Source Code for Module Bio.PDB.Chain

  1  # Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk) 
  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  """Chain class, used in Structure objects.""" 
  7   
  8  from Bio.PDB.Entity import Entity 
  9   
 10   
 11 -class Chain(Entity): 
 12 -    def __init__(self, id): 
 13          self.level="C" 
 14          Entity.__init__(self, id) 
 15   
 16      # Private methods 
 17   
 18 -    def _sort(self, r1, r2): 
 19          """Sort function for residues in a chain 
 20   
 21          Residues are first sorted according to their hetatm records. 
 22          Protein and nucleic acid residues first, hetatm residues next, 
 23          and waters last. Within each group, the residues are sorted according 
 24          to their resseq's (sequence identifiers). Finally, residues with the 
 25          same resseq's are sorted according to icode. 
 26   
 27          Arguments: 
 28          o r1, r2 - Residue objects 
 29          """ 
 30          hetflag1, resseq1, icode1=r1.id 
 31          hetflag2, resseq2, icode2=r2.id 
 32          if hetflag1!=hetflag2: 
 33              return cmp(hetflag1[0], hetflag2[0]) 
 34          elif resseq1!=resseq2: 
 35              return cmp(resseq1, resseq2) 
 36          return cmp(icode1, icode2) 
 37   
 38 -    def _translate_id(self, id): 
 39          """ 
 40          A residue id is normally a tuple (hetero flag, sequence identifier, 
 41          insertion code). Since for most residues the hetero flag and the 
 42          insertion code are blank (i.e. " "), you can just use the sequence 
 43          identifier to index a residue in a chain. The _translate_id method 
 44          translates the sequence identifier to the (" ", sequence identifier, 
 45          " ") tuple. 
 46   
 47          Arguments: 
 48          o id - int, residue resseq 
 49          """ 
 50          if isinstance(id, int): 
 51              id=(' ', id, ' ') 
 52          return id 
 53   
 54      # Special methods 
 55   
 56 -    def __getitem__(self, id): 
 57          """Return the residue with given id. 
 58   
 59          The id of a residue is (hetero flag, sequence identifier, insertion code). 
 60          If id is an int, it is translated to (" ", id, " ") by the _translate_id 
 61          method. 
 62   
 63          Arguments: 
 64          o id - (string, int, string) or int 
 65          """ 
 66          id=self._translate_id(id) 
 67          return Entity.__getitem__(self, id) 
 68   
 69 -    def __contains__(self, id): 
 70          """True if a residue with given id is present in this chain. 
 71   
 72          Arguments: 
 73          o id - (string, int, string) or int 
 74          """ 
 75          id=self._translate_id(id) 
 76          return Entity.__contains__(self, id) 
 77   
 78 -    def __delitem__(self, id): 
 79          """ 
 80          Arguments: 
 81          o id - (string, int, string) or int 
 82          """ 
 83          id=self._translate_id(id) 
 84          return Entity.__delitem__(self, id) 
 85   
 86 -    def __repr__(self): 
 87          return "<Chain id=%s>" % self.get_id() 
 88   
 89      # Public methods 
 90   
 91 -    def get_unpacked_list(self): 
 92          """Return a list of undisordered residues. 
 93   
 94          Some Residue objects hide several disordered residues 
 95          (DisorderedResidue objects). This method unpacks them, 
 96          ie. it returns a list of simple Residue objects. 
 97          """ 
 98          unpacked_list=[] 
 99          for residue in self.get_list(): 
100              if residue.is_disordered()==2: 
101                  for dresidue in residue.disordered_get_list(): 
102                      unpacked_list.append(dresidue) 
103              else: 
104                  unpacked_list.append(residue) 
105          return unpacked_list 
106   
107 -    def has_id(self, id): 
108          """Return 1 if a residue with given id is present. 
109   
110          The id of a residue is (hetero flag, sequence identifier, insertion code). 
111                  If id is an int, it is translated to (" ", id, " ") by the _translate_id 
112          method. 
113   
114          Arguments: 
115          o id - (string, int, string) or int 
116          """ 
117          id=self._translate_id(id) 
118          return Entity.has_id(self, id) 
119   
120      # Public 
121   
122 -    def get_residues(self): 
123          for r in self: 
124              yield r 
125   
126 -    def get_atoms(self): 
127          for r in self: 
128              for a in r: 
129                  yield a 
130