biotite.structure.dihedral_backbone

biotite.structure.dihedral_backbone(atom_array)[source]

Measure the characteristic backbone dihedral angles of a structure.

Parameters
atom_array: AtomArray or AtomArrayStack

The protein structure. A complete backbone, without gaps, is required here. Chain transitions are allowed, the angles at the transition are NaN. The order of the backbone atoms for each residue must be (N, CA, C).

Returns
phi, psi, omegandarray

An array containing the 3 backbone dihedral angles for every CA. ‘phi’ is not defined at the N-terminus, ‘psi’ and ‘omega’ are not defined at the C-terminus. In these places the arrays have NaN values. If an AtomArrayStack is given, the output angles are 2-dimensional, the first dimension corresponds to the model number.

Raises
BadStructureError

If the amount of backbone atoms is not equal to amount of residues times 3 (for N, CA and C).

See also

dihedral

Examples

>>> phi, psi, omega = dihedral_backbone(atom_array)
>>> print(np.stack([np.rad2deg(phi), np.rad2deg(psi)]).T)
[[     nan  -56.145]
 [ -43.980  -51.309]
 [ -66.466  -30.898]
 [ -65.219  -45.945]
 [ -64.747  -30.346]
 [ -73.136  -43.425]
 [ -64.882  -43.255]
 [ -59.509  -25.698]
 [ -77.989   -8.823]
 [ 110.784    8.079]
 [  55.244 -124.371]
 [ -57.983  -28.766]
 [ -81.834   19.125]
 [-124.057   13.401]
 [  67.931   25.218]
 [-143.952  131.297]
 [ -70.100  160.068]
 [ -69.484  145.669]
 [ -77.264  124.223]
 [ -78.100      nan]]