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NAR 2026 manuscript: sync M07_methods_similarity_mapping.tex with Overleaf edits #307

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NAR 2026 manuscript: sync M07_methods_similarity_mapping.tex with Overleaf edits #307

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4 changes: 3 additions & 1 deletion Papers/NAR_Update_2026/latex/sections/M07_methods_similarity_mapping.tex
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%% Consolidates the former methods_{reaction_similarity,atom_mapping} sections.
\subsection{Atom mapping}\label{sec:methods-mapping}

Atom mappings are generated from the workflow of Hu{\ss} \textit{et al.}~\cite{huss2022} where they refine the per-reaction output of the Reaction Decoder Tool~\cite{rahman2016} into mappings that can be used to span a metabolic reconstruction. The approach also resolves chemically equivalent atoms into symmetry groups, such as the two oxygens of CO$_2$ and the six equivalent terminal oxygens of pyrophosphate, so the ambiguity is apparent. The output is formatted and stored in the database, and can also be visualized in the UI.
Atom mappings are generated from the workflow of Hu{\ss} \textit{et al.}~\cite{huss2022} where they refine the per-reaction output of the Reaction Decoder Tool~\cite{rahman2016} into mappings that can be used to span a metabolic reconstruction.
The approach also resolves chemically equivalent atoms into symmetry groups, such as the two oxygens of CO$_2$ and the six equivalent terminal oxygens of pyrophosphate, so the ambiguity is apparent.
The output is formatted and stored in the database, and can also be visualized in the UI.