o Rŀg߁@sdZddlZddlZddlZddlmZddlmZddlm Z ddlm Z ddl m Z dd l mZdd l mZdd l mZdd l mZd dddddddZddddddddZgdZgdZgdZid d!d"d#dd$d%d&d'd(d)d*d+d,d-d.d/d0d1d2d3d4d5d6d7d8d9d:d;d<d=d>Zid d?d"d@ddAd%dBd'dCd)dDd+dEd-dFd/dGd1dHd3dId5dJd7dKd9dLd;dMd=dNZdOdPZedQZdRdSZdTdUZGdVdWdWZGdXdYdYZGdZd[d[eZ Gd\d]d]Z!       ^dcd_d`Z"dddadbZ#dS)eaSCOP: Structural Classification of Proteins. The SCOP database aims to provide a manually constructed classification of all know protein structures into a hierarchy, the main levels of which are family, superfamily and fold. * "SCOP":http://scop.mrc-lmb.cam.ac.uk/legacy/ * "Introduction":http://scop.mrc-lmb.cam.ac.uk/legacy/intro.html * "SCOP parsable files":http://scop.mrc-lmb.cam.ac.uk/legacy/parse/ The Scop object in this module represents the entire SCOP classification. It can be built from the three SCOP parsable files, modified is so desired, and converted back to the same file formats. A single SCOP domain (represented by the Domain class) can be obtained from Scop using the domain's SCOP identifier (sid). - nodeCodeDict -- A mapping between known 2 letter node codes and a longer description. The known node types are 'cl' (class), 'cf' (fold), 'sf' (superfamily), 'fa' (family), 'dm' (domain), 'sp' (species), 'px' (domain). Additional node types may be added in the future. This module also provides code to access SCOP over the WWW. Functions: - search -- Access the main CGI script (DEPRECATED, no longer available).. - _open -- Internally used function. N) urlencode)urlopen)BiopythonDeprecationWarning)SeqIO)Seq)Cla)Des)Hie)Residuesclassfold superfamilyfamilyproteinspeciesdomain)clcfsffadmsppxrrrrrrr)r r rrrrr)rorrrrrrr) #(2FZ_d)rr?皙?皙?{Gz?{Gzt?MbP?-C6?h㈵>绽|=V瞯<#B ;}:Jz5rze+1r&ze+0,7ze+0r'ze-0,3r(ze-1r)ze-1,3r*ze-2r+ze-2,3r,ze-3r-ze-4r.ze-5r/ze-10r0ze-15r1ze-20r2ze-25r3ze-50e1e0_7e0e_0_3e_1e_1_3e_2e_2_3e_3e_4e_5e_10e_15e_20e_25e_50c Cs|d}|d}|d|d}}||krdS||krdSt|dd|ddD]\}}t|}t|}||kr?dS||krFdSq,t|}t|} || krUdS|| kr[dSdS)aOrder SCOP concise classification strings (sccs). a.4.5.1 < a.4.5.11 < b.1.1.1 A sccs (e.g. a.4.5.11) compactly represents a domain's classification. The letter represents the class, and the numbers are the fold, superfamily, and family, respectively. .rrN)splitzipintlen) sccs1sccs2s1s2c1c2i1i2n1n2rTE/var/www/html/myenv/lib/python3.10/site-packages/Bio/SCOP/__init__.pycmp_sccs]s, "rVz+>?([\w_\.]*)\s+([\w\.]*)\s+\(([^)]*)\) (.