def doO3Dalign(i,
mol,
qmol,
threshold,
perfect_score,
writer,
conformerProps=None,
minEnergy=None):
pyO3As = rdMolAlign.GetO3AForProbeConfs(mol, qmol)
best_score = 0
j = 0
conf_id = -1
for pyO3A in pyO3As:
align = pyO3A.Align()
score = pyO3A.Score()
if score > best_score:
best_score = score
conf_id = j
j += 1
#utils.log("Best score = ",best_score)
if not threshold or perfect_score - best_score < threshold:
utils.log(i, align, score, Chem.MolToSmiles(mol, isomericSmiles=True))
mol.SetDoubleProp(field_O3DAScore, score)
if conformerProps and minEnergy:
eAbs = conformerProps[conf_id][(conformers.field_EnergyAbs)]
eDelta = eAbs - minEnergy
if eAbs:
mol.SetDoubleProp(conformers.field_EnergyAbs, eAbs)
if eDelta:
mol.SetDoubleProp(conformers.field_EnergyDelta, eDelta)
writer.write(mol, confId=conf_id)
return 1
return 0
def test15MultiConfs(self):
" test multi-conf alignment "
sdf = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'MolAlign',
'test_data', 'ref_e2.sdf')
suppl = Chem.SDMolSupplier(sdf, removeHs=False)
refMol = suppl[13]
sdf = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'MolAlign',
'test_data', 'probe_mol.sdf')
prbSuppl = Chem.SDMolSupplier(sdf, removeHs=False)
tms = [x for x in prbSuppl]
prbMol = tms[0]
for tm in tms[1:]:
prbMol.AddConformer(tm.GetConformer(), True)
self.failUnlessEqual(prbMol.GetNumConformers(), 50)
refParams = ChemicalForceFields.MMFFGetMoleculeProperties(refMol)
prbParams = ChemicalForceFields.MMFFGetMoleculeProperties(prbMol)
cp = Chem.Mol(prbMol)
o3s = rdMolAlign.GetO3AForProbeConfs(cp, refMol, 1, prbParams,
refParams)
for i in range(prbMol.GetNumConformers()):
cp2 = Chem.Mol(prbMol)
o3 = rdMolAlign.GetO3A(cp2, refMol, prbParams, refParams, prbCid=i)
self.failUnlessAlmostEqual(o3s[i].Align(), o3.Align(), 6)
self.failUnlessAlmostEqual(o3s[i].Score(), o3.Score(), 6)
cp = Chem.Mol(prbMol)
o3s = rdMolAlign.GetCrippenO3AForProbeConfs(cp, refMol)
for i in range(prbMol.GetNumConformers()):
cp2 = Chem.Mol(prbMol)
o3 = rdMolAlign.GetCrippenO3A(cp2, refMol, prbCid=i)
self.failUnlessAlmostEqual(o3s[i].Align(), o3.Align(), 6)
self.failUnlessAlmostEqual(o3s[i].Score(), o3.Score(), 6)
def doO3Dalign(i,
mol,
qmol,
use_crippen,
threshold,
perfect_score,
writer,
conformerProps=None,
minEnergy=None):
if use_crippen:
pyO3As = rdMolAlign.GetCrippenO3AForProbeConfs(mol, qmol)
else:
pyO3As = rdMolAlign.GetO3AForProbeConfs(mol, qmol)
if len(pyO3As) == 0:
return 0
best_score = 0
j = 0
conf_id = -1
for pyO3A in pyO3As:
align = pyO3A.Align()
score = pyO3A.Score()
if score > best_score:
best_score = score
conf_id = j
j += 1
#utils.log("Best score = ",best_score)
if not threshold or perfect_score - best_score < threshold:
utils.log("Molecule", i, align, score)
mol.SetDoubleProp(field_O3DAScore, score)
if conformerProps and minEnergy:
eAbs = conformerProps[conf_id][(conformers.field_EnergyAbs)]
eDelta = eAbs - minEnergy
if eAbs:
mol.SetDoubleProp(conformers.field_EnergyAbs, eAbs)
if eDelta:
mol.SetDoubleProp(conformers.field_EnergyDelta, eDelta)
writer.write(mol, confId=conf_id)
return 1
return 0
def test16MultithreadBug(self):
" test multi-conf alignment "
nConfs = 10
sdf = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'MolAlign',
'test_data', 'bzr_data.sdf')
bzr_ms_o = [x for x in Chem.SDMolSupplier(sdf, removeHs=False)]
bzr_ms = [Chem.Mol(x) for x in bzr_ms_o]
for m in bzr_ms:
c = m.GetConformer()
while m.GetNumConformers() < nConfs:
cc = Chem.Conformer(c)
m.AddConformer(cc, assignId=True)
#refParams = ChemicalForceFields.MMFFGetMoleculeProperties(bzr_ms_o[0])
for i, m in enumerate(bzr_ms):
#prbParams = ChemicalForceFields.MMFFGetMoleculeProperties(m)
algs = rdMolAlign.GetO3AForProbeConfs(
m,
bzr_ms_o[0],
numThreads=4 #,prbPyMMFFMolProperties=prbParams,
#refPyMMFFMolProperties=refParams
)
self.failUnlessEqual(len(algs), nConfs)
