Source Code for Module Bio.PDB.AbstractPropertyMap

  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  """Class that maps (chain_id, residue_id) to a residue property.""" 
  7   
  8   
  9   
 10 -class AbstractPropertyMap(object): 
 11 -    def __init__(self, property_dict, property_keys, property_list): 
 12          self.property_dict=property_dict 
 13          self.property_keys=property_keys 
 14          self.property_list=property_list 
 15   
 16 -    def _translate_id(self, entity_id): 
 17          return entity_id 
 18   
 19 -    def __contains__(self, id): 
 20          """True if the mapping has a property for this residue. 
 21   
 22          Example: 
 23              >>> if (chain_id, res_id) in apmap: 
 24              ...     res, prop = apmap[(chain_id, res_id)] 
 25   
 26          @param chain_id: chain id 
 27          @type chain_id: char 
 28   
 29          @param res_id: residue id 
 30          @type res_id: char 
 31          """ 
 32          translated_id = self._translate_id(id) 
 33          return (translated_id in self.property_dict) 
 34   
 35 -    def __getitem__(self, key): 
 36          """ 
 37          Return property for a residue. 
 38   
 39          @param chain_id: chain id 
 40          @type chain_id: char 
 41   
 42          @param res_id: residue id 
 43          @type res_id: int or (char, int, char) 
 44   
 45          @return: some residue property 
 46          @rtype: anything (can be a tuple) 
 47          """ 
 48          translated_id=self._translate_id(key) 
 49          return self.property_dict[translated_id] 
 50   
 51 -    def __len__(self): 
 52          """ 
 53          Return number of residues for which the property is available. 
 54   
 55          @return: number of residues 
 56          @rtype: int 
 57          """ 
 58          return len(self.property_dict) 
 59   
 60 -    def has_key(self, id): 
 61          """True if the mapping has a property for this residue. 
 62   
 63          (Obsolete; use "id in mapping" instead.) 
 64   
 65          Example: 
 66   
 67              >>> if apmap.has_key((chain_id, res_id)): 
 68              ...     res, prop = apmap[(chain_id, res_id)] 
 69   
 70          Is equivalent to: 
 71   
 72              >>> if (chain_id, res_id) in apmap: 
 73              ...     res, prop = apmap[(chain_id, res_id)] 
 74   
 75          @param chain_id: chain id 
 76          @type chain_id: char 
 77   
 78          @param res_id: residue id 
 79          @type res_id: char 
 80          """ 
 81          import warnings 
 82          from Bio import BiopythonDeprecationWarning 
 83          warnings.warn("This function is deprecated; use 'id in mapping' instead", BiopythonDeprecationWarning) 
 84          return (id in self) 
 85   
 86 -    def keys(self): 
 87          """ 
 88          Return the list of residues. 
 89   
 90          @return: list of residues for which the property was calculated 
 91          @rtype: [(chain_id, res_id), (chain_id, res_id),...] 
 92          """ 
 93          return self.property_keys 
 94   
 95 -    def __iter__(self): 
 96          """ 
 97          Iterate over the (entity, property) list. Handy alternative to 
 98          the dictionary-like access. 
 99   
100          Example: 
101              >>> for (res, property) in iter(map): 
102              ...     print res, property 
103   
104          @return: iterator 
105          """ 
106          for i in range(0, len(self.property_list)): 
107              yield self.property_list[i] 
108   
109   
110 -class AbstractResiduePropertyMap(AbstractPropertyMap): 
111 -    def __init__(self, property_dict, property_keys, property_list): 
112          AbstractPropertyMap.__init__(self, property_dict, property_keys, 
113                  property_list) 
114   
115 -    def _translate_id(self, ent_id): 
116          chain_id, res_id=ent_id 
117          if isinstance(res_id, int): 
118              ent_id=(chain_id, (' ', res_id, ' ')) 
119          return ent_id 
120   
121   
122 -class AbstractAtomPropertyMap(AbstractPropertyMap): 
123 -    def __init__(self, property_dict, property_keys, property_list): 
124          AbstractPropertyMap.__init__(self, property_dict, property_keys, 
125                  property_list) 
126   
127 -    def _translate_id(self, ent_id): 
128          if len(ent_id)==4: 
129              chain_id, res_id, atom_name, icode=ent_id 
130          else: 
131              chain_id, res_id, atom_name=ent_id 
132              icode=None 
133          if isinstance(res_id, int): 
134              ent_id=(chain_id, (' ', res_id, ' '), atom_name, icode) 
135          return ent_id 
136