for x in df.itertuples():
name = str(x.reac.label.split('_r')[0])
mol = x.prod.get_rdkit_mol()
xcontrol_name = name + "_xcontrol"
create_xcontrol(mol, xcontrol_name)
n = name + "_ts"
ts_scan(x.prod, n, charge, mult, xcontrol_name)
with open(n + "_xtbscan.log", 'r') as out:
output = out.read()
print(output)
ts_qmmol = QMMol()
xyz_file = ts_scan_xtb.read_ts_guess_structure2(output)
ts_qmmol.add_conformer(input_mol=xyz_file,
fmt='xyz',
label=n,
charge=charge,
multiplicity=mult,
read_freq=False,
charged_fragments=True)
ts_conf = ts_qmmol.conformers[0]
ts_conf.results['energy'] = ts_scan_xtb.read_ts_guess_energy(output)[0]
#print(ts_conf.results['energy'])
reac_qmconf = x.reac
def gs_conformer_search(name, rdkit_conf, chrg, mult, cpus):
""" ground state conformer search """
charged = True # hard coded for mogens
# create conformers
qmmol = QMMol()
qmmol.add_conformer(rdkit_conf, fmt='rdkit', label=name,
charged_fragments=charged, set_initial=True)
# find #-- rot bond.
mol = qmmol.get_rdkit_mol()
triple_smart = '[c]:[c]-[CH0]#[CH0]'
extra_rot_bond = int(len(mol.GetSubstructMatches(Chem.MolFromSmarts(triple_smart))) / 2)
# print compute number of conformers to find
rot_bonds = len(RotatableBonds(qmmol.initial_conformer.get_rdkit_mol())) + extra_rot_bond
num_confs = 5 + 5*rot_bonds
qmmol.create_random_conformers(threads=cpus, num_confs=num_confs)
xtb_params = {'method': 'gfn2',
'opt': 'opt',
'cpus': 1}
qmmol.calc = xTB(parameters=xtb_params)
qmmol.optimize(num_procs=cpus, keep_files=False)
# Get most stable conformer. If most stable conformer
# not identical to initial conf try second lowest.
initial_smi = Chem.MolToSmiles(Chem.RemoveHs(qmmol.initial_conformer.get_rdkit_mol()))
low_energy_conf = qmmol.nlowest(1)[0]
conf_smi = Chem.MolToSmiles(Chem.RemoveHs(low_energy_conf.get_rdkit_mol()))
i = 1
while initial_smi != conf_smi:
low_energy_conf = qmmol.nlowest(i+1)[-1]
conf_smi = Chem.MolToSmiles(Chem.RemoveHs(low_energy_conf.get_rdkit_mol()))
i += 1
if len(qmmol.conformers) < i:
sys.exit('no conformers match the initial input')
return low_energy_conf