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import math
import os
import sys
import unittest
from rdkit import Chem, DataStructs, RDConfig
from rdkit.Chem import rdMolAlign
from rdkit.Chem import rdMolTransforms as rdmt
from rdkit.Chem import rdShapeHelpers as rdshp
from rdkit.Geometry import rdGeometry as geom
class TestCase(unittest.TestCase):
def setUp(self):
pass
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.assertEqual(ovect.GetTotalVal(), 7405)
m = Chem.MolFromMolFile(fileN)
trans = rdmt.ComputeCanonicalTransform(m.GetConformer())
dims, offset = rdshp.ComputeConfDimsAndOffset(m.GetConformer(), trans=trans)
dims -= dims1
offset -= offset1
self.assertAlmostEqual(dims.Length(), 0.0, 4)
self.assertAlmostEqual(offset.Length(), 0.0, 4)
grd1 = geom.UniformGrid3D(30.0, 16.0, 10.0)
rdshp.EncodeShape(m, grd1, 0, trans)
ovect = grd1.GetOccupancyVect()
self.assertEqual(ovect.GetTotalVal(), 7405)
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)
self.assertAlmostEqual(rdshp.ShapeTanimotoDist(m, m), 0.0, 4)
self.assertAlmostEqual(rdshp.ShapeTverskyIndex(m, m, 1.0, 1.0), 1.0, 4)
rmsd = rdMolAlign.AlignMol(m, m2)
self.assertAlmostEqual(rdshp.ShapeTanimotoDist(m, m2), 0.31, 2)
self.assertAlmostEqual(rdshp.ShapeTverskyIndex(m, m2, 1.0, 1.0), 0.686, 2)
dist = rdshp.ShapeTanimotoDist(mol1=m, mol2=m2, confId1=0, confId2=0, gridSpacing=0.25,
stepSize=0.125)
self.assertAlmostEqual(dist, 0.339, 2)
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.assertAlmostEqual(dims.Length(), 0.0, 4)
self.assertAlmostEqual(offset.Length(), 0.0, 4)
rdshp.EncodeShape(m, grd, 0)
ovect = grd.GetOccupancyVect()
self.assertEqual(ovect.GetTotalVal(), 7417)
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.assertAlmostEqual(lc.Length(), 0.0, 4)
self.assertAlmostEqual(uc.Length(), 0.0, 4)
lc1 -= geom.Point3D(-8.7163, -5.3279, -3.1621)
uc1 -= geom.Point3D(10.7519, 6.0778, 3.0123)
self.assertAlmostEqual(lc1.Length(), 0.0, 3)
self.assertAlmostEqual(uc1.Length(), 0.0, 3)
lc2 -= geom.Point3D(-8.716, -5.328, -3.162)
uc2 -= geom.Point3D(10.752, 33.799, 12.557)
self.assertAlmostEqual(lc2.Length(), 0.0, 3)
self.assertAlmostEqual(uc2.Length(), 0.0, 3)
if __name__ == '__main__':
print("Testing Shape Helpers wrapper")
unittest.main()
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