Hello,
This might be trivial python question but I am stuck in calculating
the Chem.MolFromSmiles:
My smiles strings are in a pandas DataFrame (df) with SMILES column
(df.SMILES) and I have been calculating the mols (df_mol) by Pandas apply
function as below:
df_mol = df.SMILES.apply( lambda x: Chem.MolFromSmiles(x) )
While this works just fine, I would like to speed up the calculation by
vectorization either in pandas or in numpy as below:
df_mol = Chem.MolFromSmiles(df.SMILES)
df_mol = Chem.MolFromSmiles(df.SMILES.values)
However, I am getting the TypeError as below:
TypeError: No registered converter was able to produce a C++ rvalue of type
std::__1::basic_string<wchar_t, std::__1::char_traits<wchar_t>,
std::__1::allocator<wchar_t> > from this Python object of type Series
Just to provide further information on the above approach is to replace the
apply function in the snippet below with vectorization:
allDescp=[name[0] for name in Descriptors._descList]
for name in allDescp:
_= MoleculeDescriptors.MolecularDescriptorCalculator([name])
df [name] = df [smiles_column].apply(lambda x:
_.CalcDescriptors(Chem.MolFromSmiles(x))[0])
Thanks,
Ali
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