custom digests

There are a number of predefined enzymes specified for the Enzyme class contained within pythomics.proteomics. However, the class also supports arbitrary proteases based on the rules found here:

X!Tandem Protease Rules

Here is an example using a known protease,

import pythomics.proteomics.digest as digest

enzyme = digest.Enzyme(enzyme='trypsin')
print enzyme.cleave('PEPTIDESALLLLLKRAAAAAAAA')

However, for enzymes which are not specified, we can provide the pattern (as defined by the X!Tandem rules)

import pythomics.proteomics.digest as digest

enzyme = digest.Enzyme(pattern='[R]|[X]')
print enzyme.cleave('PEPTIDESALLLLLKRAAAAAAAA')
enzyme = Enzyme(pattern='[KR]|{P},[X]|[D]')
print enzyme.cleave('PEPTIDESALLLLLKRAAAAAAAA')