ó "˜ÎIc@s@ddlmZddlmZdZdefd„ƒYZdS(iÿÿÿÿ(tIntType(tEntitys'Chain class, used in Structure objects.tChaincBsYeZd„Zd„Zd„Zd„Zd„Zd„Zd„Zd„Z d„Z RS( cCsd|_tj||ƒdS(NtC(tlevelRt__init__(tselftid((s€/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Chain.pyRs c Csk|j\}}}|j\}}}||krEt|d|dƒS||kr^t||ƒSt||ƒS(sÃSort function for residues in a chain Residues are first sorted according to their hetatm records. Protein and nucleic acid residues first, hetatm residues next, and waters last. Within each group, the residues are sorted according to their resseq's (sequence identifiers). Finally, residues with the same resseq's are sorted according to icode. Arguments: o r1, r2 - Residue objects i(Rtcmp( Rtr1tr2thetflag1tresseq1ticode1thetflag2tresseq2ticode2((s€/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Chain.pyt_sorts    cCs(t|ƒtkr$d|df}n|S(sÑ 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: o id - int, residue resseq t (ttypeR(RR((s€/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Chain.pyt _translate_id*s cCs|j|ƒ}tj||ƒS(s!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: o id - (string, int, string) or int (RRt __getitem__(RR((s€/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Chain.pyR<s cCs|j|ƒ}tj||ƒS(sH Arguments: o id - (string, int, string) or int (RRt __delitem__(RR((s€/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Chain.pyRIscCsd|jƒS(Ns (tget_id(R((s€/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Chain.pyt__repr__QscCsgg}xZ|jƒD]L}|jƒdkrRx1|jƒD]}|j|ƒq8Wq|j|ƒqW|S(sèReturn 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. i(tget_listt is_disorderedtdisordered_get_listtappend(Rt unpacked_listtresiduetdresidue((s€/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Chain.pytget_unpacked_listVscCs|j|ƒ}tj||ƒS(s5Return 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: o id - (string, int, string) or int (RRthas_id(RR((s€/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Chain.pyR!fs ccs+x$|D]}x|D] }|VqWqWdS(N((Rtrta((s€/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Chain.pyt get_atomsvs  ( t__name__t __module__RRRRRRR R!R$(((s€/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Chain.pyRs       N(ttypesRRt__doc__R(((s€/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/Chain.pyts