def aa_analysis(df, property):
if property == "ncpr":
df = df[pd.notnull(df['Amino_acids'])]
df[["AA1","AA2"]] = df['Amino_acids'].str.split('/',expand=True)
isoelectric_point = []
for sequence in df["AA1"]:
try:
cdr3 = ProteinAnalysis(str(sequence))
cidercdr3 = SequenceParameters(str(sequence))
isoelectric_point.append(cidercdr3.get_NCPR())
except:
isoelectric_point.append(0)
pass
df["AA1_Iso"] = isoelectric_point
isoelectric_point2 = []
for sequence in df["AA2"]:
try:
cdr3 = ProteinAnalysis(str(sequence))
cidercdr3 = SequenceParameters(str(sequence))
isoelectric_point2.append(cidercdr3.get_NCPR())
except:
isoelectric_point2.append(0)
pass
df["AA2_Iso"] = isoelectric_point2
df["AA_Iso_Delta"] = df["AA2_Iso"] - df["AA1_Iso"]
df = df[["AA1_Iso", "AA2_Iso", "AA_Iso_Delta"]]
elif property == "uversky_hydropathy":
df = df[pd.notnull(df['Amino_acids'])]
df[["AA1","AA2"]] = df['Amino_acids'].str.split('/',expand=True)
isoelectric_point = []
for sequence in df["AA1"]:
try:
cdr3 = ProteinAnalysis(str(sequence))
cidercdr3 = SequenceParameters(str(sequence))
isoelectric_point.append(cidercdr3.get_uversky_hydropathy())
except:
isoelectric_point.append(0)
pass
df["AA1_Iso"] = isoelectric_point
isoelectric_point2 = []
for sequence in df["AA2"]:
try:
cdr3 = ProteinAnalysis(str(sequence))
cidercdr3 = SequenceParameters(str(sequence))
isoelectric_point2.append(cidercdr3.get_uversky_hydropathy())
except:
isoelectric_point2.append(0)
pass
df["AA2_Iso"] = isoelectric_point2
df["AA_Iso_Delta"] = df["AA2_Iso"] - df["AA1_Iso"]
df = df[["AA1_Iso", "AA2_Iso", "AA_Iso_Delta"]]
return df
#can't use SeqParam(seqfile=file)
#because all the sequences are appended to each other.
output = open(file + "_charge", 'w+')
for protein in [x for x in contents if x]:
header = protein[0:protein.index('\n')]
seq = protein[protein.index('\n'):-1]
print(header)
if ('X' in seq):
print("Warning: unspecified protein encountered.")
seq = seq.replace('X', '')
seq_param = SequenceParameters(seq)
#mean_net_charge is always positive, whereas
# net_charge_per_residue is alternating
net_charge = seq_param.get_NCPR(pH=7.0) * seq_param.get_length()
print(net_charge)
output.write(header)
output.write(", ")
output.write(str(7.0))
output.write(str(", "))
output.write(str(seq_param.get_molecular_weight()))
output.write(str(", "))
output.write(str(net_charge))
output.write('\n')
output.close()