% Macros:
% -------

\newcommand{\tabtab}{\rule{0.3in}{0cm}}
\newcommand{\logf}{{\tt log}}
\newcommand{\bull}{$\bullet$}

% Underline below Figure or Table
\newcommand{\underfigtab}{\vspace{-0.55cm} 
                 \begin{center} \rule{7cm}{0.2mm} \end{center}}

% Broken line for indicating a new theme without a title
\newcommand{\brokenline}{
  \hspace{1cm}
   \begin{center} 
   \rule{9mm}{0.2mm} \rule{6mm}{0.0mm} \rule{9mm}{0.2mm} 
   \rule{6mm}{0.0mm} \rule{9mm}{0.2mm} \rule{6mm}{0.0mm} \rule{9mm}{0.2mm} 
   \end{center}
  \hspace{1cm}
}

% Underline:
\newcommand{\un}[1]{\underline{#1}}

%TLS tensors:
\newcommand{\TLS}{$\bf T$, $\bf L$ and $\bf S$}

% Enlarge and shrink the page for one line:
\newcommand{\longpage}{\enlargethispage{\baselineskip}}
\newcommand{\shortpage}{\enlargethispage{-\baselineskip}}

% Ensemble average
\newcommand{\ens}[1]{\langle#1\rangle}

% Figure~placeholders (won't work for tables!!!; the placement will be screwed):
\newcommand{\figplace}{\begin{center} \fbox{\hspace{8cm} \rule{0cm}{1cm}} \end{center}}
\newcommand{\figholder}[1]{\rule{0cm}{#1}}
\newcommand{\pageinsert}{\begin{figure}[htbp] \rule{0.cm}{30cm} \end{figure}}
\newcommand{\onepage}{\pageinsert}
\newcommand{\twopages}{\onepage\onepage}
\newcommand{\threepages}{\onepage\onepage\onepage}

% Right margin notes:
\newcommand{\margnote}[1] {\marginpar{\small $\leftarrow$#1}}

\newcommand{\Sub}[1]{${\rm S}_{#1}$}
\newcommand{\Subp}[1]{${\rm S}'_{\rm #1}$}
\newcommand{\Pos}[1]{${\rm P}_{#1}$}
\newcommand{\Posp}[1]{${\rm P}'_{\rm #1}$}

