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# Copyright (c) 2019 Greg Landrum
# All rights reserved.
#
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
import os
import sys
import unittest
from rdkit import Chem, DataStructs, RDConfig
from rdkit.Chem import rdEHTTools
class TestCase(unittest.TestCase):
def setUp(self):
pass
def test1(self):
mol = Chem.MolFromMolFile(
os.path.join(RDConfig.RDBaseDir, "External", "YAeHMOP", "test_data", "benzene.mol"),
removeHs=False)
self.assertEqual(mol.GetNumAtoms(), 12)
ok, res = rdEHTTools.RunMol(mol)
self.assertTrue(ok)
chgs = res.GetAtomicCharges()
self.assertAlmostEqual(chgs[1], -0.026, places=3)
self.assertAlmostEqual(chgs[7], 0.026, places=3)
def test2(self):
mol = Chem.MolFromMolFile(
os.path.join(RDConfig.RDBaseDir, "External", "YAeHMOP", "test_data", "benzene.mol"),
removeHs=False)
self.assertEqual(mol.GetNumAtoms(), 12)
ok, res = rdEHTTools.RunMol(mol)
self.assertTrue(ok)
self.assertEqual(res.numOrbitals, 30)
self.assertEqual(res.numElectrons, 30)
cm = res.GetReducedChargeMatrix()
self.assertEqual(cm.shape, (12, res.numOrbitals))
for i in range(6):
self.assertAlmostEqual(cm[i][0], 0.161, places=3)
self.assertAlmostEqual(cm[i + 6][0], 0.005, places=3)
self.assertAlmostEqual(cm[i][6], 0.1066, places=3)
self.assertAlmostEqual(cm[i + 6][6], 0.060, places=3)
self.assertAlmostEqual(cm[i][9], 0.167, places=3)
self.assertAlmostEqual(cm[i + 6][9], 0.000, places=3)
def test3(self):
mol = Chem.MolFromMolFile(
os.path.join(RDConfig.RDBaseDir, "External", "YAeHMOP", "test_data", "benzene.mol"),
removeHs=False)
self.assertEqual(mol.GetNumAtoms(), 12)
ok, res = rdEHTTools.RunMol(mol)
self.assertTrue(ok)
opm = res.GetReducedOverlapPopulationMatrix()
self.assertEqual(opm.shape, (int(12 * 13 / 2), ))
self.assertAlmostEqual(opm[0], 2.7035, 3)
self.assertAlmostEqual(opm[2], 2.7035, 3)
self.assertAlmostEqual(opm[3], -0.0785, 3)
def test4(self):
mol = Chem.MolFromMolFile(
os.path.join(RDConfig.RDBaseDir, "External", "YAeHMOP", "test_data", "benzene.mol"),
removeHs=False)
self.assertEqual(mol.GetNumAtoms(), 12)
ok, res = rdEHTTools.RunMol(mol)
self.assertTrue(ok)
self.assertAlmostEqual(res.fermiEnergy, -12.804, places=3)
self.assertAlmostEqual(res.totalEnergy, -535.026, places=3)
def test5(self):
mol = Chem.MolFromMolFile(
os.path.join(RDConfig.RDBaseDir, "External", "YAeHMOP", "test_data", "benzene.mol"),
removeHs=False)
self.assertEqual(mol.GetNumAtoms(), 12)
ok, res = rdEHTTools.RunMol(mol, keepOverlapAndHamiltonianMatrices=True)
self.assertTrue(ok)
orbEs = res.GetOrbitalEnergies()
self.assertAlmostEqual(orbEs[0], -29.6302, places=3)
self.assertAlmostEqual(orbEs[14], -12.804, places=3)
self.assertAlmostEqual(orbEs[29], 67.0404, places=3)
hamil = res.GetHamiltonian()
self.assertAlmostEqual(hamil[0, 0], -21.4000, places=3)
self.assertAlmostEqual(hamil[0, 4], -15.3224, places=3)
self.assertAlmostEqual(hamil[4, 0], 0.0000, places=3)
overlap = res.GetOverlapMatrix()
self.assertAlmostEqual(overlap[0, 0], 1.0000, places=3)
self.assertAlmostEqual(overlap[0, 4], 0.4091, places=3)
self.assertAlmostEqual(overlap[4, 0], 0.0000, places=3)
if __name__ == '__main__':
unittest.main()
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