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%% BioMed_Central_Tex_Template_v1.05
%% %
% bmc_article.tex ver: 1.05 %
% %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% %%
%% LaTeX template for BioMed Central %%
%% journal article submissions %%
%% %%
%% <27 January 2006> %%
%% %%
%% %%
%% Uses: %%
%% cite.sty, url.sty, bmc_article.cls %%
%% ifthen.sty. multicol.sty %%
%% %%
%% %%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% %%
%% For instructions on how to fill out this Tex template %%
%% document please refer to Readme.pdf and the instructions for %%
%% authors page on the biomed central website %%
%% http://www.biomedcentral.com/info/authors/ %%
%% %%
%% Please do not use \input{...} to include other tex files. %%
%% Submit your LaTeX manuscript as one .tex document. %%
%% %%
%% All additional figures and files should be attached %%
%% separately and not embedded in the \TeX\ document itself. %%
%% %%
%% BioMed Central currently use the MikTex distribution of %%
%% TeX for Windows) of TeX and LaTeX. This is available from %%
%% http://www.miktex.org %%
%% %%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\NeedsTeXFormat{LaTeX2e}[1995/12/01]
\documentclass[10pt]{bmc_article}
% Load packages
\usepackage{url} % Formatting web addresses
\usepackage{ifthen} % Conditional
\usepackage{multicol} %Columns
\usepackage[utf8]{inputenc} %unicode support
%\usepackage[applemac]{inputenc} %applemac support if unicode package fails
%\usepackage[latin1]{inputenc} %UNIX support if unicode package fails
\urlstyle{rm}
\usepackage[citestyle=numeric-comp]{biblatex}
\setlength{\bibitemsep}{0cm}
\renewbibmacro{in:}{%
\ifentrytype{article}{}{%
\printtext{\bibstring{in}\intitlepunct}}}
\addbibresource{bmc_article.bib}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% %%
%% If you wish to display your graphics for %%
%% your own use using includegraphic or %%
%% includegraphics, then comment out the %%
%% following two lines of code. %%
%% NB: These line *must* be included when %%
%% submitting to BMC. %%
%% All figure files must be submitted as %%
%% separate graphics through the BMC %%
%% submission process, not included in the %%
%% submitted article. %%
%% %%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\def\includegraphic{}
\def\includegraphics{}
\setlength{\topmargin}{0.0cm}
\setlength{\textheight}{21.5cm}
\setlength{\oddsidemargin}{0cm}
\setlength{\textwidth}{16.5cm}
\setlength{\columnsep}{0.6cm}
\newboolean{publ}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% %%
%% You may change the following style settings %%
%% Should you wish to format your article %%
%% in a publication style for printing out and %%
%% sharing with colleagues, but ensure that %%
%% before submitting to BMC that the style is %%
%% returned to the Review style setting. %%
%% %%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%Review style settings
\newenvironment{bmcformat}{\begin{raggedright}\baselineskip20pt\sloppy\setboolean{publ}{false}}{\end{raggedright}\baselineskip20pt\sloppy}
%Publication style settings
%\newenvironment{bmcformat}{\fussy\setboolean{publ}{true}}{\fussy}
% Begin ...
