[Biojava-l] BioJava3 - Structure - Bug

[Andreas Prlic]

Hi Jose,

Thanks for spotting this. I disabled the get/setPDBline a while ago
since it essentially doubles memory usage. It would be better to have
an Atom.toPDB or a FileConvert.toPDB(Atom) class that builds up the
String output dynamically.. I will flag the method calls as
deprecated.

Andreas


2010/12/30 José Augusto Salim <jose.asalim at gmail.com>:
> Hi Andreas,
>
> I have used BioJava3 and I find some kind of bug on it. When I try to use
> the function getPBDline from Atom interface it return a blank string, it
> because in PDBFileParser when a new AtomImpl is created no pdbLine is set.
> So, I change the code for it works, just but the line:
>
> atom.setPDBline(line.trim());
>
> in PDBFileParser.java
>
> I'm sending the file for you.
>
> thanks for BioJava3 it has been very useful for my work.
>
> best regardless,
>
> ===
> José Augusto Salim
> Computer Engineer
> -------------------------------
> http://www.thezeitgeistmovement.com
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>
>