pandas integration

Installing pandas

pandas must be installed to use its functionality from within PubChemPy. It is an optional dependency, so it is not installed automatically with PubChemPy. The easiest way is to use pip:

pip install pandas

See the pandas documentation for more information.

Usage

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(["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=["smiles", "xlogp", "rotatable_bond_count"])