Do you still get the error if you move the import into the function body?
def calc_bcut(smi):
from rdkit.Chem.rdMolDescriptors import BCUT2D
mol = Chem.MolFromSmiles(smi)
return BCUT2D(mol)
On Mon, Mar 22, 2021 at 7:29 AM Patrick Walters <[email protected]> wrote:
> 2020.09.5
>
> On Mon, Mar 22, 2021 at 9:24 AM Guillaume GODIN <
> [email protected]> wrote:
>
>> Hi Pat,
>>
>>
>>
>> Hum, I’ve got same error as you.
>>
>>
>>
>> By the way I have to change code to use this
>>
>> from rdkit.Chem.rdMolDescriptors import CalcExactMolWt
>>
>> to avoid another error.
>>
>> Which version of rdkit do you use ?
>>
>>
>>
>> BR
>>
>>
>>
>> Guillaume
>>
>>
>>
>>
>>
>> *De : *Patrick Walters <[email protected]>
>> *Date : *lundi, 22 mars 2021 à 14:20
>> *À : *Guillaume GODIN <[email protected]>
>> *Cc : *rdkit-discuss <[email protected]>
>> *Objet : *Re: [*External*] Re: [Rdkit-discuss] Using the RDKit with Dask
>>
>>
>>
>> The input is just SMILES and molecule name separated by a space. I've
>> attached an example.
>>
>>
>>
>> Thanks,
>>
>>
>>
>> Pat
>>
>>
>>
>>
>>
>> On Mon, Mar 22, 2021 at 9:13 AM Guillaume GODIN <
>> [email protected]> wrote:
>>
>> Hi Pat,
>>
>>
>>
>> Do you have a small example file to proceed , or can I use esol.csv for
>> example ?
>>
>>
>>
>> Thanks
>>
>>
>>
>> Guillaume
>>
>>
>>
>> *De : *Patrick Walters <[email protected]>
>> *Date : *lundi, 22 mars 2021 à 13:51
>> *À : *rdkit-discuss <[email protected]>
>> *Objet : *[*External*] Re: [Rdkit-discuss] Using the RDKit with Dask
>>
>> Apologies, there was a bug in the code I sent in my previous message.
>> The problem is the same. Here is the corrected code in a gist.
>>
>>
>>
>> https://gist.github.com/PatWalters/ca41289a6990ebf7af1e5c44e188fccd
>>
>>
>>
>>
>>
>>
>>
>> On Mon, Mar 22, 2021 at 8:16 AM Patrick Walters <[email protected]>
>> wrote:
>>
>> Hi All,
>>
>>
>>
>> I've been trying to calculate BCUT2D descriptors in parallel with Dask
>> and get this error with the code below.
>>
>> TypeError: cannot pickle 'Boost.Python.function' object
>>
>>
>>
>> Everything works if I call mw_df, which calculates molecular weight, but
>> I get the error above if I call bcut_df. Does anyone have a workaround?
>>
>>
>>
>> Thanks,
>>
>>
>>
>> Pat
>>
>>
>>
>> #!/usr/bin/env python
>>
>> import sys
>> import dask.dataframe as dd
>> import pandas as pd
>> from rdkit import Chem
>> from rdkit.Chem.Descriptors import MolWt
>> from rdkit.Chem.rdMolDescriptors import BCUT2D
>> import time
>>
>> # -- molecular weight functions
>> def calc_mw(smi):
>> mol = Chem.MolFromSmiles(smi)
>> return MolWt(mol)
>>
>> def mw_df(df):
>> return df.SMILES.apply(calc_mw)
>>
>> # -- bcut functions
>> def bcut_df(df):
>> return df.apply(calc_bcut)
>>
>> def calc_bcut(smi):
>> mol = Chem.MolFromSmiles(smi)
>> return BCUT2D(mol)
>>
>> def main():
>> start = time.time()
>> df = pd.read_csv(sys.argv[1],sep=" ",names=["SMILES","Name"])
>> ddf = dd.from_pandas(df,npartitions=16)
>> ddf['MW'] =
>> ddf.map_partitions(mw_df,meta='float').compute(scheduler='processes')
>> ddf['BCUT'] =
>> ddf.map_partitions(bcut_df,meta='float').compute(scheduler='processes')
>> print(time.time()-start)
>> print(ddf.head())
>>
>>
>> if __name__ == "__main__":
>> main()
>>
>>
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