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

source code

    object --+
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            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