Installing Bioclipse

In the process of learning on how to create smiles structures to .png files I tried converiting a .smi file to a .sdf or .mol file using openbabel to no avial.  It seems to only want to read the first structure in the .smi list.

I came across an open source QnA forum that recommend installing dingo, but was unable to get it working at that instance in time. (However as of yesterday, dingo was updated and now works flawlessly.)

I've tried several other programs both on Ubuntu and OpenSuse but each only seems to let me work with a single smiles string at a time, and many won't take this string from the command line.


In comes Bioclipse.

I had some troubble getting Bioclipse up and running at first.  I failed in Ubuntu, and attributed it to having the default version 6 JRE, but couldn't seem to find version 5 in the repository. As it turns out, it will start to run in OpenSUSE with Sun JRE version 6. Therefore, the source, not the version that was the problem and Ubuntu users, be sure to install the sun java package if they wish to run Bioclipse.


So far in OpenSUSE I've found one hitch related to an xul runner error:

Error while booting Bioclipse: SWTErrorXPCOM error -2147467262

org.eclipse.swt.SWTError: XPCOM error -2147467262 
        at org.eclipse.swt.browser.Mozilla.error(Mozilla.java:1638)

        at org.eclipse.swt.browser.Mozilla.setText(Mozilla.java:1861)
        at org.eclipse.swt.browser.Browser.setText(Browser.java:737)

As reported here, this can be solved by editing bioclipse.ini, adding the line:

-Dorg.eclipse.swt.browser.XULRunnerPath=/usr/lib/xulrunner