INCHI-1(1)

💖 INCHI-1 💖

okay bestie, pull up a chair, because this is the manual page for inchi-1, the section 1 command that is literally the whole inchi-1 executable. yes, the entire program. it's giving "one binary to rule them all" energy and honestly? we're obsessed. 💅

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✨ NAME ✨

inchi-1 — the inchi-1 executable. that's it, that's the name, short and iconic. 🎀

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🌸 SYNOPSIS 🌸

inchi-1 inputFile [outputFile [logFile [problemFile]]] [-option[
-option...]] inchi-1 inputFiles... -AMI [-option[ -option...]]

so like two whole vibes live in here: the classic one-file run where you can optionally hand it an outputFile, a logFile, and a problemFile in that exact order, and then the -AMI era where you can just throw a whole pile of inputFiles... at it and let it cook. 🔥

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👑 OPTIONS 👑

🍓 Input

• STDIO — use the standard input/output streams. classic, minimal, effective.
• InpAux — input structures in InChI default aux. info format (for use with STDIO).
• SDF:DataHeader — read from the input SDfile the ID under this DataHeader.
• START:n — start at the n-th input structure.
• END:n — stop after the n-th input structure.
• RECORD:n — treat only the n-th input structure.
• AMI — allow multiple input files (wildcards supported). the group-chat mode fr fr.
• AMIOutStd — write output to stdout (in AMI mode).
• AMILogStd — write log to stderr (in AMI mode).
• AMIPrbNone — suppress creation of problem files (in AMI mode).

🦋 Output

• NoLabels — omit structure number, DataHeader and ID from InChI output.
• NoWarnings — suppress all warning messages. (not me ignoring my own drama 😭)
• AuxNone — omit auxiliary information.
• SaveOpt — save custom InChI creation options (non-standard InChI).
• Tabbed — separate structure number, InChI, and AuxInfo with tabs. aesthetic spacing, we love.
• MergeHash — combine InChIKey with extra hash(es) if present.
• NoInChI — do not print InChI string itself.
• OutErrInChI — on fail, print empty InChI (default: nothing).
• OutputSDF — convert InChI created with default aux. info to SDfile.
• SdfAtomsDT — output Hydrogen Isotopes to SDfile as Atoms D and T.

💜 Structure perception

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

🧚 Stereo perception modifiers (non-standard InChI)

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

🌈 Customizing InChI creation (non-standard InChI)

• SUU — always include omitted unknown/undefined stereo.
• SLUUD — make labels for unknown and undefined stereo different.
• RecMet — include reconnected metals results.
• FixedH — include 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).

⭐ Generation

• Wnumber — set time-out per structure in seconds; W0 means unlimited.
• WMnumber — set time-out per structure in milliseconds (int); WM0 means unlimited.
• LargeMolecules — treat molecules up to 32766 atoms (experimental).
• WarnOnEmptyStructure — warn and produce empty InChI for empty structure.
• Polymers — allow processing of polymers (experimental).
• Polymers105 — allow processing of polymers (experimental, legacy mode of v. 1.05).
• FoldCRU — fold polymer CRU if inner repeats occur.
• NoFrameShift — disable polymer CRU frame shift.
• NoEdits — disable polymer CRU frame shift and folding.
• NPZz — allow non-polymer-related Zz atoms (pseudo element placeholders).
• SAtZz — allow stereo at atoms connected to Zz (default: disabled).
• Key — generate InChIKey.
• XHash1 — generate hash extension (to 256 bits) for 1st block of InChIKey.
• XHash2 — generate hash extension (to 256 bits) for 2nd block of InChIKey.

💅 Conversion

• InChI2Struct — convert InChI string(s) to structure(s) in InChI aux.info format.
• InChI2InChI — convert Convert InChI string(s) into InChI string(s).

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🌸 psst, bestie: a bunch of these are marked experimental, and like — that's not me being cute, that's literally the word on the page. iykyk. treat those flags with the respect they deserve. 🫶

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and that's the whole page, no notes. this is the inchi-1 manual from 01/15/2026 — manifesting clean structures and zero warnings for you forever. slay, run your molecules, and hydrate. 💖✨🦋👑