mdtraj.baker_hubbard

mdtraj.baker_hubbard(traj, freq=0.1, exclude_water=True)

Identify hydrogen bonds based on cutoffs for the Donor-H...Acceptor distance and angle.

The criterion employed is \(\theta > 120\) and \(r_\text{H...Acceptor} < 2.5 A\).

When donor the donor is ‘N’ and the acceptor is ‘O’, this corresponds to the definition established in [R4]. The donors considered by this method are NH and OH, and the acceptors considered are O.

Parameters:

traj : md.Trajectory

An mdtraj trajectory. It must contain topology information.

freq : float, default=0.1

Return only hydrogen bonds that occur in greater this fraction of the frames in the trajectory.

exclude_water : bool, default=True

Exclude solvent molecules from consideration
Returns:

hbonds : np.array, shape=[n_hbonds, 3], dtype=int

An array containing the indices atoms involved in each of the identified hydrogen bonds. Each row contains three integer indices, (d_i, h_i, a_i), such that d_i is the index of the donor atom, h_i the index of the hydrogen atom, and a_i the index of the acceptor atom involved in a hydrogen bond which occurs (according to the definition above) in proportion greater than freq of the trajectory.

See also

kabsch_sander

Notes

[R4]Baker, E. N., and R. E. Hubbard. “Hydrogen bonding in globular proteins.” Progress in Biophysics and Molecular Biology 44.2 (1984): 97-179.

Examples

>>> md.baker_hubbard(t)
array([[  0,  10,   8],
       [  0,  11,   7],
       [ 69,  73,  54],
       [ 76,  82,  65],
       [119, 131,  89],
       [140, 148, 265],
       [166, 177, 122],
       [181, 188, 231]])
>>> label = lambda hbond : '%s -- %s' % (t.topology.atom(hbond[0]), t.topology.atom(hbond[2]))
>>> for hbond in hbonds:
>>>     print label(hbond)
GLU1-N -- GLU1-OE2 
GLU1-N -- GLU1-OE1
GLY6-N -- SER4-O
CYS7-N -- GLY5-O
TYR11-N -- VAL8-O
MET12-N -- LYS20-O
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