Example #1
0
 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))
Example #2
0
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
Example #3
0
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
Example #4
0
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
Example #5
0
def test_cysteine_count():
    scores = ManufacturabilityScores.from_amino_acids("C" * 7)
    assert scores.cysteine_count == 7
Example #6
0
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
Example #7
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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
Example #8
0
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
Example #9
0
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
Example #10
0
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
Example #11
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def test_cysteine_count():
    scores = ManufacturabilityScores.from_amino_acids("C" * 7)
    assert scores.cysteine_count == 7
Example #12
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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
Example #13
0
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
Example #14
0
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