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Get Compound 3D Structure

pubchem_get_compound_3d_structure
Read-onlyIdempotent

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).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
cidYesPubChem Compound ID. Resolve from name/SMILES with pubchem_search_compounds.
formatNoOutput format. "json" (default) returns parsed atoms and bonds. "sdf" returns the raw V2000 SDF text for passthrough to other tools.json
maxAtomsNoCap the atoms returned in the format="json" preview. atomCount always reports the full total; omitted rows are disclosed via the truncated/shownAtoms enrichment. Defaults to the first 200 atoms.
maxBondsNoCap the bonds returned in the format="json" preview. bondCount always reports the full total; omitted rows are disclosed via the truncated/shownBonds enrichment. Defaults to the first 200 bonds.
includeRawSdfNoFor format="sdf", return the complete raw V2000 SDF even when it exceeds the safe line cap. Default false: an SDF longer than 500 lines is line-capped with disclosure. No effect when format="json".
includeAlternateConformerIdsNoList the IDs of additional computed conformers beyond the default. Slower than the default response. Default: false.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
cidNoPubChem Compound ID.
sdfNoRaw V2000 SDF text. Populated when format="sdf".
atomsNoParsed atoms. Populated when format="json".
bondsNoParsed bonds. Populated when format="json".
errorNoPresent when the call failed. Absent on success.
noticeNoGuidance naming which lists were capped and how to widen them.
atomCapNoThe atom cap applied (explicit maxAtoms or the safe default), when the atom list was capped.
bondCapNoThe bond cap applied (explicit maxBonds or the safe default), when the bond list was capped.
atomCountNoNumber of atoms in the conformer.
bondCountNoNumber of bonds in the conformer.
truncatedNoTrue when the atom list, bond list, or raw SDF was capped below its total. atomCount/bondCount always report the full totals.
shownAtomsNoAtoms returned after the cap, when fewer than atomCount. Raise maxAtoms for more.
shownBondsNoBonds returned after the cap, when fewer than bondCount. Raise maxBonds for more.
conformerIdNoDefault (primary) conformer ID. Present when includeAlternateConformerIds is set.
shownSdfLinesNoSDF lines returned when format="sdf" and the raw text was line-capped. Set includeRawSdf for the full record.
alternateConformerIdsNoConformer IDs beyond the default. Present when includeAlternateConformerIds is set and alternates exist.

TDQS

A4.1/5.0
Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Annotations already convey read-only, idempotent, and open-world behavior; the description adds meaningful context by explaining the two output formats and the important caveat that large molecules, mixtures, and some salts may have no 3D coordinates. It does not cover error behavior or rate limits, but those are less critical given the read-only hint.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The three-sentence description is tightly front-loaded, beginning with the core operation and data returned, then explaining format behavior and availability limits. Every sentence earns its place and there is no redundant restatement of schema details.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness5/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

For a read-only retrieval tool with a rich output schema and complete parameter documentation, the description covers purpose, format choice, and a key failure-prone case. Truncation and safe-line details are already handled in the parameter schema, so nothing essential is missing.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

All six parameters are fully documented in the schema with defaults, enums, and truncation behavior, so the description is not required to compensate. The description briefly reinforces the format distinction and alternate conformer option but does not add substantial parameter semantics beyond the schema.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

States a specific verb and resource: retrieving a compound's default 3D conformer with atomic coordinates and bonds for one CID. The format distinction (JSON vs raw SDF) further clarifies exactly what the tool returns, setting it apart from sibling compound detail and image tools.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines3/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

Gives clear use context, such as raw SDF for docking, rendering, or conformer tools, and warns that some compounds lack computed 3D coordinates. However, it does not explicitly name sibling alternatives or state when to prefer them, leaving routing decisions mostly implicit.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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TDQS

A4.3/5.0
Disambiguation4/5

Tools cleanly separate into search (compounds, assays) and retrieval (details, structure, image, safety, xrefs, bioactivity, interactions, summary). The only mild overlap is bioactivity versus interactions, but their descriptions clarify that one focuses on assay outcomes and the other on drug-drug/food/chemical-target records.

Naming Consistency5/5

All tools follow a consistent pubchem_<verb>_<object> pattern, with get_ for retrieval and search_ for discovery. Minor variations like pubchem_get_summary still fit the same convention clearly.

Tool Count5/5

Ten tools is well-scoped for a PubChem client: search entry points, compound detail retrieval, structural representations, safety data, interaction data, and cross-reference lookups. Each tool earns its place without redundancy.

Completeness5/5

The surface covers the core PubChem workflows: finding compounds and assays, retrieving compound properties and structures, and exploring bioactivity, safety, interactions, and cross-references. Search results feed directly into retrieval tools, and paging is provided where needed, leaving no obvious dead ends.