def test_singlereaction(self):
"""
1 -1> 2
"""
session = self.Session()
session.add(Molecule(molid=1, nhits=1))
session.add(Molecule(molid=2, nhits=1))
session.add(Reaction(reactid=1, name=u'esterase',
reactant=1, product=2))
session.flush()
fill_molecules_reactions(session)
expected1 = {
u'products': {
u'esterase': {
u'nr': 1,
u'nrp': 1
}
}
}
self.assertDictEqual(self.getReactionSequence(1), expected1)
expected2 = {
u'reactants': {
u'esterase': {
u'nr': 1,
u'nrp': 1
}
}
}
self.assertDictEqual(self.getReactionSequence(2), expected2)
def test_noreactions(self):
session = self.Session()
session.add(Molecule(molid=1, nhits=1))
session.flush()
fill_molecules_reactions(session)
self.assertDictEqual(self.getReactionSequence(1), {})
def test_reactionson4molecules(self):
"""
1 -1> 2 -3> 4
1 -2> 3 -4> 4
"""
session = self.Session()
session.add(Molecule(molid=1, nhits=1))
session.add(Molecule(molid=2, nhits=1))
session.add(Molecule(molid=3, nhits=0))
session.add(Molecule(molid=4, nhits=1))
session.add(Reaction(reactid=1, name=u'esterase',
reactant=1, product=2))
session.add(Reaction(reactid=2, name=u'theogallin',
reactant=1, product=3))
session.add(Reaction(reactid=3, name=u'dehydrox',
reactant=2, product=4))
session.add(Reaction(reactid=4, name=u'reduc',
reactant=3, product=4))
session.flush()
fill_molecules_reactions(session)
expected1 = {
u'products': {u'esterase': {u'nr': 1, u'nrp': 1},
u'theogallin': {u'nr': 1}}
}
self.assertDictEqual(self.getReactionSequence(1), expected1)
expected2 = {
u'reactants': {u'esterase': {u'nr': 1, u'nrp': 1}},
u'products': {u'dehydrox': {u'nr': 1, u'nrp': 1}}
}
self.assertDictEqual(self.getReactionSequence(2), expected2)
expected3 = {
u'reactants': {u'theogallin': {u'nr': 1, u'nrp': 1}},
u'products': {u'reduc': {u'nr': 1, u'nrp': 1}}
}
self.assertDictEqual(self.getReactionSequence(3), expected3)
expected4 = {
u'reactants': {u'dehydrox': {u'nr': 1, u'nrp': 1},
u'reduc': {u'nr': 1}}
}
self.assertDictEqual(self.getReactionSequence(4), expected4)
def populateTestingDB(session):
"""Populates test db with data
Adds 1 molecule with one fragment.
Adds 1 molecule with one fragment which has 2 child fragments
of which one has another child fragment.
Run, Scan and Peak are filled to create a working run.
session
session connection to db
"""
url1 = u'<a href="http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi'
url1 += u'?cid=289">CID: 289</a>'
url2 = u'<a href="http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi'
url2 += u'?cid=152432">CID: 152432</a>'
session.add(Run(
ionisation_mode=-1, skip_fragmentation=True,
ms_intensity_cutoff=200000.0, msms_intensity_cutoff=50,
mz_precision=10, mz_precision_abs=0.002, use_all_peaks=True,
ms_filename=u'F123456.mzxml', abs_peak_cutoff=1000,
max_ms_level=3, precursor_mz_precision=10,
max_broken_bonds=4, description=u'My first description',
max_water_losses=1,
))
session.add(Molecule(
molid=72, mol=u'Molfile', refscore=1.0,
reactionsequence={
u'reactantof': {
u'esterase': {
u'nr': 2,
u'nrp': 1
}
}
},
smiles=u'C1=CC=C(C(=C1)O)O', inchikey14=u'YCIMNLLNPGFGHC',
formula=u'C6H6O2', predicted=False, nhits=1,
name=u'pyrocatechol', mim=110.03677, logp=1.231,
reference=url1
))
session.add(Scan(
scanid=641, mslevel=1, rt=933.317, lowmz=90.3916, highmz=1197.78,
basepeakmz=305.034, basepeakintensity=807577.0, totioncurrent=5957620
))
session.add_all([
# basepeak
Peak(scanid=641, mz=305.033508300781, intensity=807576.625),
# peak of molecule
Peak(scanid=641, mz=109.0295639038086, intensity=345608.65625)
])
session.add(Fragment(
fragid=948,
molid=72,
scanid=641,
mz=109.0295639038086,
mass=110.0367794368,
score=200,
parentfragid=0,
atoms=u"0,1,2,3,4,5,6,7",
deltah=-1.0,
deltappm=-1.84815979523607e-08,
formula=u"C5H4",
))
# fragments of molid=352 + scanid=870
session.add(Molecule(
predicted=False, molid=352,
mol=u"Molfile of dihydroxyphenyl-valerolactone",
formula=u"C11H12O4",
name=u"dihydroxyphenyl-valerolactone",
refscore=1.0, reactionsequence={
u'productof': {
u'theogallin': {
u'nr': 1,
u'nrp': 0
}
}
},
smiles=u"O=C1CCC(Cc2ccc(O)c(O)c2)O1",
inchikey14=u'ZNXXWTPQHVLMQT',
reference=url2,
mim=208.07355, logp=2.763, nhits=1
))
session.add_all([Scan(
scanid=870, mslevel=1, rt=1254.15, lowmz=91.0302, highmz=1171.51,
basepeakmz=287.023, basepeakintensity=1972180.0, totioncurrent=9265290
