[Biopython-dev] [biopython] Added transform and copy method to Entity in biopython.PDB (#25)

[Thomas Hamelryck]

On Sat, Feb 11, 2012 at 3:55 AM, Eric Talevich <eric.talevich at gmail.com>wrote:

> -        self.coord=numpy.dot(self.coord, rot)+tran
> +        self.coord=numpy.dot(rot, self.coord)+tran
>
>
> This will break every script that uses the transform() method if we apply
> it. It also breaks the unit test, of course, but I can change the unit test
> to match if we accept this patch.
>
> It seems to me that which way is right is a matter of how the user
> specifies the input. I'm not a thinking man, so I don't entirely trust my
> judgment on this one.
>

Indeed. This is not a bug, the method simply assumes a right-multiplying
matrix. Changing this will break many scripts for No Good Reason (TM).

Cheers,

-Thomas

-- 
Thomas Hamelryck
Assoc. Prof., University of Copenhagen, Denmark <http://www.ku.dk>
Visiting Prof., University of Leeds, UK <http://www.leeds.ac.uk>
Group leader Structural
Bioinformatics<http://www.binf.ku.dk/research/structural_bioinformatics/>
Bioinformatics center, Department of Biology
University of Copenhagen
Ole Maaloes Vej 5
DK-2200 Copenhagen N
Denmark