From: Noel O'B. <no...@ca...> - 2006-08-08 08:41:03
|
Hello Priyashree, I am copying this email to the openbabel-scripting mailing list so that other developers can help with this question. On Mon, 2006-08-07 at 15:08 -0700, pri...@ya... wrote: > I need to use pyopenbabel to obtain the outcome (i.e. similarity > measures) of tanimoto kernel, Minmax and Hybrid kernel on a SDF file > which contains a large number of molecules. Are these kernels already > implemented in this software or do I need to code them. Also in order > to implement the above kernels I will need to perform DFS on the > molecules, is this functionality provided in pyopenbabel. Also it > would be great if you could guide me to the installation process as i > am new to pyopenbabel. First of all, I am fairly sure that these methods are not present in OpenBabel. However, I know that Joerg Wegner has done a lot of work with graph kernels, and these features may be available in JOELIB2 (a Java cheminformatics library similar to OpenBabel). I have copied him into this reply. If you decide to code these yourself, either in C++ or Python, we would encourage you to donate your code to OpenBabel so that it will be available to others. We can discuss this further if you are interested. Regarding DFS specifically, I believe it is present but I am not sure where. I'm sure that Geoff can comment on this. Regarding installation, we should have an install page on the web site. At the moment we don't have one, but I will write one as soon as possible. What operating system do you use? If you are using Windows, I am afraid you will not be able to use Python to access OpenBabel, you can only use C++. Best regards, Noel |