def test1Basics(self):
fs = [
FreeChemicalFeature('Aromatic', 'Foo', Point3D(0, 0, 0)),
FreeChemicalFeature('Acceptor', 'Foo', Point3D(2, 0, 0)),
FreeChemicalFeature('Acceptor', 'Foo', Point3D(2.1, 0, 0))
]
aFmp = FeatMaps.FeatMapParams()
aFmp.radius = 2.0
bFmp = FeatMaps.FeatMapParams()
bFmp.radius = 1.0
fmps = {'Aromatic': aFmp, 'Acceptor': bFmp}
fmap = FeatMaps.FeatMap(params=fmps)
fmap.AddFeature(fs[0], 1.0)
fmap.AddFeature(fs[1], 1.0)
fmap.AddFeature(fs[2], 2.0)
fmap.AddFeature(fs[2], 2.0)
self.assertTrue(fmap.GetNumFeatures() == 4)
self.assertTrue(len(fmap.GetFeatures()) == 4)
fmap.DropFeature(3)
self.assertTrue(fmap.GetNumFeatures() == 3)
self.assertTrue(len(fmap.GetFeatures()) == 3)
f = fmap.GetFeature(0)
self.assertTrue(f.GetFamily() == 'Aromatic')
self.assertTrue(feq(f.weight, 1.0))
f = fmap.GetFeature(1)
self.assertTrue(f.GetFamily() == 'Acceptor')
self.assertTrue(feq(f.weight, 1.0))
f = fmap.GetFeature(2)
self.assertTrue(f.GetFamily() == 'Acceptor')
self.assertTrue(feq(f.weight, 2.0))
def test4FeatFeatScoreBox(self):
aFmp = FeatMaps.FeatMapParams()
aFmp.radius = 2.0
aFmp.featProfile = FeatMaps.FeatMapParams.FeatProfile.Box
fmps = {'Aromatic': aFmp}
fmap = FeatMaps.FeatMap(params=fmps)
fs = [FreeChemicalFeature('Aromatic', 'Foo', Point3D(0, 0, 0))]
fmap.AddFeature(fs[0], 1.1)
self.assertTrue(len(fmap.GetFeatures()) == 1)
sc = fmap.GetFeatFeatScore(
fmap.GetFeature(0),
FreeChemicalFeature('Aromatic', '', Point3D(1, 0, 0)))
self.assertTrue(feq(sc, 1.1))
sc = fmap.GetFeatFeatScore(
fmap.GetFeature(0),
FreeChemicalFeature('Aromatic', '', Point3D(1.5, 0, 0)))
self.assertTrue(feq(sc, 1.1))
sc = fmap.GetFeatFeatScore(
fmap.GetFeature(0),
FreeChemicalFeature('Aromatic', '', Point3D(0, 0, 0)))
self.assertTrue(feq(sc, 1.1))
sc = fmap.GetFeatFeatScore(
fmap.GetFeature(0),
FreeChemicalFeature('Aromatic', '', Point3D(2.1, 0, 0)))
self.assertTrue(feq(sc, 0))
def test5ScoreFeats(self):
aFmp = FeatMaps.FeatMapParams()
bFmp = FeatMaps.FeatMapParams()
fmps = {'Aromatic': aFmp, 'Acceptor': bFmp}
fmap = FeatMaps.FeatMap(params=fmps)
fs = [
FreeChemicalFeature('Aromatic', 'Foo', Point3D(0, 0, 0)),
FreeChemicalFeature('Acceptor', 'Foo', Point3D(2, 0, 0)),
FreeChemicalFeature('Acceptor', 'Foo', Point3D(2.1, 0, 0))
]
fmap.AddFeature(fs[0], 1.1)
fmap.AddFeature(fs[1], 1.1)
fmap.AddFeature(fs[2], 2.1)
l1 = fmap._loopOverMatchingFeats(
FreeChemicalFeature('Aromatic', '', Point3D(0, 0, 0)))
l1 = list(l1)
self.assertTrue(len(l1) == 1)
self.assertTrue(l1[0][0] == 0)
self.assertTrue(l1[0][1].GetFamily() == 'Aromatic')
