aizynthfinder
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MolecularAI
aizynthfinder process is killed after loading config.yml
Hi,
I am trying to run Retrosynthesis on a small sample of Building Blocks. From the published paper "AiZynthFinder: a fast, robust and flexible open-source software for retrosynthetic planning".
I got 2 hdf5 for policy configuration and 1 hdf5 for zinc stock from the reference: https://figshare.com/articles/dataset/AiZynthFinder_a_fast_robust_and_flexible_open-source_software_for_retrosynthetic_planning/12334577/1
My config file is shown as follows:
config.yml starts here
properties: exclude_target_from_stock: False iteration_limit: 100 time_limit: 10 cutoff_cumulative: 0.995 cutoff_number: 50 max_transforms: 5 policy: files: uspto: - ~/repos/full_uspto_03_05_19_rollout_policy.hdf5 - ~/repos/full_uspto_03_05_19_unique_templates.hdf5 stock: files: zinc: ~/repos/zinc_stock_17_04_20.hdf5
config.yml ends here
After loading the config.yml, the aizynthfinder process is unexpectedly killed without any error message. Here is the log:
log starts here
(aizynth-env) [user1@c0308a-s25 Lib-INVENT]$ aizynthcli --smiles ../sample_output/AC_SMILES_split_0.smi --config ../sample_run/config.yml --output ../sample_output/aizynthfinder_output_AC.hdf5 Setting exclude target from stock to False Setting iteration limit to 10000000 Setting time limit to 100 Setting cutoff cumulative to 0.9 Setting cutoff number to 25 Setting max transforms to 4 Loading template-based expansion policy model from ~/repos/full_uspto_03_05_19_rollout_policy.hdf5 to uspto Loading templates from ~/repos/full_uspto_03_05_19_unique_templates.hdf5 to uspto Loading stock from ~/repos/zinc_stock_17_04_20.hdf5 to zinc Killed (aizynth-env) [user1@c0308a-s25 Lib-INVENT]$
log ends here
I have tried adjusting the time limit and all other variables in my config.yml, but it will always be killed within 20 seconds. I wonder what is the cause and how I can fix it.
Thank you!
Hi, I figured that if I use the stockfile.hdf5 file from "https://github.com/SeemonJ/combinatorial-library-design-dpp/tree/main/publication_example", aizynthfinder will work.
Hello. Thanks for your respons.
My initial thought is that you ran out of memory when trying to load the rather large ZINC stock.
Looking at your input file, it appears that you are running on old version of aizynthfinder with old model files. I would recommend upgrading to the latest version and downloading the models files anew with "download_public_data" script.
