Re: [Biojava-l] modify structure

Hi Tamas, it is possible to access the content of a structure and change/add/drop groups and atoms as you wish. When talking about introducing "point mutations" I assume you want to re-label a residue's main chain atoms and drop the side chain atoms, but keep the Cb one? this would take

[Biojava-l] 1.4 vs 1.5

Recently we had a discussion whether Biojava could use the novel features of Java1.5. Since I just have moved two larger applications (633 java files) to Java1.5 I would like to share my experiences with you. Applying the new features to the source code took me two days: This was worth doing beca

Re: [Biojava-l] modify structure

Exactly... I want to keep a backbone and replace the whole sidechain asnecessary... I know this should be relatively easy, but I'm a bit lost intthe documentation... On 12/1/05, Andreas Prlic <[EMAIL PROTECTED]> wrote:>> Hi Tamas,>> it is possible to access the content of a structure and> chan

[Biojava-l] help on blast

Thanks for all your ideas. It was really useful . Parveen Date: Wed, 30 Nov 2005 09:42:51 -0800 (PST) From: "W. Eric Trull" <[EMAIL PROTECTED]> Subject: [Biojava-l] help on blast To: biojava-l@biojava.org Cc: [EMAIL PROTECTED], [EMAIL PROTECTED] Message-ID: < [EMAIL PROTECTED]> Content-Type: text/

Re: [Biojava-l] Problem with downloading Genbank-sequence

Hi, the problem is the security-policy of the container I use for my web-application. In this case it's the 'Sun Java System Application Server Platform Edition 8.1'. As Thomas Down suggested, the Server prohibits the creation of ClassLoaders, however they are needed by BioJava. So I tried to

[Biojava-l] Looking for a Fisher(like) Kernel

Hello, I have good news! I have fixed the bug in the BaumWelchTrainer class (hopefully the source in CVS will be updated soon). Now that I am able to train my Profile HMM, I would like to feed my HMM into a Fisher Kernel to perform SVM training in order to find the proper scoring threshold f

Re: [Biojava-l] modify structure

If I've got a Group , which is an amino acid, and I want to shift it by a 3Dvector (or 3 2D vectors), how may I do it?Similarly, if i want to rotate the same structure, how may I do it?If you just can show me a very short sample code, I'd really appreciate it!Thanks! On 12/1/05, Tamas Horvath <[

RE: [Biojava-l] cvs downlod install

Your problem lies here: > when i use in the folder C:\biojava\biojava-live\: > (windows) > cd demos > javac seq\TestEmbl.java > i obtain > $ javac seq\TestEmbl.java > error: cannot read: seqTestEmbl.java > 1 error Note that the java file has not been compiled. Hence when you later try to run