l1 = fmap._loopOverMatchingFeats(
FreeChemicalFeature('Acceptor', '', Point3D(0, 0, 0)))
l1 = list(l1)
self.assertTrue(len(l1) == 2)
self.assertTrue(l1[0][0] == 1)
self.assertTrue(l1[0][1].GetFamily() == 'Acceptor')
self.assertTrue(l1[1][0] == 2)
self.assertTrue(l1[1][1].GetFamily() == 'Acceptor')
def test2FeatFeatScoreGauss(self):
aFmp = FeatMaps.FeatMapParams()
aFmp.radius = 2.0
fmps = {'Aromatic':aFmp}
fmap = FeatMaps.FeatMap(params=fmps)
fs = [FreeChemicalFeature('Aromatic','Foo',Point3D(0,0,0))]
fmap.AddFeature(fs[0],1.0)
self.failUnless(len(fmap.GetFeatures())==1)
sc = fmap.GetFeatFeatScore(fmap.GetFeature(0),FreeChemicalFeature('Aromatic','',Point3D(1,0,0)))
self.failUnless(feq(sc,math.exp(-1)))
sc = fmap.GetFeatFeatScore(fmap.GetFeature(0),FreeChemicalFeature('Aromatic','',Point3D(1.5,0,0)))
self.failUnless(feq(sc,math.exp(-2.25)))
sc = fmap.GetFeatFeatScore(fmap.GetFeature(0),FreeChemicalFeature('Aromatic','',Point3D(0,0,0)))
self.failUnless(feq(sc,1.0))
sc = fmap.GetFeatFeatScore(fmap.GetFeature(0),FreeChemicalFeature('Aromatic','',Point3D(2.1,0,0)))
self.failUnless(feq(sc,0))
sc = fmap.GetFeatFeatScore(fmap.GetFeature(0),FreeChemicalFeature('Acceptor','',Point3D(1,0,0)))
self.failUnless(feq(sc,0))
sc = fmap.GetFeatFeatScore(fmap.GetFeature(0),FreeChemicalFeature('Acceptor','',Point3D(1,0,0)),
typeMatch=False)
self.failUnless(feq(sc,math.exp(-1)))
self.failUnlessRaises(IndexError,lambda: fmap.GetFeatFeatScore(fmap.GetFeature(1),FreeChemicalFeature('Aromatic','',Point3D(0,0,0))))
def get_FeatureMapScore(small_m, large_m, score_mode=FeatMaps.FeatMapScoreMode.All):
featLists = []
for m in [small_m, large_m]:
rawFeats = fdef.GetFeaturesForMol(m)
# filter that list down to only include the ones we're intereted in
featLists.append([f for f in rawFeats if f.GetFamily() in keep])
fms = [FeatMaps.FeatMap(feats=x, weights=[1] * len(x), params=fmParams) for x in featLists]
fms[0].scoreMode = score_mode
fm_score = fms[0].ScoreFeats(featLists[1]) / min(fms[0].GetNumFeatures(), len(featLists[1]))
return fm_score
def test7ScoreFeats(self):
aFmp = FeatMaps.FeatMapParams()
aFmp.radius = 2.0
aFmp.featProfile = FeatMaps.FeatMapParams.FeatProfile.Box
bFmp = FeatMaps.FeatMapParams()
bFmp.radius = 1.0
bFmp.featProfile = FeatMaps.FeatMapParams.FeatProfile.Box
fmps = {'Aromatic': aFmp, 'Acceptor': bFmp}
fmap = FeatMaps.FeatMap(params=fmps)
fs = [
FreeChemicalFeature('Aromatic', 'Foo', Point3D(0, 0, 0)),
]
fmap.AddFeature(fs[0], 1.1)
fs = [
FreeChemicalFeature('Aromatic', '', Point3D(0, 1, 0)),
FreeChemicalFeature('Acceptor', '', Point3D(1.5, 0, 0)),
