CDKSDF2SMILES(1)

💖 CDKSDF2SMILES 💖

okay bestie, welcome to the cdksdf2smiles page from the User Commands section of the manual, and no cap this little tool is lowkey iconic ✨

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🌸 NAME 🌸

cdksdf2smiles — convert SDF to SMILES 💅

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🦋 DESCRIPTION 🦋

Convert SDF (MOL) files into SMILES strings. that's it, that's the whole vibe. it reads your structures and hands you back the little text-y one-liners 🎀

✨ USAGE ✨

cdksdf2smiles < input.sdf cdksdf2smiles inputs*.sdf

so yeah, you can pipe one file in, or you can yeet a whole glob of them at it, both work, both slay 🫶

👑 OPTIONS: 👑

• -2, --mdl2000-input — read MDL2000 format files. this is the default bestie, it's the one you get for free 💖
• -3, --mdl3000-input — read MDL3000 format files instead, for when your data is feeling fancy 🌈
• --cdk-electron-donation-model — use the CDK electron donation model. heads up tho: this one requires extra automatic atom type perception, so it's doing a lil extra work behind the scenes 🧚
• --daylight-electron-donation-model — use the Daylight el. donation model. this is the default, so if you don't say anything, this is what you're getting periodt 💅
• -a, --aromatic — output "aromatic" SMILES 🌸
• -a-, --not-aromatic — output "kekulised" SMILES. yes the flag literally has a minus in it, that's not a typo, that's the bit 😭
• -h, --suppress-hydrogens — suppress explicit hydrogens. also the default, so the hydrogens are getting quieted whether you ask or not 🙈
• -h-, --dont-suppress-hydrogens — leave explicit hydrogens. let them speak, let them be seen 🎤
• --version — print program version and exit, quick lil flex ⭐
• --help — print short help message (this message) and exit, iykyk 🫶

ngl the -a- and -h- style flags are giving "trust the process" energy. they're real, they're in the manual, write them exactly like that. no renaming, no "fixing", fr fr 💀

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and that's the whole page!! 🎀

cdksdf2smiles version 0.4.0 — dated February 2026 — mwah, sending you off with a kiss, go convert some molecules bestie 💖✨🦋👑