pubchem_get_compound_3d_structure
shallowio.github.cyanheads/pubchem-mcp-server · Verify this server
Get a compound's default 3D conformer — atomic coordinates and bonds — for one CID. format="json" (default) returns atoms and bonds parsed into structured fields; format="sdf" returns the raw V2000 SDF text for passthrough to docking, rendering, or conformer tools. Optionally lists alternate conformer IDs. Not every compound has computed 3D coordinates (large molecules, mixtures, and some salts do not).
1 trials · measured 57 days ago
pubchem_get_compound_3d_structure scores 100.0/100 on Vouch's measured behaviour index, from 1 real invocation trials against io.github.cyanheads/pubchem-mcp-server, measured 25 Aug 2026 under methodology v0.2.0. Every measured component scored 100.
Component breakdown
| Component | Weight | Value |
|---|---|---|
| Reliability | 35% | not applicable |
| Schema integrity | 25% | 100.0 |
| Failure behaviour | 15% | not applicable |
| Latency | 15% | not applicable |
| Concurrency | 10% | not applicable |
Tool details
- Transport
- remote + stdio
- Credential class
- self-provisionable
- Category
- Developer infrastructure
- Input schema
- not declared
- Output schema
- not declared
- Side-effect classification
- unclassified
Score history
| Day | Score | Tier | Methodology |
|---|---|---|---|
| 2026-08-25 | 100.0 | shallow | v0.2.0 |
Probe evidence
| Probe | Outcomes |
|---|---|
| schema_integrity | pass: 1 |
Raw request/response logs are not archived yet — the outcome counts above are drawn directly from every recorded trial.
Embed this score
Available for every tool, scored or not — not a verification perk. Always links back to this page.
[](https://vouch.tools/tools/551dbf74-fc42-40c6-bae1-1d7cf592b107)