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

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

    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 polyxcalc is the GNU polyxmass software project's module where the
user makes simple mass calculations on a number of chemically-relevant
elements, like:

- initial masses to seed the calculation (if required, like saying "ok, lets
  modify this polymer sequence that I already know weighs 12500 Da);

- atoms, by choosing from a list of atoms known to the GNU polyxmass mass
  spectrometry framework;

- formulas, by writing a syntactically correct "action-formula", like
  "-H20+CH3C0OH";

- monomers, if a polymer definition type was required to be loaded by the
  calculator, since the monomers are polymer definition-specific;

- modifications, with the same provision as for monomers;

- polymer sequence, with the same provision as for monomers;

All these chemical elements may be combined into a single calculation, by
setting them all at once in the mass calculator graphical user interface. 

Each chemical element being involved into a mass calculation must be
accompanied by a count number. This count number allows two things:

- to tell GNU polyxcalc that the element should be included in the
  mass calculation a number of times. For example, one may say "I want
  to add three glycine monomers now";

- to tell GNU polyxcalc if the element involved in the mass
  calculation should be ADDED or REMOVED from the virtual molecule
  being dealt with. For example, while the user said above that he
  wanted three glycine monomers to be added, she could have said that
  she wanted the same amount of glycine monomer (3) to be REMOVED from
  the virtual molecule. To do so would have been easy, just enter "-3"
  instead of "3" in the count text entry widget !

Each computation is logged to a text view widget that the user can modify to
his taste, for later inclusion in the lab-book.

The GNU polyxcalc module is programmable in a polymer
definition-specific way.  That means that each polymer definition has
its own configuration file.  The configuration file is located in the
polymer definition's specific directory (see the GNU polyxmassdata
package for the whole filesystem explanation). Its format is trivial,
and I include below some lines from such a configuration file:


chempadkey=protonate%+H1%adds a proton
chempadkey=hydrate%+H2O1%adds a water molecule
chempadkey=0H-ylate%+O1H1%adds an hydroxyl group
chempadkey=acetylate%-H1+C2H3O1%adds an acetyl group

Happy polyxcalc'ing
