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rdkit-molecule-standardization

95 / 100 · Low risk

Fine to try.

By ma-compbio-lab/SkillFoundry (GitHub) · other · 44 stars · scanned at commit 4a8cc0c

Use this skill to standardize one small-molecule SMILES string with RDKit MolStandardize. It is for local cleanup, salt stripping, uncharging, and tautomer canonicalization, not docking or batch-library processing.

Works with any agent that supports SKILL.md skills.

What this skill can do

Install

Paste this into your terminal. It downloads exactly the version we scanned, not whatever is newest.

if [ -e ~/.agents/skills/'rdkit-molecule-standardization' ] || [ -L ~/.agents/skills/'rdkit-molecule-standardization' ]; then echo 'A skill folder named rdkit-molecule-standardization already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/ma-compbio-lab/SkillFoundry' "$d" && git -C "$d" checkout --quiet '4a8cc0cd9f923cde47a7f542d4a84b92bbabc59f' -- 'skills/drug-discovery-and-cheminformatics/rdkit-molecule-standardization' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/drug-discovery-and-cheminformatics/rdkit-molecule-standardization' ~/.agents/skills/'rdkit-molecule-standardization' && rm -rf "$d"; fi

Codex reads ~/.agents/skills directly. For Claude Code, Cursor, Copilot, Gemini CLI, Antigravity or OpenCode, also link it. For Claude Code: ln -s ~/.agents/skills/'rdkit-molecule-standardization' ~/.claude/skills/'rdkit-molecule-standardization' (other agents: ~/.cursor/skills, ~/.copilot/skills, ~/.gemini/skills, ~/.gemini/config/skills, ~/.config/opencode/skills). Or install through the finder skill, which does both.

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