INCHI_MAIN(1)

💖 INCHI_MAIN(1) 💖

okay bestie, gather round, because today we're learning inchi_main(1) — the InChI library call example that runs on the classic API. yes the classic one. she's vintage, she's reliable, she slays.

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✨ NAME ✨

inchi_main — InChI library call example, classic API. that's the whole vibe. no notes.

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🎀 SYNOPSIS 🎀

inchi_main inputFile [outputFile [logFile [problemFile]]] [-option[-option...]]

so like… you give her an inputFile (mandatory, she's not optional about it 💅), and then everything else is just vibes and brackets. outputFile, logFile, problemFile — all optional, all snuggled inside each other like nesting dolls. and then your -options. as many as you want, back to back, no spaces needed. go off queen.

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👑 OPTIONS 👑

📥 Input

this is where your data comes IN, obviously. the entrance. the red carpet.

• STDIO — use standard input/output streams. pipes and vibes only, no files required.
• InpAux — input structures arrive in the InChI default aux. info format. note: this one's for use with STDIO, so they're a package deal, iykyk.
• SDF:DataHeader — when reading from an input SDfile, grab the ID sitting under this DataHeader. she reads the label, not the tea.
• START:n — start at the n-th input structure. skip the intro, we're jumping straight into the plot.
• END:n — stop after the n-th input structure. that's a wrap, everyone go home.
• RECORD:n — treat ONLY the n-th input structure. one and done. main character energy, no ensemble cast.

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📤 Output

what she gives back. her little gifts to you 🎁

• NoLabels — omit the structure number, the DataHeader, and the ID from the InChI output. anonymous. mysterious. iconic.
• NoWarnings — suppress all warning messages. (the warnings are still happening, she's just not telling you 🙈)
• AuxNone — omit auxiliary information entirely.
• SaveOpt — save custom InChI creation options, aka non-standard InChI. she remembers what you asked for ✨
• Tabbed — separate the structure number, the InChI, and the AuxInfo with tabs. clean columns, immaculate presentation.
• MergeHash — combine the InChIKey with extra hash(es) if present.
• NoInChI — do NOT print the InChI string itself. wild, I know, it's literally in the name of the program. she contains multitudes.
• OutputSDF — convert an InChI created with default aux. info to an SDfile.
• SdfAtomsDT — output Hydrogen Isotopes to the SDfile as Atoms D and T.

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🔍 Structure perception

how she sees your molecules. reading them. understanding them. basically therapy but for atoms.

• SNon — exclude stereo. (default: include absolute stereo.)
• NEWPSOFF — both ends of the wedge point to stereocenters. (default: a narrow end.)
• LooseTSACheck — relax the criteria for ambiguous drawing when it comes to in-ring tetrahedral stereo. be cool about it.
• DoNotAddH — all H are explicit. (default: add H according to usual valences.)

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🧚 Stereo perception modifiers (non-standard InChI)

okay so these ones are the non-standard InChI girlies. she's off-script and she's thriving.

• SRel — relative stereo.
• SRac — racemic stereo.
• SUCF — use the Chiral Flag: On means Absolute stereo, Off means Relative.

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🌸 Customizing InChI creation (non-standard InChI)

more non-standard behavior. she's customizing. she's building her own lore.

• SUU — always include omitted unknown/undefined stereo. no more hiding.
• SLUUD — make the labels for unknown and undefined stereo different from each other. yes they were the same before, yes it was confusing.
• RecMet — include reconnected metals results.
• FixedH — include the Fixed H layer.
• KET — account for keto-enol tautomerism. (experimental!)
• 15T — account for 1,5-tautomerism. (experimental!)
• PT_22_00 — account for PT_22_00 tautomerism. (experimental!)
• PT_16_00 — account for PT_16_00 tautomerism. (experimental!)
• PT_06_00 — account for PT_06_00 tautomerism. (experimental!)
• PT_39_00 — account for PT_39_00 tautomerism. (experimental!)
• PT_13_00 — account for PT_13_00 tautomerism. (experimental!)
• PT_18_00 — account for PT_18_00 tautomerism. (experimental!)

okay so heads up bestie: every single one of those tautomerism options is marked experimental. that word is doing a LOT of work. treat accordingly 🔥

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⚙️ Generation

the actual making of the thing. the birth of the InChI. scream, cry, throw up 💀

• Wnumber — set the time-out per structure in seconds. W0 means unlimited. (unlimited!! she'll wait forever. romantic.)
• WMnumber — set the time-out per structure in milliseconds (int). WM0 means unlimited.
• LargeMolecules — treat molecules up to 32766 atoms. (experimental!)
• WarnOnEmptyStructure — warn and produce an empty InChI for an empty structure. she'll tell you, but she'll still do it.
• Polymers — allow processing of polymers. (experimental!)
• Polymers105 — allow processing of polymers. (experimental, and it's the legacy mode of v. 1.05 — vintage mode, quite demure of her.)
• FoldCRU — fold the polymer CRU if inner repeats occur.
• NoFrameShift — disable the polymer CRU frame shift.
• NoEdits — disable the polymer CRU frame shift AND the folding. all of it. gone.
• NPZz — allow non-polymer-related Zz atoms (those are pseudo element placeholders, fyi).
• SAtZz — allow stereo at atoms connected to Zz. (default: disabled.)
• Key — generate the InChIKey. the moment we've all been waiting for 🔥
• XHash1 — generate a hash extension (up to 256 bits) for the 1st block of the InChIKey.
• XHash2 — generate a hash extension (up to 256 bits) for the 2nd block of the InChIKey.

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🔄 Conversion

she's flexible. she can be something else. metamorphosis, but chemistry.

• InChI2Struct — test mode: Mol/SDfile → InChI → Structure → (InChI+AuxInfo). a whole round trip. a journey. she left and came back changed ✈️
• InChI2InChI — Convert Convert InChI string(s) into InChI string(s). (the doubled-up "Convert" is her little typo and we love her for it, no cap 🫶)

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🦋 that's the whole page 🦋

no SEE ALSO, no environment variables, no exit statuses, no examples — she said "keep it simple, keep it iconic." literally nothing else. that's the tea.

fr fr though: every option above is exactly as listed, nothing merged, nothing invented, nothing skipped. 40-something options and we did them ALL. we ate. 👑

peace out bestie, and happy structure parsing, your girl INCHI_MAIN(1) 💖✨🎀

source/version: INCHI_MAIN(1) — dated 01/15/2026. that's the fine print, and she's serving it with a bow. 🎀