def test3UniformGrid(self): ugrid = geom.UniformGrid3D(20, 18, 15) self.failUnless(ugrid.GetNumX() == 40) self.failUnless(ugrid.GetNumY() == 36) self.failUnless(ugrid.GetNumZ() == 30) dvect = ugrid.GetOccupancyVect() ugrid = geom.UniformGrid3D(20, 18, 15, 0.5, DataStructs.DiscreteValueType.TWOBITVALUE) dvect = ugrid.GetOccupancyVect() self.failUnless( dvect.GetValueType() == DataStructs.DiscreteValueType.TWOBITVALUE) grd = geom.UniformGrid3D(10.0, 10.0, 10.0, 0.5) grd.SetSphereOccupancy(geom.Point3D(-2.0, -2.0, 0.0), 1.5, 0.25) grd.SetSphereOccupancy(geom.Point3D(-2.0, 2.0, 0.0), 1.5, 0.25) grd.SetSphereOccupancy(geom.Point3D(2.0, -2.0, 0.0), 1.5, 0.25) grd.SetSphereOccupancy(geom.Point3D(2.0, 2.0, 0.0), 1.5, 0.25) geom.WriteGridToFile(grd, "junk.grd") grd2 = geom.UniformGrid3D(10.0, 10.0, 10.0, 0.5) grd2.SetSphereOccupancy(geom.Point3D(-2.0, -2.0, 0.0), 1.5, 0.25) grd2.SetSphereOccupancy(geom.Point3D(-2.0, 2.0, 0.0), 1.5, 0.25) grd2.SetSphereOccupancy(geom.Point3D(2.0, -2.0, 0.0), 1.5, 0.25) dist = geom.TanimotoDistance(grd, grd2) self.failUnless(dist == 0.25) dist = geom.ProtrudeDistance(grd, grd2) self.failUnless(dist == 0.25) dist = geom.ProtrudeDistance(grd2, grd) self.failUnless(dist == 0.0) grd2 = geom.UniformGrid3D(10.0, 10.0, 10.0, 0.5, DataStructs.DiscreteValueType.FOURBITVALUE) grd2.SetSphereOccupancy(geom.Point3D(-2.0, -2.0, 0.0), 1.5, 0.25, 3) grd2.SetSphereOccupancy(geom.Point3D(-2.0, 2.0, 0.0), 1.5, 0.25, 3) grd2.SetSphereOccupancy(geom.Point3D(2.0, -2.0, 0.0), 1.5, 0.25, 3) self.failUnlessRaises(ValueError, lambda: geom.TanimotoDistance(grd, grd2)) grd2 = geom.UniformGrid3D(10.0, 10.0, 10.0, 1.0) self.failUnlessRaises(ValueError, lambda: geom.TanimotoDistance(grd, grd2)) grd2 = geom.UniformGrid3D(11.0, 10.0, 10.0, 1.0) self.failUnlessRaises(ValueError, lambda: geom.TanimotoDistance(grd, grd2))
def test1Shape(self): fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'ShapeHelpers', 'test_data', '1oir.mol') m = Chem.MolFromMolFile(fileN) rdmt.CanonicalizeMol(m) dims1, offset1 = rdshp.ComputeConfDimsAndOffset(m.GetConformer()) grd = geom.UniformGrid3D(30.0, 16.0, 10.0) rdshp.EncodeShape(m, grd, 0) ovect = grd.GetOccupancyVect() self.failUnless(ovect.GetTotalVal() == 9250) m = Chem.MolFromMolFile(fileN) trans = rdmt.ComputeCanonicalTransform(m.GetConformer()) dims, offset = rdshp.ComputeConfDimsAndOffset(m.GetConformer(), trans=trans) dims -= dims1 offset -= offset1 self.failUnless(feq(dims.Length(), 0.0)) self.failUnless(feq(offset.Length(), 0.0)) grd1 = geom.UniformGrid3D(30.0, 16.0, 10.0) rdshp.EncodeShape(m, grd1, 0, trans) ovect = grd1.GetOccupancyVect() self.failUnless(ovect.GetTotalVal() == 9250) grd2 = geom.UniformGrid3D(30.0, 16.0, 10.0) rdshp.EncodeShape(m, grd2, 0) fileN2 = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'ShapeHelpers', 'test_data', '1oir_conf.mol') m2 = Chem.MolFromMolFile(fileN2) rmsd = rdMolAlign.AlignMol(m, m2) self.failUnless(feq(rdshp.ShapeTanimotoDist(m, m2), 0.2813)) dist = rdshp.ShapeTanimotoDist(mol1=m, mol2=m2, confId1=0, confId2=0, gridSpacing=0.25, stepSize=0.125) self.failUnless(feq(dist, 0.3021)) m = Chem.MolFromMolFile(fileN) cpt = rdmt.ComputeCentroid(m.GetConformer()) dims, offset = rdshp.ComputeConfDimsAndOffset(m.GetConformer()) grd = geom.UniformGrid3D(dims.x, dims.y, dims.z, 0.5, DataStructs.DiscreteValueType.TWOBITVALUE, offset) dims -= geom.Point3D(13.927, 16.97, 9.775) offset -= geom.Point3D(-4.353, 16.829, 2.782) self.failUnless(feq(dims.Length(), 0.0)) self.failUnless(feq(offset.Length(), 0.0)) rdshp.EncodeShape(m, grd, 0) ovect = grd.GetOccupancyVect() self.failUnless(ovect.GetTotalVal() == 9275) geom.WriteGridToFile(grd, '1oir_shape.grd') m = Chem.MolFromMolFile(fileN) lc, uc = rdshp.ComputeConfBox(m.GetConformer()) rdmt.CanonicalizeMol(m) lc1, uc1 = rdshp.ComputeConfBox(m.GetConformer()) lc2, uc2 = rdshp.ComputeUnionBox((lc, uc), (lc1, uc1)) lc -= geom.Point3D(-4.353, 16.829, 2.782) uc -= geom.Point3D(9.574, 33.799, 12.557) self.failUnless(feq(lc.Length(), 0.0)) self.failUnless(feq(uc.Length(), 0.0)) lc1 -= geom.Point3D(-10.7519, -6.0778, -3.0123) uc1 -= geom.Point3D(8.7163, 5.3279, 3.1621) self.failUnless(feq(lc1.Length(), 0.0)) self.failUnless(feq(uc1.Length(), 0.0)) lc2 -= geom.Point3D(-10.7519, -6.0778, -3.01226) uc2 -= geom.Point3D(9.574, 33.799, 12.557) self.failUnless(feq(lc2.Length(), 0.0)) self.failUnless(feq(uc2.Length(), 0.0))