csb.bio.io.wwpdb.AbstractResidueMapper

Class AbstractResidueMapper

object --+ | AbstractResidueMapper

Defines the base interface of all residue mappers, used to align PDB ATOM records to the real (SEQRES) sequence of a chain.

Nested Classes

__metaclass__
Metaclass for defining Abstract Base Classes (ABCs).

Instance Methods

ResidueInfo

create_gap(self, alphabet=<ProteinAlphabet: ILE=I, GLN=Q, ...>)
Create and return a new gap residue.

source code

SparseChainSequence

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

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

Class Variables

__abstractmethods__ = frozenset(['map'])

Properties

Inherited from object: __class__

Method Details

create_gap(self, alphabet=<ProteinAlphabet: ILE=I, GLN=Q, ...>)

source code

Create and return a new gap residue.

Parameters:

alphabet (enum) - sequence alphabet; a member of SequenceAlphabets which has GAP item

Returns: ResidueInfo

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 (SparseChainSequence) - sparse sequence (e.g. derived from ATOMS records)
reference (SparseChainSequence) - 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

Note: sparse's ranks won't be touched because the rank property of the underlying ResidueInfo implementation is not necessarily r/w.