1 files changed, 243 insertions, 0 deletions
diff --git a/Master/texmf-dist/doc/latex/nih/example-nih-cls.tex b/Master/texmf-dist/doc/latex/nih/example-nih-cls.tex
new file mode 100644
index 00000000000..d17a4bb807a
--- /dev/null
+++ b/Master/texmf-dist/doc/latex/nih/example-nih-cls.tex
@@ -0,0 +1,243 @@
+% This example file for NIH submissions was originally written
+% by Bruce Donald (http://www.cs.duke.edu/brd/).
+% 
+% You may freely use, modify and/or distribute this file.
+% 
+\documentclass[11pt]{nih}
+%\documentclass{article}
+%\documentclass[12pt]{article}%
+% last revision:
+\def\mydate{2005-06-09 13:58:03 brd}
+
+
+%%%%%%% Two column control
+\newif\ifdotwocol
+\dotwocoltrue   % two col
+%\dotwocolfalse   % one col
+\long\def\twocol#1#2{\ifdotwocol{#1}\else{#2}\fi}
+%%%%%%%
+
+\def\mybeforeequation{\footnotesize}
+%\def\mybeforeequation{\small}
+%\def\mybeforeequation{}
+
+\def\myafterequation{\renewcommand\baselinestretch{1.1}}
+%\def\myafterequation{}
+
+%%%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%
+
+\def\citeusmark{$^{\textstyle \star}$}
+\def\citeus#1#2{\cite{#1}}
+
+\def\crow#1#2{#2}
+
+%\usepackage{denselists}
+%\usepackage{scaledfullpage}
+\usepackage[dvips]{graphicx}
+\usepackage{color}
+\usepackage{boxedminipage}
+\usepackage{amsfonts}
+\usepackage{amsmath}
+\usepackage{url}
+%\usepackage{times}
+%\usepackage{nih}		% PHS 398 Forms
+%\usepackage{nihblank}		% For printing on Blank PHS 398 Forms
+%\usepackage{confidential}
+
+\def\Paper{grant application}
+\def\paper{application}
+\def\refappendix{Sec.}
+
+\def\poster{(Poster)}
+
+%Note from brd
+\long\def\todo#1{{\bf{To do:}} #1}
+%\long\def\todo#1{}
+\def\ICRA{IEEE International Conference on Robotics and Automation (ICRA)}
+
+\long\def\squeezable#1{#1}
+
+%\def\a5{$\alpha_{_5}$
+
+\def\a5{5}
+
+%\def\mycaptionsize{\normalsize}
+%\def\mycaptionsize{\small}
+%\def\mycaptionsize{\small}
+\def\mycaptionsize{\footnotesize}
+\def\mycodesize{\footnotesize}
+\def\myeqnsize{\small}
+
+\def\sheading#1{{\bf #1:}\ }
+\def\sheading#1{\subsubsection{#1}}
+%\def\sheading#1{\bigskip {\bf #1.}}
+
+\def\ssheading#1{\noindent {\bf #1.}\ } 
+
+\newtheorem{hypothesis}{Hypothesis}
+\long\def\hyp#1{\begin{hypothesis} #1 \end{hypothesis}}
+
+\def\cbk#1{[{\em #1}]}
+
+\def\R{\mathbb{R}}
+\def\midv{\mathop{\,|\,}}
+\def\Fscr{\mathcal{F}}
+\def\Gscr{\mathcal{G}}
+\def\Sscr{\mathcal{S}}
+\def\set#1{{\{#1\}}}
+\def\edge{\!\rightarrow\!}
+\def\dedge{\!\leftrightarrow\!}
+\newcommand{\EOP}{\nolinebreak[1]~~~\hspace*{\fill} $\Box$\vspace*{\parskip}\vspace*{1ex}}
+%my way of doing starred references
+\newcommand{\mybibitem}[1]{\bibitem{#1} 
+\label{mybiblabel:#1}}
+\newcommand{\BC}{[}
+\newcommand{\EC}{]}
+\newcommand{\mycite}[1]{\ref{mybiblabel:#1}\nocite{#1}}
+\newcommand{\starcite}[1]{\ref{mybiblabel:#1}\citeusmark\nocite{#1}}
+
+
+\def\degree{$^\circ$}
+\def\R{\mathbb{R}}
+\def\Fscr{\mathcal{F}}
+\def\set#1{{\{#1\}}}
+\def\edge{\!\rightarrow\!}
+\def\dedge{\!\leftrightarrow\!}
+
+\long\def\gobble#1{}
+\def\Jigsaw{{\sc Jigsaw}}
+\def\ahelix{\ensuremath{\alpha}-helix}
+\def\ahelices{\ensuremath{\alpha}-helices}
+\def\ahelical{$\alpha$-helical}
+\def\bstrand{\ensuremath{\beta}-strand}
+\def\bstrands{\ensuremath{\beta}-strands}
+\def\bsheet{\ensuremath{\beta}-sheet}
+\def\bsheets{\ensuremath{\beta}-sheets}
+\def\hone{{\ensuremath{^1}\rm{H}}}
+\def\htwo{{$^{2}$H}}
+\def\cthir{{\ensuremath{^{13}}\rm{C}}}
+\def\nfif{{\ensuremath{^{15}}\rm{N}}}
+\def\hn{{\rm{H}\ensuremath{^\mathrm{N}}}}
+\def\hnone{{\textup{H}\ensuremath{^1_\mathrm{N}}}}
+\def\ca{{\rm{C}\ensuremath{^\alpha}}}
+\def\catwel{{\ensuremath{^{12}}\rm{C}\ensuremath{^\alpha}}}
+\def\ha{{\rm{H}\ensuremath{^\alpha}}}
