pultar / ppqm

Enable cheminformatics and quantum chemistry

Psi Phi Package

Do you need rdkit? Do you need quantum chemistry? We got you bro.

Examples

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)

Notes on Jupyter usage

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-widgets

Please note, if you are using Jupyter Lab (not notebook) there are som additional notes to consider

Contributions

Fork, branch and use pre-commit.

Other code bases

"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.

• https://github.com/kzfm/pygamess
• https://github.com/duartegroup/autodE/
• https://github.com/JelfsMaterialsGroup/stko
• https://github.com/lukasturcani/stk
• https://github.com/MolSSI
• https://github.com/datamol-org/datamol
• https://github.com/ekwan/cctk
• https://gitlab.com/ase/ase
• https://github.com/cclib/cclib
• https://github.com/Acellera/moleculekit