\pagenumbering{roman} 

\vspace{5mm}
\begin{figure}
  \begin{center}
    \includegraphics [scale=0.25] {figures/raster/polyxmass-logo.png}
  \end{center}
  \label{fig:polyxmass-logo}
\end{figure}

\maketitle

\begin{small}
\noindent\textbf{\pxm\ User Manual}\\
Copyright (C) 2001, 2002, 2003, 2004, 2005 by Filippo \textsc{Rusconi}\\

\noindent http://www.polyxmass.org \bigskip

\noindent This documentation and all its accompanying files are part
of the \pxm project. They are software and are an integral part of
the software they document.

The \pxm project is an official GNU project package (see www.gnu.org)
released ---in its entirety--- under the GNU General Public License
and was started at the Centre National de la Recherche Scientifique
(FRANCE), that granted me the formal authorization to publish it under
this Free Software License.

This software is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or (at
your option) any later version.

A copy of the license is included in the appendix entitled ``GNU
General Public License''.

This software is distributed in the hope that it will be useful, but
WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
General Public License for more details.

You should have received a copy of the GNU General Public License
along with this software; if not, write to the Free Software
Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301,
USA.

\noindent For more details see the file \filename{COPYING} in the
\pxm\ distribution files.\\ 
\end{small}

\noindent%
\vspace{5mm}
\textbf{Revision History}
\vspace{-5mm}
\begin{itemize}
\item june 2006: addition of a section about importing a sequence from
  a raw text file.
\item april 2006: addition of a fragmentation specification example
  for the ``dna'' polymer chemistry definition that clearly
  illustrates the benefits of using the fragmentation rules (``a-B''
  fragmentation specification).
\item december 2005: minor corrections and addition of the
  Find/Replace section in the \pxe\ chapter.
\item october 2005: update the address of the Free Software Foundation
  wherever needed.
\item august-september 2005: many changes in the doc package so that
  the LaTeX source can be almost automagically translated to HTML
  using the tex4ht package.
\item july 2005: updated the \pxe\ chapter about how invalid
  characters in clipboard-imported sequences can be ``purified-out''.
  Also switched the licence from the GFDL to the GPL.
\item june 2005: update of the manual to document the window
  management features and the exporting of results reports. Also made
  adjustments to the Debian installation part due to \pxm being now
  part of Debian GNU/Linux.
\item 12$\rm ^{th}$ of february, 2005: update the \software{Fink}
  installation paragraph according to a document that was communicated
  by D$\mathrm{^r}$ Mark Tracy.
\item 24$\rm ^{th}$ of january, 2005: updated the documentation to
  reflect the addition of the m/z ratio calculations feature. Two
  chapters were affected: the one for \pxc and the one for \pxe.
\item 7$\rm ^{th}$ of december, 2004: updated the documentation to
  reflect additions in the software. Namely, the calculations of net
  electrical charges beared by polymers, and the isoelectric point
  calculations. 
\item october the 23$\mathrm{^{rd}}$ 2004, updated the documentation
  with details about the way to produce atom/polymer chemistry
  definition packages and customization, as the scripts initially set
  up in the \pxm software package were removed. 
\item october 2004, updated the documentation with the new contents of
  the \filename{sounds.dic} file and the renaming of
  \filename{monomer-modif.dic} in \filename{monicons.dic}.  Also added
  a section about self-speaking polymer sequences in the \pxe chapter. 
\item september 2004, changed the whole documentation due to a big
  refactoring of the whole \pxm software suite. 
\item february 2004, added a section on the debian package use. 
  Mentioned the fact that the configuration schema changed, for the
  configuration files of the different modules go now in
  /usr/share/polyxmass.d. 
\item november 2003, added a number of descriptions and made
  substantial modifications to the \pxe\ chapter, in particular
  pertaining to the annotation system (improved heavily recently) and
  to the user feedback that is given in the polymer sequence editor
  when the user points monomers with the mouse cursor. 
\item october 2003, additions to the \pxe\ chapter to describe the
  annotation system. Also added a small section on the creation of
  brand new polymer sequences, as this was not described before. 
\item august 2003, corrections here and there; modified the \pxc\ 
  chapter to reflect the changes in the graphical user interface and
  the chemical pad's layout configuration file. Corrected a doc bug
  about Andreas Fink leading the Fink project (which is false);
\item july 2003, big work on the polyxmassdata chapter that describes
