SMI_CANONICALISE(1)

🎀 NAME 🎀

smi_canonicalise — canonicalise SMILES, bestie 💅

Oh and hey, this whole thing lives in the User Commands corner of the manual, so if you ever forget where you found it: it's smi_canonicalise(1), section 1, the user-commands section. Noted. Slay.

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✨ DESCRIPTION ✨

🦋 USAGE 🦋

smi_canonicalise [<args>] [<files>]

That's the whole vibe. Args, files, go. 🫶

💖 DESCRIPTION 💖

Okay so real talk: smi_canonicalise reads in files full of SMILES descriptors and spits them back out using a stable atom ordering established by Graph::Nauty. Stable. Ordered. Immaculate. ✨

And if there's more than one moiety? They get ordered in lexicographic order. Alphabetical-ish, basically. The moieties are getting lined up single file and they're gonna like it. 💅

👑 OPTIONS 👑

Every flag, every default, no cap:

• --infer-hydrogens — infer hydrogen atom counts according to valency rules. [default] — yes, this is what happens unless you say otherwise ✨
• --no-infer-hydrogens — do not infer hydrogen atom counts. Do not pass go, do not count H's.
• --aromatise — aromatise Kekule structures. (experimental) — it's giving science experiment, handle with care 🧪
• --no-aromatise — do not attempt to aromatise. [default]
• --aromatisation-method STR — mark flat rings as aromatic. Two methods are supported: 'electron-cycles', which follows Richard L. Apodaca's electron cycle-based approach (default), and 'Huckel', which aims to follow H??ckel's rule as implemented in Chemistry::Ring. There's also 'external-list': it uses aromaticity defined using the --aromatic-atoms or --aromatic-bonds options. Three names, described as two, we love a mystery 😭
• --aromatic-atoms STR — a comma-separated list of 0-based aromatic atom numbers, consulted during aromaticity detection. This implies --aromatisation-method 'external-list'. It's the friend that brings the guest list.
• --aromatic-bonds STR — a comma-separated list of bonds, expressed as dash-separated pairs of 0-based aromatic atom numbers. The list gets consulted during aromaticity detection. This implies --aromatisation-method 'external-list' too. Guest list, bond edition 🎀
• --kekulise — kekulise simple aromatic structures. (experimental) — again, experimental, we're in the lab, goggles on 🥽
• --no-kekulise — do not attempt to kekulise. [default]
• --no-acyclic-aromatic-bonds — convert acyclic aromatic bonds to single. Just. Single. Living their simple life. 🦋
• --canonicalise-haloanions — canonicalise the representation of haloanions. [default] — iconic behaviour, honestly
• --no-canonicalise-haloanions — retain the input representation of haloanions. Leave them exactly as you found them, no edits, no notes.
• --canonicalise-nitro-groups — canonicalise the representation of nitro groups by converting them from *-[N+]([O-])=O to *-N(=O)=O. A glow-up, fr fr ✨
• --no-canonicalise-nitro-groups — retain the input representation of nitro groups. [default] — untouched, unbothered, in its original form 💅
• --ignore-class — ignore SMILES atom class in canonicalisation. (useful for testing)
• --preserve-order — preserve the input order of molecular entities and atoms. No rearranging, bestie, we keep the seating plan exactly as it was 🪑
• --random-order — instead of canonical, output SMILES in random order. (useful for testing) — chaos mode, lowkey iconic 🎲
• --help — print usage message and exit. Our beloved. The one flag that always has your back 🫶

Heads up bestie: --aromatise and --kekulise are marked (experimental) in the original, so don't come for me if the science gets weird 🧪😭

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And that's the whole page, mwah 💋 This was smi_canonicalise version 0.4.0+dfsg, from February 2026, and it's filed under User Commands. Go canonicalise something gorgeous. Periodt. 🌈💖