Package Bio :: Package SCOP :: Module Raf
[hide private]
[frames] | no frames]

Source Code for Module Bio.SCOP.Raf

  1  # Copyright 2001 by Gavin E. Crooks.  All rights reserved. 
  2  # This code is part of the Biopython distribution and governed by its 
  3  # license.  Please see the LICENSE file that should have been included 
  4  # as part of this package. 
  5   
  6  # Gavin E. Crooks 2001-10-10 
  7   
  8  """ASTRAL RAF (Rapid Access Format) Sequence Maps. 
  9   
 10  The ASTRAL RAF Sequence Maps record the relationship between the PDB SEQRES 
 11  records (representing the sequence of the molecule used in an experiment) to  
 12  the ATOM records (representing the atoms experimentally observed).  
 13   
 14  This data is derived from the Protein Data Bank CIF files. Known errors in the 
 15  CIF files are corrected manually, with the original PDB file serving as the 
 16  final arbiter in case of discrepancies.  
 17   
 18  Residues are referenced by residue ID. This consists of a the PDB residue 
 19  sequence number (upto 4 digits) and an optional PDB  insertion code (an 
 20  ascii alphabetic character, a-z, A-Z). e.g. "1", "10A", "1010b", "-1" 
 21   
 22  See "ASTRAL RAF Sequence Maps":http://astral.stanford.edu/raf.html 
 23   
 24  to_one_letter_code -- A mapping from the 3-letter amino acid codes found 
 25                          in PDB files to 1-letter codes.  The 3-letter codes 
 26                          include chemically modified residues. 
 27  """ 
 28   
 29  from copy import copy  
 30   
 31  from Bio.SCOP.Residues import Residues 
 32   
 33  # This table is taken from the RAF release notes, and includes the 
 34  # undocumented mapping "UNK" -> "X" 
 35  to_one_letter_code= { 
 36      'ALA':'A', 'VAL':'V', 'PHE':'F', 'PRO':'P', 'MET':'M', 
 37      'ILE':'I', 'LEU':'L', 'ASP':'D', 'GLU':'E', 'LYS':'K', 
 38      'ARG':'R', 'SER':'S', 'THR':'T', 'TYR':'Y', 'HIS':'H', 
 39      'CYS':'C', 'ASN':'N', 'GLN':'Q', 'TRP':'W', 'GLY':'G', 
 40      '2AS':'D', '3AH':'H', '5HP':'E', 'ACL':'R', 'AIB':'A', 
 41      'ALM':'A', 'ALO':'T', 'ALY':'K', 'ARM':'R', 'ASA':'D', 
 42      'ASB':'D', 'ASK':'D', 'ASL':'D', 'ASQ':'D', 'AYA':'A', 
 43      'BCS':'C', 'BHD':'D', 'BMT':'T', 'BNN':'A', 'BUC':'C', 
 44      'BUG':'L', 'C5C':'C', 'C6C':'C', 'CCS':'C', 'CEA':'C', 
 45      'CHG':'A', 'CLE':'L', 'CME':'C', 'CSD':'A', 'CSO':'C', 
 46      'CSP':'C', 'CSS':'C', 'CSW':'C', 'CXM':'M', 'CY1':'C', 
 47      'CY3':'C', 'CYG':'C', 'CYM':'C', 'CYQ':'C', 'DAH':'F', 
 48      'DAL':'A', 'DAR':'R', 'DAS':'D', 'DCY':'C', 'DGL':'E', 
 49      'DGN':'Q', 'DHA':'A', 'DHI':'H', 'DIL':'I', 'DIV':'V', 
 50      'DLE':'L', 'DLY':'K', 'DNP':'A', 'DPN':'F', 'DPR':'P', 
 51      'DSN':'S', 'DSP':'D', 'DTH':'T', 'DTR':'W', 'DTY':'Y', 
 52      'DVA':'V', 'EFC':'C', 'FLA':'A', 'FME':'M', 'GGL':'E', 
 53      'GLZ':'G', 'GMA':'E', 'GSC':'G', 'HAC':'A', 'HAR':'R', 
 54      'HIC':'H', 'HIP':'H', 'HMR':'R', 'HPQ':'F', 'HTR':'W', 
 55      'HYP':'P', 'IIL':'I', 'IYR':'Y', 'KCX':'K', 'LLP':'K', 
 56      'LLY':'K', 'LTR':'W', 'LYM':'K', 'LYZ':'K', 'MAA':'A', 
 57      'MEN':'N', 'MHS':'H', 'MIS':'S', 'MLE':'L', 'MPQ':'G', 
 58      'MSA':'G', 'MSE':'M', 'MVA':'V', 'NEM':'H', 'NEP':'H', 
 59      'NLE':'L', 'NLN':'L', 'NLP':'L', 'NMC':'G', 'OAS':'S', 
 60      'OCS':'C', 'OMT':'M', 'PAQ':'Y', 'PCA':'E', 'PEC':'C', 
 61      'PHI':'F', 'PHL':'F', 'PR3':'C', 'PRR':'A', 'PTR':'Y', 
 62      'SAC':'S', 'SAR':'G', 'SCH':'C', 'SCS':'C', 'SCY':'C', 
 63      'SEL':'S', 'SEP':'S', 'SET':'S', 'SHC':'C', 'SHR':'K', 
 64      'SOC':'C', 'STY':'Y', 'SVA':'S', 'TIH':'A', 'TPL':'W', 
 65      'TPO':'T', 'TPQ':'A', 'TRG':'K', 'TRO':'W', 'TYB':'Y', 
 66      'TYQ':'Y', 'TYS':'Y', 'TYY':'Y', 'AGM':'R', 'GL3':'G', 
 67      'SMC':'C', 'ASX':'B', 'CGU':'E', 'CSX':'C', 'GLX':'Z', 
 68      'PYX':'C', 
