Class Alignment

Container for an individual sequence alignment.

Instance Methods

__init__(self, object_ids=None, models=None, molecules=None, sequences=None, strings=None, gaps=None, msa_algorithm=None, pairwise_algorithm=None, matrix=None, gap_open_penalty=None, gap_extend_penalty=None, end_gap_open_penalty=None, end_gap_extend_penalty=None)
Set up the sequence alignment object.

Inherited from data_classes.Element: __repr__, from_xml, is_empty, to_xml

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

Properties

Inherited from object: __class__

Method Details

__init__(self, object_ids=None, models=None, molecules=None, sequences=None, strings=None, gaps=None, msa_algorithm=None, pairwise_algorithm=None, matrix=None, gap_open_penalty=None, gap_extend_penalty=None, end_gap_open_penalty=None, end_gap_extend_penalty=None)
(Constructor)

Set up the sequence alignment object.

Parameters:

• object_ids (list of str) - The list of IDs for each structural object in the alignment. In most cases this will be the data pipe name. This will be used to retrieve alignments.
• models (list of int) - The list of model numbers used in the alignment. This will be used to retrieve alignments.
• molecules (list of str) - The list of molecules used in the alignment. This will be used to retrieve alignments.
• sequences (list of str) - The list of residue sequences for the alignment as one letter codes.
• strings (list of str) - The list of alignment strings.
• gaps (numpy rank-2 int array) - The alignment gap matrix.
• msa_algorithm (str) - The global multiple sequence alignment (MSA) algorithm.
• pairwise_algorithm (str) - The pairwise sequence alignment algorithm.
• matrix (str) - The substitution matrix
• gap_open_penalty (float) - The penalty for introducing gaps, as a positive number.
• gap_extend_penalty (float) - The penalty for extending a gap, as a positive number.
• end_gap_open_penalty (float) - The optional penalty for opening a gap at the end of a sequence.
• end_gap_extend_penalty (float) - The optional penalty for extending a gap at the end of a sequence.

Overrides: object.__init__