def amino_acids():
return jsonify({
"amino_acids": [{
"one_letter_code": amino_acid.one_letter_code,
"name": amino_acid.name
} for amino_acid in AminoAcid.all()]
})
def check_partition_boundaries_sequence(self, boundaries):
# Beginning with 0
self.assertEqual(boundaries[0][1], 0)
# Each upper boundary of the current partition must match lower boundary of the next partition
for idx in range(len(boundaries) - 1):
self.assertEqual(boundaries[idx][2], boundaries[idx + 1][1])
# Last partition needs a upper limit of 60 times Tryptophan + 1 Water + 1 for the explicit boundary
upper_boundary = AminoAcid.get_haviest().mono_mass * 60 + NeutralLoss.get_by_name("H2O").mono_mass + 1
self.assertEqual(boundaries[len(boundaries) - 1][2], upper_boundary)
def calculate_mass(cls, sequence: str) -> int:
"""
Calculates the mass of the given amino acid sequence.
Parameters
----------
sequence: str
Amino acid sequence
"""
mass = H2O.mono_mass
for amino_acid_one_letter_code in sequence:
mass += AminoAcid.get_by_one_letter_code(
amino_acid_one_letter_code).mono_mass
return mass
def from_dict(cls, attributes: dict) -> Modification:
"""
Creates modification from dictionary.
Parameters
----------
attributes : dict
Dictionary of attributes with key: 'accession', 'name', 'amino_acid', 'delta', 'is_static' and 'position'
Returns
-------
Modification
"""
return Modification(
attributes["accession"],
attributes["name"],
AminoAcid.get_by_one_letter_code(attributes["amino_acid"]),
attributes["delta"],
attributes["is_static"],
ModificationPosition.from_string(attributes["position"])
)
def read_from_csv_file(cls, csv_file_path: pathlib.Path) -> List[Modification]:
"""
Reads modifications from CSV file.
Parameters
----------
csv_file_path : pathlib.Path
Path of the CSV-file
Returns
-------
List of modifications
"""
modifications = []
with csv_file_path.open("r") as csv_file:
csv_reader = csv.reader(csv_file)
# Omit header
next(csv_reader)
for row in csv_reader:
modifications.append(
Modification(row[0], row[1], AminoAcid.get_by_one_letter_code(row[2]), mass_to_int(float(row[3])), cls.string_to_is_static(row[4].lower()), ModificationPosition.from_string(row[5]))
)
return modifications
def test_mass_calculation(self):
fictional_peptide = Peptide(FICTIONAL_SEQUENCE, 0)
# If the amino acid cound test passes, we can use the counts to calculate the mass manally.
# Actually there is no external tool which supports all of our known amino acids, so we can double check the weigth.
mass = fictional_peptide.a_count * AminoAcid.get_by_one_letter_code('A').mono_mass \
+ fictional_peptide.b_count * AminoAcid.get_by_one_letter_code('B').mono_mass \
+ fictional_peptide.c_count * AminoAcid.get_by_one_letter_code('C').mono_mass \
+ fictional_peptide.d_count * AminoAcid.get_by_one_letter_code('D').mono_mass \
+ fictional_peptide.e_count * AminoAcid.get_by_one_letter_code('E').mono_mass \
+ fictional_peptide.f_count * AminoAcid.get_by_one_letter_code('F').mono_mass \
+ fictional_peptide.g_count * AminoAcid.get_by_one_letter_code('G').mono_mass \
+ fictional_peptide.h_count * AminoAcid.get_by_one_letter_code('H').mono_mass \
+ fictional_peptide.i_count * AminoAcid.get_by_one_letter_code('I').mono_mass \
+ fictional_peptide.j_count * AminoAcid.get_by_one_letter_code('J').mono_mass \
+ fictional_peptide.k_count * AminoAcid.get_by_one_letter_code('K').mono_mass \
+ fictional_peptide.l_count * AminoAcid.get_by_one_letter_code('L').mono_mass \
+ fictional_peptide.m_count * AminoAcid.get_by_one_letter_code('M').mono_mass \
+ fictional_peptide.n_count * AminoAcid.get_by_one_letter_code('N').mono_mass \
+ fictional_peptide.o_count * AminoAcid.get_by_one_letter_code('O').mono_mass \
+ fictional_peptide.p_count * AminoAcid.get_by_one_letter_code('P').mono_mass \
