bis_protein_structure.TORSION2.get_coordinates

bis_protein_structure.TORSION2.get_coordinates(final_residue, residues, chain)[source]

Retrieves the coordinates of atoms from the residues in a chain.

Parameters:

  • final_residue (int) – The total number of residues to be considered.

  • residues (dict) – A dictionary mapping residue IDs to residue names.

  • chain (Chain) – The chain object containing the residues.

Returns:

  • coord (np.ndarray) – An array of shape (final_residue, 37, 3) containing the coordinates of the atoms.

  • coord_mask (np.ndarray) – An array of shape (final_residue, 37, 1) indicating which atoms have valid coordinates.

  • unexpected_atoms (dict) – A dictionary mapping residue IDs to unexpected atom IDs found during processing.