pdb_get_polymer_entity_groups

A read tool on the Origene MCP server.

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/pdb-get-polymer-entity-groups.md

WHAT IT DOES

What pdb_get_polymer_entity_groups does on OrigeneMCP

AI agents call pdb_get_polymer_entity_groups 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 pdb_get_polymer_entity_groups is rated Low

This tool retrieves polymer entity group information from the Protein Data Bank. Despite the empty description reducing certainty, the naming convention and context of other biomedical query tools on this server strongly suggest read-only data retrieval with no side effects.

From the tool's definition Tool name 'pdb_get_polymer_entity_groups' uses the 'get' verb, suggesting data retrieval. The PDB (Protein Data Bank) context and sibling tools (clinvar_query_*, depmap_get_*) consistently retrieve biomedical data without modification.

Attacks that exploit this kind of access

RECOMMENDED RULE

The rule that runs pdb_get_polymer_entity_groups 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 pdb_get_polymer_entity_groups, this is the rule to start with:

pdb_get_polymer_entity_groups Allowed

pdb_get_polymer_entity_groups 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": {
    "pdb_get_polymer_entity_groups": {}
  }
}

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 pdb_get_polymer_entity_groups call is checked against it from then on.

FAQ

Questions about pdb_get_polymer_entity_groups

What does the pdb_get_polymer_entity_groups tool do? +

pdb_get_polymer_entity_groups is a read tool on the Origene MCP server. 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 pdb_get_polymer_entity_groups? +

Register the Origene MCP server in PolicyLayer and add a rule for pdb_get_polymer_entity_groups: 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 pdb_get_polymer_entity_groups? +

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

Can I rate-limit pdb_get_polymer_entity_groups? +

Yes. Add a rate_limit block to the pdb_get_polymer_entity_groups 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 pdb_get_polymer_entity_groups completely? +

Set action: deny in the PolicyLayer policy for pdb_get_polymer_entity_groups. 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 pdb_get_polymer_entity_groups? +

pdb_get_polymer_entity_groups 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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