+ fictional_peptide.q_count * AminoAcid.get_by_one_letter_code('Q').mono_mass \
+ fictional_peptide.r_count * AminoAcid.get_by_one_letter_code('R').mono_mass \
+ fictional_peptide.s_count * AminoAcid.get_by_one_letter_code('S').mono_mass \
+ fictional_peptide.t_count * AminoAcid.get_by_one_letter_code('T').mono_mass \
+ fictional_peptide.u_count * AminoAcid.get_by_one_letter_code('U').mono_mass \
+ fictional_peptide.v_count * AminoAcid.get_by_one_letter_code('V').mono_mass \
+ fictional_peptide.w_count * AminoAcid.get_by_one_letter_code('W').mono_mass \
+ fictional_peptide.y_count * AminoAcid.get_by_one_letter_code('Y').mono_mass \
+ fictional_peptide.z_count * AminoAcid.get_by_one_letter_code('Z').mono_mass \
+ H2O.mono_mass
self.assertEqual(mass, fictional_peptide.mass)
def test_validation(self):
static_carbamidomethylation_of_c = Modification(
'unimod:4', 'carbamidomethylation of cysteine',
AminoAcid.get_by_one_letter_code('C'), mass_to_int(57.021464),
True, ModificationPosition.ANYWHERE)
variable_oxidation_of_m = Modification(
'unimod:35', 'oxidation of methionine',
AminoAcid.get_by_one_letter_code('M'), mass_to_int(15.994915),
False, ModificationPosition.ANYWHERE)
static_custom_modification_of_n_terminal_d = Modification(
'custom:1', 'custom of aspartic acid',
AminoAcid.get_by_one_letter_code('D'), mass_to_int(10.01541), True,
ModificationPosition.N_TERMINUS)
variable_custom_modification_of_n_terminal_d = Modification(
'custom:2', 'custom of aspartic acid',
AminoAcid.get_by_one_letter_code('D'), mass_to_int(10.01541),
False, ModificationPosition.N_TERMINUS)
static_custom_modification_of_c_terminal_r = Modification(
'custom:3', 'custom of arginine',
AminoAcid.get_by_one_letter_code('R'), mass_to_int(6.153215), True,
ModificationPosition.C_TERMINUS)
variable_custom_modification_of_c_terminal_r = Modification(
'custom:4', 'custom of arginine',
AminoAcid.get_by_one_letter_code('R'), mass_to_int(6.153215),
False, ModificationPosition.C_TERMINUS)
peptide = Peptide(LEPTIN_PEPTIDE_SEQUENCE, 2)
# Static carbamidomethylation of C
expected_peptide_mass = peptide.weight + peptide.c_count * static_carbamidomethylation_of_c.delta
modification_collection = ModificationCollection(
[static_carbamidomethylation_of_c])
precursor_range = PrecursorRange(expected_peptide_mass, 0, 0)
validator = PeptideMassValidator(modification_collection, 0,
precursor_range)
self.assertTrue(validator.validate(peptide))
# This should als match with allowed variable modification (where actually none is applied)
# Static carbamidomethylation of C
# Variable oxidation of M (not considered in expected_weight)
modification_collection = ModificationCollection(
[static_carbamidomethylation_of_c, variable_oxidation_of_m])
validator = PeptideMassValidator(modification_collection, 3,
precursor_range)
self.assertTrue(validator.validate(peptide))
# Static carbamidomethylation of C
# 1 variable oxidation of M
expected_peptide_mass = peptide.weight \
+ peptide.c_count * static_carbamidomethylation_of_c.delta \
+ 1 * variable_oxidation_of_m.delta
modification_collection = ModificationCollection(
[static_carbamidomethylation_of_c, variable_oxidation_of_m])
precursor_range = PrecursorRange(expected_peptide_mass, 0, 0)
validator = PeptideMassValidator(modification_collection, 3,
precursor_range)
self.assertTrue(validator.validate(peptide))
# This should not match if no variable modifiations are allowed
# Static carbamidomethylation of C
# Variable oxidation of M (considered in expected_weight but no variable modification allowed in validation)
validator.set_maximum_number_of_variable_modifications(0)
self.assertFalse(validator.validate(peptide))