 69      'UNK':'X' 
 70      } 
 71   
 72   
73 -def normalize_letters(one_letter_code):
74 """Convert RAF one-letter amino acid codes into IUPAC standard codes. 75 76 Letters are uppercased, and "." ("Unknown") is converted to "X". 77 """ 78 if one_letter_code == '.': 79 return 'X' 80 else: 81 return one_letter_code.upper()
82
83 -class SeqMapIndex(dict):
84 """An RAF file index. 85 86 The RAF file itself is about 50 MB. This index provides rapid, random 87 access of RAF records without having to load the entire file into memory. 88 89 The index key is a concatenation of the PDB ID and chain ID. e.g 90 "2drcA", "155c_". RAF uses an underscore to indicate blank 91 chain IDs. 92 """ 93
94 - def __init__(self, filename):
95 """ 96 Arguments: 97 98 filename -- The file to index 99 """ 100 dict.__init__(self) 101 self.filename = filename 102 103 f = open(self.filename, "rU") 104 try: 105 position = 0 106 while True: 107 line = f.readline() 108 if not line: break 109 key = line[0:5] 110 if key != None: 111 self[key]=position 112 position = f.tell() 113 finally: 114 f.close()
115
116 - def __getitem__(self, key):
117 """ Return an item from the indexed file. """ 118 position = dict.__getitem__(self,key) 119 120 f = open(self.filename, "rU") 121 try: 122 f.seek(position) 123 line = f.readline() 124 record = SeqMap(line) 125 finally: 126 f.close() 127 return record
128 129
130 - def getSeqMap(self, residues):
131 """Get the sequence map for a collection of residues. 132 133 residues -- A Residues instance, or a string that can be converted into 134 a Residues instance. 135 """ 136 if isinstance(residues, basestring): 137 residues = Residues(residues) 138 139 pdbid = residues.pdbid 140 frags = residues.fragments 141 if not frags: frags =(('_','',''),) # All residues of unnamed chain 142 143 seqMap = None 144 for frag in frags: 145 chainid = frag[0] 146 if chainid=='' or chainid=='-' or chainid==' ' or chainid=='_': 147 chainid = '_' 148 id = pdbid + chainid 149 150 151 sm = self[id] 152 153 #Cut out fragment of interest 154 start = 0 155 end = len(sm.res) 156 if frag[1] : start = int(sm.index(frag[1], chainid)) 157 if frag[2] : end = int(sm.index(frag[2], chainid)+1) 158 159 sm = sm[start:end] 160 161 if seqMap == None: 162 seqMap = sm 163 else: 164 seqMap += sm 165 166 return seqMap
167 168
169 -class SeqMap(object):
170 """An ASTRAL RAF (Rapid Access Format) Sequence Map. 171 172 This is a list like object; You can find the location of particular residues 173 with index(), slice this SeqMap into fragments, and glue fragments back 174 together with extend(). 175 176 pdbid -- The PDB 4 character ID 177 178 pdb_datestamp -- From the PDB file 179 180 version -- The RAF format version. e.g. 0.01 181 182 flags -- RAF flags. (See release notes for more information.) 183 184 res -- A list of Res objects, one for each residue in this sequence map 185 """ 186
187 - def __init__(self, line=None):
188 self.pdbid = '' 189 self.pdb_datestamp = '' 190 self.version = '' 191 self.flags = '' 192 self.res = [] 193 if line: 194 self._process(line)
195 196
197 - def _process(self, line):
198 """Parses a RAF record into a SeqMap object. 199 """ 200 header_len = 38 201 202 line = line.rstrip() # no trailing whitespace 203 204 if len(line)<header_len: 205 raise ValueError("Incomplete header: "+line) 206 207 self.pdbid = line[0:4] 208 chainid = line[4:5] 209 210 self.version = line[6:10] 211 212 #Raf format versions 0.01 and 0.02 are identical for practical purposes 213 if(self.version != "0.01" and self.version !="0.02"): 214 raise ValueError("Incompatible RAF version: "+self.version) 215 216 self.pdb_datestamp = line[14:20] 217 self.flags = line[21:27] 218 219 for i in range(header_len, len(line), 7): 220 f = line[i : i+7] 221 if len(f)!=7: 222 raise ValueError("Corrupt Field: ("+f+")") 223 r = Res() 224 r.chainid = chainid 225 r.resid = f[0:5].strip() 226 r.atom = normalize_letters(f[5:6]) 227 r.seqres = normalize_letters(f[6:7]) 228 229 self.res.append(r)
