Reaction standardization#

This page explains how to do a reaction standardization in SynPlanner.

Reaction mapping#

Reaction atom-to-atom (AAM) mapping in SynPlanner is performed with GraphormerMapper, an algorithm for AAM based on a transformer neural network adopted for the direct processing of molecular graphs as sets of atoms and bonds, as opposed to SMILES/SELFIES sequence-based approaches, in combination with the Bidirectional Encoder Representations from Transformers (BERT) network. The graph transformer serves to extract molecular features that are tied to atoms and bonds. The BERT network is used for chemical transformation learning. In a benchmarking study [https://doi.org/10.1021/acs.jcim.2c00344], GraphormerMapper achieved 89.5% correctly mapped reactions on the “Golden” benchmarking data set, compared to 84.5% for IBM RxnMapper.

Reaction standardization#

The reaction data are standardized using an original protocol for reaction data curation published earlier [https://doi.org/10.1002/minf.202100119]. This protocol includes two layers: standardization of individual molecules (reactants, reagents, products) and reaction standardization. Steps for standardization of individual molecules include functional group standardization, aromatization/kekulization, valence checking, hydrogens manipulation, cleaning isotopes, and radicals, etc. The reaction standardization layer includes reaction role assignment, reaction equation balancing, and atom-to-atom mapping fixing. The duplicate reactions and erroneous reactions are removed.

The current available reaction standardizers in SynPlanner:

  • Reaction mapping (reaction atom mapping using chython from chytorch)

  • Reaction mapping fix (fix reaction mapping in reaction when needed and possible)

  • Functional groups standardization (standardization of functional groups)

  • Kekule / Aromatic form conversion (conversion between Kekule and Aromatic form when needed)

  • Atom valence validation (check atom valences)

  • Isotope validation (check and clean isotope atoms when possible)

  • Reagents validation (remove reagents from reaction)

  • Unchanged parts validation (remove unchanged parts in reaction)

  • Hydrogen manipulation (remove hydrogen atoms)

  • Ions splitting (split ions in reaction when possible)

  • Reaction rebalancing (rebalancing reaction)

  • Duplicate reaction removal (remove duplicate reactions)

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