1.1 --- a/allpy/alignment.py	Sun Nov 28 17:40:11 2010 +0300
     1.2 +++ b/allpy/alignment.py	Tue Nov 30 17:10:25 2010 +0300
     1.3 @@ -15,17 +15,13 @@
     1.4  import block
     1.5  from fasta import save_fasta
     1.6  
     1.7 -class Alignment(object):
     1.8 +class Alignment(dict):
     1.9      """ Alignment
    1.10      
    1.11 -    Mandatory data:
    1.12 -    *   body -- dict 
    1.13          {<Sequence object>:[<Monomer object>,None,<Monomer object>]}
    1.14          keys are the Sequence objects, values are the lists, which
    1.15          contain monomers of those sequences or None for gaps in the
    1.16 -        corresponding sequence of
    1.17 -        alignment
    1.18 -    
    1.19 +        corresponding sequence of alignment
    1.20      """
    1.21      # _sequences -- list of Sequence objects. Sequences don't contain gaps
    1.22      #  - see sequence.py module

     2.1 --- a/allpy/monomer.py	Sun Nov 28 17:40:11 2010 +0300
     2.2 +++ b/allpy/monomer.py	Tue Nov 30 17:10:25 2010 +0300
     2.3 @@ -89,10 +89,14 @@
     2.4      """  Amino acid """
     2.5      pass
     2.6  
     2.7 -class DNA(Monomer):
     2.8 +class DNABase(Monomer):
     2.9      """ Deoxyribonucleic acid  """
    2.10      pass
    2.11  
    2.12 +class RNABase(Monomer):
    2.13 +    """ Ribonucleic acid  """
    2.14 +    pass
    2.15 +
    2.16  # prepare all aminoacids
    2.17  
    2.18  for code3, data in AAdict.items():

     3.1 --- a/allpy/sequence.py	Sun Nov 28 17:40:11 2010 +0300
     3.2 +++ b/allpy/sequence.py	Tue Nov 30 17:10:25 2010 +0300
     3.3 @@ -14,15 +14,17 @@
     3.4  import os
     3.5  
     3.6  
     3.7 -class Sequence(object):
     3.8 +class Sequence(list):
     3.9      """ Sequence of Monomers
    3.10 +
    3.11 +    list of monomer objects (aminoacids or nucleotides)
    3.12      
    3.13      Mandatory data:
    3.14      *   name -- str with the name of sequence
    3.15      *   description -- str with description of the sequence
    3.16 -    *   monomers -- list of monomer objects (aminoacids or nucleotides)
    3.17      
    3.18      Optional (may be empty):
    3.19 +    *   source -- source of sequence
    3.20      *   pdb_chains -- list of Bio.PDB.Chain's
    3.21      *   pdb_files -- dictionary like {Bio.PDB.Chain: file_obj}
    3.22      
    3.23 @@ -212,3 +214,9 @@
    3.24                  n = len(line)
    3.25                  s += line[(n_from - number_user):(n_to - number_user)]
    3.26          return Sequence.from_str(s, name, description, monomer_kind)
    3.27 +
    3.28 +class ProteinSequence(Sequence):
    3.29 +    """ """
    3.30 +    pass
    3.31 +
    3.32 +