SDF-TO-SMI(1)

👑 NAME 👑

okay so <pink>sdf-to-smi</pink> — she converts SDF to SMILES. that's the whole personality, and honestly? iconic. ✨

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🦋 DESCRIPTION 🦋

🎀 USAGE 🎀

sdf-to-smi [<args>] [<files>]

💖 DESCRIPTION 💖

so like, <pink>sdf-to-smi</pink> takes your SDF files and just. converts them into SMILES. bestie behaviour fr fr. 🧚

✨ OPTIONS ✨

• --convert-type-8-bonds-to-covalent — turns every single type 8 bond into a plain single covalent bond. yes, all of them. 💅
• --no-adjust-charges — when she's converting those type 8 bonds, she will not be adjusting atom charges. hands off. 🙈
• --no-estimate-attached-hydrogens — do not estimate how many hydrogens are attached. she's not guessing today. 😌
• --ignore-flat-tetrahedra — when she's looking at tetrahedral chiral centers, flat tetrahedra get ignored, judged by volume threshold. this is the default vibe. ✨
• --require-tetrahedral-angles — when she's considering tetrahedral chiral centers, she ignores tetrahedra whose average bond angle is far from 109.5 degrees. geometry check, no skipping. 📐
• --planarity-threshold NUM — planarity volume threshold, measured in cubic angstroms. any tetrahedra with a chiral volume less than or equal to that number get understood as flat. default: 1e-06 ⭐
• --normalise-vectors — normalise the vectors used for the chiral volume calculation. glow-up for your vectors. 💫
• --aromatisation-method STR — the method used to mark aromatic atoms and bonds. the supported methods are:
  • 'Huckel' — marks flat rings as aromatic after making sure they follow H??ckel's rule as implemented in Chemistry::Ring.
  • 'electron-cycles' — marks flat rings as aromatic following Richard L. Apodaca's electron cycle-based approach. heads up: this one is slow for large conjugated systems 😭
  • 'external-list' — uses the aromaticity defined by the --aromatic-atoms or --aromatic-bonds options.
• --aromatic-atoms STR — a comma-separated list of 1-based aromatic atom numbers, consulted during aromaticity detection. it implies --aromatisation-method 'external-list'. 🫶
• --aromatic-bonds STR — a comma-separated list of bonds, written as dash-separated pairs of 1-based aromatic atom numbers. the list gets consulted during aromaticity detection, and it implies --aromatisation-method 'external-list'. 💜
• --mark-square-planar-centers — marks chirality in square planar centers. square girlies, this one's for you. 🔥
• --no-generate-racemates — do not attempt to fully represent racemates in non-Sohncke space groups. she's not doing it. periodt. 💅
• --remove-excess-stereochemistry — removes excess stereochemistry settings. experimental, so proceed with caution bestie 😭
• --help — prints the usage message and exits. the classic. the icon. 👑

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and that's the whole page, no cap. every flag, every default, every little detail — she kept it all. 🎀

sdf-to-smi 0.4.0+dfsg — dated February 2026. go forth and convert, bestie. mwah. 💖🌈🦋