In [1]:
import qcportal as ptl
client = ptl.FractalClient()
ds = client.get_collection("Dataset", "COMP6 DrugBank")
In [2]:
mols = ds.get_molecules()
In [3]:
mols.shape
Out[3]:
(13379, 1)
In [4]:
ds.list_values().reset_index()['method'].unique()
Out[4]:
array(['ωB97x', 'b3lyp', 'b3lyp-d3m(bj)', 'hf', 'pbe', 'pbe-d3m(bj)',
       'svwn', 'wb97m', 'wb97m-d3(bj)'], dtype=object)
In [5]:
ds.list_values().reset_index()['basis'].unique()
Out[5]:
array(['6-31g*', 'def2-tzvp'], dtype=object)
In [6]:
ds.list_values().reset_index().groupby(['method','basis']).size().reset_index()
Out[6]:
method basis 0
0 b3lyp def2-tzvp 1
1 b3lyp-d3m(bj) def2-tzvp 1
2 hf def2-tzvp 1
3 pbe def2-tzvp 1
4 pbe-d3m(bj) def2-tzvp 1
5 svwn def2-tzvp 1
6 wb97m def2-tzvp 1
7 wb97m-d3(bj) def2-tzvp 1
8 ωB97x 6-31g* 6
In [7]:
ds.list_values()
Out[7]:
keywords name
native driver program method basis
False charge gaussian ωB97x 6-31g* Unknown CM5 Charges
6-31g* Unknown Hirshfeld Charges
energy gaussian ωB97x 6-31g* Unknown Energy
gradient gaussian ωB97x 6-31g* Unknown Gradient
hirshfeld_dipole gaussian ωB97x 6-31g* Unknown Hirshfeld Dipole
spin_density gaussian ωB97x 6-31g* Unknown Spin Density
True energy psi4 b3lyp def2-tzvp scf_default B3LYP/def2-tzvp
b3lyp-d3m(bj) def2-tzvp scf_default B3LYP-D3M(BJ)/def2-tzvp
hf def2-tzvp scf_default HF/def2-tzvp
pbe def2-tzvp scf_default PBE/def2-tzvp
pbe-d3m(bj) def2-tzvp scf_default PBE-D3M(BJ)/def2-tzvp
svwn def2-tzvp scf_default SVWN/def2-tzvp
wb97m def2-tzvp scf_default WB97M/def2-tzvp
wb97m-d3(bj) def2-tzvp scf_default WB97M-D3(BJ)/def2-tzvp
In [8]:
val = ds.get_values(method='ωB97x')
In [9]:
val.columns
Out[9]:
Index(['CM5 Charges', 'Hirshfeld Charges', 'Energy', 'Gradient',
       'Hirshfeld Dipole', 'Spin Density'],
      dtype='object')
In [10]:
energy = val['Energy']
In [11]:
mols['molecule'][0].show()
In [12]:
energy[0]
Out[12]:
-636107.9519541461
In [13]:
mols['molecule'][1].show()
In [14]:
energy[1]
Out[14]:
-558044.7290289854
In [15]:
ds.list_records()
Out[15]:
driver program method basis keywords name
0 energy psi4 hf def2-tzvp scf_default HF/def2-tzvp
1 energy psi4 svwn def2-tzvp scf_default SVWN/def2-tzvp
3 energy psi4 pbe def2-tzvp scf_default PBE/def2-tzvp
5 energy psi4 b3lyp def2-tzvp scf_default B3LYP/def2-tzvp
7 energy psi4 wb97m def2-tzvp scf_default WB97M/def2-tzvp
8 energy psi4 pbe-d3m(bj) def2-tzvp scf_default PBE-D3M(BJ)/def2-tzvp
9 energy psi4 b3lyp-d3m(bj) def2-tzvp scf_default B3LYP-D3M(BJ)/def2-tzvp
10 energy psi4 wb97m-d3(bj) def2-tzvp scf_default WB97M-D3(BJ)/def2-tzvp
In [ ]: