allpy
changeset 645:88c246f20918
Fixed monomer pickling to avoid name clashes. This breaks pickle backwards-compatiblity! [see #35]
Previosly all monomer classes were stored a single namespace,
allpy.data.monomers. This caused a few name clashes, which were mostly
resolved, and one name clash, that was not. (This caused one class to be named
differently depending on the order in which modules were loaded).
Now, instead of one allpy.data.monomers module we have allpy.data.monomers
package with modules dna, rna, protein. This ensures that all name clashes are
resolved uniformly upon any sequence of modules loading.
This may also help in future to keep backward-compatibility longer in case we
replace dynaminc monomer class creation with storing the classes in the module -
if we want to retain independent loading of dna/rna/protein parts.
| author | Daniil Alexeyevsky <dendik@kodomo.fbb.msu.ru> |
|---|---|
| date | Wed, 08 Jun 2011 21:31:02 +0400 |
| parents | 0386dc31676e |
| children | e3f06e45de03 |
| files | allpy/base.py allpy/data/monomers.py allpy/data/monomers/__init__.py allpy/data/monomers/dna.py allpy/data/monomers/protein.py allpy/data/monomers/rna.py |
| diffstat | 6 files changed, 28 insertions(+), 12 deletions(-) [+] |
line diff
1.1 --- a/allpy/base.py Fri Jun 03 16:59:45 2011 +0400 1.2 +++ b/allpy/base.py Wed Jun 08 21:31:02 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 03 16:59:45 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 Wed Jun 08 21:31:02 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 Wed Jun 08 21:31:02 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