pubchem-compound-search SKILL.md skillA
pubchem-compound-search from jaechang-hits/sciagent-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add jaechang-hits/sciagent-skills/pubchem-compound-search@git:20260613.7b256f1Pins git:20260613.7b256f1 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- jaechang-hits/sciagent-skills
- Path
skills/structural-biology-drug-discovery/pubchem-compound-search/SKILL.md- Versions recorded
- 4
- Latest version
- git:20260613.7b256f1, committed Jun 13, 2026
- First version recorded
- Feb 18, 2026
- Size
- 28,306 bytes
- Repository stars
- 381
- License
- a license file GitHub does not identify
Query PubChem (110M+ compounds) directly via the PUG-REST/JSON API with plain `requests` — no SDK install required. Search by name/CID/SMILES/InChIKey/formula, retrieve properties (MW, XLogP, TPSA, H-bond counts), do similarity/substructure searches with async ListKey polling, fetch synonyms, descriptions, assay summaries, and download SDF/PNG. For local cheminformatics use rdkit; for bioactivity-centric workflows use chembl-database-bioactivity.
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
# PubChem Compound Search
## Overview
PubChem (NCBI) is the largest freely available chemical database — 110M+ compounds, 280M+ substances, and millions of bioassay records. Its **PUG-REST JSON API** is the canonical programmatic surface, and every example here uses it directly via plain `requests`. The Python `pubchempy` wrapper is *not* required; the PUG-REST URL grammar is small enough that direct calls are more transparent, easier to retry/cache, and avoid sandbox dependency issues (the library is not in `TOOL_STATUS.md`).
The URL pattern is fixed and predictable:
```
https://pubchem.ncbi.nlm.nih.gov/rest/pug/<input>/<operation>/<output>
```
- `<input>` = `compound/{name,cid,smiles,inchikey,formula}/<value>`
- `<operation>` = `cids`, `property/<list>`, `synonyms`, `description`, `assaysummary`, `JSON` (full record), `SDF`, `PNG`
- `<output>` = `JSON`, `CSV`, `TXT`, `SDF`, `PNG`
For long-running operations (similarity, substructure, formula) the API returns HTTP 202 + `{"Waiting": {"ListKey": "..."}}`; poll `compound/listkey/{key}/cids/JSON` until it returns `IdentifierList`. The skill handles this pattern in Module 4.
## When to Use
…Read the whole file at its exact version.
How to install
mdr add jaechang-hits/sciagent-skills/pubchem-compound-search@sha256:0b1ac82caaf89437The line at the top of this page pins the label git:20260613.7b256f1, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_7quej7tkk3qvu6q5)
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Versions
The registry has recorded 4 versions of this file, between Feb 18, 2026 and Jun 13, 2026, about one every 38 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260613.7b256f1 latest | 2026-06-13 | 7b256f1 | 28,306 B | A | view · diff |
| git:20260522.d4a4f76 | 2026-05-22 | d4a4f76 | 27,864 B | A | view · diff |
| git:20260428.81ea2d2 | 2026-04-28 | 81ea2d2 | 9,983 B | A | view · diff |
| git:20260218.8df1694 | 2026-02-18 | 8df1694 | 10,069 B | A | view |
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (28306 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
jaechang-hits/sciagent-skills · 381 stars · license a license file GitHub does not identify · pushed 2026-10-16 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_7quej7tkk3qvu6q5 GET https://markdownregistry.com/api/v1/resolve?ref=jaechang-hits/sciagent-skills/pubchem-compound-search GET https://markdownregistry.com/api/v1/blob/0b1ac82caaf89437a8830b3a54643b3eb9b5f1289fbaa97d92199141186aaa9b
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.