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import unittest
from rdkit import Chem
from rdkit.Chem import rdShapeAlign
from rdkit import RDConfig
datadir = RDConfig.RDBaseDir + '/External/pubchem_shape/test_data'
class TestCase(unittest.TestCase):
def setUp(self):
suppl = Chem.SDMolSupplier(datadir + '/test1.sdf')
self.ref = suppl[0]
self.probe = suppl[1]
def test1_Defaults(self):
tpl = rdShapeAlign.AlignMol(self.ref, self.probe, opt_param=0.5, max_preiters=3,
max_postiters=16)
self.assertAlmostEqual(tpl[0], 0.773, places=3)
self.assertAlmostEqual(tpl[1], 0.303, places=3)
def test2_NoColor(self):
tpl = rdShapeAlign.AlignMol(self.ref, self.probe, useColors=False, opt_param=0.5,
max_preiters=3, max_postiters=16)
self.assertAlmostEqual(tpl[0], 0.773, places=3)
self.assertAlmostEqual(tpl[1], 0.0, places=3)
def test3_FromShape(self):
shp = rdShapeAlign.PrepareConformer(self.ref)
self.assertTrue(type(shp) == rdShapeAlign.ShapeInput)
tpl = rdShapeAlign.AlignMol(shp, self.probe, opt_param=0.5, max_preiters=3, max_postiters=16)
self.assertAlmostEqual(tpl[0], 0.773, places=3)
self.assertAlmostEqual(tpl[1], 0.303, places=3)
def test4_ShapeInputOptions(self):
opts = rdShapeAlign.ShapeInputOptions()
opts.useColors = False
shp = rdShapeAlign.PrepareConformer(self.ref, -1, opts)
tpl = rdShapeAlign.AlignMol(shp, self.probe, opt_param=0.5, max_preiters=3, max_postiters=16)
self.assertAlmostEqual(tpl[0], 0.773, places=3)
self.assertAlmostEqual(tpl[1], 0.0, places=3)
opts.atomSubset = [4, 5, 6, 7, 8, 9]
shp = rdShapeAlign.PrepareConformer(self.ref, -1, opts)
self.assertAlmostEqual(shp.sov, 251.946, places=3)
self.assertAlmostEqual(shp.sof, 0.0, places=3)
opts.atomRadii = [(4, 1.9)]
shp = rdShapeAlign.PrepareConformer(self.ref, -1, opts)
self.assertAlmostEqual(shp.sov, 274.576, places=3)
with self.assertRaises(AttributeError):
opts.rhubarb = True
def test5_ShapeShapeOverlay(self):
refShp = rdShapeAlign.PrepareConformer(self.ref, -1)
probeShp = rdShapeAlign.PrepareConformer(self.probe, -1)
tpl = rdShapeAlign.AlignShapes(refShp, probeShp)
probeCp = Chem.Mol(self.probe)
rdShapeAlign.TransformConformer(refShp.shift, tpl[2], probeShp, probeCp.GetConformer(-1))
# Just show it did something. The full test is in the C++ layer.
self.assertNotEqual(self.probe.GetConformer().GetAtomPosition(0),
probeCp.GetConformer().GetAtomPosition(0))
matrix = tpl[2][:10]
with self.assertRaises(ValueError):
rdShapeAlign.TransformConformer(refShp.shift, matrix, probeShp, probeCp.GetConformer(-1))
def test6_notColorAtoms(self):
m1 = Chem.MolFromSmiles("Nc1ccccc1 |(0.392086,-2.22477,0.190651;"
"0.232269,-1.38667,0.118385;-1.06274,-0.918982,0.0342466;"
"-1.26098,0.446053,-0.0811879;-0.244035,1.36265,-0.11691;"
"1.05134,0.875929,-0.031248;1.28797,-0.499563,0.0864097)"
",atomProp:0.dummyLabel.*|")
opts = rdShapeAlign.ShapeInputOptions()
opts.notColorAtoms = [0]
shp = rdShapeAlign.PrepareConformer(m1, -1, opts)
self.assertAlmostEqual(shp.sof, 5.074, places=3)
if __name__ == '__main__':
unittest.main()
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