def testFormGen():
mf = "C6H12O3"
m0 = mass.of(mf)
t = ms.formulaTable(m0 - 0.001,
m0 + 0.001,
C=(0, 100),
H=(0, 100),
O=(0, 110),
N=0,
P=0,
S=0)
assert len(t) == 1, len(t)
assert t.mf.values == [mf]
t = ms.formulaTable(m0 - 0.005,
m0 + 0.005,
C=(0, 100),
H=(0, 100),
O=(0, 110))
t.print_()
assert len(t) == 3, len(t)
assert mf in t.mf.values
assert "C2H8N6O" in t.mf.values
assert "C5H13N2P" in t.mf.values
def testFormGen():
mf = "C6H12O3"
m0 = mass.of(mf)
t = ms.formulaTable(m0-0.001, m0+0.001, C=(0,100), H=(0, 100), O=(0, 110), N=0, P=0, S=0)
assert len(t) == 1, len(t)
assert t.mf.values == [mf]
t = ms.formulaTable(m0-0.005, m0+0.005, C=(0,100), H=(0, 100), O=(0, 110))
t.print_()
assert len(t) == 3, len(t)
assert mf in t.mf.values
assert "C2H8N6O" in t.mf.values
assert "C5H13N2P" in t.mf.values
def testAccessAndConsistency():
c12 = elements.C12
assert c12["abundance"] == abundance.C12
assert c12["abundance"] is not None
assert abs(c12["abundance"] - 0.989) < 0.001
assert c12["mass"] == mass.C12
assert c12["name"] == "Carbon"
assert c12["number"] == 6
assert mass.of("[13]C") - mass.of("C") == mass.C13 - mass.C12
assert mass.of("C", C=mass.C13) == mass.of("[13]C")
assert mass.of("C", C=elements.C13) == mass.of("[13]C")
#encoding: latin-1
import mass as _mass
_all_adducts=[("M+H" , _mass.p , 1),
("M+NH4" , _mass.of("NH3") + _mass.p , 1),
("M+Na" , _mass.Na - _mass.e , 1),
("M+H-2H2O" , _mass.p - 2*_mass.of("H2O"), 1),
("M+H-H2O" , _mass.p - _mass.of("H20") , 1),
("M+K" , _mass.K - _mass.e , 1),
("M+ACN+H" , _mass.of("C2H3N") + _mass.p , 1),
("M+ACN+Na" , _mass.of("C2H3N") + _mass.Na - _mass.e , 1),
("M+2Na-H" , _mass.of("Na2") - _mass.H - _mass.e, 1),
("M+2H" , 2*_mass.p , 2),
("M+3H" , 3*_mass.p , 3),
("M+H+Na" , _mass.p + _mass.Na - _mass.e, 2),
("M+2H+Na" , 2*_mass.p + _mass.Na - _mass.e, 3),
("M+2Na" , 2*_mass.Na - 2*_mass.e , 2),
("M+2Na+H" , _mass.p + 2*_mass.Na - 2*_mass.e, 3),
("M+Li" , _mass.Li - _mass.e , 1),
("M+CH3OH+H", _mass.of("CH4O") + _mass.p , 1),
("M-H" , -_mass.p , -1),
("M-H2O-H" , -_mass.p - _mass.of("H2O"), -1),
("M+Na-2H" , -2*_mass.p + _mass.Na , -1),
("M+Cl" , _mass.Cl + _mass.e , -1),
("M+K-2H" , -2*_mass.p + _mass.K , -1),
("M+KCl-H" , -1*_mass.p + _mass.K + _mass.Cl, -1),
("M+FA-H" , _mass.of("H2CO2")-_mass.p , -1),
("M-2H" , -2*_mass.p , -2),
("M-3H" , -3*_mass.p , -3),
#encoding: latin-1
import mass as _mass
_all_adducts = [("[M+H]+", _mass.p, 1),
("[M+NH4]+", _mass.of("NH3") + _mass.p, 1),
("[M+Na]+", _mass.Na - _mass.e, 1),
("[M+H-H2O]+", _mass.p - _mass.of("H20"), 1),
("[M+H-H4O2]+", _mass.p - 2 * _mass.of("H2O"), 1),
("[M+K]+", _mass.K - _mass.e, 1),
("[M+CH4O+H]+", _mass.of("CH4O") + _mass.p, 1),
("[M+2Na-H]+", _mass.of("Na2") - _mass.H - _mass.e, 1),
("[M+H2]2+", 2 * _mass.p, 2), ("[M+H3]3+", 3 * _mass.p, 3),
("[M+Na+H]2+", _mass.p + _mass.Na - _mass.e, 2),
("[M+H2+Na]3+", 2 * _mass.p + _mass.Na - _mass.e, 3),
