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\author{<NAME>}
\date{\today}
\title{Sasalib Manual}

\begin{document}
\maketitle
\hrule\vspace{0.5cm}
\noindent
The program/library Sasalib, including this manual, is licensed under
GPLv3, and can be downloaded from github at: 
\begin{center}
\texttt{https://github.com/mittinatten/sasalib/}
\end{center}
NB: This document is still a draft and not complete in any way.
\vspace{0.5cm}
\hrule
\section{Introduction}
The Solvent Accessible Surface Area (SASA) of a molecule gives a
measure of the surface of the molecule in contact with solvent. This
area can for example quantify how folded the conformation of a
macromolecule is, and can also be used to compare the exposed
hydrophobic surfaces of different conformations or different
molecules. To define the SASA, $A$, of given molecule, let a spherical
probe roll over the surface of the molecule, including internal
cavities. $A$ is then the surface drawn by the center of the
probe.~\cite{LnR} The probe represents a solvent molecule
(i.e.\ water), and therefore cavities that are too small for the
solvent to enter do not contribute to $A$.

Calculating Solvent Accessible Surface Areas (SASA) is a
run-of-the-mill type calculation in protein structure studies. To the
author's knowledge there are no fully open source standalone programs
for doing this. Neither are there any libraries designed to be easily
integrated in other programs. The present library is an attempt to
resolve both these issues, and is released under the GNU General
Public License 3.0.

Sasalib is a both a standalone command line program and a C library
for protein SASA calculations. The library provides a simple interface
that takes PDB-files as input. It has default parameters to allow
straightforward calculations, but also allows the user to change most
parameters of the calculation. In addition, there is a lower level
interface where the user can treat the calculation as a purely
mathematical operation on a set of spheres, specifying only
coordinates and radii. Both Lee \& Richards' \cite{LnR} and Shrake \&
Rupley's \cite{SnR} algorithms are available. They will be referred to
as L\&R and S\&R throughout this document. Future versions of the
library might include other algorithms as well.

This document is organized as follows. Section \ref{sec:howto_short}
give a brief introduction to the library, presenting the command line
interface and a short sample program that gives a general idea of how<commit_msg>Added use cases to manual.<commit_after>\documentclass[a4paper,11pt]{article}
\usepackage[utf8]{inputenc}
\usepackage[OT1]{fontenc}
\usepackage[english]{babel}
\usepackage[margin=1.2in]{geometry}
\usepackage{graphicx}
\usepackage{amsmath}
\usepackage{cite}
\usepackage[perpage,symbol]{footmisc}
\usepackage[hang,small]{caption}
%\usepackage{pslatex}

%\usepackage{fancyvrb}

\author{<NAME>}
\date{\today}
\title{Sasalib Manual}

\begin{document}
\maketitle
\hrule\vspace{0.5cm}
\noindent
The program/library Sasalib, including this manual, is licensed under
GPLv3, and can be downloaded from github at: 
\begin{center}
\texttt{https://github.com/mittinatten/sasalib/}
\end{center}
NB: This document is still a draft and not complete in any way.
\vspace{0.5cm}
\hrule
\section{Introduction}
The Solvent Accessible Surface Area (SASA) of a molecule gives a
measure of the surface of the molecule in contact with solvent. This
area can for example quantify how folded the conformation of a
macromolecule is, and can also be used to compare the exposed
hydrophobic surfaces of different conformations or different
molecules. To define the SASA, $A$, of given molecule, let a spherical
probe roll over the surface of the molecule, including internal
cavities. $A$ is then the surface drawn by the center of the
probe.~\cite{LnR} The probe represents a solvent molecule
(i.e.\ water), and therefore cavities that are too small for the
solvent to enter do not contribute to $A$.

Calculating Solvent Accessible Surface Areas (SASA) is a
run-of-the-mill type calculation in protein structure studies. To the
author's knowledge there are no fully open source standalone programs
for doing this. Neither are there any libraries designed to be easily
integrated in other programs. The present library is an attempt to
resolve both these issues, and is released under the GNU General
Public License 3.0.

Sasalib is a both a standalone command line program and a C library
for protein SASA calculations. The library provides a simple interface
that takes PDB-files as input. It has default parameters to allow
straightforward calculations, but also allows the user to change most
parameters of the calculation. In addition, there is a lower level
interface where the user can treat the calculation as a purely
mathematical operation on a set of spheres, specifying only
coordinates and radii. Both Lee \& Richards' \cite{LnR} and Shrake \&
Rupley's \cite{SnR} algorithms are available. They will be referred to
as L\&R and S\&R throughout this document. Future versions of the
library might include other algorithms as well.

In constructing the library three possible use cases were considered. 
\begin{enumerate}
\item The user has a PDB-file and wishes to calculate total SASA of
  the structure, or the SASA for certain groups or types of atoms.
\item The user has a set of cartesian coordinates for atoms and radii
  for these atoms and wants to calculate the total SASA for this object. 
\item The user is simulating a molecule and wants to sample SASA of
  different configurations during the simulation.
\end{enumerate}
For case 1 both the command-line interface (CLI) and the application
programming interface (API) can be used. Using the API gives more
flexibility in interpreting and analyzing the results. The other 2
cases can only be handled through the API. Both the API and the CLI
allow the user to set parameters for the calculation. 

This document is organized as follows. Section \ref{sec:howto_short}
give a brief introduction to the library, presenting the command line
interface and a short sample program that gives a general idea of how
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