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2de1dabdc1
* Make shape on subset of atoms in molecule. Optional radius for dummy atoms. * Re-factor. Add ShapeInputOptions. * Python wrapper for options. * Add non-standard radii option. Add function to align a shape on a shape. Add function to align conformer based on shape-shape transformation. * Python wrappers for AlignShapes and TransformConformer. * Add the new thing for Python options. * Add option for excluding atoms from color features. No partial color features if using atomSubset. * In AlignShapes, don't change the fit shape (apart from transforming it) in case it will be used again. * Rename it AlignShape to be consistent with AlignMolecule. * Response to review. * Undo clang-format * Fix botched merge. * Typo. --------- Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
81 lines
3.3 KiB
Python
81 lines
3.3 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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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], 0.303, 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], 0.303, 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, tpl[2], probeShp, probeCp.GetConformer(-1))
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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, 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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if __name__ == '__main__':
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unittest.main()
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