chemistry.pubchem.structure
Look up a compound by name or identifier and get its chemical structure representations — SMILES (isomeric + canonical), InChI, InChIKey, molecular formula, and molecular weight. Convert between chemical identifier formats (PubChem / NCBI)
This record as markdown: /tools/io-github-whiteknightonhorse-apibase/chemistry.pubchem.structure.md
What chemistry.pubchem.structure does on Apibase
AI agents call chemistry.pubchem.structure to retrieve information from Apibase without modifying anything. It is typically the context-gathering step in research, monitoring, and reporting workflows, before the agent takes action elsewhere.
| Parameter | Type | Required | Description |
|---|---|---|---|
name | string | Yes | Compound name or identifier (e.g. "caffeine", "50-78-2") — returns SMILES, InChI, InChIKey, formula |
Parameters from the server's own tool schema.
Why chemistry.pubchem.structure is rated Low
Tool retrieves chemical structure data with no side effects or external operations.
From the tool's definition Look up a compound, get structure representations, convert between identifier formats
Attacks that exploit this kind of access
The rule that runs chemistry.pubchem.structure safely
PolicyLayer is an MCP gateway: it sits between your AI agents and Apibase, and checks every tool call against a rule you set before the call runs. Nothing changes on the server itself. For chemistry.pubchem.structure, this is the rule to start with:
chemistry.pubchem.structure is read-only, so it stays allowed. Everything else on the server is denied unless you say otherwise.
The button opens the PolicyLayer dashboard: create your workspace, connect Apibase, apply this rule, and every chemistry.pubchem.structure call is checked against it from then on.
Questions about chemistry.pubchem.structure
Look up a compound by name or identifier and get its chemical structure representations — SMILES (isomeric + canonical), InChI, InChIKey, molecular formula, and molecular weight. Convert between chemical identifier formats (PubChem / NCBI). It is categorised as a Read tool in the Apibase MCP Server, which means it retrieves data without modifying state.
chemistry.pubchem.structure accepts 1 parameter: name. Required: name. The full parameter table on this page comes from the server's own tool schema.
Register the Apibase MCP server in PolicyLayer and add a rule for chemistry.pubchem.structure: allow, deny, rate-limit, or require approval. Point your MCP client at the PolicyLayer proxy URL and the rule is enforced on every call, before it reaches Apibase. Nothing to install.
chemistry.pubchem.structure is a Read tool with low risk. Read-only tools are generally safe to allow by default.
Yes. Add a rate_limit block to the chemistry.pubchem.structure rule in your PolicyLayer policy. For example, setting max: 10 and window: 60 limits the tool to 10 calls per minute. Rate limits are tracked per agent session and reset automatically.
Set action: deny in the PolicyLayer policy for chemistry.pubchem.structure. The AI agent will receive a policy violation error and cannot call the tool. You can also include a reason field to explain why the tool is blocked.
chemistry.pubchem.structure is provided by the Apibase MCP server (apibase-mcp-client). PolicyLayer sits as a proxy in front of this server to enforce policies before tool calls reach the server.
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