Help on function shrake_rupley in module mdtraj.geometry.sasa:
shrake_rupley(traj, probe_radius=0.14, n_sphere_points=960, mode='atom')
Compute the solvent accessible surface area of each atom or residue in each simulation frame.
Parameters
----------
traj : Trajectory
An mtraj trajectory.
probe_radius : float, optional
The radius of the probe, in nm.
n_sphere_points : int, optional
The number of points representing the surface of each atom, higher
values leads to more accuracy.
mode : {'atom', 'residue'}
In mode == 'atom', the extracted areas are resolved per-atom
In mode == 'residue', this is consolidated down to the
per-residue SASA by summing over the atoms in each residue.
Returns
-------
areas : np.array, shape=(n_frames, n_features)
The accessible surface area of each atom or residue in every frame.
If mode == 'atom', the second dimension will index the atoms in
the trajectory, whereas if mode == 'residue', the second
dimension will index the residues.
Notes
-----
This code implements the Shrake and Rupley algorithm, with the Golden
Section Spiral algorithm to generate the sphere points. The basic idea
is to great a mesh of points representing the surface of each atom
(at a distance of the van der waals radius plus the probe
radius from the nuclei), and then count the number of such mesh points
that are on the molecular surface -- i.e. not within the radius of another
atom. Assuming that the points are evenly distributed, the number of points
is directly proportional to the accessible surface area (its just 4*pi*r^2
time the fraction of the points that are accessible).
There are a number of different ways to generate the points on the sphere --
possibly the best way would be to do a little "molecular dyanmics" : put the
points on the sphere, and then run MD where all the points repel one another
and wait for them to get to an energy minimum. But that sounds expensive.
This code uses the golden section spiral algorithm
(picture at http://xsisupport.com/2012/02/25/evenly-distributing-points-on-a-sphere-with-the-golden-sectionspiral/)
where you make this spiral that traces out the unit sphere and then put points
down equidistant along the spiral. It's cheap, but not perfect.
The gromacs utility g_sas uses a slightly different algorithm for generating
points on the sphere, which is based on an icosahedral tesselation.
roughly, the icosahedral tesselation works something like this
http://www.ziyan.info/2008/11/sphere-tessellation-using-icosahedron.html
References
----------
.. [1] Shrake, A; Rupley, JA. (1973) J Mol Biol 79 (2): 351--71.