]
sc = fmap.ScoreFeats(fs)
self.assertTrue(feq(sc, 1.1))
msv = [-1] * 1
fsv = [-1] * 2
fsfmi = [-1] * 2
sc = fmap.ScoreFeats(fs,
mapScoreVect=msv,
featsScoreVect=fsv,
featsToFeatMapIdx=fsfmi)
self.assertTrue(feq(sc, 1.1))
self.assertTrue(feq(sum(msv), sc))
self.assertTrue(feq(sum(fsv), sc))
self.assertTrue(fsfmi == [[0], []])
fmap.scoreMode = FeatMaps.FeatMapScoreMode.Closest
sc = fmap.ScoreFeats(fs,
mapScoreVect=msv,
featsScoreVect=fsv,
featsToFeatMapIdx=fsfmi)
self.assertTrue(feq(sc, 1.1))
self.assertTrue(feq(sum(msv), sc))
self.assertTrue(feq(sum(fsv), sc))
self.assertTrue(fsfmi == [[0], []])
fmap.scoreMode = FeatMaps.FeatMapScoreMode.Best
sc = fmap.ScoreFeats(fs,
mapScoreVect=msv,
featsScoreVect=fsv,
featsToFeatMapIdx=fsfmi)
self.assertTrue(feq(sc, 1.1))
self.assertTrue(feq(sum(msv), sc))
self.assertTrue(feq(sum(fsv), sc))
self.assertTrue(fsfmi == [[0], []])
def CombineFeatMaps(fm1,
fm2,
mergeMetric=MergeMetric.NoMerge,
mergeTol=1.5,
dirMergeMode=DirMergeMode.NoMerge):
"""
the parameters will be taken from fm1
"""
res = FeatMaps.FeatMap(params=fm1.params)
__copyAll(res, fm1, fm2)
if mergeMetric != MergeMetric.NoMerge:
MergeFeatPoints(res, mergeMetric=mergeMetric, mergeTol=mergeTol)
return res
def get_FeatureMapScore(ref_mol, query_mol):
featLists = []
for m in [ref_mol, query_mol]:
rawFeats = fdef.GetFeaturesForMol(m)
# filter that list down to only include the ones we're interested in
featLists.append([f for f in rawFeats if f.GetFamily() in keep])
fms = [
FeatMaps.FeatMap(feats=x, weights=[1] * len(x), params=fmParams)
for x in featLists
]
#utils.log("Calc:", str(fms[0].ScoreFeats(featLists[1])), "/ float(min(", str(fms[0].GetNumFeatures()), str(len(featLists[1])), "))")
fm_score = fms[0].ScoreFeats(featLists[1]) / float(
min(fms[0].GetNumFeatures(), len(featLists[1])))
return fm_score
def get_FeatureMapScore(small_feats,
large_feats,
tani=False,
score_mode=FeatMaps.FeatMapScoreMode.All):
"""
Generate the feature map score.
:param small_feats:
:param large_feats:
:param tani:
:return:
"""
featLists = []
for rawFeats in [small_feats, large_feats]:
# filter that list down to only include the ones we're interested in
featLists.append(rawFeats)
fms = [
FeatMaps.FeatMap(feats=x, weights=[1] * len(x), params=fmParams)
for x in featLists
]
# set the score mode
fms[0].scoreMode = score_mode
try:
if tani:
c = fms[0].ScoreFeats(featLists[1])
A = fms[0].GetNumFeatures()
B = len(featLists[1])
if B != fms[1].GetNumFeatures():
utils.log("Why isn't B equal to number of features...?!")
