def setUp(self):
self.dataDir = os.path.join(RDConfig.RDCodeDir,
'Chem/Pharm3D/test_data')
self.fdefBlock = """
DefineFeature HAcceptor1 [N,O;H0]
Family HBondAcceptor
Weights 1.0
EndFeature
DefineFeature HDonor1 [N,O;!H0]
Family HBondDonor
Weights 1.0
EndFeature
DefineFeature Aromatic1 c1ccccc1
Family Aromatic
Weights 1.,1.,1.,1.,1.,1.
EndFeature\n"""
self.featFactory = ChemicalFeatures.BuildFeatureFactoryFromString(
self.fdefBlock)
self.feats = [
ChemicalFeatures.FreeChemicalFeature(
'HBondAcceptor', 'HAcceptor1', Geometry.Point3D(0.0, 0.0,
0.0)),
ChemicalFeatures.FreeChemicalFeature(
'HBondDonor', 'HDonor1', Geometry.Point3D(2.65, 0.0, 0.0)),
ChemicalFeatures.FreeChemicalFeature(
'Aromatic', 'Aromatic1', Geometry.Point3D(5.12, 0.908, 0.0)),
]
self.pcophore = Pharmacophore.Pharmacophore(self.feats)
self.pcophore.setLowerBound(0, 1, 2.0)
self.pcophore.setUpperBound(0, 1, 3.3)
self.pcophore.setLowerBound(0, 2, 5.0)
self.pcophore.setUpperBound(0, 2, 5.4)
self.pcophore.setLowerBound(1, 2, 2.6)
self.pcophore.setUpperBound(1, 2, 3.0)
def setUp(self):
self.fdefBlock = \
"""DefineFeature HAcceptor1 [N,O;H0]
Family HBondAcceptor
Weights 1.0
EndFeature
DefineFeature HDonor1 [N,O;!H0]
Family HBondDonor
Weights 1.0
EndFeature
DefineFeature Aromatic1 c1ccccc1
Family Aromatic
Weights 1.0,1.0,1.0,1.0,1.0,1.0
EndFeature\n"""
self.featFactory = ChemicalFeatures.BuildFeatureFactoryFromString(
self.fdefBlock)
self.feats = [
ChemicalFeatures.FreeChemicalFeature(
'HBondAcceptor', 'HAcceptor1', Geometry.Point3D(0.0, 0.0,
0.0)),
ChemicalFeatures.FreeChemicalFeature(
'HBondDonor', 'HDonor1', Geometry.Point3D(2.65, 0.0, 0.0)),
ChemicalFeatures.FreeChemicalFeature(
'Aromatic', 'Aromatic1', Geometry.Point3D(5.12, 0.908, 0.0)),
]
self.pcophore = Pharmacophore.Pharmacophore(self.feats)
def testBasic(self):
ffeat = ChemicalFeatures.FreeChemicalFeature()
ffeat.SetId(123)
pos = ffeat.GetId()
self.assertTrue(pos == 123)
ffeat.SetFamily("HBondDonor")
self.assertTrue(ffeat.GetFamily() == "HBondDonor")
ffeat.SetPos(geom.Point3D(1.0, 2.0, 3.0))
pos = ffeat.GetPos()
self.assertTrue(ptFeq(pos, geom.Point3D(1.0, 2.0, 3.0)))
ffeat.SetType("HBondDonor1")
self.assertTrue(ffeat.GetType() == "HBondDonor1")
ffeat = ChemicalFeatures.FreeChemicalFeature("HBondDonor", "HBondDonor1", geom.Point3D(1.0, 2.0,
3.0))
self.assertTrue(ffeat.GetId() == -1)
self.assertTrue(ffeat.GetFamily() == "HBondDonor")
self.assertTrue(ffeat.GetType() == "HBondDonor1")
