ó ªIc@s\dZddlmZdd d„ƒYZd„Zdd d„ƒYZdd d „ƒYZd S(s Handle the SCOP DOMain file. The DOM file has been officially deprecated. For more information see the SCOP"release notes.":http://scop.berkeley.edu/release-notes-1.55.html The DOM files for older releases can be found "elsewhere at SCOP.":http://scop.mrc-lmb.cam.ac.uk/scop/parse/ iÿÿÿÿ(tResiduestRecordcBs,eZdZdd„Zd„Zd„ZRS(sæHolds information for one SCOP domain. sid -- The SCOP ID of the entry, e.g. d1anu1 residues -- The domain definition as a Residues object hierarchy -- A string specifying where this domain is in the hierarchy. cCs5d|_g|_d|_|r1|j|ƒndS(Nt(tsidtresiduest 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/Dom.pyt__init__s    cCsw|jƒ}|jdƒ}t|ƒdkr@td|ƒ‚n|\|_}}|_t|ƒ|_||j_dS(s~Parses DOM records. Records consist of 4 tab deliminated fields; sid, pdbid, residues, hierarchy s is#I don't understand the format of %sN( trstriptsplittlent ValueErrorRRRRtpdbid(RRtcolumnsRtres((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SCOP/Dom.pyR%s cCsYg}|j|jƒ|jt|jƒjddƒƒ|j|jƒdj|ƒdS(Nt s s (tappendRtstrRtreplaceRtjoin(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/Dom.pyt__str__;s "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/Dom.pyRs  ccs x|D]}t|ƒVqWdS(s‘Iterates over a DOM file, returning a Dom 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/Dom.pytparseCs tIteratorcBs#eZdZdd„Zd„ZRS(sIterates over a DOM file. cCs_ddlm}m}t|ƒ|k rIt|ƒ|k rItdƒ‚n||_||_dS(s/Create an object that iterates over a DES file. handle -- file-like object. parser -- an optional Parser object to change the results into another form. If set to None, then the raw contents of the file will be returned. iÿÿÿÿ(tFileTypet InstanceTypes,I expected a file handle or file-like objectN(ttypesRR ttypeR t_handlet_parser(RRtparserRR ((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SCOP/Dom.pyR Rs $ cCs<|jjƒ}|sdS|jdk r8|jj|ƒS|S(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/Dom.pytnextbs N(RRRRR 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/Dom.pyROs tParsercBseZd„ZRS(cCs#ddl}|jdƒt|ƒS(sReturns a Dom.Record iÿÿÿÿNsºBio.SCOP.Dom.Parser is deprecated. Instead of parser = Dom.Parser() record = parser.parse(entry) please use record = Dom.Record(entry) (twarningstwarnR(RtentryR)((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SCOP/Dom.pyRks  (RRR(((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SCOP/Dom.pyR(jsN((((RRRRRR((((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SCOP/Dom.pyts .