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16 """ SCOP: Structural Classification of Proteins.
17
18 The SCOP database aims to provide a manually constructed classification of
19 all know protein structures into a hierarchy, the main levels of which
20 are family, superfamily and fold.
21
22 * "SCOP":http://scop.mrc-lmb.cam.ac.uk/scop/
23
24 * "Introduction":http://scop.mrc-lmb.cam.ac.uk/scop/intro.html
25
26 * "SCOP parsable files":http://scop.mrc-lmb.cam.ac.uk/scop/parse/
27
28 The Scop object in this module represents the entire SCOP classification. It
29 can be built from the three SCOP parsable files, modified is so desired, and
30 converted back to the same file formats. A single SCOP domain (represented
31 by the Domain class) can be obtained from Scop using the domain's SCOP
32 identifier (sid).
33
34
35 nodeCodeDict -- A mapping between known 2 letter node codes and a longer
36 description. The known node types are 'cl' (class), 'cf'
37 (fold), 'sf' (superfamily), 'fa' (family), 'dm' (domain),
38 'sp' (species), 'px' (domain). Additional node types may
39 be added in the future.
40
41 This module also provides code to access SCOP over the WWW.
42
43 Functions:
44 search -- Access the main CGI script.
45 _open -- Internally used function.
46
47 """
48
49 from types import *
50 import os, string
51
52 import Des
53 import Cla
54 import Hie
55 from Residues import *
56 from Bio import SeqIO
57 from Bio.Alphabet import IUPAC
58 from Bio.Seq import Seq
59
60
61 nodeCodeDict = { 'cl':'class', 'cf':'fold', 'sf':'superfamily',
62 'fa':'family', 'dm':'protein', 'sp':'species', 'px':'domain'}
63
64
65 _nodetype_to_code= { 'class': 'cl', 'fold': 'cf', 'superfamily': 'sf',
66 'family': 'fa', 'protein': 'dm', 'species': 'sp', 'domain': 'px'}
67
68 nodeCodeOrder = [ 'ro', 'cl', 'cf', 'sf', 'fa', 'dm', 'sp', 'px' ]
69
70 astralBibIds = [10,20,25,30,35,40,50,70,90,95,100]
71
72 astralEvs = [10, 5, 1, 0.5, 0.1, 0.05, 0.01, 0.005, 0.001, 1e-4, 1e-5, 1e-10, 1e-15,
73 1e-20, 1e-25, 1e-50]
74
75 astralEv_to_file = { 10: 'e+1', 5: 'e+0,7', 1: 'e+0', 0.5: 'e-0,3', 0.1: 'e-1',
76 0.05: 'e-1,3', 0.01: 'e-2', 0.005: 'e-2,3', 0.001: 'e-3',
77 1e-4: 'e-4', 1e-5: 'e-5', 1e-10: 'e-10', 1e-15: 'e-15',
78 1e-20: 'e-20', 1e-25: 'e-25', 1e-50: 'e-50' }
79
80 astralEv_to_sql = { 10: 'e1', 5: 'e0_7', 1: 'e0', 0.5: 'e_0_3', 0.1: 'e_1',
81 0.05: 'e_1_3', 0.01: 'e_2', 0.005: 'e_2_3', 0.001: 'e_3',
82 1e-4: 'e_4', 1e-5: 'e_5', 1e-10: 'e_10', 1e-15: 'e_15',
83 1e-20: 'e_20', 1e-25: 'e_25', 1e-50: 'e_50' }
84
85
87 """Order SCOP concise classification strings (sccs).
88
89 a.4.5.1 < a.4.5.11 < b.1.1.1
90
91 A sccs (e.g. a.4.5.11) compactly represents a domain's classification.
92 The letter represents the class, and the numbers are the fold,
93 superfamily, and family, respectively.
94
95 """
96
97 s1 = sccs1.split(".")
98 s2 = sccs2.split(".")