  the \pxm\ file-system hierarchy. Also added some notes on the \pxm\ 
  installation on the \OSname{Mac~OS~X} system (thanks Mark Tracy for
  these notes);
\item july 2003, continued working on the \pxe\ module's chapter. 
  Removed any proprietary font embedding. Chapter and Section titles
  now are typeset using freely available fonts (Palatino). 
\item june 2003, started a major overhaul of the document as the \pxm\ 
  software program was entirely rewritten during the last numerous
  months. The organization of the document will be modified so that
  the document reflects better the new modularity of the \pxm\ 
  software suite. 
\item july 2002, added the section on the molecular calculator
  (\pxc). 
\item july 2002, changed author's address from ``University of
  Bordeaux'' to ``Present address: Muséum national d'Histoire
  naturelle'' in Paris as I have now moved to the Laboratoire de
  biophysique. 
\item july 2002, back to the Computer Modern set of fonts in the text
  of the manual. pdflatex still best way to get to a nice pdf file. 
\item july 2002, added a description of the find/replace procedures. 
\item july 2002, made all the big pictures again better managing their
  size. The overall size of the document has fallen to 2.2 Mb, while
  it was of more than 5 Mb. 
\item april 2002, added a description of how to set some values to
  customize the program in the resources.tex file. New screen dumps
  allow to describe the process easily. 
\item april 2002, moved general-options.tex to resources.tex. 
\item april 2002, changes related to the fact that the packages are no
  more relocatable. 
\item april 2002, changes related to the fact that the directory into
  which the \pxm\ program is installed is from now on \filename{\pxmng}
  and not \filename{polyxmass}. So some  macros were edited in order
  to produce the correct typographical results. The pxm-macros.tex
  file is not dynamically regenerated from a pxm-macros.tex.in file
  upon autotools processing. That allows a very close correlation
  between the version of the software package and the version
  elements' rendering throughout all the text. 
\item april 2002, updated the chapter on the \pxm' file-system standard
  to reflect the changes in the program workings (the fact that the
  ressource files are now in a hidden directory in the user's home
  directory). 
\item april 2002, added a detailed description, in the options'
  configuration chapter, of each option available. 
\item april 2002, added a new chapter on the configuration of the
  options: file general-options.tex. 
\item end of march 2002, added a section on the chemical bridge
  support. 
\item march 2002, moved file name ``config-data.tex'' to
  ``file-system-config.tex'' and corresponding chapter title to reflect
  the real configuration issue that is dealt with in this chapter and
  to differentiate this configuration issue with the polymer chemistry
  ``configuration'' or ``definition''. 
\item march 2002, added the description of the graphical configuration
  of the \pxm\ file-system. Updated relevant parts after the
  \filename{monomer.dic} file was removed from the configuration
  files, and its contents are moved to \filename{polymer.dic}. 
\item february 2002, added a section on mass searching, as I have
  coded it these last days. 
\item february 2002, chopped polyxmass.tex into chapter parts. This is
  to allow easily producing chapters one apart from the other. 
\item february 2002, added the \fileformat{PDF} thumbnail support with
  the wonderful package from Heiko Oberdiek (thumbpdf). 
\item february 2002, changed the organization of the \pxm-specific
  chapters into one single chapter, with as many sections as needed to
  describe all aspects of \pxm' operation; 
\item january 2002, added the ``\pxm' Sequence Editor'' chapter; 
\item january 2002, added the ``Installing From The \software{rpm}
  Source Package'' section for the sake of completeness; 
\item january 2002, started writing the little (but tough) chapter on
  the \pxm' configuration data hierarchy scheme; 
\item january 2002, a wealth of corrections after careful reading of
  the last version while in Christmas holidays in Viterbo (near Rome); 
\item december 2001, added section on UNIX history\dots\ from document
  by David A. Wheeler: \emph{Secure Programming for GNU/Linux and UNIX
    HOWTO}; 
\item november 2001, switched from DocBook SGML format to \LaTeX\ 
  format
\item october 2001, initial writing, DocBook SGML format 
\end{itemize}

\cleardoublepage
\begin{small}
  \begin{flushright}
    \mbox{}\vspace{30mm}\\
    \textit{To $\mathcal{MARIA\ CECILIA}$,\vspace{5mm}\\
      To all the admirable people acting in the ``\emph{Free Software
        Movement}'' \\for a better and cleaner computing
      world,\vspace{3mm}\\
      To all the readers who helped me with this manual\dots}
  \end{flushright} 
\end{small}
\vfill

\cleardoublepage


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