2024.10 Release Notes

ASKCOS Development

Software package for the prediction of feasible synthetic routes towards a desired compound and associated tasks related to synthesis planning. Originally developed under the DARPA Make-It program and now being developed under the MLPDS Consortium.

askcos2_core

• SMILES output by handler should be canonicalized + deduplicated (Issue askcosv2_core#135)
• TaskCreate RDKit Utility Endpoint (Issue mlpds_mit/askcosv2/askcos2_core#131)
• Multiple errors in calculating "one-step calculation", blocks interactive path planner (Issue mlpds_mit/askcosv2/askcos2_core#130)
• Turn off backend caching on error (Issue mlpds_mit/askcosv2/askcos2_core#125)
• MCTS pathway enumeration gets stuck sometimes (Issue mlpds_mit/askcosv2/askcos2_core#119)
• Add ranking back to the Condition recommender (Issue mlpds_mit/askcosv2/askcos2_core#111)
• Refactor/rework backup restore to use mongo cli (MR askcosv2_core!109) ·
• [RDKit] Add to_sdfile API in rdkit (MR askcosv2_core!108)
• update env version and support email (MR askcosv2_core!107)
• add exact_match to backend option (MR askcosv2_core!106)
• add lookup_by_exact_product_smiles in reactions (MR askcosv2_core!105)
• additional error handling for atom mapping (MR askcosv2_core!104)
• retro-star value network (MR askcosv2_core!103)
• Add molecular_complexity to configs and wrappers (MR askcos2_core!102)
• store access_token in cookie and add cookie-based authentication (MR askcos2_core!101)
• add error handling and fall back to unmodified mol on alignment error (MR askcos2_core!100)
• Issues deploying custom one-step template-based retrosynthetic model (Issue mlpds_mit/askcosv2/askcos2_core#99)

askcos-vue-nginx

• Copy All Reaction ID's not working on the Aromatic C-H functionalization page (Issue askcos-vue-nginx#358)
• [Tree Builder] Result Info not displaying the settings properly (Issue askcos-vue-nginx#355)
• When adding a precursor manually on the IPP, it should be added to the display graph automatically (Issue askcos-vue-nginx#354)
• “Score” is not well explained in reaction detailed view (Issue askcos-vue-nginx#353)
• IssueAugmented transformer model for forward synthesis may fail to crash gracefully (Issue mlpds_mit/askcosv2/askcos-vue-nginx#343)
• Product Prediction Smiles Copy in Result Section copies the wrong smiles. (Issue askcos-vue-nginx#337)
• MCTS recognizes that there is a path (i.e. "first_path_time" returns a nonzero value) but does not return any paths (Issue mlpds_mit/askcosv2/askcos-vue-nginx#332)
• Setting update in askcos-vue-nginx not reflected upon rebuild, unless "empty cache and hard reload" in browser (Issue mlpds_mit/askcosv2/askcos-vue-nginx#330)
• Hovering over precursors no longer shows number of appearance (issue mlpds_mit/askcosv2/askcos-vue-nginx#321)
• Node visualization error in IPP (Issue mlpds_mit/askcosv2/askcos-vue-nginx#319)
• [Test] Improve test coverage for js files (Issue askcos-vue-nginx#271)
• Testing Task for IPP (Issue mlpds_mit/askcosv2/askcos-vue-nginx#126)
• [PWA] add functionality to check for PWA online or offline (MR askcos-vue-nginx!225)
• [IPP] Rename score to precursor score (MR askcos-vue-nginx!224)
• [SiteSelectivity] Copy to Clipboard fixed (MR askcos-vue-nginx!223)
• [MolCom] Add Molecular Complexity page (MR askcos-vue-nginx!222)
• [QM] 3D Visualization for the QM page (MR askcos-vue-nginx!220)
• [Accross all pages] Dark mode theme 🚀 (MR askcos-vue-nginx!219)
• [Auth] Cookie based authentication (MR askcos-vue-nginx!217)
• [common] Re-wrote logic for common js files (MR askcos-vue-nginx!216)
• [Result Store] Optimize results store (MR askcos-vue-nginx!215)
• [Optimize Admin] Improve Admin Page (MR askcos-vue-nginx!214)
• [QM] Fix for using rdkit api (MR askcos-vue-nginx!213)
• [Home] Show recent search history (MR askcos-vue-nginx!212)
• [Tree Builder] Fix the strategy displayed on the tree builder setting page (MR askcos-vue-nginx!211)
• [Home] Update the hero section (MR askcos-vue-nginx!210)
• Does it make sense to scale down the IPP UI? (Issue mlpds_mit/askcosv2/askcos-vue-nginx#173)
• [Testing/IPP] Chemical Node Detail - Precursors (Issue mlpds_mit/askcosv2/askcos-vue-nginx#136)
• Weird third option in ordering -> [check all sorting function if possible] - eg my result, solvent screening... (Issue mlpds_mit/askcosv2/askcos-vue-nginx#120)

molecular_complexity

• Update error handling (MR molecular_complexity!2)
• module for molecular_complexity (MR molecular_complexity!1)

retro_star

• Update pathway enumeration (MR mlpds_mit/askcosv2/tree_search/retro_star!3)

tree_search/mcts

• Update pathway enumeration (MR mlpds_mit/askcosv2/tree_search/mcts!4)

retro/template_relevance

• Serving reaxys model returns a value error when I attempt to make a prediction (Issue mlpds_mit/askcosv2/retro/template_relevance#7)
• Question: does retraining produce historian and reaction reference data? (Issue mlpds_mit/askcosv2/retro/template_relevance#3)

forward_predictor/augmented_transformer

• at_handler_fix (MR mlpds_mit/askcosv2/forward_predictor/augmented_transformer!1)

Deployment

We currently support two methods for deploying ASKCOS: Docker Compose (recommended) and Kubernetes (limited support). Docker Compose is a simpler method for deploying on a single workstation, while Kubernetes is more complex but is suitable for scaling across multiple nodes.

Hardware and Software Requirements

Please review the hardware and software requirements before proceeding to install ASKCOSv2.

Deployment options

ASKCOS is highly modularized and can be installed locally in two ways (click the links for installation instructions):

1. Full/Quickstart
2. Customizable

Upgrade Information

ASKCOSv2 can be easily upgraded by following the instructions here.

Member companies can find more deployment options on the members site