99
100 if s1[0] != s2[0]: return cmp(s1[0], s2[0])
101
102 s1 = map(int, s1[1:])
103 s2 = map(int, s2[1:])
104
105 return cmp(s1,s2)
106
107
108 _domain_re = re.compile(r">?([\w_\.]*)\s+([\w\.]*)\s+\(([^)]*)\) (.*)")
109
110 -def parse_domain(str) :
111 """Convert an ASTRAL header string into a Scop domain.
112
113 An ASTRAL (http://astral.stanford.edu/) header contains a concise
114 description of a SCOP domain. A very similar format is used when a
115 Domain object is converted into a string. The Domain returned by this
116 method contains most of the SCOP information, but it will not be located
117 within the SCOP hierarchy (i.e. The parent node will be None). The
118 description is composed of the SCOP protein and species descriptions.
119
120 A typical ASTRAL header looks like --
121 >d1tpt_1 a.46.2.1 (1-70) Thymidine phosphorylase {Escherichia coli}
122 """
123
124 m = _domain_re.match(str)
125 if (not m) : raise ValueError("Domain: "+ str)
126
127 dom = Domain()
128 dom.sid = m.group(1)
129 dom.sccs = m.group(2)
130 dom.residues = Residues(m.group(3))
131 if not dom.residues.pdbid :
132 dom.residues.pdbid= dom.sid[1:5]
133 dom.description = m.group(4).strip()
134
135 return dom
136
138 filename = "dir.%s.scop.txt_%s" % (filetype,version)
139 handle = open(os.path.join( scop_dir_path, filename))
140 return handle
141
142
144 """The entire SCOP hierarchy.
145
146 root -- The root node of the hierarchy
147 """
148 - def __init__(self, cla_handle=None, des_handle=None, hie_handle=None,
149 dir_path=None, db_handle=None, version=None):
150 """Build the SCOP hierarchy from the SCOP parsable files, or a sql backend.
151
152 If no file handles are given, then a Scop object with a single
153 empty root node is returned.
154
155 If a directory and version are given (with dir_path=.., version=...) or
156 file handles for each file, the whole scop tree will be built in memory.
157
158 If a MySQLdb database handle is given, the tree will be built as needed,
159 minimising construction times. To build the SQL database to the methods
160 write_xxx_sql to create the tables.
161
162 """
163 self._sidDict = {}
164 self._sunidDict = {}
165
166 if cla_handle==des_handle==hie_handle==dir_path==db_handle==None: return
167
168 if dir_path is None and db_handle is None:
169 if cla_handle == None or des_handle==None or hie_handle==None:
170 raise RuntimeError("Need CLA, DES and HIE files to build SCOP")
171
172 sunidDict = {}
173
174 self.db_handle = db_handle
175 try:
176
177 if db_handle:
178
179 pass
180
181 else:
182
183 if dir_path:
184 if not version :
185 raise RuntimeError("Need SCOP version to find parsable files in directory")
186 if cla_handle or des_handle or hie_handle:
187 raise RuntimeError("Cannot specify SCOP directory and specific files")
188
189 cla_handle = _open_scop_file( dir_path, version, 'cla')
190 des_handle = _open_scop_file( dir_path, version, 'des')
191 hie_handle = _open_scop_file( dir_path, version, 'hie')
192
193 root = Node()
194 domains = []
195 root.sunid=0
196 root.type='ro'
197 sunidDict[root.sunid] = root
198 self.root = root
199 root.description = 'SCOP Root'
200
201
202 records = Des.parse(des_handle)
203 for record in records:
204 if record.nodetype =='px' :
205 n = Domain()
206 n.sid = record.name
207 domains.append(n)
208 else :
209 n = Node()
210 n.sunid = record.sunid
211 n.type = record.nodetype
212 n.sccs = record.sccs
213 n.description = record.description
214
215 sunidDict[n.sunid] = n
216
217
218 records = Hie.parse(hie_handle)
219 for record in records:
220 if record.sunid not in sunidDict :
221 print record.sunid
222
223 n = sunidDict[record.sunid]
224
225 if record.parent != '' :
226
227 if record.parent not in sunidDict:
228 raise ValueError("Incomplete data?")
229
230 n.parent = sunidDict[record.parent]
231
232 for c in record.children:
233 if c not in sunidDict :
234 raise ValueError("Incomplete data?")
