\documentclass[10pt]{article} \usepackage{fullpage} \usepackage{setspace} \usepackage{parskip} \usepackage{titlesec} \usepackage[section]{placeins} \usepackage{xcolor} \usepackage{breakcites} \usepackage{lineno} \usepackage{hyphenat} \PassOptionsToPackage{hyphens}{url} \usepackage[colorlinks = true, linkcolor = blue, urlcolor = blue, citecolor = blue, anchorcolor = blue]{hyperref} \usepackage{etoolbox} \makeatletter \patchcmd\@combinedblfloats{\box\@outputbox}{\unvbox\@outputbox}{}{% \errmessage{\noexpand\@combinedblfloats could not be patched}% }% \makeatother \usepackage[round]{natbib} \let\cite\citep \renewenvironment{abstract} {{\bfseries\noindent{\abstractname}\par\nobreak}\footnotesize} {\bigskip} \titlespacing{\section}{0pt}{*3}{*1} \titlespacing{\subsection}{0pt}{*2}{*0.5} \titlespacing{\subsubsection}{0pt}{*1.5}{0pt} \usepackage{authblk} \usepackage{graphicx} \usepackage[space]{grffile} \usepackage{latexsym} \usepackage{textcomp} \usepackage{longtable} \usepackage{tabulary} \usepackage{booktabs,array,multirow} \usepackage{amsfonts,amsmath,amssymb} \providecommand\citet{\cite} \providecommand\citep{\cite} \providecommand\citealt{\cite} % You can conditionalize code for latexml or normal latex using this. \newif\iflatexml\latexmlfalse \providecommand{\tightlist}{\setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}% \AtBeginDocument{\DeclareGraphicsExtensions{.pdf,.PDF,.eps,.EPS,.png,.PNG,.tif,.TIF,.jpg,.JPG,.jpeg,.JPEG}} \usepackage[utf8]{inputenc} \usepackage[english]{babel} \begin{document} \title{3Dmol.js and NGL examples for computational chemistry} \author[1]{Alberto Pepe}% \affil[1]{Authorea}% \vspace{-1em} \date{March 28, 2024} \begingroup \let\center\flushleft \let\endcenter\endflushleft \maketitle \endgroup \sloppy \par\null \section*{Interactive visualizations} {\label{789327}} The following examples have been created using~\texttt{3dmol.js}\cite{Rego_2014}{ The figure below was created clicking on }\textbf{Insert}{ -\textgreater{} }\textbf{Interactive Figure}{ and then selecting a local file with the following code:} \par\null \begin{verbatim}
\end{verbatim}\selectlanguage{english} \begin{figure}[h!] \begin{center} \includegraphics[width=0.70\columnwidth]{figures/3dmol/static} \caption{{Example of an embedded \href{https://github.com/3dmol/3Dmol.js}{3Dmol.js figure}. Move the figure and zoom in and out. {\label{117222}}% }} \end{center} \end{figure} \texttt{3dmol.js} is presented in this paper~\cite{Rego_2014} which unwilling and emphatically provides the case for a web-first, live scientific article. \texttt{3dmol.js}'s interactive features are presented as static figures in the 18th century style~ technology of a traditional academic article. \par\null\selectlanguage{english} \begin{figure}[h!] \begin{center} \includegraphics[width=0.56\columnwidth]{figures/3dmol-2/static} \caption{{Another embedded~\href{https://github.com/3dmol/3Dmol.js}{3Dmol.js figure}. PDB structure from the 3Dmol.js server but hosting it in Authorea or calling it from another arbitrary server looks \href{http://3dmol.csb.pitt.edu/doc/tutorial-url.html}{easy enough.} {\label{174742}}% }} \end{center} \end{figure} An alternative to\texttt{3Dmol.js} is \texttt{NGL}, seen in action in Fig.~{\ref{595403}}~ \par\null\selectlanguage{english} \begin{figure}[h!] \begin{center} \includegraphics[width=0.56\columnwidth]{figures/ngl/static} \caption{{Embedded \href{https://github.com/arose/ngl}{NGL viewer} in action. The PDB file is hosted at~\href{https://www.rcsb.org/}{RCSB PDB}, and called via code. {\label{595403}}% }} \end{center} \end{figure} \section*{} {\label{801660}} \section*{Jupyter and executable notebooks} {\label{801660}}\selectlanguage{english} \begin{figure}[h!] \begin{center} \includegraphics[width=0.70\columnwidth]{figures/plot/plot} \caption{{Figure and Jupyter Notebook from \href{https://paperstack.uchicago.edu:8001/chartdetails.jsp?paperId=5b0ef8381f87c63760acb909}{QRESP}, for testing purposes {\label{148284}}% }} \end{center} \end{figure} \selectlanguage{english} \FloatBarrier \bibliographystyle{plainnat} \bibliography{bibliography/converted_to_latex.bib% } \end{document}