[Joelib-devel] coordinate transformation bug

[Joerg K. W. <we...@in...>]

Hi Thijs,

please use the developer mailing list, to avoid me answering questions 
multiple times and a more descriptive subject than 'bug'.
You can also use the bug-tracking system.

good point :-)
Actually i've never tested this class, because the rotamere generation 
sources are still not complete ported from the stalled OELib.

The original C++ class is ctransform.cpp.
So, if you're familiar with C++ and pointer references you can have a 
look at your own at OELib or his successor OpenBabel.

I will have a look, but actually i'm not working actively at the rotamer 
generation, but i think it should be:
System.arraycopy(in_xyz, 3 * 2, y, 0, 3);
System.arraycopy(in_xyz, 3 * 3, z, 0, 3);

Because the API docu, i've now added,says:
in_xyz  A length 12 array containing 4 coordinates
(0,0,0), (1,0,0), (0,1,0) and (0,0,1) from the initial
reference frame transformed into the final reference frame

If this not works, i closer look at the matrix transformation is required.

Kind regards, Joerg


> Hi,
> 
> I was playing around a bit with your resources and found what i think is 
> a a bug.
> 
> class:joelib.math.JOECoordTrans
> method: public boolean setup(double[] in_xyz)
> line 509
> 
>     public boolean setup(double[] in_xyz)
>     {
>         //Copy coordinate array
>         double[] xyz = new double[12];
>         double[] y = new double[4];
> 
>         //;xyz[3*2];
>         double[] z = new double[4];
> 
>         //xyz[3*3];
>         int i;
> 
>         //for (i=0 ; i<12 ; i++) xyz[i] = in_xyz[i];
>         System.arraycopy(in_xyz, 0, xyz, 0, 12);
>         System.arraycopy(in_xyz, 3 * 2, y, 0, 4);
>         System.arraycopy(in_xyz, 3 * 3, z, 0, 4);
> Here it goes wrong, since element (3*3) + 4 = 12 does not exist in xyz, and
> i get an arrayindexoutofbounds exception
> 
> The solution is not obvious to me,
> 
> Hopefully you can help me out.
> 
> Thijs Beuming
> 
> 


-- 
Dipl. Chem. Joerg K. Wegner
Center of Bioinformatics Tuebingen (ZBIT)
Department of Computer Architecture
Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
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