This file is part of the "GNU polyxmass" project.

The "GNU polyxmass" 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.

Copyright (C) 2000,2001,2002,2003 Filippo Rusconi

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    This program 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.

    This program 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 program; if not, write to the Free Software
    Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
    USA

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README:

GNU polyxdef is the GNU polyxmass software project's module where the
user makes/modifies polymer chemistry definitions. Those polymer
chemistry definitions are then saved to a disk file under an xml-based
format that will be understandable by other modules in the GNU
polyxmass software suite.

The GNU polyxdef graphical user interface (GUI) module makes it very
easy to define brand new polymer chemistry by defining a number of
chemically-relevant elements:

- the monomers that the polymer sequence may be made of (through
  polymerization of these into a single molecule);

- the left and right end caps that put the polymer sequence, after
  polymerization has terminated, in its finished state (for example,
  a protein has a left end cap "H" and a right end cap "OH");

- the chemical cleavages that can occur in the polymer sequence (chemical
  means either enzymatic, like endo-proteolysis, or actually chemical,
  like methanolysis or cyanogen bromide cleavage);

- the gas-phase fragmentations that the polymer sequence may undergo;

Once the polymer definition is finished, the file should be saved into
a directory where the programs of the GNU polyxmass mass spectrometry
framework will be able to find them (see the GNU polyxmassdata package
for examples of such configuration arrangements).


Happy polyxdef'ing