tani_score = float(c) / (A + B - c)
return tani_score
else:
fm_score = fms[0].ScoreFeats(featLists[1]) / min(
fms[0].GetNumFeatures(), len(featLists[1]))
return fm_score
except ZeroDivisionError:
utils.log("ZeroDivisionError")
return 0
if tani:
tani_score = float(c) / (A + B - c)
return tani_score
else:
fm_score = fms[0].ScoreFeats(featLists[1]) / min(
fms[0].GetNumFeatures(), len(featLists[1]))
return fm_score
def get_fm_score(self,
small_m=None,
large_m=None,
score_mode=FeatMaps.FeatMapScoreMode.All):
'''
Get the feature-map score for a small molecule vs. a large molecule
:param small_m: rdkit mol object for the small molecule
:param large_m: rdkit mol object for the large molecule
:param score_mode: default = featuremaps score, defined in init
:return: the value of the feature map score
'''
if not small_m and not self.reference:
raise Exception(
'Reference molecule not set! Please specify or provide to init'
)
if not large_m and not self.target_s:
raise Exception(
'Target molecule(s) not set! Please specify or provide to init'
)
if not small_m:
small_m = self.reference
if not large_m:
large_m = self.target_s
feat_lists = []
for m in [small_m, large_m]:
rawFeats = self.fdef.GetFeaturesForMol(m)
# filter that list down to only include the ones we're interested in
feat_lists.append(
[f for f in rawFeats if f.GetFamily() in self.keep])
fms = [
FeatMaps.FeatMap(feats=x,
weights=[1] * len(x),
params=self.fmParams) for x in feat_lists
]
fms[0].scoreMode = score_mode
fm_score = fms[0].ScoreFeats(feat_lists[1]) / min(
fms[0].GetNumFeatures(), len(feat_lists[1]))
return fm_score
def Parse(self, featMap=None):
if featMap is None:
featMap = FeatMaps.FeatMap()
l = self._NextLine().strip()
while l:
splitL = l.split('=')
if len(splitL) == 1:
keyword = splitL[0].strip().lower()
if keyword == 'beginpoints':
pts = self.ParseFeatPointBlock()
for pt in pts:
featMap.AddFeatPoint(pt)
elif keyword == 'beginparams':
featMap.params = self.ParseParamBlock()
else:
raise FeatMapParseError(
'Unrecognized keyword %s on line %d' %
(keyword, self._lineNum))
else:
keyword = splitL[0].strip().lower()
val = splitL[1].strip()
if keyword == 'scoremode':
try:
featMap.scoreMode = getattr(FeatMaps.FeatMapScoreMode,
val)
except AttributeError:
raise FeatMapParseError(
'ScoreMode %s not recognized on line %d' %
(val, self._lineNum))
elif keyword == 'dirscoremode':
try:
featMap.dirScoreMode = getattr(
FeatMaps.FeatDirScoreMode, val)
except AttributeError:
raise FeatMapParseError(
'DirScoreMode %s not recognized on line %d' %
(val, self._lineNum))
else:
raise FeatMapParseError(
'Unrecognized keyword %s on line %d' %
(keyword, self._lineNum))
l = self._NextLine().strip()
return featMap
def test3FeatFeatScoreTriangle(self):
aFmp = FeatMaps.FeatMapParams()
aFmp.width = 2.0
aFmp.radius = 3.0
aFmp.featProfile=FeatMaps.FeatMapParams.FeatProfile.Triangle
fmps = {'Aromatic':aFmp}
fmap = FeatMaps.FeatMap(params=fmps)
fs = [FreeChemicalFeature('Aromatic','Foo',Point3D(0,0,0))]
fmap.AddFeature(fs[0],1.0)
self.failUnless(len(fmap.GetFeatures())==1)
sc = fmap.GetFeatFeatScore(fmap.GetFeature(0),FreeChemicalFeature('Aromatic','',Point3D(1,0,0)))
self.failUnless(feq(sc,0.5))
sc = fmap.GetFeatFeatScore(fmap.GetFeature(0),FreeChemicalFeature('Aromatic','',Point3D(1.5,0,0)))
self.failUnless(feq(sc,0.25))
sc = fmap.GetFeatFeatScore(fmap.GetFeature(0),FreeChemicalFeature('Aromatic','',Point3D(0,0,0)))