*)cCsxt|}|s td|t}|d|_|d|_t|d|_|jj s2|jdd|j_ |d |_ |S)abConvert an ASTRAL header string into a Scop domain. An ASTRAL (http://astral.stanford.edu/) header contains a concise description of a SCOP domain. A very similar format is used when a Domain object is converted into a string. The Domain returned by this method contains most of the SCOP information, but it will not be located within the SCOP hierarchy (i.e. The parent node will be None). The description is composed of the SCOP protein and species descriptions. A typical ASTRAL header looks like -- >d1tpt_1 a.46.2.1 (1-70) Thymidine phosphorylase {Escherichia coli} zDomain: rr&) _domain_rematch ValueErrorDomaingroupsidsccsr residuespdbidstrip description)termmdomrTrTrU parse_domains    rhcCs&d|d|}ttj||}|S)Nzdir.z .scop.txt_)openospathjoin) scop_dir_pathversionfiletypefilenamehandlerTrTrU_open_scop_filesrrc@seZdZdZ      dddZddZddZd d Zd d Zd dZ ddZ ddZ d ddZ ddZ ddZddZddZddZdS)!ScopzKThe entire SCOP hierarchy. root -- The root node of the hierarchy NcCsi|_i|_tdd|||||fDrdS|dur.|dur.|dus*|dus*|dur.tdi}||_z |r8n|r\|s@td|sF|sF|rJtdt||d}t||d}t||d }t}g} d |_d |_|||j<||_ d |_ t |} | D],} | j d krt} | j| _| | nt} | j| _| j | _| j| _| j | _ | || j<qyt |} | D];} | j|vrt| j|| j} | jdkr| j|vrtd|| j| _| jD]} | |vrtd| j|| qqi}t |} | D]"} || j} | j| jksJ| j| jks J| j| _| || j<q||_||_t| |_W|r;|r+||r2||r=|dSdSdS|rX|rI||rP||rY|www)a0Build the SCOP hierarchy from the SCOP parsable files, or a sql backend. If no file handles are given, then a Scop object with a single empty root node is returned. If a directory and version are given (with dir_path=.., version=...) or file handles for each file, the whole scop tree will be built in memory. If a MySQLdb database handle is given, the tree will be built as needed, minimising construction times. To build the SQL database to the methods write_xxx_sql to create the tables. css|]}|duVqdSNrT).0hrTrTrU s z Scop.__init__..Nz)Need CLA, DES and HIE files to build SCOPz5Need SCOP version to find parsable files in directoryz0Cannot specify SCOP directory and specific filescladeshierrz SCOP RootrzIncomplete data?)_sidDict _sunidDictall RuntimeError db_handlerrNodesunidtyperootrdr parsenodetyper]namer_appendr`r printparentr\childrenrratuple_domainsclose)self cla_handle des_handle hie_handledir_pathrrn sunidDictrdomainsrecordsrecordncsidDictrTrTrU__init__s                        z Scop.__init__cCs |dS)zGet root node.r)getNodeBySunidrrTrTrUgetRoot)s z Scop.getRootcCB||jvr |j|S|jr|j|d||jvr|j|SdSdS)zReturn a domain from its sid.)r_N)r|rgetDomainFromSQL)rr_rTrTrUgetDomainBySid-     zScop.getDomainBySidcCr)zReturn a node from its sunid.rN)r}rr)rrrTrTrUr8rzScop.getNodeBySunidcCs|jr |dS|jS)z,Return an ordered tuple of all SCOP Domains.r)rrgetDescendentsrrrTrTrU getDomainsCszScop.getDomainscC2t|jdddD] }|t|q dS)z1Build an HIE SCOP parsable file from this object.cS|jSrtrxrTrTrUMz Scop.write_hie..keyN)sortedr}valueswritestr toHieRecordrrqrrTrTrU write_hieJzScop.write_hiecCs<t|jdddD]}||jkr|t|q dS)z0Build a DES SCOP parsable file from this object.cSrrtrrrTrTrUrSrz Scop.write_des..rN)rr}rrrr toDesRecordrrTrTrU write_desPs  zScop.write_descCr)z0Build a CLA SCOP parsable file