csb.bio.sequence.StructureAlignment

Class StructureAlignment

object --+ | AbstractAlignment --+ | StructureAlignment

Multiple structure alignment. Similar to a SequenceAlignment, but the alignment holds the actual csb.bio.structure.ProteinResidue objects, taken from the corresponding source csb.bio.structure.Chains.

Instance Methods

Inherited from AbstractAlignment: __getitem__, __init__, __iter__, add, format, gap_at, subregion

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

Static Methods

StructureAlignment

parse(string, provider, id_factory=None, strict=True)
Create a new StructureAlignment from an mFASTA string.

source code

Class Variables

__abstractmethods__ = frozenset([])

Properties

Inherited from AbstractAlignment: columns, length, rows, size

Inherited from object: __class__

Method Details

parse(string, provider, id_factory=None, strict=True)
Static Method

source code

Create a new StructureAlignment from an mFASTA string. See csb.bio.io.fasta.StructureAlignmentFactory for details.

Parameters:

string (str) - MSA-formatted string
provider (csb.bio.io.wwpdb.StructureProvider) - data source for all structures found in the alignment
strict (bool) - see AbstractAlignment
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.

Returns: StructureAlignment

Nested Classes
Inherited from `AbstractAlignment`: `__metaclass__`

Class StructureAlignment

parse(string, provider, id_factory=None, strict=True) Static Method

parse(string, provider, id_factory=None, strict=True)
Static Method