# pdb_get_nonpolymer_entity

A read tool on the OrigeneMCP MCP server.

Agent View of the PolicyLayer registry record for `pdb_get_nonpolymer_entity`. HTML page: https://policylayer.com/tools/gentel-lab-origenemcp/pdb-get-nonpolymer-entity

## Facts

- Tool: `pdb_get_nonpolymer_entity`
- Server: OrigeneMCP (`gentel-lab/origenemcp`) — https://policylayer.com/tools/gentel-lab-origenemcp.md
- Homepage: https://github.com/GENTEL-lab/OrigeneMCP
- Risk category: Read (Low risk)
- Registry record: grade C, identity unverified
- Server rate-limited: no
- Parameters: 0
- Recommended policy verdict: Allowed

## Example call (MCP tools/call, JSON-RPC 2.0)

```json
{
  "jsonrpc": "2.0",
  "id": 1,
  "method": "tools/call",
  "params": {
    "name": "pdb_get_nonpolymer_entity",
    "arguments": {}
  }
}
```

## Why pdb_get_nonpolymer_entity is rated Low

This tool retrieves structural or metadata information about nonpolymer entities (ligands, ions, etc.) from the PDB database. Retrieval operations have no side effects and pose minimal risk as they only query public biomedical data. Classified as Read with low severity due to its informational nature and no capability to modify or delete data.

From the tool's own definition: "Tool name 'pdb_get_nonpolymer_entity' indicates retrieval of nonpolymer entity information from PDB (Protein Data Bank), a public biomedical database."

## Use case

AI agents call pdb_get_nonpolymer_entity 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.

## Recommended policy (PolicyLayer)

Verdict: **Allowed**. Enforced by the PolicyLayer MCP gateway (https://policylayer.com/mcp-gateway) before a call reaches OrigeneMCP:

```json
{
  "version": "1",
  "default": "deny",
  "tools": {
    "pdb_get_nonpolymer_entity": {}
  }
}
```

## Other tools on OrigeneMCP (438)

- `post_vep_hgvs` — Execute — https://policylayer.com/tools/gentel-lab-origenemcp/post-vep-hgvs.md
- `post_vep_id` — Execute — https://policylayer.com/tools/gentel-lab-origenemcp/post-vep-id.md
- `post_ga4gh_features_search` — Other — https://policylayer.com/tools/gentel-lab-origenemcp/post-ga4gh-features-search.md
- `post_lookup_id` — Other — https://policylayer.com/tools/gentel-lab-origenemcp/post-lookup-id.md
- `check_genome_accessions` — Read — https://policylayer.com/tools/gentel-lab-origenemcp/check-genome-accessions.md
- `check_virus_accessions` — Read — https://policylayer.com/tools/gentel-lab-origenemcp/check-virus-accessions.md
- `clinvar_find_single_mutation` — Read — https://policylayer.com/tools/gentel-lab-origenemcp/clinvar-find-single-mutation.md
- `clinvar_get_best_refseqid_by_sequence` — Read — https://policylayer.com/tools/gentel-lab-origenemcp/clinvar-get-best-refseqid-by-sequence.md
- `clinvar_query_sequence_variants` — Read — https://policylayer.com/tools/gentel-lab-origenemcp/clinvar-query-sequence-variants.md
- `clinvar_query_variant_significance` — Read — https://policylayer.com/tools/gentel-lab-origenemcp/clinvar-query-variant-significance.md
- `depmap_comprehensive_analysis` — Read — https://policylayer.com/tools/gentel-lab-origenemcp/depmap-comprehensive-analysis.md
- `depmap_get_dependency` — Read — https://policylayer.com/tools/gentel-lab-origenemcp/depmap-get-dependency.md
- `depmap_get_expression` — Read — https://policylayer.com/tools/gentel-lab-origenemcp/depmap-get-expression.md
- `depmap_get_mutation` — Read — https://policylayer.com/tools/gentel-lab-origenemcp/depmap-get-mutation.md
- `ensembl_get_genes_by_band` — Read — https://policylayer.com/tools/gentel-lab-origenemcp/ensembl-get-genes-by-band.md
- `get_activity` — Read — https://policylayer.com/tools/gentel-lab-origenemcp/get-activity.md
- `get_activity_by_id` — Read — https://policylayer.com/tools/gentel-lab-origenemcp/get-activity-by-id.md
- `get_activity_by_ids` — Read — https://policylayer.com/tools/gentel-lab-origenemcp/get-activity-by-ids.md
- `get_activity_supplementary_data_by_activity` — Read — https://policylayer.com/tools/gentel-lab-origenemcp/get-activity-supplementary-data-by-activity.md
- `get_activity_supplementary_data_by_activity_by_id` — Read — https://policylayer.com/tools/gentel-lab-origenemcp/get-activity-supplementary-data-by-activity-by-id.md
- `get_activity_supplementary_data_by_activity_by_ids` — Read — https://policylayer.com/tools/gentel-lab-origenemcp/get-activity-supplementary-data-by-activity-by-ids.md
- `get_alignment_region` — Read — https://policylayer.com/tools/gentel-lab-origenemcp/get-alignment-region.md
- `get_all_interaction_partners_of_the_protein_set` — Read — https://policylayer.com/tools/gentel-lab-origenemcp/get-all-interaction-partners-of-the-protein-set.md
- `get_archive_id` — Read — https://policylayer.com/tools/gentel-lab-origenemcp/get-archive-id.md
- `get_assay` — Read — https://policylayer.com/tools/gentel-lab-origenemcp/get-assay.md
- `get_assay_by_id` — Read — https://policylayer.com/tools/gentel-lab-origenemcp/get-assay-by-id.md
- `get_assay_by_ids` — Read — https://policylayer.com/tools/gentel-lab-origenemcp/get-assay-by-ids.md
- `get_assay_class` — Read — https://policylayer.com/tools/gentel-lab-origenemcp/get-assay-class.md
- `get_assay_class_by_id` — Read — https://policylayer.com/tools/gentel-lab-origenemcp/get-assay-class-by-id.md
- `get_assay_class_by_ids` — Read — https://policylayer.com/tools/gentel-lab-origenemcp/get-assay-class-by-ids.md
- …and 408 more: https://policylayer.com/tools/gentel-lab-origenemcp.md

## For agents

This record is a snapshot. Live verdicts and the full registry:

- Check every server in your MCP config at once: `npx -y policylayer stack`
- Vet a server before you add it: install the mcp-precheck skill — `npx skills add https://policylayer.com` (skill text: https://policylayer.com/skill.md)
- Query the registry over MCP: endpoint `https://api.policylayer.com/mcp` — tools `check_mcp_server`, `check_mcp_stack`, `check_tool`, `search_registry`, `get_change_events`

---

Source: the PolicyLayer MCP registry — one continuously verified record per MCP server. Full record: https://policylayer.com/registry?q=gentel-lab-origenemcp · API: https://policylayer.com/registry/api · Policy library: https://policylayer.com/policies/gentel-lab-origenemcp