Hi Brian,
This is due to the way all parallel Python packages handle message transfer
across processes. They pickle the message sent, and RDKit's default
molecule object is not pickle safe (if such a term exists). You have to
convert molecule objects to PropertyMol ones that are pickle safe.
Best,
Christos Kannas
Sent from my Galaxy Note 4.
On 2 Mar 2015 17:50, "Bennion, Brian" <benni...@llnl.gov> wrote:
> Hello,
>
> I am relatively new to rdkit but have found it to be very useful in
> creating compounds with the reaction functions.
>
> Currently my project involves taking a handful of scaffolds and creating
> shrubbery for these scaffolds based on available precursor compounds. I
> found that creating more than a few hundred compounds takes much to long (i
> am not very patient). It would be best if I could create 100K compounds an
> a few hours. Again, I have a perfectly working serial script that does
> want I need.
>
> That is when I found parallel python and spent a few days learning how to
> get the two projects to play with each other.
>
> I am stuck at a point where I make a command:
> molename=m.GetOpt("_Name")
> and this stops the program with:
>
> An error has occured during the function execution
> Traceback (most recent call last):
> File "/usr/lib/python2.7/site-packages/ppworker.py", line 90, in run
> __result = __f(*__args)
> File "<string>", line 31, in synthesize
> KeyError: '_Name'
>
> It seems that the parallel process does not know what this command is
> supposed to do.
> The parallel process is started with this code.
> for index in xrange(parts):
> starti = start+index*step
> endi = min(start+(index+1)*step, end)
> # Submit a job which will synthesize a number of compounds
> # synthesize - the function
> # give starting info to synthesize (hash, starti, endi) - tuple with
> arguments for synthesize
> # () - tuple with functions on which function synthesize depends
> # ("Allchem",) - tuple with module names which must be imported before
> synthesize execution
> jobs.append(job_server.submit(synthesize, (ms1, ms2,rxnR1, rxnR23,
> oxime, starti, endi), (),
> ("rdkit","rdkit.Chem","rdkit.Chem.AllChem","rdkit.Chem.Draw",)))
>
>
> I am naive to think that these two python modules can not play together?
> Or can I fix a mistake I have made somewhere
>
>
> Brian
>
>
>
>
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