J. Cheminf. 2011, 3, 33

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Chemical Markup Language (cml, mrv)

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InChIKey (inchikey)

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InChI format (inchi)

IUPAC/NIST molecular identifier

Read Options

X <Option string>
 List of InChI options
n molecule name follows InChI on same line
a add InChI string to molecule name

Write Options

Standard InChI is written unless certain InChI options are used
K output InChIKey only
t add molecule name after InChI

ignore less important warnings

These are: ‘Omitted undefined stereo’ ‘Charges were rearranged’ ‘Proton(s) added/removed’ ‘Metal was disconnected’

a output auxiliary information
l display InChI log
r recalculate InChI; normally an input InChI is reused

recalculate wedge and hash bonds(2D structures only)

Uniqueness options (see also --unique and --sort which are more versatile)

u output only unique molecules
U output only unique molecules and sort them

compare first molecule to others

This can also be done with InChICompare format:

babel first.smi second.mol third.cml -ok
T <param>

truncate InChI according to various parameters

See below for possible truncation parameters.

X <Option string>

Additional InChI options

See InChI documentation. These options should be space delimited in a single quoted string.

  • Structure perception (compatible with stdInChI): NEWPSOFF, DoNotAddH, SNon
  • Stereo interpretation (produces non-standard InChI): SRel, SRac, SUCF, ChiralFlagON, ChiralFlagOFF
  • InChI creation options (produces non-standard InChI): SUU, SLUUD, FixedH, RecMet, KET, 15T

The following options are for convenience, e.g. -xF but produce non-standard InChI.

F include fixed hydrogen layer
M include bonds to metal


Truncation parameters used with -xT:

/formula formula only
/connect formula and connectivity only
/nostereo ignore E/Z and sp3 stereochemistry
/sp3 ignore sp3 stereochemistry
/noEZ ignore E/Z steroeochemistry
/nochg ignore charge and protonation
/noiso ignore isotopes

Note that these can also be combined, e.g. /nochg/noiso