for filename in sorted(glob.glob(filenames, recursive=True)):
if re.search("slurm", filename):
continue
try:
output_file = GaussianFile.read_file(filename)
if len(output_file.energies) > 0:
mol = output_file.get_molecule()
ensemble.add_molecule(mol,
energy=output_file.energies[-1] * 627.509)
except:
print(f"skipping f{filename} due to error...")
print(f"{len(ensemble.molecules)} conformers before elimination of redundant")
ensemble.eliminate_redundant(cutoff=0.6)
print(f"{len(ensemble.molecules)} conformers after elimination of redundant")
best_confs = ensemble.get_within_cutoff(cutoff=10)
for idx, molecule in enumerate(best_confs):
GaussianFile.write_molecule_to_file(
f"conformer_v2_{idx:03d}.gjf", molecule,
"#p opt freq=noraman m062x/6-31g(d) scrf=(smd,solvent=diethylether)",
None)
for idx, molecule in enumerate(
list(ensemble.molecules[np.argsort(ensemble.energies)])):
items = [idx + 1, np.sort(ensemble.energies)[idx]]
for atoms in to_rotate:
items.append(molecule.get_dihedral(*atoms))
#### Usage: ``python generate_conformers.py``
output_file = XYZFile.read_file("CpG.xyz")
mol = output_file.molecule.assign_connectivity()
ensemble = ConformationalEnsemble()
angles = [0, 60, 120, 180, 240, 241, 300]
for x in angles:
for y in angles:
mol.set_dihedral(1, 7, 6, 8, x)
mol.set_dihedral(23, 24, 25, 1, y)
ensemble.add_molecule(mol, copy=True)
old_num = len(ensemble)
ensemble = ensemble.eliminate_redundant()
new_num = len(ensemble)
print(
f"originally {old_num} conformers, but after eliminating redundant there are {new_num}!"
)
count = 0
for molecule in ensemble.molecules:
x = int(round(molecule.get_dihedral(1, 7, 6, 8)))
y = int(round(molecule.get_dihedral(23, 24, 25, 1)))
if molecule.check_for_conflicts():
GaussianFile.write_molecule_to_file(f"CpG_{x}_{y}.gjf",
molecule,
route_card="#p opt b3lyp/6-31g(d)")
count += 1
else: