def test1(self):
suppl = Chem.SDMolSupplier(
os.path.join(RDConfig.RDCodeDir, 'Chem', 'Subshape',
'test_data/5ht3ligs.sdf'))
builder = SubshapeBuilder.SubshapeBuilder()
builder.gridDims = (20., 20., 10)
builder.gridSpacing = 0.5
builder.winRad = 4.
ms = []
shapes = []
for m in suppl:
m = Chem.AddHs(m, addCoords=True)
AllChem.CanonicalizeConformer(m.GetConformer())
ms.append(m)
shape = builder(m, terminalPtsOnly=True)
shapes.append(shape)
self.assertTrue(len(ms) == 4)
self.assertTrue(len(shapes) == 4)
self.assertTrue([len(x.skelPts) for x in shapes] == [5, 5, 5, 5])
refShape = builder.GenerateSubshapeShape(ms[0])
self.assertTrue(len(refShape.skelPts) == 15)
aligner = SubshapeAligner.SubshapeAligner()
aligner.shapeDistTol = .30
algStore = []
for i, s1 in enumerate(shapes):
if not i or not s1:
algStore.append([])
continue
m1 = ms[i]
alignments = aligner.GetSubshapeAlignments(ms[0], refShape, m1, s1,
builder)
algStore.append(alignments)
self.assertEqual([len(x) for x in algStore], [0, 2, 39, 0])
algStore = []
for i, s1 in enumerate(shapes):
if not i or not s1:
algStore.append([])
continue
m1 = ms[i]
alignments = list(aligner(ms[0], refShape, m1, s1, builder))
algStore.append(alignments)
self.assertTrue([len(x) for x in algStore] == [0, 2, 39, 0])
pruned = []
for i, mi in enumerate(ms):
alignments = algStore[i]
pruned.append(
SubshapeAligner.ClusterAlignments(mi,
alignments,
builder,
neighborTol=0.15))
self.assertTrue([len(x) for x in pruned] == [0, 2, 29, 0])
def test1(self):
filename = os.path.join(os.path.dirname(os.path.abspath(__file__)),
'test_data', '5ht3ligs.sdf')
suppl = Chem.SDMolSupplier(filename)
builder = SubshapeBuilder.SubshapeBuilder()
builder.gridDims = (20., 20., 10)
builder.gridSpacing = 0.5
builder.winRad = 4.
ms = []
shapes = []
for m in suppl:
m = Chem.AddHs(m, addCoords=True)
AllChem.CanonicalizeConformer(m.GetConformer())
ms.append(m)
shape = builder(m, terminalPtsOnly=True)
shapes.append(shape)
self.assertEqual(len(ms), 4)
self.assertEqual(len(shapes), 4)
self.assertEqual([len(x.skelPts) for x in shapes], [5, 5, 5, 5])
refShape = builder.GenerateSubshapeShape(ms[0])
self.assertEqual(len(refShape.skelPts), 16)
aligner = SubshapeAligner.SubshapeAligner()
aligner.shapeDistTol = .30
algStore = []
for i, s1 in enumerate(shapes):
if not i or not s1:
algStore.append([])
continue
m1 = ms[i]
alignments = aligner.GetSubshapeAlignments(ms[0], refShape, m1, s1, builder)
algStore.append(alignments)
self.assertEqual([len(x) for x in algStore], [0, 5, 28, 0])
algStore = []
for i, s1 in enumerate(shapes):
if not i or not s1:
algStore.append([])
continue
m1 = ms[i]
alignments = list(aligner(ms[0], refShape, m1, s1, builder))
algStore.append(alignments)
self.assertEqual([len(x) for x in algStore], [0, 5, 28, 0])
pruned = []
for i, mi in enumerate(ms):
alignments = algStore[i]
pruned.append(SubshapeAligner.ClusterAlignments(
mi, alignments, builder, neighborTol=0.15))
self.assertEqual([len(x) for x in pruned], [0, 4, 12, 0])
