Package csb :: Package bio :: Package io :: Module wwpdb :: Class CombinedResidueMapper

Class CombinedResidueMapper

           object --+    
                    |    
AbstractResidueMapper --+
                        |
                       CombinedResidueMapper

The best of both worlds: attempts to map the residues using FastResidueMapper, but upon failure secures success by switching to RobustResidueMapper.

Nested Classes
Inherited from `AbstractResidueMapper`: `__metaclass__`

Instance Methods

SparseChainSequence

map(self, sparse, reference)
Map sparse's residues to reference. source code

Inherited from AbstractResidueMapper: create_gap

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __init__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Class Variables
	FAST = `<csb.bio.io.wwpdb.FastResidueMapper object at 0x7fe0c57...`
	ROBUST = `<csb.bio.io.wwpdb.RobustResidueMapper object at 0x7fe...`
	__abstractmethods__ = `frozenset([])`

Properties
Inherited from `object`: `__class__`

Method Details

map(self, sparse, reference)

source code

Map sparse's residues to reference. Return all sparse residues, aligned over reference, with artificial gap residues inserted at relevant positions. The resulting sequence of sparse residues will always have the same length as the reference sequence.

Parameters:

sparse - sparse sequence (e.g. derived from ATOMS records)
reference - reference, complete sequence (e.g. derived from SEQRES records)

Returns: SparseChainSequence

all sparse residues, optimally aligned over reference (with gaps)

Raises:

ResidueMappingError - if the specified sequences are not alignable

Overrides: AbstractResidueMapper.map

(inherited documentation)

Class Variable Details

FAST

Value:

<csb.bio.io.wwpdb.FastResidueMapper object at 0x7fe0c57c3a50>

ROBUST

Value:

<csb.bio.io.wwpdb.RobustResidueMapper object at 0x7fe0c57c3ad0>