("[M+Na2]2+", 2 * _mass.Na - 2 * _mass.e, 2),
("[M+H+Na2]3+", _mass.p + 2 * _mass.Na - 2 * _mass.e, 3),
("[M-H]-", -_mass.p, -1),
("[M-H-H2O]-", -_mass.p - _mass.of("H2O"), -1),
("[M+Na-H2]-", -2 * _mass.p + _mass.Na, -1),
("[M+Cl]-", -(_mass.p - _mass.Cl), -1),
("[M+K-H2]-", -2 * _mass.p + _mass.K, -1),
("[M-H2]2-", -2 * _mass.p, -2), ("[M-H3]3-", -3 * _mass.p, -3)]
_shortname = lambda key: key[1:].split("]")[0].replace("+", "_plus_")\
.replace("-", "_minus_")
labels = [_a[0] for _a in _all_adducts]
namedLabels = [_shortname(_a) for _a in labels]
#encoding: latin-1
import mass as _mass
_all_adducts = [("M+H", _mass.p, 1), ("M+NH4", _mass.of("NH3") + _mass.p, 1),
("M+Na", _mass.Na - _mass.e, 1),
("M+H-2H2O", _mass.p - 2 * _mass.of("H2O"), 1),
("M+H-H2O", -_mass.of("OH") - _mass.e, 1),
("M+K", _mass.K - _mass.e, 1),
("M+ACN+H", _mass.of("C2H3N") + _mass.p, 1),
("M+ACN+Na", _mass.of("C2H3N") + _mass.Na - _mass.e, 1),
("M+2Na-H", _mass.of("Na2") - _mass.H - _mass.e, 1),
("M+2H", 2 * _mass.p, 2), ("M+3H", 3 * _mass.p, 3),
("M+H+Na", _mass.p + _mass.Na - _mass.e, 2),
("M+2H+Na", 2 * _mass.p + _mass.Na - _mass.e, 3),
("M+2Na", 2 * _mass.Na - 2 * _mass.e, 2),
("M+2Na+H", _mass.p + 2 * _mass.Na - 2 * _mass.e, 3),
("M+Li", _mass.Li - _mass.e, 1),
("M+CH3OH+H", _mass.of("CH4O") + _mass.p, 1),
("M-H", -_mass.p, -1),
("M-H2O-H", -_mass.p - _mass.of("H2O"), -1),
("M+Na-2H", -2 * _mass.p + _mass.Na, -1),
("M+Cl", _mass.Cl + _mass.e, -1),
("M+K-2H", -2 * _mass.p + _mass.K, -1),
("M+KCl-H", -1 * _mass.p + _mass.K + _mass.Cl, -1),
("M+FA-H", _mass.of("H2CO2") - _mass.p, -1),
("M-2H", -2 * _mass.p, -2), ("M-3H", -3 * _mass.p, -3),
("M+CH3COO", _mass.of("H4C2O2") - _mass.p, -1),
("M+F", _mass.F - _mass.e, -1), ("M", 0.0, 0)]
_shortname = lambda key: key.replace("+", "_plus_").replace("-", "_minus_")
#encoding: latin-1
import mass as _mass
_all_adducts=[("[M+H]+" , _mass.p , 1),
("[M+NH4]+" , _mass.of("NH3") + _mass.p , 1),
("[M+Na]+" , _mass.Na - _mass.e , 1),
("[M+H-H2O]+" , _mass.p - _mass.of("H20") , 1),
("[M+H-H4O2]+", _mass.p - 2*_mass.of("H2O"), 1),
("[M+K]+" , _mass.K - _mass.e , 1),
("[M+CH4O+H]+", _mass.of("CH4O") + _mass.p , 1),
("[M+2Na-H]+" , _mass.of("Na2") - _mass.H - _mass.e, 1),
("[M+H2]2+" , 2*_mass.p , 2),
("[M+H3]3+" , 3*_mass.p , 3),
("[M+Na+H]2+" , _mass.p + _mass.Na - _mass.e, 2),
("[M+H2+Na]3+", 2*_mass.p + _mass.Na - _mass.e, 3),
("[M+Na2]2+" , 2*_mass.Na - 2*_mass.e , 2),
("[M+H+Na2]3+", _mass.p + 2*_mass.Na - 2*_mass.e, 3),
("[M-H]-" , -_mass.p , -1),
("[M-H-H2O]-" , -_mass.p - _mass.of("H2O"), -1),
("[M+Na-H2]-" , -2*_mass.p + _mass.Na , -1),
("[M+Cl]-" , -(_mass.p - _mass.Cl) , -1),
("[M+K-H2]-" , -2*_mass.p + _mass.K , -1),
("[M-H2]2-" , -2*_mass.p , -2),
("[M-H3]3-" , -3*_mass.p , -3)
]
_shortname = lambda key: key[1:].split("]")[0].replace("+", "_plus_")\
.replace("-", "_minus_")
