Installing JME

The recommended molecular editor for Pathway Tools is Marvin. However, JME is a simpler and smaller applet, but it needs OpenBabel as well, which makes the overall installation more complicated.

JME applet distribution, version 2004.01 or later

Request this by email from Peter Ertl at Novartis (peter.ertl@pharma.novartis.com ). Obtaining and using JME is free of charge. More information about JME, including the license and instructions for using it, can be found at http://www.molinspiration.com/jme/. The distribution will arrive as an email attachment in the form of a ZIP archive. It should be unzipped into a newly created directory in the file system. On UNIX platforms, the command to execute in a shell would look like:

unzip jme-0401.zip

An additional required installation step is to set the shell environment variable JME_PATH to the full directory path in which the JME distribution was unzipped. It is best to do this in one of your shell init scripts such as .cshrc or .login. For example, in csh syntax:

setenv JME_PATH /example/of/full/jme/path

OpenBabel version 1.100.2 or later

This is a format converter between many 2D molecular structure file formats. It is currently needed if a Pathway Tools compound that contains aromatic rings needs to be edited. JME does not currently understand the aromatic bond type directly, and babel is used for converting the aromatic bonds to the alternating single/double bond patterns that JME understands. OpenBabel is completely open source and the source code can be downloaded from http://openbabel.sourceforge.net/.

Build the program by following its installation instructions. This should result in an executable program called babel. This program must be installed in a directory location that is mentioned in the PATH shell environment variable. If babel is not installed or not found, aromatic bonds will show up in JME labeled with a question mark (?), and it will be necessary for the curator to manually change the bond types of the aromatic substructures to an appropriate pattern of alternating single/double bonds.