ASKCOS/ASKCOS: ASKCOS v0.4.1 Public Release

Release Notes User notes:

• New site selectivity module to predict the most likely site of aromatic C-H functionalization
• New clustering of one-step retrosynthetic predictions in the Interactive Path Planning user interface
• New visualization of tree builder results in the Interactive Path Planning user interface
• The entire expanded graph is now able to be explored, instead of only pathways that were resolved
• The tree builder is now more resilient for large, complex molecules and long expansion times
• Updated webpage to view molecules in the buyables database, adding the ability to add and delete entries
• Improved API error handling
• Molecular weights of compounds are now shown in the forward predictor results
• New impurity predictor module
• New reaction atom-mapping module
• Upgrade to rdkit version 2019.03.3
• Migration of rdchiral to standalone pypi package - rdchiral development can now be found at https://github.com/connorcoley/rdchiral
• Improved buyables lookup consistency
• Canonicalizes SMILES strings before lookup in buyables module
• Improved granularity of feedback after buyable upload
• Improved handling of reaction templates in rdchiral for "hypervalent" nitrogens - significant improvement for nitration reactions

• Support for Kubernetes deployment
• Option included to not preload retrosynthetic templates upon deployment, and instead create the templates on-the-fly as needed
• Groundwork for unit tests
• Enabled option to skip https, despite this not being recommended
• Data and models migrated to a separate repository (https://github.com/ASKCOS/askcos-data)
• Docker builds are now much, much, much faster
• Chemhistorian data migrated to mongodb (increases initialization mongodb seeding time, but decreases memory footprint)
• All dependencies, including third-party docker images, are now pinned to specific versions
• Celery dependency upgraded to 4.4
• Seeding of mongo db now occurs using the backend "app" service
• Template relevance and fast filter models moved to Tensorflow serving containers

• Reduced likelihood of "Connection reset by peer" errors in tree builder
• Format of the synthesis predictor export is now csv
• Link to export Reaxys reactions supporting a given template now works again
• No more Docker images are built on-the-fly
• Results saved with old versions of ASKCOS should now be able to be restored to newer versions
• Fixed restart config for nginx service