Do you need rdkit? Do you need quantum chemistry? We got you bro.
Assume all codesnippets below are using RDKit molecule objs
molecule = Chem.MolFromSmiles("O")
Chem.AddHydrogens(molecule)
AllChem.UFFOptimizeMolecule(molecule)Optimize using XTB
from ppqm import XtbCalculator
xc = XtbCalculator()
molecule2 = xc.optimize(molecule, return_copy=True)Example of using GAMESS calculator and using specific options. As you notice, GAMESS needs a lot of settings to work with.
from ppqm import GamessCalculator
# Let's set the complicated GAMESS settings
gamess_options = {
"scr": "/tmp/node/scr/space/slurm/id",
"cmd": "/opt/gamess/rungms",
"gamess_scr": "~/scr",
"gamess_userscr": "~/userscr",
}
gc = GamessCalculator(**gamess_options)
# Now that we have gamess setup, we can then the GAMESS options we all know
# and love. Knowing exactly what keywords to set in GAMESS, you'll have to
# read the manual
calculation_option = {
"runtyp": "optimize",
"statpt": {
"opttol": 0.005,
"nstep": 300,
"projct": False,
}
}
# We then use the options to get properties for the molecule.
# The return will be a list of dictionaries, per conformer in the molobj.
results = gc.calculate(molecule, calculation_option)
for properties in results:
print(properties)Example notebooks uses nglview to visualize the molecules in notebooks
# install nglview
conda install nglview -c conda-forge
# install plugin for jupyter lab
jupyter labextension install nglview-js-widgetsPlease note, if you are using Jupyter Lab (not notebook) there are som additional notes to consider
Fork, branch and use pre-commit.
"is this the first python wrapper for quantum chemistry?" No, check the others and find the one right for your project. Know one, not on the list? Add it.