Package data_store :: Module seq_align :: Class Alignment
[hide private]
[frames] | no frames]

Class Alignment

source code


Container for an individual sequence alignment.

Instance Methods [hide private]
 
__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.
source code

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 [hide private]

Inherited from object: __class__

Method Details [hide private]

__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)

source code 

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__