mdtraj.kabsch_sander¶

mdtraj.kabsch_sander(traj)¶

Compute the Kabsch-Sander hydrogen bond energy between each pair of residues in every frame.

Hydrogen bonds are defined using an electrostatic definition, assuming partial charges of -0.42 e and +0.20 e to the carbonyl oxygen and amide hydrogen respectively, their opposites assigned to the carbonyl carbon and amide nitrogen. A hydrogen bond is identified if E in the following equation is less than -0.5 kcal/mol:

\[E = 0.42 \cdot 0.2 \cdot 33.2 kcal/(mol \cdot nm) * \ (1/r_{ON} + 1/r_{CH} - 1/r_{OH} - 1/r_{CN})\]

Parameters:

traj : md.Trajectory

An mdtraj trajectory. It must contain topology information.

Returns:

matrices : list of scipy.sparse.csr_matrix

The return value is a list of length equal to the number of frames in the trajectory. Each element is an n_residues x n_residues sparse matrix, where the existence of an entry at row i, column j with value x means that there exists a hydrogen bond between a backbone CO group at residue i with a backbone NH group at residue j whose Kabsch-Sander energy is less than -0.5 kcal/mol (the threshold for existence of the “bond”). The exact value of the energy is given by the value x.