IUPAC InChI and InChIKey

Codename: inchi, inchikey

Contents

IUPAC InChI format

The Marvin beans and applications are able to import and export IUPAC InChI files, and export IUPAC InChIKey files. This function does not work in the applets (except signed applets).

The export makes an inchi with AuxInfo by default. The import requires an inchi string (AuxInfo is optional). Without AuxInfo, the generated molecule does not include coordinates.

At the moment Linux, Windows and Mac platforms are supported, but we will also add Sun and possibly HP Unix.

Since Marvin 5.5 the InChI 1.03 version is integrated. Since Marvin 5.5 Marvin uses the jni-inchi sourceforge project to call the native c code. Since Marvin 5.2.5 InChIKey export format is also included.

Export options

Export options can be specified in the format string. The format descriptor and the options are separated by a colon, the options by commas.

... Basic options for aromatization and H atom adding/removal
SNon Exclude stereo (Deafult: Include Absolute stereo)
SRel Relative stereo
SRac Racemic stereo
SUCF Use Chiral Flag: On means Absolute stereo, Off - Relative
ChiralFlagON Use Chiral Flag (Absolute stereo)
ChiralFlagOFF Do not use Chiral Flag (relative stereo)
SUU Include omitted unknown/undefined stereo
NEWPS Narrow end of wedge points to stereocenter (default: both)
RecMet Include reconnected metals results
FixedH Mobile H Perception Off (Default: On)
AuxNone Omit auxiliary information (default: Include)
NoADP Disable Aggressive Deprotonation (for testing only)
Compress Compressed output
DoNotAddH Don't add H according to usual valences: all H are explicit
Key Exports the InChIKey as well

Known Issues

References

InchiExport uses the InChI format, InChITM Material is © IUPAC 2005