def test_compute_random_coil_chemical_shifts_pH_low():
seq = 'ARNDE'
temperature = 30
pHs = [-1.0, -1, 15.0, 15]
for pH in pHs:
with pytest.raises(SSException):
nmr.compute_random_coil_chemical_shifts(seq,
temperature=temperature,
pH=pH,
use_ggxgg=True,
use_perdeuteration=False)
def test_compute_random_coil_chemical_shifts_extreme_temperatures():
seq = 'ARNDE'
temperatures = [
-273.15, # absolute zero (celcius)
-273,
100.1,
101
]
for temperature in temperatures:
with pytest.raises(SSException):
nmr.compute_random_coil_chemical_shifts(seq,
temperature=temperature,
use_ggxgg=True,
use_perdeuteration=False)
def test_simple_temp():
"""Tests the ability of the function randCoilChemShifts to accurately predict random coil chemical shifts in different temperature conditions.
"""
output = nmr.compute_random_coil_chemical_shifts("ACDE",
temperature=15,
pH=6.5,
use_ggxgg=True,
use_perdeuteration=False,
asFloat=True)
control = [{
"Res": "A",
"Index": 0,
"CA": 52.695,
"CB": 18.967,
"CO": 177.864,
"N": 126.057,
"HN": 8.519,
"HA": 4.357
}, {
"Res": "C",
"Index": 1,
"CA": 58.584,
"CB": 29.752,
"CO": 174.436,
"N": 118.754,
"HN": 8.466,
"HA": 4.500
}, {
"Res": "D",
"Index": 2,
"CA": 54.701,
"CB": 40.940,
"CO": 176.465,
"N": 122.592,
"HN": 8.476,
"HA": 4.609
}, {
"Res": "E",
"Index": 3,
"CA": 56.941,
"CB": 30.167,
"CO": 176.755,
"N": 121.337,
"HN": 8.426,
"HA": 4.263
}]
for i in range(4):
amino_acid = output[i]
assert amino_acid == control[i]
def test_simple_ph():
"""Tests the ability of the function randCoilChemShifts to accurately predict random coil chemical shifts in different pH conditions.
"""
output = nmr.compute_random_coil_chemical_shifts("ACDE",
temperature=25,
pH=4,
use_ggxgg=True,
use_perdeuteration=False,
asFloat=True)
control = [{
"Res": "A",
"Index": 0,
"CA": 52.673,
"CB": 19.015,
"CO": 177.793,
"N": 126.005,
"HN": 8.429,
"HA": 4.364
}, {
"Res": "C",
"Index": 1,
"CA": 58.575,
"CB": 29.764,
"CO": 174.410,
"N": 118.672,
"HN": 8.396,
"HA": 4.500
}, {
"Res": "D",
"Index": 2,
"CA": 53.868,
"CB": 39.252,
"CO": 175.702,
"N": 121.615,
"HN": 8.476,
"HA": 4.675
}, {
"Res": "E",
"Index": 3,
"CA": 56.281,
"CB": 29.080,
"CO": 176.324,
"N": 120.696,
"HN": 8.281,
"HA": 4.340
}]
for i in range(4):
amino_acid = output[i]
assert amino_acid == control[i]
def test_simple_undeut():
"""Tests the ability of the function randCoilChemShifts to accurately predict random coil chemical shifts for unperdeuterated proteins
"""
output = nmr.compute_random_coil_chemical_shifts("ACDE",
temperature=25,
pH=6.5,
use_ggxgg=True,
use_perdeuteration=False,
asFloat=True)
control = [{
"Res": "A",
"Index": 0,
"CA": 52.673,
"CB": 19.015,
"CO": 177.793,
"N": 126.005,
"HN": 8.429,
"HA": 4.364
}, {
"Res": "C",
"Index": 1,
"CA": 58.575,
"CB": 29.764,
"CO": 174.410,
"N": 118.672,
"HN": 8.396,
"HA": 4.500
}, {
"Res": "D",
"Index": 2,
"CA": 54.728,
"CB": 41.005,
"CO": 176.417,
"N": 122.553,
"HN": 8.414,
"HA": 4.608
}, {
"Res": "E",
"Index": 3,
"CA": 56.950,
"CB": 30.213,
"CO": 176.706,
"N": 121.300,
"HN": 8.362,
"HA": 4.266
}]
for i in range(4):
amino_acid = output[i]
assert amino_acid == control[i]
def test_simple_deut():
"""Tests the ability of the function randCoilChemShifts to accurately predict random coil chemical shifts for perdeuterated proteins.
"""
output = nmr.compute_random_coil_chemical_shifts("ACDE",
temperature=25,
pH=6.5,
use_ggxgg=True,
use_perdeuteration=True,
asFloat=True)
control = [{
"Res": "A",
"Index": 0,
"CA": 51.993,
"CB": 18.015,
"CO": 177.793,
"N": 126.005,
"HN": 8.429,
"HA": "*.***"
}, {
"Res": "C",
"Index": 1,
"CA": 58.025,
"CB": 29.054,
"CO": 174.410,
"N": 118.672,
"HN": 8.396,
"HA": "*.***"
}, {
"Res": "D",
"Index": 2,
"CA": 54.178,
"CB": 40.295,
"CO": 176.417,
"N": 122.553,
"HN": 8.414,
"HA": "*.***"
}, {
"Res": "E",
"Index": 3,
"CA": 56.260,
"CB": 29.243,
"CO": 176.706,
"N": 121.300,
"HN": 8.362,
"HA": "*.***"
}]
for i in range(4):
amino_acid = output[i]
assert amino_acid == control[i]
def test_simple_phos():
"""Tests the ability of the function randCoilChemShifts to accurately predict random coil chemical shifts for phosphorylated amino acids.
