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  1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 %% 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}