o RŀgR@s:dZddlmZGdddZddZGdddeZd S) aqHandle 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) )Residuesc@s*eZdZdZd ddZddZddZdS) RecordaLHolds information for one SCOP domain. Attributes: - 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 dictionary, keys are nodetype, values are sunid, describing the location of this domain in the SCOP hierarchy. See the Scop module for a description of nodetypes. This used to be a list of (key,value) tuples in older versions of Biopython (see Bug 3109). NcCs4d|_d|_d|_d|_i|_|r||dSdS)zInitialize the class.N)sidresiduessccssunid hierarchy_process)selfliner @/var/www/html/myenv/lib/python3.10/site-packages/Bio/SCOP/Cla.py__init__'szRecord.__init__c Cs|}|d}t|dkrtd||\|_}}|_|_}t||_||j_ t |j|_|dD]}|d\}}t ||j |<q6dS)N z!I don't understand the format of ,=) rstripsplitlen ValueErrorrrrrrpdbidintr ) r r columnsrrr htkeyvaluer r rr 1s    zRecord._processcCspg}||j|t|jd7}||j||j|ddd|j Ddt t|dS)zCRepresent the SCOP classification record as a tab-separated string. rcss&|]\}}d|t|fVqdS)rN)joinstr).0rrr r r Is z!Record.__str__..r ) appendrr rrrrrr itemsmap)r sr r r__str__@s    zRecord.__str__)N)__name__ __module__ __qualname____doc__rr r(r r r rrs   rccs&|D] }|dr qt|VqdS)zmIterate over a CLA file as Cla records for each line. Arguments: - handle - file-like object. #N) startswithr)handler r r rparseQs   r0c@s eZdZdZddZddZdS)Indexz?A CLA file indexed by SCOP identifiers for rapid random access.cCst|||_t|j-}d} |}|sn|drqt|}|j}|dur-|||<|}qWddS1s=wYdS)zWCreate CLA index. Arguments: - filename - The file to index Tr-N) dictrfilenameopenreadliner.rrtell)r r4fpositionr recordrr r rras$   "zIndex.__init__cCsVt||}t|j}|||}t|}Wd|S1s$wY|S)z%Return an item from the indexed file.N)r3 __getitem__r5r4seekr6r)r rr9r8r r:r r rr;xs     zIndex.__getitem__N)r)r*r+r,rr;r r r rr1^s r1N)r,rrrr0r3r1r r r rs  :