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 polyxedit is the GNU polyxmass software project's module where the
user performs the following tasks on a polymer sequence:

- edit or create a polymer sequence. Editing an existing polymer
  sequence simply involves opening its file from disk and start making
  changes in the polymer sequence editor. Creating a polymer sequence
  involves actually more steps: 1) give the GNU polyxedit program the
  name of a non-existent file; 2) tell the GNU polyxedit program what
  polymer definition type the polymer sequence will be (will it be a
  protein or a saccharide?...)

- perform a wide number of chemically-relevant modifications on the
  active polymer sequence. Such actions can be one of the following:

  - changing the polymer sequence by editing it;

  - annotating the polymer sequence or any monomer in the sequence,
    with no limitation to the number of annotations whatsoever;

  - modifying the polymer sequence by modifying either the polymer
    sequence itself (on its left/right ends) or any number of monomers
    in the polymer sequence;

  - cleaving a polymer sequence using a specific cleavage pattern;

  - gas-phase fragmenting a polymer sequence using specific
    fragmentation patterns;

- arbitrary mass search operations on the polymer sequence;

- mass finding operations on the results of any chemical action that
  had previously provided an array of oligomers (like cleaving or
  fragmenting a polymer sequence, for example);

- determination of the composition of the polymer sequence or any
  selected region of this polymer sequence. There are two different
  types of compositions that GNU polyxedit can compute:
  
  - the monomeric composition, that lists in a table the number of
    each monomer encountered in the polymer sequence;
  
  - the elemental composition that lists in a formula the number of
    each atomic element encountered in the polymer sequence;

  These computations are extremely configurable, as to what chemical
  modification, left/right cap should be taken into account...

- each time a chemically relevant action takes place in the polymer
  sequence editor, the mass calculation engine is triggered and new
  masses are re-computed real-time;

- the sequence file is saved in an xml-based file format


Happy polyxedit'ing