from this object.cSrrtrrrTrTrUrZrz Scop.write_cla..rN)rr|rrr toClaRecordrrTrTrU write_claWrzScop.write_clac CsX|dur |dur dS|j}|r%|d||}|dur!dS|d}|d||}|durd}|ddkrZt|d}|d|g}|D] }||dqL||_n%t|d}|d ||\|_ |_ } t |j |_ | |j _ ||j |j <|\|_|_|_|_|dd kr|d ||d|_t|j|_||j|j<dSdS) z4Load a node from the SQL backend using sunid or sid.Nz"SELECT sunid FROM cla WHERE sid=%srz SELECT * FROM des WHERE sunid=%srrscop%SELECT child FROM hie WHERE parent=%sz3select sid, residues, pdbid from cla where sunid=%sr%SELECT parent FROM hie WHERE child=%s)rcursorexecutefetchonerfetchallrrr]r_rar rbr|rrr`rdrrHr}) rrr_curresdatarrrrbrTrTrUr]sF            zScop.getDomainFromSQLcCsft|t|jkr dS|j}|d|d|jd|j|}|dur1||dSdS)z!Get ascendents using SQL backend.NzSELECT z from cla WHERE =%sr) nodeCodeOrderindexrrrrrrr)rnoderrresultrTrTrUgetAscendentFromSQLs zScop.getAscendentFromSQLc Cst|t|jkr gSg}|jdkr+|D]}|||D]}||q q|S|j}|dkr|d|jd|d|j | }|D]Z}t |d|j vrt |d}|\|_ |_|_|_t |j |_ ||j |j <|d|j |d|_|d |j g} | D] }| |dq| |_||j t |dqJ|S|d |jd |j | }|D]N}t |d|j vrt|d}|dd \|_ |_} |_|_|_|_|_t|j|_| |j_t |j |_ ||j |j <||j|j<||j t |dq|S) zGet descendents of a node using the database backend. This avoids repeated iteration of SQL calls and is therefore much quicker than repeatedly calling node.getChildren(). rrzOSELECT DISTINCT des.sunid,des.type,des.sccs,description FROM cla,des WHERE cla.z =%s AND cla.z =des.sunidrrrrzpSELECT cla.sunid,sid,pdbid,residues,cla.sccs,type,description,sp FROM cla,des where cla.sunid=des.sunid and cla.r)rrr getChildrengetDescendentsFromSQLrrrrrrrHr}rr`rdrrrr]r_rar rbr|) rrrdes_listrdrrrrrbrTrTrUrs             zScop.getDescendentsFromSQLc CsX|}|d|d|jD]}|jD]}|d|jd|jdqqdS)zWrite HIE data to SQL database.zDROP TABLE IF EXISTS hiezNCREATE TABLE hie (parent INT, child INT, PRIMARY KEY (child), INDEX (parent) )zINSERT INTO hie VALUES (,)N)rrr}rrr)rrqrprrTrTrU write_hie_sqls  zScop.write_hie_sqlcCs|}|d|d|jD]7}|}|d|j|j|jj|j|j | dj| dj| dj| dj| dj| d j|jf qd S) zWrite CLA data to SQL database.zDROP TABLE IF EXISTS clazCREATE TABLE cla (sunid INT, sid CHAR(8), pdbid CHAR(4), residues VARCHAR(50), sccs CHAR(10), cl INT, cf INT, sf INT, fa INT, dm INT, sp INT, px INT, PRIMARY KEY (sunid), INDEX (SID) )zhz$Node.getChildren..)rrrrTrrUrcs zNode.getChildrencCs|jdur|jS|j|jS)zReturn the parent of this Node.N)rrrrrTrTrUrjs zNode.getParentcCs|tvrt|}|g}|jr|j||S|dj|krA|djdkr%gSg}|D]}|D]}||q/|}q)|dj|ks|S)zReturn a list of all descendant nodes of the given type. Node type can be a two letter code or longer description, e.g. 'fa' or 'family'. rr)_nodetype_to_coderrrrr)r node_typenodes child_listrchildrTrTrUrqs   zNode.getDescendentscCsd|tvrt|}|jr|j||S|}|j|krdS|j|kr0|jdkr'dS|}|j|ks |S)zReturn the ancenstor node of the given type, or None. Node type can be a two letter code or longer description, e.g. 