"""
output = nmr.compute_random_coil_chemical_shifts("(sep)(tpo)(ptr)",
temperature=25,
pH=6.5,
use_ggxgg=True,
use_perdeuteration=False,
asFloat=True)
control = [{
"Res": "SEP",
"Index": 0,
"CA": 58.483,
"CB": 65.876,
"CO": 174.762,
"N": 119.143,
"HN": 9.005,
"HA": 4.440
}, {
"Res": "TPO",
"Index": 1,
"CA": 62.641,
"CB": 71.984,
"CO": 174.201,
"N": 117.185,
"HN": 8.913,
"HA": 4.261
}, {
"Res": "PTR",
"Index": 2,
"CA": 57.802,
"CB": 38.635,
"CO": 175.690,
"N": 122.211,
"HN": 8.087,
"HA": 4.585
}]
for i in range(3):
amino_acid = output[i]
assert amino_acid == control[i]
def test_simple_types():
"""Tests the ability of the function randCoilChemShifts to accurately predict random coil chemical shifts for all 20 amino acid types.
"""
output = nmr.compute_random_coil_chemical_shifts("ACDEFGHIKLMNPQRSTVWY",
temperature=25,
pH=6.5,
use_ggxgg=True,
use_perdeuteration=False,
asFloat=True)
control = [{
"Res": "A",
"Index": 0,
"CA": 52.673,
"CB": 19.015,
"CO": 177.793,
"N": 126.005,
"HN": 8.429,
"HA": 4.364
}, {
"Res": "C",
"Index": 1,
"CA": 58.575,
"CB": 29.764,
"CO": 174.410,
"N": 118.672,
"HN": 8.396,
"HA": 4.500
}, {
"Res": "D",
"Index": 2,
"CA": 54.896,
"CB": 40.919,
"CO": 176.273,
"N": 122.765,
"HN": 8.403,
"HA": 4.540
}, {
"Res": "E",
"Index": 3,
"CA": 56.873,
"CB": 30.051,
"CO": 176.341,
"N": 120.831,
"HN": 8.335,
"HA": 4.225
}, {
"Res": "F",
"Index": 4,
"CA": 57.900,
"CB": 39.333,
"CO": 176.236,
"N": 119.924,
"HN": 8.186,
"HA": 4.637
}, {
"Res": "G",
"Index": 5,
"CA": 45.364,
"CB": "**.***",
"CO": 173.150,
"N": 112.203,
"HN": 8.145,
"HA": 3.909
}, {
"Res": "H",
"Index": 6,
"CA": 55.775,
"CB": 29.978,
"CO": 174.752,
"N": 118.609,
"HN": 8.137,
"HA": 4.631
}, {
"Res": "I",
"Index": 7,
"CA": 61.170,
"CB": 38.698,
"CO": 175.946,
"N": 122.883,
"HN": 8.143,
"HA": 4.135
}, {
"Res": "K",
"Index": 8,
"CA": 56.199,
"CB": 32.866,
"CO": 176.184,
"N": 126.438,
"HN": 8.474,
"HA": 4.309
}, {
"Res": "L",
"Index": 9,
"CA": 55.223,
"CB": 42.321,
"CO": 177.352,
"N": 124.735,
"HN": 8.114,
"HA": 4.339
}, {
"Res": "M",
"Index": 10,
"CA": 55.397,
"CB": 32.878,
"CO": 175.653,
"N": 121.485,
"HN": 8.400,
"HA": 4.502
}, {
"Res": "N",
"Index": 11,
"CA": 51.159,
"CB": 38.132,
"CO": 173.163,
"N": 121.161,
"HN": 8.416,
"HA": 4.957
}, {
"Res": "P",
"Index": 12,
"CA": 63.418,
"CB": 32.272,
"CO": 176.884,
"N": "***.***",
"HN": "*.***",
"HA": 4.423
}, {
"Res": "Q",
"Index": 13,
"CA": 55.989,
"CB": 29.081,
"CO": 176.161,
"N": 120.570,
"HN": 8.503,
"HA": 4.305
}, {
"Res": "R",
"Index": 14,
"CA": 56.205,
"CB": 30.960,
"CO": 176.358,
"N": 123.141,
"HN": 8.392,
"HA": 4.407
}, {
"Res": "S",
"Index": 15,
"CA": 58.326,
"CB": 63.811,
"CO": 174.642,
"N": 117.860,
"HN": 8.452,
"HA": 4.549
}, {
"Res": "T",
"Index": 16,
"CA": 62.004,
"CB": 69.725,
"CO": 174.464,
"N": 116.881,
"HN": 8.182,
"HA": 4.350
}, {
"Res": "V",
"Index": 17,
"CA": 62.918,
"CB": 32.654,
"CO": 175.762,
"N": 122.829,
"HN": 8.103,
"HA": 3.984
}, {
"Res": "W",
"Index": 18,
"CA": 57.244,
"CB": 29.237,
"CO": 175.644,
"N": 124.340,
"HN": 8.098,
"HA": 4.638
}, {
"Res": "Y",
"Index": 19,
"CA": 57.632,
"CB": 38.892,
"CO": 174.936,
"N": 122.232,
"HN": 7.732,
"HA": 4.438
}]
for i in range(20):
amino_acid = output[i]
assert amino_acid == control[i]