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21b3c4e6f1
* Add MolTransforms library. * Transform to inertial frame of reference before overlay. * Vital fix of typo in comment. * Tidy up debugging cruft. * Comment in CMakeLists.txt. * Fix python wrappers. * Extra tidy. * Response to review. * Tidy includes. --------- Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
149 lines
6.3 KiB
Python
149 lines
6.3 KiB
Python
import unittest
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from rdkit import Chem
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from rdkit.Chem import rdShapeAlign
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from rdkit import RDConfig
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from rdkit.Geometry import Point3D
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datadir = RDConfig.RDBaseDir + '/External/pubchem_shape/test_data'
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class TestCase(unittest.TestCase):
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def setUp(self):
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suppl = Chem.SDMolSupplier(datadir + '/test1.sdf')
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self.ref = suppl[0]
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self.probe = suppl[1]
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def test1_Defaults(self):
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tpl = rdShapeAlign.AlignMol(self.ref, self.probe, opt_param=0.5, max_preiters=3,
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max_postiters=16)
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self.assertAlmostEqual(tpl[0], 0.773, places=3)
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self.assertAlmostEqual(tpl[1], 0.305, places=3)
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def test2_NoColor(self):
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tpl = rdShapeAlign.AlignMol(self.ref, self.probe, useColors=False, opt_param=0.5,
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max_preiters=3, max_postiters=16)
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self.assertAlmostEqual(tpl[0], 0.773, places=3)
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self.assertAlmostEqual(tpl[1], 0.0, places=3)
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def test3_FromShape(self):
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shp = rdShapeAlign.PrepareConformer(self.ref)
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self.assertTrue(type(shp) == rdShapeAlign.ShapeInput)
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tpl = rdShapeAlign.AlignMol(shp, self.probe, opt_param=0.5, max_preiters=3, max_postiters=16)
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self.assertAlmostEqual(tpl[0], 0.773, places=3)
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self.assertAlmostEqual(tpl[1], 0.305, places=3)
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def test4_ShapeInputOptions(self):
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opts = rdShapeAlign.ShapeInputOptions()
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opts.useColors = False
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shp = rdShapeAlign.PrepareConformer(self.ref, -1, opts)
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tpl = rdShapeAlign.AlignMol(shp, self.probe, opt_param=0.5, max_preiters=3, max_postiters=16)
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self.assertAlmostEqual(tpl[0], 0.773, places=3)
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self.assertAlmostEqual(tpl[1], 0.0, places=3)
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opts.atomSubset = [4, 5, 6, 7, 8, 9]
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shp = rdShapeAlign.PrepareConformer(self.ref, -1, opts)
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self.assertAlmostEqual(shp.sov, 251.946, places=3)
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self.assertAlmostEqual(shp.sof, 0.0, places=3)
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opts.atomRadii = [(4, 1.9)]
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shp = rdShapeAlign.PrepareConformer(self.ref, -1, opts)
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self.assertAlmostEqual(shp.sov, 274.576, places=3)
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with self.assertRaises(AttributeError):
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opts.rhubarb = True
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def test5_ShapeShapeOverlay(self):
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refShp = rdShapeAlign.PrepareConformer(self.ref, -1)
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probeShp = rdShapeAlign.PrepareConformer(self.probe, -1)
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tpl = rdShapeAlign.AlignShapes(refShp, probeShp)
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probeCp = Chem.Mol(self.probe)
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rdShapeAlign.TransformConformer(refShp.shift, refShp.inertialRot, tpl[2], probeShp, probeCp.GetConformer(-1))
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self.assertEqual(len(refShp.inertialRot), 9)
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self.assertAlmostEqual(refShp.inertialRot[0], -0.926125, places=6)
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self.assertAlmostEqual(refShp.inertialRot[8], -0.852890, places=6)
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# Just show it did something. The full test is in the C++ layer.