# Lets replace two Js with Ms and test 3 applied variable oxidations of M
# Static carbamidomethylation of C
# 3 Variable oxidation of M
peptide = Peptide(LEPTIN_PEPTIDE_SEQUENCE.replace('J', 'M', 2), 2)
expected_peptide_mass = peptide.weight \
+ peptide.c_count * static_carbamidomethylation_of_c.delta \
+ 3 * variable_oxidation_of_m.delta
modification_collection = ModificationCollection(
[static_carbamidomethylation_of_c, variable_oxidation_of_m])
precursor_range = PrecursorRange(expected_peptide_mass, 0, 0)
validator = PeptideMassValidator(modification_collection, 3,
precursor_range)
self.assertTrue(validator.validate(peptide))
# This should fail with only 2 allowed variable modifications
validator.set_maximum_number_of_variable_modifications(2)
self.assertFalse(validator.validate(peptide))
# Test variable n-terminal
# Variable n-terminal modification of D
# Static carbamidomethylation of C
# 2 variable oxidation of M
expected_peptide_mass = peptide.weight \
+ variable_custom_modification_of_n_terminal_d.delta \
+ peptide.c_count * static_carbamidomethylation_of_c.delta \
+ 2 * variable_oxidation_of_m.delta
modification_collection = ModificationCollection([
static_carbamidomethylation_of_c, variable_oxidation_of_m,
variable_custom_modification_of_n_terminal_d
])
precursor_range = PrecursorRange(expected_peptide_mass, 0, 0)
validator = PeptideMassValidator(modification_collection, 3,
precursor_range)
self.assertTrue(validator.validate(peptide))
# This should fail with only 2 allowed variable modifications
validator.set_maximum_number_of_variable_modifications(2)
self.assertFalse(validator.validate(peptide))
# Test static n-terminal modification
# Static n-terminal modification of D
# Static carbamidomethylation of C
# 2 variable oxidation of M
expected_peptide_mass = peptide.weight \
+ static_custom_modification_of_n_terminal_d.delta \
+ peptide.c_count * static_carbamidomethylation_of_c.delta \
+ 2 * variable_oxidation_of_m.delta
modification_collection = ModificationCollection([
static_carbamidomethylation_of_c, variable_oxidation_of_m,
static_custom_modification_of_n_terminal_d
])
precursor_range = PrecursorRange(expected_peptide_mass, 0, 0)
validator = PeptideMassValidator(modification_collection, 3,
precursor_range)
self.assertTrue(validator.validate(peptide))
# Test variable n-terminal
# Variable c-terminal modification of R
# Static carbamidomethylation of C
# 2 variable oxidation of M
expected_peptide_mass = peptide.weight \
+ variable_custom_modification_of_c_terminal_r.delta \
+ peptide.c_count * static_carbamidomethylation_of_c.delta \
+ 2 * variable_oxidation_of_m.delta
modification_collection = ModificationCollection([
static_carbamidomethylation_of_c, variable_oxidation_of_m,
variable_custom_modification_of_c_terminal_r
])
precursor_range = PrecursorRange(expected_peptide_mass, 0, 0)
validator = PeptideMassValidator(modification_collection, 3,
precursor_range)
self.assertTrue(validator.validate(peptide))
# This should fail with only 2 allowed variable modifications
validator.set_maximum_number_of_variable_modifications(2)
self.assertFalse(validator.validate(peptide))
# Test static n-terminal modification
# Static c-terminal modification of R
# Static carbamidomethylation of C
# 2 variable oxidation of M
expected_peptide_mass = peptide.weight \
+ static_custom_modification_of_c_terminal_r.delta \
+ peptide.c_count * static_carbamidomethylation_of_c.delta \
+ 2 * variable_oxidation_of_m.delta
modification_collection = ModificationCollection([
static_carbamidomethylation_of_c, variable_oxidation_of_m,
static_custom_modification_of_c_terminal_r
])
precursor_range = PrecursorRange(expected_peptide_mass, 0, 0)
validator = PeptideMassValidator(modification_collection, 3,
precursor_range)
self.assertTrue(validator.validate(peptide))