Firewall when aromatizing???

I am using Molecule::aromatize() (actually since I am not specifying


an integer parameter as required in Molecule::aromatize(int), I'm


invoking the inherited aromatize() from class MoleculeGraph)





I am getting a SECURITY exception. The API simply says:


Throws:


java.lang.SecurityException - cannot load module because of a security problem (firewall)





Can someone explain this to me and/or tell me how to get around the


security exception. Is this caused by my particular machine's firewall???





Would it help for me to (instead) invoke Molecule::aromatize(int)??


If so, what algorithm should I use? (what int parameter should I


pass it? API says the parameter specifies which algorithm to use)





I am applying the method to a LIST of Molecules.....the exception is


only being thrown on SOME of them (probably only the ones with


aromatics!!)





I need to aromatize() in order to use class MolSearch methods


(findFirst(), etc), or so says the API.





Thanks,





Kevin

I have never seen this kind of problem in Marvin.


Which jar do you use for aromatization? Which version of Marvin/JChem have you got?


Do you use Marvin API from a JSP?

I am experiencing this on another machine (not the one I am at now) so


I am unsure of the versions....only that they were the ones I downloaded


from your website in December (3 months ago).





At this time I am NOT using .jsp....I'm working on "back end" code, so


I'm writing Java classes and use main() programs for testing in a


"DOS window" (using MS Windows XP).





Later today I can check the exact versions. In this case, I do not think


Marvin Sketch is involved at all....its just the Java method throwing


the Security exception when I run my test program in a DOS (WinXP


console window).





Kevin

OK, very strange...I returned to my development machine and without


changing anything, could not reproduce the error!??!! I did REBOOT


the machine....I guess that fixes most problems in WINDOWS, right??





I did have a bug:

Code:

private fun (Molecule[] list) {    int i;    for (i=0; i<list.length; i++)        list[i].aromatize(); }

It turned out some of the elements of the array were NULL....but tonight I


was getting a NULL POINTER EXCEPTION (not a SECURITY EXCEPTION).





Maybe it was that strange herbal tea I was drinking last night?? ;)





Anyway, problem gone! Sorry for the 'wild goose chase'!





Thanks,





Kevin

Hi Kevin,





The security exception occurs when a Marvin module jar file (in this case the aromatization module) could not be loaded. The most frequent cause for this is when a firewall is blocking the access in case of Marvin applets, that's why the exception mentions firewall.





I am glad the problem is over, whatever caused the .jar file inaccessibility.





Best regards,


Szabolcs