'fa' or 'family'. Nr)rrrrr)rrrrTrTrUrs    zNode.getAscendentrt) rrrrrrrrrrrrrTrTrTrUr(s     rc@s2eZdZdZd ddZddZddZd d ZdS) r]zA SCOP domain. A leaf node in the Scop hierarchy. Attributes: - sid - The SCOP domain identifier. e.g. ``"d5hbib_"`` - residues - A Residue object. It defines the collection of PDB atoms that make up this domain. NcCstj||dd|_d|_dS)z Initialize a SCOP Domain object.rr{N)rrr_rarrTrTrUrs zDomain.__init__cCsg}||j||j|dt|jd|s%||jn|}|}||j|d|jdd|S)z&Represent the SCOP Domain as a string.(r{}r)rr_r`rrarrdrl)rrrrrTrTrUrs    zDomain.__str__cCst|}|j|_|Sr)rrr_rrrTrTrUrs zDomain.toDesRecordcCs^t}|j|_|j|_|j|_|j|_|}|jdkr-t|j|j|j<| }|jdks|S)zReturn a Cla.Record.r) rrr_rar`rr hierarchyrr)rrrrTrTrUrs  zDomain.toClaRecordrt)rrrrrrrrrTrTrTrUr]s   r]c@sveZdZdZ dddZddZddZdd d Zd d Zd dZ ddZ ddZ ddZ ddZ ddZddZdS)AstralzRepresentation of the ASTRAL database. Abstraction of the ASTRAL database, which has sequences for all the SCOP domains, as well as clusterings by percent id or evalue. NcCs|dur|dur|durtd|std||_||_|sI|sI|dus(|dur,td||_tj|d||_d|jd}tj|j|}|rUtt |d|_ ||_ i|_ i|_ i|_i|_dS) amInitialize the astral database. You must provide either a directory of SCOP files: - dir_path - string, the path to location of the scopseq-x.xx directory (not the directory itself), and - version -a version number. or, a FASTA file: - astral_file - string, a path to a fasta file (which will be loaded in memory) or, a MYSQL database: - db_handle - a database handle for a MYSQL database containing a table 'astral' with the astral data in it. This can be created using writeToSQL. NzXNeed either file handle, or (dir_path + version), or database handle to construct Astralz)Must provide a Scop instance to constructz!must provide dir_path and versionzscopseq-zastral-scopdom-seqres-all-z.fafasta)rrrrnrjrkrlrto_dictr fasta_dict astral_file EvDatasets EvDatahash IdDatasets IdDatahash)rrrnrrrrTrTrUrs, zAstral.__init__cCsv||jvr6|jr|t||j|<n#|jstdd}d|t||jf}tj |j|}| ||j|<|j|S)z Get domains clustered by evalue.No scopseq directory specifiedastral-scopdom-seqres-sel-gsz%s-e100m-%s-%s.id) rrgetAstralDomainsFromSQLastralEv_to_sqlrkrastralEv_to_filernrjrlgetAstralDomainsFromFilerid file_prefixrprTrTrUdomainsClusteredByEvs  zAstral.domainsClusteredByEvcCs~||jvr:|jr|dt||j|<n%|jstdd}|d|d|jd}tj|j|}| ||j|<|j|S)z-Get domains clustered by percentage identity.rrrz-bib-rz.id) rrrrrkrrnrjrlrrrTrTrUdomainsClusteredById's  zAstral.domainsClusteredByIdcs||dur |dur td|st|}g} |}|sn |}||q|r,|dd|D}fdd|D}|S)z;Get the scop domains from a file containing a list of sids.Nz%You must provide a filename or handleTcSsg|] }|ddkr|qS)rrrT)ruarTrTrUrFz3Astral.getAstralDomainsFromFile..crrTrrrrrTrUrGr)rrireadlinerstriprr)rrp file_handledomslinerTrrUr6s" zAstral.getAstralDomainsFromFilecs:j}|d|d|}fdd|D}|S)zLoad