Source Code for Module csb.bio.io.dssp

  1  """ 
  2  DSSP Parser 
  3  """ 
  4   
  5  import csb.core 
  6  import csb.io 
  7   
  8  from csb.bio.structure import SecStructures, UnknownSecStructureError 
  9   
 10   
 11 -class DSSPParseError(ValueError): 
 12      pass 
 13   
 14   
 15 -class ResidueAssignmentInfo(object): 
 16       
 17 -    def __init__(self, residue_id, accession, chain, secondary_structure, phi, psi): 
 18           
 19          self.residue_id = residue_id 
 20          self.accession = accession 
 21          self.chain = chain 
 22          self.secondary_structure = secondary_structure 
 23          self.phi = phi 
 24          self.psi = psi 
 25           
 26   
 27 -class DSSPParser(object): 
 28      """ 
 29      Simple DSSP Secondary Structure Parser. 
 30      """ 
 31       
 32 -    def parse(self, dssp_file): 
 33          """ 
 34          @param dssp_file: source DSSP file to parse 
 35          @type dssp_file: str 
 36          @return: a dictionary of L{ResidueAssignmentInfo} objects 
 37          @rtype: dict 
 38          """ 
 39           
 40          data = {} 
 41          start = False 
 42          offset = 0                  # assume old DSSP format 
 43          accession = None 
 44           
 45          for line in open(dssp_file): 
 46               
 47              if not start: 
 48                   
 49                  if line.startswith('HEADER'): 
 50                      accession = line[62:66].strip().lower() 
 51                        
 52                  elif line.startswith('  #  RESIDUE'): 
 53                      if len(line) >= 140: 
 54                          offset = 4  # the new DSSP format            
 55                      start = True 
 56              else: 
 57                  if line[13] == '!': 
 58                      continue                 
 59                   
 60                  residue_id = line[6:11].strip() 
 61                  chain = line[11]          
 62                  try: 
 63                      ss = line[16].strip() 
 64                      if ss == '': 
 65                          ss = SecStructures.Gap 
 66                      else: 
 67                          ss = csb.core.Enum.parse(SecStructures, ss)   
 68                  except csb.core.EnumValueError as e: 
 69                      raise UnknownSecStructureError(str(e))  
 70                  phi = float(line[104 + offset : 109 + offset]) 
 71                  psi = float(line[110 + offset : 115 + offset]) 
 72                   
 73                   
 74                  if chain not in data: 
 75                      data[chain] = {} 
 76                   
 77                  data[chain][residue_id] = ResidueAssignmentInfo(residue_id, accession, chain, ss, phi, psi) 
 78                   
 79          return data 
 80   
 81 -class StrideParser(object): 
 82      """ 
 83      Simple STRIDE Secondary Structure Parser. 
 84      """ 
 85       
 86 -    def parse(self, stride_file): 
 87          """ 
 88          @param stride_file: source STRIDE file to parse 
 89          @type stride_file: str 
 90          @return: a dictionary of L{ResidueAssignmentInfo} objects 
 91          @rtype: dict 
 92          """ 
 93           
 94          data = {} 
 95           
 96          for line in open(stride_file): 
 97              if line.startswith('ASG '): 
 98                   
 99                  fields = line.split() 
100                   
101                  residue_id = fields[3] 
102                  chain = fields[2] 
103                  accession = fields[-1].lower() 
104                  try: 
105                      ss = csb.core.Enum.parse(SecStructures, fields[5])   
106                  except csb.core.EnumValueError as e: 
107                      raise UnknownSecStructureError(str(e))  
108                  phi = float(fields[7]) 
109                  psi = float(fields[8]) 
110                   
111                  if chain not in data: 
112                      data[chain] = {} 
113                   
114                  data[chain][residue_id] = ResidueAssignmentInfo(residue_id, accession, chain, ss, phi, psi) 
115                   
116          return data 
117   
118       
119 -def get(accession, prefix='http://www.pdb.org/pdb/files/'): 
120      """ 
121      Download and parse a DSSP entry. 
122   
123      @param accession: accession number of the entry 
124      @type accession: str 
125      @param prefix: download URL prefix 
126      @type prefix: str 
127   
128      @return: see L{DSSPParser.parse} 
129      @rtype: dict 
130      """ 
131      dssp = csb.io.TempFile() 
132   
133      browser = csb.io.urllib.urlopen(prefix + accession.lower() + '.dssp') 
134      dssp.write(browser.read().decode('utf-8')) 
135      dssp.flush() 
136   
137      return DSSPParser().parse(dssp.name) 
138