I3DSequence
#
- class biotite.structure.alphabet.I3DSequence(sequence='')[source]#
Bases:
Sequence
Representation of a structure in the 3Di structural alphabet. [1]
- Parameters:
- sequenceiterable object, optional
The 3Di sequence. This may either be a list or a string. May take upper or lower case letters. By default the sequence is empty.
See also
to_3di
Create 3Di sequences from a structure.
References
- copy(new_seq_code=None)#
Copy the object.
- Parameters:
- new_seq_codendarray, optional
If this parameter is set, the sequence code is set to this value, rather than the original sequence code.
- Returns:
- copy
A copy of this object.
- static dtype(alphabet_size)#
Get the sequence code dtype required for the given size of the alphabet.
- Parameters:
- alpahabet_sizeint
The size of the alphabet.
- Returns:
- dtype
The
dtype
, that is large enough to store symbol codes, that are encoded by anAlphabet
of the given size.
- get_alphabet()#
Get the
Alphabet
of theSequence
.This method must be overwritten, when subclassing
Sequence
.- Returns:
- alphabetAlphabet
Sequence
alphabet.
- get_symbol_frequency()#
Get the number of occurences of each symbol in the sequence.
If a symbol does not occur in the sequence, but it is in the alphabet, its number of occurences is 0.
- Returns:
- frequencydict
A dictionary containing the symbols as keys and the corresponding number of occurences in the sequence as values.
- is_valid()#
Check, if the sequence contains a valid sequence code.
A sequence code is valid, if at each sequence position the code is smaller than the size of the alphabet.
Invalid code means that the code cannot be decoded into symbols. Furthermore invalid code can lead to serious errors in alignments, since the substitution matrix is indexed with an invalid index.
- Returns:
- validbool
True, if the sequence is valid, false otherwise.
- reverse(copy=True)#
Reverse the
Sequence
.- Parameters:
- copybool, optional
If set to False, the code
ndarray
of the returned sequence is an array view to the sequence code of this object. In this case, manipulations on the returned sequence would also affect this object. Otherwise, the sequence code is copied.
- Returns:
- reversedSequence
The reversed
Sequence
.
Examples
>>> dna_seq = NucleotideSequence("ACGTA") >>> dna_seq_rev = dna_seq.reverse() >>> print(dna_seq_rev) ATGCA
Gallery#

Searching for structural homologs in a protein structure database