1.1 --- a/allpy/base.py	Tue Jul 12 23:38:54 2011 +0400
     1.2 +++ b/allpy/base.py	Tue Jul 12 23:52:54 2011 +0400
     1.3 @@ -52,11 +52,13 @@
     1.4          vars(module)[TheMonomer.__name__] = TheMonomer
     1.5          if not is_modified:
     1.6              cls.by_code1[code1] = TheMonomer
     1.7 -        cls.by_code3[code3] = TheMonomer
     1.8 +        if code3 not in cls.by_code3 or not is_modified:
     1.9 +            cls.by_code3[code3] = TheMonomer
    1.10          cls.by_name[name] = TheMonomer
    1.11          # We duplicate distinguished long names into Monomer itself, so that we
    1.12          # can use Monomer.from_code3 to create the relevant type of monomer.
    1.13 -        Monomer.by_code3[code3] = TheMonomer
    1.14 +        if code3 not in Monomer.by_code3 or not is_modified:
    1.15 +            Monomer.by_code3[code3] = TheMonomer
    1.16          Monomer.by_name[name] = TheMonomer
    1.17  
    1.18      @classmethod

     2.1 --- a/test/test_base.py	Tue Jul 12 23:38:54 2011 +0400
     2.2 +++ b/test/test_base.py	Tue Jul 12 23:52:54 2011 +0400
     2.3 @@ -36,6 +36,11 @@
     2.4      assert m.code3 == "ALA"
     2.5      assert m.name == "Alanine"
     2.6  
     2.7 +    # This actually tests for proper overriding when there are many monomers
     2.8 +    # with the same code3. The unmodified one takes precedence.
     2.9 +    m = b.Monomer.from_code3('SEC')
    2.10 +    assert m.name == "Selenocysteine"
    2.11 +
    2.12  def assert_alignment(alignment, *body):
    2.13      """Helper: check if alignment representation matches strings of body"""
    2.14      s = StringIO()