1.1 --- a/lib/project.py	Thu Oct 21 01:00:18 2010 +0400
     1.2 +++ b/lib/project.py	Fri Oct 22 17:07:21 2010 +0400
     1.3 @@ -129,9 +129,9 @@
     1.4                  else:
     1.5                      alignment_list.append(None)
     1.6              if "description" in vars():#if there's no description
     1.7 -                sequences.append(sequence.Sequence(name,monomers,description))
     1.8 +                sequences.append(sequence.Sequence(monomers,name,description))
     1.9              else:
    1.10 -                sequences.append(sequence.Sequence(name,monomers))
    1.11 +                sequences.append(sequence.Sequence(monomers,name))
    1.12              alignment[sequences[-1]]=alignment_list
    1.13          return sequences,alignment
    1.14      

     2.1 --- a/lib/sequence.py	Thu Oct 21 01:00:18 2010 +0400
     2.2 +++ b/lib/sequence.py	Fri Oct 22 17:07:21 2010 +0400
     2.3 @@ -1,5 +1,5 @@
     2.4  #!/usr/bin/python
     2.5 -import monomer
     2.6 +from monomer import AminoAcidType
     2.7  from Bio.PDB import PDBParser, CaPPBuilder
     2.8  from Bio.Seq import Seq
     2.9  from allpy_pdb import Pdb
    2.10 @@ -12,12 +12,12 @@
    2.11      *   name -- str with the name of sequence
    2.12      *   description -- str with description of the sequence
    2.13      *   monomers -- list of monomer objects (aminoacids or nucleotides)
    2.14 -    *   pdb_chain -- list of Bio.PDB.Chain's
    2.15 +    *   pdb_chains -- list of Bio.PDB.Chain's
    2.16      
    2.17      TODO: class Protein: container of multiple Sequences,
    2.18            class ProteinMononer: container of multiple Monomers
    2.19      """
    2.20 -    def __init__(self, name, monomers, description=""):
    2.21 +    def __init__(self, monomers, name='', description=""):
    2.22          self.name = name
    2.23          self.description = description
    2.24          self.monomers = monomers 
    2.25 @@ -47,6 +47,9 @@
    2.26          print sequence
    2.27          # FIXME: align and map
    2.28          
    2.29 +    @staticmethod
    2.30 +    def from_fasta(self, fasta_str, name='', description='', type=AminoAcidType):
    2.31 +        seq = Sequence([])
    2.32  
    2.33          
    2.34