# 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 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/docs.md): ```bash npm install apify-client ``` In Python projects, use official [Python client library](https://docs.apify.com/api/client/python/docs.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/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 — 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 '' with your token const client = new ApifyClient({ 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 '' with your token. client = ApifyClient("") # 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 " ] } } } ``` ## OpenAPI specification ```json { "openapi": "3.0.1", "info": { "title": "PubChem Scraper — Chemical Compound Data", "description": "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.", "version": "0.1", "x-build-id": "Br550x4zfED906WE5" }, "servers": [ { "url": "https://api.apify.com/v2" } ], "paths": { "/acts/ponderable_hydrometer~pubchem-scraper/run-sync-get-dataset-items": { "post": { "operationId": "run-sync-get-dataset-items-ponderable_hydrometer-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/ponderable_hydrometer~pubchem-scraper/runs": { "post": { "operationId": "runs-sync-ponderable_hydrometer-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/ponderable_hydrometer~pubchem-scraper/run-sync": { "post": { "operationId": "run-sync-ponderable_hydrometer-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": { "names": { "title": "Compound names", "type": "array", "description": "Chemical names to look up, e.g. [\"aspirin\",\"caffeine\",\"glucose\"].", "items": { "type": "string" } }, "cids": { "title": "PubChem CIDs", "type": "array", "description": "Specific PubChem Compound IDs, e.g. [\"2244\",\"2519\"].", "items": { "type": "string" } }, "properties": { "title": "Properties (override)", "type": "array", "description": "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.", "items": { "type": "string" } }, "includeSynonyms": { "title": "Include synonyms", "type": "boolean", "description": "Also fetch common names/synonyms for each compound (extra request per compound).", "default": false }, "maxSynonyms": { "title": "Max synonyms", "minimum": 1, "type": "integer", "description": "Cap on synonyms returned per compound.", "default": 20 }, "maxResultsPerName": { "title": "Max CIDs per name", "minimum": 1, "type": "integer", "description": "How many matching compounds to keep per name (a name may map to several CIDs).", "default": 1 } } }, "runsResponseSchema": { "type": "object", "properties": { "data": { "type": "object", "properties": { "id": { "type": "string" }, "actId": { "type": "string" }, "userId": { "type": "string" }, "startedAt": { "type": "string", "format": "date-time", "example": "2025-01-08T00:00:00.000Z" }, "finishedAt": { "type": "string", "format": "date-time", "example": "2025-01-08T00:00:00.000Z" }, "status": { "type": "string", "example": "READY" }, "meta": { "type": "object", "properties": { "origin": { "type": "string", "example": "API" }, "userAgent": { "type": "string" } } }, "stats": { "type": "object", "properties": { "inputBodyLen": { "type": "integer", "example": 2000 }, "rebootCount": { "type": "integer", "example": 0 }, "restartCount": { "type": "integer", "example": 0 }, "resurrectCount": { "type": "integer", "example": 0 }, "computeUnits": { "type": "integer", "example": 0 } } }, "options": { "type": "object", "properties": { "build": { "type": "string", "example": "latest" }, "timeoutSecs": { "type": "integer", "example": 300 }, "memoryMbytes": { "type": "integer", "example": 1024 }, "diskMbytes": { "type": "integer", "example": 2048 } } }, "buildId": { "type": "string" }, "defaultKeyValueStoreId": { "type": "string" }, "defaultDatasetId": { "type": "string" }, "defaultRequestQueueId": { "type": "string" }, "buildNumber": { "type": "string", "example": "1.0.0" }, "containerUrl": { "type": "string" }, "usage": { "type": "object", "properties": { "ACTOR_COMPUTE_UNITS": { "type": "integer", "example": 0 }, "DATASET_READS": { "type": "integer", "example": 0 }, "DATASET_WRITES": { "type": "integer", "example": 0 }, "KEY_VALUE_STORE_READS": { "type": "integer", "example": 0 }, "KEY_VALUE_STORE_WRITES": { "type": "integer", "example": 1 }, "KEY_VALUE_STORE_LISTS": { "type": "integer", "example": 0 }, "REQUEST_QUEUE_READS": { "type": "integer", "example": 0 }, "REQUEST_QUEUE_WRITES": { "type": "integer", "example": 0 }, "DATA_TRANSFER_INTERNAL_GBYTES": { "type": "integer", "example": 0 }, "DATA_TRANSFER_EXTERNAL_GBYTES": { "type": "integer", "example": 0 }, "PROXY_RESIDENTIAL_TRANSFER_GBYTES": { "type": "integer", "example": 0 }, "PROXY_SERPS": { "type": "integer", "example": 0 } } }, "usageTotalUsd": { "type": "number", "example": 0.00005 }, "usageUsd": { "type": "object", "properties": { "ACTOR_COMPUTE_UNITS": { "type": "integer", "example": 0 }, "DATASET_READS": { "type": "integer", "example": 0 }, "DATASET_WRITES": { "type": "integer", "example": 0 }, "KEY_VALUE_STORE_READS": { "type": "integer", "example": 0 }, "KEY_VALUE_STORE_WRITES": { "type": "number", "example": 0.00005 }, "KEY_VALUE_STORE_LISTS": { "type": "integer", "example": 0 }, "REQUEST_QUEUE_READS": { "type": "integer", "example": 0 }, "REQUEST_QUEUE_WRITES": { "type": "integer", "example": 0 }, "DATA_TRANSFER_INTERNAL_GBYTES": { "type": "integer", "example": 0 }, "DATA_TRANSFER_EXTERNAL_GBYTES": { "type": "integer", "example": 0 }, "PROXY_RESIDENTIAL_TRANSFER_GBYTES": { "type": "integer", "example": 0 }, "PROXY_SERPS": { "type": "integer", "example": 0 } } } } } } } } } } ```