ffeat = ChemicalFeatures.FreeChemicalFeature("HBondDonor", "HBondDonor1",
geom.Point3D(1.0, 2.0, 3.0), id=123)
self.assertTrue(ffeat.GetId() == 123)
self.assertTrue(ffeat.GetFamily() == "HBondDonor")
self.assertTrue(ffeat.GetType() == "HBondDonor1")
pos = ffeat.GetPos()
self.assertTrue(ptFeq(pos, geom.Point3D(1.0, 2.0, 3.0)))
ffeat = ChemicalFeatures.FreeChemicalFeature(id=123, type="HBondDonor1", family="HBondDonor",
loc=geom.Point3D(1.0, 2.0, 3.0))
self.assertTrue(ffeat.GetId() == 123)
self.assertTrue(ffeat.GetFamily() == "HBondDonor")
self.assertTrue(ffeat.GetType() == "HBondDonor1")
pos = ffeat.GetPos()
self.assertTrue(ptFeq(pos, geom.Point3D(1.0, 2.0, 3.0)))
def test4Search(self):
featFactory = ChemicalFeatures.BuildFeatureFactory(os.path.join(self.dataDir,
'BaseFeatures.fdef'))
activeFeats = [ChemicalFeatures.FreeChemicalFeature('Acceptor',
Geometry.Point3D(0.0, 0.0, 0.0)),
ChemicalFeatures.FreeChemicalFeature('Donor',
Geometry.Point3D(0.0, 0.0, 0.0)),
ChemicalFeatures.FreeChemicalFeature('Aromatic',
Geometry.Point3D(0.0, 0.0, 0.0))]
pcophore= Pharmacophore.Pharmacophore(activeFeats)
pcophore.setLowerBound(0,1,2.251)
pcophore.setUpperBound(0,1,2.451)
pcophore.setUpperBound2D(0,1,3)
pcophore.setLowerBound(0,2,4.970)
pcophore.setUpperBound(0,2,5.170)
pcophore.setUpperBound2D(0,2,6)
pcophore.setLowerBound(1,2,2.681)
pcophore.setUpperBound(1,2,2.881)
pcophore.setUpperBound2D(1,2,6)
inF = gzip.open(os.path.join(self.dataDir,'cdk2-syn-clip100.pkl.gz'),'rb')
nDone = 0
nMatches = 0
nHits = 0
while 1:
try:
name,molPkl,boundsMat = cPickle.load(inF, encoding='latin1')
if PY3:
molPkl = bytes(molPkl, encoding='latin1')
except:
break
nDone += 1
mol = Chem.Mol(molPkl)
boundsMat = rdDistGeom.GetMoleculeBoundsMatrix(mol)
DG.DoTriangleSmoothing(boundsMat)
canMatch,matches = EmbedLib.MatchPharmacophoreToMol(mol,featFactory,
pcophore)
if canMatch:
nMatches+=1
r = EmbedLib.MatchPharmacophore(matches,boundsMat,pcophore,
useDownsampling=True,use2DLimits=True,
mol=mol)
failed,bm,match,details = r
if not failed:
nHits+=1
self.assertEqual(nDone,100)
self.assertEqual(nMatches,93)
#print 'nhits:',nHits
self.assertEqual(nHits,67)
def initFromLines(self, lines):
import re
spaces = re.compile('[\ \t]+')
feats = []
rads = []
for lineNum, line in enumerate(lines):
txt = line.split('#')[0].strip()
if txt:
splitL = spaces.split(txt)
if len(splitL) < 5:
logger.error(
'Input line %d only contains %d fields, 5 are required. Read failed.'
