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% Inline citations.
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% Allow the maths blocks to be broken!!!
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% Set the graphics path to the parent relax directory.
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% Make the index.
\makeindex


% Start the document.
%%%%%%%%%%%%%%%%%%%%%

\begin{document}

% Include the hyphenation rules.
\include{hyphenation}


\frontmatter


% Title page.
%%%%%%%%%%%%%

\begin{titlepage}
\begin{center}

% Vertical centering.
\vspace*{\stretch{2}}

% Title.
{\Huge \textbf{relax}}
\vspace{\stretch{1}}

% relax version number.
{\LARGE \textbf{\input{relax_version}}}
\vspace{\stretch{1}}

\centerline{
  \includegraphics[
    width=\textwidth,
    bb=14 14 793 342
  ]
  {images/ulysses}
}
\vspace{\stretch{2}}

% Subtitle.
{\huge \textbf{Molecular dynamics by}}
\vspace{\stretch{0.5}}

{\huge \textbf{NMR data analysis}}
\vspace{\stretch{1}}

% Date.
{\large \today}
\vspace*{\stretch{2}}

\end{center}
\end{titlepage}


% Table of Contents.
%%%%%%%%%%%%%%%%%%%%

\tableofcontents


% List of Figures.
%%%%%%%%%%%%%%%%%%

\newpage
\listoffigures


% List of Tables.
%%%%%%%%%%%%%%%%%

\newpage
\listoftables


% Abbreviations.
%%%%%%%%%%%%%%%%

\chapter*{Abbreviations}

\begin{description}
  \item[AIC:]  Akaike's Information Criteria (model selection method)
  \item[AICc:]  small sample size corrected AIC (model selection method)
  \item[API:]  application programming interface
  \item[ANOVA:]  analysis of variance (field of statistics)
  \item[BC:]  back calculation
  \item[BIC:]  Bayesian Information Criteria (model selection method)
  \item[BFGS:]  Broyden-Fletcher-Goldfarb-Shanno (optimisation method)
  \item[$C(\tau)$:]  correlation function
  \item[$\chi^2$:]  chi-squared function
  \item[CG:]  conjugate gradient (optimisation)
  \item[CPMG:]  the Carr-Purcell-Meiboom-Gill pulse sequence
  \item[CR72:]  the \citet{CarverRichards72} relaxation dispersion model
  \item[CSA:]  chemical shift anisotropy
  \item[CV:]  cross validation
  \item[CVS:]  Concurrent Versions System (open source version control system)
  \item[$\Diff$:]  the set of diffusion tensor parameters
  \item[$\Diff_\Par$:]  the eigenvalue of the spheroid diffusion tensor corresponding to the unique axis of the tensor
  \item[$\Diff_\Per$:]  the eigenvalue of the spheroid diffusion tensor corresponding to the two axes perpendicular to the unique axis
  \item[$\Diff_a$:]  the anisotropic component of the Brownian rotational diffusion tensor
  \item[$\Diff_{iso}$:]  the isotropic component of the Brownian rotational diffusion tensor
  \item[$\Diff_r$:]  the rhombic component of the Brownian rotational diffusion tensor
  \item[$\Diff_{ratio}$:]  the ratio of $\Diff_\Par$ to $\Diff_\Per$