% Programs:
\newcommand{\GROMOS} {\mbox{\sc Gromos}}
\newcommand{\COMPARER} {\mbox{\sc Comparer}}
\newcommand{\ALIGNER} {\mbox{\sc Aligner}}
\newcommand{\MOLSCRIPT} {\mbox{\sc Molscript}}
\newcommand{\CLUSTALV} {\mbox{\sc Clustalv}}
\newcommand{\CHARMM} {\mbox{\sc Charmm}}
\newcommand{\XPLOR} {\mbox{\sc X-PLOR}}
\newcommand{\QUANTA} {\htmladdnormallink{\mbox{\sc Quanta}}
           {http://www.msi.com/info/products/QUANTA.html}}
\newcommand{\WEBLAB} {\htmladdnormallink{\mbox{\sc Weblab}}
           {http://www.msi.com/weblab/index.html}}
\newcommand{\INSIGHT} {\htmladdnormallink{\mbox{\sc InsightII}}
           {http://www.msi.com/info/products/InsightII.html}}
\newcommand{\GENEEXPLORER} {\htmladdnormallink{\mbox{\sc GeneExplorer}}
           {http://www.msi.com/info/life/molbio/index.html}}
\newcommand{\RASMOL} {\mbox{\sc Rasmol}}
\newcommand{\GRASP} {\mbox{\sc Grasp}}
\newcommand{\MATCHMAKER} {\mbox{\sc MatchMaker}}
\newcommand{\PROFIT} {\mbox{\sc Profit}}
\newcommand{\MODELLER} {\mbox{\sc Modeller}}
\newcommand{\MOULDER} {\mbox{\sc Moulder}}
\newcommand{\MOD} {\mbox{\sc Mod}}
\newcommand{\RESTRAIN} {\mbox{\sc Restrain}}
\newcommand{\MNYFIT} {\mbox{\sc Mnyfit}}
\newcommand{\FRODO} {\mbox{\sc Frodo}}
\newcommand{\ARIADNE} {\mbox{\sc Ariadne}}
\newcommand{\DISMAN} {\mbox{\sc Disman}}
\newcommand{\COMPOSER} {\mbox{\sc Composer}}
\newcommand{\LOPAL} {\mbox{\sc Lopal}}
\newcommand{\KITSCH} {\mbox{\sc Kitsch}}
\newcommand{\PHYLIP} {\mbox{\sc Phylip}}
\newcommand{\PROCHECK} {\mbox{\sc Procheck}}
\newcommand{\DRAWTREE} {\mbox{\sc Drawtree}}
\newcommand{\DRAWGRAM} {\mbox{\sc Drawgram}}
\newcommand{\ALIGN} {\mbox{\sc Align}}
\newcommand{\JOY} {\mbox{\sc Joy}}
\newcommand{\TOP} {\mbox{\sc Top}}
\newcommand{\MDT} {\mbox{\sc Mdt}}
\newcommand{\XS} {\mbox{\sc Xs}}
\newcommand{\DIH} {\mbox{\sc Dih}}
\newcommand{\PLOT} {\mbox{\sc Plot}}
\newcommand{\LSQ} {\mbox{\sc Lsq}}
\newcommand{\CORR} {\mbox{\sc Corr}}
\newcommand{\PSA} {\mbox{\sc Psa}}
\newcommand{\DISULF} {\mbox{\sc Disulf}}
\newcommand{\GETCSR} {\mbox{\sc Getcsr}}
\newcommand{\SSTRUC} {\mbox{\sc Sstruc}}
\newcommand{\DSSP} {\mbox{\sc Dssp}}
\newcommand{\THREADER} {\mbox{\sc Threader}}
\newcommand{\ACC} {\mbox{\sc Acc}}
\newcommand{\HBD} {\mbox{\sc Hbd}}
\newcommand{\NGH} {\mbox{\sc Ngh}}
\newcommand{\CNT} {\mbox{\sc Cnt}}
\newcommand{\THREED} {\mbox{\sc 3d}}
\newcommand{\UHBD} {\mbox{\sc Uhbd}}
\newcommand{\ELLIPSOID} {\mbox{\sc Ellipsoid}}
\newcommand{\RAMA} {\mbox{\sc Rama}}
\newcommand{\DDM} {\mbox{\sc Ddm}}
\newcommand{\TLSFIT} {\mbox{\sc Tlsfit}}
\newcommand{\PRINCONE} {\mbox{\sc Princ1}}
\newcommand{\PRINCTWO} {\mbox{\sc Princ2}}

% Computers, OS:
\newcommand{\PROLOG} {\mbox{\sc Prolog}}
\newcommand{\FORTRAN} {\mbox{\sc Fortran}}
\newcommand{\VAX} {\mbox{\sc Vax}}
\newcommand{\UNIX} {\mbox{\sc Unix}}
\newcommand{\PostScript} {\mbox{\sc PostScript}}
\newcommand{\XENIX} {\mbox{\sc Xenix}}

% AA, AA^2, \pH, pKa, kcat, Km, Ki, Biso, oC, tab
\newcommand{\tab } {\rule{1cm}{0cm}}
\newcommand{\RMS}{\mbox{\sc Rms}}
\newcommand{\DRMS}{\mbox{\sc Drms}}
\newcommand{\Ang}{\mbox{\AA}}
\newcommand{\kB}{\mbox{$k_B$}}
\newcommand{\Angsq}{\mbox{\Ang\sups{2}}}
\newcommand{\pH}{{\it p}H}
\newcommand{\pKa}{{\it p}K\subs{a}}
\newcommand{\dGw}{$\Delta G_{\mbox{H\subs{2}O}}$}
\newcommand{\kcat } {\mbox{\it k\subs{cat}}}
\newcommand{\Km } {\mbox{\it K\subs{M}}}
\newcommand{\Ki } {\mbox{\it K\subs{i}}}
\newcommand{\Biso } {\mbox{\it B\subs{iso}}}

%Greek characters
\newcommand{\al}{$\alpha$}
\newcommand{\be}{$\beta$}
\newcommand{\ga}{$\gamma$}
\newcommand{\de}{$\delta$}
\newcommand{\ep}{$\epsilon$}
\newcommand{\micro}{$\mu$}

\input{macros-latex.inc}