\begin{document}
\begin{bmcformat}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% %%
%% Enter the title of your article here %%
%% %%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\title{The Chemistry Development Kit (CDK). 3. Atom typing, Rendering, Molecular Formula, ...}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% %%
%% Enter the authors here %%
%% %%
%% Ensure \and is entered between all but %%
%% the last two authors. This will be %%
%% replaced by a comma in the final article %%
%% %%
%% Ensure there are no trailing spaces at %%
%% the ends of the lines %%
%% %%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\author{
Egon L Willighagen$^{1}$% // FIXED FIRST AUTHOR
\email{Egon L Willighagen - egon.willighagen@ki.se}
\and
Miguel Rojas Cherto$^2$%
\email{Miguel Rojas Cherto - steinbeck@ebi.ac.uk}
\and
You C B Here$^3$%
\email{You C B Here - you.here@example.org}
\and
C D K Project\correspondingauthor$^98$% // FIXED SECOND BUT LAST AUTHOR
\email{C D K Project - cdk-devel@lists.sourceforge.net}
\and
Rajarshi Guha$^99$% // FIXED ONE BUT LAST AUTHOR
\email{Rajarshi Guha - steinbeck@ebi.ac.uk}
\and
Christoph Steinbeck$^100$% // FIXED LAST AUTHOR
\email{Christoph Steinbeck - steinbeck@ebi.ac.uk}
}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% %%
%% Enter the authors' addresses here %%
%% %%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\address{
\iid(1)Division of Molecular Toxicology, Institute of Environmental Medicine, Karolinska Institutet, SE-17177 Stockholm, Sweden\\
\iid(2)Division of Analytical Biosciences, Leiden/Amsterdam Center for Drug Research, Leiden, The Netherlands \\
\iid(3)Example Ltd., Glasgow, UK \\
\iid(98)\url{http://cdk.sourceforge.net/} \\
\iid(99)NIH Center for Translational Therapeutics, 9800 Medical Center Drive, Rockville, MD 20878, USA \\
\iid(100)Chemoinformatics and Metabolism team, European Bioinformatics Institute, Hinxton, UK
}
\maketitle
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% %%
%% The Abstract begins here %%
%% %%
%% The Section headings here are those for %%
%% a Research article submitted to a %%
%% BMC-Series journal. %%
%% %%
%% If your article is not of this type, %%
%% then refer to the Instructions for %%
%% authors on http://www.biomedcentral.com %%
%% and change the section headings %%
%% accordingly. %%
%% %%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\begin{abstract}
% Do not use inserted blank lines (ie \\) until main body of text.
\paragraph*{Background:}
Cheminformatics is a well-established field with many applications in chemistry,
drug discovery, and the life sciences. Particularly in the latter field, however,
molecular properties are not well-understood yet, and the interaction between
molecules and larger systems remains a challenge to be modeled. Therefore, the
development of new data mining and pattern recognition continues to be important
and the need for access to a cheminformatics library that one can change remains.
\paragraph*{Results:}
We here report the 1.4 series of the Chemistry Development Kit and outline how
it evolved since the previous report. We demonstrate the new APIs we introduced
in this version and discuss the extensive quality control mechanism we have
adopted. New APIs have been introduced for substructure searching, rendering of
molecules, handling of molecular formulas, atom type perception, and InChI
support. At a quality control side we have introduced automated building,
extensive unit and use case testing, and adopted peer review.
\paragraph*{Conclusions:}
With this paper we have shown the continued effort to provide a free, Open Source
cheminformatics library, and show that such colleborative projects can survive for
a long period. We have taken advantage from the community support, and show
that an open source cheminformatics project can act as a peer reviewed
publishing platform for scientific computating software.
\end{abstract}
\ifthenelse{\boolean{publ}}{\begin{multicols}{2}}{}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% %%
%% The Main Body begins here %%
%% %%
%% The Section headings here are those for %%
%% a Research article submitted to a %%
%% BMC-Series journal. %%
%% %%
%% If your article is not of this type, %%
%% then refer to the instructions for %%
%% authors on: %%
%% http://www.biomedcentral.com/info/authors%%
%% and change the section headings %%
%% accordingly. %%
%% %%
%% See the Results and Discussion section %%
%% for details on how to create sub-sections%%
%% %%
%% use \cite{...} to cite references %%
%% \cite{koon} and %%
%% \cite{oreg,khar,zvai,xjon,schn,pond} %%
%% \nocite{smith,marg,hunn,advi,koha,mouse}%%
%% %%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%
%% Background %%
%%
\section*{Background}
Open Source cheminformatics state \ldots (EGON)
Adoption of the CDK ... Cinfony~\cite{OBoyle2008}, and other bindings \ldots ...
