ó ªIc@sldZddlTdd d„ƒYZddd„ƒYZddd„ƒYZd „Zd efd „ƒYZd S(st Handle the SCOP CLAssification file, which describes SCOP domains. The file format is described in the scop "release notes.":http://scop.mrc-lmb.cam.ac.uk/scop/release-notes.html The latest CLA file can be found "elsewhere at SCOP.":http://scop.mrc-lmb.cam.ac.uk/scop/parse/ "Release 1.73": http://scop.mrc-lmb.cam.ac.uk/scop/parse/dir.cla.scop.txt_1.73 (July 2008) iÿÿÿÿ(t*tRecordcBs,eZdZdd„Zd„Zd„ZRS(s÷Holds information for one SCOP domain sid -- SCOP identifier. e.g. d1danl2 residues -- The domain definition as a Residues object sccs -- SCOP concise classification strings. e.g. b.1.2.1 sunid -- SCOP unique identifier for this domain hierarchy -- A sequence of tuples (nodetype, sunid) describing the location of this domain in the SCOP hierarchy. See the Scop module for a description of nodetypes. cCsGd|_d|_d|_d|_g|_|rC|j|ƒndS(Nt(tsidtNonetresiduestsccstsunidt hierarchyt_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/Cla.pyt__init__&s     c Csã|jƒ}|jdƒ}t|ƒdkr@td|ƒ‚n|\|_}}|_|_}t|ƒ|_||j_ t |jƒ|_xN|jdƒD]=}|jdƒ\}}t |ƒ}|j j ||gƒqžWdS(Ns is#I don't understand the format of %st,t=( trstriptsplittlent ValueErrorRRRtResiduesRtpdbidtintRtappend( R R tcolumnsRRRthttkeytvalue((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SCOP/Cla.pyR /s !  cCs»g}|j|jƒ|t|jƒjdƒ7}|j|jƒ|j|jƒg}x0|jD]%}|jdjt t|ƒƒƒqbW|jdj|ƒƒdjt t|ƒƒdS(Nt RR s s ( RRtstrRRRRRtjointmap(R tsthR((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SCOP/Cla.pyt__str__?s#N(t__name__t __module__t__doc__RR 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/Cla.pyRs tIteratorcBs,eZdZdd„Zd„Zd„ZRS(sIterates over a CLA file. cCs{ddl}|jdtƒddlm}m}t|ƒ|k ret|ƒ|k retdƒ‚n||_||_ dS(sCreate an object that iterates over a CLA 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.Cla.Iterator is deprecated. Please use Bio.SCOP.Cla.parse() instead.(tFileTypet InstanceTypes,I expected a file handle or file-like object( twarningstwarntDeprecationWarningttypesR&R'ttypet TypeErrort_handlet_parser(R thandletparserR(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/Cla.pyR Ps $ cCsWx1|jjƒ}|sdS|ddkrPqqW|jdk rS|jj|ƒS|S(sRetrieve the next CLA record.it#N(R.treadlineRR/tparse(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/Cla.pytnextbscCst|jdƒS(N(titerR5R(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/Cla.pyt__iter__lsN(R"R#R$RR R5R7(((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SCOP/Cla.pyR%Ms  tParsercBs eZdZd„Zd„ZRS(s(Parses tab-deliminated CLA records. cCs ddl}|jdtƒdS(NiÿÿÿÿsºBio.SCOP.Cla.Parser is deprecated. Instead of parser = Cla.Parser() record = parser.parse(entry) please use record = Cla.Record(entry) (R(R)R*(R R(((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SCOP/Cla.pyR ss  cCs t|ƒS(sReturns a Cla Record (R(R tentry((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SCOP/Cla.pyR4€s(R"R#R$R R4(((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SCOP/Cla.pyR8ps ccs5x.|D]&}|jdƒr"qnt|ƒVqWdS(s‰Iterates over a CLA file, returning a Cla record for each line in the file. Arguments: handle -- file-like object. R2N(t startswithR(R0R ((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SCOP/Cla.pyR4…s tIndexcBs eZdZd„Zd„ZRS(sXA CLA file indexed by SCOP identifiers, allowing rapid random access into a file.cCsžtj|ƒ||_t|jƒ}zgd}xZtrŠ|jƒ}|sMPnt|ƒ}|j}|dkr{|||R=tseekR3RRA(R RRCRBR RD((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SCOP/Cla.pyRE¬s   (R"R#R$R RE(((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SCOP/Cla.pyR;“s N((((R$RRR%R8R4R<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/Cla.pyts  6#