235 n.children.append(sunidDict[c])
236
237
238
239 sidDict = {}
240 records = Cla.parse(cla_handle)
241 for record in records:
242 n = sunidDict[record.sunid]
243 assert n.sccs == record.sccs
244 assert n.sid == record.sid
245 n.residues = record.residues
246 sidDict[n.sid] = n
247
248
249 self._sunidDict = sunidDict
250 self._sidDict = sidDict
251 self._domains = tuple(domains)
252
253 finally:
254 if dir_path :
255
256 if cla_handle : cla_handle.close()
257 if des_handle : des_handle.close()
258 if hie_handle : hie_handle.close()
259
260
263
264
265 - def getDomainBySid(self, sid) :
266 """Return a domain from its sid"""
267 if sid in self._sidDict:
268 return self._sidDict[sid]
269 if self.db_handle:
270 self.getDomainFromSQL(sid=sid)
271 if sid in self._sidDict:
272 return self._sidDict[sid]
273 else:
274 return None
275
276
278 """Return a node from its sunid"""
279 if sunid in self._sunidDict:
280 return self._sunidDict[sunid]
281 if self.db_handle:
282 self.getDomainFromSQL(sunid=sunid)
283 if sunid in self._sunidDict:
284 return self._sunidDict[sunid]
285 else:
286 return None
287
288
289 - def getDomains(self) :
290 """Returns an ordered tuple of all SCOP Domains"""
291 if self.db_handle:
292 return self.getRoot().getDescendents('px')
293 else:
294 return self._domains
295
296
297
306
307
317
318
327
328
329 - def getDomainFromSQL(self, sunid=None, sid=None):
330 """Load a node from the SQL backend using sunid or sid"""
331 if sunid==sid==None: return None
332
333 cur = self.db_handle.cursor()
334
335 if sid:
336 cur.execute("SELECT sunid FROM cla WHERE sid=%s", sid)
337 res = cur.fetchone()
338 if res is None:
339 return None
340 sunid = res[0]
341
342 cur.execute("SELECT * FROM des WHERE sunid=%s", sunid)
343 data = cur.fetchone()
344
345 if data is not None:
346 n = None
347
348
349 if data[1] != "px":
350 n = Node(scop=self)
351
352 cur.execute("SELECT child FROM hie WHERE parent=%s", sunid)
353 children = []
354 for c in cur.fetchall():
355 children.append(c[0])
356 n.children = children
357
358
359 else:
360 n = Domain(scop=self)
361 cur.execute("select sid, residues, pdbid from cla where sunid=%s",
362 sunid)
363
364 [n.sid,n.residues,pdbid] = cur.fetchone()
365 n.residues = Residues(n.residues)
366 n.residues.pdbid=pdbid
367 self._sidDict[n.sid] = n
368
369 [n.sunid,n.type,n.sccs,n.description] = data
370
371 if data[1] != 'ro':
372 cur.execute("SELECT parent FROM hie WHERE child=%s", sunid)
373 n.parent = cur.fetchone()[0]
374
375 n.sunid = int(n.sunid)
376
377 self._sunidDict[n.sunid] = n
378
379
391
392
394 """Get descendents of a node using the database backend. This avoids
395 repeated iteration of SQL calls and is therefore much quicker than
396 repeatedly calling node.getChildren().
