pandas, convert DataFrame to MultiIndex'ed DataFrame
You need set_index:
print (df2.head()) resultx y z 0.0 0.0 0.000000 NaN 0.025126 0.0 0.050251 0.0 0.075377 0.0 0.100503 0.0print (df.set_index(['x','y','z']).head()) resultx y z 0.0 0.0 0.000000 NaN 0.025126 0.0 0.050251 0.0 0.075377 0.0 0.100503 0.0If need compare both DataFrames, need replace NaN to same values, else get False:
print (df.set_index(['x','y','z']).eq(df2).all())result Falsedtype: boolprint (np.nan == np.nan)Falseprint (df.fillna(1).set_index(['x','y','z']).eq(df2.fillna(1)).all())result Truedtype: bool