Hi Pat,
What I found useful in the past is to make the imports inside of the
functions for dask. Not very elegant, but works.
Best,
Maciek
pon., 22 mar 2021, 14:30 użytkownik Patrick Walters
napisał:
> 2020.09.5
>
> On Mon, Mar 22, 2021 at 9:24 AM Guillaume GODIN <
>
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 wrote:
> 2020.09.5
>
> On Mon, Mar 22, 2021
Thanks, Greg. Yutong Zhao sent me the same solution and I was just about
to post his fix to the list. It's funny how I posted to the list and a
colleague had the answer.
Thanks all, the RDKit community is awesome!
On Mon, Mar 22, 2021 at 9:55 AM Greg Landrum wrote:
> Hi Pat,
>
> Solution,
Hi Pat,
Solution, either change your calc_bcut function to:
def calc_bcut(smi):
from rdkit.Chem.rdMolDescriptors import BCUT2D
mol = Chem.MolFromSmiles(smi)
return BCUT2D(mol)
or change the import on line 8 at the top to:
from rdkit.Chem import rdMolDescriptors
and do:
def
2020.09.5
On Mon, Mar 22, 2021 at 9:24 AM Guillaume GODIN <
guillaume.go...@firmenich.com> 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.
>
>
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
Date : lundi, 22 mars 2021 à 14:20
À : Guillaume GODIN
Hi Pat,
Do you have a small example file to proceed , or can I use esol.csv for example
?
Thanks
Guillaume
De : Patrick Walters
Date : lundi, 22 mars 2021 à 13:51
À : rdkit-discuss
Objet : [*External*] Re: [Rdkit-discuss] Using the RDKit with Dask
Apologies, there was a bug in the code I
Hi,
did you try to do something along these lines already?:
https://stackoverflow.com/questions/7089386/pickling-boost-python-functions
Peter
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 <
guillaume.go...@firmenich.com> wrote:
> Hi Pat,
>
>
>
> Do you have a small example file to proceed , or can I use esol.csv for
> example
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 wrote:
> Hi All,
>
> I've been trying to
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
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