Individual skill

rdkit-chemdraw-cdxml

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 reaction through a Mol silently drops arrows and text; this skill shows the XML layer that preserves them. For pure molecular analysis (descriptors, fingerprints, SMARTS) use rdkit-cheminformatics; for multi-format 3D conversion use openbabel.

skills/structural-biology-drug-discovery/rdkit-chemdraw-cdxml/SKILL.md

Source commit 55c1bd3e863d11bf5a853d24bcdda10c88e6eddf

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Observed behavior

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Last checked

Nov 5, 2026

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