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()