230 231
232 - def index(self, resid, chainid="_"):
233 for i in range(0, len(self.res)): 234 if self.res[i].resid == resid and self.res[i].chainid == chainid: 235 return i 236 raise KeyError("No such residue "+chainid+resid)
237
238 - def __getitem__(self, index):
239 if not isinstance(index, slice): 240 raise NotImplementedError 241 s = copy(self) 242 s.res = s.res[index] 243 return s
244
245 - def append(self, res):
246 """Append another Res object onto the list of residue mappings.""" 247 self.res.append(res)
248
249 - def extend(self, other):
250 """Append another SeqMap onto the end of self. 251 252 Both SeqMaps must have the same PDB ID, PDB datestamp and 253 RAF version. The RAF flags are erased if they are inconsistent. This 254 may happen when fragments are taken from different chains. 255 """ 256 if not isinstance(other, SeqMap): 257 raise TypeError("Can only extend a SeqMap with a SeqMap.") 258 if self.pdbid != other.pdbid: 259 raise TypeError("Cannot add fragments from different proteins") 260 if self.version != other.version: 261 raise TypeError("Incompatible rafs") 262 if self.pdb_datestamp != other.pdb_datestamp: 263 raise TypeError("Different pdb dates!") 264 if self.flags != other.flags: 265 self.flags = '' 266 self.res += other.res
267
268 - def __iadd__(self, other):
269 self.extend(other) 270 return self
271
272 - def __add__(self, other):
273 s = copy(self) 274 s.extend(other) 275 return s
276
277 - def getAtoms(self, pdb_handle, out_handle):
278 """Extract all relevant ATOM and HETATOM records from a PDB file. 279 280 The PDB file is scanned for ATOM and HETATOM records. If the 281 chain ID, residue ID (seqNum and iCode), and residue type match 282 a residue in this sequence map, then the record is echoed to the 283 output handle. 284 285 This is typically used to find the coordinates of a domain, or other 286 residue subset. 287 288 pdb_handle -- A handle to the relevant PDB file. 289 290 out_handle -- All output is written to this file like object. 291 """ 292 #This code should be refactored when (if?) biopython gets a PDB parser 293 294 #The set of residues that I have to find records for. 295 resSet = {} 296 for r in self.res: 297 if r.atom=='X' : #Unknown residue type 298 continue 299 chainid = r.chainid 300 if chainid == '_': 301 chainid = ' ' 302 resid = r.resid 303 resSet[(chainid,resid)] = r 304 305 resFound = {} 306 for line in pdb_handle.xreadlines(): 307 if line.startswith("ATOM ") or line.startswith("HETATM"): 308 chainid = line[21:22] 309 resid = line[22:27].strip() 310 key = (chainid, resid) 311 if key in resSet: 312 res = resSet[key] 313 atom_aa = res.atom 314 resName = line[17:20] 315 if resName in to_one_letter_code: 316 if to_one_letter_code[resName] == atom_aa: 317 out_handle.write(line) 318 resFound[key] = res 319 320 if len(resSet) != len(resFound): 321 #for k in resFound.keys(): 322 # del resSet[k] 323 #print resSet 324 325 raise RuntimeError('I could not find at least one ATOM or HETATM' \ 326 +' record for each and every residue in this sequence map.')
327 328
329 -class Res(object):
330 """ A single residue mapping from a RAF record. 331 332 chainid -- A single character chain ID. 333 334 resid -- The residue ID. 335 336 atom -- amino acid one-letter code from ATOM records. 337 338 seqres -- amino acid one-letter code from SEQRES records. 339 """
340 - def __init__(self):
341 self.chainid = '' 342 self.resid = '' 343 self.atom = '' 344 self.seqres = ''
345 346
347 -def parse(handle):
348 """Iterates over a RAF file, returning a SeqMap object for each line 349 in the file. 350 351 Arguments: 352 353 handle -- file-like object. 354 """ 355 for line in handle: 356 yield SeqMap(line)
357