RipdZddlmZddlmZddlmZddlmZer ddlm Z ddl m Z Gdd ed Z y ) z'Chain class, used in Structure objects.)Optional) TYPE_CHECKING)Entity)IC_Chain)Model)ResidueceZdZdZdZdZdZdZdZdZ dZ d Z d Z d Z d Zd ZdZdZddeddfdZ ddededzdedzfdZy)ChainzDefine Chain class. Chain is an object of type Entity, stores residues and includes a method to access atoms from residues. cLd|_d|_tj||y)zInitialize the class.CN)levelinternal_coordr__init__selfids E/home/agent/.friday_env/lib/python3.12/site-packages/Bio/PDB/Chain.pyrzChain.__init__s "b!ct|trW|jdk(r|jdk7ry|jdk7r|jdk(ry|j|jkDStS)z(Validate if id is greater than other.id. r isinstancer rNotImplementedrothers r__gt__z Chain.__gt__#U eU #ww#~%((c/CEHHOww))! !rct|trW|jdk(r|jdk7ry|jdk7r|jdk(ry|j|jk\StS)z1Validate if id is greater or equal than other.id.rrrrrs r__ge__z Chain.__ge__/U eU #ww#~%((c/CEHHOww%((**! !rct|trW|jdk(r|jdk7ry|jdk7r|jdk(ry|j|jkStS)z%Validate if id is less than other.id.rrrrrs r__lt__z Chain.__lt__;rrct|trW|jdk(r|jdk7ry|jdk7r|jdk(ry|j|jkStS)z.Validate if id is less or equal than other id.rrrrrs r__le__z Chain.__le__Gr!rcz t|}t|trd|df}|S#t$rY"t$rY,wxYw)aTranslate sequence identifier to tuple form (PRIVATE). A residue id is normally a tuple (hetero flag, sequence identifier, insertion code). Since for most residues the hetero flag and the insertion code are blank (i.e. " "), you can just use the sequence identifier to index a residue in a chain. The _translate_id method translates the sequence identifier to the (" ", sequence identifier, " ") tuple. Arguments: - id - int, residue resseq r)int ValueError TypeErrorrrs r _translate_idzChain._translate_idSsK RB b# r3B      s $ :::cP|j|}tj||S)a!Return the residue with given id. The id of a residue is (hetero flag, sequence identifier, insertion code). If id is an int, it is translated to (" ", id, " ") by the _translate_id method. Arguments: - id - (string, int, string) or int )r*r __getitem__rs rr,zChain.__getitem__ks'   #!!$++rcP|j|}tj||S)zCheck if a residue with given id is present in this chain. Arguments: - id - (string, int, string) or int )r*r __contains__rs rr.zChain.__contains__ys'   #""4,,rcP|j|}tj||S)zWDelete item. Arguments: - id - (string, int, string) or int )r*r __delitem__rs rr0zChain.__delitem__s'   #!!$++rc*d|jdS)zReturn the chain identifier.z )get_idrs r__repr__zChain.__repr__sDKKM?!,,rcg}|jD]M}|jdk(r'|jD]}|j|=|j|O|S)zReturn a list of undisordered residues. Some Residue objects hide several disordered residues (DisorderedResidue objects). This method unpacks them, ie. it returns a list of simple Residue objects. )get_list is_disordereddisordered_get_listappend)r unpacked_listresiduedresidues rget_unpacked_listzChain.get_unpacked_listsm }} .G$$&!+ ' ; ; =3H!((23$$W-  . rcP|j|}tj||S)a0Return 1 if a residue with given id is present. The id of a residue is (hetero flag, sequence identifier, insertion code). If id is an int, it is translated to (" ", id, " ") by the _translate_id method. Arguments: - id - (string, int, string) or int )r*rhas_idrs rrAz Chain.has_ids%   #}}T2&&rc#$K|Ed{y7w)zReturn residues.Nr4s r get_residueszChain.get_residuess s c#NK|jD] }|Ed{y7w)zReturn atoms from residues.N)rD)rrs r get_atomszChain.get_atomss(""$ ALL  s %#%verbosereturnNcv|jst|||_|jj|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 )rHN)rratom_to_internal_coordinates)rrHs rrKz"Chain.atom_to_internal_coordinatess3"""*4"9D  888Irstartfinc|jr|jj|||y|jdn|jj}td|d|d)aCreate/update atom coordinates from internal coordinates. :param verbose bool: default False describe runtime problems :param: start, fin integers optional sequence positions for begin, end of subregion to process. N.B. this activates serial residue assembly, residue CA will be at origin :raises Exception: if any chain does not have .internal_coord attribute )rHrLrMNz Structure z Chain z' does not have internal coordinates set)rinternal_to_atom_coordinatesparent Exception)rrHrLrM structures rrOz"Chain.internal_to_atom_coordinatess`       < <u# = !% 39K9KId$ r)F)FNN)__name__ __module__ __qualname____doc__rrr r#r%r*r,r.r0r5r?rArDrGboolrKr'rOrCrrr r s " " " " "0 ,-,-  '" JD JT J  Tz4Z rr )rrN) rVtypingrrBio.PDB.EntityrBio.PDB.internal_coordsr Bio.PDB.ModelrBio.PDB.Residuerr rCrrr]s3. !,#'MF% &Mr