pandas integration

Getting pandas

pandas must be installed to use its functionality from within PubChemPy. The easiest way is to use pip:

pip install pandas

See the pandas documentation for more information.


It is possible for get_compounds, get_substances and get_properties to return a pandas DataFrame:

df1 = pcp.get_compounds('C20H41Br', 'formula', as_dataframe=True)
df2 = pcp.get_substances([1, 2, 3, 4], as_dataframe=True)
df3 = pcp.get_properties(['isomeric_smiles', 'xlogp', 'rotatable_bond_count'], 'C20H41Br', 'formula', as_dataframe=True)

An existing list of Compound objects can be converted into a dataframe, optionally specifying the desired columns:

cs = pcp.get_compounds('C20H41Br', 'formula')
df4 = pcp.compounds_to_frame(cs, properties=['isomeric_smiles', 'xlogp', 'rotatable_bond_count'])