rdkit-chemdraw-cdxml SKILL.md skillA
rdkit-chemdraw-cdxml 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/rdkit-chemdraw-cdxml@git:20260806.7705408Pins git:20260806.7705408 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/rdkit-chemdraw-cdxml/SKILL.md- Versions recorded
- 5
- Latest version
- git:20260806.0d18706, committed Aug 6, 2026
- First version recorded
- Aug 3, 2026
- Size
- 27,795 bytes
- Repository stars
- 381
- License
- a license file GitHub does not identify
Read, write, and edit ChemDraw CDX/CDXML files with RDKit's rdkit.Chem.rdChemDraw plus direct XML editing, always paired with a rendered PNG. Parse molecules and reactions from .cdxml/.cdx, write structures with good 2D depiction, and hand-build or modify the parts RDKit cannot write: reaction arrows, plus signs, schemes/steps, and text/labels. Use for reaction schemes, synthesis routes, mechanisms, retrosynthesis, or SI figures. Critical: RDKit writes structures only — round-tripping a…
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
# RDKit ChemDraw / CDXML Toolkit ## Overview CDXML is an XML serialization of ChemDraw's object tree (CDX is its binary form). RDKit 2022.09+ exposes an optional Revvity ChemDraw parser at `rdkit.Chem.rdChemDraw` that reads molecules **and** reactions and writes molecule structures. RDKit cannot write **arrows, plus signs, schemes, or text** — those are built or edited at the XML level. This skill covers the full read → depict → annotate → write → modify → render loop. ## Output contract A `.cdxml` is not viewable without ChemDraw, and **you cannot run ChemDraw here** — so the rendered PNG is the only evidence the file is correct. Therefore: - **Deliver `<name>.cdxml` and `<name>.png` together, matching basenames** — never the CDXML alone. `build_scheme()` and Module 9 write both; the helper raises if the PNG cannot be produced. - **Validate before delivering** with `scripts/check_scheme.py` (rebuilds each molecule from the drawing, sanitizes, checks mass balance across arrows, and critiques layout). Drive it to zero problems. …
Read the whole file at its exact version.
How to install
mdr add jaechang-hits/sciagent-skills/rdkit-chemdraw-cdxml@sha256:b2e9e5e7507cb0a0The line at the top of this page pins the label git:20260806.7705408, 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_3nmolsbjzb7hk74u)
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Versions
The registry has recorded 5 versions of this file, between Aug 3, 2026 and Aug 6, 2026, more than one a day.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260806.0d18706 latest | 2026-08-06 | 0d18706 | 27,795 B | A | view · diff |
| git:20260806.7705408 | 2026-08-06 | 7705408 | 26,740 B | A | view · diff |
| git:20260803.7152b9d | 2026-08-03 | 7152b9d | 25,767 B | A | view · diff |
| git:20260803.94e6d5d | 2026-08-03 | 94e6d5d | 24,893 B | A | view · diff |
| git:20260803.baa8a71 | 2026-08-03 | baa8a71 | 25,036 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 (27795 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_3nmolsbjzb7hk74u GET https://markdownregistry.com/api/v1/resolve?ref=jaechang-hits/sciagent-skills/rdkit-chemdraw-cdxml GET https://markdownregistry.com/api/v1/blob/b2e9e5e7507cb0a06de4d901ca855f9bac3d4c1c47a88bb4b9c95304021e73be
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.