397 """
398 if nodeCodeOrder.index(type) <= nodeCodeOrder.index(node.type): return []
399
400 des_list = []
401
402
403
404 if node.type == 'ro':
405 for c in node.getChildren():
406 for d in self.getDescendentsFromSQL(c,type):
407 des_list.append(d)
408 return des_list
409
410 cur = self.db_handle.cursor()
411
412
413 if type != 'px':
414 cur.execute("SELECT DISTINCT des.sunid,des.type,des.sccs,description FROM \
415 cla,des WHERE cla."+node.type+"=%s AND cla."+type+"=des.sunid", (node.sunid))
416 data = cur.fetchall()
417 for d in data:
418 if int(d[0]) not in self._sunidDict:
419 n = Node(scop=self)
420 [n.sunid,n.type,n.sccs,n.description] = d
421 n.sunid=int(n.sunid)
422 self._sunidDict[n.sunid] = n
423
424 cur.execute("SELECT parent FROM hie WHERE child=%s", n.sunid)
425 n.parent = cur.fetchone()[0]
426
427 cur.execute("SELECT child FROM hie WHERE parent=%s", n.sunid)
428 children = []
429 for c in cur.fetchall():
430 children.append(c[0])
431 n.children = children
432
433
434 des_list.append( self._sunidDict[int(d[0])] )
435
436 else:
437 cur.execute("SELECT cla.sunid,sid,pdbid,residues,cla.sccs,type,description,sp\
438 FROM cla,des where cla.sunid=des.sunid and cla."+node.type+"=%s",
439 node.sunid)
440
441 data = cur.fetchall()
442 for d in data:
443 if int(d[0]) not in self._sunidDict:
444 n = Domain(scop=self)
445
446
447 [n.sunid,n.sid, pdbid,n.residues,n.sccs,n.type,n.description,
448 n.parent] = d[0:8]
449 n.residues = Residues(n.residues)
450 n.residues.pdbid = pdbid
451 n.sunid = int(n.sunid)
452 self._sunidDict[n.sunid] = n
453 self._sidDict[n.sid] = n
454
455
456 des_list.append( self._sunidDict[int(d[0])] )
457
458 return des_list
459
460
461
462
464 """Write HIE data to SQL database"""
465 cur = handle.cursor()
466
467 cur.execute("DROP TABLE IF EXISTS hie")
468 cur.execute("CREATE TABLE hie (parent INT, child INT, PRIMARY KEY (child),\
469 INDEX (parent) )")
470
471 for p in self._sunidDict.values():
472 for c in p.children:
473 cur.execute("INSERT INTO hie VALUES (%s,%s)" % (p.sunid, c.sunid))
474
475
477 """Write CLA data to SQL database"""
478 cur = handle.cursor()
479
480 cur.execute("DROP TABLE IF EXISTS cla")
481 cur.execute("CREATE TABLE cla (sunid INT, sid CHAR(8), pdbid CHAR(4),\
482 residues VARCHAR(50), sccs CHAR(10), cl INT, cf INT, sf INT, fa INT,\
483 dm INT, sp INT, px INT, PRIMARY KEY (sunid), INDEX (SID) )")
484
485 for n in self._sidDict.values():
486 c = n.toClaRecord()
487 cur.execute( "INSERT INTO cla VALUES (%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s)",
488 (n.sunid, n.sid, c.residues.pdbid, c.residues, n.sccs,
489 n.getAscendent('cl').sunid, n.getAscendent('cf').sunid,
490 n.getAscendent('sf').sunid, n.getAscendent('fa').sunid,
491 n.getAscendent('dm').sunid, n.getAscendent('sp').sunid,
492 n.sunid ))
493
494
496 """Write DES data to SQL database"""
497 cur = handle.cursor()
498
499 cur.execute("DROP TABLE IF EXISTS des")
500 cur.execute("CREATE TABLE des (sunid INT, type CHAR(2), sccs CHAR(10),\
501 description VARCHAR(255),\
502 PRIMARY KEY (sunid) )")
503
504 for n in self._sunidDict.values():
505 cur.execute( "INSERT INTO des VALUES (%s,%s,%s,%s)",
506 ( n.sunid, n.type, n.sccs, n.description ) )
507
508
509
511 """ A node in the Scop hierarchy
512
513 sunid -- SCOP unique identifiers. e.g. '14986'
514
515 parent -- The parent node
516
517 children -- A list of child nodes
518
519 sccs -- SCOP concise classification string. e.g. 'a.1.1.2'
520
521 type -- A 2 letter node type code. e.g. 'px' for domains
522
523 description --
524
525 """
527 """Create a Node in the scop hierarchy. If a Scop instance is provided to the
528 constructor, this will be used to lookup related references using the SQL
529 methods. If no instance is provided, it is assumed the whole tree exists
530 and is connected."""
