Source Code for Module csb.bio.io.vasco

  1  """ 
  2  VASCO Chemical Shift format parser. 
  3  """ 
  4   
  5  import csb.core 
  6   
  7   
  8 -class ShiftInfo(object): 
  9   
 10 -    def __init__(self, residue_id, amino_acid, nucleus, 
 11                   shift, element, secondary_structure): 
 12   
 13          self.residue_id = residue_id 
 14          self.nucleus = nucleus 
 15          self.element = element 
 16          self.amino_acid = amino_acid 
 17          self.shift = shift 
 18          self.secondary_structure = secondary_structure 
 19   
 20 -    def __str__(self): 
 21          return '{0.amino_acid} {0.nucleus} {0.shift}'.format(self) 
 22   
 23      __repr__ = __str__ 
 24   
 25           
 26 -class ChemicalShiftContainer(csb.core.DictionaryContainer): 
 27   
 28 -    def __init__(self, bmrb_id='', pdb_id='', sequence='', 
 29                   chain='', exptype=''): 
 30           
 31          self.bmrb_id = bmrb_id 
 32          self.pdb_id = pdb_id 
 33          self.sequence = sequence 
 34          self.chain = chain 
 35          self.exptype = exptype 
 36           
 37          super(ChemicalShiftContainer, self).__init__() 
 38   
 39 -class VascoStructureParser(object): 
 40      """ 
 41      Simple Vasco Parser 
 42      """ 
 43   
 44 -    def __init__(self): 
 45          self._stream  = None 
 46   
 47 -    def parse(self, file_name, ignore_outliers=True): 
 48          """ 
 49          @param file_name: source  file to parse 
 50          @type file_name: str 
 51          @return: a L{ChemicalShiftContainer} of L{ShiftInfo} objects 
 52          @rtype: dict 
 53          """ 
 54          self._stream  = open(file_name) 
 55          shifts = self._parse_header() 
 56   
 57          self._parse_shifts(shifts, ignore_outliers=ignore_outliers) 
 58          self._stream.close() 
 59   
 60          return shifts 
 61           
 62 -    def _parse_header(self): 
 63   
 64          bmrb_id = '' 
 65          pdb_id = '' 
 66          sequence = '' 
 67          chain = '' 
 68          exptype = '' 
 69          self._stream.seek(0) 
 70           
 71          while True: 
 72              try: 
 73                  line = next(self._stream) 
 74              except StopIteration : 
 75                  break 
 76   
 77              if line.startswith('#'): 
 78                  if line[2:].startswith('BMRB ORIGIN'): 
 79                      bmrb_id = line[20:].strip() 
 80                  elif line[2:].startswith('PDB ORIGIN'): 
 81                      pdb_id = line[20:].strip() 
 82                  elif line[2:].startswith('SEQUENCE PDB'): 
 83                      sequence = line[20:].strip() 
 84                      chain = line[17] 
 85                  elif line[2:].startswith('PDB EXPTYPE'): 
 86                      exptype = line[20:].strip() 
 87              else: 
 88                  break 
 89   
 90            
 91          return ChemicalShiftContainer(bmrb_id, pdb_id, chain, 
 92                                        sequence, exptype ) 
 93               
 94       
 95 -    def _parse_shifts(self, data, ignore_outliers=True): 
 96   
 97          while True: 
 98              try: 
 99                  line = next(self._stream) 
100              except StopIteration: 
101                  break 
102   
103              if ignore_outliers and "Shift outlier" in line: 
104                  continue 
105         
106              chain_id = line[7] 
107              res_code = line[9:14].strip() 
108              res_label = line[16:19].strip() 
109              res_ss = line[21] 
110              nucleus_name = line[23:28].strip() 
111              nucleus_element = line[41] 
112              shift = float(line[43:52]) 
113   
114              info = ShiftInfo(res_code, res_label, 
115                               nucleus_name, shift, 
116                               nucleus_element, res_ss) 
117   
118              if not chain_id in data: 
119                  data.append(chain_id, csb.core.OrderedDict()) 
120   
121              if not res_code in data[chain_id]: 
122                  data[chain_id][res_code] = {} 
123   
124               
125              data[chain_id][res_code][nucleus_name] = info 
126