def xyz2AC_huckel(atomicNumList, xyz, charge):
import numpy as np
mol = get_proto_mol(atomicNumList)
conf = Chem.Conformer(mol.GetNumAtoms())
for i in range(mol.GetNumAtoms()):
conf.SetAtomPosition(i, (xyz[i][0], xyz[i][1], xyz[i][2]))
mol.AddConformer(conf)
num_atoms = len(atomicNumList)
AC = np.zeros((num_atoms, num_atoms)).astype(int)
mol_huckel = Chem.Mol(mol)
mol_huckel.GetAtomWithIdx(0).SetFormalCharge(
charge) #mol charge arbitrarily added to 1st atom
passed, result = rdEHTTools.RunMol(mol_huckel)
opop = result.GetReducedOverlapPopulationMatrix()
tri = np.zeros((num_atoms, num_atoms))
tri[np.tril(np.ones(
(num_atoms, num_atoms),
dtype=bool))] = opop #lower triangular to square matrix
for i in range(num_atoms):
for j in range(i + 1, num_atoms):
pair_pop = abs(tri[j, i])
if pair_pop >= 0.15: #arbitry cutoff for bond. May need adjustment
AC[i, j] = 1
AC[j, i] = 1
return AC, mol
def saveimg(smile, pltnm):
atorvastatin = Chem.MolFromSmiles(smile)
mh = Chem.AddHs(atorvastatin)
rdDistGeom.EmbedMolecule(mh)
_, res = rdEHTTools.RunMol(mh)
static_chgs = res.GetAtomicCharges()[:atorvastatin.GetNumAtoms()]
d = Draw.MolDraw2DCairo(400, 400)
SimilarityMaps.GetSimilarityMapFromWeights(atorvastatin,
list(static_chgs),
draw2d=d)
d.FinishDrawing()
thing = show_png(d.GetDrawingText())
name = "http://localhost:5006/fol/static/" + pltnm + ".png"
thing.save(
"C:\\Users\\patil.py\\Documents\\11F-Drive\\PFastWebLocalApp\\FlavorTool\\fol\\static\\"
+ pltnm + ".png")
p = figure(x_range=(0, 1),
y_range=(0, 1),
toolbar_location=None,
plot_width=200,
plot_height=200)
p.xgrid.grid_line_color = None
p.ygrid.grid_line_color = None
p.axis.visible = False
thing = WheelZoomTool()
p.add_tools(thing)
p.toolbar.active_scroll = thing
p.image_url(url=[name], x=0, y=1, w=1, h=1)
return p
def _getMolWithEHTcharges(self, mol : Chem.Mol):
"""
Prepare the molecule and calculate the charges.
TODO: perhaps this should be divided into more methods for more flexibility...
:param mol:
:return:
"""
mol_ = Chem.RemoveHs(mol)
mol_ = Chem.AddHs(mol_)
Chem.EmbedMolecule(mol_)
# should create two output files ('run.out' and 'nul') TODO: maybe this is not really needed or even desirable in the final version?
passed, res = rdEHTTools.RunMol(mol_)
nat = len(mol_.GetAtoms())
charges = res.GetAtomicCharges()
if not self.includeHs:
mol_ = Chem.RemoveHs(mol)
# creates a mol object with charges set as double properties on atoms of that mol object
for i in range(nat):
if i < len(mol_.GetAtoms()):
mol_.GetAtomWithIdx(i).SetDoubleProp('EHTcharge', charges[i])
else:
break
return mol_
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 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 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 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)
cm = res.GetReducedChargeMatrix()
self.assertEqual(cm.shape, (12, 12))
self.assertAlmostEqual(cm[0][0], 0.161, places=3)
self.assertAlmostEqual(cm[1][0], 0.118, places=3)
self.assertAlmostEqual(cm[11][10], 0.004, 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 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)
def xyz2AC_huckel(atomicNumList, xyz, charge):
"""
args
atomicNumList - atom type list
xyz - coordinates
charge - molecule charge
returns
ac - atom connectivity
mol - rdkit molecule
"""
mol = get_proto_mol(atomicNumList)
conf = Chem.Conformer(mol.GetNumAtoms())
for i in range(mol.GetNumAtoms()):
conf.SetAtomPosition(i, (xyz[i][0], xyz[i][1], xyz[i][2]))
mol.AddConformer(conf)
num_atoms = len(atomicNumList)
AC = np.zeros((num_atoms, num_atoms)).astype(int)
mol_huckel = Chem.Mol(mol)
mol_huckel.GetAtomWithIdx(0).SetFormalCharge(
charge) #mol charge arbitrarily added to 1st atom
# Run in temporary path because rdkit generates empty "nul" and "run.out" output files
with in_temp_path(cleanup=True) as path:
passed, result = rdEHTTools.RunMol(mol_huckel)
opop = result.GetReducedOverlapPopulationMatrix()
tri = np.zeros((num_atoms, num_atoms))
tri[np.tril(np.ones(
(num_atoms, num_atoms),
dtype=bool))] = opop #lower triangular to square matrix
for i in range(num_atoms):
for j in range(i + 1, num_atoms):
pair_pop = abs(tri[j, i])
if pair_pop >= 0.15: #arbitry cutoff for bond. May need adjustment
AC[i, j] = 1
AC[j, i] = 1
return AC, mol
