Sequence_Cider.py

from localcider.sequenceParameters import SequenceParameters


# Create a Cider sequence object for sequence parameter calculation
def create_Seq_Object(sequence):
    SeqOb = SequenceParameters(sequence)
    return SeqOb


# We need to pass a Seq_object to calculate following sequence feature
# Calculate the kappa value which describe the charge residue dispersion
def calculate_kappa(SeqOb):
    kappa = SeqOb.get_kappa()
    return kappa


# Calculate the fraction of charge residue in the sequence
def calculate_FCR(SeqOb):
    FCR = SeqOb.get_FCR()
    return FCR


# Calculate the net charge per residue in the sequence (+ for positive - for negative)
def calculate_NCPR(SeqOb):
    NCPR = SeqOb.get_NCPR()
    return NCPR


# Calculate the hydrophobicity of the sequence
def calculate_mean_hydropathy(SeqOb):
    mean_hydropathy = SeqOb.get_mean_hydropathy()
    return mean_hydropathy


# Calculate the fraction of expanding residue(E/D/R/K/P) in the sequence
def calculate_fraction_expanding(SeqOb):
    fraction_expanding = SeqOb.get_fraction_expanding()
    return fraction_expanding


# Calculate the charge residue dispersion raw value
def calculate_delta(SeqOb):
    delta = SeqOb.get_delta()
    return delta


# This function is to calculate all parameters and return to main function with a dictionary
def Cider_calculation(sequence):
    SeqOb = create_Seq_Object(sequence)
    kappa = calculate_kappa(SeqOb)
    FCR = calculate_FCR(SeqOb)
    NCPR = calculate_NCPR(SeqOb)
    mean_hydropathy = calculate_mean_hydropathy(SeqOb)
    fraction_expanding = calculate_fraction_expanding(SeqOb)
    delta = calculate_delta(SeqOb)
    dict_parameter = {'kappa': kappa, 'FCR': FCR, 'NCPR': NCPR, 'Hydrophobicity': mean_hydropathy
        , 'Expanding': fraction_expanding, 'delta': delta}
    return dict_parameter