def test4Github252(self):
fdef = os.path.join(RDConfig.RDDataDir, 'BaseFeatures.fdef')
feat_factory = ChemicalFeatures.BuildFeatureFactory(fdef)
m1 = Chem.MolFromSmiles('Cc1ccccc1')
feats = feat_factory.GetFeaturesForMol(m1)
self.assertRaises(RuntimeError, lambda: Pharmacophore.Pharmacophore(feats))
AllChem.Compute2DCoords(m1)
Pharmacophore.Pharmacophore(feats)
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 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
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:
_, molPkl, boundsMat = pickle.load(inF, encoding='latin1')
molPkl = bytes(molPkl, encoding='latin1')
except Exception:
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 = r[0]
if not failed:
nHits += 1
self.assertEqual(nDone, 100)
self.assertEqual(nMatches, 93)
# print 'nhits:',nHits
self.assertEqual(nHits, 67)
from rdkit import Chem
from rdkit import RDConfig
from rdkit import Geometry
from rdkit.Chem import AllChem
from rdkit.Chem import ChemicalFeatures
from rdkit.Chem.Pharm3D import Pharmacophore
from rdkit.Chem.FeatMaps import FeatMapPoint
# feature Def
feat_def = "BaseFeatures_seri.fdef"
feat_fact = AllChem.BuildFeatureFactoryFromString(file(feat_def, "r").read())
# Get Pharmacophore from q_mol
q_mol = Chem.SDMolSupplier(sys.argv[1])[0]
feats = feat_fact.GetFeaturesForMol(q_mol)
pcophore = Pharmacophore.Pharmacophore(feats)
# GetFeatures As nested list
# [[x,y,x],
# [x,y,z],
# [x,y,z]]
pos_list = []
for feat in feats:
geom = list(feat.GetPos())
pos_list.append(geom)
for i in range(len(pos_list)):
print pos_list[i], feats[i].GetFamily()
def get_distance(feats):
dist_list = []