), Scan(
scanid=871, mslevel=2, rt=1254.93, lowmz=51.5211, highmz=216.864,
basepeakmz=163.076, basepeakintensity=279010.0, totioncurrent=809307,
precursormz=207.0663147, precursorintensity=293096.0,
precursorscanid=870
), Scan(
scanid=872, mslevel=3, rt=1256.77, lowmz=50.3338, highmz=172.155,
basepeakmz=119.087, basepeakintensity=17387.0, totioncurrent=236842,
precursormz=163.0762329, precursorintensity=6163.73,
precursorscanid=871
)])
session.add_all([
# basepeak
Peak(scanid=870, mz=287.022979736328, intensity=1972180.625),
# peak of molecule
Peak(scanid=870, mz=207.066284179688, intensity=293095.84375),
# basepeak and peak of frag 1709
Peak(scanid=871, mz=163.076232910156, intensity=279010.28125),
# peak of frag 1708
Peak(scanid=871, mz=123.04508972168, intensity=211603.046875),
# basepeak and peak of frag 1710
Peak(scanid=872, mz=119.086540222168, intensity=17386.958984375),
])
session.add_all([Fragment(
fragid=1707, molid=352, scanid=870, mass=208.0735588736,
mz=207.066284179688, score=100, parentfragid=0,
atoms=u"0,1,2,3,4,5,6,7,8,9,10,11,12,13,14", deltah=-1,
deltappm=-8.18675317722029e-09,
formula=u"C3H5O3",
), Fragment(
fragid=1708, molid=352, scanid=871, mass=123.0446044689,
mz=123.04508972167969, score=201, parentfragid=1707,
atoms=u"6,7,8,9,10,11,12,13,14", deltah=0,
deltappm=3.943698856902144e-12,
formula=u"C3H5O3",
), Fragment(
fragid=1709, molid=352, scanid=871, mass=164.08372962939995,
mz=163.07623291015625, score=65, parentfragid=1707,
atoms=u"3,4,5,6,7,8,9,10,11,12,13,14", deltah=-1,
deltappm=-1.235815738001507e-08,
formula=u"C3H5O3",
), Fragment(
fragid=1710, scanid=872, molid=352, mass=116.0626002568,
mz=119.08654022216797, score=4, parentfragid=1709,
atoms=u"4,5,6,7,8,9,11,13,14", deltah=3,
deltappm=5.0781684060061766e-08,
formula=u"C3H5O3",
)])
session.flush()
def populateWithUseAllPeaks(session):
""" Dataset with multiple fragments of same molecule on lvl1 scan """
session.add(Run(
ionisation_mode=-1, skip_fragmentation=True,
ms_intensity_cutoff=200000.0, msms_intensity_cutoff=50,
mz_precision=10, mz_precision_abs=0.002, use_all_peaks=False,
ms_filename=u'F123456.mzxml', abs_peak_cutoff=1000,
max_ms_level=3, precursor_mz_precision=10,
max_broken_bonds=4, description=u'My second description',
max_water_losses=1,
))
session.add(Molecule(
molid=12,
refscore=0.119004,
reactionsequence=['sulfation_(aromatic_hydroxyl)'],
smiles=u'Oc1ccc(CC2OC(=O)CC2)cc1OS(O)(=O)=O',
inchikey14=u'YAXFVDUJDAQPTJ',
formula=u'C11H12O7S',
predicted=True,
name=u'5-(3,4)-dihydroxyphenyl-g-valerolactone (F)',
mol=u'Molfile',
reference=u'',
mim=288.0303734299,
logp=1.9027,
nhits=1
))
session.add_all([Scan(
scanid=1,
mslevel=1,
rt=0.503165,
lowmz=286.529,
highmz=288.239,
basepeakmz=287.023,
basepeakintensity=39047000.0,
totioncurrent=49605000.0,
precursorscanid=0
), Scan(
scanid=2,
mslevel=2,
rt=0.544193333333333,
lowmz=66.8575,
highmz=288.026,
basepeakmz=207.066,
basepeakintensity=32485600.0,
totioncurrent=42005700.0,
precursormz=287.0231323,
precursorintensity=39047000.0,
precursorscanid=1
)])
session.add_all([Peak(
scanid=1,
mz=287.015686035156,
intensity=1058332.875
), Peak(
scanid=1,
mz=287.023132324219,
intensity=39047040.0
), Peak(
scanid=2,
mz=207.066223144531,
intensity=32485624.0
), Peak(
scanid=2,
mz=287.022827148438,
intensity=6491798.0
)])
session.add_all([Fragment(
fragid=17,
molid=12,
scanid=1,
mz=287.015686035156,
mass=288.0303734299,
score=0.0,
parentfragid=0,
atoms=u'0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18',
deltah=-1.0,
deltappm=-7.046696487857745e-09,
formula=u"C4H6O2",
), Fragment(
fragid=18,
molid=12,
scanid=1,
mz=287.023132324219,
mass=288.0303734299,
score=0.5,
parentfragid=0,
atoms=u'0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18',
deltah=-1.0,
deltappm=-7.020570507205176e-09,
formula=u"C4H6O2",
), Fragment(
fragid=19,
molid=12,
scanid=2,
mz=207.066223144531,
mass=207.0657338415,
score=0.5,
parentfragid=18,
atoms=u'0,1,2,3,4,5,6,7,8,9,10,11,12,13,14',
deltah=0.0,
deltappm=2.3630267823129625e-12,
formula=u"C4H6O2",
), Fragment(
fragid=20,
molid=12,
scanid=2,
mz=287.022827148438,
mass=288.0303734299,
score=0.0,
parentfragid=18,
atoms=u'0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18',
deltah=-1.0,
deltappm=-7.021641217476223e-09,
formula=u"C4H6O2",
)])