INCHI-1(1)

NAME
inchi-1 - inchi-1 executable

SYNOPSIS

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

OPTIONS

Input

    • STDIO: Use standard input/output streams

    • 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 n-th input structure

    • END:n: Stop after n-th input structure

    • RECORD:n: Treat only n-th input structure

    • AMI: Allow multiple input files (wildcards supported)

    • 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

    • AuxNone: Omit auxiliary information

    • SaveOpt: Save custom InChI creation options (non-standard InChI)

    • Tabbed: Separate structure number, InChI, and AuxInfo with tabs

    • 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)