[Biopython] geometry.py

[ezgi karaca]

Hello Frederico,

In the code, we had a small scaling error and a typo, they are fixed
right now. You can get the current version from the same link:
http://nmr.chem.uu.nl/~joao/f/geometry.py

Just to make things clear, this is how we calculate the dimensions:

1. We calculate the gyration tensor of the protein (the geometrical
one, we don't consider the masses)

2. We diagonalize the gyration tensor and get the eigenvalues of it

3. We take the square roots of the eigenvalues, and those correspond
to the length of the semi-axis of ellipsoid

We got this procedure from the following reference: *Vondrasek J
(2011) Gyration- and Inertia-Tensor-Based Collective Coordinates for
Metadynamics. Application on the Conformational Behavior of
Polyalanine Peptides and Trp-Cage Folding - The Journal of Physical
Chemistry A*

 As João has indicated, Dmax and the maximum axis length should not be
exactly the same, since we average out the coordinates while
calculating the gyration tensor. But, of course they should at least
be close to each other. So, please test the current version to see how
well it matches with your calculations and hopefully this version will
give us more reasonable results!

Cheers,

Ezgi