SMI_ISOMORPHISM(1)

💖 SMI_ISOMORPHISM(1) 💖

okay bestie so this is smi_isomorphism, a little user command that lives in section 1 of the manual, and it is literally here to tell you whether two SMILES strings are the same molecule in disguise. no cap.

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✨ NAME ✨

smi_isomorphism — detect isomorphism between SMILES 🧪

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🌸 DESCRIPTION 🌸

🎀 USAGE 🎀

smi_isomorphism [<args>] [<files>]

🦋 DESCRIPTION (the actual tea) 🦋

so here's the vibe: smi_isomorphism reads in files, and every file has three tab-separated columns, like this:

<ID> <SMILES_1> <SMILES_2>

then, for every single line, it tries to detect isomorphism between <SMILES_1> and <SMILES_2>. 💅

and here's the part that's giving main character energy: if it doesn't clock immediate isomorphism, it doesn't just give up and go home. nope. it performs step-by-step simplifications — in order — to try and lead both SMILES to isomorphism. obsessed, honestly. 🔥

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👑 OPTIONS 👑

• --remove-alkali-bonds — adds alkali bond removal to the list of simplifications. bye bye alkali bonds, you're not invited to the party 🫶
• --remove-metal-bonds — adds metal bond removal to the list of simplifications. metals, you're also getting yeeted 💀
• --print-side-of-superfluous-moieties — identifies which of the compared sides has superfluous molecular entities. like, one side is doing too much and this tells you which 🙈
• --check-isomorphism — performs an extra isomorphism check on molecular entities that were detected as isomorphic, by comparing their canonical representations. double-checking? we love a thorough queen ⭐
• --help — print usage message and exit. classic, iconic, always there for you 🎀

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ok so real talk: if immediate isomorphism isn't detected, the simplifications run in order, so the order matters — that's the whole point of the "step-by-step" thing. don't skip ahead, bestie. 💜

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anyway that's the whole page, slay, go compare some SMILES 💖✨

this manual page is for smi_isomorphism version 0.4.0+dfsg, and it's dated February 2026. 💅🌸 mwah, bye bestie!