pdb_get_nonpolymer_entity_groups
A read tool on the Origene MCP server.
This record as markdown: /tools/gentel-lab-origenemcp/pdb-get-nonpolymer-entity-groups.md
What pdb_get_nonpolymer_entity_groups does on OrigeneMCP
AI agents call pdb_get_nonpolymer_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.
Why pdb_get_nonpolymer_entity_groups is rated Low
Based on naming convention, this tool queries PDB database to retrieve information about non-polymer entity groups—a metadata lookup with no side effects. The 'get_' prefix across sibling tools (get_dependency, get_expression) consistently indicates read operations. No modification, execution, deletion, or financial action is implied.
From the tool's definition Tool name 'pdb_get_nonpolymer_entity_groups' indicates retrieval of PDB (Protein Data Bank) entity group information. The 'get' prefix strongly suggests read/retrieval operation. Description is empty, limiting specificity.
Attacks that exploit this kind of access
The rule that runs pdb_get_nonpolymer_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_nonpolymer_entity_groups, this is the rule to start with:
pdb_get_nonpolymer_entity_groups 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 OrigeneMCP, apply this rule, and every pdb_get_nonpolymer_entity_groups call is checked against it from then on.
Questions about pdb_get_nonpolymer_entity_groups
pdb_get_nonpolymer_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.
Register the Origene MCP server in PolicyLayer and add a rule for pdb_get_nonpolymer_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.
pdb_get_nonpolymer_entity_groups 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 pdb_get_nonpolymer_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.
Set action: deny in the PolicyLayer policy for pdb_get_nonpolymer_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.
pdb_get_nonpolymer_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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