From 0d292b8ba5714a8659cac00944464ca2adad796c Mon Sep 17 00:00:00 2001 From: Andrew Freiburger Date: Fri, 2 Oct 2026 08:34:04 -0500 Subject: [PATCH] NAR 2026: sync M07_methods_similarity_mapping.tex with Overleaf edits Co-Authored-By: Claude Opus 5.5 (1M context) --- .../latex/sections/M07_methods_similarity_mapping.tex | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/Papers/NAR_Update_2026/latex/sections/M07_methods_similarity_mapping.tex b/Papers/NAR_Update_2026/latex/sections/M07_methods_similarity_mapping.tex index 89ed64f7..e7643b09 100644 --- a/Papers/NAR_Update_2026/latex/sections/M07_methods_similarity_mapping.tex +++ b/Papers/NAR_Update_2026/latex/sections/M07_methods_similarity_mapping.tex @@ -1,4 +1,6 @@ %% 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.