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

-w

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

-s

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

-e

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

Comments

Truncation parameters used with -xT:

/formula

formula only

/connect

formula and connectivity only

/nostereo

ignore E/Z and sp3 stereochemistry

/nosp3

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