1.1 --- a/lib/block.py	Mon Oct 25 00:03:35 2010 +0400
     1.2 +++ b/lib/block.py	Mon Oct 25 13:30:11 2010 +0400
     1.3 @@ -68,7 +68,7 @@
     1.4      timeout=config.timeout, minsize=config.minsize, 
     1.5      ac_new_atoms=config.ac_new_atoms,
     1.6      ac_count=config.ac_count):
     1.7 -        """ returns length-sorted list of blocks, representing GCs
     1.8 +        """ Returns length-sorted list of blocks, representing GCs
     1.9          
    1.10          max_delta -- threshold of distance spreading
    1.11          timeout -- Bron-Kerbosh timeout (then fast O(n ln n) algorithm)

     2.1 --- a/lib/graph.py	Mon Oct 25 00:03:35 2010 +0400
     2.2 +++ b/lib/graph.py	Mon Oct 25 13:30:11 2010 +0400
     2.3 @@ -51,9 +51,11 @@
     2.4          
     2.5      @staticmethod
     2.6      def line(k1, k2):
     2.7 +        """ Construct object, representing line of graph """
     2.8          return frozenset([k1, k2])
     2.9      
    2.10      def bounded(self, k1, k2):
    2.11 +        """ Return if these two nodes of the graph are bounded with line """
    2.12          return k1 == k2 or Graph.line(k1, k2) in self.lines
    2.13      
    2.14      def count_one(self, node):
    2.15 @@ -94,6 +96,7 @@
    2.16      
    2.17      def drop_nodes(self, nodes):
    2.18          """ Run drop_node for each of given nodes
    2.19 +        
    2.20          Returns if nodes was not empty (ugly beauty)
    2.21          """
    2.22          for node in nodes:

     3.1 --- a/lib/monomer.py	Mon Oct 25 00:03:35 2010 +0400
     3.2 +++ b/lib/monomer.py	Mon Oct 25 13:30:11 2010 +0400
     3.3 @@ -73,6 +73,7 @@
     3.4      def from_code1(code1):
     3.5          return index_code1_protein[code1.upper()]
     3.6      def instance(self):
     3.7 +        """ Returns new AminoAcid object of this type """
     3.8          return AminoAcid(self)
     3.9  
    3.10  
    3.11 @@ -86,4 +87,7 @@
    3.12  for code3, data in AAdict.items():
    3.13      code1, m_type, is_modified, none, name = data
    3.14      if m_type == 'p':
    3.15 -        aat = AminoAcidType(name, code1, code3, is_modified)
    3.16 +        AminoAcidType(name, code1, code3, is_modified)
    3.17 +
    3.18 +del code3, data, code1, m_type, is_modified, none, name
    3.19 +

     4.1 --- a/lib/project.py	Mon Oct 25 00:03:35 2010 +0400
     4.2 +++ b/lib/project.py	Mon Oct 25 13:30:11 2010 +0400
     4.3 @@ -52,6 +52,7 @@
     4.4              self.sequences,self.alignment=Project.from_fasta(args[0])
     4.5  
     4.6      def __len__(self):
     4.7 +        """ Returns width, ie length of each sequence with gaps """
     4.8          return max([len(line) for line in self.alignment.values()])
     4.9  
    4.10      def thickness(self):

     5.1 --- a/lib/sequence.py	Mon Oct 25 00:03:35 2010 +0400
     5.2 +++ b/lib/sequence.py	Mon Oct 25 13:30:11 2010 +0400
     5.3 @@ -33,9 +33,14 @@
     5.4          return len(self.monomers)
     5.5      
     5.6      def __str__(self):
     5.7 +        """ Returns sequence in one-letter code """
     5.8          return ''.join([monomer.type.code1 for monomer in self.monomers])
     5.9          
    5.10      def __eq__(self, other):
    5.11 +        """ Returns if all corresponding monomers of this sequences are equal
    5.12 +        
    5.13 +        If lengths of sequences are not equal, returns False
    5.14 +        """ 
    5.15          return len(self) == len(other) and \
    5.16          all([a==b for a, b in zip(self.monomers, other.monomers)])
    5.17      
    5.18 @@ -61,12 +66,16 @@
    5.19          
    5.20      @staticmethod
    5.21      def from_str(fasta_str, name='', description='', monomer_kind=AminoAcidType):
    5.22 +        """ Import data from one-letter code
    5.23 +        
    5.24 +        monomer_kind is class, inherited from MonomerType
    5.25 +        """
    5.26          monomers = [monomer_kind.from_code1(aa).instance() for aa in fasta_str]
    5.27          return Sequence(monomers, name, description)
    5.28  
    5.29      @staticmethod
    5.30      def from_pdb_chain(chain):
    5.31 -        """ returns Sequence with Monomers with link to Bio.PDB.Residue
    5.32 +        """ Returns Sequence with Monomers with link to Bio.PDB.Residue
    5.33          
    5.34          chain is Bio.PDB.Chain
    5.35          """