Source Code for Module Bio.PDB.parse_pdb_header'

  1  #!/usr/bin/env python 
  2  # 
  3  # parse_pdb_header.py 
  4  # parses header of PDB files into a python dictionary. 
  5  # emerged from the Columba database project www.columba-db.de. 
  6  # 
  7  # author: Kristian Rother 
  8  # 
  9  # license: same as BioPython, read LICENSE.TXT from current BioPython release. 
 10  # 
 11  # last modified: 9.2.2004 
 12  # 
 13  # Added some small changes: the whole PDB file is not read in anymore, but just 
 14  # until the first ATOM record (faster). I also split parse_pdb_header into 
 15  # parse_pdb_header and parse_pdb_header_list, because parse_pdb_header_list 
 16  # can be more easily reused in PDBParser. 
 17  # 
 18  # Thomas, 19/03/04 
 19  # 
 20  # Renamed some clearly private functions to _something (ie. parse_pdb_header_list 
 21  # is now _parse_pdb_header_list) 
 22  # Thomas 9/05/04 
 23   
 24  """Parse the header of a PDB file.""" 
 25   
 26  # For 'with' on Python 2.5/Jython 2.5 
 27  from __future__ import with_statement 
 28  import re 
 29   
 30  from Bio import File 
 31   
 32   
 33 -def _get_journal(inl): 
 34      # JRNL        AUTH   L.CHEN,M.DOI,F.S.MATHEWS,A.Y.CHISTOSERDOV,           2BBK   7 
 35      journal="" 
 36      for l in inl: 
 37          if re.search("\AJRNL",l): 
 38              journal+=l[19:72].lower() 
 39      journal=re.sub("\s\s+"," ",journal) 
 40      return journal 
 41   
 42   
 43 -def _get_references(inl): 
 44      # REMARK   1 REFERENCE 1                                                  1CSE  11 
 45      # REMARK   1  AUTH   W.BODE,E.PAPAMOKOS,D.MUSIL                           1CSE  12 
 46      references=[] 
 47      actref="" 
 48      for l in inl: 
 49          if re.search("\AREMARK   1",l): 
 50              if re.search("\AREMARK   1 REFERENCE",l): 
 51                  if actref!="": 
 52                      actref=re.sub("\s\s+"," ",actref) 
 53                      if actref!=" ": 
 54                          references.append(actref) 
 55                      actref="" 
 56              else: 
 57                  actref+=l[19:72].lower() 
 58   
 59      if actref!="": 
 60          actref=re.sub("\s\s+"," ",actref) 
 61          if actref!=" ": 
 62              references.append(actref) 
 63      return references 
 64   
 65   
 66  # bring dates to format: 1909-01-08 
 67 -def _format_date(pdb_date): 
 68      """Converts dates from DD-Mon-YY to YYYY-MM-DD format.""" 
 69      date="" 
 70      year=int(pdb_date[7:]) 
 71      if year<50: 
 72          century=2000 
 73      else: 
 74          century=1900 
 75      date=str(century+year)+"-" 
 76      all_months=['xxx','Jan','Feb','Mar','Apr','May','Jun','Jul', 
 77      'Aug','Sep','Oct','Nov','Dec'] 
 78      month=str(all_months.index(pdb_date[3:6])) 
 79      if len(month)==1: 
 80          month = '0'+month 
 81      date = date+month+'-'+pdb_date[:2] 
 82      return date 
 83   
 84   
 85 -def _chop_end_codes(line): 
 86      """Chops lines ending with  '     1CSA  14' and the like.""" 
 87      return re.sub("\s\s\s\s+[\w]{4}.\s+\d*\Z","",line) 
 88   
 89   
 90 -def _chop_end_misc(line): 
 91      """Chops lines ending with  '     14-JUL-97  1CSA' and the like.""" 
 92      return re.sub("\s\s\s\s+.*\Z","",line) 
 93   
 94   
 95 -def _nice_case(line): 
 96      """Makes A Lowercase String With Capitals.""" 
 97      l=line.lower() 
 98      s="" 
 99      i=0 
100      nextCap=1 
101      while i<len(l): 
102          c=l[i] 
103          if c>='a' and c<='z' and nextCap: 
104              c=c.upper() 
105              nextCap=0 
106          elif c==' ' or c=='.' or c==',' or c==';' or c==':' or c=='\t' or\ 
107               c=='-' or c=='_': 
108              nextCap=1 
109          s+=c 
110          i+=1 
111      return s 
112   
113   
114 -def parse_pdb_header(infile): 
115      """ 
116      Returns the header lines of a pdb file as a dictionary. 
117   
118      Dictionary keys are: head, deposition_date, release_date, structure_method, 
119      resolution, structure_reference, journal_reference, author and 
120      compound. 
