Codename: inchi, inchikey
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 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 Woff Do not display warnings
JNI-InChI is Copyright � 2006-2010, Sam Adams. JNI-InChI is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License e as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. (See GPL, LGPL licence.)
The modified source, that we use in our program to locate and download dlls, is available here.
The compiled version (jni-inchi_07.jar) is in the lib directory of the installed marvin. If you find any bugs, we recommend asking for a bugfix on our technical support forum, instead of modifying the source.
InchiExport uses the InChI format, InChITM Material is © IUPAC 2005