Installing InChi

InChi (International Chemical Identifier -- see www.inchi.info) is a character string that uniquely identifies a chemical structure. After a compound structure editor like Marvin has beed used to modify a structure, it is possible to have the InChi recomputed by means of an external program.

The InChi program is not developed by SRI International, and is not included in the Pathway Tools distribution. The so-called "Standard InChi" should be used to allow for the easiest comparison between different chemical databases. (There are other variations of InChi, which make comparisons harder.) Obtaining and using InChi is free of charge.

Downloading

Download the following InChi distribution, for Linux and MSWindows: http://www.iupac.org/inchi/download/STDINCHI-1-BIN.zip

For Mac OSX, try this binary, compiled from source code: http://bioinformatics.ai.sri.com/ptools/inchi-macosx/stdinchi-1

Installation in Linux

On UNIX platforms, uncompress the downloaded archive file using the command 
unzip STDINCHI-1-BIN.zip
Pathway Tools needs to find the stdinchi-1 executable by searching the directories listed in the PATH environment variable. You'd want to add the following to one of the user's shell init scripts such as .cshrc or .login. For example, in csh syntax: 
setenv PATH /replace/with/full/inchi/path:$PATH
Restart Pathway Tools.

Installation on Mac OSX

Unfortunately, at this time, there appears to be no prebuilt executable included in the official InChi distribution. It has to be compiled from source code, that is available in a separate distribution. We have compiled such an executable, which appears to work. See the Download section. Please ensure that the execute flags are set for this executable.

Pathway Tools needs to find the stdinchi-1 executable by searching the directories listed in the PATH environment variable. For Mac OS X, bash is the default shell, so you'd want to add the following to your .bashrc file (located in your home directory): 

export PATH=/replace/with/full/inchi/path:$PATH
Restart Pathway Tools.

Installation in MSWindows

Unzip the downloaded archive file into a newly created local directory (e.g., C:\Program Files\InChi).

Next, you need to edit the environment variable called Path, and set it to the full directory path in which the file stdinchi-1.exe was installed. To do so: right-click on the "My Computer" icon (on the desktop), and choose "Properties". In the window that opens, click on the "Advanced" tab, then click on the "Environment Variables" button. A window like the one depicted in the Figure below will open.

Under "System Variables", select the Path entry (which should already exist) and click the "Edit" button. In the resulting popup, add the full path of the stdinchi-1.exe file to the Variable value, using the semicolon character as a separator.

Restart Pathway Tools.