mirror of
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315939f7ae
* add test for conformer canonicalization inverting stereo * Fix problem with canonicalizeConformer inverting stereo * response to review cleanup fix the other tests affected by this change
103 lines
3.5 KiB
Python
103 lines
3.5 KiB
Python
import math
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import os
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import sys
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import unittest
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from rdkit import Chem, DataStructs, RDConfig
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from rdkit.Chem import rdMolAlign
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from rdkit.Chem import rdMolTransforms as rdmt
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from rdkit.Chem import rdShapeHelpers as rdshp
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from rdkit.Geometry import rdGeometry as geom
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class TestCase(unittest.TestCase):
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def setUp(self):
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pass
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def test1Shape(self):
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fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'ShapeHelpers', 'test_data',
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'1oir.mol')
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m = Chem.MolFromMolFile(fileN)
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rdmt.CanonicalizeMol(m)
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dims1, offset1 = rdshp.ComputeConfDimsAndOffset(m.GetConformer())
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grd = geom.UniformGrid3D(30.0, 16.0, 10.0)
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rdshp.EncodeShape(m, grd, 0)
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ovect = grd.GetOccupancyVect()
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self.assertEqual(ovect.GetTotalVal(), 7405)
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m = Chem.MolFromMolFile(fileN)
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trans = rdmt.ComputeCanonicalTransform(m.GetConformer())
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dims, offset = rdshp.ComputeConfDimsAndOffset(m.GetConformer(), trans=trans)
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dims -= dims1
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offset -= offset1
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self.assertAlmostEqual(dims.Length(), 0.0, 4)
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self.assertAlmostEqual(offset.Length(), 0.0, 4)
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grd1 = geom.UniformGrid3D(30.0, 16.0, 10.0)
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rdshp.EncodeShape(m, grd1, 0, trans)
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ovect = grd1.GetOccupancyVect()
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self.assertEqual(ovect.GetTotalVal(), 7405)
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grd2 = geom.UniformGrid3D(30.0, 16.0, 10.0)
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rdshp.EncodeShape(m, grd2, 0)
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fileN2 = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'ShapeHelpers', 'test_data',
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'1oir_conf.mol')
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m2 = Chem.MolFromMolFile(fileN2)
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self.assertAlmostEqual(rdshp.ShapeTanimotoDist(m, m), 0.0, 4)
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self.assertAlmostEqual(rdshp.ShapeTverskyIndex(m, m, 1.0, 1.0), 1.0, 4)
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rmsd = rdMolAlign.AlignMol(m, m2)
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self.assertAlmostEqual(rdshp.ShapeTanimotoDist(m, m2), 0.31, 2)
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self.assertAlmostEqual(rdshp.ShapeTverskyIndex(m, m2, 1.0, 1.0), 0.686, 2)
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dist = rdshp.ShapeTanimotoDist(mol1=m, mol2=m2, confId1=0, confId2=0, gridSpacing=0.25,
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stepSize=0.125)
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self.assertAlmostEqual(dist, 0.339, 2)
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m = Chem.MolFromMolFile(fileN)
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cpt = rdmt.ComputeCentroid(m.GetConformer())
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dims, offset = rdshp.ComputeConfDimsAndOffset(m.GetConformer())
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grd = geom.UniformGrid3D(dims.x, dims.y, dims.z, 0.5, DataStructs.DiscreteValueType.TWOBITVALUE,
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offset)
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dims -= geom.Point3D(13.927, 16.97, 9.775)
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offset -= geom.Point3D(-4.353, 16.829, 2.782)
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self.assertAlmostEqual(dims.Length(), 0.0, 4)
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self.assertAlmostEqual(offset.Length(), 0.0, 4)
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rdshp.EncodeShape(m, grd, 0)
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ovect = grd.GetOccupancyVect()
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self.assertEqual(ovect.GetTotalVal(), 7417)
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geom.WriteGridToFile(grd, '1oir_shape.grd')
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m = Chem.MolFromMolFile(fileN)
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lc, uc = rdshp.ComputeConfBox(m.GetConformer())
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rdmt.CanonicalizeMol(m)
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lc1, uc1 = rdshp.ComputeConfBox(m.GetConformer())
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lc2, uc2 = rdshp.ComputeUnionBox((lc, uc), (lc1, uc1))
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lc -= geom.Point3D(-4.353, 16.829, 2.782)
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uc -= geom.Point3D(9.574, 33.799, 12.557)
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self.assertAlmostEqual(lc.Length(), 0.0, 4)
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self.assertAlmostEqual(uc.Length(), 0.0, 4)
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lc1 -= geom.Point3D(-8.7163, -5.3279, -3.1621)
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uc1 -= geom.Point3D(10.7519, 6.0778, 3.0123)
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self.assertAlmostEqual(lc1.Length(), 0.0, 3)
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self.assertAlmostEqual(uc1.Length(), 0.0, 3)
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lc2 -= geom.Point3D(-8.716, -5.328, -3.162)
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uc2 -= geom.Point3D(10.752, 33.799, 12.557)
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self.assertAlmostEqual(lc2.Length(), 0.0, 3)
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self.assertAlmostEqual(uc2.Length(), 0.0, 3)
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if __name__ == '__main__':
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print("Testing Shape Helpers wrapper")
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unittest.main()
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