csb.bio.io.wwpdb.FastResidueMapper

Class FastResidueMapper

object --+ | AbstractResidueMapper --+ | FastResidueMapper

RegExp-based residue mapper. Fails on heavily malformed input (i.e. it cannot insert gaps in the reference), but it is very fast (linear) and memory efficient.

Instance Methods

__init__(self)
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

CODEC = 'utf-8'

DELIMITER = u').*?('

FORBIDDEN_CHARS = set(['(', ')', '*', '-', '.', '?', '^'])

MAX_FRAGMENTS = 20

MIN_UNICODE_CHAR = 300

PATTERN = u'^.*?({0}).*?$'

__abstractmethods__ = frozenset([])

Properties

Inherited from object: __class__

Method Details

init(self)
(Constructor)

source code

x.__init__(...) initializes x; see help(type(x)) for signature

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)

Nested Classes
Inherited from `AbstractResidueMapper`: `__metaclass__`

Class FastResidueMapper

__init__(self) (Constructor)

map(self, sparse, reference)

init(self)
(Constructor)