def setUp(self):
self.paramTxt = """
BeginParams
family=Acceptor radius=0.5 profile=Box
EndParams
"""
self.p = FeatMapParser.FeatMapParser()
def test_FeatMapParser(self):
# We can use a string
p = FeatMapParser.FeatMapParser(data=self.data)
fm = p.Parse()
self.assertEqual(fm.GetNumFeatures(), 3)
self.assertEqual([x.GetFamily() for x in fm.GetFeatures()],
['Acceptor', 'Aromatic', 'Acceptor'])
# We can use a list of strings
p = FeatMapParser.FeatMapParser(data=self.data.split('\n'))
fm = p.Parse()
self.assertEqual(fm.GetNumFeatures(), 3)
self.assertEqual([x.GetFamily() for x in fm.GetFeatures()],
['Acceptor', 'Aromatic', 'Acceptor'])
# and a stream
with closing(StringIO(self.data)) as file:
p = FeatMapParser.FeatMapParser(file=file)
fm = p.Parse()
self.assertEqual(fm.GetNumFeatures(), 3)
self.assertEqual([x.GetFamily() for x in fm.GetFeatures()],
['Acceptor', 'Aromatic', 'Acceptor'])
def test_ParseErrors(self):
# Typos in scoreMode or dirscoreMode section
data = "scoreMode = typo\nbeginParams\nfamily=Acceptor radius=1.5\nEndParams"
p = FeatMapParser.FeatMapParser(data=data)
self.assertRaises(FeatMapParser.FeatMapParseError, p.Parse)
data = "dirscoremode = typo\nbeginParams\nfamily=Acceptor radius=1.5\nEndParams"
p = FeatMapParser.FeatMapParser(data=data)
self.assertRaises(FeatMapParser.FeatMapParseError, p.Parse)
data = "typo = All\nbeginParams\nfamily=Acceptor radius=1.5\nEndParams"
p = FeatMapParser.FeatMapParser(data=data)
self.assertRaises(FeatMapParser.FeatMapParseError, p.Parse)
# Typos in paramBlock
data = "beginTypo\nfamily=Acceptor radius=1.5\nEndParams"
p = FeatMapParser.FeatMapParser(data=data)
self.assertRaises(FeatMapParser.FeatMapParseError, p.Parse)
data = "beginParams\nfamily=Acceptor radius=1.5\nEndTypo"
p = FeatMapParser.FeatMapParser(data=data)
self.assertRaises(FeatMapParser.FeatMapParseError, p.Parse)
data = "beginParams\ntypo=Acceptor radius=1.5\nEndParams"
p = FeatMapParser.FeatMapParser(data=data)
self.assertRaises(FeatMapParser.FeatMapParseError, p.Parse)
data = "beginParams\nprofile=Typo\nEndParams"
p = FeatMapParser.FeatMapParser(data=data)
self.assertRaises(FeatMapParser.FeatMapParseError, p.Parse)
# Typos in points block
data = "BeginPoints\npos=(1.0, 0.0, 5.0, 4.0)\nEndPoints"
p = FeatMapParser.FeatMapParser(data=data)
self.assertRaises(ValueError, p.Parse)
data = "BeginPoints\npos=(1.0, 0.0, 5.0) typo=Acceptor\nEndPoints"
p = FeatMapParser.FeatMapParser(data=data)
self.assertRaises(FeatMapParser.FeatMapParseError, p.Parse)
def test1Basics(self):
p = FeatMapParser.FeatMapParser()
p.SetData(self.data)
fm = p.Parse()
self.assertTrue(fm.scoreMode == FeatMaps.FeatMapScoreMode.Best)
self.assertTrue(fm.dirScoreMode == FeatMaps.FeatDirScoreMode.DotFullRange)
self.assertTrue(fm.GetNumFeatures() == 3)
feats = fm.GetFeatures()
self.assertTrue(feq(feats[0].weight, 1.25))
self.assertTrue(feq(feats[1].weight, 2.0))
self.assertTrue(feq(feats[2].weight, 1.25))
self.assertTrue(len(feats[0].featDirs) == 1)
self.assertTrue(len(feats[1].featDirs) == 2)
self.assertTrue(len(feats[2].featDirs) == 0)
fams = [x.GetFamily() for x in feats]
self.assertTrue(fams == ['Acceptor', 'Aromatic', 'Acceptor'])
def test1Basics(self):
txt = """
ScoreMode=Best
DirScoreMode=DotFullRange
BeginParams
family=Aromatic radius=2.5 width=1.0 profile=Triangle
family=Acceptor radius=1.5
EndParams
# optional
BeginPoints
family=Acceptor pos=(1.0, 0.0, 5.0) weight=1.25 dir=(1, 1, 0)
family=Aromatic pos=(0.0,1.0,0.0) weight=2.0 dir=(0,0,1) dir=(0,0,-1)
family=Acceptor pos=(1.0,1.0,2.0) weight=1.25
EndPoints
"""
p = FeatMapParser.FeatMapParser()
p.SetData(txt)
fm = p.Parse()
self.assertTrue(fm.scoreMode == FeatMaps.FeatMapScoreMode.Best)
self.assertTrue(
fm.dirScoreMode == FeatMaps.FeatDirScoreMode.DotFullRange)
self.assertTrue(fm.GetNumFeatures() == 3)
feats = fm.GetFeatures()
self.assertTrue(feq(feats[0].weight, 1.25))
self.assertTrue(feq(feats[1].weight, 2.0))
self.assertTrue(feq(feats[2].weight, 1.25))
self.assertTrue(len(feats[0].featDirs) == 1)
self.assertTrue(len(feats[1].featDirs) == 2)
self.assertTrue(len(feats[2].featDirs) == 0)
fams = [x.GetFamily() for x in feats]
self.assertTrue(fams == ['Acceptor', 'Aromatic', 'Acceptor'])