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README
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#Copyright (c) 2013-2015 Aram H Markosyan. All rights reserved.
#
# This file is part of PumpKin (see http://www.pumpkin-tool.org).
# Please see the COPYRIGHT_and_LICENSE file for the copyright notice,
# disclaimer, contact information and the GNU Lesser General Public License.
#
# PumpKin 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) version 2.
#
# PumpKin 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 terms and conditions of the GNU General
# Public License for more details.
#
# You should have received a copy of the GNU Lesser 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
###############################################################################
Download
=================================
Before installing PumpKin, the user should have installed the GLPK package.
For this we recommend tools like MacPorts (www.macports.org) or
Fink (www.finkproject.org) for Mac OS X and package management systems for
GNU/Linux distributions. The windows user can get installation instructions
at (winglpk.sourceforge.net).
The full source code of PumpKin is available at:
http://www.pumpkin-tool.org
After the download user should do:
1. Copy the pumpkin distribution file to a working directory.
2. Unpack the distribution file with the following command:
$ gzip -d pumpkin-X.Y.tar.gz
After unpacking the distribution file is automatically renamed to ‘pumpkin- X.Y.tar’.
3. Unarchive the distribution file with the following command:
$ tar -x < pumpkin-X.Y.tar
It automatically creates the subdirectory ‘pumpkin-X.Y’ containing the pumpkin distribution.
Description of this Package
=================================
The PumpKin package contains the folling files:
Copyright_and_License
README
User manual.pdf
src/
Makefile
PumpKin.cpp
pk_Array.h
pk_IO.cpp
pk_Pathways.cpp
pk_Print.cpp
pk_Array.cpp
pk_DataTypes.h
pk_IO.h
pk_Pathways.h
pk_Print.h
Examples/
ZDPlasKin/
Input_10/
input.txt
qt_conditions_list.txt
qt_matrix.txt
qt_reactions_list.txt
qt_conditions.txt
qt_densities.txt
qt_rates.txt
qt_species_list.txt
Input_20/
input.txt
qt_conditions_list.txt
qt_matrix.txt
qt_reactions_list.txt
qt_conditions.txt
qt_densities.txt
qt_rates.txt
qt_species_list.txt
Global_Kin/
--------------------------------------
The package consists of the following C++ files:
PumpKin.cpp
pk_DataTypes.h
pk_Array.h, pk_Array.cpp
pk_IO.h, pk_IO.cpp
pk_Print.h, pk_Print.cpp
pk_Pathways.h, pk_Pathways.cpp
--------------------------------------
a. PumpKin.cpp -- is the user defined file to run PumpKin and make output.
b. pk_DataTypes.h -- contains all the abstract structures which store the data like rates etc.
c. pk_Array.h(.cpp) -- multidimensional dynamic array structures
d. pk_IO.h(.cpp) -- contains all the input routines to read input data
e. pk_Print.h(.cpp) -- contains all the printing (output) routines
g. pk_Pathways.h(.cpp) -- performs all operations over pathways. The core of algorithm is implemented in these files.
PumpKin Installation Information
=================================
The simplest way to build this package is:
1. `cd' to the directory containing the package's source code:
$ cd pumpkin-X.Y/src
2. Type make to buid it:
$ make
To run simple examples provided with package type:
$ ./pumpkin Examples/ZDPlasKin/Input_10
$ ./pumpkin Examples/ZDPlasKin/Input_20
or
$ ./pumpkin Examples/Global_Kin