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self.assertNotEqual(self.probe.GetConformer().GetAtomPosition(0),
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probeCp.GetConformer().GetAtomPosition(0))
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matrix = tpl[2][:10]
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with self.assertRaises(ValueError):
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rdShapeAlign.TransformConformer(refShp.shift, refShp.inertialRot, matrix, probeShp, probeCp.GetConformer(-1))
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def test6_notColorAtoms(self):
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m1 = Chem.MolFromSmiles("Nc1ccccc1 |(0.392086,-2.22477,0.190651;"
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"0.232269,-1.38667,0.118385;-1.06274,-0.918982,0.0342466;"
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"-1.26098,0.446053,-0.0811879;-0.244035,1.36265,-0.11691;"
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"1.05134,0.875929,-0.031248;1.28797,-0.499563,0.0864097)"
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",atomProp:0.dummyLabel.*|")
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opts = rdShapeAlign.ShapeInputOptions()
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opts.notColorAtoms = [0]
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shp = rdShapeAlign.PrepareConformer(m1, -1, opts)
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self.assertAlmostEqual(shp.sof, 5.074, places=3)
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def test7_customFeatures(self):
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m1 = Chem.MolFromSmiles(
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"O=CC=O |(-1.75978,0.148897,0;-0.621382,-0.394324,0;0.624061,0.3656,.1;1.7571,-0.120174,.1)|")
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opts = rdShapeAlign.ShapeInputOptions()
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opts.customFeatures = ((1, Point3D(-1.75978, 0.148897,
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0), 1.0), (2, Point3D(1.7571, -0.120174, 0.1), 1.0))
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shp = rdShapeAlign.PrepareConformer(m1, -1, opts)
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self.assertEqual(len(shp.coord), 18)
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m2 = Chem.Mol(m1)
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opts2 = rdShapeAlign.ShapeInputOptions()
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opts2.customFeatures = ((2, Point3D(-1.75978, 0.148897,
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0), 1.0), (1, Point3D(1.7571, -0.120174, 0.1), 1.0))
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shp2 = rdShapeAlign.PrepareConformer(m2, -1, opts2)
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tpl = rdShapeAlign.AlignShapes(shp, shp2, opt_param=0.5)
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self.assertAlmostEqual(tpl[0], 1.000, places=3)
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self.assertAlmostEqual(tpl[1], 0.997, places=3)
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tf = tpl[2]
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self.assertGreater(0.0, tf[0])
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self.assertLess(0.0, tf[3 * 3])
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# check the getter:
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cfs = opts2.customFeatures
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self.assertEqual(len(cfs), 2)
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self.assertEqual(cfs[0][0], 2)
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self.assertEqual(cfs[1][0], 1)
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def test8_customFeatures(self):
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m1 = Chem.MolFromSmiles(
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"O=CC=O |(-1.75978,0.148897,0;-0.621382,-0.394324,0;0.624061,0.3656,.1;1.7571,-0.120174,.1)|")
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opts = rdShapeAlign.ShapeInputOptions()
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opts.customFeatures = ((1, Point3D(-1.75978, 0.148897,
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0), 1.0), (2, Point3D(1.7571, -0.120174, 0.1), 1.0))
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m2 = Chem.Mol(m1)
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opts2 = rdShapeAlign.ShapeInputOptions()
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opts2.customFeatures = ((2, Point3D(-1.75978, 0.148897,
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0), 1.0), (1, Point3D(1.7571, -0.120174, 0.1), 1.0))
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tpl = rdShapeAlign.AlignMol(m1, m2, opts, opts2, opt_param=0.5)
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self.assertAlmostEqual(tpl[0], 1.000, places=3)
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self.assertAlmostEqual(tpl[1], 0.997, places=3)
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def test9_FixedScore(self):
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# Just to make sure it's there and returns a value.
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opts = rdShapeAlign.ShapeInputOptions()
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tpl = rdShapeAlign.ScoreMol(self.ref, self.ref, opts, opts)
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self.assertAlmostEqual(tpl[0], 1.0, places=3)
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self.assertAlmostEqual(tpl[1], 1.0, places=3)
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opts = rdShapeAlign.ShapeInputOptions()
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opts.useColors = False
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opts.normalize = False
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shp = rdShapeAlign.PrepareConformer(self.ref, -1, opts)
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tpl = rdShapeAlign.ScoreMol(shp, self.probe, opts)
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self.assertAlmostEqual(tpl[0], 0.0, places=3)
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self.assertAlmostEqual(tpl[1], 0.0, places=3)
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opts.useColors = True
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shp1 = rdShapeAlign.PrepareConformer(self.probe, -1, opts)
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shp2 = rdShapeAlign.PrepareConformer(self.probe, -1, opts)
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tpl = rdShapeAlign.ScoreShape(shp1, shp2, True)
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self.assertAlmostEqual(tpl[0], 1.0, places=3)
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self.assertAlmostEqual(tpl[1], 1.0, places=3)
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if __name__ == '__main__':
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unittest.main()
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