ó ªIc@sLdZdd d„ƒYZd„Zdd d„ƒYZdd d„ƒYZdS( sC Handle the SCOP DEScription file. The file format is described in the scop "release notes.":http://scop.berkeley.edu/release-notes-1.55.html The latest DES file can be found "elsewhere at SCOP.":http://scop.mrc-lmb.cam.ac.uk/scop/parse/ "Release 1.55":http://scop.berkeley.edu/parse/des.cla.scop.txt_1.55 (July 2001) tRecordcBs,eZdZdd„Zd„Zd„ZRS(sCHolds information for one node in the SCOP hierarchy. sunid -- SCOP unique identifiers nodetype -- One of 'cl' (class), 'cf' (fold), 'sf' (superfamily), 'fa' (family), 'dm' (protein), 'sp' (species), 'px' (domain). Additional node types may be added. sccs -- SCOP concise classification strings. e.g. b.1.2.1 name -- The SCOP ID (sid) for domains (e.g. d1anu1), currently empty for other node types description -- e.g. "All beta proteins","Fibronectin type III", cCsGd|_d|_d|_d|_d|_|rC|j|ƒndS(Nt(tsunidtnodetypetsccstnamet descriptiont_process(tselftline((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SCOP/Des.pyt__init__#s     cCs|jƒ}|jdƒ}t|ƒdkr@td|ƒ‚n|\}|_|_|_|_|jdkr|d|_nt|ƒ|_ dS(s“Parses DES records. Records consist of 5 tab deliminated fields, sunid, node type, sccs, node name, node description. s is#I don't understand the format of %st-RN( trstriptsplittlent ValueErrorRRRRtintR(RR tcolumnsR((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SCOP/Des.pyR,s ! cCs‰g}|j|jƒ|j|jƒ|j|jƒ|jrR|j|jƒn |jdƒ|j|jƒdjtt|ƒƒdS(NR s s ( tappendRRRRRtjointmaptstr(Rts((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SCOP/Des.pyt__str__Ds  N(t__name__t __module__t__doc__tNoneR RR(((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SCOP/Des.pyRs ccs x|D]}t|ƒVqWdS(s‡Iterates over a DES file, returning a Des record for each line in the file. Arguments: handle -- file-like object N(R(thandleR ((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SCOP/Des.pytparseQs tIteratorcBs,eZdZdd„Zd„Zd„ZRS(sIterates over a DES file. cCs{ddl}|jdtƒddlm}m}t|ƒ|k ret|ƒ|k retdƒ‚n||_||_ dS(s.Create an object that iterates over a DES file. handle -- file-like object. parser -- an optional Parser object to chang the results into another form. If set to None, then the raw contents of the file will be returned. iÿÿÿÿNsMBio.SCOP.Des.Iterator is deprecated. Please use Bio.SCOP.Des.parse() instead.(tFileTypet InstanceTypes,I expected a file handle or file-like object( twarningstwarntDeprecationWarningttypesRR ttypet TypeErrort_handlet_parser(RRtparserR!RR ((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SCOP/Des.pyR _s $ cCsWx1|jjƒ}|sdS|ddkrPqqW|jdk rS|jj|ƒS|S(sRetrieve the next DES record.it#N(R'treadlineRR(R(RR ((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SCOP/Des.pytnextqscCst|jdƒS(N(titerR,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/SCOP/Des.pyt__iter__{sN(RRRRR 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/SCOP/Des.pyR\s  tParsercBseZd„Zd„ZRS(cCs ddl}|jdtƒdS(NiÿÿÿÿsºBio.SCOP.Des.Parser is deprecated. Instead of parser = Des.Parser() record = parser.parse(entry) please use record = Des.Record(entry) (R!R"R#(RR!((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SCOP/Des.pyR €s  cCs t|ƒS(sReturns a Des Record (R(Rtentry((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SCOP/Des.pyRs(RRR R(((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SCOP/Des.pyR/s N((((RRRRR/(((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SCOP/Des.pyts? #