def testAtomMatch(self):
fdefBlock = \
"""
DefineFeature HAcceptor1 [#7,#8]
Family HBondAcceptor
Weights 1.0
EndFeature
DefineFeature Arom1 a1aaaaa1
Family Aromatic
Weights 1.0,1.0,1.0,1.0,1.0,1.0
EndFeature
"""
cfac = ChemicalFeatures.BuildFeatureFactoryFromString(fdefBlock)
self.failUnless(cfac.GetNumFeatureDefs() == 2)
mol = Chem.MolFromSmiles('n1ccccc1')
feats = cfac.GetFeaturesForMol(mol)
self.failUnless(len(feats)==2)
m = ChemicalFeatures.GetAtomMatch(feats)
self.failIf(m)
mol = Chem.MolFromSmiles('c1ccccc1N')
feats = cfac.GetFeaturesForMol(mol)
self.failUnless(len(feats)==2)
m = ChemicalFeatures.GetAtomMatch(feats)
self.failUnless(len(m)==2)
def ConstrainedEnum(matches,mol,pcophore,bounds,use2DLimits=False,
index=0,soFar=[]):
""" Enumerates the list of atom mappings a molecule
has to a particular pharmacophore.
We do check distance bounds here.
"""
nMatches = len(matches)
if index>=nMatches:
yield soFar,[]
elif index==nMatches-1:
for entry in matches[index]:
nextStep = soFar+[entry]
if index != 0:
atomMatch = _checkMatch(nextStep,mol,bounds,pcophore,use2DLimits)
else:
atomMatch = ChemicalFeatures.GetAtomMatch(nextStep)
if atomMatch:
yield soFar+[entry],atomMatch
else:
for entry in matches[index]:
nextStep = soFar+[entry]
if index != 0:
atomMatch = _checkMatch(nextStep,mol,bounds,pcophore,use2DLimits)
if not atomMatch:
continue
for val in ConstrainedEnum(matches,mol,pcophore,bounds,use2DLimits=use2DLimits,
index=index+1,soFar=nextStep):
if val:
yield val
def GetAllPharmacophoreMatches(matches,
bounds,
pcophore,
useDownsampling=0,
progressCallback=None,
use2DLimits=False,
mol=None,
verbose=False):
res = []
nDone = 0
for match in CombiEnum(matches):
atomMatch = ChemicalFeatures.GetAtomMatch(match)
if atomMatch and use2DLimits and mol:
pass2D = Check2DBounds(atomMatch, mol, pcophore)
if verbose:
print('..', atomMatch)
print(' ..Pass2d:', pass2D)
else:
pass2D = True
if atomMatch and pass2D and \
CoarseScreenPharmacophore(atomMatch,bounds,pcophore,verbose=verbose):
if verbose:
print(' ..CoarseScreen: Pass')
bm = bounds.copy()
if verbose:
print('pre update:')
for row in bm:
print(' ', ' '.join(['% 4.2f' % x for x in row]))
bm = UpdatePharmacophoreBounds(bm, atomMatch, pcophore)
sz = bm.shape[0]
if verbose:
print('pre downsample:')
for row in bm:
print(' ', ' '.join(['% 4.2f' % x for x in row]))
if useDownsampling:
indices = []
for entry in atomMatch:
indices += list(entry)
bm = DownsampleBoundsMatrix(bm, indices)
if verbose:
print('post downsample:')
for row in bm:
print(' ', ' '.join(['% 4.2f' % x for x in row]))
if DG.DoTriangleSmoothing(bm):
res.append(match)
elif verbose:
print('cannot smooth')
nDone += 1
if progressCallback:
progressCallback(nDone)
return res
def _checkMatch(match, mol, bounds, pcophore, use2DLimits):
""" **INTERNAL USE ONLY**
checks whether a particular atom match can be satisfied by
a molecule
"""
atomMatch = ChemicalFeatures.GetAtomMatch(match)
if not atomMatch:
return None
elif use2DLimits:
if not Check2DBounds(atomMatch, mol, pcophore):
return None
if not CoarseScreenPharmacophore(atomMatch, bounds, pcophore):
return None
return atomMatch