ASTRAL domains from the MySQL database. Load a set of astral domains from a column in the astral table of a MYSQL database (which can be created with writeToSQL(...). zSELECT sid FROM astral WHERE z=1csg|] }j|dqS)rr rrrTrUrSrz2Astral.getAstralDomainsFromSQL..)rrrr)rcolumnrrrTrrUrJs zAstral.getAstralDomainsFromSQLcCs<|jdur |j|jS|j}|d|t|dS)z2Get the seq record of a given domain from its sid.Nz#SELECT seq FROM astral WHERE sid=%sr)rrseqrrrr)rrrrTrTrU getSeqBySidWs    zAstral.getSeqBySidcCs ||jS)z"Return seq associated with domain.)rr_)rrrTrTrUgetSeq`s z Astral.getSeqcC<||jvri|j|<||D] }d|j||<q|j|S)z5Get domains clustered by sequence identity in a dict.r)rrrrrrTrTrUhashedDomainsByIdd   zAstral.hashedDomainsByIdcCr)z*Get domains clustered by evalue in a dict.r)rrrrTrTrUhashedDomainsByEvlrzAstral.hashedDomainsByEvcC|||vS)zCReturn true if the domain is in the astral clusters for percent ID.)rrrgrrTrTrU isDomainInIdtzAstral.isDomainInIdcCr)z@Return true if the domain is in the ASTRAL clusters for evalues.)rrrTrTrU isDomainInEvxrzAstral.isDomainInEvcCs|}|d|d|jD]}|d||j|jfqtD]"}|dt|d||D]}|dt|d|jq4q"tD]"}|dt |d| |D]}|d t |d|jqYqGd S) z.Write the ASTRAL database to a MYSQL database.zDROP TABLE IF EXISTS astralz>CREATE TABLE astral (sid CHAR(8), seq TEXT, PRIMARY KEY (sid))z+INSERT INTO astral (sid,seq) values (%s,%s)zALTER TABLE astral ADD (idz TINYINT)zUPDATE astral SET idz=1 WHERE sid=%szALTER TABLE astral ADD (zUPDATE astral SET N) rrrr astralBibIdsrrr_ astralEvsrr)rrrrgirevrTrTrU writeToSQL|s,   zAstral.writeToSQL)NNNNNr)rrrrrrrrrrrrrrrr!rTrTrTrUrs 1    r/http://scop.mrc-lmb.cam.ac.uk/legacy/search.cgic KsXtdt||||||d}i} |D] \} } | dur!| | | <q| |t|| S)aAccess SCOP search and return a handle to the results (DEPRECATED). Access search.cgi and return a handle to the results. See the online help file for an explanation of the parameters: http://scop.mrc-lmb.cam.ac.uk/legacy/help.html Raises an IOError if there's a network error. This function is now DEPRECATED and will be removed in a future release of Biopython because this search.cgi API is no longer available with SCOP now hosted the the EBI. zuThe SCOP search function is deprecated and will be removed as the CGI based SCOP search is no longer availble online.)pdbrr_dispdirlocN)warningswarnritemsupdate_open) r#rr_r$r%r&cgikeywdsparams variableskvrTrTrUsearchs  r2cCsD|duri}t|}|r|r|d|7}t|}|St||d}|S)zOpen a handle to SCOP and return it (PRIVATE). Open a handle to SCOP. cgi is the URL for the cgi script to access. params is a dictionary with the options to pass to it. get is a boolean that describes whether a GET should be used. N?)r)rr)r,r.getoptionsrqrTrTrUr+s   r+)NNNNNNr")Nr)$rrjrer' urllib.parserurllib.requestrBiorrBio.Seqrr{rr r r nodeCodeDictrrrrrrrVcompilerZrhrrrsrr]rr2r+rTrTrTrUs            $x;@ $