cPickle.dump(s2,file('test_data/square2.shp.pkl','wb+'))
ns1 = b.CombineSubshapes(s1,s2)
b.GenerateSubshapeSkeleton(ns1)
cPickle.dump(ns1,file('test_data/combined.shp.pkl','wb+'))
else:
s1 = cPickle.load(file('test_data/square1.shp.pkl','rb'))
s2 = cPickle.load(file('test_data/square2.shp.pkl','rb'))
#ns1 = cPickle.load(file('test_data/combined.shp.pkl','rb'))
ns1=cPickle.load(file('test_data/combined.shp.pkl','rb'))
v = MolViewer()
SubshapeObjects.DisplaySubshape(v,s1,'shape1')
SubshapeObjects.DisplaySubshape(v,ns1,'ns1')
#SubshapeObjects.DisplaySubshape(v,s2,'shape2')
a = SubshapeAligner.SubshapeAligner()
pruneStats={}
algs =a.GetSubshapeAlignments(None,ns1,m1,s1,b,pruneStats=pruneStats)
print len(algs)
print pruneStats
import os,tempfile
from rdkit import Geometry
fName = tempfile.mktemp('.grd')
Geometry.WriteGridToFile(ns1.coarseGrid.grid,fName)
v.server.loadSurface(fName,'coarse','',2.5)
os.unlink(fName)
fName = tempfile.mktemp('.grd')
Geometry.WriteGridToFile(ns1.medGrid.grid,fName)
v.server.loadSurface(fName,'med','',2.5)
os.unlink(fName)
def test1(self):
# computeCanonicalTransform returns more approximate eigenvalues/eigencvectors
# when built against the native RDKit PowerEigenSolver, so unit test results
# differ slightly
builtAgainstEigen3 = hasattr(AllChem, 'ComputePrincipalAxesAndMomentsFromGyrationMatrix')
if builtAgainstEigen3:
expectedSkelPts = 15
expectedAlgs = [0, 5, 21, 0]
prunedAlgs = [0, 4, 11, 0]
else:
expectedSkelPts = 16
expectedAlgs = [0, 5, 28, 0]
prunedAlgs = [0, 4, 12, 0]
filename = os.path.join(os.path.dirname(os.path.abspath(__file__)),
'test_data', '5ht3ligs.sdf')
suppl = Chem.SDMolSupplier(filename)
builder = SubshapeBuilder.SubshapeBuilder()
builder.gridDims = (20., 20., 10)
builder.gridSpacing = 0.5
builder.winRad = 4.
ms = []
shapes = []
for m in suppl:
m = Chem.AddHs(m, addCoords=True)
AllChem.CanonicalizeConformer(m.GetConformer())
ms.append(m)
shape = builder(m, terminalPtsOnly=True)
shapes.append(shape)
self.assertEqual(len(ms), 4)
self.assertEqual(len(shapes), 4)
self.assertEqual([len(x.skelPts) for x in shapes], [5, 5, 5, 5])
refShape = builder.GenerateSubshapeShape(ms[0])
self.assertEqual(len(refShape.skelPts), expectedSkelPts)
aligner = SubshapeAligner.SubshapeAligner()
aligner.shapeDistTol = .30
algStore = []
for i, s1 in enumerate(shapes):
if not i or not s1:
algStore.append([])
continue
m1 = ms[i]
alignments = aligner.GetSubshapeAlignments(ms[0], refShape, m1, s1, builder)
algStore.append(alignments)
self.assertEqual([len(x) for x in algStore], expectedAlgs)
algStore = []
for i, s1 in enumerate(shapes):
if not i or not s1:
algStore.append([])
continue
m1 = ms[i]
alignments = list(aligner(ms[0], refShape, m1, s1, builder))
algStore.append(alignments)
self.assertEqual([len(x) for x in algStore], expectedAlgs)
pruned = []
for i, mi in enumerate(ms):
alignments = algStore[i]
pruned.append(SubshapeAligner.ClusterAlignments(
mi, alignments, builder, neighborTol=0.15))
self.assertEqual([len(x) for x in pruned], prunedAlgs)