  \item[$\Diff_x$:]  the eigenvalue of the Brownian rotational diffusion tensor in which the corresponding eigenvector defines the x-axis of the tensor
  \item[$\Diff_y$:]  the eigenvalue of the Brownian rotational diffusion tensor in which the corresponding eigenvector defines the y-axis of the tensor
  \item[$\Diff_z$:]  the eigenvalue of the Brownian rotational diffusion tensor in which the corresponding eigenvector defines the z-axis of the tensor
  \item[DPL94:]  the \citet{Davis94} relaxation dispersion model
  \item[DQ:]  double quantum
  \item[$\epsilon_i$:]  elimination value
  \item[FSF:]  Free Software Foundation
  \item[GNU:]  GNU's Not Unix!
  \item[GPG:]  GNU Privacy Guard (software)
  \item[GPL:]  GNU general public licence
  \item[GUI:]  graphical user interface
  \item[ID string:]  identification string
  \item[IT99:]  the \citet{IshimaTorchia99} relaxation dispersion model
  \item[$J(\omega)$:]  spectral density function
  \item[LM63:]  the \citet{LuzMeiboom63} relaxation dispersion model
  \item[M61:]  the \citet{Meiboom61} relaxation dispersion model
  \item[MC:]  Monte Carlo (simulations)
  \item[MD:]  molecular dynamics (simulations)
  \item[MMQ:]  proton-heteronuclear SQ, ZQ, DQ, and MQ data (multi-multiple quantum)
  \item[MP05:]  the \citet{MiloushevPalmer05} relaxation dispersion model
  \item[MPI:]  message passing interface
  \item[MQ:]  multiple quantum
  \item[NMR:]  if you do not know this one, do not read further
  \item[NNTP:]  network news transfer protocol
  \item[NOE:]  nuclear Overhauser effect
  \item[NS:]  numeric solution
  \item[ORD:]  optical rotatory dispersion
  \item[OS:]  operating system
  \item[PCS:]  pseudocontact shift
  \item[PDB:]  Protein Data Bank
  \item[pdf:]  probability distribution function
  \item[PRE:]  paramagnetic relaxation enhancement
  \item[$r$:]  bond length
  \item[$\Rone$:]  spin-lattice relaxation rate
  \item[$\Rtwo$:]  spin-spin relaxation rate
  \item[$R_{ex}$:]  chemical exchange relaxation rate
  \item[RDC:]  residual dipolar coupling
  \item[RMSD:]  root-mean-square deviation
  \item[ROE:]  rotating-frame Overhauser effect
  \item[RSDM:]  reduced spectral density mapping
  \item[RSS:]  rich site summary (web feed format)
  \item[$S^2$, $S^2_f$, and $S^2_s$:]  model-free generalised order parameters
  \item[SVN:]  Apache Subversion (open source version control system)
  \item[$\tau_e$, $\tau_f$, and $\tau_s$:]  model-free effective internal correlation times
  \item[$\tau_m$:]  global rotational correlation time
  \item[TP02:]  the \citet{TrottPalmer02} relaxation dispersion model
  \item[TAP03:]  the \citet{Trott03} relaxation dispersion model
  \item[TSMFK01:]  the \citet{Tollinger01} relaxation dispersion model
  \item[UI:]  user interface
  \item[XML:]  extensible markup language
  \item[ZQ:]  zero quantum
\end{description}

