B ‰°b”ã@shdZddlmZddlmZmZiZded<ded<ded <d ed<Gdd „d eƒZGdd„deƒZdS)z)Residue class, used by Structure objects.é)ÚPDBConstructionException)ÚEntityÚDisorderedEntityWrapperéÚNéZCAéÚCéÚOc@sXeZdZdZdd„Zdd„Zdd„Zdd „Zd d„Zdd „Z dd„Z dd„Zdd„ZdS)ÚResiduez4Represents a residue. A Residue object stores atoms.cCs.d|_d|_||_||_d|_t ||¡dS)zInitialize the class.ÚRrN)ÚlevelÚ disorderedÚresnameÚsegidZinternal_coordrÚ__init__)ÚselfÚidrr©rú.lib/python3.7/site-packages/Bio/PDB/Residue.pyrszResidue.__init__cCs*| ¡}| ¡\}}}||||f}d|S)zReturn the residue full id.z&)Úget_resnameÚget_id)rrÚhetflagÚresseqÚicodeÚfull_idrrrÚ__repr__!szResidue.__repr__cCs2| ¡}| |¡r"td||fƒ‚t ||¡dS)z}Add an Atom object. Checks for adding duplicate atoms, and raises a PDBConstructionException if so. z#Atom %s defined twice in residue %sN)rZhas_idrrÚadd)rÚatomZatom_idrrrr(s zResidue.addcCs d|_dS)zSet the disordered flag.rN)r)rrrrÚflag_disordered5szResidue.flag_disorderedcCs|jS)z2Return 1 if the residue contains disordered atoms.)r)rrrrÚ is_disordered9szResidue.is_disorderedcCs|jS)zReturn the residue name.)r)rrrrr=szResidue.get_resnamecCs>| ¡}g}x,|D]$}| ¡r,|| ¡7}q| |¡qW|S)z5Return the list of all atoms, unpack DisorderedAtoms.)Zget_listr!Údisordered_get_listÚappend)rZ atom_listZundisordered_atom_listrrrrÚget_unpacked_listAs zResidue.get_unpacked_listcCs|jS)zReturn the segment identifier.)r)rrrrÚ get_segidLszResidue.get_segidccs|EdHdS)z Return atoms.Nr)rrrrÚ get_atomsPszResidue.get_atomsN) Ú__name__Ú __module__Ú__qualname__Ú__doc__rrrr r!rr$r%r&rrrrrs rc@s@eZdZdZdd„Zdd„Zdd„Zdd „Zd d„Zdd „Z dS)ÚDisorderedResiduezÁDisorderedResidue 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)zInitialize the class.N)rr)rrrrrr\szDisorderedResidue.__init__cCs8|jr0| ¡}| ¡\}}}||||f}d|SdSdS)z*Return disordered residue full identifier.z0zN)Ú child_dictrr)rrrrrrrrrr`szDisorderedResidue.__repr__cCsV| ¡}| ¡dksH| ¡}| ¡\}}}| |¡td||||fƒ‚| |¡dS)zAdd atom to residue.rz2Blank altlocs in duplicate residue %s (%s, %i, %s)N)Zdisordered_getr!rrrr)rrÚresiduerZhetrrrrrrjs zDisorderedResidue.addcCsx| ¡D]}| ¡q WdS)z,Sort the atoms in the child Residue objects.N)r"Úsort)rr-rrrr.zszDisorderedResidue.sortcCs>| ¡}| ¡}| |¡| |¡r(t‚|||<| |¡dS)zrAdd a residue object and use its resname as key. Arguments: - residue - Residue object N)rZ get_parentZ set_parentZdisordered_has_idÚAssertionErrorÚdisordered_select)rr-rÚchainrrrÚdisordered_adds z DisorderedResidue.disordered_addcCsX|j|}|j|k}|j|=| ¡|rH|jrHtt|jƒƒ}| |¡n|jsTd|_dS)z—Remove a child residue from the DisorderedResidue. Arguments: - resname - name of the child residue to remove, as a string. N)r,Zselected_childZ detach_parentÚnextÚiterr0)rrr-Zis_selectedZchildrrrÚdisordered_removeŽs z#DisorderedResidue.disordered_removeN) r'r(r)r*rrrr.r2r5rrrrr+Us r+N) r*ZBio.PDB.PDBExceptionsrZBio.PDB.EntityrrZ_atom_name_dictrr+rrrrÚs@