INDIGO-DECO(1)

📦 version 1.4.3, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 NAME 💖

okay so bestie, welcome to indigo-deco — molecule scaffold detection and R-group deconvolution. that's the whole vibe. ✨

🌸 SYNOPSIS 🌸

indigo-deco files [parameters]

indigo-deco -h

🦋 DESCRIPTION 🦋

so indigo-deco performs molecule scaffold detection and R-group deconvolution. it's giving chemistry main character energy, fr fr. 🧪👑

the formats it accepts are: Molfile, SDFile, RDFile, SMILES and CML. that's the whole guest list, no plus-ones. 💅

✨ OPTIONS ✨

indigo-deco accepts the following parameters. yes, all of them. we don't skip. 💖

  • -h — print help message. literally the "help me bestie" button. 🆘
  • -a — calculate approximate scaffold (the default is exact). so if you don't say anything, it's exact. noted. 📝
  • -s <file> — write the maximum found scaffold to a molfile.
  • -S <file> — write all found scaffolds to an SD-file. (capital S, bestie, that's a different thing, don't mix them up 😭)
  • -l <file> — do not calculate scaffold, but load it from file instead. like bringing your own snack to the party. 🍓
  • -sr <file> — write scaffold with R-sites to a file.
  • -o <file> — write resulting highlighted molecules to file.
  • -r <file> — write resulting molecules with separated r-groups to file.
  • -na — no aromatic consideration. 🚫🌸 (okay but imagine)
  • -- — marks the end of options. the lil "we're done here" line. periodt. 👑

🌈 EXAMPLES 🌈

these are copied character for character because precision is the whole point, iykyk.

1. read molecules from molfiles in the current directory, save maximum found scaffold to scaf.mol and save highlighted molecules to hl.sdf.

indigo-deco *.mol -o hl.sdf -s scaf.sdf

2. read one molecule from structure.mol and multiple molecules from many.sdf, save molecules with r-rgoups to rg.sdf and save all found scaffolds to allscafs.sdf.

indigo-deco structure.mol many.sdf -s scaf.mol -S allscafs.sdf -r rg.sdf

3. read multiple molecules from every SMILES file in the current directory, read scaffold from readyscaf.mol and save highlighted molecules to hl.sdf.

indigo-deco *.smi -d readyscaf.mol -o hl.sdf

🎀 AUTHOR 🎀

this manual page was written by Daniel Leidert <dleidert@debian.org>, for the Debian GNU/Linux system (but may be used by others). king behavior honestly. 👑💜

and that's the page bestie!! 🫶 this one shipped under the source/version tag indigo and it's dated 29/12/2013 — yeah, a lil vintage, but the lore is immaculate. mwah, go detect some scaffolds. 💖✨🎀

📦 where this page comes from