def test_calculate_conformer(self):
if os.path.exists(os.path.expandvars("$AUTOTST/test/species")):
shutil.rmtree(os.path.expandvars("$AUTOTST/test/species"))
conformer = Conformer(smiles='CC', index=0)
result = self.job.calculate_conformer(conformer=conformer)
self.assertTrue(result)
conformer = Conformer(smiles='CC(Cl)(Cl)Cl', index=0)
result = self.job.calculate_conformer(conformer=conformer)
self.assertFalse(result)
def get_rdkit_mol(self,
rmg_molecule=None,
reaction_family="H_Abstraction",
distance_data=None):
"""
A method to create an rdkit geometry... slightly different than that of the conformer method
returns both the rdkit_molecule and the bm
"""
if not rmg_molecule:
rmg_molecule = self.rmg_molecule
rdkit_molecule = Chem.RWMol(
Conformer().get_rdkit_mol(rmg_molecule=rmg_molecule))
labels, atom_match = self.get_labels(rmg_molecule, reaction_family)
for i, atom in enumerate(rmg_molecule.atoms):
assert atom.number == rdkit_molecule.GetAtoms()[i].GetAtomicNum()
if len(labels) == 3:
rd_copy = rdkit_molecule.__copy__()
lbl1, lbl2, lbl3 = labels
if not rd_copy.GetBondBetweenAtoms(lbl1, lbl2):
rd_copy.AddBond(lbl1,
lbl2,
order=rdkit.Chem.rdchem.BondType.SINGLE)
else:
rd_copy.AddBond(lbl2,
lbl3,
order=rdkit.Chem.rdchem.BondType.SINGLE)
self._pseudo_geometry = rd_copy
logging.info("Initially embedded molecule")
bm = None
if distance_data:
logging.info("Getting bounds matrix")
bm = self.get_bounds_matrix(rdkit_molecule=rdkit_molecule)
if len(labels) > 0:
logging.info("Editing bounds matrix")
bm = self.edit_matrix(rmg_molecule, bm, labels, distance_data)
logging.info("Performing triangle smoothing on bounds matrix.")
DistanceGeometry.DoTriangleSmoothing(bm)
logging.info("Now attempting to embed using edited bounds matrix.")
rdkit_molecule = self.rd_embed(rdkit_molecule,
10000,
bm=bm,
match=atom_match)[0]
return rdkit_molecule, bm
def test_load_conformer_attributes(self):
charge = 0
mult = 1
label = 'CC(C)C'
base = 'CC{C}C'
self.orca.conformer = Conformer(smiles='CC(C)C')
self.orca.load_conformer_attributes()
self.assertTrue([charge,mult,label,base] ==
[self.orca.charge,self.orca.mult,self.orca.label,self.orca.base])
def get_angles(self):
test_conf = Conformer()
test_conf.rmg_molecule = self.rmg_molecule
try:
test_conf._rdkit_molecule = self._pseudo_geometry
except:
self.get_rdkit_mol()
test_conf._rdkit_molecule = self._pseudo_geometry
test_conf._ase_molecule = self.ase_molecule
return test_conf.get_angles()
def get_rdkit_mol(self):
"""
A method to create an rdkit geometry... slightly different than that of the conformer method
returns both the rdkit_molecule and the bm
"""
self.rdkit_molecule = Conformer(
rmg_molecule=self.rmg_molecule).get_rdkit_mol()
self.get_labels()
for i, atom in enumerate(self.rmg_molecule.atoms):
assert atom.number == self.rdkit_molecule.GetAtoms(
)[i].GetAtomicNum()
if len(self.labels) == 3:
rd_copy = Chem.RWMol(self.rdkit_molecule.__copy__())
lbl1, lbl2, lbl3 = self.labels
if not rd_copy.GetBondBetweenAtoms(lbl1, lbl2):
rd_copy.AddBond(lbl1,
lbl2,
order=rdkit.Chem.rdchem.BondType.SINGLE)
elif not rd_copy.GetBondBetweenAtoms(lbl2, lbl3):
rd_copy.AddBond(lbl2,
lbl3,
order=rdkit.Chem.rdchem.BondType.SINGLE)
self._pseudo_geometry = rd_copy
logging.info("Initially embedded molecule")
self.bm = None
if self.distance_data:
logging.info("Getting bounds matrix")
self.bm = self.get_bounds_matrix()
if len(self.labels) > 0:
logging.info("Editing bounds matrix")
self.bm = self.edit_matrix()
logging.info("Performing triangle smoothing on bounds matrix.")
DistanceGeometry.DoTriangleSmoothing(self.bm)
logging.info("Now attempting to embed using edited bounds matrix.")
self.rd_embed()
return self.rdkit_molecule
def setUp(self):
self.conformer = Conformer("NC(O)C=CC")
self.conformer.get_molecules()
def test_conformer_calc(self):
autotst_gaussian_confomer = Gaussian(conformer=Conformer(
smiles='CCC')).get_conformer_calc()
calc_dict = autotst_gaussian_confomer.todict()
self.assertIsInstance(autotst_gaussian_confomer, ASEGaussian)
self.assertIsInstance(calc_dict, dict)
def get_angles(self):
return Conformer().get_angles(self._pseudo_geometry, self.ase_molecule)
def get_bonds(self):
return Conformer().get_bonds(self._pseudo_geometry, self.ase_molecule,
self.rmg_molecule)
def setUp(self):
self.conformer = Conformer(smiles='CC')
def setUp(self):
conf = Conformer(smiles='C')
self.orca = Orca(conformer=conf, directory=os.path.expandvars(
"$AUTOTST/autotst/calculator/fod"))
def get_torsions(self):
test_conf = Conformer()
test_conf.rmg_molecule = self.rmg_molecule
test_conf.rdkit_molecule = self._pseudo_geometry
test_conf.ase_molecule = self.ase_molecule
return test_conf.get_torsions()
def test_calculate_conformer(self):
conformer = Conformer(smiles='CC', index=0)
result = self.job.calculate_conformer(conformer=conformer)
self.assertTrue(result)
def setUp(self):
self.conformer = Conformer("CC(C)C=CC")
self.conformer_3rad = Conformer("[C]=[CH]")
self.conformer_4rad = Conformer("[C]=[C]")