Ri6 ddZddlmZddlmZddlmZer ddlmZddl m Z Gdded Z y ) z'Model class, used in Structure objects.) TYPE_CHECKING)Entity)IC_Chain)Chain) StructurecTeZdZdZd dZdZdZdZdZd de d dfd Z d de d dfd Z y)ModelzThe object representing a model in a structure. In a structure derived from an X-ray crystallography experiment, only a single model will be present (with some exceptions). NMR structures normally contain many different models. Nc`d|_|||_n||_tj||y)zYInitialize. Arguments: - id - int - serial_num - int MN)level serial_numr__init__)selfidr s E/home/agent/.friday_env/lib/python3.12/site-packages/Bio/PDB/Model.pyrzModel.__init__s-   DO(DOb!c*d|jdS)zReturn model identifier.z )get_idrs r__repr__zModel.__repr__*sDKKM?!,,rc#$K|Ed{y7w)zReturn chains.Nrs r get_chainszModel.get_chains.s s c#NK|jD] }|Ed{y7w)zReturn residues.N)r)rcs r get_residueszModel.get_residues2s&" ALL   %#%c#NK|jD] }|Ed{y7w)z Return atoms.N)r)rrs r get_atomszModel.get_atoms7s(""$ ALL  rverbosereturncP|jD]}|j|y)zCreate/update internal coordinates from Atom X,Y,Z coordinates. Internal coordinates are bond length, angle and dihedral angles. :param verbose bool: default False describe runtime problems N)ratom_to_internal_coordinatesrr"chns rr%z"Model.atom_to_internal_coordinates<(??$ 6C  , ,W 5 6rcP|jD]}|j|y)zCreate/update atom coordinates from internal coordinates. :param verbose bool: default False describe runtime problems :raises Exception: if any chain does not have .pic attribute N)rinternal_to_atom_coordinatesr&s rr*z"Model.internal_to_atom_coordinatesGr(r)N)F) __name__ __module__ __qualname____doc__rrrrr!boolr%r*rrrr r sF" -  6D 6T 6 6D 6T 6rr )rrN) r.typingrBio.PDB.EntityrBio.PDB.internal_coordsr Bio.PDB.ChainrBio.PDB.Structurerr rrrr5s. . !,#+>6F' (>6r