I’m still learning QCArchive. I posted qcportal with reaction dataset. And today I tried to retrieve of drug bank from qcportal. QCportal provides not only calculated numeric data but also 3D mol view by using py3Dmol.
OK let’s go to code. get_molecule method provides many data from qcportal web server.
import qcportal as ptl client = ptl.FractalClient() ds = client.get_collection("Dataset", "COMP6 DrugBank") mols = ds.get_molecules() mols.shape > (13379, 1)
What kinds of data in the dataset? It is easy to do it, just call some methods.
ds.list_values().reset_index()['method'].unique() > array(['ωB97x', 'b3lyp', 'b3lyp-d3m(bj)', 'hf', 'pbe', 'pbe-d3m(bj)', 'svwn', 'wb97m', 'wb97m-d3(bj)'], dtype=object) ds.list_values().reset_index()['basis'].unique() > array(['6-31g*', 'def2-tzvp'], dtype=object) ds.list_values()
This dataset has not only data from psi4 but also gaussian!.
I got data from method=’wB97x’
val = ds.get_values(method='ωB97x') val.columns > Index(['CM5 Charges', 'Hirshfeld Charges', 'Energy', 'Gradient', 'Hirshfeld Dipole', 'Spin Density'], dtype='object')
I got energy from the data and visualize molecules.
energy = val['Energy'] mols['molecule'].show() energy > -636107.9519541461
Py3Dmol works very well. I could get QC energy of molecule in drug bank and could render molecule as 3D object.
It is very cool!
My whole code is uploaded following URL.
Have a nice week end! ;)