def isoelectric_point(self):
"""Calculate the isoelectric point.
Uses the module IsoelectricPoint to calculate the pI of a protein.
"""
aa_content = self.count_amino_acids()
ie_point = IsoelectricPoint.IsoelectricPoint(self.sequence, aa_content)
return ie_point.pi()
def calc_region_charges(seq, cur_window):
"""Perform calculation of charges via isoelectric points for a sequence.
"""
# internal small regions, so do not deal with C and N terminal charges
IsoelectricPoint.pKcterminal = {}
IsoelectricPoint.pKnterminal = {}
cur_pos = 0
region_charges = []
while cur_pos < len(seq) - cur_window:
cur_seq = seq[cur_pos:cur_pos + cur_window]
prot_analysis = ProtParam.ProteinAnalysis(str(cur_seq))
ie_calc = IsoelectricPoint.IsoelectricPoint(
cur_seq, prot_analysis.count_amino_acids())
region_charges.append(ie_calc.pi())
cur_pos += 1
return region_charges
def charge_at_pH(self, pH):
"""Calculate the charge of a protein at given pH."""
aa_content = self.count_amino_acids()
charge = IsoelectricPoint.IsoelectricPoint(self.sequence, aa_content)
return charge.charge_at_pH(pH)