1.1 --- a/allpy/structure.py	Wed Mar 16 19:45:56 2011 +0300
     1.2 +++ b/allpy/structure.py	Wed Mar 16 19:50:06 2011 +0300
     1.3 @@ -64,7 +64,7 @@
     1.4      """
     1.5  
     1.6      def set_pdb_chain(self, pdb_file, pdb_id, pdb_chain='A', pdb_model=0):
     1.7 -        """ Reads Pdb chain from file
     1.8 +        """ Read Pdb chain from file
     1.9  
    1.10          and align each Monomer with PDB.Residue (TODO)
    1.11          """
    1.12 @@ -92,7 +92,7 @@
    1.13  
    1.14      @classmethod
    1.15      def from_pdb_chain(cls, chain):
    1.16 -        """ Returns Sequence with Monomers with link to Bio.PDB.Residue
    1.17 +        """ Return Sequence with Monomers with link to Bio.PDB.Residue
    1.18  
    1.19          chain is Bio.PDB.Chain
    1.20          """
    1.21 @@ -111,9 +111,9 @@
    1.22          return sequence
    1.23  
    1.24      def auto_pdb(self, conformity=None, pdb_getter=download_pdb):
    1.25 -        """ Adds pdb information to each monomer
    1.26 +        """ Add pdb information to each monomer
    1.27  
    1.28 -        Returns if information has been successfully added
    1.29 +        Return if information has been successfully added
    1.30          TODO: conformity_file
    1.31  
    1.32          id-format lava flow
    1.33 @@ -129,7 +129,7 @@
    1.34          return True
    1.35  
    1.36      def save_pdb(self, out_filename, new_chain=None, new_model=None):
    1.37 -        """ Saves pdb_chain to out_file """
    1.38 +        """ Save pdb_chain to out_file """
    1.39          class MySelect(Select):
    1.40              def accept_chain(myselect, chain):
    1.41                  if chain == self.pdb_chain:
    1.42 @@ -182,7 +182,7 @@
    1.43      def geometrical_cores(self, max_delta=config.delta,
    1.44      timeout=config.timeout, minsize=config.minsize,
    1.45      ac_new_atoms=config.ac_new_atoms, ac_count=config.ac_count):
    1.46 -        """ Returns length-sorted list of GCs
    1.47 +        """ Return length-sorted list of GCs
    1.48          GC is set of columns
    1.49  
    1.50          * max_delta -- threshold of distance spreading
    1.51 @@ -195,8 +195,8 @@
    1.52          * ac_count -- max number of cores (including main core)
    1.53              0 means infinity
    1.54  
    1.55 -        cost is calculated as 1 / (delta + 1)
    1.56 -            delta in [0, +inf) => cost in (0, 1]
    1.57 +        weight is calculated as 1 / (delta + 1)
    1.58 +            delta in [0, +inf) => weight in (0, 1]
    1.59          """
    1.60          graph = Graph()
    1.61          for i, column1 in enumerate(self.columns):
    1.62 @@ -237,7 +237,7 @@
    1.63      def blocks3d(self, max_delta=config.delta,
    1.64      timeout=config.timeout, timeout_2=config.timeout_2,
    1.65      min_width=config.min_width, primary_cliques=False):
    1.66 -        """ Returns length-sorted list of reliable blocks
    1.67 +        """ Return length-sorted list of reliable blocks
    1.68  
    1.69          * max_delta -- threshold of distance spreading
    1.70          * timeout -- Bron-Kerbosh timeout (couple cores)
    1.71 @@ -407,7 +407,7 @@
    1.72      def save_pdb(self, out_file):
    1.73          """ Save all sequences
    1.74  
    1.75 -        returns {sequence: (new_chain, new_model)}
    1.76 +        return {sequence: (new_chain, new_model)}
    1.77          """
    1.78          map = {}
    1.79          chains = "ABCDEFGHIJKLMNOPQRSTUVWXYZ"