self.failUnless(feq(sc,1.0))
sc = fmap.GetFeatFeatScore(fmap.GetFeature(0),FreeChemicalFeature('Aromatic','',Point3D(2.1,0,0)))
self.failUnless(feq(sc,0))
def test8ScoreFeatDirs(self):
aFmp = FeatMaps.FeatMapParams()
aFmp.radius = 2.0
aFmp.featProfile = FeatMaps.FeatMapParams.FeatProfile.Box
fmps = {'Acceptor': aFmp}
fmap = FeatMaps.FeatMap(params=fmps)
fmap.dirScoreMode = FeatMaps.FeatDirScoreMode.DotFullRange
fs = [
FreeChemicalFeature('Acceptor', 'Foo', Point3D(0, 0, 0)),
]
fs[0].featDirs = [Point3D(0, 1, 0)]
fmap.AddFeature(fs[0], 1.1)
fs = [
FreeChemicalFeature('Acceptor', '', Point3D(1.0, 0, 0)),
]
fs[0].featDirs = [Point3D(0, 1, 0)]
sc = fmap.ScoreFeats(fs)
self.assertTrue(feq(sc, 1.1))
fs[0].featDirs = [Point3D(0, -1, 0)]
sc = fmap.ScoreFeats(fs)
self.assertTrue(feq(sc, -1.1))
fs[0].featDirs = [Point3D(0, 0, 1)]
sc = fmap.ScoreFeats(fs)
self.assertTrue(feq(sc, 0.0))
fmap.dirScoreMode = FeatMaps.FeatDirScoreMode.DotPosRange
fs[0].featDirs = [Point3D(0, -1, 0)]
sc = fmap.ScoreFeats(fs)
self.assertTrue(feq(sc, 0))
fs[0].featDirs = [Point3D(0, 1, 0)]
sc = fmap.ScoreFeats(fs)
self.assertTrue(feq(sc, 1.1))
def create_feature_map(mol):
feats = get_raw_features(mol)
return FeatMaps.FeatMap(feats=feats,
weights=[1] * len(feats),
params=fmaps.params)
def test6ScoreFeats(self):
aFmp = FeatMaps.FeatMapParams()
aFmp.radius = 2.0
bFmp = FeatMaps.FeatMapParams()
bFmp.radius = 1.0
# use box scoring to make math easier... the other scoring
# functions are tested above
aFmp.featProfile = FeatMaps.FeatMapParams.FeatProfile.Box
bFmp.featProfile = FeatMaps.FeatMapParams.FeatProfile.Box
fmps = {'Aromatic': aFmp, 'Acceptor': bFmp}
fmap = FeatMaps.FeatMap(params=fmps)
fs = [
FreeChemicalFeature('Aromatic', 'Foo', Point3D(0, 0, 0)),
FreeChemicalFeature('Acceptor', 'Foo', Point3D(2, 0, 0)),
FreeChemicalFeature('Acceptor', 'Foo', Point3D(2.1, 0, 0))
]
fmap.AddFeature(fs[0], 1.1)
fmap.AddFeature(fs[1], 1.1)
fmap.AddFeature(fs[2], 2.1)
fs = [
FreeChemicalFeature('Aromatic', '', Point3D(0, 1, 0)),
FreeChemicalFeature('Acceptor', '', Point3D(1.5, 0, 0)),
]
sc = fmap.ScoreFeats(fs)
self.assertTrue(feq(sc, 4.3))
msv = [-1] * 3
fsv = [-1] * 2
fsfmi = [None] * 2
sc = fmap.ScoreFeats(fs,
mapScoreVect=msv,
featsScoreVect=fsv,
featsToFeatMapIdx=fsfmi)
self.assertTrue(feq(sc, 4.3))
self.assertTrue(feq(sum(msv), sc))
self.assertTrue(feq(sum(fsv), sc))
self.assertTrue(fsfmi == [[0], [1, 2]])
# make sure we reset the vectors internally:
sc = fmap.ScoreFeats(fs,
mapScoreVect=msv,
featsScoreVect=fsv,
featsToFeatMapIdx=fsfmi)
self.assertTrue(feq(sc, 4.3))
self.assertTrue(feq(sum(msv), sc))
self.assertTrue(feq(sum(fsv), sc))
self.assertTrue(fsfmi == [[0], [1, 2]])
fmap.scoreMode = FeatMaps.FeatMapScoreMode.Closest
sc = fmap.ScoreFeats(fs,
mapScoreVect=msv,
featsScoreVect=fsv,
featsToFeatMapIdx=fsfmi)
self.assertTrue(feq(sc, 2.1))
self.assertTrue(feq(sum(msv), sc))
self.assertTrue(feq(sum(fsv), sc))
self.assertTrue(fsfmi == [[0], [1]])
fmap.scoreMode = FeatMaps.FeatMapScoreMode.Best
sc = fmap.ScoreFeats(fs,
mapScoreVect=msv,
featsScoreVect=fsv,
featsToFeatMapIdx=fsfmi)
self.assertTrue(feq(sc, 3.2))
self.assertTrue(feq(sum(msv), sc))
self.assertTrue(feq(sum(fsv), sc))
self.assertTrue(fsfmi == [[0], [2]])
def getFeatureMap(mol):
feats = getRawFeatures(mol)
return FeatMaps.FeatMap(feats=feats,
weights=[1] * len(feats),
params=fmParams)