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 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 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 ParseParamBlock(self):
paramLineSplitter = re.compile(r'([a-zA-Z]+) *= *(\S+)')
params = {}
l = self._NextLine()
while l and l != 'EndParams':
param = FeatMaps.FeatMapParams()
vals = paramLineSplitter.findall(l)
for name, val in vals:
name = name.lower()
if name == 'family':
family = val
elif name == 'radius':
param.radius = float(val)
elif name == 'width':
param.width = float(val)
elif name == 'profile':
try:
param.featProfile = getattr(param.FeatProfile, val)
except AttributeError:
raise FeatMapParseError(
'Profile %s not recognized on line %d' %
(val, self._lineNum))
else:
raise FeatMapParseError(
'FeatMapParam option %s not recognized on line %d' %
(name, self._lineNum))
params[family] = param
l = self._NextLine()
if l != 'EndParams':
raise FeatMapParseError('EndParams line not found')
return params
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 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 __init__(self, reference: str = None, target_s: str = None):
'''
Setup of the SuCOS scoring class. If you do not set reference or target_s, you will have to feed them
as rdkit mol objects to each class method/function.
Sets: self.reference: an rdkit mol object of the reference mol
self.target_s: a list of rdkit mol objects for the target mols
:param reference: an sdf or mol file containing the reference (hit) molecule
:param target_s: an sdf or mol file containing one or multiple molecules to compare against reference
'''
self.fdef = AllChem.BuildFeatureFactory(
os.path.join(RDConfig.RDDataDir, 'BaseFeatures.fdef'))
self.fmParams = {}
for k in self.fdef.GetFeatureFamilies():
self.fparams = FeatMaps.FeatMapParams()
self.fmParams[k] = self.fparams
self.keep = ('Donor', 'Acceptor', 'NegIonizable', 'PosIonizable',
'ZnBinder', 'Aromatic', 'Hydrophobe', 'LumpedHydrophobe')
if reference:
refs = Chem.SDMolSupplier(reference, sanitize=True)
self.reference = [x for x in refs if x][0]
if target_s:
tgts = Chem.SDMolSupplier(target_s, sanitize=True)
self.target_s = [x for x in tgts if x]
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))
import argparse, os, sys, gzip
import numpy as np
from rdkit import Chem, rdBase, RDConfig
from rdkit.Chem import AllChem, rdShapeHelpers
from rdkit.Chem.FeatMaps import FeatMaps
import utils
### start function definitions #########################################
# Setting up the features to use in FeatureMap
fdef = AllChem.BuildFeatureFactory(os.path.join(RDConfig.RDDataDir, 'BaseFeatures.fdef'))
fmParams = {}
for k in fdef.GetFeatureFamilies():
fparams = FeatMaps.FeatMapParams()
fmParams[k] = fparams
keep = ('Donor', 'Acceptor', 'NegIonizable', 'PosIonizable', 'ZnBinder',
'Aromatic', 'Hydrophobe', 'LumpedHydrophobe')
def filterFeature(f):
result = f.GetFamily() in keep
# TODO - nothing ever seems to be filtered. Is this expected?
if not result:
utils.log("Filtered out feature type", f.GetFamily())
return result
def getRawFeatures(mol):
rawFeats = fdef.GetFeaturesForMol(mol)
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]])