Calculate Radius of Gyration for a PDB File

[alirezaomidi]

Setup

Radius of gyration is mathematically the root mean square distance of a polymer's atoms from its center of mass, and has its own applications in structural biology and chemistry. It would be great if we could use biopython to calculate it. Specifically, a code like this would be nice:

from Bio.PDB.PDBParser import PDBParser
from Bio.PDB.RG import GyrationRadius

parser = PDBParser()
structure = parser.get_structure("1a8o", "Tests/PDB/1A8O.pdb")
model = structure[0]
rg = GyrationRadius(model)

What do you guys think?

[erik-whiting]

For whatever it's worth, this isn't the first time someone has tried to find a way to do this with Biopython: https://www.biostars.org/p/281805/ it also seems like there's a few existing examples of how to do this:

• From scikit-mobility
• an example with PyMOL
• A small but archived script from a molecular biologist
• This (possibly irrelevant) example from AdKGromacs

So maybe it's worth having and not too much trouble to implement?