Package csb :: Package bio :: Package io :: Module wwpdb :: Class RobustResidueMapper |
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# Class RobustResidueMapper

source code

               object --+
                        |
    AbstractResidueMapper --+
                            |
                           RobustResidueMapper

Exhaustive residue mapper, which uses Needleman-Wunsch global alignment. Much slower (quadratic), but fail-proof even with incompatible sequences (can insert gaps in both the `sparse` and the `reference` sequence).

Nested Classes
| GlobalAligner
Inherited from `AbstractResidueMapper`: `__metaclass__`

Instance Methods
__init__(self, match=1, mismatch=-10, gap=0) x.__init__(...) initializes x; see help(type(x)) for signature | source code
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__`, `__new__`, `__reduce__`, `__reduce_ex__`, `__repr__`, `__setattr__`, `__sizeof__`, `__str__`, `__subclasshook__`

Class Variables
| __abstractmethods__ = ``frozenset([``])``

Properties
Inherited from `object`: `__class__`

Method Details

### __init__(self, match=1, mismatch=-10, gap=0) (Constructor) | source code
x.__init__(...) initializes x; see help(type(x)) for signature Parameters: `match` (float) - score for a match `mismatch` (float) - score for a mismatch (by default mismatches are heavily penalized, while gaps are allowed) `gap` (float) - gap penalty Overrides: object.__init__ (inherited documentation)

### 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)