search_pubchem_by_smiles

Search PubChem for compounds matching a SMILES string.

SERVEROrigeneMCP SOURCEgentel-lab/origenemcp

Low RISK CLASS

Category Read

Parameters 00 required

Recommended Allowedsee the rule below

Registry record Grade C, identity unverified Pull the record →

This record as markdown: /tools/gentel-lab-origenemcp/search-pubchem-by-smiles.md

WHAT IT DOES

What search_pubchem_by_smiles does on OrigeneMCP

AI agents call search_pubchem_by_smiles to retrieve information from OrigeneMCP without modifying anything. It is typically the context-gathering step in research, monitoring, and reporting workflows, before the agent takes action elsewhere.

RISK

Why search_pubchem_by_smiles is rated Low

This is a read-only operation that queries a public chemistry database (PubChem) using a molecular identifier (SMILES notation). It retrieves matching compound information with no side effects, no data modification, and no execution of arbitrary code. The blast radius of misuse is minimal—an agent could retrieve irrelevant chemical compound data, but this poses no security, financial, or system integrity risk.

From the tool's definition Tool name 'search_pubchem_by_smiles' and description 'Search PubChem for compounds matching a SMILES string' indicate a query operation that retrieves data from PubChem without modifying, executing, or deleting anything.

Attacks that exploit this kind of access

RECOMMENDED RULE

The rule that runs search_pubchem_by_smiles safely

PolicyLayer is an MCP gateway: it sits between your AI agents and OrigeneMCP, and checks every tool call against a rule you set before the call runs. Nothing changes on the server itself. For search_pubchem_by_smiles, this is the rule to start with:

search_pubchem_by_smiles Allowed

search_pubchem_by_smiles is read-only, so it stays allowed. Everything else on the server is denied unless you say otherwise.

View as policy code

policy.json

{
  "version": "1",
  "default": "deny",
  "tools": {
    "search_pubchem_by_smiles": {}
  }
}

ALLOW ONLY THIS TOOL → Instant setup, no code required.

The button opens the PolicyLayer dashboard: create your workspace, connect OrigeneMCP, apply this rule, and every search_pubchem_by_smiles call is checked against it from then on.

FAQ

Questions about search_pubchem_by_smiles

What does the search_pubchem_by_smiles tool do? +

Search PubChem for compounds matching a SMILES string. It is categorised as a Read tool in the OrigeneMCP MCP Server, which means it retrieves data without modifying state.

How do I enforce a policy on search_pubchem_by_smiles? +

Register the Origene MCP server in PolicyLayer and add a rule for search_pubchem_by_smiles: 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 OrigeneMCP. Nothing to install.

What risk level is search_pubchem_by_smiles? +

search_pubchem_by_smiles is a Read tool with low risk. Read-only tools are generally safe to allow by default.

Can I rate-limit search_pubchem_by_smiles? +

Yes. Add a rate_limit block to the search_pubchem_by_smiles 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.

How do I block search_pubchem_by_smiles completely? +

Set action: deny in the PolicyLayer policy for search_pubchem_by_smiles. 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.

What MCP server provides search_pubchem_by_smiles? +

search_pubchem_by_smiles is provided by the Origene MCP server (gentel-lab/origenemcp). PolicyLayer sits as a proxy in front of this server to enforce policies before tool calls reach the server.

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