531 self.sunid=''
532 self.parent = None
533 self.children=[]
534 self.sccs = ''
535 self.type =''
536 self.description =''
537 self.scop=scop
538
547
549 """Return an Hie.Record"""
550 rec = Hie.Record()
551 rec.sunid = str(self.sunid)
552 if self.getParent() :
553 rec.parent = str(self.getParent().sunid)
554 else:
555 rec.parent = '-'
556 for c in self.getChildren() :
557 rec.children.append(str(c.sunid))
558 return rec
559
561 """Return a Des.Record"""
562 rec = Des.Record()
563 rec.sunid = str(self.sunid)
564 rec.nodetype = self.type
565 rec.sccs = self.sccs
566 rec.description = self.description
567 return rec
568
570 """Return a list of children of this Node"""
571 if self.scop is None:
572 return self.children
573 else:
574 return map ( self.scop.getNodeBySunid, self.children )
575
577 """Return the parent of this Node"""
578 if self.scop is None:
579 return self.parent
580 else:
581 return self.scop.getNodeBySunid( self.parent )
582
584 """ Return a list of all decendent nodes of the given type. Node type can a
585 two letter code or longer description. e.g. 'fa' or 'family'
586 """
587 if node_type in _nodetype_to_code:
588 node_type = _nodetype_to_code[node_type]
589
590 nodes = [self]
591 if self.scop:
592 return self.scop.getDescendentsFromSQL(self,node_type)
593 while nodes[0].type != node_type:
594 if nodes[0].type == 'px' : return []
595 child_list = []
596 for n in nodes:
597 for child in n.getChildren():
598 child_list.append( child )
599 nodes = child_list
600
601 return nodes
602
603
605 """ Return the ancenstor node of the given type, or None.Node type can a
606 two letter code or longer description. e.g. 'fa' or 'family'"""
607 if node_type in _nodetype_to_code:
608 node_type = _nodetype_to_code[node_type]
609
610 if self.scop:
611 return self.scop.getAscendentFromSQL(self,node_type)
612 else:
613 n = self
614 if n.type == node_type: return None
615 while n.type != node_type:
616 if n.type == 'ro': return None
617 n = n.getParent()
618
619 return n
620
621
622
623 -class Domain(Node) :
624 """ A SCOP domain. A leaf node in the Scop hierarchy.
625
626 sid -- The SCOP domain identifier. e.g. 'd5hbib_'
627
628 residues -- A Residue object. It defines the collection
629 of PDB atoms that make up this domain.
630 """
631 - def __init__(self,scop=None) :
632 Node.__init__(self,scop=scop)
633 self.sid = ''
634 self.residues = None
635
636 - def __str__(self) :
637 s = []
638 s.append(self.sid)
639 s.append(self.sccs)
640 s.append("("+str(self.residues)+")")
641
642 if not self.getParent() :
643 s.append(self.description)
644 else :
645 sp = self.getParent()
646 dm = sp.getParent()
647 s.append(dm.description)
648 s.append("{"+sp.description+"}")
649
650 return " ".join(s)
651
652 - def toDesRecord(self):
653 """Return a Des.Record"""
654 rec = Node.toDesRecord(self)
655 rec.name = self.sid
656 return rec
657
658 - def toClaRecord(self) :
659 """Return a Cla.Record"""
660 rec = Cla.Record()
661 rec.sid = self.sid
662 rec.residues = self.residues
663 rec.sccs = self.sccs
664 rec.sunid = self.sunid
665
666 n = self
667 while n.sunid != 0:
668 rec.hierarchy.append( (n.type, str(n.sunid)) )
669 n = n.getParent()
670
671 rec.hierarchy.reverse()
672
673 return rec
674
676 """Abstraction of the ASTRAL database, which has sequences for all the SCOP domains,
677 as well as clusterings by percent id or evalue.
678 """
679
680 - def __init__( self, dir_path=None, version=None, scop=None, ind_file=None,
681 astral_file=None, db_handle=None):
682 """
683 Initialise the astral database.
684
685 You must provide either a directory of SCOP files:
686
687 dir_path - string, the path to location of the scopseq-x.xx directory
688 (not the directory itself), and
689 version -a version number.
