def test_resp_noopt_orient(self, dmso_opt, ref):
charge_options = psiresp.ChargeOptions(equivalent_methyls=True)
orientation_options = psiresp.OrientationOptions(n_reorientations=2)
r = self.cls.from_molecules([dmso_opt],
orientation_options=orientation_options)
charges = r.run(charge_constraint_options=charge_options)
assert_allclose(charges, ref, rtol=0.05, atol=1e-4)
def test_resp_opt(self, ref):
mol = [mol_from_file(self.molfile)]
orientation_options = psiresp.OrientationOptions(n_reorientations=2)
charge_options = psiresp.ChargeOptions(equivalent_methyls=True)
r = self.cls.from_molecules(mol,
optimize_geometry=True,
orientation_options=orientation_options)
charges = r.run(charge_options=charge_options)
assert_allclose(charges, ref, rtol=0.05, atol=1e-3)
def test_resp_noopt(self, ref):
orientation_options = psiresp.OrientationOptions(n_reorientations=2)
opt = [mol_from_file('{}_c1_ATB_opt.xyz'.format(self.molname))]
charge_options = psiresp.ChargeOptions(equivalent_methyls=True)
r = self.cls.from_molecules(opt,
optimize_geometry=False,
orientation_options=orientation_options)
charges = r.run(charge_options=charge_options)
# no idea which point density ATB uses
assert_allclose(charges, ref, rtol=0.05, atol=1e-3)
def nme2ala2(self):
mols = [mol_from_file(f) for f in self.nme2ala2_names]
orient = [(5, 18, 19), (19, 18, 5), (6, 19, 20), (20, 19, 6)]
or_options = psiresp.OrientationOptions(reorientations=orient,
keep_original=False)
chrconstrs = {0: [20, 21, 22, 23, 24, 25], 0.6163: [18], -0.5722: [19]}
chrequivs = [[10, 14], [11, 12, 13, 15, 16, 17]]
ch_options = psiresp.ChargeOptions(charge_equivalences=chrequivs,
charge_constraints=chrconstrs,
equivalent_sp3_hydrogens=False)
resp = psiresp.Resp.from_molecules(
mols,
charge=0,
orientation_options=or_options,
charge_constraint_options=ch_options,
optimize_geometry=self.opt,
name='nme2ala2')
return resp
def methylammonium(self):
mols = [mol_from_file(f) for f in self.methylammonium_names]
orient = [(1, 5, 7), (7, 5, 1)]
or_options = psiresp.OrientationOptions(reorientations=orient,
keep_original=False)
chrconstrs = []
chrequivs = [[6, 7, 8]]
ch_options = psiresp.ChargeOptions(charge_equivalences=chrequivs,
charge_constraints=chrconstrs,
equivalent_sp3_hydrogens=False)
resp = psiresp.Resp.from_molecules(
mols,
charge=1,
multiplicity=1,
orientation_options=or_options,
charge_constraint_options=ch_options,
optimize_geometry=self.opt,
name='methylammonium')
return resp