Package csb :: Package bio :: Package io :: Module fasta :: Class StructureAlignmentFactory

Class StructureAlignmentFactory

object --+
         |
        StructureAlignmentFactory

Protein structure alignment parser.

In order to construct the structural alignment, this factory needs a PDB structure provider: an object, whose provider.get method returns a csb.bio.structute.Structure for a given sequence identifier. Sequence identifiers on the other hand need to be split into 'accession number' and 'chain ID'. By default this is done using a standard PDB Entry ID factory, but clients are free to provide custom factories. An id_factory must be a callable, which accepts a single string identifier and returns an EntryID object.

Instance Methods

__init__(self, provider, id_factory=None, strict=True)
x.__init__(...) initializes x; see help(type(x)) for signature

source code

SequenceAlignment

make_alignment(self, string)
Build a protein structure alignment given a multi-FASTA string and the current structure provider. source code

ChainSequence

make_entry(self, row, chain)
Build a protein structure alignment entry, given a sequence alignment entry and its corresponding source PDB chain.

source code

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

Properties
EntryID	id_factory Current csb.bio.io.wwpdb.EntryID factory instance in use
enum item	product_type Default sequence type of the alignment rows - a member of SequenceTypes
StructureProvider	provider Current csb.bio.io.wwpdb.StructureProvider instance in use
bool	strict True if strict mode is enabled
Inherited from `object`: `__class__`

Method Details

init(self, provider, id_factory=None, strict=True)
(Constructor)

source code

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

Parameters:

provider (csb.bio.io.wwpdb.StructureProvider) - data source for all structures found in the alignment
id_factory (callable) - callable factory, which transforms a sequence ID into a csb.bio.io.wwpdb.EntryID object. By default this is csb.bio.io.wwpdb.EntryID.create.
strict (bool) - if True, raise exception on duplicate sequence identifiers. See csb.bio.sequence.AbstractAlignment for details

Overrides: object.__init__

(inherited documentation)

make_alignment(self, string)

source code

Build a protein structure alignment given a multi-FASTA string and the current structure provider.

Parameters:

string (str) - alignment string

Returns: SequenceAlignment

Raises:

SequenceError - when an aligned sequence is not a proper subsequence of its respective source PDB chain
StructureNotFoundError - if provider can't provide a structure for a given sequence ID
InvalidEntryIDError - if a given sequence ID cannot be parsed

make_entry(self, row, chain)

source code

Build a protein structure alignment entry, given a sequence alignment entry and its corresponding source PDB chain.

Parameters:

row (AbstractSequence, SequenceAdapter) - sequence alignment entry (sequence with gaps)
chain (csb.bio.structure.Chain) - source PDB chain

Returns: ChainSequence

gapped chain sequence, containing cloned residues from the source chain (except for the gaps)

Raises:

SequenceError - when row is not a proper subsequence of chain

Property Details

id_factory

Current csb.bio.io.wwpdb.EntryID factory instance in use

Get Method:: unreachable.id_factory(self) - Current csb.bio.io.wwpdb.EntryID factory instance in use
Type:: EntryID

product_type

Default sequence type of the alignment rows - a member of SequenceTypes

Get Method:: unreachable.product_type(self) - Default sequence type of the alignment rows - a member of SequenceTypes
Type:: enum item

provider

Current csb.bio.io.wwpdb.StructureProvider instance in use

Get Method:: unreachable.provider(self) - Current csb.bio.io.wwpdb.StructureProvider instance in use
Type:: StructureProvider

strict

True if strict mode is enabled

Get Method:: unreachable.strict(self) - True if strict mode is enabled
Type:: bool

Class StructureAlignmentFactory

__init__(self, provider, id_factory=None, strict=True) (Constructor)

make_alignment(self, string)

make_entry(self, row, chain)

id_factory

product_type

provider

strict

init(self, provider, id_factory=None, strict=True)
(Constructor)