AI agents call get_atom_info to retrieve information from Vmd without modifying anything — typically the context-gathering step in research, monitoring, and reporting workflows, before the agent takes action elsewhere.
This tool queries and returns information about atoms in loaded molecular structures (residue names, IDs, atom names, indices). It performs no side effects, does not modify data, does not execute code or commands, and does not delete or create resources. It is a straightforward data retrieval operation typical of Read category tools.
From the tool's definition Tool name 'get_atom_info' and description 'Return residue names, residue IDs, atom names, and indices for atoms matching' indicate retrieval of molecular structure metadata without modification or execution.
Attacks that exploit this kind of access
Return residue names, residue IDs, atom names, and indices for atoms matching. It is categorised as a Read tool in the Vmd MCP Server, which means it retrieves data without modifying state.
Register the Vmd MCP server in PolicyLayer and add a rule for get_atom_info: 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 Vmd. Nothing to install.
get_atom_info 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 get_atom_info 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 get_atom_info. 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.
get_atom_info is provided by the Vmd MCP server (omararias-gaguancela/vmd-mcp). PolicyLayer sits as a proxy in front of this server to enforce policies before tool calls reach the server.
Every MCP server has a record like this.
Type a name, get the same breakdown: verified identity, auth posture, risk grade, capabilities, recommended policy.
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