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import os
import sys
import unittest
import math
from rdkit import RDConfig
from rdkit import DataStructs
from rdkit import Chem
from rdkit.Chem import rdMolAlign
from rdkit.Geometry import rdGeometry as geom
from rdkit.Chem import rdShapeHelpers as rdshp
from rdkit.Chem import rdMolTransforms as rdmt
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(-10.7519, -6.0778, -3.0123)
uc1 -= geom.Point3D(8.7163, 5.3279, 3.1621)
self.assertAlmostEqual(lc1.Length(), 0.0, 4)
self.assertAlmostEqual(uc1.Length(), 0.0, 3)
lc2 -= geom.Point3D(-10.7519, -6.0778, -3.01226)
uc2 -= geom.Point3D(9.574, 33.799, 12.557)
self.assertAlmostEqual(lc2.Length(), 0.0, 4)
self.assertAlmostEqual(uc2.Length(), 0.0, 4)
if __name__ == '__main__':
print("Testing Shape Helpers wrapper")
unittest.main()
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