1.1 --- a/allpy/base.py	Fri Jun 10 15:33:16 2011 +0400
     1.2 +++ b/allpy/base.py	Fri Jun 10 15:37:20 2011 +0400
     1.3 @@ -37,8 +37,9 @@
     1.4          name = name.strip().capitalize()
     1.5          code1 = code1.upper()
     1.6          code3 = code3.upper()
     1.7 +        module = vars(data.monomers)[cls.type]
     1.8          TheMonomer.__name__ = re.sub(r"\W", "_", name)
     1.9 -        TheMonomer.__module__ = data.monomers.__name__
    1.10 +        TheMonomer.__module__ = module.__name__
    1.11          TheMonomer.name = name
    1.12          TheMonomer.code1 = code1
    1.13          TheMonomer.code3 = code3
    1.14 @@ -46,11 +47,9 @@
    1.15          # Save the class in data.monomers so that it can be pickled
    1.16          # Some names are not unique, we append underscores to them
    1.17          # in order to fix it.
    1.18 -        # XXX: this WILL fail with dna 0AV != rna A2M, which both have
    1.19 -        # name "2'-O-METHYLADENOSINE 5'-(DIHYDROGEN PHOSPHATE)"
    1.20 -        while TheMonomer.__name__ in vars(data.monomers):
    1.21 +        while TheMonomer.__name__ in vars(module):
    1.22              TheMonomer.__name__ += "_"
    1.23 -        vars(data.monomers)[TheMonomer.__name__] = TheMonomer
    1.24 +        vars(module)[TheMonomer.__name__] = TheMonomer
    1.25          if not is_modified:
    1.26              cls.by_code1[code1] = TheMonomer
    1.27          cls.by_code3[code3] = TheMonomer

     2.1 --- a/allpy/data/monomers.py	Fri Jun 10 15:33:16 2011 +0400
     2.2 +++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
     2.3 @@ -1,7 +0,0 @@
     2.4 -"""This module stores classes for all monomer objects.
     2.5 -
     2.6 -These classes are currently created on-the-fly and not stored here directly.
     2.7 -For implementation details please see base.Monomer._subclass and
     2.8 -base.Monomer.initialize.
     2.9 -"""
    2.10 -pass

     3.1 --- /dev/null	Thu Jan 01 00:00:00 1970 +0000
     3.2 +++ b/allpy/data/monomers/__init__.py	Fri Jun 10 15:37:20 2011 +0400
     3.3 @@ -0,0 +1,9 @@
     3.4 +"""This package stores classes for all monomer objects.
     3.5 +
     3.6 +These classes are currently created on-the-fly and not stored here directly.
     3.7 +For implementation details please see base.Monomer._subclass and
     3.8 +base.Monomer.initialize.
     3.9 +"""
    3.10 +import protein
    3.11 +import dna
    3.12 +import rna

     4.1 --- /dev/null	Thu Jan 01 00:00:00 1970 +0000
     4.2 +++ b/allpy/data/monomers/dna.py	Fri Jun 10 15:37:20 2011 +0400
     4.3 @@ -0,0 +1,5 @@
     4.4 +"""Classes for DNA monomers.
     4.5 +
     4.6 +Contents of this module are created on-the-fly, see `allpy.base.Monomer`.
     4.7 +"""
     4.8 +pass

     5.1 --- /dev/null	Thu Jan 01 00:00:00 1970 +0000
     5.2 +++ b/allpy/data/monomers/protein.py	Fri Jun 10 15:37:20 2011 +0400
     5.3 @@ -0,0 +1,5 @@
     5.4 +"""Classes for protein monomers.
     5.5 +
     5.6 +Contents of this module are created on-the-fly, see `allpy.base.Monomer`.
     5.7 +"""
     5.8 +pass

     6.1 --- /dev/null	Thu Jan 01 00:00:00 1970 +0000
     6.2 +++ b/allpy/data/monomers/rna.py	Fri Jun 10 15:37:20 2011 +0400
     6.3 @@ -0,0 +1,5 @@
     6.4 +"""Classes for RNA monomers.
     6.5 +
     6.6 +Contents of this module are created on-the-fly, see `allpy.base.Monomer`.
     6.7 +"""
     6.8 +pass