1.1 --- a/allpy/pdb.py	Wed Jan 19 20:33:51 2011 +0300
     1.2 +++ b/allpy/pdb.py	Thu Jan 20 21:51:24 2011 +0300
     1.3 @@ -75,8 +75,12 @@
     1.4                  #~ model = parse[5]
     1.5      #~ return code, chain, model
     1.6  
     1.7 -class Sequence(base.Sequence):
     1.8 -    """Sequence with associated PDB structure.
     1.9 +class SequenceMixin(base.Sequence):
    1.10 +    """Mixin for adding PDB data to a Sequence.
    1.11 +
    1.12 +    Please note: since this is a mixin, no objects of this class should be
    1.13 +    created. This class is intended to be subclassed together with one of
    1.14 +    Sequence classes.
    1.15  
    1.16      Attributes:
    1.17  
    1.18 @@ -221,7 +225,13 @@
    1.19          return chain in self.pdb_secstr and monomer in self.pdb_secstr[chain]
    1.20  
    1.21  
    1.22 -class Alignment(base.Alignment):
    1.23 +class AlignmentMixin(base.Alignment):
    1.24 +    """Mixin to add 3D properties to alignments.
    1.25 +
    1.26 +    Please note: since this is a mixin, no objects of this class should be
    1.27 +    created. This class is intended to be subclassed together with one of
    1.28 +    Alignment classes.
    1.29 +    """
    1.30  
    1.31      def secstr(self, sequence, pdb_chain, gap='-'):
    1.32          """ Returns string representing secondary structure """
    1.33 @@ -229,7 +239,13 @@
    1.34          (sequence.pdb_secstr[pdb_chain][m] if sequence.secstr_has(pdb_chain, m) else gap)
    1.35          for m in self.body[sequence]])
    1.36  
    1.37 -class Block(base.Block):
    1.38 +class BlockMixin(base.Block):
    1.39 +    """Mixin to add 3D properties to blocks.
    1.40 +
    1.41 +    Please note: since this is a mixin, no objects of this class should be
    1.42 +    created. This class is intended to be subclassed together with one of
    1.43 +    Block classes.
    1.44 +    """
    1.45  
    1.46      def geometrical_cores(self, max_delta=config.delta,
    1.47      timeout=config.timeout, minsize=config.minsize,