Abstract
In the past two decades a lot of different formats for molecules and reactions have been created. These formats were mostly developed for the purposes of identifiers, representation, classification, analysis and data exchange. A lot of efforts have been made on molecule formats but only few for reactions where the endeavors have been made mostly by companies leading to proprietary formats. Here, we present ReactionCode: a new open-source format that allows one to encode and decode a reaction into multi-layer machine readable code, which aggregates reactants and products into a condensed graph of reaction (CGR). This format is flexible and can be used in a context of reaction similarity searching and classification. It is also designed for database organization, machine learning applications and as a new transform reaction language.
Highlights
Different proprietary and open formats for reactions have been invented over the past 50 years
They implemented a format based on rules to generate new molecules and integrated it in the first computer-aided organic synthesis program: OCSS (Organic Chemical Simulation of Synthesis) [1]
This project split to give birth to LHASA (Logic and Heuristics Applied to Synthetic Analysis) [2,3,4] and SECS (Simulation and Evaluation of Chemical Synthesis) [5]
Summary
Different proprietary and open formats for reactions have been invented over the past 50 years. They implemented a format based on rules to generate new molecules and integrated it in the first computer-aided organic synthesis program: OCSS (Organic Chemical Simulation of Synthesis) [1]. This project split to give birth to LHASA (Logic and Heuristics Applied to Synthetic Analysis) [2,3,4] and SECS (Simulation and Evaluation of Chemical Synthesis) [5]. The LHASA team designed the language CHMTRN (CHeMistryTRaNslator), while the SECS group created the ALCHEM (A Language for CHEMistry) language [6] After their launch, diverse additional reaction transform languages came up along the implementation of programs such as CLASS and IGOR & IGOR2.
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