121      """ 
122      header = [] 
123      with File.as_handle(infile, 'r') as f: 
124          for l in f: 
125              record_type=l[0:6] 
126              if (record_type=='ATOM  ' or record_type=='HETATM' or 
127                      record_type=='MODEL '): 
128                  break 
129              else: 
130                  header.append(l) 
131      return _parse_pdb_header_list(header) 
132   
133   
134 -def _parse_pdb_header_list(header): 
135      # database fields 
136      dict={'name':"", 
137          'head':'', 
138          'deposition_date' : "1909-01-08", 
139          'release_date' : "1909-01-08", 
140          'structure_method' : "unknown", 
141          'resolution' : 0.0, 
142          'structure_reference' : "unknown", 
143          'journal_reference' : "unknown", 
144          'author' : "", 
145          'compound':{'1':{'misc':''}},'source':{'1':{'misc':''}}} 
146   
147      dict['structure_reference'] = _get_references(header) 
148      dict['journal_reference'] = _get_journal(header) 
149      comp_molid="1" 
150      src_molid="1" 
151      last_comp_key="misc" 
152      last_src_key="misc" 
153   
154      for hh in header: 
155          h=re.sub("[\s\n\r]*\Z","",hh) # chop linebreaks off 
156          #key=re.sub("\s.+\s*","",h) 
157          key = h[:6].strip() 
158          #tail=re.sub("\A\w+\s+\d*\s*","",h) 
159          tail = h[10:].strip() 
160          # print key+":"+tail 
161   
162          # From here, all the keys from the header are being parsed 
163          if key=="TITLE": 
164              name=_chop_end_codes(tail).lower() 
165              if 'name' in dict: 
166                  dict['name'] += " "+name 
167              else: 
168                  dict['name']=name 
169          elif key=="HEADER": 
170              rr=re.search("\d\d-\w\w\w-\d\d",tail) 
171              if rr is not None: 
172                  dict['deposition_date']=_format_date(_nice_case(rr.group())) 
173              head=_chop_end_misc(tail).lower() 
174              dict['head']=head 
175          elif key=="COMPND": 
176              tt=re.sub("\;\s*\Z","",_chop_end_codes(tail)).lower() 
177              # look for E.C. numbers in COMPND lines 
178              rec = re.search('\d+\.\d+\.\d+\.\d+',tt) 
179              if rec: 
180                  dict['compound'][comp_molid]['ec_number']=rec.group() 
181                  tt=re.sub("\((e\.c\.)*\d+\.\d+\.\d+\.\d+\)","",tt) 
182              tok=tt.split(":") 
183              if len(tok)>=2: 
184                  ckey=tok[0] 
185                  cval=re.sub("\A\s*","",tok[1]) 
186                  if ckey=='mol_id': 
187                      dict['compound'][cval]={'misc':''} 
188                      comp_molid=cval 
189                      last_comp_key="misc" 
190                  else: 
191                      dict['compound'][comp_molid][ckey]=cval 
192                      last_comp_key=ckey 
193              else: 
194                  dict['compound'][comp_molid][last_comp_key]+=tok[0]+" " 
195          elif key=="SOURCE": 
196              tt=re.sub("\;\s*\Z","",_chop_end_codes(tail)).lower() 
197              tok=tt.split(":") 
198              # print tok 
199              if len(tok)>=2: 
200                  ckey=tok[0] 
201                  cval=re.sub("\A\s*","",tok[1]) 
202                  if ckey=='mol_id': 
203                      dict['source'][cval]={'misc':''} 
204                      comp_molid=cval 
205                      last_src_key="misc" 
206                  else: 
207                      dict['source'][comp_molid][ckey]=cval 
208                      last_src_key=ckey 
209              else: 
210                  dict['source'][comp_molid][last_src_key]+=tok[0]+" " 
211          elif key=="KEYWDS": 
212              kwd=_chop_end_codes(tail).lower() 
213              if 'keywords' in dict: 
214                  dict['keywords']+=" "+kwd 
215              else: 
216                  dict['keywords']=kwd 
217          elif key=="EXPDTA": 
218              expd=_chop_end_codes(tail) 
219              # chop junk at end of lines for some structures 
220              expd=re.sub('\s\s\s\s\s\s\s.*\Z','',expd) 
221              # if re.search('\Anmr',expd,re.IGNORECASE): expd='nmr' 
222              # if re.search('x-ray diffraction',expd,re.IGNORECASE): expd='x-ray diffraction' 
223              dict['structure_method']=expd.lower() 
224          elif key=="CAVEAT": 
225              # make Annotation entries out of these!!! 
226              pass 
227          elif key=="REVDAT": 
228              rr=re.search("\d\d-\w\w\w-\d\d",tail) 
229              if rr is not None: 
230                  dict['release_date']=_format_date(_nice_case(rr.group())) 
231          elif key=="JRNL": 
232              # print key,tail 
233              if 'journal' in dict: 
234                  dict['journal']+=tail 
235              else: 
236                  dict['journal']=tail 
237          elif key=="AUTHOR": 
238              auth = _nice_case(_chop_end_codes(tail)) 
239              if 'author' in dict: 
240                  dict['author']+=auth 
241              else: 
242                  dict['author']=auth 
243          elif key=="REMARK": 
244              if re.search("REMARK   2 RESOLUTION.",hh): 
245                  r=_chop_end_codes(re.sub("REMARK   2 RESOLUTION.",'',hh)) 
246                  r=re.sub("\s+ANGSTROM.*","",r) 
247                  try: 
248                      dict['resolution']=float(r) 
249                  except: 
250                      #print 'nonstandard resolution',r 
251                      dict['resolution']=None 
252          else: 
253              # print key 
254              pass 
255      if dict['structure_method']=='unknown': 
256          if dict['resolution']>0.0: 
257              dict['structure_method']='x-ray diffraction' 
258      return dict 
259   
260  if __name__=='__main__': 
261      # Reads a PDB file passed as argument, parses its header, extracts 
262      # some data and returns it as a dictionary. 
263      import sys 
264      filename = sys.argv[1] 
265      handle = open(filename,'r') 
266      data_dict = parse_pdb_header(handle) 
267      handle.close() 
268   
269      # print the dictionary 
270      for k, y in data_dict.iteritems(): 
271          print "-"*40 
272          print k 
273          print y 
274