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
------------------------------------------------------------------------------
Dive into the World of Parallel Programming The Go Parallel Website, sponsored
by Intel and developed in partnership with Slashdot Media, is your hub for all
things parallel software development, from weekly thought leadership blogs to
news, videos, case studies, tutorials and more. Take a look and join the
conversation now. http://goparallel.sourceforge.net/
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
