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HADDOCK scriptorium - geometrical properties of a molecule

HOW TO CALCULATE GEOMETRICAL PROPERTIES OF A MOLECULE

geometry.py is a python module, which is composed of three functions (to make use of the geometry module, you should have Biopython installed): 

  1. center_of_mass: calculates the center of mass of a molecule. It can be run in two modes: geometric=False or geometric=Truegeometric=False assumes that all the atoms present in the molecule has the same mass. 
  2. calculate_shape_paramcalculates the dimensions of the smallest ellipsoid into which the input molecule can fit (a, b,c, see Ellipsoid-wiki), radius of gyration and anisotropy value, A (for interpretation of it, see below). 
  3. calculate_moment_of_inertia_tensor: calculates the moment of inertia tensor.

Usage:

To use any of the above given functions, you should first import the PDBParser of Biopython and parse your structure with it:

from Bio.PDB import PDBParser
P = PDBParser()
s = P.get_structure('id', 'structure.pdb')

And after that you can make use of the each function as follows:

from geometry import center_of_mass
print center_of_mass(s, False)
from geometry import calculate_gyration_tensor
print calculate_shape_param(s)
from geometry import calculate_moment_of_inertia_tensor
print calculate_moment_of_inertia_tensor(s)

How to interpret the anisotrpy value, A (see Ellipsoid-wiki):

If A=0: The molecule is spherical
If A>0: The molecule is prolate
If A<0: The molecule is oblate
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And the following article describing the WeNMR portals should be cited:
Wassenaar et al. (2012). WeNMR: Structural Biology on the Grid.J. Grid. Comp., 10:743-767.

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WeNMR is an e-Infrastructure project funded under the 7th framework of the EU. Contract no. 261572

WestLife, the follow up project of WeNMR is a Virtual Research Environment e-Infrastructure project funded under Horizon 2020. Contract no. 675858

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