o Rŀg@sdZddlmZddlmZddlmZddlmZddlmZer.ddl m Z ddl m Z ed d d Z iZd ed <ded<ded<ded<Gdd d edZGdddeZdS)z)Residue class, used by Structure objects.) TYPE_CHECKING)TypeVar)DisorderedEntityWrapper)Entity)PDBConstructionException)Atom)Chain _ResidueTResidue)boundNCACOc @sveZdZdZddZddZ ddeded ed efd d Zd dZ ddZ ddZ ddZ ddZ ddZddZdS)r z4Represents a residue. A Residue object stores atoms.cCs.d|_d|_||_||_d|_t||dS)Initialize the class.RrN)level disorderedresnamesegidinternal_coordr__init__)selfidrrrC/var/www/html/myenv/lib/python3.10/site-packages/Bio/PDB/Residue.pyr"s zResidue.__init__cCs*|}|\}}}||||f}d|S)zReturn the residue full id.z&) get_resnameget_idrrhetflagresseqicodefull_idrrr__repr__+s zResidue.__repr__Frothercompare_coordinatesreturncCs8t|t|s dS|j|jko|j|jkot|||S)aCompare this residue to the other residue using a strict definition of equality. The residues are equal if they have the same name, identifier, and their constituent atoms are strictly equal. :param other: The residue to compare this residue to :type other: Residue :param compare_coordinates: Whether to compare the coordinates of the atoms :type compare_coordinates: bool :return: Whether the residues are strictly equal :rtype: bool F) isinstancetyperrrstrictly_equals)rr(r)rrrr-2s   zResidue.strictly_equalscCs6|}||rtd|d|t||dS)z}Add an Atom object. Checks for adding duplicate atoms, and raises a PDBConstructionException if so. zAtom z defined twice in residue N)r!has_idrradd)ratomatom_idrrrr/Js  z Residue.addcCs d|_dS)zSet the disordered flag.r Nrrrrrflag_disorderedWs zResidue.flag_disorderedcC|jS)z2Return 1 if the residue contains disordered atoms.r2r3rrr is_disordered[zResidue.is_disorderedcCr5)zReturn the residue name.)rr3rrrr _r7zResidue.get_resnamecCs:|}g}|D]}|r||7}q||q|S)z5Return the list of all atoms, unpack DisorderedAtoms.)get_listr6disordered_get_listappend)r atom_listundisordered_atom_listr0rrrget_unpacked_listcs zResidue.get_unpacked_listcCr5)zReturn the segment identifier.)rr3rrr get_segidnr7zResidue.get_segidccs|EdHdS)z Return atoms.Nrr3rrr get_atomsrszResidue.get_atomsN)F)__name__ __module__ __qualname____doc__rr'r boolr-r/r4r6r r=r>r?rrrrr s*    )rrc@s@eZdZdZddZddZddZdd Zd d Zd d Z dS)DisorderedResiduezDisorderedResidue is a wrapper around two or more Residue objects. It is used to represent point mutations (e.g. there is a Ser 60 and a Cys 60 residue, each with 50 % occupancy). cCst||dS)rN)rr)rrrrrr~szDisorderedResidue.__init__cCs4|jr|}|\}}}||||f}d|SdS)z*Return disordered residue full identifier.z0z) child_dictr r!r"rrrr's  zDisorderedResidue.__repr__cCsV|}|dkr$|}|\}}}||td||||f||dS)zAdd atom to residue.rz2Blank altlocs in duplicate residue %s (%s, %i, %s)N)disordered_getr6r r!r/r)rr0residuerhetr$r%rrrr/s   zDisorderedResidue.addcCs|D]}|qdS)z,Sort the atoms in the child Residue objects.N)r9sort)rrHrrrrJs  zDisorderedResidue.sortcCs>|}|}||||rJ|||<||dS)zrAdd a residue object and use its resname as key. Arguments: - residue - Residue object N)r get_parent set_parentdisordered_has_iddisordered_select)rrHrchainrrrdisordered_adds  z DisorderedResidue.disordered_addcCs^|j|}|j|u}|j|=||r%|jr%tt|j}||dS|js-d|_dSdS)zRemove a child residue from the DisorderedResidue. Arguments: - resname - name of the child residue to remove, as a string. N)rFselected_child detach_parentnextiterrN)rrrH is_selectedchildrrrdisordered_removes    z#DisorderedResidue.disordered_removeN) r@rArBrCrr'r/rJrPrWrrrrrEws  rEN)rCtypingrrBio.PDB.EntityrrBio.PDB.PDBExceptionsr Bio.PDB.Atomr Bio.PDB.Chainrr _atom_name_dictr rErrrrs"        X