is there any documentation provided concerning the wrappers for Jfatcat and Jce (combinatorial extensions) I'm assuming it's within the PDB tools in Biopython... as in Bio.PDB.---- but I cant seem to find it. Thanks.
There are no such wrappers in Biopython - what makes you think there would be? Would you like to write wrappers as a contribution to Biopython?
Well I tried to do something about it, writing a wrapper or using python subprocess module to make us of the functionality of that web program... however I failed, since I don't have the slightest clue of how these wrappers work, I only use them. However in BioJava there's a class that implements the Jce approach as present in the PDB website. http://biojava.org/wiki/BioJava:CookBook:PDB:align and I was thinking that there might be similar module in python that implements the same algorithm, however I cant seem to find anything like it. I think I'm just gonna implement that bit in Java and the make a connection between the Java code in a python script.
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these are two java GUI-webstart applications: what do you mean with "python wrappers" ?
I know there are GUI web apps for them two, which work perfectly fine, that's why you make use of wrappers which is basically using the functionality of those apps inside our python code, by calling their methods with specific parameters. However I can't seem to find any documentation or any online example of someone implementing those wrappers.