% (lineNum, len(splitL)))
return
fName = splitL[0]
try:
xP = float(splitL[1])
yP = float(splitL[2])
zP = float(splitL[3])
rad = float(splitL[4])
except ValueError:
logger.error(
'Error parsing a number of line %d. Read failed.' %
(lineNum))
return
feats.append(
ChemicalFeatures.FreeChemicalFeature(
fName, fName, Geometry.Point3D(xP, yP, zP)))
rads.append(rad)
self._initializeFeats(feats, rads)
def testPickle(self):
ffeat = ChemicalFeatures.FreeChemicalFeature(
"HBondDonor", "HBondDonor1", geom.Point3D(1.0, 2.0, 3.0), 123)
pkl = cPickle.dumps(ffeat)
ffeat2 = cPickle.loads(pkl, encoding='bytes')
self.assertTrue(ffeat2.GetId() == ffeat.GetId())
self.assertTrue(ffeat2.GetFamily() == ffeat.GetFamily())
self.assertTrue(ffeat2.GetType() == ffeat.GetType())
self.assertTrue(ptFeq(ffeat2.GetPos(), ffeat.GetPos()))
# Check that the old pickled versions have not been broken
inF = open(
os.path.join(RDConfig.RDBaseDir,
'Code/ChemicalFeatures/Wrap/testData/feat.pkl'), 'rb')
ffeat2 = cPickle.load(inF, encoding='bytes')
# this version (1.0) does not have an id in the byte stream
self.assertTrue(ffeat2.GetFamily() == ffeat.GetFamily())
self.assertTrue(ffeat2.GetType() == ffeat.GetType())
self.assertTrue(ptFeq(ffeat2.GetPos(), ffeat.GetPos()))
# Test the new version also has the id and works as expected
# uncomment the following to generate (overrwrite) new version of pickled
# data file
#cPickle.dump(ffeat,file(os.path.join(RDConfig.RDBaseDir, 'Code/ChemicalFeatures/Wrap/testData/featv2.pkl'),'wb+'))
inF = open(
os.path.join(RDConfig.RDBaseDir,
'Code/ChemicalFeatures/Wrap/testData/featv2.pkl'),
'rb')
ffeat2 = cPickle.load(inF, encoding='bytes')
self.assertTrue(ffeat2.GetId() == ffeat.GetId())
self.assertTrue(ffeat2.GetFamily() == ffeat.GetFamily())
self.assertTrue(ffeat2.GetType() == ffeat.GetType())
self.assertTrue(ptFeq(ffeat2.GetPos(), ffeat.GetPos()))
def _initializeFeats(self, feats):
self._feats = []
for feat in feats:
if isinstance(feat, ChemicalFeatures.MolChemicalFeature):
pos = feat.GetPos()
newFeat = ChemicalFeatures.FreeChemicalFeature(feat.GetFamily(), feat.GetType(),
Geometry.Point3D(pos[0], pos[1], pos[2]))
self._feats.append(newFeat)
else:
self._feats.append(feat)
def _initializeFeats(self, feats, radii):
if len(feats) != len(radii):
raise ValueError('len(feats)!=len(radii)')
self._feats = []
self._radii = []
for feat, rad in zip(feats, radii):
if isinstance(feat, ChemicalFeatures.MolChemicalFeature):
pos = feat.GetPos()
newFeat = ChemicalFeatures.FreeChemicalFeature(feat.GetFamily(), feat.GetType(),
Geometry.Point3D(pos[0], pos[1], pos[2]))
else:
newFeat = feat
self._feats.append(newFeat)
self._radii.append(rad)
def to_rdkit(self) -> Tuple[rdkitPharmacophore.Pharmacophore, List[float]]:
""" Returns an rdkit pharmacophore with the pharmacophoric_points from the original pharmacophore.
rdkit pharmacophores do not store the pharmacophoric_points radii, so they are returned as well.
Returns
-------
rdkit_pharmacophore : rdkit.Chem.Pharm3D.Pharmacophore
The rdkit pharmacophore.
radii : list of float
List with the radius in angstroms of each pharmacophoric point.
"""
rdkit_element_name = { # dictionary to map openpharmacophore feature names to rdkit feature names
"aromatic ring": "Aromatic",
"hydrophobicity": "Hydrophobe",
"hb acceptor": "Acceptor",
"hb donor": "Donor",
"positive charge": "PosIonizable",
"negative charge": "NegIonizable",
}
points = []
radii = []
for element in self._pharmacophoric_points:
feat_name = rdkit_element_name[element.feature_name]
center = puw.get_value(element.center, to_unit="angstroms")
center = Geometry.Point3D(center[0], center[1], center[2])
points.append(ChemicalFeatures.FreeChemicalFeature(
feat_name,
center
))
radius = puw.get_value(element.radius, to_unit="angstroms")
radii.append(radius)
rdkit_pharmacophore = rdkitPharmacophore.Pharmacophore(points)
return rdkit_pharmacophore, radii