allpy
view allpy/markup.py @ 642:a1307c0bb030
Added necessary hooks for monomer pickling [closes #35]
Current implementation is lazy and does not store all monomer classes
explicitly in some module. They are still generated on the fly.
Some monomer classes have the same name as per PDB database. In order to avoid
name clashes, we add underscores to classes, if same name class already exists.
WARNING.
This may and WILL cause trouble, if such clashes occur between different types
of monomers, in which case different names will be generated for the same class
depending on the order of loading modules.
The only example of such clash in the current database is dna monomer "0AV" and
rna "A2M", which both have name "2'-O-METHYLADENOSINE 5'-(DIHYDROGEN PHOSPHATE)"
author | Daniil Alexeyevsky <dendik@kodomo.fbb.msu.ru> |
---|---|
date | Fri, 03 Jun 2011 16:49:44 +0400 |
parents | 3566d253c994 |
children |
line source
4 """ object for use as key for default value """
7 """ Markup for Sequence or Alignment
9 container is iterable collection of items.
10 item is object getting markup data (new attribute).
12 container: Alignment, item: Column
13 container: Sequence, item: Monomer
15 Markup stored in attributes of item is internal value.
16 When export or import, it is mapped to or from external value.
17 Internal value could be of any type.
18 External value should be single character.
20 Data:
21 * name -- name (str) of attribute of object
22 * container
23 * map_out -- dict, mapping internal values to external
24 * map_in -- dict, mapping external values to internal
26 map_in and map_out can have key markup.default, which used when
27 input key is not in map. To drop this defaults, drop this key
28 from map_out and map_in dicts. In this case to_string() and
29 from_string() methods can raise KeyError
30 """
33 """ Note: add convenient defaults to maps """
55 """ return internal value for given item
57 markup[monomer] <==> monomer.name, where name is markup.name
58 """
62 """ set attribute of item to value """
66 """ return item has attribute
68 usage: if item in markup
69 """
73 """ delete all attributes from items """
78 """ return string representing markup """
87 @classmethod
89 """ return new markup
91 add (or replaces) attributes to items
92 """
104 """ return list of tuples (item, self[item]) for items with attribute """
110 """ return list of items for with attribute is determined """