Radius of gyration
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This script does calcualate the radius of gyration of a molecule.
Thanks to Tsjerk Wassenaar for posting this script on the pymol-users mailing list!
from pymol import cmd
from itertools import izip
import math
def rgyrate(selection='(all)', quiet=1):
'''
DESCRIPTION
Radius of gyration
USAGE
rgyrate [ selection ]
'''
quiet = int(quiet)
model = cmd.get_model(selection).atom
x = [i.coord for i in model]
mass = [i.get_mass() for i in model]
xm = [(m*i,m*j,m*k) for (i,j,k),m in izip(x,mass)]
tmass = sum(mass)
rr = sum(mi*i+mj*j+mk*k for (i,j,k),(mi,mj,mk) in izip(x,xm))
mm = sum((sum(i)/tmass)**2 for i in izip(*xm))
rg = math.sqrt(rr/tmass - mm)
if not quiet:
print "Radius of gyration: %.2f" % (rg)
return rg
cmd.extend("rgyrate", rgyrate)
# vi:expandtab