690
691 or, a FASTA file:
692
693 astral_file - string, a path to a fasta file (which will be loaded in memory)
694
695 or, a MYSQL database:
696
697 db_handle - a database handle for a MYSQL database containing a table
698 'astral' with the astral data in it. This can be created
699 using writeToSQL.
700
701 Note that the ind_file argument is deprecated.
702 """
703 if ind_file :
704 raise RuntimeError("The ind_file (index file) argument is deprecated")
705
706 if astral_file==dir_path==db_handle==None:
707 raise RuntimeError("Need either file handle, or (dir_path + "\
708 + "version) or database handle to construct Astral")
709 if not scop:
710 raise RuntimeError("Must provide a Scop instance to construct")
711
712 self.scop = scop
713 self.db_handle = db_handle
714
715
716 if not astral_file and not db_handle:
717 if dir_path == None or version == None:
718 raise RuntimeError("must provide dir_path and version")
719
720 self.version = version
721 self.path = os.path.join( dir_path, "scopseq-%s" % version)
722 astral_file = "astral-scopdom-seqres-all-%s.fa" % self.version
723 astral_file = os.path.join (self.path, astral_file)
724
725 if astral_file:
726
727 self.fasta_dict = SeqIO.to_dict(SeqIO.parse(open(astral_file), "fasta"))
728
729 self.astral_file = astral_file
730 self.EvDatasets = {}
731 self.EvDatahash = {}
732 self.IdDatasets = {}
733 self.IdDatahash = {}
734
735
737 """get domains clustered by evalue"""
738 if id not in self.EvDatasets:
739 if self.db_handle:
740 self.EvDatasets[id] = self.getAstralDomainsFromSQL(astralEv_to_sql[id])
741
742 else:
743 if not self.path:
744 raise RuntimeError("No scopseq directory specified")
745
746 file_prefix = "astral-scopdom-seqres-sel-gs"
747 filename = "%s-e100m-%s-%s.id" % (file_prefix, astralEv_to_file[id] ,
748 self.version)
749 filename = os.path.join(self.path,filename)
750 self.EvDatasets[id] = self.getAstralDomainsFromFile(filename)
751 return self.EvDatasets[id]
752
753
755 """get domains clustered by percent id"""
756 if id not in self.IdDatasets:
757 if self.db_handle:
758 self.IdDatasets[id] = self.getAstralDomainsFromSQL("id"+str(id))
759
760 else:
761 if not self.path:
762 raise RuntimeError("No scopseq directory specified")
763
764 file_prefix = "astral-scopdom-seqres-sel-gs"
765 filename = "%s-bib-%s-%s.id" % (file_prefix, id, self.version)
766 filename = os.path.join(self.path,filename)
767 self.IdDatasets[id] = self.getAstralDomainsFromFile(filename)
768 return self.IdDatasets[id]
769
770
771 - def getAstralDomainsFromFile(self,filename=None,file_handle=None):
772 """Get the scop domains from a file containing a list of sids"""
773 if file_handle == filename == none:
774 raise RuntimeError("You must provide a filename or handle")
775 if not file_handle:
776 file_handle = open(filename)
777 doms = []
778 while 1:
779 line = file_handle.readline()
780 if not line:
781 break
782 line = line.rstrip()
783 doms.append(line)
784 if filename:
785 file_handle.close()
786
787 doms = filter( lambda a: a[0]=='d', doms )
788 doms = map( self.scop.getDomainBySid, doms )
789 return doms
790
791 - def getAstralDomainsFromSQL(self, column):
792 """Load a set of astral domains from a column in the astral table of a MYSQL
793 database (which can be created with writeToSQL(...)"""
