dihedral_side_chain

biotite.structure.dihedral_side_chain(atoms)

Measure the side chain \(\chi\) dihedral angles of amino acid residues.

Parameters:

atomsAtomArray or AtomArrayStack

The protein structure to measure the side chain dihedral angles for.

Returns:

chindarray, shape=(m, n, 4) or shape=(n, 4), dtype=float

An array containing the up to four side chain dihedral angles for every amino acid residue. Trailing \(\chi\) angles that are not defined for an amino acid are filled with \(NaN\) values. The same is True for all residues that are not canonical amino acids.

Notes

By convention, the \(\chi_2\) angle of leucine is defined using CD1 instead of CD2.

Examples

>>> res_ids, res_names = get_residues(atom_array)
>>> dihedrals = dihedral_side_chain(atom_array)
>>> for res_id, res_name, dihedrals in zip(res_ids, res_names, dihedrals):
...     print(f"{res_name.capitalize()}{res_id:<2d}:", dihedrals)
Asn1 : [-1.180 -0.066    nan    nan]
Leu2 : [0.923 1.866   nan   nan]
Tyr3 : [-2.593 -1.487    nan    nan]
Ile4 : [-0.781 -0.972    nan    nan]
Gln5 : [-2.557  1.410 -1.776    nan]
Trp6 : [3.117 1.372   nan   nan]
Leu7 : [-1.33  3.08   nan   nan]
Lys8 : [ 1.320  1.734  3.076 -2.022]
Asp9 : [-1.623  0.909    nan    nan]
Gly10: [nan nan nan nan]
Gly11: [nan nan nan nan]
Pro12: [-0.331  0.539    nan    nan]
Ser13: [-1.067    nan    nan    nan]
Ser14: [-2.514    nan    nan    nan]
Gly15: [nan nan nan nan]
Arg16: [ 1.032 -3.063  1.541 -1.568]
Pro17: [ 0.522 -0.601    nan    nan]
Pro18: [ 0.475 -0.577    nan    nan]
Pro19: [ 0.561 -0.602    nan    nan]
Ser20: [-1.055    nan    nan    nan]