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% Citations.
%%%%%%%%%%%%

\begin{spacedpara}
\tolerance=1000
\include{citations}
\end{spacedpara}


%%%%%%%%%%%%%%
% Main text. %
%%%%%%%%%%%%%%

\mainmatter
\begin{spacedpara}


% Layout of the document.
%%%%%%%%%%%%%%%%%%%%%%%%%

\part{The basics}
\include{intro}
\include{install}
\include{infrastruct}
\include{data_model}

\part{The specific analyses}
\include{curvefit}
\include{noe}
\include{model-free}
\include{jw_mapping}
\include{consistency_tests}
\include{n_state}
\include{dispersion}

\part{Power users}
\include{develop}

\part{Advanced topics}
\include{optimisation}
\include{maths}

\part{Reference}
\include{functions}
\include{licence}


% End of the main chapters.
%%%%%%%%%%%%%%%%%%%%%%%%%%%

\end{spacedpara}



% Bibliography.
%%%%%%%%%%%%%%%

\bibliographystyle{relax}
\bibliography{bibliography}



% Index.
%%%%%%%%

% Cross-referencing.
\index{AIC|see{model selection, AIC}}
\index{AICc|see{model selection, AICc}}
\index{anisotropic diffusion|see{diffusion, anisotropic}}
\index{ANOVA model selection|see{model selection, ANOVA}}
\index{asymmetric diffusion|see{diffusion, ellipsoid (asymmetric)}}
\index{Augmented Lagrangian|see{optimisation, constraint algorithm, Method of Multipliers}}
\index{axially symmetric diffusion|see{diffusion, spheroid (axially symmetric)}}
\index{Bayesian model selection|see{model selection, Bayesian}}
\index{BFGS|see{optimisation, algorithm, BFGS}}
\index{BIC|see{model selection, BIC}}
\index{Bootstrap model selection|see{model selection, Bootstrap}}
\index{Brownian diffusion|see{diffusion, Brownian}}
\index{bzip2|see{compression, bzip2}}
\index{C module compilation|see{SCons, C module compilation}}
\index{Cauchy point|see{optimisation, algorithm, Cauchy point}}
\index{CG-Steihaug|see{optimisation, algorithm, CG-Steihaug}}
\index{cross rate|see{relaxation rate, cross rate}}
\index{cross-relaxation|see{relaxation rate, cross-relaxation}}
\index{cross-validation model selection|see{model selection, cross-validation}}
\index{Dasha|see{software, Dasha}}
\index{dogleg|see{optimisation, algorithm, dogleg}}
\index{exact trust region|see{optimisation, algorithm, exact trust region}}
\index{ellipsoidal diffusion|see{diffusion, ellipsoid (asymmetric)}}
\index{Fletcher-Reeves|see{optimisation, algorithm, Fletcher-Reeves}}
\index{Frequentist model selection|see{model selection, Frequentist}}
\index{GNU/Linux|see{Operating system, GNU/\ Lin\-ux}}
\index{Grace|see{software, Grace}}
\index{GUI|see{User interface, GUI}}
\index{gzip|see{compression, gzip}}
\index{Hestenes-Stiefel|see{optimisation, algorithm, Hestenes-Stiefel}}
\index{Hypothesis testing model selection|see{model selection, Hypothesis testing}}
\index{isotropic diffusion|see{diffusion, sphere (isotropic)}}
\index{keyword argument|see{argument, keyword}}
\index{Kullback-Leibler discrepancy|see{discrepancy, Kullback-Leibler}}
\index{Levenberg-Marquardt|see{optimisation, algorithm, Levenberg-Marquardt}}
\index{Linux|see{Operating system, GNU/\-Lin\-ux}}
\index{Logarithmic barrier|see{optimisation, constraint algorithm, Logarithmic barrier}}
\index{longitudinal relaxation|see{relaxation rate, spin-lattice}}
\index{Mac OS X|see{Operating system, Mac OS X}}
\index{Method of Multipliers|see{optimisation, constraint algorithm, Method of Multipliers}}
\index{minfx|see{optimisation, minfx}}
\index{Modelfree|see{software, Modelfree}}
\index{MOLMOL|see{software, MOLMOL}}
\index{MS Windows|see{Operating system, MS Windows}}
\index{Nelder-Mead simplex|see{optimisation, algorithm, Nelder-Mead simplex}}
\index{Newton|see{optimisation, algorithm, Newton}}
\index{Newton-Raphson|see{optimisation, algorithm, Newton}}
\index{Newton-CG|see{optimisation, algorithm, New\-ton-CG}}
\index{NMRView|see{software, NMRView}}
\index{OpenDX|see{software, OpenDX}}
\index{OpenMPI|see{MPI, OpenMPI}}
\index{OS X|see{Operating system, Mac OS X}}
\index{PCS|see{Pseudo-contact shift}}
\index{Polak-Ribi\`ere|see{optimisation, algorithm, Polak-Ribi\`ere}}
\index{Polak-Ribi\`ere +|see{optimisation, algorithm, Polak-Ribi\`ere +}}
\index{PyMOL|see{software, PyMOL}}
\index{R1@$\Rone$|see{relaxation rate, spin-lattice}}
\index{R2@$\Rtwo$|see{relaxation rate, spin-spin}}
\index{RDC|see{Residual dipolar couplings}}
\index{relax|see{software, relax}}
\index{simplex algorithm|see{optimisation, algorithm, Nelder-Mead simplex}}
\index{Sparky|see{software, Sparky}}
\index{spherical diffusion|see{diffusion, sphere (isotropic)}}
\index{spheroidal diffusion|see{diffusion, spheroid (axially symmetric)}}
\index{spin-lattice relaxation|see{relaxation rate, spin-lattice}}
\index{spin-spin relaxation|see{relaxation rate, spin-spin}}
\index{steepest descent|see{optimisation, algorithm, steepest descent}}
\index{step-length|see{optimisation, step-length selection algorithm}}
\index{SVN|see{Subversion}}
\index{svnmerge.py|see{Subversion, svnmerge.py}}
\index{Tensor|see{software, Tensor}}
\index{transverse relaxation|see{relaxation rate, spin-spin}}
\index{Windows|see{Operating system, MS Windows}}
\index{Unix|see{Operating system, Unix}}
\index{XEasy|see{software, XEasy}}

\printindex


\end{document}