Recent prominent use cases of the CDK~\cite{Steinbeck2003,Steinbeck2006} \ldots (EGON)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Results and Discussion %%
%%
\section*{Results and Discussion}
\subsection*{New Functionality}
Everyone is invited to contribute and write up the functionality they contributed;
only requirement: the code must have been incorporated into the main CDK library by the
time of submission of this paper.
\subsubsection*{Atom Typing}
The CDK has adopted a new atom typing algorithm \ldots (EGON)
\subsubsection*{Rendering API}
Initiated by ...
\subsubsection*{Molecular Formula}
....
\subsubsection*{SMARTS parser}
....
\subsubsection*{Partial charges and Delocalization}
....
\subsubsection*{New Builders}
....
\subsubsection*{InChI integration}
.... jni-inchi dep, atom numbering, tautomer generation
\subsection*{Improved Coding Standards}
\subsubsection*{Peer review}
\subsubsection*{Modularization}
\subsubsection*{Documentation}
Initially done with DocCheck, replaced by OpenJavaDocCheck ...
\subsubsection*{Unit testing}
\subsubsection*{Code Quality}
PMD ...
\subsubsection*{Git, branching, and patches}
%%%%%%%%%%%%%%%%%%%%%%
\section*{Conclusions}
Text for this section \ldots
%%%%%%%%%%%%%%%%%%
\section*{Methods}
\subsection*{Peer Review: Automated}
\subsubsection*{PMD}
\subsubsection*{JavaDoc Checks}
\subsection*{Peer Review: Manual}
\subsection*{Unit Testing}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\section*{Authors contributions}
Text for this section \ldots
%%%%%%%%%%%%%%%%%%%%%%%%%%%
\section*{Acknowledgements}
\ifthenelse{\boolean{publ}}{\small}{}
Text for this section \ldots
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% The Bibliography %%
%% %%
%% Bmc_article.bst will be used to %%
%% create a .BBL file for submission, which includes %%
%% XML structured for BMC. %%
%% %%
%% %%
%% Note that the displayed Bibliography will not %%
%% necessarily be rendered by Latex exactly as specified %%
%% in the online Instructions for Authors. %%
%% %%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
{\ifthenelse{\boolean{publ}}{\footnotesize}{\small}
\printbibliography
}
%%%%%%%%%%%
\ifthenelse{\boolean{publ}}{\end{multicols}}{}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% %%
%% Figures %%
%% %%
%% NB: this is for captions and %%
%% Titles. All graphics must be %%
%% submitted separately and NOT %%
%% included in the Tex document %%
%% %%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%
%% Do not use \listoffigures as most will included as separate files
%\section*{Figures}
% \subsection*{Figure 1 - Sample figure title}
% A short description of the figure content
% should go here.
%
% \subsection*{Figure 2 - Sample figure title}
% Figure legend text.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% %%
%% Tables %%
%% %%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Use of \listoftables is discouraged.
%%
%\section*{Tables}
% \subsection*{Table 1 - Sample table title}
% Here is an example of a \emph{small} table in \LaTeX\ using
% \verb|\tabular{...}|. This is where the description of the table
% should go. \par \mbox{}
% \par
% \mbox{
% \begin{tabular}{|c|c|c|}
% \hline \multicolumn{3}{|c|}{My Table}\\ \hline
% A1 & B2 & C3 \\ \hline
% A2 & ... & .. \\ \hline
% A3 & .. & . \\ \hline
% \end{tabular}
% }
% \subsection*{Table 2 - Sample table title}
% Large tables are attached as separate files but should
% still be described here.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% %%
%% Additional Files %%
%% %%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%\section*{Additional Files}
% \subsection*{Additional file 1 --- Sample additional file title}
% Additional file descriptions text (including details of how to
% view the file, if it is in a non-standard format or the file extension). This might
% refer to a multi-page table or a figure.
%
% \subsection*{Additional file 2 --- Sample additional file title}
% Additional file descriptions text.
\end{bmcformat}
\end{document}