+\def\cb{{\rm{C}\ensuremath{^\beta}}}
+\def\hb{{\rm{H}\ensuremath{^\beta}}}
+\def\hg{{\rm{H}\ensuremath{^\gamma}}}
+\def\dnn{{\ensuremath{d_{\mathrm{NN}}}}}
+\def\dan{{\ensuremath{d_{\alpha \mathrm{N}}}}}
+\def\jconst{{\ensuremath{^{3}\mathrm{J}_{\mathrm{H}^{\mathrm{N}}\mathrm{H}^{\alpha}}}} }
+\def\cbfb{{CBF-$\beta$}}
+
+\newtheorem{defn}{Definition}
+\newtheorem{claim}{Claim}
+
+    \gobble{
+    \psfrag{CO}[][]{\colorbox{white}{C}}
+    \psfrag{OO}[][]{\colorbox{white}{O}}
+    \psfrag{CA}[][]{\colorbox{white}{\ca}}
+    \psfrag{HA}[][]{\colorbox{white}{\ha}}
+    \psfrag{CB}[][]{\colorbox{white}{\cb}}
+    \psfrag{HB}[][]{\colorbox{white}{\hb}}
+    \psfrag{HN}[][]{\colorbox{white}{\hn}}
+    \psfrag{N15}[][]{\colorbox{white}{\nfif}}
+    \psfrag{dnn}[][]{\dnn}
+    \psfrag{dan}[][]{\dan}
+    \psfrag{phi}[][]{$\phi$}
+    }
+
+\newenvironment{closeenumerate}{\begin{list}{\arabic{enumi}.}{\topsep=0in\itemsep=0in\parsep=0in\usecounter{enumi}}}{\end{list}}
+\def\CR{\hspace{0pt}}           % ``invisible'' space for line break
+
+
+
+\newif\ifdbspacing
+%\dbspacingtrue  % For double spacing
+\dbspacingfalse  % For normal spacing
+
+\ifdbspacing
+ \doublespacing
+ \newcommand{\capspacing}{\doublespace\mycaptionsize}
+\else
+ \newcommand{\capspacing}{\mycaptionsize}
+\fi
+
+\def\rulefigure{\smallskip\hrule}
+
+% \def\codesize{\normalsize}
+\def\codesize{\small}
+
+% Can use macros \be, \ee, \en as shortcuts
+%  for \begin{enumerate}, \end{enumerate}, \item
+%  respectively.
+
+\def\be{\begin{enumerate}}   % Begin Enumerate
+\def\ee{\end{enumerate}}     % End Enumerate
+\def\en{\item}               % ENtry (item)
+\def\bi{\begin{itemize}}     % Begin Itemize
+\def\ei{\end{itemize}}       % End Itemize
+\def\bv{\begin{verbatim}}    % Begin Verbatim
+\def\ev{\end{verbatim}}      % End Verbatim
+
+\def\matlab{{\sc matlab} }
+\def\amber{{\sc amber} }
+\def\KS{{$K^*$}}
+\def\KSM{{K^*}} % K-Star Math
+\def\KSTM{{\tilde{K}^*}}  % K-Star Tilde Math (appx K*)
+\def\KOP{{$K^{\dagger}_{o}$}}  % K-Star Optimal partial
+\def\KOPM{{K^{\dagger}_{o}}}  % K-Star Optimal partial Math
+\def\KP{{$K^{\dagger}$}}  % K-Star partial
+\def\KPM{{K^{\dagger}}}  % K-Star partial Math
+\def\KTPM{{\tilde{K}^{\dagger}}}  % K-Star Tilde partial Math
+\def\KD{{$K_{_D}$}}
+\def\KA{{$K_{_A}$}}
+\def\qpM{{q_{_P}}}
+\def\qlM{{q_{_L}}}
+\def\qplM{{q_{_{PL}}}}
+\def\qSplM{{q^*_{_{PL}}}}
+\def\KSO{{$K^*_{o}$}} % K-Star Optimal
+\def\KSOM{{K^*_{o}}}  % K-Star Optimal Math
+\def\CBFB{{CBF-$\beta$}}   % Core binding factor beta
+\def\argmin{\mathop{\mathrm{argmin}}}
+\def\rhl#1{{\em \underline{RYAN}: *\{{#1}\}*}}
+\def\set#1{{\left\{ #1 \right\}}}
+\def\Escr{{\mathcal{E}}}
+\def\Jscr{{\mathcal{J}}}
+\def\Kscr{{\mathcal{K}}}
+\def\th{{$^{{\mathrm{th}}}$}}
+
+\newtheorem{proposition}{Proposition}
+\newtheorem{lemma}{Lemma}
+
+
+
+\begin{document}
+
+\bigskip
+
+\appendix 
+
+%\mydate
+
+\setcounter{page}{20} % or whatever
+
+%\noindent{\Large\bf Research Plan}
+
+\section{Specific Aims}
+
+\noindent Realization of novel molecular function requires the ability
+to alter molecular complex formation. Enzymatic function can be
+altered by changing enzyme-substrate interactions via modification of
+an enzyme's active site. A redesigned enzyme may either perform a
+novel reaction on its native substrates or its native reaction on
+novel substrates.  We propose a novel algorithm for protein redesign,
+which searches over possible active site mutations and combines a
+statistical mechanics-derived ensemble-based approach to computing the
+binding constant with the speed and completeness of a branch-and-bound
+pruning algorithm. We will develop an efficient$\ldots$
+
+\end{document}
+
+