allpy
view allpy/markup.py @ 701:8ca932b9e951
structure/SequenceMixin: add resi_begin and resi_end parameters to PDB loader
Optional arguments resi_begin and resi_end where added to methods
set_pdb_chain() and auto_pdb() of SequenceMixin.
These arguments can be used to restrict range of pdb residues,
that can be connected with monomers from sequence.
These arguments are tuples like (hetero_flag, sequence_id, insertion_code).
See biopdb documantation for more information.
closes #61
author | boris <bnagaev@gmail.com> |
---|---|
date | Wed, 06 Jul 2011 20:49:31 +0200 |
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 """