alphabets

Alphabets for the protein sequences.

polyclonal.alphabets.AAS = ('A', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'K', 'L', 'M', 'N', 'P', 'Q', 'R', 'S', 'T', 'V', 'W', 'Y')

Amino-acid one-letter codes alphabetized, doesn’t include stop or gap.

Type:

tuple

polyclonal.alphabets.AAS_WITHGAP = ('A', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'K', 'L', 'M', 'N', 'P', 'Q', 'R', 'S', 'T', 'V', 'W', 'Y', '-')

Amino-acid one-letter codes alphabetized plus gap as -.

Type:

tuple

polyclonal.alphabets.AAS_WITHSTOP = ('A', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'K', 'L', 'M', 'N', 'P', 'Q', 'R', 'S', 'T', 'V', 'W', 'Y', '*')

Amino-acid one-letter codes alphabetized plus stop as *.

Type:

tuple

polyclonal.alphabets.AAS_WITHSTOP_WITHGAP = ('A', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'K', 'L', 'M', 'N', 'P', 'Q', 'R', 'S', 'T', 'V', 'W', 'Y', '*', '-')

Amino-acid one-letter codes plus stop as * and gap as -.

Type:

tuple

polyclonal.alphabets.biochem_order_aas(alphabet)

Put amino-acids in “biochemical order” so ones with similar properties are nearby.

Parameters:

alphabet (array-like) – Amino-acid characters, can include stop (*) and gap (-).

Returns:

Contains the alphabet in biochemical order

Return type:

tuple

Example

>>> biochem_order_aas(AAS_WITHSTOP_WITHGAP)
... 
('R', 'K', 'H', 'D', 'E', 'Q', 'N', 'S', 'T', 'Y', 'W', 'F', 'A', 'I', 'L', 'M',
'V', 'G', 'P', 'C', '-', '*')