restype_atom37_to_rigid_group

Sparse encoding 21 types of amino acid. Each amino acid contains the rigid group the atoms belong to. Shape is \((21, 37)\) .

8 groups are

  • 0 - backbone-group Main chain rigid group corresponding to torsion angle backbone between atoms \(N-C\alpha-C-C\beta\) in amino acid. CA is the origin point, C is on positive x-axis and N is on X-Y plane.

  • 1 - pre-omega-group Rigid group corresponding to torsion angle pre-omega between atoms \(N_i-C\alpha_i-N_{i-1}-C\alpha_{i-1}\) in amino acid.

  • 2 - phi-group Rigid group corresponding to torsion angle phi between atoms \(C_i-C\alpha_i-N_i-C_{i+1}\) in amino acid.

  • 3 - psi-group Rigid group corresponding to torsion angle psi between atoms \(N_{i-1}-C_i-C\alpha_i-N_i\) in amino acid.

  • 4 - chi1-group

  • 5 - chi2-group

  • 6 - chi3-group

  • 7 - chi4-group

chi1,2,3,4-group correspond to torsion angles in the amino acids in chi_angle_atoms . Torsion angles are determined by the coordinates of four atoms [A, B, C, D]. Atom B and C constitute the axis of rotation, in x-axis. The third atom C is the origin point. Atom B is on the negative x-axis. The first atom A is on X-Y plane. So we can determine the coordinate of the fourth atom D.

from mindsponge.common import residue_constants
print(residue_constants.restype_atom37_to_rigid_group)