def __new__(cls, peptide):
return VaccinePeptideBase.__new__(
cls,
mutant_protein_fragment="",
mutant_epitope_predictions="",
wildtype_epitope_predictions="",
mutant_epitope_score="",
wildtype_epitope_score="",
num_mutant_epitopes_to_keep="",
manufacturability_scores=ManufacturabilityScores.from_amino_acids(
peptide))
def test_n_terminal_cysteine():
scores = ManufacturabilityScores.from_amino_acids("C" + 6 * "A")
assert scores.difficult_n_terminal_residue
scores = ManufacturabilityScores.from_amino_acids(7 * "A")
assert not scores.difficult_n_terminal_residue
def max_7mer_gravy_score():
scores = ManufacturabilityScores.from_amino_acids("H" * 3 + "A" * 7)
# hydropathy of alanine is 1.8, histidine is -3.2
# from Kyte & Doolittle 1982
assert scores.max_7mer_gravy_score == 1.8
def cterm_7mer_gravy_score():
scores = ManufacturabilityScores.from_amino_acids("QLFY" + "A" * 7)
# hydropathy of alanine is 1.8 from Kyte & Doolittle 1982
assert scores.cterm_7mer_gravy_score == 1.8
def test_cysteine_count():
scores = ManufacturabilityScores.from_amino_acids("C" * 7)
assert scores.cysteine_count == 7
def test_asp_pro_bond_count():
scores = ManufacturabilityScores.from_amino_acids("A" * 7)
assert scores.asparagine_proline_bond_count == 0
scores = ManufacturabilityScores.from_amino_acids("NP" + "A" * 7 + "NP")
assert scores.asparagine_proline_bond_count == 2
def test_c_terminal_proline():
scores = ManufacturabilityScores.from_amino_acids("A" * 6 + "P")
assert scores.c_terminal_proline
scores = ManufacturabilityScores.from_amino_acids("A" * 7)
assert not scores.c_terminal_proline
def test_n_terminal_glutamic_acid():
scores = ManufacturabilityScores.from_amino_acids("E" + 6 * "A")
assert scores.difficult_n_terminal_residue
scores = ManufacturabilityScores.from_amino_acids(7 * "A")
assert not scores.difficult_n_terminal_residue
def max_7mer_gravy_score():
scores = ManufacturabilityScores.from_amino_acids("H" * 3 + "A" * 7)
# hydropathy of alanine is 1.8, histidine is -3.2
# from Kyte & Doolittle 1982
assert scores.max_7mer_gravy_score == 1.8
def cterm_7mer_gravy_score():
scores = ManufacturabilityScores.from_amino_acids("QLFY" + "A" * 7)
# hydropathy of alanine is 1.8 from Kyte & Doolittle 1982
assert scores.cterm_7mer_gravy_score == 1.8
def test_cysteine_count():
scores = ManufacturabilityScores.from_amino_acids("C" * 7)
assert scores.cysteine_count == 7
def test_asp_pro_bond_count():
scores = ManufacturabilityScores.from_amino_acids("A" * 7)
assert scores.asparagine_proline_bond_count == 0
scores = ManufacturabilityScores.from_amino_acids("NP" + "A" * 7 + "NP")
assert scores.asparagine_proline_bond_count == 2
def test_n_terminal_glutamine():
scores = ManufacturabilityScores.from_amino_acids("Q" + 6 * "A")
assert scores.difficult_n_terminal_residue
scores = ManufacturabilityScores.from_amino_acids(7 * "A")
assert not scores.difficult_n_terminal_residue
def test_c_terminal_proline():
scores = ManufacturabilityScores.from_amino_acids("A" * 6 + "P")
assert scores.c_terminal_proline
scores = ManufacturabilityScores.from_amino_acids("A" * 7)
assert not scores.c_terminal_proline