Dear Stamatia,
If the molecules are processed completely independently by your code, it
may be simpler to split the SDF into chunks (e.g. with csplit in a bash
script) and then run separate instances of your python code on each chunk,
wait until all are finished and finally collate the output. Thus
Hi Stamatia,
Yes, SDMolSupplier is not thread safe.
My guess is due to the nature of SDF file where a molecule record needs
multiple lines and you do not know a-priory the number of lines per
molecule in order to split the file to different threads/processes.
Given that your proposed approach is
Hello everyone,
We have been writing a script that searches though a large number of molecules
within different files for a common substructure. To speed this up we have been
attempting to run this script in parallel-see scripts below. However online the
tutorial notes make reference to proble
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