omega_yfw_example.py

## Code snippet for calculating the omega aro value for the WT A1-LCD sequence, as 
## described in Martin, E. W., Holehouse, A. S., Peran, I., Farag, M., Incicco, J. J., 
## Bremer, A., Grace, C. R., Soranno, A., Pappu, R. V. & Mittag, T. Valence and 
## patterning of aromatic residues determine the phase behavior of prion-like domains. 
## Science 367, 694–699 (2020).
##
## This requires the localcider package (https://pypi.org/project/localcider/)
##

from localcider.sequenceParameters import SequenceParameters

A1 = 'GSMASASSSQRGRSGSGNFGGGRGGGFGGNDNFGRGGNFSGRGGFGGSRGGGGYGGSGDGYNGFGNDGSNFGGGGSYNDFGNYNNQSSNFGPMKGGNFGGRSSGGGGGGGQYFAKPRNQGGYGGSSSSSSYGSGRRF'

# build the SequenceParameters object from the sequence
S = SequenceParameters(A1)

# Compute the omega_aro patterning parameter for the WT sequence 
# (corresponds to the vertical 'WT' line on Figure 4A

omega_aro = S.get_kappa_X(['Y','F','W'])
print('WT A1 Omega_aro: %1.3f' %(omega_aro))