run the Actor and wait for it to finish const run = await client.actor("logiover/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 '' with your token. client = ApifyClient("") # Prepare the Actor input run_input = { "names": [ "aspirin", "caffeine", "glucose", "ibuprofen", "acetaminophen", "dopamine", "serotonin", "melatonin", "testosterone", "estradiol", "cortisol", "cholesterol", "adrenaline", "ascorbic acid", "penicillin", "morphine", "nicotine", "ethanol", "benzene", "acetone", "formaldehyde", "toluene", "chloroform", "methanol", "water", ], "proxyConfiguration": { "useApifyProxy": True }, } # Run the Actor and wait for it to finish run = client.actor("logiover/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", "glucose", "ibuprofen", "acetaminophen", "dopamine", "serotonin", "melatonin", "testosterone", "estradiol", "cortisol", "cholesterol", "adrenaline", "ascorbic acid", "penicillin", "morphine", "nicotine", "ethanol", "benzene", "acetone", "formaldehyde", "toluene", "chloroform", "methanol", "water" ], "proxyConfiguration": { "useApifyProxy": true } }' | apify call logiover/pubchem-scraper --silent --output-dataset ``` ## MCP server setup ```json { "mcpServers": { "apify": { "command": "npx", "args": [ "mcp-remote", "https://mcp.apify.com/?tools=logiover/pubchem-scraper", "--header", "Authorization: Bearer " ] } } } ``` ## OpenAPI specification ```json { "openapi": "3.0.1", "info": { "title": "PubChem Scraper — Compounds, Properties & SMILES", "description": "Scrape PubChem by name, CID, or formula search. Extract molecular formula, weight, SMILES, InChIKey, IUPAC name, XLogP, and synonyms for drug discovery, cheminformatics, and research. No API key needed.", "version": "1.0", "x-build-id": "Uc1zwLZ7nMX3j7GK0" }, "servers": [ { "url": "https://api.apify.com/v2" } ], "paths": { "/acts/logiover~pubchem-scraper/run-sync-get-dataset-items": { "post": { "operationId": "run-sync-get-dataset-items-logiover-pubchem-scraper", "x-openai-isConsequential": false, "summary": "Executes an Actor, waits for its completion, and returns Actor's dataset items in response.", "tags": [ "Run Actor" ], "requestBody": { "required": true, "content": { "application/json": { "schema": { "$ref": "#/components/schemas/inputSchema" } } } }, "parameters": [ { "name": "token", "in": "query", "required": true, "schema": { "type": "string" }, "description": "Enter your Apify token here" } ], "responses": { "200": { "description": "OK" } } } }, "/acts/logiover~pubchem-scraper/runs": { "post": { "operationId": "runs-sync-logiover-pubchem-scraper", "x-openai-isConsequential": false, "summary": "Executes an Actor and returns information about the initiated run in response.", "tags": [ "Run Actor" ], "requestBody": { "required": true, "content": { "application/json": { "schema": { "$ref": "#/components/schemas/inputSchema" } } } }, "parameters": [ { "name": "token", "in": "query", "required": true, "schema": { "type": "string" }, "description": "Enter your Apify token here" } ], "responses": { "200": { "description": "OK", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/runsResponseSchema" } } } } } } }, "/acts/logiover~pubchem-scraper/run-sync": { "post": { "operationId": "run-sync-logiover-pubchem-scraper", "x-openai-isConsequential": false, "summary": "Executes an Actor, waits for completion, and returns the OUTPUT from Key-value store in response.", "tags": [ "Run Actor" ], "requestBody": { "required": true, "content": { "application/json": { "schema": { "$ref": "#/components/schemas/inputSchema" } } } }, "parameters": [ { "name": "token", "in": "query", "required": true, "schema": { "type": "string" }, "description": "Enter your Apify token here" } ], "responses": { "200": { "description": "OK" } } } } }, "components": { "schemas": { "inputSchema": { "type": "object", "properties": { "mode": { "title": "Search mode", "enum": [ "byName", "byCid", "search" ], "type": "string", "description": "How to look up compounds: By Name (list of chemical names), By CID (list of PubChem CIDs), or Search / Keyword (name keyword returning multiple CIDs).", "default": "byName" }, "names": { "title": "Chemical names", "type": "array", "description": "List of chemical names to look up (used when mode = By Name). Leave empty to browse popular compounds. Example: [\"aspirin\", \"caffeine\"].", "items": { "type": "string" } }, "cids": { "title": "PubChem CIDs", "type": "array", "description": "List of numeric PubChem Compound IDs to look up (used when mode = By CID). Example: [2244, 2519].", "items": { "type": "string" } }, "searchQuery": { "title": "Search query", "type": "string", "description": "Keyword or partial name for compound search (used when mode = Search / Keyword). Example: \"acetaminophen\" or \"vitamin\"." }, "maxResults": { "title": "Max results", "minimum": 1, "maximum": 10000, "type": "integer", "description": "Maximum number of compounds to return. Applies to search mode (name list / CID list are processed in full unless very large).", "default": 200 }, "proxyConfiguration": { "title": "Proxy configuration", "type": "object", "description": "Proxy settings. 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