794 cur = self.db_handle.cursor()
795 cur.execute("SELECT sid FROM astral WHERE "+column+"=1")
796 data = cur.fetchall()
797 data = map( lambda x: self.scop.getDomainBySid(x[0]), data)
798
799 return data
800
801
803 """get the seq record of a given domain from its sid"""
804 if self.db_handle is None:
805 return self.fasta_dict[domain].seq
806
807 else:
808 cur = self.db_handle.cursor()
809 cur.execute("SELECT seq FROM astral WHERE sid=%s", domain)
810 return Seq(cur.fetchone()[0])
811
813 """Return seq associated with domain"""
814 return self.getSeqBySid(domain.sid)
815
816
817 - def hashedDomainsById(self,id):
818 """Get domains clustered by sequence identity in a dict"""
819 if id not in self.IdDatahash:
820 self.IdDatahash[id] = {}
821 for d in self.domainsClusteredById(id):
822 self.IdDatahash[id][d] = 1
823 return self.IdDatahash[id]
824
825 - def hashedDomainsByEv(self,id):
826 """Get domains clustered by evalue in a dict"""
827 if id not in self.EvDatahash:
828 self.EvDatahash[id] = {}
829 for d in self.domainsClusteredByEv(id):
830 self.EvDatahash[id][d] = 1
831 return self.EvDatahash[id]
832
833
834 - def isDomainInId(self,dom,id):
835 """Returns true if the domain is in the astral clusters for percent ID"""
836 return dom in self.hashedDomainsById(id)
837
838 - def isDomainInEv(self,dom,id):
839 """Returns true if the domain is in the ASTRAL clusters for evalues"""
840 return dom in self.hashedDomainsByEv(id)
841
842
844 """Write the ASTRAL database to a MYSQL database"""
845 cur = db_handle.cursor()
846
847 cur.execute("DROP TABLE IF EXISTS astral")
848 cur.execute("CREATE TABLE astral (sid CHAR(8), seq TEXT, PRIMARY KEY (sid))")
849
850 for dom in self.fasta_dict.keys():
851 cur.execute( "INSERT INTO astral (sid,seq) values (%s,%s)",
852 (dom, self.fasta_dict[dom].seq.data))
853
854
855 for i in astralBibIds:
856 cur.execute("ALTER TABLE astral ADD (id"+str(i)+" TINYINT)")
857
858 for d in self.domainsClusteredById(i):
859 cur.execute("UPDATE astral SET id"+str(i)+"=1 WHERE sid=%s",
860 d.sid)
861
862 for ev in astralEvs:
863 cur.execute("ALTER TABLE astral ADD ("+astralEv_to_sql[ev]+" TINYINT)")
864
865 for d in self.domainsClusteredByEv(ev):
866
867 cur.execute("UPDATE astral SET "+astralEv_to_sql[ev]+"=1 WHERE sid=%s",
868 d.sid)
869
870 -def search(pdb=None, key=None, sid=None, disp=None, dir=None, loc=None,
871 cgi='http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi', **keywds):
872 """search(pdb=None, key=None, sid=None, disp=None, dir=None, loc=None,
873 cgi='http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi', **keywds)
874
875 Access search.cgi and return a handle to the results. See the
876 online help file for an explanation of the parameters:
877 http://scop.mrc-lmb.cam.ac.uk/scop/help.html
878
879 Raises an IOError if there's a network error.
880
881 """
882 params = {'pdb' : pdb, 'key' : key, 'sid' : sid, 'disp' : disp,
883 'dir' : dir, 'loc' : loc}
884 variables = {}
885 for k in params.keys():
886 if params[k] is not None:
887 variables[k] = params[k]
888 variables.update(keywds)
889 return _open(cgi, variables)
890
891 -def _open(cgi, params={}, get=1):
892 """_open(cgi, params={}, get=1) -> UndoHandle
893
894 Open a handle to SCOP. cgi is the URL for the cgi script to access.
895 params is a dictionary with the options to pass to it. get is a boolean
896 that describes whether a GET should be used. Does some
897 simple error checking, and will raise an IOError if it encounters one.
898
899 """
900 import urllib
901 from Bio import File
902
903 options = urllib.urlencode(params)
904 if get:
905 fullcgi = cgi
906 if options:
907 fullcgi = "%s?%s" % (cgi, options)
908 handle = urllib.urlopen(fullcgi)
909 else:
910 handle = urllib.urlopen(cgi, options)
911
912
913 uhandle = File.UndoHandle(handle)
914
915 return uhandle
916